From https://github.com/taverna/taverna-ui-exts master
diff --git a/taverna-workbench-loop-ui/pom.xml b/taverna-workbench-loop-ui/pom.xml
new file mode 100644
index 0000000..f639bea
--- /dev/null
+++ b/taverna-workbench-loop-ui/pom.xml
@@ -0,0 +1,71 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna.t2</groupId>
+ <artifactId>ui-exts</artifactId>
+ <version>2.0-SNAPSHOT</version>
+
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>loop-ui</artifactId>
+ <packaging>bundle</packaging>
+ <name>Loop layer contextual view</name>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>contextual-views-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+
+
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>file-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>edits-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>helper-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>beanshell-activity-ui</artifactId>
+ <version>${t2.ui.activities.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>edits-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>file-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>contextual-views-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>selection-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+ </dependencies>
+</project>
\ No newline at end of file
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/ActivityGenerator.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/ActivityGenerator.java
new file mode 100644
index 0000000..9bd68e8
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/ActivityGenerator.java
@@ -0,0 +1,195 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.loop;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Set;
+import java.util.Map.Entry;
+
+import net.sf.taverna.t2.workbench.loop.comparisons.Comparison;
+import net.sf.taverna.t2.workbench.loop.comparisons.EqualTo;
+import net.sf.taverna.t2.workbench.loop.comparisons.IsGreaterThan;
+import net.sf.taverna.t2.workbench.loop.comparisons.IsLessThan;
+import net.sf.taverna.t2.workbench.loop.comparisons.Matches;
+import net.sf.taverna.t2.workbench.loop.comparisons.NotEqualTo;
+import net.sf.taverna.t2.workbench.loop.comparisons.NotMatches;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+import uk.org.taverna.scufl2.api.core.Processor;
+import uk.org.taverna.scufl2.api.port.InputActivityPort;
+import uk.org.taverna.scufl2.api.port.InputProcessorPort;
+import uk.org.taverna.scufl2.api.port.OutputActivityPort;
+import uk.org.taverna.scufl2.api.port.OutputPort;
+import uk.org.taverna.scufl2.api.port.OutputProcessorPort;
+
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+public class ActivityGenerator {
+
+ private static final String LOOP_PORT = "loop";
+
+ private static final String SCRIPT = "script";
+
+ public static URI BEANSHELL_ACTIVITY = URI
+ .create("http://ns.taverna.org.uk/2010/activity/beanshell");
+
+ public static URI BEANSHELL_CONFIG = BEANSHELL_ACTIVITY.resolve("#Config");
+
+
+ public static final double DEFAULT_DELAY_S = 0.2;
+ public static final String COMPARE_PORT = "comparePort";
+ public static final String COMPARISON = "comparison";
+ public static final String CUSTOM_COMPARISON = "custom";
+ public static final String COMPARE_VALUE = "compareValue";
+ public static final String IS_FEED_BACK = "isFeedBack";
+ public static final String DELAY = "delay";
+
+ private static Logger logger = Logger.getLogger(ActivityGenerator.class);
+ private final ObjectNode loopProperties;
+ private final Processor processorToCompare;
+ private static Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ public ActivityGenerator(ObjectNode configuration,
+ Processor processorToCompare) {
+ this.loopProperties = configuration;
+ this.processorToCompare = processorToCompare;
+ }
+
+ protected Activity generateActivity() {
+ Activity beanshell = new Activity();
+ beanshell.setType(BEANSHELL_ACTIVITY);
+ Configuration config = generateBeanshellConfig(beanshell);
+ // TODO: Where to put the config?
+ return beanshell;
+ }
+
+ private Configuration generateBeanshellConfig(Activity beanshell) {
+ Configuration config = scufl2Tools.createConfigurationFor(beanshell, BEANSHELL_CONFIG);
+ generateInputPorts(beanshell);
+ generateOutputPorts(beanshell);
+ config.getJsonAsObjectNode().put(SCRIPT, generateScript());
+ return config;
+ }
+
+ protected static List<Comparison> comparisons = Arrays.asList(
+ new EqualTo(), new NotEqualTo(), new Matches(), new NotMatches(),
+ new IsGreaterThan(), new IsLessThan());
+
+ protected static Comparison getComparisonById(String id) {
+ if (id == null || id.isEmpty()) {
+ return comparisons.get(0);
+ }
+ for (Comparison potentialComparison : comparisons) {
+ if (potentialComparison.getId().equals(id)) {
+ return potentialComparison;
+ }
+ }
+ return null;
+ }
+
+ @SuppressWarnings("boxing")
+ private String generateScript() {
+ Map<String, String> replacements = new HashMap<String, String>();
+ replacements.put("${loopPort}", LOOP_PORT);
+ replacements.put("${port}", loopProperties.findValue(COMPARE_PORT).asText());
+ replacements.put("${value}", beanshellString(loopProperties
+ .findValue(COMPARE_VALUE).asText()));
+
+
+ // as seconds
+ Double delay = loopProperties.findPath(DELAY).asDouble(DEFAULT_DELAY_S);
+ // as milliseconds
+ delay = Math.max(0.0, delay) * 1000;
+ // as integer (for Thread.sleep)
+ replacements.put("${delay}", Integer.toString(delay.intValue()));
+
+ String template = getComparisonById(
+ loopProperties.findValue(COMPARISON).asText()).getScriptTemplate();
+
+ if (delay > 0.0) {
+ template += "\nif (\"true\".matches(${loopPort})) {\n";
+ template += " Thread.sleep(${delay});\n";
+ template += "}";
+ }
+
+ String script = template;
+ for (Entry<String, String> mapping : replacements.entrySet()) {
+ script = script.replace(mapping.getKey(), mapping.getValue());
+ }
+ return script;
+ }
+
+ private String beanshellString(String value) {
+ value = value.replace("\\", "\\\\");
+ value = value.replace("\n", "\\n");
+ value = value.replace("\"", "\\\"");
+ return '"' + value + '"';
+ }
+
+ private void generateInputPorts(Activity beanshell) {
+ if (processorToCompare == null) {
+ return;
+ }
+ for (OutputProcessorPort procOut : processorToCompare.getOutputPorts()) {
+ // Any of the outputs are available to the script, giving
+ // a custom script that compares multiple outputs a better
+ // starting point.
+ String portName = procOut.getName();
+ if (portName.equals(loopProperties.findValue(COMPARE_PORT).asText()) ||
+ (loopProperties.findValue(IS_FEED_BACK).asBoolean())) {
+ InputActivityPort input = new InputActivityPort(beanshell, portName);
+ input.setDepth(procOut.getDepth());
+ input.setParent(beanshell);
+ }
+ }
+ }
+
+ private void generateOutputPorts(Activity beanshell) {
+ OutputActivityPort loopPort = new OutputActivityPort(beanshell, LOOP_PORT);
+ loopPort.setDepth(0);
+ loopPort.setGranularDepth(0);
+ if (processorToCompare == null) {
+ return;
+ }
+ if (! loopProperties.findValue(IS_FEED_BACK).asBoolean()) {
+ return;
+ }
+ for (InputProcessorPort procIn : processorToCompare.getInputPorts()) {
+ String portName = procIn.getName();
+ if (processorToCompare.getOutputPorts().containsName(portName)) {
+ OutputActivityPort actOut = new OutputActivityPort(beanshell, portName);
+ actOut.setDepth(procIn.getDepth());
+ actOut.setGranularDepth(procIn.getDepth());
+ }
+ }
+ }
+}
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/AddLoopFactory.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/AddLoopFactory.java
new file mode 100644
index 0000000..f23650c
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/AddLoopFactory.java
@@ -0,0 +1,125 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.loop;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import net.sf.taverna.t2.workbench.MainWindow;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.AddLayerFactorySPI;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+import uk.org.taverna.scufl2.api.core.Processor;
+
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+public class AddLoopFactory implements AddLayerFactorySPI {
+
+ private static final URI LOOP_TYPE = URI.create("http://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Loop");
+
+
+ private static Logger logger = Logger.getLogger(AddLoopFactory.class);
+ private static final JsonNodeFactory JSON_NODE_FACTORY = JsonNodeFactory.instance;
+ private static Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private SelectionManager selectionManager;
+ private ApplicationConfiguration applicationConfig;
+
+ public boolean canAddLayerFor(Processor processor) {
+ return findLoopLayer(processor) == null;
+ }
+
+
+ public ObjectNode findLoopLayer(Processor processor) {
+ List<Configuration> configs = scufl2Tools.configurationsFor(processor, selectionManager.getSelectedProfile());
+ for (Configuration config : configs) {
+ if (config.getJson().has("loop")) {
+ return (ObjectNode) config.getJson().get("loop");
+ }
+ }
+ return null;
+ }
+
+ @SuppressWarnings("serial")
+ public Action getAddLayerActionFor(final Processor processor) {
+ return new AbstractAction("Add looping") {
+
+ public void actionPerformed(ActionEvent e) {
+ ObjectNode loopLayer = findLoopLayer(processor);
+ if (loopLayer == null) {
+ loopLayer = JSON_NODE_FACTORY.objectNode();
+ }
+ // Pop up the configure loop dialog
+ LoopConfigureAction loopConfigureAction = new LoopConfigureAction(
+ MainWindow.getMainWindow(), null, processor, loopLayer,
+ selectionManager.getSelectedProfile(), editManager,
+ fileManager, getApplicationConfig());
+ loopConfigureAction.actionPerformed(e);
+ }
+ };
+ }
+
+ @Override
+ public boolean canCreateLayerClass(URI dispatchLayerType) {
+ return dispatchLayerType.equals(LOOP_TYPE);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public SelectionManager getSelectionManager() {
+ return selectionManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+
+ public ApplicationConfiguration getApplicationConfig() {
+ return applicationConfig;
+ }
+
+
+ public void setApplicationConfig(ApplicationConfiguration applicationConfig) {
+ this.applicationConfig = applicationConfig;
+ }
+
+}
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopAddMenuAction.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopAddMenuAction.java
new file mode 100644
index 0000000..e7b6e87
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopAddMenuAction.java
@@ -0,0 +1,73 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.workbench.loop;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import uk.org.taverna.scufl2.api.core.Processor;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+
+public class LoopAddMenuAction extends AbstractContextualMenuAction {
+
+ public static final URI configureRunningSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/configureRunning");
+
+ private static final URI LOOP_ADD_URI = URI
+ .create("http://taverna.sf.net/2008/t2workbench/loopAdd");
+
+ private static final String LOOP_ADD = "Loop add";
+
+ public LoopAddMenuAction() {
+ super(configureRunningSection, 20, LOOP_ADD_URI);
+ }
+
+ private AddLoopFactory addLoopFactory;
+
+ @SuppressWarnings("serial")
+ @Override
+ protected Action createAction() {
+ return new AbstractAction("Looping...") {
+ public void actionPerformed(ActionEvent e) {
+ //Loop loopLayer = null;
+ Processor p = (Processor) getContextualSelection().getSelection();
+ addLoopFactory.getAddLayerActionFor(p).actionPerformed(e);
+ //LoopConfigureMenuAction.configureLoopLayer(p, e); // Configuration dialog pop up is now done from getAddLayerActionFor()
+ }
+ };
+ }
+
+ public boolean isEnabled() {
+ Object selection = getContextualSelection().getSelection();
+ return (super.isEnabled() && (selection instanceof Processor) && (LoopConfigureMenuAction.getLoopLayer((Processor)selection) == null));
+ }
+
+ public void setAddLoopFactory(AddLoopFactory addLoopFactory) {
+ this.addLoopFactory = addLoopFactory;
+ }
+
+
+
+}
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopConfigurationPanel.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopConfigurationPanel.java
new file mode 100644
index 0000000..88efb1a
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopConfigurationPanel.java
@@ -0,0 +1,588 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.loop;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Properties;
+
+import javax.swing.AbstractAction;
+import javax.swing.Box;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+import javax.swing.border.EmptyBorder;
+
+import net.sf.taverna.t2.activities.beanshell.views.BeanshellConfigurationPanel;
+import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
+import net.sf.taverna.t2.workbench.loop.comparisons.Comparison;
+import net.sf.taverna.t2.workbench.ui.Utils;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+import uk.org.taverna.scufl2.api.core.Processor;
+import uk.org.taverna.scufl2.api.profiles.Profile;
+
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+/**
+ * UI for {@link LoopConfiguration}
+ *
+ * @author Stian Soiland-Reyes
+ *
+ */
+@SuppressWarnings("serial")
+public class LoopConfigurationPanel extends JPanel {
+
+ private static final String CONDITION_ACTIVITY = "conditionActivity";
+ private static final String DEFAULT_DELAY_S = "0.5";
+ protected ObjectNode configuration;
+
+ private static final Scufl2Tools scufl2tools = new Scufl2Tools();
+ private ApplicationConfiguration applicationConfig;
+
+
+ protected final Processor processor;
+
+ protected JPanel headerPanel = new JPanel();
+ protected JPanel optionsPanel = new JPanel();
+ protected JPanel configPanel = new JPanel();
+ protected JPanel customPanel = new JPanel();
+
+ protected JLabel valueTypeLabel = new JLabel("the string");
+
+ protected JTextField valueField = new JTextField("", 15);
+
+ protected JLabel delayLabel = new JLabel("adding a delay of ");
+ protected JTextField delayField = new JTextField(
+ Double.toString(ActivityGenerator.DEFAULT_DELAY_S), 4);
+ protected JLabel secondsLabel = new JLabel(" seconds between the loops.");
+
+ private JComboBox<String> portCombo;
+ private JComboBox<Comparison> comparisonCombo;
+ private JButton customizeButton;
+
+ protected ObjectNode loopLayer;
+ private Object Comparison;
+ private Activity originalCondition = null;
+ private Profile profile;
+
+ public LoopConfigurationPanel(Processor processor, ObjectNode loopLayer,
+ Profile profile, ApplicationConfiguration applicationConfig) {
+ this.processor = processor;
+ this.loopLayer = loopLayer;
+ this.profile = profile;
+ this.applicationConfig = applicationConfig;
+ this.setBorder(new EmptyBorder(10,10,10,10));
+ initialise();
+ setConfiguration(loopLayer);
+ }
+
+ public ObjectNode getConfiguration() {
+ uiToConfig();
+ return loopLayer.deepCopy();
+ }
+
+ private static Logger logger = Logger
+ .getLogger(LoopConfigurationPanel.class);
+
+ protected void uiToConfig() {
+ String comparisonStr = configuration.path(ActivityGenerator.COMPARISON).asText();
+ if (comparisonStr.isEmpty()) {
+ comparisonStr = ActivityGenerator.CUSTOM_COMPARISON;
+ }
+ if (comparisonStr.equals(ActivityGenerator.CUSTOM_COMPARISON)
+ && ! configuration.path(CONDITION_ACTIVITY).asText().isEmpty()) {
+ // Ignore values
+ } else {
+ configuration.put("runFirst", true);
+ if (portCombo.getSelectedItem() == null) {
+ // unconfigured port
+ configuration.remove(ActivityGenerator.COMPARE_PORT);
+ configuration.putNull(CONDITION_ACTIVITY);
+ return;
+ } else {
+ configuration.put(ActivityGenerator.COMPARE_PORT,
+ ((String) portCombo.getSelectedItem()));
+ }
+
+ Comparison comparison = (Comparison) comparisonCombo
+ .getSelectedItem();
+ if (comparison == null) {
+ configuration.remove(ActivityGenerator.COMPARISON);
+ configuration.putNull(CONDITION_ACTIVITY);
+ return;
+ } else {
+ configuration
+ .put(ActivityGenerator.COMPARISON, comparison.getId());
+ }
+ configuration.put(ActivityGenerator.COMPARE_VALUE, valueField
+ .getText());
+ configuration.put(ActivityGenerator.DELAY, Double.parseDouble(delayField.getText()));
+ configuration.put(ActivityGenerator.IS_FEED_BACK, feedBackCheck.isSelected());
+
+ // Generate activity
+ ActivityGenerator activityGenerator = new ActivityGenerator(
+ configuration, processor);
+ configuration.put(CONDITION_ACTIVITY, activityGenerator.generateActivity().getName());
+ }
+ }
+
+ public class ResetAction extends AbstractAction {
+ public ResetAction() {
+ super("Clear");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ configuration.putNull(CONDITION_ACTIVITY);
+ configToUi();
+ }
+ }
+
+ private final class CustomizeAction implements ActionListener {
+
+
+// public CustomizeAction() {
+// super();
+// //putValue(NAME, "Customise loop condition");
+// }
+
+ public void actionPerformed(ActionEvent e) {
+ uiToConfig();
+
+ String conditionName = configuration.path(CONDITION_ACTIVITY).asText();
+
+ Activity condition = profile.getActivities().getByName(conditionName);
+ if (condition == null) {
+ condition = new Activity();
+ profile.getActivities().add(condition);
+ configuration.put(CONDITION_ACTIVITY, condition.getName());
+ condition.setType(ActivityGenerator.BEANSHELL_ACTIVITY);
+ Configuration config = scufl2tools.createConfigurationFor(condition, ActivityGenerator.BEANSHELL_CONFIG);
+ } else if (!(condition.getType().equals(ActivityGenerator.BEANSHELL_ACTIVITY))) {
+ logger.warn("Can't configure unsupported loop condition of service type "
+ + condition.getType());
+ return;
+ }
+
+ Frame owner = Utils.getParentFrame(LoopConfigurationPanel.this);
+
+
+ final BeanshellConfigurationPanel beanshellConfigView = new BeanshellConfigurationPanel(
+ condition, applicationConfig);
+
+ final JDialog dialog = new HelpEnabledDialog(owner, "Customize looping", true);
+ dialog.setLayout(new BorderLayout());
+ dialog.add(beanshellConfigView, BorderLayout.NORTH);
+ dialog.setSize(600, 600);
+ JPanel buttonPanel = new JPanel();
+
+ buttonPanel.setLayout(new FlowLayout(FlowLayout.RIGHT));
+
+ JButton applyButton = new JButton(new AbstractAction() {
+
+ public void actionPerformed(ActionEvent e) {
+ if (beanshellConfigView.isConfigurationChanged()) {
+ beanshellConfigView.noteConfiguration();
+// beanshellActivity.configure(beanshellConfigView
+// .getConfiguration());
+// configuration.setCondition(beanshellActivity);
+ Configuration config = beanshellConfigView.getConfiguration();
+ // TODO: Do we need to store this somehow?
+ configuration.put(
+ ActivityGenerator.COMPARISON,
+ ActivityGenerator.CUSTOM_COMPARISON);
+ }
+ dialog.setVisible(false);
+ configToUi();
+ }
+
+ });
+ applyButton.setText("Apply");
+
+ buttonPanel.add(applyButton);
+ JButton closeButton = new JButton(new AbstractAction() {
+
+ public void actionPerformed(ActionEvent e) {
+ dialog.setVisible(false);
+ }
+ });
+ closeButton.setText("Cancel");
+ buttonPanel.add(closeButton);
+ dialog.add(buttonPanel, BorderLayout.SOUTH);
+ dialog.setLocationRelativeTo(customizeButton);
+ dialog.setVisible(true);
+
+ }
+ }
+
+ public void setConfiguration(ObjectNode configuration) {
+ this.configuration = configuration.deepCopy();
+ configToUi();
+ }
+
+ protected void configToUi() {
+
+
+ String comparisonId;
+
+ if (configuration.has(ActivityGenerator.COMPARISON)) {
+ comparisonId = configuration.get(ActivityGenerator.COMPARISON)
+ .asText();
+ } else {
+ comparisonId = ActivityGenerator.CUSTOM_COMPARISON;
+ }
+
+ if (comparisonId.equals(ActivityGenerator.CUSTOM_COMPARISON)
+ && configuration.has("conditionalActivity")) {
+ configPanel.setVisible(false);
+ customPanel.setVisible(true);
+ } else {
+ configPanel.setVisible(true);
+ customPanel.setVisible(false);
+ }
+
+ portCombo.setSelectedItem(configuration.get(ActivityGenerator.COMPARE_PORT).asText());
+ if (portCombo.getSelectedIndex() == -1
+ && portCombo.getModel().getSize() > 0) {
+ portCombo.setSelectedIndex(0);
+ }
+
+ Comparison comparison = ActivityGenerator
+ .getComparisonById(comparisonId);
+ comparisonCombo.setSelectedItem(comparison);
+ if (comparisonCombo.getSelectedIndex() == -1
+ && comparisonCombo.getModel().getSize() > 0) {
+ comparisonCombo.setSelectedIndex(0);
+ }
+
+ valueField.setText(configuration.get(ActivityGenerator.COMPARE_VALUE).asText());
+
+ if (configuration.has(ActivityGenerator.DELAY)) {
+ delayField.setText(configuration.get(ActivityGenerator.DELAY).asText());
+ } else {
+ delayField.setText(DEFAULT_DELAY_S);
+ }
+
+ feedBackCheck.setSelected(configuration.get(ActivityGenerator.IS_FEED_BACK).asBoolean());
+ updateFeedbackHelp();
+ }
+
+ private void initialise() {
+ removeAll();
+ setLayout(new GridBagLayout());
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+ gbc.gridx = 0;
+ gbc.weightx = 0.1;
+
+ makeHeader();
+ add(headerPanel, gbc);
+
+ makeConfigPanel();
+ gbc.weighty = 0.1;
+ gbc.anchor = GridBagConstraints.CENTER;
+ gbc.fill = GridBagConstraints.BOTH;
+ add(configPanel, gbc);
+
+ makeCustomPanel();
+ add(customPanel, gbc);
+
+ makeOptions();
+ add(optionsPanel, gbc);
+ }
+
+ protected void makeCustomPanel() {
+ customPanel.removeAll();
+ customPanel.setLayout(new GridBagLayout());
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.anchor = GridBagConstraints.LINE_START;
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.gridwidth = 2;
+ gbc.weightx = 0.1;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+
+ JLabel helpLabel = new JLabel(
+ "<html><body>"
+ + "The service <strong>" + processor.getName() + "</strong> will be "
+ + "invoked repeatedly as "
+ + "long as the <em>customized loop condition service</em> returns a string equal "
+ + "to <strong>\"true\"</strong> on its output port <code>loop</code>."
+// + "<br><br>"
+// + "Input ports of the condition service will be populated with values from "
+// + "the <em>corresponding output ports</em> of the main service invocation "
+// + "(as long as they are also "
+// + "<strong>connected</strong> in the containing workflow)."
+// + "<br><br> "
+//
+// + "Any <em>matching "
+// + "output ports</em> from the condition service will provide the corresponding "
+// + "<em>inputs</em> to the main service while looping. You will need to connect "
+// + "the <em>initial inputs</em> in the containing workflow."
+ + "</body></html>");
+ customPanel.add(helpLabel, gbc);
+
+ gbc.weightx = 0.1;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.gridx = 0;
+ gbc.gridy++;
+ gbc.gridwidth = 1;
+ gbc.anchor = GridBagConstraints.EAST;
+ JPanel customiseButtonPanel = new JPanel(new FlowLayout());
+ customiseButtonPanel.setBorder(new EmptyBorder(10,0,0,0));
+ customizeButton = new JButton("Customize loop condition");
+ customizeButton.addActionListener(new CustomizeAction());
+ customiseButtonPanel.add(customizeButton);
+ customiseButtonPanel.add(new JButton(new ResetAction()));
+ customPanel.add(customiseButtonPanel, gbc);
+
+ }
+
+ protected void makeConfigPanel() {
+ configPanel.removeAll();
+ configPanel.setLayout(new GridBagLayout());
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.anchor = GridBagConstraints.LINE_START;
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.gridwidth = 4;
+ gbc.weightx = 0.1;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ JLabel invokedRepeatedlyLabel = new JLabel(
+
+ "<html><body>The service <strong>" + processor.getName() + "</strong> " +
+ "will be invoked repeatedly <em>until</em> its output port</body></html>");
+ invokedRepeatedlyLabel.setBorder(new EmptyBorder(10,0,10,0)); // give some top and bottom border to the label
+ configPanel.add(invokedRepeatedlyLabel, gbc);
+ gbc.ipadx = 4;
+ gbc.ipady = 4;
+
+ gbc.weightx = 0.0;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ gbc.gridx = 0;
+ gbc.gridy = 1;
+ gbc.gridwidth = 1;
+ List<String> activityOutputPorts = getActivityOutputPorts();
+ portCombo = new JComboBox(activityOutputPorts.toArray());
+ configPanel.add(portCombo, gbc);
+
+ comparisonCombo = new JComboBox(ActivityGenerator.comparisons.toArray());
+ comparisonCombo.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ Comparison selectedComparison = (Comparison) comparisonCombo
+ .getSelectedItem();
+ if (selectedComparison != null) {
+ valueTypeLabel.setText("the "
+ + selectedComparison.getValueType());
+ }
+ }
+ });
+ if (comparisonCombo.getSelectedIndex() == -1) {
+ comparisonCombo.setSelectedIndex(0);
+ }
+ gbc.gridx = 1;
+ gbc.gridy = 1;
+ configPanel.add(comparisonCombo, gbc);
+
+ gbc.gridx = 2;
+ gbc.gridy = 1;
+ valueTypeLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ configPanel.add(valueTypeLabel, gbc);
+
+ gbc.gridx = 3;
+ gbc.gridy = 1;
+ gbc.weightx = 0.5; // request all extra space
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ configPanel.add(valueField, gbc);
+
+ gbc.gridx = 0;
+ gbc.gridy = 2;
+ gbc.weightx = 0.0;
+ configPanel.add(delayLabel, gbc);
+
+ gbc.gridx = 1;
+ gbc.gridx = 1;
+ gbc.gridy = 2;
+ gbc.weightx = 0.0;
+ delayField.setHorizontalAlignment(JTextField.RIGHT);
+ configPanel.add(delayField, gbc);
+
+ gbc.gridx = 2;
+ gbc.gridy = 2;
+ gbc.gridwidth = 2;
+ gbc.weightx = 0.5; // request all extra space
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ configPanel.add(secondsLabel, gbc);
+
+ if (activityOutputPorts.isEmpty()) {
+ JLabel warningLabel = new JLabel(
+ "<html><body><strong>Warning:</strong><br>"
+ + "<i>No single value output ports detected on the main service, "
+ + "cannot use built-in comparisons. You may still add a customized " +
+ "looping script</i></body></html>");
+ gbc.gridx = 0;
+ gbc.gridy++;
+ gbc.gridwidth = 4;
+ gbc.weightx = 0.1;
+ gbc.fill = GridBagConstraints.BOTH;
+ gbc.gridy++;
+ configPanel.add(warningLabel, gbc);
+ invokedRepeatedlyLabel.setVisible(false);
+ portCombo.setVisible(false);
+ comparisonCombo.setVisible(false);
+ portWarning.setVisible(false);
+ valueTypeLabel.setVisible(false);
+ valueField.setVisible(false);
+ delayField.setVisible(false);
+ delayLabel.setVisible(false);
+ secondsLabel.setVisible(false);
+ }
+
+ gbc.gridy++;
+ gbc.gridx = 0;
+ gbc.weightx = 0.1;
+ gbc.gridwidth = 4;
+ gbc.weightx = 0.1;
+ gbc.fill = GridBagConstraints.BOTH;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ gbc.insets = new Insets(10, 0, 10, 0);
+ configPanel.add(portWarning, gbc);
+
+ gbc.insets = new Insets(0, 0, 0, 0);
+ gbc.weightx = 0.1;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.gridx = 0;
+ gbc.gridy++;
+ gbc.gridwidth = 4;
+ gbc.anchor = GridBagConstraints.LAST_LINE_END;
+ JPanel customiseButtonPanel = new JPanel(new FlowLayout());
+ customizeButton = new JButton("Customize loop condition");
+ customizeButton.addActionListener(new CustomizeAction());
+ customiseButtonPanel.add(customizeButton);
+ configPanel.add(customiseButtonPanel, gbc);
+
+ // filler
+ gbc.gridy++;
+ gbc.fill = GridBagConstraints.BOTH;
+ gbc.gridx = 4;
+ gbc.weightx = 0.1;
+ gbc.weighty = 0.1;
+ gbc.gridwidth = 4;
+ configPanel.add(Box.createGlue(), gbc);
+ }
+
+ private List<String> getActivityOutputPorts() {
+ // Should already be sorted
+ return new ArrayList<>(processor.getOutputPorts().getNames());
+ }
+
+ protected JCheckBox feedBackCheck = new JCheckBox(
+ "Enable output port to input port feedback");
+ private JLabel portWarning = new JLabel(
+ "<html><body><small>Note that for Taverna to be able to execute this loop, "
+ + "the output port <strong>must</strong> be connected to an input of another service "
+ + "or a workflow output port.</small></body></html>");
+
+ protected void makeOptions() {
+ optionsPanel.removeAll();
+ optionsPanel.setLayout(new GridBagLayout());
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.weightx = 0.1;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ feedBackCheck.setBorder(new EmptyBorder(0,0,10,0));
+ optionsPanel.add(feedBackCheck, gbc);
+ feedBackCheck.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ updateFeedbackHelp();
+ }
+ });
+ updateFeedbackHelp();
+
+ gbc.gridy = 1;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ optionsPanel.add(feedbackHelp, gbc);
+ }
+
+ protected void updateFeedbackHelp() {
+ feedbackHelp.setEnabled(feedBackCheck.isSelected());
+ Color color;
+ if (feedBackCheck.isSelected()) {
+ color = valueTypeLabel.getForeground();
+ } else {
+ // Work around
+ // http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4303706
+ // and assume gray is the 'disabled' colour in our Look n Feel
+ color = Color.gray;
+ }
+ feedbackHelp.setForeground(color);
+
+ }
+
+ JLabel feedbackHelp = new JLabel(
+ "<html><small>"
+ + "<p>When feedback is enabled, the value of the output port is used as input " +
+ "the next time the loop in invoked. The input and output ports used for feedback "
+ + "<strong>must</strong> have the same <strong>name</strong> and <strong>depth</strong>."
+ + "</p><br>"
+
+ + "<p>Feedback can be useful for looping over a nested workflow, "
+ + "where the nested workflow's output determines its next input value.</p><br>"
+
+ + "<p>In order to use feedback looping, you must provide an initial value to the input port by "
+ + "connecting it to the output of a previous service or workflow input port."
+ + "The output port used as feedback also has to be connected to a downstream service " +
+ "or a workflow output port.</p>"
+
+ + "</small></html>");
+
+ protected void makeHeader() {
+ headerPanel.removeAll();
+ headerPanel.setLayout(new BorderLayout());
+ //headerPanel.add(new ShadedLabel("Looping for service"
+ // + processor.getLocalName(), ShadedLabel.ORANGE));
+ }
+}
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopConfigureAction.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopConfigureAction.java
new file mode 100644
index 0000000..0b7ad8f
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopConfigureAction.java
@@ -0,0 +1,262 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.workbench.loop;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+
+import org.apache.log4j.Logger;
+
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.core.Processor;
+import uk.org.taverna.scufl2.api.profiles.Profile;
+
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
+
+/**
+ * @author Alan R Williams
+ * @author Stian Soiland-Reyes
+ *
+ */
+@SuppressWarnings("serial")
+public class LoopConfigureAction extends AbstractAction {
+
+ private static Logger logger = Logger.getLogger(LoopConfigureAction.class);
+
+ private final EditManager editManager;
+ private final FileManager fileManager;
+
+ private final Frame owner;
+ private final ObjectNode loopLayer;
+ private final LoopContextualView contextualView;
+ private final Processor processor;
+ private final Profile profile;
+
+ private ApplicationConfiguration applicationConfig;
+
+
+ protected LoopConfigureAction(Frame owner,
+ LoopContextualView contextualView, Processor processor,
+ ObjectNode loopLayer, Profile profile, EditManager editManager,
+ FileManager fileManager, ApplicationConfiguration applicationConfig) {
+ super("Configure");
+ this.owner = owner;
+ this.contextualView = contextualView;
+ this.loopLayer = loopLayer;
+ this.profile = profile;
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.processor = processor;
+ this.applicationConfig = applicationConfig;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ String title = "Looping for service " + processor.getName();
+ final JDialog dialog = new HelpEnabledDialog(owner, title, true);
+ LoopConfigurationPanel loopConfigurationPanel = new LoopConfigurationPanel(
+ processor, loopLayer, profile, applicationConfig);
+ dialog.add(loopConfigurationPanel, BorderLayout.CENTER);
+
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout(new FlowLayout());
+
+ JButton okButton = new JButton(new OKAction(dialog, loopConfigurationPanel));
+ buttonPanel.add(okButton);
+
+ JButton resetButton = new JButton(new ResetAction(loopConfigurationPanel));
+ buttonPanel.add(resetButton);
+
+ JButton cancelButton = new JButton(new CancelAction(dialog));
+ buttonPanel.add(cancelButton);
+
+ dialog.add(buttonPanel, BorderLayout.SOUTH);
+ dialog.pack();
+ dialog.setSize(650, 430);
+ dialog.setLocationRelativeTo(null);
+ dialog.setVisible(true);
+ }
+
+ protected class CancelAction extends AbstractAction {
+ private final JDialog dialog;
+
+ protected CancelAction(JDialog dialog) {
+ super("Cancel");
+ this.dialog = dialog;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ dialog.setVisible(false);
+ if (contextualView != null) {
+ contextualView.refreshView();
+ }
+ }
+
+ }
+
+ protected class OKAction extends AbstractAction {
+ private final JDialog dialog;
+ private final LoopConfigurationPanel loopConfigurationPanel;
+
+ protected OKAction(JDialog dialog, LoopConfigurationPanel loopConfigurationPanel) {
+ super("OK");
+ this.dialog = dialog;
+ this.loopConfigurationPanel = loopConfigurationPanel;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ try {
+
+ List<Edit<?>> compoundEdit = new ArrayList<Edit<?>>();
+ LoopConfiguration configuration = loopConfigurationPanel.getConfiguration();
+ compoundEdit.add(edits.getConfigureEdit(loopLayer, configuration));
+ compoundEdit.addAll(checkPortMappings(configuration.getCondition()));
+
+ editManager.doDataflowEdit(fileManager.getCurrentDataflow(), new CompoundEdit(
+ compoundEdit));
+ dialog.setVisible(false);
+ if (contextualView != null) {
+ contextualView.refreshView();
+ }
+ } catch (RuntimeException ex) {
+ logger.warn("Could not configure looping", ex);
+ JOptionPane.showMessageDialog(owner, "Could not configure looping",
+ "An error occured when configuring looping: " + ex.getMessage(),
+ JOptionPane.ERROR_MESSAGE);
+ } catch (EditException ex) {
+ logger.warn("Could not configure looping", ex);
+ JOptionPane.showMessageDialog(owner, "Could not configure looping",
+ "An error occured when configuring looping: " + ex.getMessage(),
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+ protected List<Edit<?>> checkPortMappings(Activity<?> conditionActivity) {
+
+ List<Edit<?>> compoundEdit = new ArrayList<Edit<?>>();
+ if (processor.getActivityList().isEmpty()) {
+ return compoundEdit;
+ }
+ Set<String> newInputs = new HashSet<String>();
+ Set<String> newOutputs = new HashSet<String>();
+
+ Activity<?> firstProcessorActivity;
+ firstProcessorActivity = processor.getActivityList().get(0);
+ if (conditionActivity != null) {
+ for (OutputPort condOutPort : conditionActivity.getOutputPorts()) {
+ String portName = condOutPort.getName();
+ Map<String, String> mapping = firstProcessorActivity.getInputPortMapping();
+ if (!mapping.containsKey(portName)) {
+ if (mapping.containsKey(portName)) {
+ logger.warn("Can't re-map input for " + "conditional output "
+ + portName);
+ }
+ for (InputPort inputPort : firstProcessorActivity.getInputPorts()) {
+ if (inputPort.equals(portName)) {
+ Edit<Activity<?>> edit = edits.getAddActivityInputPortMappingEdit(
+ firstProcessorActivity, portName, portName);
+ compoundEdit.add(edit);
+ newInputs.add(portName);
+ }
+ }
+ }
+ }
+ for (InputPort condInPort : conditionActivity.getInputPorts()) {
+ String portName = condInPort.getName();
+ Map<String, String> mapping = firstProcessorActivity.getOutputPortMapping();
+ if (!mapping.containsValue(portName)) {
+ for (OutputPort outputPort : firstProcessorActivity.getOutputPorts()) {
+ if (outputPort.equals(portName)) {
+ if (mapping.containsKey(portName)) {
+ logger.warn("Can't re-map output for " + "conditional input "
+ + portName);
+ }
+ Edit<Activity<?>> edit = edits.getAddActivityOutputPortMappingEdit(
+ firstProcessorActivity, portName, portName);
+ logger.info("Mapping for conditional non-outgoing activity port binding "
+ + portName);
+ compoundEdit.add(edit);
+ newOutputs.add(portName);
+ }
+ }
+ }
+ }
+ }
+ // Remove any stale bindings that no longer match neither
+ // conditional activity or the processor output ports
+ for (String processorIn : firstProcessorActivity.getInputPortMapping().keySet()) {
+ if (newInputs.contains(processorIn)) {
+ continue;
+ }
+ boolean foundMatch = false;
+ for (InputPort processorPort : processor.getInputPorts()) {
+ if (processorPort.getName().equals(processorIn)) {
+ foundMatch = true;
+ break;
+ }
+ }
+ if (!foundMatch) {
+ Edit<Activity<?>> edit = edits.getRemoveActivityInputPortMappingEdit(
+ firstProcessorActivity, processorIn);
+ logger.info("Removing stale input port binding " + processorIn);
+ compoundEdit.add(edit);
+ }
+ }
+ for (String processorOut : firstProcessorActivity.getOutputPortMapping().keySet()) {
+ if (newInputs.contains(processorOut)) {
+ continue;
+ }
+ boolean foundMatch = false;
+ for (OutputPort processorPort : processor.getOutputPorts()) {
+ if (processorPort.getName().equals(processorOut)) {
+ foundMatch = true;
+ break;
+ }
+ }
+ if (!foundMatch) {
+ Edit<Activity<?>> edit = edits.getRemoveActivityOutputPortMappingEdit(
+ firstProcessorActivity, processorOut);
+ logger.info("Removing stale output port binding " + processorOut);
+ compoundEdit.add(edit);
+ }
+ }
+
+ return compoundEdit;
+ }
+ }
+
+ protected class ResetAction extends AbstractAction {
+ private LoopConfigurationPanel loopConfigurationPanel;
+
+ protected ResetAction(LoopConfigurationPanel loopConfigurationPanel) {
+ super("Reset");
+ this.loopConfigurationPanel = loopConfigurationPanel;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (contextualView != null) {
+ contextualView.refreshView();
+ }
+ loopConfigurationPanel.setConfiguration(loopLayer.getConfiguration());
+ }
+
+ }
+
+}
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopConfigureMenuAction.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopConfigureMenuAction.java
new file mode 100644
index 0000000..3d6700d
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopConfigureMenuAction.java
@@ -0,0 +1,97 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.workbench.loop;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+import uk.org.taverna.scufl2.api.core.Processor;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+
+public class LoopConfigureMenuAction extends AbstractContextualMenuAction {
+
+ public static final URI configureRunningSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/configureRunning");
+
+ private static final URI LOOP_CONFIGURE_URI = URI
+ .create("http://taverna.sf.net/2008/t2workbench/loopConfigure");
+
+ private static final String LOOP_CONFIGURE = "Loop configure";
+
+ private EditManager editManager;
+
+ private FileManager fileManager;
+
+ public LoopConfigureMenuAction() {
+ super(configureRunningSection, 20, LOOP_CONFIGURE_URI);
+ }
+
+ @SuppressWarnings("serial")
+ @Override
+ protected Action createAction() {
+ return new AbstractAction("Looping...") {
+ public void actionPerformed(ActionEvent e) {
+ Processor p = (Processor) getContextualSelection().getSelection();
+ configureLoopLayer(p, e);
+ }
+ };
+ }
+
+ public void configureLoopLayer(Processor p, ActionEvent e) {
+ ObjectNode loopLayer = getLoopLayer(p);
+ if (loopLayer != null) {
+ LoopConfigureAction loopConfigureAction = new LoopConfigureAction(null, null, loopLayer, editManager, fileManager);
+ loopConfigureAction.actionPerformed(e);
+ }
+ }
+
+ public static ObjectNode getLoopLayer(Processor p) {
+ for (DispatchLayer dl : p.getDispatchStack().getLayers()) {
+ if (dl instanceof Loop) {
+ result = (Loop) dl;
+ break;
+ }
+ }
+ return result;
+ }
+
+ public boolean isEnabled() {
+ Object selection = getContextualSelection().getSelection();
+ return (super.isEnabled() && (selection instanceof Processor) && (getLoopLayer((Processor)selection) != null));
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+}
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopContextualView.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopContextualView.java
new file mode 100644
index 0000000..c22f376
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopContextualView.java
@@ -0,0 +1,172 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.loop;
+
+import java.awt.Frame;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.util.Properties;
+
+import javax.swing.Action;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.loop.comparisons.Comparison;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.scufl2.api.core.Processor;
+
+/**
+ * View of a processor, including it's iteration stack, activities, etc.
+ *
+ * @author Stian Soiland-Reyes
+ *
+ */
+public class LoopContextualView extends ContextualView {
+
+ private static final long serialVersionUID = 1L;
+
+ private static Logger logger = Logger.getLogger(LoopContextualView.class);
+
+ private EditManager editManager;
+ private FileManager fileManager;
+
+ private Loop loopLayer;
+
+ private JPanel panel;
+
+ private Processor processor;
+
+ public LoopContextualView(Processor processor, EditManager editManager, FileManager fileManager) {
+ super();
+ this.loopLayer = loopLayer;
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.processor = processor;
+ initialise();
+ initView();
+ }
+
+ @Override
+ public Action getConfigureAction(Frame owner) {
+ return new LoopConfigureAction(owner, this, processor, editManager, fileManager);
+ }
+
+ @Override
+ public void refreshView() {
+ initialise();
+ }
+
+ private void initialise() {
+ if (panel == null) {
+ panel = new JPanel();
+ } else {
+ panel.removeAll();
+ }
+ panel.setLayout(new GridBagLayout());
+ updateUIByConfig();
+ }
+
+ @Override
+ public JComponent getMainFrame() {
+ return panel;
+ }
+
+ @Override
+ public String getViewTitle() {
+ return "Loop of " + processor.getLocalName();
+ }
+
+ protected void updateUIByConfig() {
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.gridx = 0;
+ gbc.gridy = 1;
+ gbc.weightx = 0.1;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+
+ StringBuilder description = new StringBuilder("<html><body>");
+ Properties properties = loopLayer.getConfiguration().getProperties();
+ if (properties.getProperty(ActivityGenerator.COMPARISON,
+ ActivityGenerator.CUSTOM_COMPARISON).equals(
+ ActivityGenerator.CUSTOM_COMPARISON)) {
+ Activity<?> condition = loopLayer.getConfiguration().getCondition();
+ if (condition != null) {
+ description.append("Looping using custom conditional ");
+ if (condition instanceof BeanshellActivity) {
+ String script = ((BeanshellActivity)condition).getConfiguration().getScript();
+ if (script != null) {
+ if (script.length() <= 100) {
+ description.append("<pre>\n");
+ description.append(script);
+ description.append("</pre>\n");
+ }
+ }
+ }
+ } else {
+ description.append("<i>Unconfigured, will not loop</i>");
+ }
+ } else {
+ description.append("The service will be invoked repeatedly ");
+ description.append("until<br> its output <strong>");
+ description.append(properties
+ .getProperty(ActivityGenerator.COMPARE_PORT));
+ description.append("</strong> ");
+
+ Comparison comparison = ActivityGenerator
+ .getComparisonById(properties
+ .getProperty(ActivityGenerator.COMPARISON));
+ description.append(comparison.getName());
+
+ description.append(" the " + comparison.getValueType() + ": <pre>");
+ description.append(properties
+ .getProperty(ActivityGenerator.COMPARE_VALUE));
+ description.append("</pre>");
+
+ String delay = properties.getProperty(ActivityGenerator.DELAY, "");
+ try {
+ if (Double.parseDouble(delay) > 0) {
+ description.append("adding a delay of " + delay
+ + " seconds between loops.");
+ }
+ } catch (NumberFormatException ex) {
+ }
+ }
+ description.append("</body></html>");
+
+ panel.add(new JLabel(description.toString()), gbc);
+ gbc.gridy++;
+
+ revalidate();
+ }
+
+
+
+ @Override
+ public int getPreferredPosition() {
+ return 400;
+ }
+
+}
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopContextualViewFactory.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopContextualViewFactory.java
new file mode 100644
index 0000000..d222849
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopContextualViewFactory.java
@@ -0,0 +1,53 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.loop;
+
+import java.util.Arrays;
+import java.util.List;
+
+import uk.org.taverna.scufl2.api.core.Processor;
+
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+
+public class LoopContextualViewFactory implements ContextualViewFactory<Processor> {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+
+ public boolean canHandle(Object selection) {
+ return selection instanceof Processor;
+ }
+
+ public List<ContextualView> getViews(Processor selection) {
+ return Arrays.asList(new ContextualView[] {new LoopContextualView(selection, editManager, fileManager)});
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+}
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopRemoveMenuAction.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopRemoveMenuAction.java
new file mode 100644
index 0000000..12a9592
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/LoopRemoveMenuAction.java
@@ -0,0 +1,92 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.workbench.loop;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.scufl2.api.core.Processor;
+
+public class LoopRemoveMenuAction extends AbstractContextualMenuAction {
+
+ private static Logger logger = Logger
+ .getLogger(LoopRemoveMenuAction.class);
+
+ public static final URI configureRunningSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/configureRunning");
+
+ private static final URI LOOP_REMOVE_URI = URI
+ .create("http://taverna.sf.net/2008/t2workbench/loopRemove");
+
+ private static final String LOOP_REMOVE = "Loop remove";
+
+ public LoopRemoveMenuAction() {
+ super(configureRunningSection, 25, LOOP_REMOVE_URI);
+ }
+
+ private EditManager editManager;
+ private FileManager fileManager;
+
+
+ @SuppressWarnings("serial")
+ @Override
+ protected Action createAction() {
+ return new AbstractAction("Disable looping") {
+ public void actionPerformed(ActionEvent e) {
+ Processor p = (Processor) getContextualSelection().getSelection();
+ Loop loopLayer = LoopConfigureMenuAction.getLoopLayer(p);
+ Edit<DispatchStack> deleteEdit = editManager.getEdits().getDeleteDispatchLayerEdit(
+ p.getDispatchStack(), loopLayer);
+ // TODO: Should warn before removing "essential" layers
+ try {
+ editManager.doDataflowEdit(fileManager.getCurrentDataflow(),
+ deleteEdit);
+ } catch (EditException ex) {
+ logger.warn("Could not remove layer " + loopLayer, ex);
+ }
+
+ }
+ };
+ }
+
+ public boolean isEnabled() {
+ Object selection = getContextualSelection().getSelection();
+ return (super.isEnabled() && (selection instanceof Processor) && (LoopConfigureMenuAction.getLoopLayer((Processor)selection) != null));
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+}
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/Comparison.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/Comparison.java
new file mode 100644
index 0000000..608030c
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/Comparison.java
@@ -0,0 +1,47 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.loop.comparisons;
+
+import net.sf.taverna.t2.workbench.loop.LoopConfigurationPanel;
+
+/**
+ * A comparison beanshell template for {@link LoopConfigurationPanel}.
+ * <p>
+ * A comparison is a template for generating a beanshell that can be used for
+ * comparisons in say the {@link Loop} layer.
+ *
+ * @author Stian Soiland-Reyes
+ *
+ */
+public abstract class Comparison {
+
+ public String toString() {
+ return getName();
+ }
+
+ public abstract String getId();
+
+ public abstract String getName();
+
+ public abstract String getValueType();
+
+ public abstract String getScriptTemplate();
+}
\ No newline at end of file
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/EqualTo.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/EqualTo.java
new file mode 100644
index 0000000..dbfb8f5
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/EqualTo.java
@@ -0,0 +1,40 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.loop.comparisons;
+
+public class EqualTo extends Comparison {
+
+ public String getId() {
+ return "EqualTo";
+ }
+
+ public String getName() {
+ return "is equal to";
+ }
+
+ public String getScriptTemplate() {
+ return "${loopPort} = \"\" + ! ${port}.equals(${value}); ";
+ }
+
+ public String getValueType() {
+ return "string";
+ }
+}
\ No newline at end of file
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/IsGreaterThan.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/IsGreaterThan.java
new file mode 100644
index 0000000..fc6f56b
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/IsGreaterThan.java
@@ -0,0 +1,40 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.loop.comparisons;
+
+public class IsGreaterThan extends Comparison {
+
+ public String getId() {
+ return "IsGreaterThan";
+ }
+
+ public String getName() {
+ return "is greater than";
+ }
+
+ public String getScriptTemplate() {
+ return "${loopPort} = \"\" + (! (Double.parseDouble(${port}) > Double.parseDouble(${value})));";
+ }
+
+ public String getValueType() {
+ return "number";
+ }
+}
\ No newline at end of file
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/IsLessThan.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/IsLessThan.java
new file mode 100644
index 0000000..d5fe38c
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/IsLessThan.java
@@ -0,0 +1,40 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.loop.comparisons;
+
+public class IsLessThan extends Comparison {
+
+ public String getId() {
+ return "IsLessThan";
+ }
+
+ public String getName() {
+ return "is less than";
+ }
+
+ public String getScriptTemplate() {
+ return "${loopPort} = \"\" + (! (Double.parseDouble(${port}) < Double.parseDouble(${value})));";
+ }
+
+ public String getValueType() {
+ return "number";
+ }
+}
\ No newline at end of file
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/Matches.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/Matches.java
new file mode 100644
index 0000000..fa84aeb
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/Matches.java
@@ -0,0 +1,40 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.loop.comparisons;
+
+public class Matches extends Comparison {
+
+ public String getId() {
+ return "Matches";
+ }
+
+ public String getName() {
+ return "matches";
+ }
+
+ public String getScriptTemplate() {
+ return "${loopPort} = \"\" + ! ${port}.matches(${value});";
+ }
+
+ public String getValueType() {
+ return "regular expression";
+ }
+}
\ No newline at end of file
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/NotEqualTo.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/NotEqualTo.java
new file mode 100644
index 0000000..9c73835
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/NotEqualTo.java
@@ -0,0 +1,40 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.loop.comparisons;
+
+public class NotEqualTo extends Comparison {
+
+ public String getId() {
+ return "NotEqualTo";
+ }
+
+ public String getName() {
+ return "is not equal to";
+ }
+
+ public String getScriptTemplate() {
+ return "${loopPort} = \"\" + ${port}.equals(${value});";
+ }
+
+ public String getValueType() {
+ return "string";
+ }
+}
\ No newline at end of file
diff --git a/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/NotMatches.java b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/NotMatches.java
new file mode 100644
index 0000000..803d5d7
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/java/net/sf/taverna/t2/workbench/loop/comparisons/NotMatches.java
@@ -0,0 +1,40 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.loop.comparisons;
+
+public class NotMatches extends Comparison {
+
+ public String getId() {
+ return "NotMatches";
+ }
+
+ public String getName() {
+ return "does not match";
+ }
+
+ public String getScriptTemplate() {
+ return "${loopPort} = \"\" + ${port}.matches(${value});";
+ }
+
+ public String getValueType() {
+ return "regular expression";
+ }
+}
\ No newline at end of file
diff --git a/taverna-workbench-loop-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-workbench-loop-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
new file mode 100644
index 0000000..1956a3f
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
@@ -0,0 +1,3 @@
+net.sf.taverna.t2.workbench.loop.LoopConfigureMenuAction
+net.sf.taverna.t2.workbench.loop.LoopAddMenuAction
+net.sf.taverna.t2.workbench.loop.LoopRemoveMenuAction
diff --git a/taverna-workbench-loop-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.AddLayerFactorySPI b/taverna-workbench-loop-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.AddLayerFactorySPI
new file mode 100644
index 0000000..52eafc4
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.AddLayerFactorySPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.workbench.loop.AddLoopFactory
diff --git a/taverna-workbench-loop-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-workbench-loop-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
new file mode 100644
index 0000000..9150066
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
@@ -0,0 +1 @@
+net.sf.taverna.t2.workbench.loop.LoopContextualViewFactory
diff --git a/taverna-workbench-loop-ui/src/main/resources/META-INF/spring/loop-ui-context-osgi.xml b/taverna-workbench-loop-ui/src/main/resources/META-INF/spring/loop-ui-context-osgi.xml
new file mode 100644
index 0000000..4abb75f
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/resources/META-INF/spring/loop-ui-context-osgi.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="AddLoopFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.AddLayerFactorySPI" />
+
+ <service ref="LoopConfigureMenuAction" auto-export="interfaces" />
+ <service ref="LoopAddMenuAction" auto-export="interfaces" />
+ <service ref="LoopRemoveMenuAction" auto-export="interfaces" />
+
+ <service ref="LoopContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+
+ <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
+ <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
+ <reference id="selectionManager" interface="net.sf.taverna.t2.workbench.selection.SelectionManager" />
+ <reference id="applicationConfig" interface="uk.org.taverna.configuration.app.ApplicationConfiguration"/>
+</beans:beans>
diff --git a/taverna-workbench-loop-ui/src/main/resources/META-INF/spring/loop-ui-context.xml b/taverna-workbench-loop-ui/src/main/resources/META-INF/spring/loop-ui-context.xml
new file mode 100644
index 0000000..4c2133c
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/main/resources/META-INF/spring/loop-ui-context.xml
@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="AddLoopFactory" class="net.sf.taverna.t2.workbench.loop.AddLoopFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="applicationConfig" ref="applicationConfig" />
+ </bean>
+
+ <bean id="LoopConfigureMenuAction" class="net.sf.taverna.t2.workbench.loop.LoopConfigureMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ </bean>
+ <bean id="LoopAddMenuAction" class="net.sf.taverna.t2.workbench.loop.LoopAddMenuAction">
+ <property name="addLoopFactory">
+ <ref local="AddLoopFactory"/>
+ </property>
+ </bean>
+ <bean id="LoopRemoveMenuAction" class="net.sf.taverna.t2.workbench.loop.LoopRemoveMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ </bean>
+
+ <bean id="LoopContextualViewFactory" class="net.sf.taverna.t2.workbench.loop.LoopContextualViewFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ </bean>
+
+</beans>
diff --git a/taverna-workbench-loop-ui/src/test/java/net/sf/taverna/t2/workbench/loop/ShowContextualView.java b/taverna-workbench-loop-ui/src/test/java/net/sf/taverna/t2/workbench/loop/ShowContextualView.java
new file mode 100644
index 0000000..3e3d121
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/test/java/net/sf/taverna/t2/workbench/loop/ShowContextualView.java
@@ -0,0 +1,121 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.loop;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+
+import uk.org.taverna.scufl2.api.container.WorkflowBundle;
+import uk.org.taverna.scufl2.api.core.Processor;
+
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.edits.impl.EditManagerImpl;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.file.impl.FileManagerImpl;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.selection.impl.SelectionManagerImpl;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.impl.ContextualViewComponent;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactoryRegistry;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.impl.ContextualViewFactoryRegistryImpl;
+
+/**
+ * A standalone application to show contextual views
+ * <p>
+ * The application shows a JFrame containing a contextual view, together with
+ * buttons which will select items in the {@link SelectionManager} for a
+ * (rather) empty current dataflow.
+ *
+ * @author Stian Soiland-Reyes.
+ *
+ */
+public class ShowContextualView {
+
+ public static void main(String[] args) throws Exception {
+ EditManager editManager = new EditManagerImpl();
+ FileManager fileManager = new FileManagerImpl(editManager);
+ ContextualViewFactoryRegistry contextualViewFactoryRegistry = new ContextualViewFactoryRegistryImpl();
+ SelectionManagerImpl selectionMan = new SelectionManagerImpl();
+ selectionMan.setFileManager(fileManager);
+ selectionMan.setEditManager(editManager);
+ new ShowContextualView(editManager, fileManager,selectionMan, contextualViewFactoryRegistry).showFrame();
+ }
+
+ private SelectionManager selectionManager;
+ private FileManager fileManager;
+ private EditManager editManager;
+ private ContextualViewFactoryRegistry contextualViewFactoryRegistry;
+
+ private uk.org.taverna.scufl2.api.core.Processor processor;
+
+ private WorkflowBundle currentDataflow;
+
+ public ShowContextualView(EditManager editManager, FileManager fileManager, final SelectionManager selectionManager, ContextualViewFactoryRegistry contextualViewFactoryRegistry) {
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.selectionManager = selectionManager;
+ this.contextualViewFactoryRegistry = contextualViewFactoryRegistry;
+ currentDataflow = fileManager.newDataflow();
+ makeProcessor();
+
+ }
+
+ private void makeProcessor() {
+ processor = new Processor(currentDataflow.getMainWorkflow(), "Hello");
+ }
+
+ private List getSelections() {
+ return Arrays.asList(processor, currentDataflow);
+ }
+
+ private Component makeSelectionButtons() {
+ JPanel buttons = new JPanel();
+ for (final Object selection : getSelections()) {
+ buttons.add(new JButton(new AbstractAction("" + selection) {
+ public void actionPerformed(ActionEvent e) {
+ selectionManager.getDataflowSelectionModel(
+ currentDataflow).setSelection(
+ Collections.<Object> singleton(selection));
+ }
+ }));
+ }
+ return buttons;
+ }
+
+ protected void showFrame() {
+ JFrame frame = new JFrame(getClass().getName());
+ ContextualViewComponent contextualViewComponent = new ContextualViewComponent(editManager, selectionManager, contextualViewFactoryRegistry);
+ frame.add(contextualViewComponent, BorderLayout.CENTER);
+
+ frame.add(makeSelectionButtons(), BorderLayout.NORTH);
+ frame.setSize(400, 400);
+ frame.setVisible(true);
+ }
+
+}
diff --git a/taverna-workbench-loop-ui/src/test/resources/log4j.properties b/taverna-workbench-loop-ui/src/test/resources/log4j.properties
new file mode 100644
index 0000000..850ede3
--- /dev/null
+++ b/taverna-workbench-loop-ui/src/test/resources/log4j.properties
@@ -0,0 +1,10 @@
+log4j.rootLogger=WARN, CONSOLE
+log4j.logger.net.sf.taverna.t2=INFO
+#log4j.logger.net.sf.taverna.t2.ui=DEBUG
+
+#log4j.logger.org.apache.commons.httpclient=ERROR
+
+# Default output to console
+log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
+log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
+log4j.appender.CONSOLE.layout.ConversionPattern=%-5p %d{ISO8601} (%c:%L) - %m%n
\ No newline at end of file
diff --git a/taverna-workbench-menu-items/pom.xml b/taverna-workbench-menu-items/pom.xml
new file mode 100644
index 0000000..c7007e3
--- /dev/null
+++ b/taverna-workbench-menu-items/pom.xml
@@ -0,0 +1,73 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna.t2</groupId>
+ <artifactId>ui-exts</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>menu-items</artifactId>
+ <packaging>bundle</packaging>
+ <name>Additional menu items</name>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>menu-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>report-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>selection-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>workbench-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>design-ui</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>graph-view</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>workflow-view</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.lang</groupId>
+ <artifactId>ui</artifactId>
+ <version>${t2.lang.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.commons</groupId>
+ <artifactId>taverna-services-api</artifactId>
+ <version>0.1.0-SNAPSHOT</version>
+ </dependency>
+
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>stringconstant-activity-ui</artifactId>
+ <version>${t2.ui.activities.version}</version>
+ </dependency>
+ <!-- TODO remove dependencies on implementations -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>contextual-views-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency>
+ </dependencies>
+</project>
\ No newline at end of file
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/AbstractConnectPortMenuActions.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/AbstractConnectPortMenuActions.java
new file mode 100644
index 0000000..2bbed5b
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/AbstractConnectPortMenuActions.java
@@ -0,0 +1,268 @@
+package net.sf.taverna.t2.ui.menu.items.activityport;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.Action;
+import javax.swing.Icon;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.common.NamedSet;
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.core.Processor;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.port.InputPort;
+import uk.org.taverna.scufl2.api.port.InputProcessorPort;
+import uk.org.taverna.scufl2.api.port.InputWorkflowPort;
+import uk.org.taverna.scufl2.api.port.OutputProcessorPort;
+import uk.org.taverna.scufl2.api.port.OutputWorkflowPort;
+import uk.org.taverna.scufl2.api.port.Port;
+import uk.org.taverna.scufl2.api.port.ProcessorPort;
+import uk.org.taverna.scufl2.api.port.ReceiverPort;
+import uk.org.taverna.scufl2.api.port.SenderPort;
+import uk.org.taverna.scufl2.api.port.WorkflowPort;
+import uk.org.taverna.scufl2.api.profiles.Profile;
+
+import net.sf.taverna.t2.lang.ui.ShadedLabel;
+import net.sf.taverna.t2.ui.menu.AbstractMenuCustom;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+import net.sf.taverna.t2.ui.menu.MenuManager;
+import net.sf.taverna.t2.ui.menu.MenuManager.ComponentFactory;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.configuration.workbench.WorkbenchConfiguration;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+
+public abstract class AbstractConnectPortMenuActions extends AbstractMenuCustom
+ implements ContextualMenuComponent {
+
+ protected ActivityIconManager activityIconManager;
+ protected ContextualSelection contextualSelection;
+ protected MenuManager menuManager;
+ protected WorkbenchConfiguration workbenchConfiguration;
+ protected ColourManager colourManager;
+ private EditManager editManager;
+
+ public static final String CONNECT_AS_INPUT_TO = "Connect as input to...";
+ public static final String CONNECT_WITH_OUTPUT_FROM = "Connect with output from...";
+
+ public static final String SERVICE_INPUT_PORTS = "Service input ports";
+ public static final String SERVICE_OUTPUT_PORTS = "Service output ports";
+
+ public static final String NEW_WORKFLOW_INPUT_PORT = "New workflow input port...";
+ public static final String NEW_WORKFLOW_OUTPUT_PORT = "New workflow output port...";
+
+ public static final String WORKFLOW_INPUT_PORTS = "Workflow input ports";
+ public static final String WORKFLOW_OUTPUT_PORTS = "Workflow output ports";
+
+ public static final String SERVICES = "Services";
+
+ private Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ public AbstractConnectPortMenuActions(URI parentId, int positionHint) {
+ super(parentId, positionHint);
+ }
+
+ public ContextualSelection getContextualSelection() {
+ return contextualSelection;
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ this.customComponent = null;
+ }
+
+ @Override
+ protected Component createCustomComponent() {
+ Workflow workflow = (Workflow) getContextualSelection().getParent();
+ Profile profile = workflow.getParent().getMainProfile();
+ Port port = getSelectedPort();
+ // Component component =
+ // getContextualSelection().getRelativeToComponent();
+
+ String label;
+ if (port instanceof ReceiverPort) {
+ label = CONNECT_WITH_OUTPUT_FROM;
+ } else {
+ label = CONNECT_AS_INPUT_TO;
+ }
+ JMenu connectMenu = new JMenu(new DummyAction(label,
+ WorkbenchIcons.datalinkIcon));
+ addPortMenuItems(workflow, port, connectMenu);
+ addProcessorMenuItems(workflow, profile, port, connectMenu);
+ return connectMenu;
+ }
+
+ private Port getSelectedPort() {
+ Port port = (Port) getContextualSelection().getSelection();
+ return port;
+ }
+
+ protected void addPortMenuItems(Workflow workflow, Port port, JMenu connectMenu) {
+ Color workflowPortColour = colourManager.getPreferredColour(WorkflowPort.class.getCanonicalName());
+
+ boolean addedPorts = false;
+ if (port instanceof SenderPort) {
+ connectMenu.add(new ShadedLabel(WORKFLOW_OUTPUT_PORTS, workflowPortColour));
+ for (OutputWorkflowPort outputWorkflowPort : workflow.getOutputPorts()) {
+ ConnectPortsAction connectPortsAction =
+ new ConnectPortsAction(workflow, (SenderPort) port, outputWorkflowPort, editManager);
+ connectPortsAction.putValue(Action.SMALL_ICON, WorkbenchIcons.outputIcon);
+ connectPortsAction.putValue(Action.NAME, outputWorkflowPort.getName());
+ connectMenu.add(new JMenuItem(connectPortsAction));
+ addedPorts = true;
+ }
+ } else if (port instanceof ReceiverPort) {
+ connectMenu.add(new ShadedLabel(WORKFLOW_INPUT_PORTS, workflowPortColour));
+ for (InputWorkflowPort inputWorkflowPort : workflow.getInputPorts()) {
+ ConnectPortsAction connectPortsAction =
+ new ConnectPortsAction(workflow, inputWorkflowPort, (ReceiverPort) port, editManager);
+ connectPortsAction.putValue(Action.SMALL_ICON, WorkbenchIcons.inputIcon);
+ connectPortsAction.putValue(Action.NAME, inputWorkflowPort.getName());
+ connectMenu.add(new JMenuItem(connectPortsAction));
+ addedPorts = true;
+ }
+ }
+ if (addedPorts) {
+ connectMenu.addSeparator();
+ }
+ CreateAndConnectDataflowPortAction newDataflowPortAction = new CreateAndConnectDataflowPortAction(
+ workflow, port, getSuggestedName(port), contextualSelection.getRelativeToComponent(), editManager);
+
+ if (port instanceof ReceiverPort) {
+ newDataflowPortAction.putValue(Action.NAME, NEW_WORKFLOW_INPUT_PORT);
+ } else if (port instanceof SenderPort) {
+ newDataflowPortAction.putValue(Action.NAME, NEW_WORKFLOW_OUTPUT_PORT);
+ }
+ newDataflowPortAction.putValue(Action.SMALL_ICON, WorkbenchIcons.newIcon);
+ connectMenu.add(new JMenuItem(newDataflowPortAction));
+ }
+
+ /**
+ * @param port
+ * @return
+ */
+ private String getSuggestedName(Port port) {
+ String suggestedName;
+ if (port instanceof ProcessorPort) {
+ suggestedName = ((ProcessorPort) port).getParent().getName() + "_" + port.getName();
+ } else {
+ suggestedName = port.getName();
+ }
+ return suggestedName;
+ }
+
+ protected void addProcessorMenuItems(Workflow dataflow, Profile profile,
+ final Port targetPort, JMenu connectMenu) {
+ final Set<Processor> processors = findProcessors(dataflow, targetPort);
+ if (processors.isEmpty()) {
+ return;
+ }
+ connectMenu.add(new ShadedLabel(SERVICES, colourManager.getPreferredColour(Processor.class.getCanonicalName())));
+
+ List<JMenuItem> menuItems = new ArrayList<JMenuItem>();
+ for (Processor processor : processors) {
+ Activity activity = scufl2Tools.processorBindingForProcessor(processor, profile).getBoundActivity();
+ Icon icon = activityIconManager.iconForActivity(activity);
+ final Color processorPortColour = colourManager.getPreferredColour(ProcessorPort.class.getCanonicalName());
+
+ JMenu processorMenu = new JMenu(new DummyAction(processor.getName(), icon));
+ List<JMenuItem> processorMenuItems = new ArrayList<JMenuItem>();
+ if (targetPort instanceof ReceiverPort) {
+ processorMenu.add(new ShadedLabel(SERVICE_OUTPUT_PORTS,
+ processorPortColour));
+ menuItems.add(processorMenu);
+ for (OutputProcessorPort outputProcessorPort : processor.getOutputPorts()) {
+ ConnectPortsAction connectPortsAction = new ConnectPortsAction(dataflow,
+ outputProcessorPort, (ReceiverPort) targetPort, editManager);
+ connectPortsAction.putValue(Action.SMALL_ICON,
+ WorkbenchIcons.outputPortIcon);
+ connectPortsAction.putValue(Action.NAME, outputProcessorPort.getName());
+ processorMenuItems.add(new JMenuItem(connectPortsAction));
+ }
+ } else if (targetPort instanceof SenderPort) {
+ processorMenu.add(new ShadedLabel(SERVICE_INPUT_PORTS,
+ processorPortColour));
+ menuItems.add(processorMenu);
+ for (InputProcessorPort inputProcessorPort : processor.getInputPorts()) {
+ ConnectPortsAction connectPortsAction = new ConnectPortsAction(dataflow,
+ (SenderPort) targetPort, inputProcessorPort, editManager);
+ connectPortsAction.putValue(Action.SMALL_ICON,
+ WorkbenchIcons.inputPortIcon);
+ connectPortsAction.putValue(Action.NAME, inputProcessorPort.getName());
+ processorMenuItems.add(new JMenuItem(connectPortsAction));
+ }
+ }
+
+ menuManager.addMenuItemsWithExpansion(processorMenuItems,
+ processorMenu, workbenchConfiguration.getMaxMenuItems(),
+ new ComponentFactory() {
+ public Component makeComponent() {
+ if (targetPort instanceof InputPort) {
+ return new ShadedLabel(SERVICE_OUTPUT_PORTS, processorPortColour);
+ } else {
+ return new ShadedLabel(SERVICE_INPUT_PORTS, processorPortColour);
+ }
+ }
+ });
+ }
+ menuManager.addMenuItemsWithExpansion(menuItems, connectMenu,
+ workbenchConfiguration.getMaxMenuItems(),
+ new ComponentFactory() {
+ public Component makeComponent() {
+ return new ShadedLabel(SERVICES, colourManager
+ .getPreferredColour(Processor.class
+ .getCanonicalName()));
+ }
+ });
+ }
+
+ protected Set<Processor> findProcessors(Workflow dataflow, Port targetPort) {
+ Set<Processor> possibleProcessors = new HashSet<Processor>();
+ if (targetPort instanceof InputProcessorPort) {
+ InputProcessorPort inputProcessorPort = (InputProcessorPort) targetPort;
+ possibleProcessors = scufl2Tools.possibleUpStreamProcessors(dataflow, inputProcessorPort.getParent());
+ } else if (targetPort instanceof OutputProcessorPort) {
+ OutputProcessorPort outputProcessorPort = (OutputProcessorPort) targetPort;
+ possibleProcessors = scufl2Tools.possibleDownStreamProcessors(dataflow, outputProcessorPort.getParent());
+ } else {
+ // Probably a dataflow port, everything is allowed
+ possibleProcessors = dataflow.getProcessors();
+ }
+ return possibleProcessors;
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setMenuManager(MenuManager menuManager) {
+ this.menuManager = menuManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setWorkbenchConfiguration(WorkbenchConfiguration workbenchConfiguration) {
+ this.workbenchConfiguration = workbenchConfiguration;
+ }
+
+ public void setColourManager(ColourManager colourManager) {
+ this.colourManager = colourManager;
+ }
+
+}
\ No newline at end of file
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ActivityInputPortSection.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ActivityInputPortSection.java
new file mode 100644
index 0000000..89414d6
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ActivityInputPortSection.java
@@ -0,0 +1,67 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.activityport;
+
+import java.net.URI;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractMenuSection;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+import net.sf.taverna.t2.ui.menu.DefaultContextualMenu;
+import uk.org.taverna.scufl2.api.port.InputProcessorPort;
+
+public class ActivityInputPortSection extends AbstractMenuSection implements
+ ContextualMenuComponent {
+
+ private static final String ACTIVITY_INPUT_PORT = "Service input port: ";
+ public static final URI activityInputPortSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/activityInputPort");
+ private ContextualSelection contextualSelection;
+
+ public ActivityInputPortSection() {
+ super(DefaultContextualMenu.DEFAULT_CONTEXT_MENU, 10,
+ activityInputPortSection);
+ }
+
+ public ContextualSelection getContextualSelection() {
+ return contextualSelection;
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return getContextualSelection().getSelection() instanceof InputProcessorPort;
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ this.action = null;
+ }
+
+ @Override
+ protected Action createAction() {
+ InputProcessorPort port = (InputProcessorPort) getContextualSelection().getSelection();
+ String name = ACTIVITY_INPUT_PORT + port.getName();
+ return new DummyAction(name);
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ActivityOutputPortSection.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ActivityOutputPortSection.java
new file mode 100644
index 0000000..b26cff9
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ActivityOutputPortSection.java
@@ -0,0 +1,67 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.activityport;
+
+import java.net.URI;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractMenuSection;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+import net.sf.taverna.t2.ui.menu.DefaultContextualMenu;
+import uk.org.taverna.scufl2.api.port.OutputProcessorPort;
+
+public class ActivityOutputPortSection extends AbstractMenuSection implements
+ ContextualMenuComponent {
+
+ private static final String ACTIVITY_OUTPUT_PORT = "Service output port: ";
+ public static final URI activityOutputPortSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/activityOutputPort");
+ private ContextualSelection contextualSelection;
+
+ public ActivityOutputPortSection() {
+ super(DefaultContextualMenu.DEFAULT_CONTEXT_MENU, 10,
+ activityOutputPortSection);
+ }
+
+ public ContextualSelection getContextualSelection() {
+ return contextualSelection;
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return getContextualSelection().getSelection() instanceof OutputProcessorPort;
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ this.action = null;
+ }
+
+ @Override
+ protected Action createAction() {
+ OutputProcessorPort port = (OutputProcessorPort) getContextualSelection().getSelection();
+ String name = ACTIVITY_OUTPUT_PORT + port.getName();
+ return new DummyAction(name);
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/AddInputPortDefaultValueAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/AddInputPortDefaultValueAction.java
new file mode 100644
index 0000000..414ffac
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/AddInputPortDefaultValueAction.java
@@ -0,0 +1,150 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.menu.items.activityport;
+
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JOptionPane;
+
+import net.sf.taverna.t2.activities.stringconstant.views.StringConstantConfigView;
+import net.sf.taverna.t2.workbench.design.actions.DataflowEditAction;
+import net.sf.taverna.t2.workbench.edits.CompoundEdit;
+import net.sf.taverna.t2.workbench.edits.Edit;
+import net.sf.taverna.t2.workbench.edits.EditException;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workflow.edits.AddChildEdit;
+import net.sf.taverna.t2.workflow.edits.AddDataLinkEdit;
+import net.sf.taverna.t2.workflow.edits.AddProcessorEdit;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+import uk.org.taverna.scufl2.api.core.DataLink;
+import uk.org.taverna.scufl2.api.core.Processor;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.iterationstrategy.CrossProduct;
+import uk.org.taverna.scufl2.api.port.InputProcessorPort;
+import uk.org.taverna.scufl2.api.port.OutputActivityPort;
+import uk.org.taverna.scufl2.api.port.OutputProcessorPort;
+import uk.org.taverna.scufl2.api.profiles.ProcessorBinding;
+import uk.org.taverna.scufl2.api.profiles.ProcessorOutputPortBinding;
+import uk.org.taverna.scufl2.api.profiles.Profile;
+
+/**
+ * Action for adding a default value to an input port of a processor.
+ *
+ * @author Alex Nenadic
+ */
+@SuppressWarnings("serial")
+public class AddInputPortDefaultValueAction extends DataflowEditAction {
+
+ private static Logger logger = Logger.getLogger(AddInputPortDefaultValueAction.class);
+
+ private static final URI STRING_CONSTANT = URI
+ .create("http://ns.taverna.org.uk/2010/activity/constant");
+
+ private InputProcessorPort inputPort;
+
+ private final ServiceRegistry serviceRegistry;
+
+ public AddInputPortDefaultValueAction(Workflow workflow, InputProcessorPort inputPort,
+ Component component, EditManager editManager, SelectionManager selectionManager,
+ ServiceRegistry serviceRegistry) {
+ super(workflow, component, editManager, selectionManager);
+ this.inputPort = inputPort;
+ this.serviceRegistry = serviceRegistry;
+ putValue(SMALL_ICON, WorkbenchIcons.inputValueIcon);
+ putValue(NAME, "Set constant value");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ try {
+ Activity activity = new Activity();
+ activity.setType(STRING_CONSTANT);
+ Configuration configuration = new Configuration();
+ configuration.setType(STRING_CONSTANT.resolve("#Config"));
+ configuration.getJsonAsObjectNode().put("string", "");
+ configuration.setConfigures(activity);
+
+ StringConstantConfigView configView = new StringConstantConfigView(activity,
+ configuration, serviceRegistry);
+
+ int answer = JOptionPane.showConfirmDialog(component, configView,
+ "Text constant value", JOptionPane.OK_CANCEL_OPTION);
+ if (answer != JOptionPane.CANCEL_OPTION) {
+
+ configView.noteConfiguration();
+ configuration.setJson(configView.getJson());
+
+ Profile profile = selectionManager.getSelectedProfile();
+
+ Processor processor = new Processor();
+ processor.setName(inputPort.getName() + "_value");
+
+ CrossProduct crossProduct = new CrossProduct();
+ crossProduct.setParent(processor.getIterationStrategyStack());
+
+ ProcessorBinding processorBinding = new ProcessorBinding();
+ processorBinding.setBoundProcessor(processor);
+ processorBinding.setBoundActivity(activity);
+
+ // create activity port
+ OutputActivityPort activityPort = new OutputActivityPort(activity, "value");
+ activityPort.setDepth(0);
+ activityPort.setGranularDepth(0);
+ // create processor port
+ OutputProcessorPort processorPort = new OutputProcessorPort(processor,
+ activityPort.getName());
+ processorPort.setDepth(0);
+ processorPort.setGranularDepth(0);
+ // add a new port binding
+ new ProcessorOutputPortBinding(processorBinding, activityPort, processorPort);
+
+ // Add a data link between the string constant processor's output port
+ // and the processor containing the passed inputPort.
+ DataLink datalink = new DataLink();
+ datalink.setReceivesFrom(processorPort);
+ datalink.setSendsTo(inputPort);
+
+ List<Edit<?>> editList = new ArrayList<Edit<?>>();
+ editList.add(new AddChildEdit<Profile>(profile, activity));
+ editList.add(new AddChildEdit<Profile>(profile, configuration));
+ editList.add(new AddChildEdit<Profile>(profile, processorBinding));
+ editList.add(new AddProcessorEdit(dataflow, processor));
+ editList.add(new AddDataLinkEdit(dataflow, datalink));
+
+ editManager.doDataflowEdit(dataflow.getParent(), new CompoundEdit(editList));
+
+ }
+ } catch (EditException ex) {
+ logger.error("Adding default value for input port failed", ex);
+ }
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ConnectInputPortMenuActions.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ConnectInputPortMenuActions.java
new file mode 100644
index 0000000..f22ebbc
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ConnectInputPortMenuActions.java
@@ -0,0 +1,41 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.activityport;
+
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.port.InputProcessorPort;
+
+public class ConnectInputPortMenuActions extends AbstractConnectPortMenuActions
+ implements ContextualMenuComponent {
+
+ public ConnectInputPortMenuActions() {
+ super(ActivityInputPortSection.activityInputPortSection, 20);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof InputProcessorPort
+ && getContextualSelection().getParent() instanceof Workflow;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ConnectOutputPortMenuActions.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ConnectOutputPortMenuActions.java
new file mode 100644
index 0000000..2bb3ec0
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ConnectOutputPortMenuActions.java
@@ -0,0 +1,41 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.activityport;
+
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.port.OutputProcessorPort;
+
+
+public class ConnectOutputPortMenuActions extends AbstractConnectPortMenuActions {
+
+ public ConnectOutputPortMenuActions() {
+ super(ActivityOutputPortSection.activityOutputPortSection, 20);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof OutputProcessorPort
+ && getContextualSelection().getParent() instanceof Workflow;
+ }
+
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ConnectPortsAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ConnectPortsAction.java
new file mode 100644
index 0000000..f10fedf
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/ConnectPortsAction.java
@@ -0,0 +1,68 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.activityport;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+
+import net.sf.taverna.t2.workbench.edits.Edit;
+import net.sf.taverna.t2.workbench.edits.EditException;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workflow.edits.AddDataLinkEdit;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.scufl2.api.core.DataLink;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.port.ReceiverPort;
+import uk.org.taverna.scufl2.api.port.SenderPort;
+
+@SuppressWarnings("serial")
+public class ConnectPortsAction extends AbstractAction {
+ private static Logger logger = Logger.getLogger(ConnectPortsAction.class);
+ private final Workflow workflow;
+ private final ReceiverPort receiverPort;
+ private final SenderPort senderPort;
+ private final EditManager editManager;
+
+ public ConnectPortsAction(Workflow workflow,
+ SenderPort senderPort, ReceiverPort receiverPort, EditManager editManager) {
+ super("Connect " + senderPort.getName() + " to " + receiverPort.getName());
+ this.workflow = workflow;
+ this.receiverPort = receiverPort;
+ this.senderPort = senderPort;
+ this.editManager = editManager;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ DataLink dataLink = new DataLink();
+ dataLink.setReceivesFrom(senderPort);
+ dataLink.setSendsTo(receiverPort);
+ Edit<Workflow> edit = new AddDataLinkEdit(workflow, dataLink);
+ try {
+ editManager.doDataflowEdit(workflow.getParent(), edit);
+ } catch (EditException ex) {
+ logger.warn("Can't create connection between " + senderPort
+ + " and " + receiverPort, ex);
+ }
+ }
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/CreateAndConnectDataflowPortAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/CreateAndConnectDataflowPortAction.java
new file mode 100644
index 0000000..534f4ca
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/CreateAndConnectDataflowPortAction.java
@@ -0,0 +1,226 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.activityport;
+
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.AbstractAction;
+
+import net.sf.taverna.t2.lang.ui.ValidatingUserInputDialog;
+import net.sf.taverna.t2.workbench.design.ui.DataflowInputPortPanel;
+import net.sf.taverna.t2.workbench.design.ui.DataflowOutputPortPanel;
+import net.sf.taverna.t2.workbench.edits.CompoundEdit;
+import net.sf.taverna.t2.workbench.edits.Edit;
+import net.sf.taverna.t2.workbench.edits.EditException;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workflow.edits.AddChildEdit;
+import net.sf.taverna.t2.workflow.edits.AddDataLinkEdit;
+import net.sf.taverna.t2.workflow.edits.AddWorkflowInputPortEdit;
+import net.sf.taverna.t2.workflow.edits.AddWorkflowOutputPortEdit;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.scufl2.api.core.DataLink;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.port.DepthPort;
+import uk.org.taverna.scufl2.api.port.InputPort;
+import uk.org.taverna.scufl2.api.port.InputWorkflowPort;
+import uk.org.taverna.scufl2.api.port.OutputPort;
+import uk.org.taverna.scufl2.api.port.OutputWorkflowPort;
+import uk.org.taverna.scufl2.api.port.Port;
+import uk.org.taverna.scufl2.api.port.ReceiverPort;
+import uk.org.taverna.scufl2.api.port.SenderPort;
+
+/**
+ * Action to create a dataflow input/output port and connect it to the specified
+ * processor/activity output/input port.
+ * <p>
+ * The created dataflow port name will be taken from the name of the provided
+ * port.
+ *
+ * @author Stian Soiland-Reyes
+ *
+ */
+@SuppressWarnings("serial")
+public class CreateAndConnectDataflowPortAction extends AbstractAction {
+
+ private static final String VALID_PORT_NAME_REGEX = "[\\p{L}\\p{Digit}_.]+";
+ private static final Dimension INPUT_PORT_DIALOGUE_SIZE = new Dimension(400, 250);
+ private static final Dimension OUTPUT_PORT_DIALOGUE_SIZE = new Dimension(400, 200);
+
+ private static final String INVALID_WORKFLOW_OUTPUT_PORT_NAME = "Invalid workflow output port name.";
+ private static final String DUPLICATE_WORKFLOW_OUTPUT_PORT_NAME = "Duplicate workflow output port name.";
+ private static final String SET_THE_WORKFLOW_OUTPUT_PORT_NAME = "Set the workflow output port name.";
+ private static final String ADD_WORKFLOW_OUTPUT_PORT = "Add workflow output port";
+ private static final String SET_THE_INPUT_PORT_LIST_DEPTH = "Set the input port list depth.";
+ private static final String SET_THE_INPUT_PORT_TYPE = "Set the input port type.";
+ private static final String INVALID_WORKFLOW_INPUT_PORT_NAME = "Invalid workflow input port name.";
+ private static final String DUPLICATE_WORKFLOW_INPUT_PORT_NAME = "Duplicate workflow input port name.";
+ private static final String SET_THE_WORKFLOW_INPUT_PORT_NAME = "Set the workflow input port name.";
+ private static final String ADD_WORKFLOW_INPUT_PORT = "Add workflow input port";
+ private static Logger logger = Logger.getLogger(CreateAndConnectDataflowPortAction.class);
+ private final Workflow workflow;
+
+ private final Port port;
+ private final String suggestedName;
+ private final Component parentComponent;
+ private final EditManager editManager;
+
+ /**
+ * Action for creating a Workflow input/output port and linking it to the
+ * specified port.
+ * <p>
+ * If the provided port is an InputPort then a
+ * Workflow OutputPort will be created and linked. Vice versa, if the
+ * provided port is an OutputPort, a Workflow InputPort will be created.
+ *
+ * @param workflow
+ * Workflow where to create the Workflow input/output port
+ * @param port
+ * Existing Processor port to connect to
+ * @param suggestedName
+ * suggested port name
+ * @param parentComponent
+ * Component to be parent of any pop-ups
+ */
+ public CreateAndConnectDataflowPortAction(Workflow workflow, Port port,
+ String suggestedName, Component parentComponent, EditManager editManager) {
+ super("Connect to new workflow port");
+ this.workflow = workflow;
+ this.port = port;
+ this.suggestedName = suggestedName;
+ this.parentComponent = parentComponent;
+ this.editManager = editManager;
+ if (!(port instanceof InputPort || port instanceof OutputPort)) {
+ throw new IllegalArgumentException("Port " + port
+ + " must be either an InputPort or OutputPort");
+ }
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (port instanceof ReceiverPort) {
+ InputWorkflowPort inputWorkflowPort = new InputWorkflowPort();
+ inputWorkflowPort.setName(suggestedName);
+ workflow.getInputPorts().addWithUniqueName(inputWorkflowPort);
+ workflow.getInputPorts().remove(inputWorkflowPort);
+ if (port instanceof DepthPort) {
+ inputWorkflowPort.setDepth(((DepthPort) port).getDepth());
+ } else {
+ inputWorkflowPort.setDepth(0);
+ }
+ showDialogue(inputWorkflowPort);
+
+ } else if (port instanceof SenderPort) {
+ OutputWorkflowPort outputWorkflowPort = new OutputWorkflowPort();
+ outputWorkflowPort.setName(suggestedName);
+ workflow.getOutputPorts().addWithUniqueName(outputWorkflowPort);
+ workflow.getOutputPorts().remove(outputWorkflowPort);
+ showDialogue(outputWorkflowPort);
+ } else {
+ throw new IllegalStateException("Port " + port
+ + " must be either an InputPort or OutputPort");
+ }
+
+ }
+
+ protected void showDialogue(InputWorkflowPort portTemplate) {
+ Set<String> usedInputPorts = new HashSet<String>();
+ for (InputWorkflowPort usedInputPort : workflow.getInputPorts()) {
+ usedInputPorts.add(usedInputPort.getName());
+ }
+ DataflowInputPortPanel inputPanel = new DataflowInputPortPanel();
+
+ ValidatingUserInputDialog vuid = new ValidatingUserInputDialog(
+ ADD_WORKFLOW_INPUT_PORT, inputPanel);
+ vuid.addTextComponentValidation(inputPanel.getPortNameField(),
+ SET_THE_WORKFLOW_INPUT_PORT_NAME, usedInputPorts,
+ DUPLICATE_WORKFLOW_INPUT_PORT_NAME, VALID_PORT_NAME_REGEX,
+ INVALID_WORKFLOW_INPUT_PORT_NAME);
+ vuid.addMessageComponent(inputPanel.getSingleValueButton(),
+ SET_THE_INPUT_PORT_TYPE);
+ vuid.addMessageComponent(inputPanel.getListValueButton(),
+ SET_THE_INPUT_PORT_LIST_DEPTH);
+ vuid.setSize(INPUT_PORT_DIALOGUE_SIZE);
+
+ inputPanel.setPortName(portTemplate.getName());
+ inputPanel.setPortDepth(portTemplate.getDepth());
+
+ if (vuid.show(parentComponent)) {
+ InputWorkflowPort inputWorkflowPort = new InputWorkflowPort();
+ inputWorkflowPort.setName(inputPanel.getPortName());
+ inputWorkflowPort.setDepth(inputPanel.getPortDepth());
+ List<Edit<?>> editList = new ArrayList<Edit<?>>();
+ editList.add(new AddWorkflowInputPortEdit(workflow, inputWorkflowPort));
+ DataLink dataLink = new DataLink();
+ dataLink.setReceivesFrom(inputWorkflowPort);
+ dataLink.setSendsTo((ReceiverPort) port);
+ editList.add(new AddDataLinkEdit(workflow, dataLink));
+ try {
+ CompoundEdit compoundEdit = new CompoundEdit(editList);
+ editManager.doDataflowEdit(workflow.getParent(), compoundEdit);
+ } catch (EditException ex) {
+ logger.warn("Can't create or connect new input port", ex);
+ }
+
+ }
+ }
+
+ protected void showDialogue(OutputWorkflowPort portTemplate) {
+ Set<String> usedOutputPorts = new HashSet<String>();
+ for (OutputWorkflowPort usedInputPort : workflow.getOutputPorts()) {
+ usedOutputPorts.add(usedInputPort.getName());
+ }
+ DataflowOutputPortPanel outputPanel = new DataflowOutputPortPanel();
+
+ ValidatingUserInputDialog vuid = new ValidatingUserInputDialog(
+ ADD_WORKFLOW_OUTPUT_PORT, outputPanel);
+ vuid.addTextComponentValidation(outputPanel.getPortNameField(),
+ SET_THE_WORKFLOW_OUTPUT_PORT_NAME, usedOutputPorts,
+ DUPLICATE_WORKFLOW_OUTPUT_PORT_NAME,
+ VALID_PORT_NAME_REGEX, INVALID_WORKFLOW_OUTPUT_PORT_NAME);
+ vuid.setSize(OUTPUT_PORT_DIALOGUE_SIZE);
+ outputPanel.setPortName(portTemplate.getName());
+
+ if (vuid.show(parentComponent)) {
+ OutputWorkflowPort outputWorkflowPort = new OutputWorkflowPort();
+ outputWorkflowPort.setName(outputPanel.getPortName());
+ List<Edit<?>> editList = new ArrayList<Edit<?>>();
+ editList.add(new AddWorkflowOutputPortEdit(workflow, outputWorkflowPort));
+ DataLink dataLink = new DataLink();
+ dataLink.setReceivesFrom((SenderPort) port);
+ dataLink.setSendsTo(outputWorkflowPort);
+ editList.add(new AddDataLinkEdit(workflow, dataLink));
+ try {
+ CompoundEdit compoundEdit = new CompoundEdit(editList);
+ editManager.doDataflowEdit(workflow.getParent(), compoundEdit);
+ } catch (EditException ex) {
+ logger.warn("Can't create or connect new workflow output port", ex);
+ }
+ }
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/SetConstantInputPortValueMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/SetConstantInputPortValueMenuAction.java
new file mode 100644
index 0000000..30a91c6
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/SetConstantInputPortValueMenuAction.java
@@ -0,0 +1,73 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.activityport;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.port.InputProcessorPort;
+
+public class SetConstantInputPortValueMenuAction extends AbstractContextualMenuAction {
+
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+ private ServiceRegistry serviceRegistry;
+
+ public SetConstantInputPortValueMenuAction() {
+ super(ActivityInputPortSection.activityInputPortSection, 10);
+ }
+
+ @Override
+ public synchronized Action getAction() {
+ SetDefaultInputPortValueAction action = (SetDefaultInputPortValueAction) super.getAction();
+ action.updateStatus();
+ return action;
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof InputProcessorPort
+ && getContextualSelection().getParent() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+ return new SetDefaultInputPortValueAction(editManager, selectionManager, serviceRegistry);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/SetDefaultInputPortValueAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/SetDefaultInputPortValueAction.java
new file mode 100644
index 0000000..302aaf6
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/activityport/SetDefaultInputPortValueAction.java
@@ -0,0 +1,171 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.menu.items.activityport;
+
+import java.awt.event.ActionEvent;
+import java.util.Set;
+
+import javax.swing.AbstractAction;
+import javax.swing.JOptionPane;
+
+import net.sf.taverna.t2.lang.observer.Observable;
+import net.sf.taverna.t2.lang.observer.Observer;
+import net.sf.taverna.t2.lang.observer.SwingAwareObserver;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+import net.sf.taverna.t2.workbench.selection.DataflowSelectionModel;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.selection.events.DataflowSelectionMessage;
+import net.sf.taverna.t2.workbench.selection.events.PerspectiveSelectionEvent;
+import net.sf.taverna.t2.workbench.selection.events.SelectionManagerEvent;
+import net.sf.taverna.t2.workbench.selection.events.WorkflowBundleSelectionEvent;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.container.WorkflowBundle;
+import uk.org.taverna.scufl2.api.port.InputProcessorPort;
+
+/**
+ * An action that sets a default value to a processor's input port, in case
+ * the input port is selected on the Graph View.
+ *
+ * @author Alex Nenadic
+ */
+@SuppressWarnings("serial")
+public class SetDefaultInputPortValueAction extends AbstractAction {
+
+ /* Current workflow's selection model event observer. */
+ private Observer<DataflowSelectionMessage> workflowSelectionObserver = new DataflowSelectionObserver();
+
+ private final EditManager editManager;
+ private final SelectionManager selectionManager;
+ private final ServiceRegistry serviceRegistry;
+
+ private Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ public SetDefaultInputPortValueAction(EditManager editManager,
+ SelectionManager selectionManager, ServiceRegistry serviceRegistry) {
+ super();
+ this.editManager = editManager;
+ this.selectionManager = selectionManager;
+ this.serviceRegistry = serviceRegistry;
+ putValue(SMALL_ICON, WorkbenchIcons.inputValueIcon);
+ putValue(NAME, "Constant value");
+ putValue(SHORT_DESCRIPTION, "Add a constant value for an input port");
+ setEnabled(false);
+
+ selectionManager.addObserver(new SelectionManagerObserver());
+
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ WorkflowBundle workflowBundle = selectionManager.getSelectedWorkflowBundle();
+ DataflowSelectionModel dataFlowSelectionModel = selectionManager
+ .getDataflowSelectionModel(workflowBundle);
+ // Get selected port
+ Set<Object> selectedWFComponents = dataFlowSelectionModel.getSelection();
+ if (selectedWFComponents.size() > 1) {
+ JOptionPane.showMessageDialog(null,
+ "Only one workflow component should be selected for this action.", "Warning",
+ JOptionPane.WARNING_MESSAGE);
+ } else {
+ Object selectedWFComponent = selectedWFComponents.toArray()[0];
+ if (selectedWFComponent instanceof InputProcessorPort) {
+ new AddInputPortDefaultValueAction(workflowBundle.getMainWorkflow(),
+ (InputProcessorPort) selectedWFComponent, null, editManager,
+ selectionManager, serviceRegistry).actionPerformed(e);
+ }
+ }
+ }
+
+ /**
+ * Check if action should be enabled or disabled and update its status.
+ */
+ public void updateStatus() {
+ WorkflowBundle workflowBundle = selectionManager.getSelectedWorkflowBundle();
+ DataflowSelectionModel selectionModel = selectionManager
+ .getDataflowSelectionModel(workflowBundle);
+
+ // List of all selected objects in the graph view
+ Set<Object> selection = selectionModel.getSelection();
+
+ if (selection.isEmpty()) {
+ setEnabled(false);
+ } else {
+ // Take the first selected item - we only support single selections anyway
+ Object selected = selection.toArray()[0];
+ if (selected instanceof InputProcessorPort) {
+ // If this input port is not already connected to something - enable the button
+ setEnabled(scufl2Tools.datalinksTo((InputProcessorPort) selected).isEmpty());
+ }
+ }
+ }
+
+ /**
+ * Observes events on workflow Selection Manager, i.e. when a workflow
+ * node is selected in the graph view, and enables/disables this action accordingly.
+ */
+ private final class DataflowSelectionObserver implements Observer<DataflowSelectionMessage> {
+
+ public void notify(Observable<DataflowSelectionMessage> sender,
+ DataflowSelectionMessage message) throws Exception {
+ updateStatus();
+ }
+ }
+
+ private final class SelectionManagerObserver extends SwingAwareObserver<SelectionManagerEvent> {
+
+ private static final String DESIGN_PERSPECTIVE_ID = "net.sf.taverna.t2.ui.perspectives.design.DesignPerspective";
+
+ @Override
+ public void notifySwing(Observable<SelectionManagerEvent> sender,
+ SelectionManagerEvent message) {
+ if (message instanceof WorkflowBundleSelectionEvent) {
+ WorkflowBundleSelectionEvent workflowBundleSelectionEvent = (WorkflowBundleSelectionEvent) message;
+ WorkflowBundle oldFlow = workflowBundleSelectionEvent
+ .getPreviouslySelectedWorkflowBundle();
+ WorkflowBundle newFlow = workflowBundleSelectionEvent.getSelectedWorkflowBundle();
+ // Update the buttons status as current dataflow has changed
+ updateStatus();
+
+ // Remove the workflow selection model listener from the previous (if any)
+ // and add to the new workflow (if any)
+ if (oldFlow != null) {
+ selectionManager.getDataflowSelectionModel(oldFlow).removeObserver(
+ workflowSelectionObserver);
+ }
+
+ if (newFlow != null) {
+ selectionManager.getDataflowSelectionModel(newFlow).addObserver(
+ workflowSelectionObserver);
+ }
+ } else if (message instanceof PerspectiveSelectionEvent) {
+ PerspectiveSelectionEvent perspectiveSelectionEvent = (PerspectiveSelectionEvent) message;
+ if (DESIGN_PERSPECTIVE_ID.equals(perspectiveSelectionEvent.getSelectedPerspective().getID())) {
+ updateStatus();
+ } else {
+ setEnabled(false);
+ }
+ }
+ }
+
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/annotated/AnnotatedConfigureMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/annotated/AnnotatedConfigureMenuAction.java
new file mode 100644
index 0000000..7933940
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/annotated/AnnotatedConfigureMenuAction.java
@@ -0,0 +1,77 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.annotated;
+
+import java.awt.event.ActionEvent;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.JOptionPane;
+
+import net.sf.taverna.t2.annotation.Annotated;
+import net.sf.taverna.t2.annotation.AnnotationBeanSPI;
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.ui.menu.items.contextualviews.ConfigureSection;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.annotated.AnnotatedContextualView;
+
+public class AnnotatedConfigureMenuAction extends AbstractContextualMenuAction {
+ private static final String ANNOTATE = "Annotate...";
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+ private List<AnnotationBeanSPI> annotationBeans;
+
+ public AnnotatedConfigureMenuAction() {
+ super(ConfigureSection.configureSection, 40);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled() && (getContextualSelection().getSelection() instanceof Annotated);
+ }
+
+ @SuppressWarnings("serial")
+ @Override
+ protected Action createAction() {
+ return new AbstractAction(ANNOTATE) {
+ public void actionPerformed(ActionEvent e) {
+ AnnotatedContextualView view = new AnnotatedContextualView((Annotated) getContextualSelection().getSelection(),
+ editManager, selectionManager, annotationBeans);
+ JOptionPane.showMessageDialog(null, view.getMainFrame(), "Annotation", JOptionPane.PLAIN_MESSAGE);
+ }
+ };
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setAnnotationBeans(List<AnnotationBeanSPI> annotationBeans) {
+ this.annotationBeans = annotationBeans;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ConfigureRunningContextualMenuSection.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ConfigureRunningContextualMenuSection.java
new file mode 100644
index 0000000..9c459e2
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ConfigureRunningContextualMenuSection.java
@@ -0,0 +1,50 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.contextualviews;
+
+import java.net.URI;
+
+import net.sf.taverna.t2.ui.menu.AbstractMenu;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+
+public class ConfigureRunningContextualMenuSection extends AbstractMenu
+implements ContextualMenuComponent {
+ public static final String CONFIGURE_RUNNING = "Configure running";
+ public static final URI configureRunningSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/configureRunning");
+ private ContextualSelection contextualSelection;
+
+ public ConfigureRunningContextualMenuSection() {
+ super(ConfigureSection.configureSection, 45, configureRunningSection, CONFIGURE_RUNNING);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return true;
+// return super.isEnabled() && contextualSelection instanceof Processor;
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ConfigureSection.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ConfigureSection.java
new file mode 100644
index 0000000..0f1a17f
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ConfigureSection.java
@@ -0,0 +1,61 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.contextualviews;
+
+import java.net.URI;
+
+import net.sf.taverna.t2.ui.menu.AbstractMenuSection;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+
+/**
+ * Menu section containing the actions to add service templates, i.e. activities
+ * than are not readily runnable but need to be configured first. The actual actions that
+ * go into this menu can be found in the ui modules for the activities.
+ *
+ * @author Alex Nenadic
+ *
+ */
+public class ConfigureSection extends AbstractMenuSection
+ implements ContextualMenuComponent {
+
+ public static final URI configureSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/configure");
+ private ContextualSelection contextualSelection;
+
+ public ConfigureSection() {
+ super(EditSection.editSection, 100, configureSection);
+ }
+
+ public ContextualSelection getContextualSelection() {
+ return contextualSelection;
+ }
+
+ @Override
+ public boolean isEnabled() {
+ Object selection = getContextualSelection().getSelection();
+ return super.isEnabled();
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ }
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/EditSection.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/EditSection.java
new file mode 100644
index 0000000..d23ec6e
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/EditSection.java
@@ -0,0 +1,73 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.contextualviews;
+
+import java.net.URI;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.lang.ui.ShadedLabel;
+import net.sf.taverna.t2.ui.menu.AbstractMenuSection;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+import net.sf.taverna.t2.ui.menu.DefaultContextualMenu;
+
+/**
+ * Menu section containing the actions to add service templates, i.e. activities
+ * than are not readily runnable but need to be configured first. The actual actions that
+ * go into this menu can be found in the ui modules for the activities.
+ *
+ * @author Alex Nenadic
+ *
+ */
+public class EditSection extends AbstractMenuSection
+ implements ContextualMenuComponent {
+
+ private static final String EDIT = "Edit";
+ public static final URI editSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/edit");
+ private ContextualSelection contextualSelection;
+
+ public EditSection() {
+ super(DefaultContextualMenu.DEFAULT_CONTEXT_MENU, 10, editSection);
+ }
+
+ public ContextualSelection getContextualSelection() {
+ return contextualSelection;
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled();
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ }
+
+ @Override
+ protected Action createAction() {
+ DummyAction action = new DummyAction(EDIT);
+ // Set the colour for the section
+ action.putValue(AbstractMenuSection.SECTION_COLOR, ShadedLabel.ORANGE);
+ return action;
+ }
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/InsertSection.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/InsertSection.java
new file mode 100644
index 0000000..c1e21f6
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/InsertSection.java
@@ -0,0 +1,63 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.contextualviews;
+
+import java.net.URI;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractMenuSection;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+import net.sf.taverna.t2.ui.menu.DefaultContextualMenu;
+import uk.org.taverna.scufl2.api.core.Workflow;
+
+public class InsertSection extends AbstractMenuSection implements
+ ContextualMenuComponent {
+
+ private static final String INSERT = "Insert";
+ public static final URI insertSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/insert");
+ private ContextualSelection contextualSelection;
+
+ public InsertSection() {
+ super(DefaultContextualMenu.DEFAULT_CONTEXT_MENU, 20, insertSection);
+ }
+
+ public ContextualSelection getContextualSelection() {
+ return contextualSelection;
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof Workflow;
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ }
+
+ @Override
+ protected Action createAction() {
+ return new DummyAction(INSERT);
+ }
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/PasteMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/PasteMenuAction.java
new file mode 100644
index 0000000..8f9b1f9
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/PasteMenuAction.java
@@ -0,0 +1,74 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.contextualviews;
+
+import java.net.URI;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.ui.menu.MenuManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.actions.PasteGraphComponentAction;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.core.Workflow;
+
+public class PasteMenuAction extends AbstractContextualMenuAction {
+
+ private static final URI PASTE_SERVICE_URI = URI
+ .create("http://taverna.sf.net/2008/t2workbench/paste#pasteServiceComponent");
+
+ private EditManager editManager;
+ private MenuManager menuManager;
+ private SelectionManager selectionManager;
+ private ServiceRegistry serviceRegistry;
+
+ public PasteMenuAction() {
+ super(EditSection.editSection, 20, PASTE_SERVICE_URI);
+ }
+
+ @Override
+ protected Action createAction() {
+ return PasteGraphComponentAction.getInstance(editManager, menuManager, selectionManager, serviceRegistry);
+ }
+
+ public boolean isEnabled() {
+ return super.isEnabled() && (getContextualSelection().getSelection() instanceof Workflow);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setMenuManager(MenuManager menuManager) {
+ this.menuManager = menuManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ShowConfigureMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ShowConfigureMenuAction.java
new file mode 100644
index 0000000..49c07a2
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ShowConfigureMenuAction.java
@@ -0,0 +1,165 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.contextualviews;
+
+import java.awt.KeyboardFocusManager;
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.net.URI;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.KeyStroke;
+import javax.swing.text.JTextComponent;
+
+import net.sf.taverna.t2.ui.menu.AbstractMenuAction;
+import net.sf.taverna.t2.ui.menu.DesignOnlyAction;
+import net.sf.taverna.t2.ui.menu.MenuManager;
+import net.sf.taverna.t2.workbench.design.actions.EditDataflowInputPortAction;
+import net.sf.taverna.t2.workbench.design.actions.EditDataflowOutputPortAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.DataflowSelectionModel;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.merge.MergeConfigurationView;
+import net.sf.taverna.t2.workbench.ui.workflowview.WorkflowView;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.container.WorkflowBundle;
+import uk.org.taverna.scufl2.api.core.DataLink;
+import uk.org.taverna.scufl2.api.core.Processor;
+import uk.org.taverna.scufl2.api.port.InputWorkflowPort;
+import uk.org.taverna.scufl2.api.port.OutputWorkflowPort;
+
+public class ShowConfigureMenuAction extends AbstractMenuAction {
+
+ private static Logger logger = Logger.getLogger(ShowConfigureMenuAction.class);
+
+ public static final URI GRAPH_DETAILS_MENU_SECTION = URI
+ .create("http://taverna.sf.net/2008/t2workbench/menu#graphDetailsMenuSection");
+
+ private static final URI SHOW_CONFIGURE_URI = URI
+ .create("http://taverna.sf.net/2008/t2workbench/menu#graphMenuShowConfigureComponent");
+
+ private EditManager editManager;
+
+ private SelectionManager selectionManager;
+
+ private MenuManager menuManager;
+
+ private Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ public ShowConfigureMenuAction() {
+ super(GRAPH_DETAILS_MENU_SECTION, 20, SHOW_CONFIGURE_URI);
+ }
+
+ @Override
+ protected Action createAction() {
+ return new ShowConfigureAction();
+ }
+
+ @SuppressWarnings("serial")
+ protected class ShowConfigureAction extends AbstractAction implements DesignOnlyAction {
+
+ private boolean enabled;
+
+ ShowConfigureAction() {
+ super();
+ putValue(NAME, "Configure");
+ putValue(SHORT_DESCRIPTION, "Configure selected component");
+ putValue(Action.ACCELERATOR_KEY, KeyStroke.getKeyStroke(KeyEvent.VK_ENTER, 0, false));
+
+ KeyboardFocusManager focusManager = KeyboardFocusManager
+ .getCurrentKeyboardFocusManager();
+ focusManager.addPropertyChangeListener(new PropertyChangeListener() {
+ public void propertyChange(PropertyChangeEvent e) {
+ String prop = e.getPropertyName();
+ if ("focusOwner".equals(prop)) {
+ if (e.getNewValue() instanceof JTextComponent) {
+ ShowConfigureAction.super.setEnabled(false);
+ } else {
+ ShowConfigureAction.this.setEnabled(enabled);
+ }
+ }
+ }
+ });
+ }
+
+ @Override
+ public void setEnabled(boolean enabled) {
+ this.enabled = enabled;
+ super.setEnabled(enabled);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ WorkflowBundle workflowBundle = selectionManager.getSelectedWorkflowBundle();
+ DataflowSelectionModel dataFlowSelectionModel = selectionManager
+ .getDataflowSelectionModel(workflowBundle);
+ // Get selected port
+ Set<Object> selectedWFComponents = dataFlowSelectionModel.getSelection();
+ if (selectedWFComponents.size() > 0) {
+ Object component = selectedWFComponents.iterator().next();
+ if (component instanceof Processor) {
+ Action action = WorkflowView.getConfigureAction((Processor) component,
+ menuManager);
+ if (action != null) {
+ action.actionPerformed(e);
+ }
+ } else if (component instanceof DataLink) {
+ DataLink dataLink = (DataLink) component;
+ if (dataLink.getMergePosition() != null) {
+ List<DataLink> datalinks = scufl2Tools.datalinksTo(dataLink.getSendsTo());
+ MergeConfigurationView mergeConfigurationView = new MergeConfigurationView(
+ datalinks, editManager, selectionManager);
+ mergeConfigurationView.setLocationRelativeTo(null);
+ mergeConfigurationView.setVisible(true);
+ }
+ } else if (component instanceof InputWorkflowPort) {
+ InputWorkflowPort port = (InputWorkflowPort) component;
+ new EditDataflowInputPortAction(port.getParent(), port, null, editManager,
+ selectionManager).actionPerformed(e);
+ } else if (component instanceof OutputWorkflowPort) {
+ OutputWorkflowPort port = (OutputWorkflowPort) component;
+ new EditDataflowOutputPortAction(port.getParent(), port, null, editManager,
+ selectionManager).actionPerformed(e);
+ }
+ }
+ }
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setMenuManager(MenuManager menuManager) {
+ this.menuManager = menuManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ShowDetailsContextualMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ShowDetailsContextualMenuAction.java
new file mode 100644
index 0000000..27a47de
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ShowDetailsContextualMenuAction.java
@@ -0,0 +1,65 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.contextualviews;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.workbench.ui.Workbench;
+
+import org.apache.log4j.Logger;
+
+public class ShowDetailsContextualMenuAction extends AbstractContextualMenuAction {
+ private static final String SHOW_DETAILS = "Show details";
+ private String namedComponent = "contextualView";
+
+ private static Logger logger = Logger.getLogger(ShowDetailsContextualMenuAction.class);
+ private Workbench workbench;
+
+ public ShowDetailsContextualMenuAction() {
+ super(ConfigureSection.configureSection, 40);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled();
+ // FIXME: Should we list all the applicable types here?
+ // && getContextualSelection().getSelection() instanceof Processor;
+ }
+
+ @SuppressWarnings("serial")
+ @Override
+ protected Action createAction() {
+ return new AbstractAction(SHOW_DETAILS) {
+ public void actionPerformed(ActionEvent e) {
+ workbench.makeNamedComponentVisible(namedComponent);
+ }
+ };
+ }
+
+ public void setWorkbench(Workbench workbench) {
+ this.workbench = workbench;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ShowDetailsMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ShowDetailsMenuAction.java
new file mode 100644
index 0000000..ae9fee3
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ShowDetailsMenuAction.java
@@ -0,0 +1,81 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.contextualviews;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.KeyStroke;
+
+import net.sf.taverna.t2.ui.menu.AbstractMenuAction;
+import net.sf.taverna.t2.ui.menu.DesignOnlyAction;
+import net.sf.taverna.t2.workbench.ui.Workbench;
+
+public class ShowDetailsMenuAction extends AbstractMenuAction {
+ private static final URI SHOW_DETAILS_URI = URI
+ .create("http://taverna.sf.net/2008/t2workbench/menu#graphMenuShowDetailsComponent");
+
+ private static final String SHOW_DETAILS = "Details";
+ private String namedComponent = "contextualView";
+
+ private Workbench workbench;
+
+ public ShowDetailsMenuAction() {
+ super(ShowConfigureMenuAction.GRAPH_DETAILS_MENU_SECTION, 20, SHOW_DETAILS_URI);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled();
+ // FIXME: Should we list all the applicable types here?
+ // && getContextualSelection().getSelection() instanceof Processor;
+ }
+
+ @Override
+ protected Action createAction() {
+ return new ShowDetailsAction();
+ }
+
+ protected class ShowDetailsAction extends AbstractAction implements DesignOnlyAction {
+
+ ShowDetailsAction() {
+ super();
+ putValue(NAME, "Show details");
+ putValue(SHORT_DESCRIPTION, "Show details of selected component");
+ putValue(Action.ACCELERATOR_KEY,
+ KeyStroke.getKeyStroke(KeyEvent.VK_ENTER, InputEvent.SHIFT_DOWN_MASK));
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ workbench.makeNamedComponentVisible(namedComponent);
+ }
+
+ }
+
+ public void setWorkbench(Workbench workbench) {
+ this.workbench = workbench;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ShowReportsContextualMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ShowReportsContextualMenuAction.java
new file mode 100644
index 0000000..c9d7279
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/contextualviews/ShowReportsContextualMenuAction.java
@@ -0,0 +1,103 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.contextualviews;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.Icon;
+
+import net.sf.taverna.t2.lang.ui.icons.Icons;
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.workbench.report.ReportManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.Workbench;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.scufl2.api.container.WorkflowBundle;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.validation.Status;
+
+public class ShowReportsContextualMenuAction extends AbstractContextualMenuAction {
+
+ private static final String SHOW_REPORTS = "Show validation report";
+ private String namedComponent = "reportView";
+ private ReportManager reportManager;
+ private Workbench workbench;
+ private SelectionManager selectionManager;
+
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ShowReportsContextualMenuAction.class);
+
+ public ShowReportsContextualMenuAction() {
+ /** Right below ShowDetailsContextualMenuAction
+ */
+ super(ConfigureSection.configureSection, 41);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled();
+ }
+
+ @SuppressWarnings("serial")
+ @Override
+ protected Action createAction() {
+ WorkflowBundle parent;
+ if (getContextualSelection().getParent() instanceof Workflow) {
+ parent = ((Workflow)getContextualSelection().getParent()).getParent();
+ } else {
+ parent = selectionManager.getSelectedWorkflowBundle();
+ }
+ Status status = Status.OK;
+ if (reportManager != null) {
+// status = reportManager.getStatus(parent.getMainProfile(), (WorkflowBean) getContextualSelection().getSelection());
+ }
+
+ Icon icon = null;
+ if (status == Status.WARNING) {
+ icon = Icons.warningIcon;
+ } else if (status == Status.SEVERE) {
+ icon = Icons.severeIcon;
+ }
+
+ return new AbstractAction(SHOW_REPORTS, icon) {
+ public void actionPerformed(ActionEvent e) {
+ workbench.makeNamedComponentVisible(namedComponent);
+ }
+ };
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setReportManager(ReportManager reportManager) {
+ this.reportManager = reportManager;
+ }
+
+ public void setWorkbench(Workbench workbench) {
+ this.workbench = workbench;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/controllink/ConditionSection.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/controllink/ConditionSection.java
new file mode 100644
index 0000000..3f67def
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/controllink/ConditionSection.java
@@ -0,0 +1,71 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.controllink;
+
+import java.net.URI;
+
+import javax.swing.Action;
+
+import uk.org.taverna.scufl2.api.core.BlockingControlLink;
+import uk.org.taverna.scufl2.api.core.ControlLink;
+
+import net.sf.taverna.t2.ui.menu.AbstractMenuSection;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+import net.sf.taverna.t2.ui.menu.DefaultContextualMenu;
+
+public class ConditionSection extends AbstractMenuSection implements
+ ContextualMenuComponent {
+
+ private static final String CONTROL_LINK = "Control link: ";
+ public static final URI conditionSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/condition");
+ private ContextualSelection contextualSelection;
+
+ public ConditionSection() {
+ super(DefaultContextualMenu.DEFAULT_CONTEXT_MENU, 10, conditionSection);
+ }
+
+ public ContextualSelection getContextualSelection() {
+ return contextualSelection;
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof BlockingControlLink;
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ this.action = null;
+ }
+
+ @Override
+ protected Action createAction() {
+ BlockingControlLink controllink = (BlockingControlLink) getContextualSelection()
+ .getSelection();
+ String name = CONTROL_LINK + controllink.getBlock().getName()
+ + " RUNS_AFTER " + controllink.getUntilFinished().getName();
+ return new DummyAction(name);
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/controllink/RemoveConditionMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/controllink/RemoveConditionMenuAction.java
new file mode 100644
index 0000000..68e32e2
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/controllink/RemoveConditionMenuAction.java
@@ -0,0 +1,67 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.controllink;
+
+import java.awt.Component;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.workbench.design.actions.RemoveConditionAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import uk.org.taverna.scufl2.api.core.ControlLink;
+import uk.org.taverna.scufl2.api.core.Workflow;
+
+public class RemoveConditionMenuAction extends AbstractContextualMenuAction {
+
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+
+ public RemoveConditionMenuAction() {
+ super(ConditionSection.conditionSection, 10);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof ControlLink
+ && getContextualSelection().getParent() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+ Workflow dataflow = (Workflow) getContextualSelection().getParent();
+ ControlLink controlLink = (ControlLink) getContextualSelection()
+ .getSelection();
+ Component component = getContextualSelection().getRelativeToComponent();
+ return new RemoveConditionAction(dataflow, controlLink, component, editManager, selectionManager);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/datalink/LinkSection.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/datalink/LinkSection.java
new file mode 100644
index 0000000..aee08ea
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/datalink/LinkSection.java
@@ -0,0 +1,73 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.datalink;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import uk.org.taverna.scufl2.api.core.DataLink;
+
+import net.sf.taverna.t2.ui.menu.AbstractMenuSection;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+import net.sf.taverna.t2.ui.menu.DefaultContextualMenu;
+
+public class LinkSection extends AbstractMenuSection implements
+ ContextualMenuComponent {
+
+ public static final URI linkSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/link");
+ private ContextualSelection contextualSelection;
+
+ public LinkSection() {
+ super(DefaultContextualMenu.DEFAULT_CONTEXT_MENU, 10, linkSection);
+ }
+
+ public ContextualSelection getContextualSelection() {
+ return contextualSelection;
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof DataLink;
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ this.action = null;
+ }
+
+ @SuppressWarnings("serial")
+ @Override
+ protected Action createAction() {
+ DataLink link = (DataLink) getContextualSelection().getSelection();
+ String name = "Data link: " + link.getReceivesFrom().getName() + " -> " + link.getSendsTo().getName();
+ return new AbstractAction(name) {
+ public void actionPerformed(ActionEvent e) {
+ }
+ };
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/datalink/RemoveLinkMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/datalink/RemoveLinkMenuAction.java
new file mode 100644
index 0000000..c672f99
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/datalink/RemoveLinkMenuAction.java
@@ -0,0 +1,66 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.datalink;
+
+import java.awt.Component;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.workbench.design.actions.RemoveDatalinkAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import uk.org.taverna.scufl2.api.core.DataLink;
+import uk.org.taverna.scufl2.api.core.Workflow;
+
+public class RemoveLinkMenuAction extends AbstractContextualMenuAction {
+
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+
+ public RemoveLinkMenuAction() {
+ super(LinkSection.linkSection, 10);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof DataLink
+ && getContextualSelection().getParent() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+ Workflow workflow = (Workflow) getContextualSelection().getParent();
+ DataLink datalink = (DataLink) getContextualSelection().getSelection();
+ Component component = getContextualSelection().getRelativeToComponent();
+ return new RemoveDatalinkAction(workflow, datalink, component, editManager, selectionManager);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/ConnectDataflowInputPortMenuActions.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/ConnectDataflowInputPortMenuActions.java
new file mode 100644
index 0000000..15e8424
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/ConnectDataflowInputPortMenuActions.java
@@ -0,0 +1,42 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.ports;
+
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.port.InputWorkflowPort;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.items.activityport.AbstractConnectPortMenuActions;
+
+public class ConnectDataflowInputPortMenuActions extends
+ AbstractConnectPortMenuActions implements ContextualMenuComponent {
+
+ public ConnectDataflowInputPortMenuActions() {
+ super(WorkflowInputPortSection.inputPort, 20);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof InputWorkflowPort
+ && getContextualSelection().getParent() instanceof Workflow;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/ConnectDataflowOutputPortMenuActions.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/ConnectDataflowOutputPortMenuActions.java
new file mode 100644
index 0000000..d99a361
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/ConnectDataflowOutputPortMenuActions.java
@@ -0,0 +1,42 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.ports;
+
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.port.OutputWorkflowPort;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.items.activityport.AbstractConnectPortMenuActions;
+
+public class ConnectDataflowOutputPortMenuActions extends
+ AbstractConnectPortMenuActions implements ContextualMenuComponent {
+
+ public ConnectDataflowOutputPortMenuActions() {
+ super(WorkflowOutputPortSection.outputPort, 20);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof OutputWorkflowPort
+ && getContextualSelection().getParent() instanceof Workflow;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/EditDataflowInputPortMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/EditDataflowInputPortMenuAction.java
new file mode 100644
index 0000000..77c25f5
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/EditDataflowInputPortMenuAction.java
@@ -0,0 +1,68 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.ports;
+
+import java.awt.Component;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.workbench.design.actions.EditDataflowInputPortAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.port.InputWorkflowPort;
+
+public class EditDataflowInputPortMenuAction extends
+ AbstractContextualMenuAction {
+
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+
+ public EditDataflowInputPortMenuAction() {
+ super(WorkflowInputPortSection.inputPort, 10);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof InputWorkflowPort
+ && getContextualSelection().getParent() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+ Workflow workflow = (Workflow) getContextualSelection().getParent();
+ InputWorkflowPort inport = (InputWorkflowPort) getContextualSelection()
+ .getSelection();
+ Component component = getContextualSelection().getRelativeToComponent();
+ return new EditDataflowInputPortAction(workflow, inport, component, editManager, selectionManager);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/EditDataflowOutputPortMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/EditDataflowOutputPortMenuAction.java
new file mode 100644
index 0000000..0f406dd
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/EditDataflowOutputPortMenuAction.java
@@ -0,0 +1,68 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.ports;
+
+import java.awt.Component;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.workbench.design.actions.EditDataflowOutputPortAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.port.OutputWorkflowPort;
+
+public class EditDataflowOutputPortMenuAction extends
+ AbstractContextualMenuAction {
+
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+
+ public EditDataflowOutputPortMenuAction() {
+ super(WorkflowOutputPortSection.outputPort, 10);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof OutputWorkflowPort
+ && getContextualSelection().getParent() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+ Workflow workflow = (Workflow) getContextualSelection().getParent();
+ OutputWorkflowPort outport = (OutputWorkflowPort) getContextualSelection()
+ .getSelection();
+ Component component = getContextualSelection().getRelativeToComponent();
+ return new EditDataflowOutputPortAction(workflow, outport, component, editManager, selectionManager);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/RemoveDataflowInputPortMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/RemoveDataflowInputPortMenuAction.java
new file mode 100644
index 0000000..f5e2fc1
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/RemoveDataflowInputPortMenuAction.java
@@ -0,0 +1,68 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.ports;
+
+import java.awt.Component;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.workbench.design.actions.RemoveDataflowInputPortAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.port.InputWorkflowPort;
+
+public class RemoveDataflowInputPortMenuAction extends
+ AbstractContextualMenuAction {
+
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+
+ public RemoveDataflowInputPortMenuAction() {
+ super(WorkflowInputPortSection.inputPort, 10);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof InputWorkflowPort
+ && getContextualSelection().getParent() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+ Workflow workflow = (Workflow) getContextualSelection().getParent();
+ InputWorkflowPort inport = (InputWorkflowPort) getContextualSelection()
+ .getSelection();
+ Component component = getContextualSelection().getRelativeToComponent();
+ return new RemoveDataflowInputPortAction(workflow, inport, component, editManager, selectionManager);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/RemoveDataflowOutputPortMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/RemoveDataflowOutputPortMenuAction.java
new file mode 100644
index 0000000..da775a5
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/RemoveDataflowOutputPortMenuAction.java
@@ -0,0 +1,68 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.ports;
+
+import java.awt.Component;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.workbench.design.actions.RemoveDataflowOutputPortAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.port.OutputWorkflowPort;
+
+public class RemoveDataflowOutputPortMenuAction extends
+ AbstractContextualMenuAction {
+
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+
+ public RemoveDataflowOutputPortMenuAction() {
+ super(WorkflowOutputPortSection.outputPort, 10);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof OutputWorkflowPort
+ && getContextualSelection().getParent() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+ Workflow workflow = (Workflow) getContextualSelection().getParent();
+ OutputWorkflowPort outport = (OutputWorkflowPort) getContextualSelection()
+ .getSelection();
+ Component component = getContextualSelection().getRelativeToComponent();
+ return new RemoveDataflowOutputPortAction(workflow, outport, component, editManager, selectionManager);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/WorkflowInputPortSection.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/WorkflowInputPortSection.java
new file mode 100644
index 0000000..1a0d8ef
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/WorkflowInputPortSection.java
@@ -0,0 +1,73 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.ports;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import uk.org.taverna.scufl2.api.port.InputWorkflowPort;
+
+import net.sf.taverna.t2.ui.menu.AbstractMenuSection;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+import net.sf.taverna.t2.ui.menu.DefaultContextualMenu;
+
+public class WorkflowInputPortSection extends AbstractMenuSection implements
+ ContextualMenuComponent {
+
+ public static final URI inputPort = URI
+ .create("http://taverna.sf.net/2009/contextMenu/inputPort");
+ private ContextualSelection contextualSelection;
+
+ public WorkflowInputPortSection() {
+ super(DefaultContextualMenu.DEFAULT_CONTEXT_MENU, 10, inputPort);
+ }
+
+ public ContextualSelection getContextualSelection() {
+ return contextualSelection;
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof InputWorkflowPort;
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ this.action = null;
+ }
+
+ @SuppressWarnings("serial")
+ @Override
+ protected Action createAction() {
+ InputWorkflowPort proc = (InputWorkflowPort) getContextualSelection().getSelection();
+ String name = "Workflow input port: " + proc.getName();
+ return new AbstractAction(name) {
+ public void actionPerformed(ActionEvent e) {
+ }
+ };
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/WorkflowOutputPortSection.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/WorkflowOutputPortSection.java
new file mode 100644
index 0000000..e387f9e
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/ports/WorkflowOutputPortSection.java
@@ -0,0 +1,73 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.ports;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import uk.org.taverna.scufl2.api.port.OutputWorkflowPort;
+
+import net.sf.taverna.t2.ui.menu.AbstractMenuSection;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+import net.sf.taverna.t2.ui.menu.DefaultContextualMenu;
+
+public class WorkflowOutputPortSection extends AbstractMenuSection implements
+ ContextualMenuComponent {
+
+ public static final URI outputPort = URI
+ .create("http://taverna.sf.net/2009/contextMenu/outputPort");
+ private ContextualSelection contextualSelection;
+
+ public WorkflowOutputPortSection() {
+ super(DefaultContextualMenu.DEFAULT_CONTEXT_MENU, 10, outputPort);
+ }
+
+ public ContextualSelection getContextualSelection() {
+ return contextualSelection;
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof OutputWorkflowPort;
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ this.action = null;
+ }
+
+ @SuppressWarnings("serial")
+ @Override
+ protected Action createAction() {
+ OutputWorkflowPort proc = (OutputWorkflowPort) getContextualSelection().getSelection();
+ String name = "Workflow output port: " + proc.getName();
+ return new AbstractAction(name) {
+ public void actionPerformed(ActionEvent e) {
+ }
+ };
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/processor/ConditionMenuActions.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/processor/ConditionMenuActions.java
new file mode 100644
index 0000000..a3e569b
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/processor/ConditionMenuActions.java
@@ -0,0 +1,118 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.processor;
+
+import java.awt.Component;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+import net.sf.taverna.t2.lang.ui.ShadedLabel;
+import net.sf.taverna.t2.ui.menu.AbstractMenuCustom;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+import net.sf.taverna.t2.ui.menu.items.contextualviews.ConfigureSection;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.design.actions.AddConditionAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.core.Processor;
+import uk.org.taverna.scufl2.api.core.Workflow;
+
+public class ConditionMenuActions extends AbstractMenuCustom implements
+ ContextualMenuComponent {
+
+ private ContextualSelection contextualSelection;
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+ private ActivityIconManager activityIconManager;
+ private Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ public ConditionMenuActions() {
+ super(ConfigureSection.configureSection, 80 );
+ }
+
+ public ContextualSelection getContextualSelection() {
+ return contextualSelection;
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof Processor
+ && getContextualSelection().getParent() instanceof Workflow;
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ this.customComponent = null;
+ }
+
+ @Override
+ protected Component createCustomComponent() {
+
+ Workflow workflow = (Workflow) getContextualSelection().getParent();
+ Processor processor = (Processor) getContextualSelection()
+ .getSelection();
+ Component component = getContextualSelection().getRelativeToComponent();
+
+ List<AddConditionAction> conditions = getAddConditionActions(workflow,
+ processor, component);
+ if (conditions.isEmpty()) {
+ return null;
+ }
+ JMenu conditionMenu = new JMenu("Run after");
+ conditionMenu.setIcon(WorkbenchIcons.controlLinkIcon);
+ conditionMenu.add(new ShadedLabel("Services:", ShadedLabel.ORANGE));
+ conditionMenu.addSeparator();
+ for (AddConditionAction addConditionAction : conditions) {
+ conditionMenu.add(new JMenuItem(addConditionAction));
+ }
+ return conditionMenu;
+ }
+
+ protected List<AddConditionAction> getAddConditionActions(
+ Workflow workflow, Processor targetProcessor, Component component) {
+ List<AddConditionAction> actions = new ArrayList<AddConditionAction>();
+ for (Processor processor : scufl2Tools.possibleUpStreamProcessors(workflow, targetProcessor)) {
+ actions.add(new AddConditionAction(workflow, processor,
+ targetProcessor, component, editManager, selectionManager, activityIconManager));
+ }
+ return actions;
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/processor/ProcessorSection.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/processor/ProcessorSection.java
new file mode 100644
index 0000000..b2bde61
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/processor/ProcessorSection.java
@@ -0,0 +1,58 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.processor;
+
+import java.net.URI;
+
+import uk.org.taverna.scufl2.api.core.Processor;
+
+import net.sf.taverna.t2.ui.menu.AbstractMenuSection;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+import net.sf.taverna.t2.ui.menu.items.contextualviews.EditSection;
+
+public class ProcessorSection extends AbstractMenuSection implements
+ ContextualMenuComponent {
+
+ public static final URI processorSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/processor");
+ private ContextualSelection contextualSelection;
+
+ public ProcessorSection() {
+ super(EditSection.editSection, 200, processorSection);
+ }
+
+ public ContextualSelection getContextualSelection() {
+ return contextualSelection;
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof Processor;
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ this.action = null;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/processor/RemoveProcessorMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/processor/RemoveProcessorMenuAction.java
new file mode 100644
index 0000000..e9c8fb4
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/processor/RemoveProcessorMenuAction.java
@@ -0,0 +1,67 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.processor;
+
+import java.awt.Component;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.workbench.design.actions.RemoveProcessorAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import uk.org.taverna.scufl2.api.core.Processor;
+import uk.org.taverna.scufl2.api.core.Workflow;
+
+public class RemoveProcessorMenuAction extends AbstractContextualMenuAction {
+
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+
+ public RemoveProcessorMenuAction() {
+ super(ProcessorSection.processorSection, 100);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof Processor
+ && getContextualSelection().getParent() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+ Workflow workflow = (Workflow) getContextualSelection().getParent();
+ Processor processor = (Processor) getContextualSelection()
+ .getSelection();
+ Component component = getContextualSelection().getRelativeToComponent();
+ return new RemoveProcessorAction(workflow, processor, component, editManager, selectionManager);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/processor/RenameProcessorMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/processor/RenameProcessorMenuAction.java
new file mode 100644
index 0000000..a077726
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/processor/RenameProcessorMenuAction.java
@@ -0,0 +1,68 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.processor;
+
+import java.awt.Component;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.ui.menu.items.contextualviews.ConfigureSection;
+import net.sf.taverna.t2.workbench.design.actions.RenameProcessorAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import uk.org.taverna.scufl2.api.core.Processor;
+import uk.org.taverna.scufl2.api.core.Workflow;
+
+public class RenameProcessorMenuAction extends AbstractContextualMenuAction {
+
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+
+ public RenameProcessorMenuAction() {
+ super(ConfigureSection.configureSection, 60);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof Processor
+ && getContextualSelection().getParent() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+ Workflow workflow = (Workflow) getContextualSelection().getParent();
+ Processor processor = (Processor) getContextualSelection()
+ .getSelection();
+ Component component = getContextualSelection().getRelativeToComponent();
+ return new RenameProcessorAction(workflow, processor, component, editManager, selectionManager);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/workflow/CreateInputMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/workflow/CreateInputMenuAction.java
new file mode 100644
index 0000000..6a3b880
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/workflow/CreateInputMenuAction.java
@@ -0,0 +1,62 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.workflow;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.ui.menu.items.contextualviews.InsertSection;
+import net.sf.taverna.t2.workbench.design.actions.AddDataflowInputAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import uk.org.taverna.scufl2.api.core.Workflow;
+
+public class CreateInputMenuAction extends AbstractContextualMenuAction {
+
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+
+ public CreateInputMenuAction() {
+ super(InsertSection.insertSection, 10);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+ return new AddDataflowInputAction((Workflow) getContextualSelection()
+ .getSelection(), getContextualSelection()
+ .getRelativeToComponent(), editManager, selectionManager);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/workflow/CreateOutputMenuAction.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/workflow/CreateOutputMenuAction.java
new file mode 100644
index 0000000..226258c
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/workflow/CreateOutputMenuAction.java
@@ -0,0 +1,62 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.workflow;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.ui.menu.items.contextualviews.InsertSection;
+import net.sf.taverna.t2.workbench.design.actions.AddDataflowOutputAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import uk.org.taverna.scufl2.api.core.Workflow;
+
+public class CreateOutputMenuAction extends AbstractContextualMenuAction {
+
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+
+ public CreateOutputMenuAction() {
+ super(InsertSection.insertSection, 20);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+ return new AddDataflowOutputAction((Workflow) getContextualSelection()
+ .getSelection(), getContextualSelection()
+ .getRelativeToComponent(), editManager, selectionManager);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/workflow/WorkflowServiceTemplatesSection.java b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/workflow/WorkflowServiceTemplatesSection.java
new file mode 100644
index 0000000..d461b5e
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/java/net/sf/taverna/t2/ui/menu/items/workflow/WorkflowServiceTemplatesSection.java
@@ -0,0 +1,76 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.ui.menu.items.workflow;
+
+import java.net.URI;
+
+import javax.swing.Action;
+
+import uk.org.taverna.scufl2.api.core.Workflow;
+
+import net.sf.taverna.t2.lang.ui.ShadedLabel;
+import net.sf.taverna.t2.ui.menu.AbstractMenuSection;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+import net.sf.taverna.t2.ui.menu.DefaultContextualMenu;
+
+/**
+ * Menu section containing the actions to add service templates, i.e. activities
+ * than are not readily runnable but need to be configured first. The actual actions that
+ * go into this menu can be found in the ui modules for the activities.
+ *
+ * @author Alex Nenadic
+ *
+ */
+public class WorkflowServiceTemplatesSection extends AbstractMenuSection
+ implements ContextualMenuComponent {
+
+ private static final String SERVICE_TEMPLATES = "Service templates";
+ public static final URI serviceTemplatesSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/serviceTemplates");
+ private ContextualSelection contextualSelection;
+
+ public WorkflowServiceTemplatesSection() {
+ super(DefaultContextualMenu.DEFAULT_CONTEXT_MENU, 30, serviceTemplatesSection);
+ }
+
+ public ContextualSelection getContextualSelection() {
+ return contextualSelection;
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && getContextualSelection().getSelection() instanceof Workflow;
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ }
+
+ @Override
+ protected Action createAction() {
+ DummyAction action = new DummyAction(SERVICE_TEMPLATES);
+ // Set the colour for the section
+ action.putValue(AbstractMenuSection.SECTION_COLOR, ShadedLabel.ORANGE);
+ return action;
+ }
+}
diff --git a/taverna-workbench-menu-items/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-workbench-menu-items/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
new file mode 100644
index 0000000..47f3e0e
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
@@ -0,0 +1,46 @@
+net.sf.taverna.t2.ui.menu.items.activityport.ActivityInputPortSection
+net.sf.taverna.t2.ui.menu.items.activityport.SetConstantInputPortValueMenuAction
+net.sf.taverna.t2.ui.menu.items.activityport.ConnectInputPortMenuActions
+
+net.sf.taverna.t2.ui.menu.items.activityport.ActivityOutputPortSection
+net.sf.taverna.t2.ui.menu.items.activityport.ConnectOutputPortMenuActions
+
+net.sf.taverna.t2.ui.menu.items.controllink.ConditionSection
+net.sf.taverna.t2.ui.menu.items.controllink.RemoveConditionMenuAction
+
+net.sf.taverna.t2.ui.menu.items.contextualviews.ConfigureRunningContextualMenuSection
+net.sf.taverna.t2.ui.menu.items.contextualviews.ShowDetailsMenuAction
+net.sf.taverna.t2.ui.menu.items.contextualviews.ShowDetailsContextualMenuAction
+net.sf.taverna.t2.ui.menu.items.contextualviews.ShowConfigureMenuAction
+net.sf.taverna.t2.ui.menu.items.contextualviews.ShowReportsContextualMenuAction
+
+net.sf.taverna.t2.ui.menu.items.workflow.CreateInputMenuAction
+net.sf.taverna.t2.ui.menu.items.workflow.CreateOutputMenuAction
+net.sf.taverna.t2.ui.menu.items.contextualviews.InsertSection
+net.sf.taverna.t2.ui.menu.items.workflow.WorkflowServiceTemplatesSection
+net.sf.taverna.t2.ui.menu.items.contextualviews.EditSection
+net.sf.taverna.t2.ui.menu.items.contextualviews.ConfigureSection
+net.sf.taverna.t2.ui.menu.items.contextualviews.PasteMenuAction
+
+net.sf.taverna.t2.ui.menu.items.datalink.LinkSection
+net.sf.taverna.t2.ui.menu.items.datalink.RemoveLinkMenuAction
+
+net.sf.taverna.t2.ui.menu.items.merge.MergeSection
+net.sf.taverna.t2.ui.menu.items.merge.RemoveMergeMenuAction
+
+net.sf.taverna.t2.ui.menu.items.ports.ConnectDataflowInputPortMenuActions
+net.sf.taverna.t2.ui.menu.items.ports.ConnectDataflowOutputPortMenuActions
+net.sf.taverna.t2.ui.menu.items.ports.EditDataflowInputPortMenuAction
+net.sf.taverna.t2.ui.menu.items.ports.EditDataflowOutputPortMenuAction
+net.sf.taverna.t2.ui.menu.items.ports.RemoveDataflowInputPortMenuAction
+net.sf.taverna.t2.ui.menu.items.ports.RemoveDataflowOutputPortMenuAction
+net.sf.taverna.t2.ui.menu.items.ports.WorkflowInputPortSection
+net.sf.taverna.t2.ui.menu.items.ports.WorkflowOutputPortSection
+
+net.sf.taverna.t2.ui.menu.items.processor.ConditionMenuActions
+net.sf.taverna.t2.ui.menu.items.processor.ProcessorSection
+net.sf.taverna.t2.ui.menu.items.processor.RenameProcessorMenuAction
+net.sf.taverna.t2.ui.menu.items.processor.RemoveProcessorMenuAction
+
+net.sf.taverna.t2.ui.menu.items.annotated.AnnotatedConfigureMenuAction
+
diff --git a/taverna-workbench-menu-items/src/main/resources/META-INF/spring/menu-items-context-osgi.xml b/taverna-workbench-menu-items/src/main/resources/META-INF/spring/menu-items-context-osgi.xml
new file mode 100644
index 0000000..b7ba9e4
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/resources/META-INF/spring/menu-items-context-osgi.xml
@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="ActivityInputPortSection" auto-export="interfaces" />
+ <service ref="ActivityOutputPortSection" auto-export="interfaces" />
+ <service ref="AnnotatedConfigureMenuAction" auto-export="interfaces" />
+ <service ref="ConditionMenuActions" auto-export="interfaces" />
+ <service ref="ConditionSection" auto-export="interfaces" />
+ <service ref="ConfigureRunningContextualMenuSection" auto-export="interfaces" />
+ <service ref="ConfigureSection" auto-export="interfaces" />
+ <service ref="ConnectDataflowInputPortMenuActions" auto-export="interfaces" />
+ <service ref="ConnectDataflowOutputPortMenuActions" auto-export="interfaces" />
+ <service ref="ConnectInputPortMenuActions" auto-export="interfaces" />
+ <service ref="ConnectOutputPortMenuActions" auto-export="interfaces" />
+ <service ref="CreateInputMenuAction" auto-export="interfaces" />
+ <service ref="CreateOutputMenuAction" auto-export="interfaces" />
+ <service ref="EditDataflowInputPortMenuAction" auto-export="interfaces" />
+ <service ref="EditDataflowOutputPortMenuAction" auto-export="interfaces" />
+ <service ref="EditSection" auto-export="interfaces" />
+ <service ref="InsertSection" auto-export="interfaces" />
+ <service ref="LinkSection" auto-export="interfaces" />
+ <service ref="PasteMenuAction" auto-export="interfaces" />
+ <service ref="ProcessorSection" auto-export="interfaces" />
+ <service ref="RemoveConditionMenuAction" auto-export="interfaces" />
+ <service ref="RemoveDataflowInputPortMenuAction" auto-export="interfaces" />
+ <service ref="RemoveDataflowOutputPortMenuAction" auto-export="interfaces" />
+ <service ref="RemoveLinkMenuAction" auto-export="interfaces" />
+ <service ref="RemoveProcessorMenuAction" auto-export="interfaces" />
+ <service ref="RenameProcessorMenuAction" auto-export="interfaces" />
+ <service ref="SetConstantInputPortValueMenuAction" auto-export="interfaces" />
+ <service ref="ShowConfigureMenuAction" auto-export="interfaces" />
+ <service ref="ShowDetailsContextualMenuAction" auto-export="interfaces" />
+ <service ref="ShowDetailsMenuAction" auto-export="interfaces" />
+ <service ref="ShowReportsContextualMenuAction" auto-export="interfaces" />
+ <service ref="WorkflowInputPortSection" auto-export="interfaces" />
+ <service ref="WorkflowOutputPortSection" auto-export="interfaces" />
+ <service ref="WorkflowServiceTemplatesSection" auto-export="interfaces" />
+
+ <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
+ <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
+ <reference id="menuManager" interface="net.sf.taverna.t2.ui.menu.MenuManager" />
+ <reference id="reportManager" interface="net.sf.taverna.t2.workbench.report.ReportManager" cardinality="0..1" />
+ <reference id="selectionManager" interface="net.sf.taverna.t2.workbench.selection.SelectionManager" />
+ <reference id="workbench" interface="net.sf.taverna.t2.workbench.ui.Workbench" cardinality="0..1" />
+ <reference id="workbenchConfiguration" interface="net.sf.taverna.t2.workbench.configuration.workbench.WorkbenchConfiguration" />
+ <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
+ <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
+ <reference id="serviceRegistry" interface="uk.org.taverna.commons.services.ServiceRegistry" />
+
+ <list id="annotationBeans" interface="net.sf.taverna.t2.annotation.AnnotationBeanSPI"/>
+
+</beans:beans>
diff --git a/taverna-workbench-menu-items/src/main/resources/META-INF/spring/menu-items-context.xml b/taverna-workbench-menu-items/src/main/resources/META-INF/spring/menu-items-context.xml
new file mode 100644
index 0000000..6208a72
--- /dev/null
+++ b/taverna-workbench-menu-items/src/main/resources/META-INF/spring/menu-items-context.xml
@@ -0,0 +1,124 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="ActivityInputPortSection" class="net.sf.taverna.t2.ui.menu.items.activityport.ActivityInputPortSection" />
+ <bean id="ActivityOutputPortSection" class="net.sf.taverna.t2.ui.menu.items.activityport.ActivityOutputPortSection" />
+ <bean id="ConditionMenuActions" class="net.sf.taverna.t2.ui.menu.items.processor.ConditionMenuActions">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ </bean>
+ <bean id="AnnotatedConfigureMenuAction" class="net.sf.taverna.t2.ui.menu.items.annotated.AnnotatedConfigureMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="annotationBeans" ref="annotationBeans" />
+ </bean>
+ <bean id="ConditionSection" class="net.sf.taverna.t2.ui.menu.items.controllink.ConditionSection" />
+ <bean id="ConfigureRunningContextualMenuSection" class="net.sf.taverna.t2.ui.menu.items.contextualviews.ConfigureRunningContextualMenuSection" />
+ <bean id="ConfigureSection" class="net.sf.taverna.t2.ui.menu.items.contextualviews.ConfigureSection" />
+ <bean id="ConnectDataflowInputPortMenuActions" class="net.sf.taverna.t2.ui.menu.items.ports.ConnectDataflowInputPortMenuActions">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="workbenchConfiguration" ref="workbenchConfiguration" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="colourManager" ref="colourManager" />
+ </bean>
+ <bean id="ConnectDataflowOutputPortMenuActions" class="net.sf.taverna.t2.ui.menu.items.ports.ConnectDataflowOutputPortMenuActions">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="workbenchConfiguration" ref="workbenchConfiguration" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="colourManager" ref="colourManager" />
+ </bean>
+ <bean id="ConnectInputPortMenuActions" class="net.sf.taverna.t2.ui.menu.items.activityport.ConnectInputPortMenuActions">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="workbenchConfiguration" ref="workbenchConfiguration" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="colourManager" ref="colourManager" />
+ </bean>
+ <bean id="ConnectOutputPortMenuActions" class="net.sf.taverna.t2.ui.menu.items.activityport.ConnectOutputPortMenuActions">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="workbenchConfiguration" ref="workbenchConfiguration" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="colourManager" ref="colourManager" />
+ </bean>
+ <bean id="CreateInputMenuAction" class="net.sf.taverna.t2.ui.menu.items.workflow.CreateInputMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="CreateOutputMenuAction" class="net.sf.taverna.t2.ui.menu.items.workflow.CreateOutputMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="EditDataflowInputPortMenuAction" class="net.sf.taverna.t2.ui.menu.items.ports.EditDataflowInputPortMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="EditDataflowOutputPortMenuAction" class="net.sf.taverna.t2.ui.menu.items.ports.EditDataflowOutputPortMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="EditSection" class="net.sf.taverna.t2.ui.menu.items.contextualviews.EditSection" />
+ <bean id="InsertSection" class="net.sf.taverna.t2.ui.menu.items.contextualviews.InsertSection" />
+ <bean id="LinkSection" class="net.sf.taverna.t2.ui.menu.items.datalink.LinkSection" />
+ <bean id="PasteMenuAction" class="net.sf.taverna.t2.ui.menu.items.contextualviews.PasteMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+ <bean id="ProcessorSection" class="net.sf.taverna.t2.ui.menu.items.processor.ProcessorSection" />
+ <bean id="RemoveConditionMenuAction" class="net.sf.taverna.t2.ui.menu.items.controllink.RemoveConditionMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="RemoveDataflowInputPortMenuAction" class="net.sf.taverna.t2.ui.menu.items.ports.RemoveDataflowInputPortMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="RemoveDataflowOutputPortMenuAction" class="net.sf.taverna.t2.ui.menu.items.ports.RemoveDataflowOutputPortMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="RemoveLinkMenuAction" class="net.sf.taverna.t2.ui.menu.items.datalink.RemoveLinkMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="RemoveProcessorMenuAction" class="net.sf.taverna.t2.ui.menu.items.processor.RemoveProcessorMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="RenameProcessorMenuAction" class="net.sf.taverna.t2.ui.menu.items.processor.RenameProcessorMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="SetConstantInputPortValueMenuAction" class="net.sf.taverna.t2.ui.menu.items.activityport.SetConstantInputPortValueMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+ <bean id="ShowConfigureMenuAction" class="net.sf.taverna.t2.ui.menu.items.contextualviews.ShowConfigureMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="ShowDetailsContextualMenuAction" class="net.sf.taverna.t2.ui.menu.items.contextualviews.ShowDetailsContextualMenuAction">
+ <property name="workbench" ref="workbench" />
+ </bean>
+ <bean id="ShowDetailsMenuAction" class="net.sf.taverna.t2.ui.menu.items.contextualviews.ShowDetailsMenuAction">
+ <property name="workbench" ref="workbench" />
+ </bean>
+ <bean id="ShowReportsContextualMenuAction" class="net.sf.taverna.t2.ui.menu.items.contextualviews.ShowReportsContextualMenuAction">
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="reportManager" ref="reportManager" />
+ <property name="workbench" ref="workbench" />
+ </bean>
+ <bean id="WorkflowInputPortSection" class="net.sf.taverna.t2.ui.menu.items.ports.WorkflowInputPortSection" />
+ <bean id="WorkflowOutputPortSection" class="net.sf.taverna.t2.ui.menu.items.ports.WorkflowOutputPortSection" />
+ <bean id="WorkflowServiceTemplatesSection" class="net.sf.taverna.t2.ui.menu.items.workflow.WorkflowServiceTemplatesSection" />
+
+</beans>
diff --git a/taverna-workbench-parallelize-ui/pom.xml b/taverna-workbench-parallelize-ui/pom.xml
new file mode 100644
index 0000000..6fba337
--- /dev/null
+++ b/taverna-workbench-parallelize-ui/pom.xml
@@ -0,0 +1,42 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna.t2</groupId>
+ <artifactId>ui-exts</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>parallelize-ui</artifactId>
+ <packaging>bundle</packaging>
+ <name>Parallelize layer contextual view</name>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>contextual-views-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>menu-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>edits-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>selection-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>${jackson-databind.version}</version>
+ </dependency>
+ </dependencies>
+</project>
diff --git a/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeConfigurationPanel.java b/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeConfigurationPanel.java
new file mode 100644
index 0000000..f951da6
--- /dev/null
+++ b/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeConfigurationPanel.java
@@ -0,0 +1,99 @@
+package net.sf.taverna.t2.workbench.parallelize;
+
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.border.EmptyBorder;
+
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+@SuppressWarnings("serial")
+public class ParallelizeConfigurationPanel extends JPanel {
+
+ private ObjectNode json;
+ private JTextField maxJobsField = new JTextField(10);
+ private final String processorName;
+
+ public ParallelizeConfigurationPanel(Configuration configuration, String processorName) {
+ if (configuration.getJson().has("parallelize")) {
+ json = (ObjectNode) configuration.getJson().get("parallelize").deepCopy();
+ } else {
+ json = configuration.getJsonAsObjectNode().objectNode();
+ }
+ this.processorName = processorName;
+ this.setLayout(new GridBagLayout());
+ this.setBorder(new EmptyBorder(10,10,10,10));
+ populate();
+ }
+
+ public void populate() {
+ this.removeAll();
+ GridBagConstraints gbc = new GridBagConstraints();
+ JLabel jobs = new JLabel("<html><body>Maximum numbers of items to process at the same time</body></html>");
+
+ jobs.setBorder(new EmptyBorder(0,0,0,10));
+ gbc.weightx = 0.8;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ this.add(jobs, gbc);
+ if (json.has("maximumJobs")) {
+ maxJobsField.setText(json.get("maximumJobs").asText());
+ } else {
+ maxJobsField.setText("1");
+ }
+ gbc.weightx = 0.2;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ this.add(maxJobsField, gbc);
+ gbc.weightx = 0.1;
+ this.add(new JPanel(), gbc);
+
+ gbc.gridy=1;
+ gbc.gridx=0;
+ gbc.gridwidth=3;
+ gbc.weightx=0;
+ gbc.anchor = GridBagConstraints.SOUTH;
+ gbc.fill = GridBagConstraints.BOTH;
+ gbc.weighty = 1.0;
+ JLabel explanationLabel = new JLabel("<html><body><small>" +
+ "The service <b>" + processorName + "</b> will be invoked as soon as the required inputs " +
+ "for an iteration are available, but no more than the maximum number of items " +
+ "will be invoked at the same time."
+ + "</small></body></html>");
+ this.add(explanationLabel, gbc);
+
+ this.setPreferredSize(new Dimension(350, 170));
+ }
+
+ public boolean validateConfig() {
+ String errorText = "";
+ int maxJobs = -1;
+ try {
+ maxJobs = Integer.parseInt(maxJobsField.getText());
+ if (maxJobs < 1) {
+ errorText += "The maximum number of items must be a positive integer.\n";
+ }
+ }
+ catch (NumberFormatException e) {
+ errorText += "The maximum number of items must be an integer.\n";
+ }
+
+ if (errorText.length() > 0) {
+ JOptionPane.showMessageDialog(this, errorText, "", JOptionPane.ERROR_MESSAGE);
+ return false;
+ }
+ return true;
+ }
+
+ public JsonNode getJson() {
+ json.put("maximumJobs", maxJobsField.getText());
+ return json;
+ }
+
+}
diff --git a/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeConfigureAction.java b/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeConfigureAction.java
new file mode 100644
index 0000000..6727c59
--- /dev/null
+++ b/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeConfigureAction.java
@@ -0,0 +1,185 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.workbench.parallelize;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.util.Iterator;
+import java.util.Map.Entry;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+
+import net.sf.taverna.t2.workbench.edits.Edit;
+import net.sf.taverna.t2.workbench.edits.EditException;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workflow.edits.AddChildEdit;
+import net.sf.taverna.t2.workflow.edits.ChangeJsonEdit;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+import uk.org.taverna.scufl2.api.core.Processor;
+import uk.org.taverna.scufl2.api.profiles.Profile;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+/**
+ * @author alanrw
+ * @author David Withers
+ */
+@SuppressWarnings("serial")
+public class ParallelizeConfigureAction extends AbstractAction {
+
+ private Frame owner;
+ private final Processor processor;
+ private final ParallelizeContextualView parallelizeContextualView;
+
+ private EditManager editManager;
+
+ private static Logger logger = Logger.getLogger(ParallelizeConfigureAction.class);
+
+ private final Scufl2Tools scufl2Tools = new Scufl2Tools();
+ private final SelectionManager selectionManager;
+
+ public ParallelizeConfigureAction(Frame owner,
+ ParallelizeContextualView parallelizeContextualView,
+ Processor processor, EditManager editManager, SelectionManager selectionManager) {
+ super("Configure");
+ this.owner = owner;
+ this.parallelizeContextualView = parallelizeContextualView;
+ this.processor = processor;
+ this.editManager = editManager;
+ this.selectionManager = selectionManager;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ String processorName = processor.getName();
+ String title = "Parallel jobs for service " + processorName;
+ final JDialog dialog = new HelpEnabledDialog(owner, title, true);
+ Configuration configuration;
+ try {
+ configuration = scufl2Tools.configurationFor(processor, selectionManager.getSelectedProfile());
+ } catch (IndexOutOfBoundsException ex) {
+ configuration = new Configuration();
+ }
+ ParallelizeConfigurationPanel parallelizeConfigurationPanel = new ParallelizeConfigurationPanel(configuration, processorName);
+ dialog.add(parallelizeConfigurationPanel, BorderLayout.CENTER);
+
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout(new FlowLayout());
+
+ JButton okButton = new JButton(new OKAction(dialog,
+ parallelizeConfigurationPanel));
+ buttonPanel.add(okButton);
+
+ JButton resetButton = new JButton(new ResetAction(
+ parallelizeConfigurationPanel));
+ buttonPanel.add(resetButton);
+
+ JButton cancelButton = new JButton(new CancelAction(dialog));
+ buttonPanel.add(cancelButton);
+
+ dialog.add(buttonPanel, BorderLayout.SOUTH);
+ dialog.pack();
+ dialog.setLocationRelativeTo(null);
+ dialog.setVisible(true);
+ }
+
+ public class ResetAction extends AbstractAction {
+
+ private final ParallelizeConfigurationPanel parallelizeConfigurationPanel;
+
+ public ResetAction(ParallelizeConfigurationPanel parallelizeConfigurationPanel) {
+ super("Reset");
+ this.parallelizeConfigurationPanel = parallelizeConfigurationPanel;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ parallelizeConfigurationPanel.populate();
+ }
+
+ }
+
+ public class OKAction extends AbstractAction {
+
+ private final ParallelizeConfigurationPanel parallelizeConfigurationPanel;
+ private final JDialog dialog;
+
+ public OKAction(JDialog dialog, ParallelizeConfigurationPanel parallelizeConfigurationPanel) {
+ super("OK");
+ this.dialog = dialog;
+ this.parallelizeConfigurationPanel = parallelizeConfigurationPanel;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (parallelizeConfigurationPanel.validateConfig()) {
+ try {
+ try {
+ Configuration configuration = scufl2Tools.configurationFor(processor, selectionManager.getSelectedProfile());
+ ObjectNode json = configuration.getJsonAsObjectNode().deepCopy();
+ ObjectNode parallelizeNode = null;
+ if (json.has("parallelize")) {
+ parallelizeNode = (ObjectNode) json.get("parallelize");
+ } else {
+ parallelizeNode = json.objectNode();
+ json.put("parallelize", parallelizeNode);
+ }
+ JsonNode newParallelizeNode = parallelizeConfigurationPanel.getJson();
+ Iterator<Entry<String, JsonNode>> fields = newParallelizeNode.fields();
+ while (fields.hasNext()) {
+ Entry<String, JsonNode> entry = fields.next();
+ parallelizeNode.set(entry.getKey(), entry.getValue());
+ }
+ Edit<Configuration> edit = new ChangeJsonEdit(configuration, json);
+ editManager.doDataflowEdit(selectionManager.getSelectedWorkflowBundle(), edit);
+ } catch (IndexOutOfBoundsException ex) {
+ Configuration configuration = new Configuration();
+ configuration.setConfigures(processor);
+ ObjectNode json = configuration.getJsonAsObjectNode();
+ json.put("parallelize", parallelizeConfigurationPanel.getJson());
+ Edit<Profile> edit = new AddChildEdit<Profile>(selectionManager.getSelectedProfile(), configuration);
+ editManager.doDataflowEdit(selectionManager.getSelectedWorkflowBundle(), edit);
+ }
+ dialog.setVisible(false);
+ if (parallelizeContextualView != null) {
+ parallelizeContextualView.refreshView();
+ }
+ } catch (EditException e1) {
+ logger.warn("Could not configure jobs", e1);
+ JOptionPane.showMessageDialog(owner, "Could not configure jobs",
+ "An error occured when configuring jobs: " + e1.getMessage(),
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ }
+
+ }
+
+ public class CancelAction extends AbstractAction {
+
+ private final JDialog dialog;
+
+ public CancelAction(JDialog dialog) {
+ super("Cancel");
+ this.dialog = dialog;
+
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ dialog.setVisible(false);
+ }
+
+ }
+
+}
diff --git a/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeConfigureMenuAction.java b/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeConfigureMenuAction.java
new file mode 100644
index 0000000..194d81e
--- /dev/null
+++ b/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeConfigureMenuAction.java
@@ -0,0 +1,77 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.workbench.parallelize;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import uk.org.taverna.scufl2.api.core.Processor;
+
+public class ParallelizeConfigureMenuAction extends AbstractContextualMenuAction {
+
+ public static final URI configureRunningSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/configureRunning");
+
+ private static final URI PARALLELIZE_CONFIGURE_URI = URI
+ .create("http://taverna.sf.net/2008/t2workbench/parallelizeConfigure");
+
+ public static URI TYPE = URI.create("http://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Parallelize");
+
+ private EditManager editManager;
+
+ private SelectionManager selectionManager;
+
+ public ParallelizeConfigureMenuAction() {
+ super(configureRunningSection, 10, PARALLELIZE_CONFIGURE_URI);
+ }
+
+ @SuppressWarnings("serial")
+ @Override
+ protected Action createAction() {
+ return new AbstractAction("Parallel jobs...") {
+ public void actionPerformed(ActionEvent e) {
+ Processor processor = (Processor) getContextualSelection().getSelection();
+ ParallelizeConfigureAction parallelizeConfigureAction = new ParallelizeConfigureAction(
+ null, null, processor, editManager, selectionManager);
+ parallelizeConfigureAction.actionPerformed(e);
+ }
+ };
+ }
+
+ public boolean isEnabled() {
+ return super.isEnabled() && (getContextualSelection().getSelection() instanceof Processor);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeContextualView.java b/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeContextualView.java
new file mode 100644
index 0000000..22d2da1
--- /dev/null
+++ b/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeContextualView.java
@@ -0,0 +1,130 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.parallelize;
+
+import java.awt.BorderLayout;
+import java.awt.Frame;
+import java.util.List;
+
+import javax.swing.Action;
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
+
+import net.sf.taverna.t2.lang.ui.ReadOnlyTextArea;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+import uk.org.taverna.scufl2.api.core.Processor;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+/**
+ * View of a processor, including it's iteration stack, activities, etc.
+ *
+ * @author Alan R Williams
+ *
+ */
+@SuppressWarnings("serial")
+public class ParallelizeContextualView extends ContextualView {
+
+ private final Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ private Processor processor;
+
+ private JPanel panel;
+
+ private final EditManager editManager;
+
+ private final SelectionManager selectionManager;
+
+ public ParallelizeContextualView(Processor processor, EditManager editManager, SelectionManager selectionManager) {
+ super();
+ this.processor = processor;
+ this.editManager = editManager;
+ this.selectionManager = selectionManager;
+ initialise();
+ initView();
+ }
+
+ @Override
+ public void refreshView() {
+ initialise();
+ }
+
+ private void initialise() {
+ if (panel == null) {
+ panel = createPanel();
+ } else {
+ panel.removeAll();
+ }
+
+ JTextArea textArea = new ReadOnlyTextArea();
+ textArea.setEditable(false);
+ String maxJobs = "1";
+ for (Configuration configuration : scufl2Tools.configurationsFor(processor, selectionManager.getSelectedProfile())) {
+ JsonNode processorConfig = configuration.getJson();
+ if (processorConfig.has("parallelize")) {
+ JsonNode parallelizeConfig = processorConfig.get("parallelize");
+ if (parallelizeConfig.has("maximumJobs")) {
+ maxJobs = parallelizeConfig.get("maximumJobs").asText();
+ }
+ }
+ }
+ textArea.setText("The maximum number of jobs is " + maxJobs);
+ textArea.setBackground(panel.getBackground());
+ panel.add(textArea, BorderLayout.CENTER);
+ revalidate();
+ }
+
+
+ @Override
+ public JComponent getMainFrame() {
+ return panel;
+ }
+
+ @Override
+ public String getViewTitle() {
+ return "Parallel jobs";
+ }
+
+ protected JPanel createPanel() {
+ JPanel result = new JPanel();
+ result.setLayout(new BorderLayout());
+
+
+ return result;
+ }
+
+ @Override
+ public int getPreferredPosition() {
+ return 400;
+ }
+
+ @Override
+ public Action getConfigureAction(Frame owner) {
+ return new ParallelizeConfigureAction(owner, this, processor, editManager, selectionManager);
+ }
+
+
+}
diff --git a/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeContextualViewFactory.java b/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeContextualViewFactory.java
new file mode 100644
index 0000000..f9ff7e7
--- /dev/null
+++ b/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeContextualViewFactory.java
@@ -0,0 +1,56 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.parallelize;
+
+import java.net.URI;
+import java.util.Arrays;
+import java.util.List;
+
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+import uk.org.taverna.scufl2.api.core.Processor;
+
+public class ParallelizeContextualViewFactory implements ContextualViewFactory<Processor> {
+
+ public static URI TYPE = URI.create("http://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Parallelize");
+
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+
+ public boolean canHandle(Object selection) {
+ return selection instanceof Processor;
+ }
+
+ public List<ContextualView> getViews(Processor selection) {
+ return Arrays.asList(new ContextualView[] {new ParallelizeContextualView(selection, editManager, selectionManager)});
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-parallelize-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-workbench-parallelize-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
new file mode 100644
index 0000000..edd7b2d
--- /dev/null
+++ b/taverna-workbench-parallelize-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
@@ -0,0 +1 @@
+net.sf.taverna.t2.workbench.parallelize.ParallelizeConfigureMenuAction
diff --git a/taverna-workbench-parallelize-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-workbench-parallelize-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
new file mode 100644
index 0000000..8b94f86
--- /dev/null
+++ b/taverna-workbench-parallelize-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
@@ -0,0 +1 @@
+net.sf.taverna.t2.workbench.parallelize.ParallelizeContextualViewFactory
diff --git a/taverna-workbench-parallelize-ui/src/main/resources/META-INF/spring/parallelize-ui-context-osgi.xml b/taverna-workbench-parallelize-ui/src/main/resources/META-INF/spring/parallelize-ui-context-osgi.xml
new file mode 100644
index 0000000..1859672
--- /dev/null
+++ b/taverna-workbench-parallelize-ui/src/main/resources/META-INF/spring/parallelize-ui-context-osgi.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="ParallelizeConfigureMenuAction" auto-export="interfaces" />
+
+ <service ref="ParallelizeContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+
+ <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
+ <reference id="selectionManager" interface="net.sf.taverna.t2.workbench.selection.SelectionManager" />
+
+</beans:beans>
diff --git a/taverna-workbench-parallelize-ui/src/main/resources/META-INF/spring/parallelize-ui-context.xml b/taverna-workbench-parallelize-ui/src/main/resources/META-INF/spring/parallelize-ui-context.xml
new file mode 100644
index 0000000..1d1fdd4
--- /dev/null
+++ b/taverna-workbench-parallelize-ui/src/main/resources/META-INF/spring/parallelize-ui-context.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="ParallelizeConfigureMenuAction" class="net.sf.taverna.t2.workbench.parallelize.ParallelizeConfigureMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+
+ <bean id="ParallelizeContextualViewFactory" class="net.sf.taverna.t2.workbench.parallelize.ParallelizeContextualViewFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+
+</beans>
diff --git a/taverna-workbench-perspective-biocatalogue/LocalTestLauncher.bat b/taverna-workbench-perspective-biocatalogue/LocalTestLauncher.bat
new file mode 100644
index 0000000..1c7f299
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/LocalTestLauncher.bat
@@ -0,0 +1,14 @@
+@echo off
+echo.
+echo.
+del biocatalogue-perspective-local-launch.jar
+echo Deleted old JAR file if it was there.
+cd target\classes
+jar cfM ..\..\biocatalogue-perspective-local-launch.jar *.*
+cd ..\..
+echo JAR assembly done, launching app...
+
+java -cp .;.\biocatalogue-perspective-local-launch.jar;c:/Users/Sergey/.m2/repository/net/sf/taverna/t2/workbench/ui-api/0.2/ui-api-0.2.jar;c:\Users\Sergey\.m2\repository\net\sf\taverna\t2\lang\ui\1.0\ui-1.0.jar;c:\Users\Sergey\.m2\repository\net\sf\taverna\t2\ui-components\workflow-view\1.0\workflow-view-1.0.jar;c:\Users\Sergey\.m2\repository\net\sf\taverna\t2\ui-activities\wsdl-activity-ui\0.7\wsdl-activity-ui-0.7.jar;C:\Users\Sergey\.m2\repository\log4j\log4j\1.2.13\log4j-1.2.13.jar;C:\Users\Sergey\.m2\repository\net\sf\taverna\t2\workbench\commons-icons\0.2\commons-icons-0.2.jar;c:\Users\Sergey\.m2\repository\BrowserLauncher2\BrowserLauncher2\1.3\BrowserLauncher2-1.3.jar;C:\Users\Sergey\.m2\repository\jdom\jdom\1.0\jdom-1.0.jar;"c:\Program Files\Java\xmlbeans-2.4.0\lib\xbean.jar";"c:\Program Files\Java\xmlbeans-2.4.0\lib\jsr173_1.0_api.jar";.\lib\lablib-checkboxtree-3.1.jar;.\lib\core-renderer.jar;.\lib\commons-lang-2.4.jar net.sf.taverna.t2.ui.perspectives.biocatalogue.TestJFrameForLocalLaunch
+
+del biocatalogue-perspective-local-launch.jar
+echo Cleanup done - deleted old the JAR file that was used for the current launch.
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/lib/core-renderer.jar b/taverna-workbench-perspective-biocatalogue/lib/core-renderer.jar
new file mode 100644
index 0000000..871fabf
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/lib/core-renderer.jar
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/log4j.properties b/taverna-workbench-perspective-biocatalogue/log4j.properties
new file mode 100644
index 0000000..fcd1d0c
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/log4j.properties
@@ -0,0 +1,4 @@
+log4j.rootLogger=DEBUG, A1
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
diff --git a/taverna-workbench-perspective-biocatalogue/pom.xml b/taverna-workbench-perspective-biocatalogue/pom.xml
new file mode 100644
index 0000000..3f5457a
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/pom.xml
@@ -0,0 +1,183 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna.t2</groupId>
+ <artifactId>ui-exts</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>perspective-biocatalogue</artifactId>
+ <name>BioCatalogue Perspective</name>
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository</url>
+ </repository>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>fuse</id>
+ <name>fuseRepository</name>
+ <url>http://repo.fusesource.com/maven2-all/</url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>
+ http://www.mygrid.org.uk/maven/snapshot-repository
+ </url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <!-- <dependency> <groupId>net.sf.taverna.t2.ui-api</groupId> <artifactId>perspective-core</artifactId>
+ <version>${t2.ui.api.version}</version> </dependency> -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>workflowmodel-impl</artifactId>
+ <version>${t2.core.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>menu-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>file-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.lang</groupId>
+ <artifactId>ui</artifactId>
+ <version>${t2.lang.version}</version>
+ </dependency>
+ <!-- required for providing contextual views in the bottom-left area of
+ Design perspective -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>contextual-views-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <!-- required for inserting a SOAP processor into the current workflow -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>wsdl-activity-ui</artifactId>
+ <version>${t2.ui.activities.version}</version>
+ </dependency>
+ <!-- required for importing REST processors into the current workflow -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>rest-activity-ui</artifactId>
+ <version>${t2.ui.activities.version}</version>
+ </dependency>
+ <!-- required for inserting a processor into the current workflow -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>workflow-view</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+ <!-- required registering with and opening help window -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>helper</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-app-configuration-api</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.jdom</groupId>
+ <artifactId>com.springsource.org.jdom</artifactId>
+ <version>${jdom.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.log4j</groupId>
+ <artifactId>com.springsource.org.apache.log4j</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.xmlbeans</groupId>
+ <artifactId>xmlbeans</artifactId>
+ <version>2.5.0</version>
+ </dependency>
+
+ <!-- FlyingSaucer XHTML Renderer -->
+ <!-- (it is critical to use version R8, not any earlier ones - e.g. R8pre2,
+ etc.) -->
+ <dependency>
+ <groupId>org.xhtmlrenderer</groupId>
+ <artifactId>core-renderer</artifactId>
+ <version>${org.xhtmlrenderer.core-renderer.version}</version>
+ <exclusions>
+ <exclusion>
+ <groupId>bouncycastle</groupId>
+ <artifactId>bcprov-jdk14</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>bouncycastle</groupId>
+ <artifactId>bcmail-jdk14</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+
+ <!-- At least StringEscapeUtils class is used from this library -->
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>com.springsource.org.apache.commons.lang</artifactId>
+ <version>${commons.lang.version}</version>
+ </dependency>
+
+ <!-- Gson: Java to Json conversion -->
+ <dependency>
+ <groupId>com.google.code.gson</groupId>
+ <artifactId>gson</artifactId>
+ <version>${gson.version}</version>
+ </dependency>
+ </dependencies>
+
+ <build>
+ <!-- Adds "xmlbeans:xmlbeans" Maven2 goal to compile the API binding classes
+ from XSD schema. -->
+ <plugins>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>xmlbeans-maven-plugin</artifactId>
+ <version>2.3.3</version>
+ <executions>
+ <execution>
+ <goals>
+ <goal>xmlbeans</goal>
+ </goals>
+ </execution>
+ </executions>
+ <inherited>true</inherited>
+ <configuration>
+ <!-- "javaSource=1.5" is required to make use of generics and have getXXXList()
+ methods available, not just getXXXArrray() -->
+ <javaSource>1.5</javaSource>
+ <download>true</download>
+ <schemaDirectory>src/main/xsd</schemaDirectory>
+ <!-- Default is target/generated-sources/xmlbeans - which the Maven
+ plugin should be able to add to the Project classpath -->
+ <!-- <sourceGenerationDirectory>src/main/java</sourceGenerationDirectory> -->
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+</project>
diff --git a/taverna-workbench-perspective-biocatalogue/schema_compilation/move_scomp_results_into_project.bat b/taverna-workbench-perspective-biocatalogue/schema_compilation/move_scomp_results_into_project.bat
new file mode 100644
index 0000000..3786d7c
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/schema_compilation/move_scomp_results_into_project.bat
@@ -0,0 +1,29 @@
+@echo off
+
+echo This will replace the JAR file with compiled API classes
+pause
+del ..\lib\biocatalogue_api_classes.jar
+move biocatalogue_api_classes.jar ..\lib\
+echo JAR file replaced
+echo.
+
+REM replace the sources of API classes
+echo This will delete *ALL* files in \src\main\java\org\biocatalogue
+echo \src\main\java\org\purl
+echo \src\main\java\org\w3
+pause
+
+rd /S /Q ..\src\main\java\org\biocatalogue
+rd /S /Q ..\src\main\java\org\purl
+rd /S /Q ..\src\main\java\org\w3
+
+move /Y org\biocatalogue ..\src\main\java\org
+move /Y org\purl ..\src\main\java\org
+move /Y org\w3 ..\src\main\java\org
+rd org
+
+echo Sources of API classes replaced
+echo.
+
+echo Done!
+pause
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/schema_compilation/scomp_compile_from_web.bat b/taverna-workbench-perspective-biocatalogue/schema_compilation/scomp_compile_from_web.bat
new file mode 100644
index 0000000..ee10a50
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/schema_compilation/scomp_compile_from_web.bat
@@ -0,0 +1,9 @@
+@echo off
+
+REM -src . -- put source files here
+REM -srconly -- only sources, no compiling of java classes, no jar bundling
+REM -compiler -- where to find javac
+REM -javasource -- which JAVA version to aim for (1.5 uses generics)
+REM -dl -- allows download of referenced schemas
+
+scomp -src . -srconly -compiler "%JAVA_HOME%\bin\javac.exe" -javasource 1.5 -dl http://www.biocatalogue.org/2009/xml/rest/schema-v1.xsd
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/schema_compilation/scomp_compile_from_web_to_jar.bat b/taverna-workbench-perspective-biocatalogue/schema_compilation/scomp_compile_from_web_to_jar.bat
new file mode 100644
index 0000000..dd66206
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/schema_compilation/scomp_compile_from_web_to_jar.bat
@@ -0,0 +1,9 @@
+@echo off
+
+REM -src . -- put source files here
+REM -compiler -- where to find javac
+REM -javasource -- which JAVA version to aim for (1.5 uses generics)
+REM -out -- specifies the name of the target JAR file
+REM -dl -- allows download of referenced schemas
+
+scomp -src . -compiler "%JAVA_HOME%\bin\javac.exe" -javasource 1.5 -out biocatalogue_api_classes.jar -dl http://www.biocatalogue.org/2009/xml/rest/schema-v1.xsd
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/doc/BioCatalogue Plugin Documentation.odt b/taverna-workbench-perspective-biocatalogue/src/main/doc/BioCatalogue Plugin Documentation.odt
new file mode 100644
index 0000000..85056d7
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/doc/BioCatalogue Plugin Documentation.odt
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/help/Index-TOC-Map-Additions.txt b/taverna-workbench-perspective-biocatalogue/src/main/help/Index-TOC-Map-Additions.txt
new file mode 100644
index 0000000..8d6c953
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/help/Index-TOC-Map-Additions.txt
@@ -0,0 +1,20 @@
+/* http://www.mygrid.org.uk/taverna2_1/helpset/toc.xml */
+
+<tocitem text="BioCatalogue Plugin" target="biocatalogue-plugin" expand="false">
+ <tocitem text="Feature Overview" target="biocatalogue-plugin-features"/>
+ <tocitem text="Feedback" target="biocatalogue-plugin-feedback"/>
+</tocitem>
+
+
+
+/* http://www.mygrid.org.uk/taverna2_1/helpset/index.xml */
+
+<indexitem text="BioCatalogue Plugin" target="biocatalogue-plugin"/>
+
+
+
+/* http://www.mygrid.org.uk/taverna2_1/helpset/map.xml */
+
+<mapID target="biocatalogue-plugin" url="html/biocatalogue-plugin.html"/>
+<mapID target="biocatalogue-plugin-features" url="html/biocatalogue-plugin-features.html"/>
+<mapID target="biocatalogue-plugin-feedback" url="html/biocatalogue-plugin-feedback.html"/>
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin-features.html b/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin-features.html
new file mode 100644
index 0000000..ece2949
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin-features.html
@@ -0,0 +1,113 @@
+<html>
+ <head>
+ <meta content="text/html; charset=MacRoman" http-equiv="Content-Type">
+ <link rel="stylesheet" href="./basic.css" type="text/css">
+ <meta name="generator" content="Helen">
+ <title>BioCatalogue Plugin - Features</title>
+ </head>
+ <body>
+ <h2>
+ BioCatalogue Plugin - Features
+ </h2>
+
+ <h3>
+ BioCatalogue Perspective
+ </h3>
+ <p>
+ This perspective is designed for searching and browsing the BioCatalogue
+ data. It aids with discovery of Processors that may be used in a workflow.
+ </p>
+
+ <p>
+ In the BioCatalogue perspective you may:
+ <ul>
+ <li>Search for Web Services by free text queries of by tags;</li>
+ <li>Filter search results by the same set of criteria as available on the BioCatalogue website;</li>
+ <li>Save favourite filters and search queries for re-use at a later point;</li>
+ <li>View search history;</li>
+ <li>Immediately see the types and monitoring statuses of all found Web
+ Services directly in the results listings;</li>
+ <li>Preview Web Services.</li>
+ </ul>
+ </p>
+
+ <p>
+ Web Service previews display a similar set of information to
+ that shown on the BioCatalogue website: service description,
+ type, location, provider and other details are shown. Listing
+ of all operations and their descriptions within that Web Service
+ is shown. Any operation may be added directly into the current
+ workflow or into the Service Panel in the Design Perspective
+ for later use.
+ </p>
+
+ <h3>
+ Integration into Design Perspective
+ </h3>
+
+ <p>
+ <ul>
+ <li>Any Web Service operations added to the Service Panel from the BioCatalogue
+ perspective can be dragged into the Workflow Diagram like any other Processors.
+ They are saved by the plugin, so that when Taverna is restarted, those services
+ can still be found in the Service Panel.
+ </li>
+ <li>Right mouse click on a Processor in the Workflow Explorer or Workflow Diagram
+ will display options provided by the plugin - for all WSDL Processors it is
+ possible to check their monitoring status or launch the Processor Preview.
+ </li>
+ <li>Right mouse click on an empty space in the Workflow Diagram will let to launch
+ the workflow "health check" - currently this feature will identify a list of all
+ WSDL activities in a workflow and will fetch the latest monitoring data about
+ each of the from BioCatalogue.
+ </li>
+ <li>"Details" tab in the contextual view area (bottom-left corner of the Design
+ Perspective) will display information about the WSDL Processors and their
+ input or output ports (if they are registered in BioCatalogue). These contextual
+ views are only shown if BioCatalogue knows how to handle the selected type of
+ workflow element.
+ </li>
+ </ul>
+ </p>
+
+
+ <h3>
+ Choosing the BioCatalogue Instance to Work With
+ </h3>
+
+ <p>
+ The BioCatalogue is an open-source project and anyone can setup their
+ own instance of the BioCatalogue software. By default, the plugin is
+ configured to use the main BioCatalogue website
+ (at <font color="blue">http://www.biocatalogue.org</font>) as a source
+ of data.
+ </p>
+ <p>
+ Should this be necessary, the plugin can be configured to use another
+ instance of BioCatalogue. This can be done through the Preferences dialog
+ of Taverna by going to: <pre>File -> Preferences -> BioCatalogue</pre>
+ </p>
+
+
+ <h3>
+ Known Issues and Missing Functionality
+ </h3>
+
+ <p>
+ Below are the most important known issues. These will be fixed in the later releases.
+ </p>
+
+ <p>
+ <ul>
+ <li>Previews are only available for SOAP services, but not REST services
+ or users, registries, service providers.
+ </li>
+ <li>Search history, favourite search queries and filters are not persisted.
+ This means that this data will only be available for the current working
+ session and will be lost after Taverna is switched off.
+ </li>
+ <li>Only read access to the BioCatalogue data is currently provided.</li>
+ </ul>
+ </p>
+ </body>
+</html>
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin-feedback.html b/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin-feedback.html
new file mode 100644
index 0000000..b2c48b4
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin-feedback.html
@@ -0,0 +1,28 @@
+<html>
+ <head>
+ <meta content="text/html; charset=MacRoman" http-equiv="Content-Type">
+ <link rel="stylesheet" href="./basic.css" type="text/css">
+ <meta name="generator" content="Helen">
+ <title>BioCatalogue Plugin - Feedback</title>
+ </head>
+ <body>
+ <h2>
+ BioCatalogue Plugin - Feedback
+ </h2>
+ <p>
+ Please provide us with your feedback to help improve the BioCatalogue plugin.
+ In order to do so, please go to <em>About</em> tab in the <em>BioCatalogue perspective</em>
+ and click the "Leave feedback" button - you will be taken to a web page with a form
+ to fill in and submit your comments.
+ </p>
+ <p>
+ Developers are very interested to hear:
+ <ul>
+ <li>suggestions regarding the existing functionality;</li>
+ <li>new feature requests;</li>
+ <li>ideas for improving the user interfaces;</li>
+ <li>any other feedback you may have.</li>
+ </ul>
+ </p>
+ </body>
+</html>
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin.html b/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin.html
new file mode 100644
index 0000000..152b935
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin.html
@@ -0,0 +1,54 @@
+<html>
+ <head>
+ <meta content="text/html; charset=MacRoman" http-equiv="Content-Type">
+ <link rel="stylesheet" href="./basic.css" type="text/css">
+ <meta name="generator" content="Helen">
+ <title>BioCatalogue Plugin</title>
+ </head>
+ <body>
+ <h2>
+ BioCatalogue Plugin
+ </h2>
+ <h3><small>Version: 0.1.1 (alpha)</small></h3>
+ <p>
+ The <em>BioCatalogue plugin</em> is intended to provide access to the data held
+ in the <em>BioCatalogue Web Services Registry</em> directly from <em>Taverna Workbench</em>.
+ </p>
+ <p>
+ In its current state the plugin is designed to:
+ <ul>
+ <li>display the integration capabilities with both BioCatalogue and Taverna;</li>
+ <li>provide a general idea of the kinds of data that can be fetched
+ from the Biocatalogue through its REST API;
+ </li>
+ <li>attempt to make the workflow composition process easier and provide useful
+ contextual data to help with understanding of existing workflows.
+ </li>
+ </ul>
+ </p>
+ <p>
+ This release has made the plugin compatible with the latest version of
+ Taverna - 2.2. Several important bugs were also fixed, however more new
+ functionality will be added soon.
+ </p>
+ <p>
+ To learn more about the available functionality, please see the <a href=
+ "./biocatalogue-plugin-features.html">feature list</a>.
+ </p>
+ <p><b>
+ Please note that this is an incomplete version of the BioCatalogue plugin.
+ You may see notifications that certain pieces of functionality have not been
+ implemented yet; some features are not yet fully stable, which means that
+ occasionally you may see unexpected error messages.
+ </b></p>
+ <p>
+ Any <a href="./biocatalogue-plugin-feedback.html">feedback</a> will be greatly apppreciated - it
+ will help to understand the true needs of the user community and develop
+ a complete version of this plugin later in the year.
+ </p>
+ <p>
+ This version of the plugin was developed by Sergejs Aleksejevs as part of his
+ final year project on the undergraduate Computer Science course at the University of Manchester.
+ </p>
+ </body>
+</html>
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/BioCataloguePluginConstants.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/BioCataloguePluginConstants.java
new file mode 100644
index 0000000..791b544
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/BioCataloguePluginConstants.java
@@ -0,0 +1,77 @@
+package net.sf.taverna.biocatalogue.model;
+
+import java.io.File;
+
+
+/**
+ * This class contains the collection of important constants,
+ * which are used throughout the BioCatalogue plugin.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class BioCataloguePluginConstants
+{
+ public static final String APP_VISIBLE_NAME = "Service Catalogue Plugin";
+ public static final String APP_PREFIX = "T2ServiceCataloguePlugin:";
+
+
+ public static final boolean PERFORM_API_RESPONSE_TIME_LOGGING = true;
+ public static final boolean PERFORM_API_XML_DATA_BINDING_TIME_LOGGING = true;
+ public static final String API_OPERATION_LOG_FILENAME = "service_catalogue_api.log";
+
+
+ public static final int DEFAULT_SCROLL = 15; // default vertical scroll increment to be used in all JScrollPane instances within the plugin
+ public static final int DEFAULT_TOOLTIP_DURATION = 10000; // default duration of visibility of tooltips (in "ms")
+ public static final int DEFAULT_THREAD_STARTUP_TIME = 10; // this is the time (in "ms") that we think the system takes at most to start a new thread
+
+ public static final int API_DEFAULT_REQUESTED_TAG_COUNT_PER_PAGE = 50;
+ public static final int API_DEFAULT_REQUESTED_WEB_SERVICE_COUNT_PER_PAGE = 20;
+ public static final int API_DEFAULT_REQUESTED_SOAP_OPERATION_COUNT_PER_PAGE = 20;
+ public static final int API_DEFAULT_REQUESTED_REST_METHOD_COUNT_PER_PAGE = 20;
+ public static final int API_DEFAULT_REQUESTED_USER_COUNT_PER_PAGE = 20;
+ public static final int API_DEFAULT_REQUESTED_SERVICE_PROVIDER_COUNT_PER_PAGE = 20;
+
+
+ public static final int SEARCH_HISTORY_LENGTH = 50; // maximum number of search history items to store (if exceeded, oldest will be removed)
+ public static final int FAVOURITE_SEARCHES_LENGTH = 30; // maximum number of favourite search settings to store (if exceeded, oldest will be removed)
+ public static final int FAVOURITE_FILTERS_LENGTH = 30; // maximum number of favourite service filters to store (if exceeded, oldest will be removed)
+ public static final int RESOURCE_PREVIEW_HISTORY_LENGTH = 50;
+
+ public static final int RESOURCE_PREVIEW_BROWSER_PREFERRED_WIDTH = 750;
+ public static final int RESOURCE_PREVIEW_BROWSER_PREFERRED_HEIGHT = 600;
+
+ public static final String ACTION_FILTER_FOUND_SERVICES = APP_PREFIX + "filterFoundServices:";
+ public static final String ACTION_FILTER_BY_CATEGORY = APP_PREFIX + "filterByCategory:";
+ public static final String ACTION_SHOW_IN_WEB_BROWSER = APP_PREFIX + "showInWebBrowser:";
+ public static final String ACTION_SHOW_TAG_SELECTION_DIALOG = APP_PREFIX + "showTagSelectionDialgog";
+ public static final String ACTION_PREVIEW_CURRENT_FILTER = APP_PREFIX + "previewCurrentFilter";
+ public static final String ACTION_PREVIEW_RESOURCE = APP_PREFIX + "preview:";
+ public static final String ACTION_PREVIEW_SOAP_OPERATION_AFTER_LOOKUP = APP_PREFIX + "previewSoapOperationAfterLookup:";
+ public static final String ACTION_PREVIEWED_SERVICE_HEALTH_CHECK = APP_PREFIX + "previewedServiceHealthCheck";
+ public static final String ACTION_TAG_SEARCH_PREFIX = APP_PREFIX + "tag:";
+
+
+
+ public static final String CONFIG_FILE_FOLDER_WHEN_RUNNING_STANDALONE = ".Taverna2-ServiceCatalogue Plugin";
+
+
+
+ // ---------------------------- CONTEXTUAL VIEWS --------------------------------
+
+ // this value currently makes contextual views generated by this
+ // plugin the to be the last in the list
+ public static final int CONTEXTUAL_VIEW_PREFERRED_POSITION = 600;
+
+
+
+ // ------------------------------------------------------------------------------
+
+ /*
+ * Some of the settings are determined during the runtime - hence are non-final.
+ *
+ * These are set in MainComponent.initialiseEnvironment()
+ */
+
+ public static File CONFIG_FILE_FOLDER = new File(ApplicationRuntime.getInstance().getApplicationHomeDir(), "conf");
+ public static File LOG_FILE_FOLDER = new File(ApplicationRuntime.getInstance().getApplicationHomeDir(), "logs");
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/HTTPMethodInterpreter.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/HTTPMethodInterpreter.java
new file mode 100644
index 0000000..ecd4cf1
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/HTTPMethodInterpreter.java
@@ -0,0 +1,46 @@
+package net.sf.taverna.biocatalogue.model;
+
+import org.apache.log4j.Logger;
+import org.biocatalogue.x2009.xml.rest.HttpVerb;
+
+import net.sf.taverna.t2.activities.rest.RESTActivity.HTTP_METHOD;
+
+/**
+ * Very simple class for translating HTTP method values returned
+ * by the BioCatalogue API into the set of values that are used
+ * by the REST activity.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class HTTPMethodInterpreter
+{
+ // deny instantiation of this class
+ private HTTPMethodInterpreter() { }
+
+ public static HTTP_METHOD getHTTPMethodForRESTActivity(HttpVerb.Enum httpVerb)
+ {
+ switch (httpVerb.intValue()) {
+ case HttpVerb.INT_GET: return HTTP_METHOD.GET;
+ case HttpVerb.INT_POST: return HTTP_METHOD.POST;
+ case HttpVerb.INT_PUT: return HTTP_METHOD.PUT;
+ case HttpVerb.INT_DELETE: return HTTP_METHOD.DELETE;
+ default:
+ String errorMsg = "Unable to translate " + httpVerb.toString() + " to correct representation for REST activity;\n" +
+ "this HTTP method wasn't supported at the time of implementation.";
+ Logger.getLogger(HTTPMethodInterpreter.class).error(errorMsg);
+ throw new UnsupportedHTTPMethodException(errorMsg);
+ }
+ }
+
+
+ public static class UnsupportedHTTPMethodException extends IllegalArgumentException
+ {
+ public UnsupportedHTTPMethodException() {
+ /* empty constructor */
+ }
+
+ public UnsupportedHTTPMethodException(String message) {
+ super(message);
+ }
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/LoadingExpandedResource.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/LoadingExpandedResource.java
new file mode 100644
index 0000000..cbd3f2e
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/LoadingExpandedResource.java
@@ -0,0 +1,41 @@
+package net.sf.taverna.biocatalogue.model;
+
+import org.biocatalogue.x2009.xml.rest.ResourceLink;
+import org.biocatalogue.x2009.xml.rest.impl.ResourceLinkImpl;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class LoadingExpandedResource extends ResourceLinkImpl
+{
+ private boolean nowLoading;
+ private ResourceLink associatedObj;
+
+ public LoadingExpandedResource(ResourceLink associatedObj)
+ {
+ super(ResourceLink.type);
+
+ this.associatedObj = associatedObj;
+ this.nowLoading = true;
+ }
+
+ public ResourceLink getAssociatedObj() {
+ return associatedObj;
+ }
+
+ public boolean isLoading() {
+ return (nowLoading);
+ }
+ public void setLoading(boolean isLoading) {
+ this.nowLoading = isLoading;
+ }
+
+ public String getHref() {
+ return (associatedObj.getHref());
+ }
+
+ public String getResourceName() {
+ return (associatedObj.getResourceName());
+ }
+}
+
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/LoadingResource.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/LoadingResource.java
new file mode 100644
index 0000000..a003075
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/LoadingResource.java
@@ -0,0 +1,39 @@
+package net.sf.taverna.biocatalogue.model;
+
+import org.biocatalogue.x2009.xml.rest.ResourceLink;
+import org.biocatalogue.x2009.xml.rest.impl.ResourceLinkImpl;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class LoadingResource extends ResourceLinkImpl
+{
+ private boolean nowLoading;
+ private ResourceLink associatedObj;
+
+ public LoadingResource(String resourceURL, String resourceName) {
+ super(ResourceLink.type);
+
+ associatedObj = ResourceLink.Factory.newInstance();
+ associatedObj.setHref(resourceURL);
+ associatedObj.setResourceName(resourceName);
+
+ this.nowLoading = false;
+ }
+
+ public String getHref() {
+ return (associatedObj.getHref());
+ }
+
+ public String getResourceName() {
+ return (associatedObj.getResourceName());
+ }
+
+ public boolean isLoading() {
+ return (nowLoading);
+ }
+ public void setLoading(boolean isLoading) {
+ this.nowLoading = isLoading;
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Pair.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Pair.java
new file mode 100644
index 0000000..b694db8
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Pair.java
@@ -0,0 +1,30 @@
+package net.sf.taverna.biocatalogue.model;
+
+/**
+ * Trivial class to represent a generic pair of objects.
+ * Any types of objects can be used.
+ *
+ * @author Sergejs Aleksejevs
+ *
+ * @param <T1> Type of the first object.
+ * @param <T2> Type of the second object.
+ */
+public class Pair<T1,T2>
+{
+ private final T1 firstObject;
+ private final T2 secondObject;
+
+ public Pair(T1 firstObject, T2 secondObject) {
+ this.firstObject = firstObject;
+ this.secondObject = secondObject;
+ }
+
+ public T1 getFirstObject() {
+ return firstObject;
+ }
+
+ public T2 getSecondObject() {
+ return secondObject;
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Resource.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Resource.java
new file mode 100644
index 0000000..3095863
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Resource.java
@@ -0,0 +1,506 @@
+package net.sf.taverna.biocatalogue.model;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.Icon;
+import javax.swing.JOptionPane;
+import javax.swing.ListCellRenderer;
+
+import net.sf.taverna.biocatalogue.model.connectivity.BeansForJSONLiteAPI;
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
+import net.sf.taverna.biocatalogue.ui.search_results.RESTMethodListCellRenderer;
+import net.sf.taverna.biocatalogue.ui.search_results.SOAPOperationListCellRenderer;
+import net.sf.taverna.biocatalogue.ui.search_results.ServiceListCellRenderer;
+import net.sf.taverna.t2.workbench.MainWindow;
+
+import org.apache.log4j.Logger;
+import org.biocatalogue.x2009.xml.rest.Registry;
+import org.biocatalogue.x2009.xml.rest.ResourceLink;
+import org.biocatalogue.x2009.xml.rest.RestMethod;
+import org.biocatalogue.x2009.xml.rest.RestMethods;
+import org.biocatalogue.x2009.xml.rest.Service;
+import org.biocatalogue.x2009.xml.rest.ServiceProvider;
+import org.biocatalogue.x2009.xml.rest.Services;
+import org.biocatalogue.x2009.xml.rest.SoapOperation;
+import org.biocatalogue.x2009.xml.rest.SoapOperations;
+import org.biocatalogue.x2009.xml.rest.User;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class Resource
+{
+ /**
+ * A single point of definition of the types of resources that the BioCatalogue plugin
+ * "knows" about. This enum provides various details about resource types -
+ * display names for single items of that type, names of collections of items of that
+ * type, icons to represent the items of a particular type, etc.
+ *
+ * @author Sergejs Aleksejevs
+ */
+ public static enum TYPE
+ {
+ // the order is important - all these types will appear in the user interface
+ // in the same order as listed here
+ @SuppressWarnings("serial")
+ SOAPOperation (SoapOperation.class, SoapOperations.class, BeansForJSONLiteAPI.SOAPOperationsIndex.class, "WSDL service", "WSDL services",
+ "WSDL services can be directly imported into the current workflow or Service Panel",
+ ResourceManager.getIconFromTaverna(ResourceManager.SOAP_OPERATION_ICON), true, true, true, false, true, true, true, true,
+ SOAPOperationListCellRenderer.class, BioCatalogueClient.API_SOAP_OPERATIONS_URL,
+ new HashMap<String,String>() {{
+ }},
+ new HashMap<String,String>(BioCatalogueClient.API_INCLUDE_ANCESTORS) {{
+ put(BioCatalogueClient.API_PER_PAGE_PARAMETER, ""+BioCataloguePluginConstants.API_DEFAULT_REQUESTED_SOAP_OPERATION_COUNT_PER_PAGE);
+ }},
+ BioCataloguePluginConstants.API_DEFAULT_REQUESTED_SOAP_OPERATION_COUNT_PER_PAGE,
+ BioCatalogueClient.API_SOAP_OPERATION_FILTERS_URL),
+
+ @SuppressWarnings("serial")
+ RESTMethod (RestMethod.class, RestMethods.class, BeansForJSONLiteAPI.RESTMethodsIndex.class, "REST service", "REST services",
+ "REST services can be directly imported into the current workflow or Service Panel",
+ ResourceManager.getIconFromTaverna(ResourceManager.REST_METHOD_ICON), true, true, true, false, true, false, true, true,
+ RESTMethodListCellRenderer.class, BioCatalogueClient.API_REST_METHODS_URL,
+ new HashMap<String,String>() {{
+ }},
+ new HashMap<String,String>(BioCatalogueClient.API_INCLUDE_ANCESTORS) {{
+ put(BioCatalogueClient.API_PER_PAGE_PARAMETER, ""+BioCataloguePluginConstants.API_DEFAULT_REQUESTED_REST_METHOD_COUNT_PER_PAGE);
+ }},
+ BioCataloguePluginConstants.API_DEFAULT_REQUESTED_REST_METHOD_COUNT_PER_PAGE,
+ BioCatalogueClient.API_REST_METHOD_FILTERS_URL); //,
+
+ // TODO - the following resource types have been disabled, as no actions for them can be done yet
+ // -- they are still to be implemented; if the following types are uncommented, they will be
+ // automatically searchable and visible in BioCatalogue Exploration tab; ListCellRenderers, however,
+ // would need to be added first.
+// @SuppressWarnings("serial")
+// Service (Service.class, Services.class, BeansForJSONLiteAPI.ServicesIndex.class, "Web service", "Web services",
+// "<html>Web services represent collections of WSDL services or REST services.<br>" +
+// "They cannot be directly imported into the current workflow or Service Panel,<br>" +
+// "but they may contain much more information about individual WSDL or REST<br>" +
+// "services and also provide some context for their usage.</html>",
+// ResourceManager.getImageIcon(ResourceManager.SERVICE_ICON), true, true, true, false, false, false, true,
+// ServiceListCellRenderer.class, BioCatalogueClient.API_SERVICES_URL,
+// new HashMap<String,String>(BioCatalogueClient.API_INCLUDE_SUMMARY) {{
+// }},
+// new HashMap<String,String>() {{
+// put(BioCatalogueClient.API_PER_PAGE_PARAMETER, ""+BioCataloguePluginConstants.API_DEFAULT_REQUESTED_WEB_SERVICE_COUNT_PER_PAGE);
+// }},
+// BioCataloguePluginConstants.API_DEFAULT_REQUESTED_WEB_SERVICE_COUNT_PER_PAGE,
+// BioCatalogueClient.API_SERVICE_FILTERS_URL),
+//
+// ServiceProvider (ServiceProvider.class, ServiceProviders.class, BeansForJSONLiteAPI.ServiceProvidersIndex.class, "Service Provider", "Service Providers", "",
+// ResourceManager.getImageIcon(ResourceManager.SERVICE_PROVIDER_ICON), false, false, false, false, false, false, false,
+// ServiceProviderListCellRenderer.class, BioCatalogueClient.API_SERVICE_PROVIDERS_URL,
+// new HashMap<String,String>() {{
+// }},
+// new HashMap<String,String>() {{
+// put(BioCatalogueClient.API_PER_PAGE_PARAMETER, ""+BioCataloguePluginConstants.API_DEFAULT_REQUESTED_SERVICE_PROVIDER_COUNT_PER_PAGE);
+// }},
+// BioCataloguePluginConstants.API_DEFAULT_REQUESTED_SERVICE_PROVIDER_COUNT_PER_PAGE,
+// null),
+//
+// User (User.class, Users.class, BeansForJSONLiteAPI.UsersIndex.class, "User", "Users", "",
+// ResourceManager.getImageIcon(ResourceManager.USER_ICON), false, false, true, false, false, false, false,
+// UserListCellRenderer.class, BioCatalogueClient.API_USERS_URL,
+// new HashMap<String,String>() {{
+// }},
+// new HashMap<String,String>() {{
+// put(BioCatalogueClient.API_PER_PAGE_PARAMETER, ""+BioCataloguePluginConstants.API_DEFAULT_REQUESTED_USER_COUNT_PER_PAGE);
+// }},
+// BioCataloguePluginConstants.API_DEFAULT_REQUESTED_USER_COUNT_PER_PAGE,
+// BioCatalogueClient.API_USER_FILTERS_URL);
+
+
+ @SuppressWarnings("unchecked")
+ private Class xmlbeansGeneratedClass;
+ @SuppressWarnings("unchecked")
+ private Class xmlbeansGeneratedCollectionClass;
+ private Class<?> jsonLiteAPIBindingBeanClass;
+ private String resourceTypeName;
+ private String resourceCollectionName;
+ private String resourceTabTooltip;
+ private Icon icon;
+ private boolean defaultType;
+ private boolean suitableForTagSearch;
+ private boolean suitableForFiltering;
+ private boolean suitableForOpeningInPreviewBrowser;
+ private boolean suitableForAddingToServicePanel;
+ private boolean suitableForAddingToWorkflowDiagram;
+ private boolean suitableForHealthCheck;
+ private Class<? extends ListCellRenderer> resultListingCellRendererClass;
+ private String apiResourceCollectionIndex;
+ private Map<String,String> apiResourceCollectionIndexSingleExpandedResourceAdditionalParameters;
+ private Map<String,String> apiResourceCollectionIndexAdditionalParameters;
+ private int apiResourceCountPerIndexPage;
+ private String apiResourceCollectionFilters;
+ private final boolean suitableForAddingAllToServicePanel;
+
+ @SuppressWarnings("unchecked")
+ TYPE(Class xmlbeansGeneratedClass, Class xmlbeansGeneratedCollectionClass, Class<?> jsonLiteAPIBindingBeanClass,
+ String resourceTypeName, String resourceCollectionName, String resourceTabTooltip, Icon icon,
+ boolean defaultType, boolean suitableForTagSearch, boolean suitableForFiltering, boolean suitableForOpeningInPreviewBrowser,
+ boolean suitableForAddingToServicePanel, boolean suitableForAddingAllToServicePanel, boolean suitableForAddingToWorkflowDiagram,
+ boolean suitableForHealthCheck, Class<? extends ListCellRenderer> resultListingCellRendererClass,
+ String apiResourceCollectionIndex, Map<String,String> apiResourceCollectionIndexSingleExpandedResourceAdditionalParameters,
+ Map<String,String> apiResourceCollectionIndexAdditionalParameters, int apiResourceCountPerIndexListingPage,
+ String apiResourceCollectionFilters)
+ {
+ this.xmlbeansGeneratedClass = xmlbeansGeneratedClass;
+ this.xmlbeansGeneratedCollectionClass = xmlbeansGeneratedCollectionClass;
+ this.jsonLiteAPIBindingBeanClass = jsonLiteAPIBindingBeanClass;
+ this.resourceTypeName = resourceTypeName;
+ this.resourceCollectionName = resourceCollectionName;
+ this.resourceTabTooltip = resourceTabTooltip;
+ this.icon = icon;
+ this.defaultType = defaultType;
+ this.suitableForTagSearch = suitableForTagSearch;
+ this.suitableForFiltering = suitableForFiltering;
+ this.suitableForOpeningInPreviewBrowser = suitableForOpeningInPreviewBrowser;
+ this.suitableForAddingToServicePanel = suitableForAddingToServicePanel;
+ this.suitableForAddingAllToServicePanel = suitableForAddingAllToServicePanel;
+ this.suitableForAddingToWorkflowDiagram = suitableForAddingToWorkflowDiagram;
+ this.suitableForHealthCheck = suitableForHealthCheck;
+ this.resultListingCellRendererClass = resultListingCellRendererClass;
+ this.apiResourceCollectionIndex = apiResourceCollectionIndex;
+ this.apiResourceCollectionIndexSingleExpandedResourceAdditionalParameters = apiResourceCollectionIndexSingleExpandedResourceAdditionalParameters;
+ this.apiResourceCollectionIndexAdditionalParameters = apiResourceCollectionIndexAdditionalParameters;
+ this.apiResourceCountPerIndexPage = apiResourceCountPerIndexListingPage;
+ this.apiResourceCollectionFilters = apiResourceCollectionFilters;
+ }
+
+
+
+ @SuppressWarnings("unchecked")
+ public Class getXmlBeansGeneratedClass() {
+ return this.xmlbeansGeneratedClass;
+ }
+
+ /**
+ * @return Class that represents collection of resources of this type,
+ * as represented by XmlBeans.
+ */
+ @SuppressWarnings("unchecked")
+ public Class getXmlBeansGeneratedCollectionClass() {
+ return this.xmlbeansGeneratedCollectionClass;
+ }
+
+
+ /**
+ * @return Class of the bean to be used when de-serialising JSON
+ * data received from the 'Lite' BioCatalogue JSON API's index
+ * of resources of this type.
+ */
+ public Class<?> getJsonLiteAPIBindingBeanClass() {
+ return this.jsonLiteAPIBindingBeanClass;
+ }
+
+
+ /**
+ * @return Display name of a type of a single item belonging to that type.
+ * (E.g. 'User' or 'Service')
+ */
+ public String getTypeName() {
+ return this.resourceTypeName;
+ }
+
+ /**
+ * @return Display name of a collection of items of this type.
+ * (E.g. 'Users' or 'Services').
+ */
+ public String getCollectionName() {
+ return this.resourceCollectionName;
+ }
+
+ /**
+ * @return HTML-formatted string that can be used as a tooltip
+ * for tabs in BioCatalogue Exploration tab of BioCatalogue
+ * perspective.
+ */
+ public String getCollectionTabTooltip() {
+ return this.resourceTabTooltip;
+ }
+
+ /**
+ * @return Small icon that represents this resource type.
+ */
+ public Icon getIcon() {
+ return this.icon;
+ }
+
+ /**
+ * @return <code>true</code> - if used for search by default;<br/>
+ * <code>false</code> - otherwise.
+ */
+ public boolean isDefaultSearchType() {
+ return this.defaultType;
+ }
+
+ /**
+ * Resources not of all resource types can be searched for by tags (although every resource type
+ * can be searched for by a free-text query).
+ *
+ * @return <code>true</code> if resources of this type can be searched for by tags,<br/>
+ * <code>false</code> otherwise.
+ */
+ public boolean isSuitableForTagSearch() {
+ return this.suitableForTagSearch;
+ }
+
+ /**
+ * Not all resource types are suitable for filtering - for example, there are no
+ * filters available for service providers in BioCatalogue.
+ *
+ * @return <code>true</code> indicates that tab dedicated to displaying search
+ * results of this resource type can have a filter tree.
+ */
+ public boolean isSuitableForFiltering() {
+ return this.suitableForFiltering;
+ }
+
+ /**
+ * @return <code>true</code> indicates that "Preview" option can be made
+ * available for items of this type, as preview factory would be implemented
+ * for such resources.
+ */
+ public boolean isSuitableForOpeningInPreviewBrowser() {
+ return this.suitableForOpeningInPreviewBrowser;
+ }
+
+ public boolean isSuitableForAddingToServicePanel() {
+ return this.suitableForAddingToServicePanel;
+ }
+
+ public boolean isSuitableForAddingToWorkflowDiagram() {
+ return this.suitableForAddingToWorkflowDiagram;
+ }
+
+ /**
+ * @return <code>true</code> indicates that monitoring data can be obtained
+ * from BioCatalougue for this type of resource.
+ */
+ public boolean isSuitableForHealthCheck() {
+ return this.suitableForHealthCheck;
+ }
+
+
+ /**
+ * This method helps to defer instantiation of ListCellRenderers
+ * until they are first accessed - it is because construction of
+ * the renderers requires knowledge of all available resource types,
+ * therefore they cannot be instantiated until after Resource class
+ * has been fully loaded.
+ *
+ * @return {@link ListCellRenderer} for this type of resources or
+ * <code>null</code> if an error has occurred during
+ * instantiation of required renderer.
+ */
+ public ListCellRenderer getResultListingCellRenderer() {
+ try {
+ return this.resultListingCellRendererClass.newInstance();
+ }
+ catch (Exception e) {
+ Logger.getLogger(Resource.class).error("Unable to instantiate search results ListCellRenderer for " +
+ this.getCollectionName(), e);
+ JOptionPane.showMessageDialog(MainWindow.getMainWindow(),
+ "Taverna was unable to instantiate ListCellRenderer for " + this.getCollectionName() + ".\n\n" +
+ "This may make Taverna unstable.", "Service Catalogue Plugin", JOptionPane.ERROR_MESSAGE);
+ return null;
+ }
+ }
+
+ /**
+ * @return URL in the BioCatalogue API that provides an index of the collection of
+ * all resources of this type.
+ */
+ public String getAPIResourceCollectionIndex() {
+ return apiResourceCollectionIndex;
+ }
+
+ /**
+ * @return Keys and values for any additional URL parameters that need to be included into the
+ * BioCatalogue API requests that are made in order to fetch all necessary additional
+ * details for a *single* expanded entry in the search results listing.
+ */
+ public Map<String,String> getResourceCollectionIndexSingleExpandedResourceAdditionalParameters() {
+ return apiResourceCollectionIndexSingleExpandedResourceAdditionalParameters;
+ }
+
+ /**
+ * @return Keys and values for any additional URL parameters that need to be included into the
+ * requests sent to filtered indexes of collections of this type in the BioCatalogue API.
+ */
+ public Map<String,String> getAPIResourceCollectionIndexAdditionalParameters() {
+ return apiResourceCollectionIndexAdditionalParameters;
+ }
+
+ /**
+ * @return Number of resources of this type that one page of search results from
+ * the API will contain.
+ */
+ public int getApiResourceCountPerIndexPage() {
+ return apiResourceCountPerIndexPage;
+ }
+
+ /**
+ * @return BioCatalogue API URL that provides a collection of filters for the
+ * resource of this type.
+ */
+ public String getAPIResourceCollectionFiltersURL() {
+ return apiResourceCollectionFilters;
+ }
+
+
+ /**
+ * This method is useful for adding / removing tabs into the results view - provides
+ * and index for the tabbed view to place a tab, relevant to a particular resource type.
+ * This helps to preserve the order of tabs after adding / removing them.
+ *
+ * @return Zero-based index of this resource type in the <code>RESOURCE_TYPE</code> enum or
+ * <code>-1</code> if not found (which is impossible under normal conditions).
+ */
+ public int index()
+ {
+ TYPE[] values = TYPE.values();
+ for (int i = 0; i < values.length; i++) {
+ if (this == values[i]) {
+ return (i);
+ }
+ }
+ return (-1);
+ }
+
+
+
+ /**
+ * @return the suitableForAddingAllToServicePanel
+ */
+ public boolean isSuitableForAddingAllToServicePanel() {
+ return suitableForAddingAllToServicePanel;
+ }
+
+ };
+
+
+
+ // ----------------------------- RESOURCE CLASS -------------------------------
+
+
+ // current resource data
+ private final TYPE resourceType;
+ private final String resourceURL;
+ private final String resourceTitle;
+
+
+ public Resource(String resourceURL, String resourceTitle)
+ {
+ this.resourceURL = extractPureResourceURLFromPreviewActionCommand(resourceURL);
+ this.resourceTitle = resourceTitle;
+ this.resourceType = getResourceTypeFromResourceURL(resourceURL);
+ }
+
+ public TYPE getType() {
+ return resourceType;
+ }
+
+ public String getURL() {
+ return resourceURL;
+ }
+
+ public String getTitle() {
+ return resourceTitle;
+ }
+
+
+
+ public boolean equals(Object other)
+ {
+ if (other instanceof Resource)
+ {
+ // compare by all components
+ Resource otherRes = (Resource)other;
+ return (this.resourceType == otherRes.resourceType &&
+ this.resourceTitle.equals(otherRes.resourceTitle) &&
+ this.resourceURL.equals(otherRes.resourceURL));
+ }
+ else {
+ // other object is of different type
+ return (false);
+ }
+ }
+
+
+ /**
+ * @param url Either URL of the resource in BioCatalogue or preview action command
+ * ({@link BioCataloguePluginConstants#ACTION_PREVIEW_RESOURCE}).
+ * @return Type of this resource according to the BioCatalogue URL that points to this
+ * resource or <code>null</code> if the type of the resource couldn't be determined.
+ */
+ public static TYPE getResourceTypeFromResourceURL(String url)
+ {
+ String pureURL = extractPureResourceURLFromPreviewActionCommand(url);
+
+// if (pureURL.startsWith(BioCatalogueClient.API_SERVICES_URL)) return(TYPE.Service);
+// else
+ if (pureURL.startsWith(BioCatalogueClient.API_SOAP_OPERATIONS_URL)) {
+ return(TYPE.SOAPOperation);
+ }
+ if (pureURL.startsWith(BioCatalogueClient.API_REST_METHODS_URL)) {
+ return(TYPE.RESTMethod);
+ }
+// else if (pureURL.startsWith(BioCatalogueClient.API_SERVICE_PROVIDERS_URL)) return(TYPE.ServiceProvider); // TODO - re-enable these lines as soon as ServiceProvider and User type are started to be used
+// else if (pureURL.startsWith(BioCatalogueClient.API_USERS_URL)) return(TYPE.User);
+ return (null);
+ }
+
+
+ /**
+ * @param previewActionCommand Either resource preview action command or a 'pure' resource URL already.
+ * @return A "pure" resource URL in BioCatalogue with the action prefix
+ * ({@link BioCataloguePluginConstants#ACTION_PREVIEW_RESOURCE}) removed.
+ */
+ public static String extractPureResourceURLFromPreviewActionCommand(String previewActionCommand)
+ {
+ return (previewActionCommand.startsWith(BioCataloguePluginConstants.ACTION_PREVIEW_RESOURCE) ?
+ previewActionCommand.substring(BioCataloguePluginConstants.ACTION_PREVIEW_RESOURCE.length()) :
+ previewActionCommand);
+ }
+
+
+ /**
+ * @param resource
+ * @return Display name for listings of items.
+ */
+ public static String getDisplayNameForResource(ResourceLink resource)
+ {
+ if (resource instanceof SoapOperation) {
+ return ((SoapOperation)resource).getName();
+ }
+ else if (resource instanceof RestMethod)
+ {
+ RestMethod restMethod = (RestMethod)resource;
+ return (restMethod.getName() == null || restMethod.getName().length() == 0 ?
+ restMethod.getEndpointLabel() :
+ restMethod.getName());
+ }
+ else if (resource instanceof Service) {
+ return ((Service)resource).getName();
+ }
+ else if (resource instanceof ServiceProvider) {
+ return ((ServiceProvider)resource).getName();
+ }
+ else if (resource instanceof User) {
+ return ((User)resource).getName();
+ }
+ else if (resource instanceof Registry) {
+ return ((Registry)resource).getName();
+ }
+ else if (resource instanceof LoadingResource) {
+ return (resource.getResourceName());
+ }
+ else {
+ return ("ERROR: ITEM NOT RECOGNISED - Item is of known generic type from the Service Catalogue Plugin, but not specifically recognised" + resource.toString());
+ }
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/ResourceManager.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/ResourceManager.java
new file mode 100644
index 0000000..666cd6c
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/ResourceManager.java
@@ -0,0 +1,326 @@
+package net.sf.taverna.biocatalogue.model;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.GraphicsConfiguration;
+import java.awt.GraphicsDevice;
+import java.awt.GraphicsEnvironment;
+import java.awt.image.BufferedImage;
+import java.net.URL;
+import java.util.HashMap;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.t2.activities.rest.ui.servicedescription.RESTActivityIcon;
+import net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLActivityIcon;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.BioCataloguePerspective;
+
+/**
+ * This class will be a single point of lookup of all resource files.
+ * (Icons, images, CSS files, etc).
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class ResourceManager
+{
+ // subfolders, where some icons / other resources are kept
+ public static final String FAMFAMFAM_PATH = "famfamfam_silk/"; // free collection of icons
+ public static final String SERVICE_ICONS_PATH = "service_icons/"; // icons related to web services (e.g. service types)
+ public static final String FOLDS_PATH = "folds/"; // icons for 'folding' menus (like 'Search for...')
+ public static final String TRISTATE_TREE_ICONS_PATH = "tristate_checkbox/"; // icons for the tri-state filtering tree
+
+ // all known resources to follow
+ public static final int FAVICON = 1;
+
+ public static final int INFORMATION_ICON_LARGE = 10;
+
+ public static final int SPINNER_STILL = 20;
+ public static final int SPINNER = 21;
+ public static final int BAR_LOADER_GREY = 25;
+ public static final int BAR_LOADER_GREY_STILL = 26;
+ public static final int BAR_LOADER_ORANGE = 30;
+ public static final int BAR_LOADER_ORANGE_STILL = 31;
+
+ public static final int FOLD_ICON = 40;
+ public static final int UNFOLD_ICON = 41;
+ public static final int FOLD_ICON_16x16 = 42;
+ public static final int UNFOLD_ICON_16x16 = 43;
+
+ public static final int SERVICE_TYPE_SOAP_ICON = 50;
+ public static final int SERVICE_TYPE_REST_ICON = 51;
+ public static final int SERVICE_TYPE_MULTITYPE_ICON = 65;
+ public static final int SERVICE_TYPE_UNKNOWN_ICON = 70;
+
+ public static final int TRISTATE_CHECKBOX_CHECKED_ICON = 80;
+ public static final int TRISTATE_CHECKBOX_PARTIAL_ICON = 82;
+ public static final int TRISTATE_CHECKBOX_UNCHECKED_ICON = 85;
+ public static final int UNCHECKED_ICON = 86;
+
+ public static final int SERVICE_STATUS_PASSED_ICON = 100;
+ public static final int SERVICE_STATUS_PASSED_ICON_LARGE = 101;
+ public static final int SERVICE_STATUS_WARNING_ICON = 110;
+ public static final int SERVICE_STATUS_WARNING_ICON_LARGE = 111;
+ public static final int SERVICE_STATUS_FAILED_ICON = 120;
+ public static final int SERVICE_STATUS_FAILED_ICON_LARGE = 121;
+ public static final int SERVICE_STATUS_UNCHECKED_ICON = 130;
+ public static final int SERVICE_STATUS_UNCHECKED_ICON_LARGE = 131;
+ public static final int SERVICE_STATUS_UNKNOWN_ICON = 140;
+
+ public static final int UNKNOWN_RESOURCE_TYPE_ICON = 200;
+ public static final int USER_ICON = 205;
+ public static final int REGISTRY_ICON = 210;
+ public static final int SERVICE_PROVIDER_ICON = 215;
+ public static final int SERVICE_ICON = 220;
+ public static final int SOAP_OPERATION_ICON = 225;
+ public static final int REST_METHOD_ICON = 227;
+ public static final int SERVICE_CATEGORY_ICON = 230;
+ public static final int WSDL_DOCUMENT_ICON = 235;
+ public static final int TAG_ICON = 240;
+
+ public static final int OPEN_IN_BIOCATALOGUE_ICON = 310;
+ public static final int SEARCH_ICON = 315;
+ public static final int HISTORY_ICON = 320;
+ public static final int REFRESH_ICON = 330;
+ public static final int FAVOURITE_ICON = 335;
+ public static final int TICK_ICON = 340;
+ public static final int CROSS_ICON = 341;
+ public static final int WARNING_ICON = 342;
+ public static final int ERROR_ICON = 343;
+ public static final int SAVE_ICON = 345;
+ public static final int DELETE_ITEM_ICON = 350;
+ public static final int CLEAR_ICON = 355;
+ public static final int LOCKED_ICON = 360;
+ public static final int UNLOCKED_ICON = 365;
+
+ public static final int BACK_ICON = 370;
+ public static final int FORWARD_ICON = 375;
+ public static final int FILTER_ICON = 380;
+ public static final int PREVIEW_ICON = 385;
+ public static final int SUGGESTION_TO_USER_ICON = 390;
+ public static final int ADD_PROCESSOR_TO_WORKFLOW_ICON = 395;
+ public static final int ADD_PROCESSOR_AS_FAVOURITE_ICON = 396;
+ public static final int EXECUTE_HEALTH_CHECK_ICON = 397;
+ public static final int ADD_ALL_SERVICES_AS_FAVOURITE_ICON = 398;
+
+ public static final int SELECT_ALL_ICON = 400;
+ public static final int DESELECT_ALL_ICON = 405;
+ public static final int EXPAND_ALL_ICON = 410;
+ public static final int COLLAPSE_ALL_ICON = 420;
+
+ public static final int SORT_BY_NAME_ICON = 450;
+ public static final int SORT_BY_COUNTS_ICON = 455;
+
+ public static final int STYLES_CSS = 1000;
+
+
+ /**
+ * Simple method to retrieve relative path of a required resource.
+ */
+ public static String getResourceRelPath(int resourceId)
+ {
+ String resPath = "";
+
+ switch (resourceId) {
+ case FAVICON: resPath += "favicon.png";
+ break;
+ case INFORMATION_ICON_LARGE: resPath += "info-sphere-35.png";
+ break;
+ case SPINNER_STILL: resPath += "ajax-loader-still.gif";
+ break;
+ case SPINNER: resPath += "ajax-loader.gif";
+ break;
+ case BAR_LOADER_GREY: resPath += "ajax-loader-grey-bert2.gif";
+ break;
+ case BAR_LOADER_GREY_STILL: resPath += "ajax-loader-grey-bert2-still.png";
+ break;
+ case BAR_LOADER_ORANGE: resPath += "ajax-loader-orange-bert2.gif";
+ break;
+ case BAR_LOADER_ORANGE_STILL: resPath += "ajax-loader-orange-bert2-still.png";
+ break;
+ case FOLD_ICON: resPath += FOLDS_PATH + "fold.png";
+ break;
+ case UNFOLD_ICON: resPath += FOLDS_PATH + "unfold.png";
+ break;
+ case FOLD_ICON_16x16: resPath += FOLDS_PATH + "fold_16x16.png";
+ break;
+ case UNFOLD_ICON_16x16: resPath += FOLDS_PATH + "unfold_16x16.png";
+ break;
+ case SERVICE_TYPE_SOAP_ICON: resPath += SERVICE_ICONS_PATH + "service_type_soap.png";
+ break;
+ case SERVICE_TYPE_REST_ICON: resPath += SERVICE_ICONS_PATH + "service_type_rest.png";
+ break;
+ case SERVICE_TYPE_MULTITYPE_ICON: resPath += SERVICE_ICONS_PATH + "service_type_multitype.png";
+ break;
+ case SERVICE_TYPE_UNKNOWN_ICON: resPath += SERVICE_ICONS_PATH + "service_type_unknown.png";
+ break;
+ case SERVICE_STATUS_PASSED_ICON: resPath += FAMFAMFAM_PATH + "accept.png";
+ break;
+ case SERVICE_STATUS_PASSED_ICON_LARGE: resPath += "tick-sphere-35.png";
+ break;
+ case SERVICE_STATUS_WARNING_ICON: resPath += FAMFAMFAM_PATH + "error.png";
+ break;
+ case SERVICE_STATUS_WARNING_ICON_LARGE: resPath += "pling-sphere-35.png";
+ break;
+ case SERVICE_STATUS_FAILED_ICON: resPath += FAMFAMFAM_PATH + "exclamation.png";
+ break;
+ case SERVICE_STATUS_FAILED_ICON_LARGE: resPath += "cross-sphere-35.png";
+ break;
+ case SERVICE_STATUS_UNCHECKED_ICON: resPath += FAMFAMFAM_PATH + "help.png";
+ break;
+ case SERVICE_STATUS_UNCHECKED_ICON_LARGE: resPath += "query-sphere-35.png";
+ break;
+ case SERVICE_STATUS_UNKNOWN_ICON: resPath += FAMFAMFAM_PATH + "grey_circle.png";
+ break;
+ case TRISTATE_CHECKBOX_CHECKED_ICON: resPath += TRISTATE_TREE_ICONS_PATH + "tristate_checkbox_checked.png";
+ break;
+ case TRISTATE_CHECKBOX_PARTIAL_ICON: resPath += TRISTATE_TREE_ICONS_PATH + "tristate_checkbox_partial.png";
+ break;
+ case TRISTATE_CHECKBOX_UNCHECKED_ICON: resPath += TRISTATE_TREE_ICONS_PATH + "tristate_checkbox_unchecked.png";
+ break;
+ case UNCHECKED_ICON: resPath += "unchecked.png";
+ break;
+ case UNKNOWN_RESOURCE_TYPE_ICON: resPath += FAMFAMFAM_PATH + "grey_circle.png";
+ break;
+ case USER_ICON: resPath += FAMFAMFAM_PATH + "user.png";
+ break;
+ case REGISTRY_ICON: resPath += FAMFAMFAM_PATH + "remote_resource.png";
+ break;
+ case SERVICE_PROVIDER_ICON: resPath += FAMFAMFAM_PATH + "chart_organisation.png";
+ break;
+ case SERVICE_ICON: resPath += "favicon.png";
+ break;
+ case SOAP_OPERATION_ICON: resPath += FAMFAMFAM_PATH + "plugin.png";
+ break;
+ case REST_METHOD_ICON: resPath += FAMFAMFAM_PATH + "plugin.png";
+ break;
+ case SERVICE_CATEGORY_ICON: resPath += FAMFAMFAM_PATH + "text_list_numbers.png";
+ break;
+ case TAG_ICON: resPath += FAMFAMFAM_PATH + "tag_blue.png";
+ break;
+ case WSDL_DOCUMENT_ICON: resPath += FAMFAMFAM_PATH + "page_white_code.png";
+ break;
+ case OPEN_IN_BIOCATALOGUE_ICON: resPath += FAMFAMFAM_PATH + "magnifier.png";
+ break;
+ case SEARCH_ICON: resPath += FAMFAMFAM_PATH + "magnifier.png";
+ break;
+ case HISTORY_ICON: resPath += FAMFAMFAM_PATH + "folder_explore.png";
+ break;
+ case REFRESH_ICON: resPath += FAMFAMFAM_PATH + "arrow_refresh.png";
+ break;
+ case FAVOURITE_ICON: resPath += FAMFAMFAM_PATH + "star.png";
+ break;
+ case TICK_ICON: resPath += FAMFAMFAM_PATH + "tick.png";
+ break;
+ case CROSS_ICON: resPath += FAMFAMFAM_PATH + "cross.png";
+ break;
+ case WARNING_ICON: resPath += FAMFAMFAM_PATH + "error.png";
+ break;
+ case ERROR_ICON: resPath += FAMFAMFAM_PATH + "exclamation.png";
+ break;
+ case SAVE_ICON: resPath += FAMFAMFAM_PATH + "disk.png";
+ break;
+ case DELETE_ITEM_ICON: resPath += FAMFAMFAM_PATH + "cross.png";
+ break;
+ case CLEAR_ICON: resPath += "trash.png";
+ break;
+ case LOCKED_ICON: resPath += FAMFAMFAM_PATH + "lock.png";
+ break;
+ case UNLOCKED_ICON: resPath += FAMFAMFAM_PATH + "lock_open.png";
+ break;
+ case BACK_ICON: resPath += FAMFAMFAM_PATH + "arrow_left.png";
+ break;
+ case FORWARD_ICON: resPath += FAMFAMFAM_PATH + "arrow_right.png";
+ break;
+ case FILTER_ICON: resPath += FAMFAMFAM_PATH + "arrow_join (flipped vertically).png";
+ break;
+ case PREVIEW_ICON: resPath += FAMFAMFAM_PATH + "magnifier.png";
+ break;
+ case SUGGESTION_TO_USER_ICON: resPath += FAMFAMFAM_PATH + "lightbulb.png";
+ break;
+ case ADD_PROCESSOR_TO_WORKFLOW_ICON: resPath += "open_in_BioCatalogue.png";
+ break;
+ case ADD_PROCESSOR_AS_FAVOURITE_ICON: resPath += FAMFAMFAM_PATH + "star.png";
+ break;
+ case ADD_ALL_SERVICES_AS_FAVOURITE_ICON:resPath += FAMFAMFAM_PATH + "multiple_star.png";
+ break;
+ case EXECUTE_HEALTH_CHECK_ICON: resPath += FAMFAMFAM_PATH + "information.png";
+ break;
+ case SELECT_ALL_ICON: resPath += FAMFAMFAM_PATH + "tick.png";
+ break;
+ case DESELECT_ALL_ICON: resPath += FAMFAMFAM_PATH + "cross.png";
+ break;
+ case EXPAND_ALL_ICON: resPath += FAMFAMFAM_PATH + "text_linespacing.png";
+ break;
+ case COLLAPSE_ALL_ICON: resPath += FAMFAMFAM_PATH + "text_linespacing (collapse).png";
+ break;
+ case SORT_BY_NAME_ICON: resPath += FAMFAMFAM_PATH + "style.png";
+ break;
+ case SORT_BY_COUNTS_ICON: resPath += FAMFAMFAM_PATH + "sum.png";
+ break;
+ case STYLES_CSS: resPath += "styles.css";
+ break;
+ default: return (null);
+ }
+
+ return (resPath);
+ }
+
+
+ private static URL getResourceLocalURL(int resourceId) {
+ return (BioCataloguePerspective.class.getResource(getResourceRelPath(resourceId)));
+ }
+
+ private static HashMap<Integer, ImageIcon> iconMap = new HashMap<Integer, ImageIcon>();
+
+ public static ImageIcon getImageIcon(int iconId)
+ {
+ ImageIcon result = iconMap.get(iconId);
+ if (result == null) {
+ result = new ImageIcon(getResourceLocalURL(iconId));
+ iconMap.put(iconId, result);
+ }
+ return result;
+ }
+
+ public static ImageIcon getImageIcon(URL resourceLocalURL) {
+ return (new ImageIcon(resourceLocalURL));
+ }
+
+
+ public static Icon getIconFromTaverna(int iconId) {
+ switch (iconId) {
+ case SOAP_OPERATION_ICON: return (WSDLActivityIcon.getWSDLIcon());
+ case REST_METHOD_ICON: return (RESTActivityIcon.getRESTActivityIcon());
+ default: return (drawMissingIcon());
+ }
+ }
+
+
+ /**
+ * This method would be called by other methods in this class
+ * when they were unable to load requested icon.
+ *
+ * @return A 16x16 pixel icon that represents a missing icon -
+ * a red cross.
+ */
+ private static ImageIcon drawMissingIcon()
+ {
+ int w = 16;
+ int h = 16;
+ GraphicsEnvironment ge = GraphicsEnvironment.getLocalGraphicsEnvironment();
+ GraphicsDevice gd = ge.getDefaultScreenDevice();
+ GraphicsConfiguration gc = gd.getDefaultConfiguration();
+
+ BufferedImage image = gc.createCompatibleImage(w, h, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D g = image.createGraphics();
+ g.setColor(Color.RED);
+ g.setStroke(new BasicStroke(3, BasicStroke.CAP_SQUARE, BasicStroke.JOIN_MITER));
+ g.drawLine(4, 4, 12, 12);
+ g.drawLine(12, 4, 4, 12);
+ g.dispose();
+
+ return new ImageIcon(image);
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/ResourcePreviewContent.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/ResourcePreviewContent.java
new file mode 100644
index 0000000..7dc1fce
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/ResourcePreviewContent.java
@@ -0,0 +1,38 @@
+package net.sf.taverna.biocatalogue.model;
+
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
+
+/**
+ * Helper class to hold all data about the generated preview.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class ResourcePreviewContent
+{
+ private Resource resource;
+ private JComponent jcContent;
+
+ public ResourcePreviewContent(Resource resource, JComponent content)
+ {
+ this.resource = resource;
+ this.jcContent = content;
+ }
+
+ public Resource getResource() {
+ return(this.resource);
+ }
+
+ public JComponent getContent() {
+ return(this.jcContent);
+ }
+
+
+ public static ResourcePreviewContent createDummyInstance()
+ {
+ Resource r = new Resource(BioCatalogueClient.API_USERS_URL + "/1", "Dummy user");
+ return (new ResourcePreviewContent(r, new JLabel("dummy content - JLabel")));
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/SoapOperationIdentity.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/SoapOperationIdentity.java
new file mode 100644
index 0000000..df16566
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/SoapOperationIdentity.java
@@ -0,0 +1,77 @@
+package net.sf.taverna.biocatalogue.model;
+
+/**
+ * Identifies a SOAP operation (or "processor" in Taverna terms)
+ * in the most straightforward way - by WSDL location and operation name.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class SoapOperationIdentity extends SoapServiceIdentity
+{
+ public static final String ACTION_STRING_SEPARATOR = "===";
+
+ private final String operationName;
+ private final String description;
+
+ public SoapOperationIdentity(String wsdlLocation, String operationName, String description) {
+ super(wsdlLocation);
+ this.operationName = operationName;
+ this.description = description;
+ }
+
+ public SoapOperationIdentity(Object errorDetails) {
+ super(errorDetails);
+ this.operationName = null;
+ this.description = null;
+ }
+
+ public String getOperationName() {
+ return operationName;
+ }
+
+ public String getDescription() {
+ return description;
+ }
+
+
+ /**
+ * @return String that can be placed into an action command (i.e. into JClickableLabel)
+ * to identify a SOAP operation - WSDL location and operation name are concatenated
+ * with <code>SoapOperationIdentity.ACTION_STRING_SEPARATOR</code>.
+ */
+ public String toActionString() {
+ return (getWsdlLocation() + ACTION_STRING_SEPARATOR + this.operationName);
+ }
+
+
+ /**
+ * @param actionString String that includes WSDL location appended by
+ * <code>SoapOperationIdentity.ACTION_STRING_SEPARATOR</code>
+ * and by the operation name of a SOAP operations.
+ * <br/>
+ * The action string may either contain only WSDL location and operation
+ * name (which are joined by a specified separator) OR the action string
+ * may start from <code>BioCataloguePluginConstants.ACTION_PREVIEW_SOAP_OPERATION_AFTER_LOOKUP</code>.
+ * @return Instance of this class initialised with the values from the <code>actionString</code>
+ * or <code>null</code> if an error occurred.
+ */
+ public static SoapOperationIdentity fromActionString(String actionString)
+ {
+ if (actionString == null) return (null);
+
+ // remove the prefix if it is present
+ if (actionString.startsWith(BioCataloguePluginConstants.ACTION_PREVIEW_SOAP_OPERATION_AFTER_LOOKUP)) {
+ actionString = actionString.substring(BioCataloguePluginConstants.ACTION_PREVIEW_SOAP_OPERATION_AFTER_LOOKUP.length());
+ }
+
+ String[] parts = actionString.split(ACTION_STRING_SEPARATOR);
+ if (parts == null || parts.length != 2 ||
+ parts[0].length() == 0 || parts[1].length() == 0)
+ {
+ return (null);
+ }
+
+ return (new SoapOperationIdentity(parts[0], parts[1], null));
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/SoapOperationPortIdentity.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/SoapOperationPortIdentity.java
new file mode 100644
index 0000000..6910e23
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/SoapOperationPortIdentity.java
@@ -0,0 +1,26 @@
+package net.sf.taverna.biocatalogue.model;
+
+public class SoapOperationPortIdentity extends SoapOperationIdentity
+{
+ private String portName;
+ private boolean isInput;
+
+ public SoapOperationPortIdentity(String wsdlLocation, String operationName, String portName, boolean isInput) {
+ super(wsdlLocation, operationName, null);
+ this.portName = portName;
+ this.isInput = isInput;
+ }
+
+ public SoapOperationPortIdentity(Object errorDetails) {
+ super(errorDetails);
+ }
+
+ public String getPortName() {
+ return portName;
+ }
+
+ public boolean isInput() {
+ return isInput;
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/SoapProcessorIdentity.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/SoapProcessorIdentity.java
new file mode 100644
index 0000000..814a701
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/SoapProcessorIdentity.java
@@ -0,0 +1,27 @@
+package net.sf.taverna.biocatalogue.model;
+
+/**
+ * Identifies a SOAP Processor in Taverna terms. Adds a local name
+ * attribute to the details available in <code>SoapOperationIdentity</code>.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class SoapProcessorIdentity extends SoapOperationIdentity
+{
+ private final String localName;
+
+ public SoapProcessorIdentity(String wsdlLocation, String operationName, String localName) {
+ super(wsdlLocation, operationName, null);
+ this.localName = localName;
+ }
+
+ public SoapProcessorIdentity(Object errorDetails) {
+ super(errorDetails);
+ this.localName = null;
+ }
+
+ public String getLocalName() {
+ return localName;
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/SoapServiceIdentity.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/SoapServiceIdentity.java
new file mode 100644
index 0000000..a015ad2
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/SoapServiceIdentity.java
@@ -0,0 +1,45 @@
+package net.sf.taverna.biocatalogue.model;
+
+/**
+ * Identifies a SOAP service in the most straightforward
+ * way - by WSDL location.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class SoapServiceIdentity
+{
+ private final String wsdlLocation;
+
+ // this variable holds an object that will be displayable
+ private final Object errorDetails;
+
+ public SoapServiceIdentity(String wsdlLocation) {
+ this.wsdlLocation = wsdlLocation;
+ this.errorDetails = null;
+ }
+
+ public SoapServiceIdentity(Object errorDetails) {
+ this.errorDetails = errorDetails;
+ this.wsdlLocation = null;
+ }
+
+ public String getWsdlLocation() {
+ return (wsdlLocation);
+ }
+
+ public boolean hasError() {
+ return (errorDetails != null);
+ }
+
+ /**
+ * @return Returned object contains an object that may be displayed
+ * in a JOptionPane or printed (in other words defining a
+ * sensible way of displaying itself), which has details of
+ * an error that has occurred which prevented from populating
+ * this instance with the actual details of their SOAP service.
+ */
+ public Object getErrorDetails() {
+ return (errorDetails);
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Tag.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Tag.java
new file mode 100644
index 0000000..e1ca6b9
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Tag.java
@@ -0,0 +1,218 @@
+package net.sf.taverna.biocatalogue.model;
+
+import java.io.Serializable;
+import java.util.Comparator;
+
+import org.apache.commons.lang.StringEscapeUtils;
+
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class Tag implements Serializable
+{
+ private static final long serialVersionUID = 784872111173271581L;
+
+ private String tagURI; // URI to use on BioCatalogue to fetch all tagged items
+ private String tagNamespace; // namespace where this tag is defined
+ private String tagDisplayName; // only the actual tag (for display within the tag cloud)
+ private String fullTagName; // full tag name - including namespace
+ private int itemCount; // count of tagged items
+
+
+ /**
+ * Constructs a Tag instance from primitive components.
+ * All values are set directly, no internal inference made.
+ *
+ * @param tagURI
+ * @param tagNamespace
+ * @param tagDisplayName
+ * @param fullTagName
+ * @param itemCount
+ */
+ public Tag(String tagURI, String tagNamespace, String tagDisplayName, String fullTagName, int itemCount)
+ {
+ this.tagURI = tagURI;
+ this.tagNamespace = tagNamespace;
+ this.tagDisplayName = tagDisplayName;
+ this.setFullTagName(fullTagName);
+ this.itemCount = itemCount;
+ }
+
+
+ /**
+ * Constructs Tag instance from an XML representation of the Tag from BioCatalogue API.
+ *
+ * @param xmlTag
+ */
+ public Tag(org.biocatalogue.x2009.xml.rest.Tag xmlTag)
+ {
+ // these values come directly from the XML data obtained via the API
+ this.tagURI = xmlTag.getHref();
+ this.fullTagName = xmlTag.getName();
+ this.itemCount = xmlTag.getTotalItemsCount().intValue();
+
+ // NB! Namespace and the display name need to be inferred 'manually'.
+ // First - set the namespace; it's value is taken from the 'namespace'
+ // attribute of the tag URI.
+ this.tagNamespace = Util.extractURLParameter(this.tagURI, "namespace");
+
+ // Now set the display name; if full tag name is not a part of any ontology,
+ // display name will be identical to the full name.
+ if (this.fullTagName.startsWith("<") && this.fullTagName.endsWith(">")) {
+ int iStart = this.fullTagName.lastIndexOf('#') + 1;
+ this.tagDisplayName = this.fullTagName.substring(iStart, this.fullTagName.length() - 1);
+ }
+ else {
+ this.tagDisplayName = this.fullTagName;
+ }
+ }
+
+
+ // *** Various getters and setters ***
+
+ public void setTagURI(String tagURI) {
+ this.tagURI = tagURI;
+ }
+
+ public String getTagURI() {
+ return tagURI;
+ }
+
+
+ public void setTagNamespace(String tagNamespace) {
+ this.tagNamespace = tagNamespace;
+ }
+
+ public String getTagNamespace() {
+ return tagNamespace;
+ }
+
+
+ public void setTagDisplayName(String tagDisplayName) {
+ this.tagDisplayName = tagDisplayName;
+ }
+
+ public String getTagDisplayName() {
+ return tagDisplayName;
+ }
+
+
+ public void setFullTagName(String fullTagName) {
+ this.fullTagName = fullTagName;
+ }
+
+ /**
+ * @return Unique and unambiguous name of this tag on BioCatalogue:<br/>
+ * <ul>
+ * <li>for tags with no namespaces, they it is just plain text names;</li>
+ * <li>for those with namespaces, it will have the following form:<br/>
+ * "<code>< http://www.mygrid.org.uk/ontology#retrieving ></code>" (without spaces, though), where
+ * the first part before the '#' symbol is the namespace and the second part
+ * is the actual tag within that namespace.</li></ul>
+ */
+ public String getFullTagName() {
+ return fullTagName;
+ }
+
+
+ public int getItemCount() {
+ return itemCount;
+ }
+
+ public void setItemCount(int itemCount) {
+ this.itemCount = itemCount;
+ }
+
+
+ // *** Tag Comparators ***
+
+ public static class ReversePopularityComparator implements Comparator<Tag>
+ {
+ public ReversePopularityComparator() {
+ super();
+ }
+
+ public int compare(Tag t1, Tag t2)
+ {
+ if (t1.getItemCount() == t2.getItemCount()) {
+ // in case of the same popularity, compare by full tag names (which are unique)
+ return (t1.getFullTagName().compareTo(t2.getFullTagName()));
+ }
+ else {
+ // popularity isn't the same; arrange by popularity (more popular first)
+ return (t2.getItemCount() - t1.getItemCount());
+ }
+ }
+ }
+
+
+ public static class AlphanumericComparator implements Comparator<Tag>
+ {
+ public AlphanumericComparator() {
+ super();
+ }
+
+ public int compare(Tag t1, Tag t2) {
+ // full tag names are unique on BioCatalogue
+ return (t1.getFullTagName().compareTo(t2.getFullTagName()));
+ }
+ }
+
+ public static class AlphabeticalIgnoreCaseComparator implements Comparator<Tag>
+ {
+ public AlphabeticalIgnoreCaseComparator() {
+ super();
+ }
+
+ public int compare(Tag t1, Tag t2) {
+ // full tag names are unique on BioCatalogue
+ return (t1.getTagDisplayName().compareToIgnoreCase(t2.getTagDisplayName()));
+ }
+ }
+
+ /**
+ * This makes sure that things like instanceOf() and remove() in List interface
+ * work properly - this way resources are treated to be the same if they store
+ * identical data, rather than they simply hold the same reference.
+ */
+ public boolean equals(Object other) {
+ // could only be equal to another Tag object, not anything else
+ if (! (other instanceof Tag)) return (false);
+
+ // 'other' object is a Tag; equality is based on the data stored
+ // in the current and 'other' Tag instances
+ Tag otherTag = (Tag)other;
+ return (this.itemCount == otherTag.itemCount && this.fullTagName.equals(otherTag.fullTagName));
+ }
+
+
+ public String toString()
+ {
+ return ("Tag (" + this.fullTagName + ", " + this.itemCount + ")");
+ }
+
+
+ /**
+ * This method is used to generate the tooltip to be shown over the tag
+ * in the tagcloud. Shown text will contain the full tag name, namespace
+ * and frequency.
+ *
+ * @return HTML encoded string ready to be put into the tooltip.
+ */
+ public String getTagCloudTooltip()
+ {
+ StringBuilder tooltip = new StringBuilder("<html>");
+
+ tooltip.append(" <b>" + (this.fullTagName.length() > this.tagDisplayName.length() ? "Full tag" : "Tag") + ": </b>" + StringEscapeUtils.escapeHtml(this.fullTagName));
+ if (this.tagNamespace != null && this.tagNamespace.length() > 0) {
+ tooltip.append("<br> <b>Namespace: </b>" + StringEscapeUtils.escapeHtml(this.tagNamespace));
+ }
+ tooltip.append("<br> <b>Frequency: </b>" + this.itemCount);
+ tooltip.append("</html>");
+
+ return tooltip.toString();
+ }
+
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Util.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Util.java
new file mode 100644
index 0000000..06b30e3
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Util.java
@@ -0,0 +1,793 @@
+package net.sf.taverna.biocatalogue.model;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.ObjectStreamClass;
+import java.io.UnsupportedEncodingException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLDecoder;
+import java.net.URLEncoder;
+import java.util.Calendar;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.BorderFactory;
+import javax.swing.JLabel;
+
+import net.sf.taverna.raven.appconfig.ApplicationRuntime;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.BioCataloguePerspective;
+
+import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.log4j.Logger;
+
+/**
+ * Class containing various reusable helper methods.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class Util
+
+
+{
+
+ private static Logger logger = Logger.getLogger(Util.class);
+
+
+ /**
+ * Makes sure that one component (for example, a window) is centered horizontally and vertically
+ * relatively to the other component. This is achieved by aligning centers of the two components.
+ *
+ * This method can be used even if the 'dependentComponent' is larger than the 'mainComponent'. In
+ * this case it is probably only useful for centering windows against each other rather than
+ * components inside a container.
+ *
+ * Method also makes sure that the dependent component will not be placed above the screen's upper
+ * edge and to the left of the left edge.
+ */
+ public static void centerComponentWithinAnother(Component mainComponent, Component dependentComponent)
+ {
+ int iMainComponentCenterX = (int)Math.round(mainComponent.getLocationOnScreen().getX() + (mainComponent.getWidth() / 2));
+ int iPosX = iMainComponentCenterX - (dependentComponent.getWidth() / 2);
+ if (iPosX < 0) iPosX = 0;
+
+ int iMainComponentCenterY = (int)Math.round(mainComponent.getLocationOnScreen().getY() + (mainComponent.getHeight() / 2));
+ int iPosY = iMainComponentCenterY - (dependentComponent.getHeight() / 2);
+ if (iPosY < 0) iPosY = 0;
+
+ dependentComponent.setLocation(iPosX, iPosY);
+ }
+
+
+ /**
+ * The parameter is the class name to be processed; class name is likely to be in
+ * the form <class_name>$<integer_value>, where the trailing part starting with
+ * the $ sign indicates the anonymous inner class within the base class. This will
+ * strip out that part of the class name to get the base class name.
+ */
+ public static String getBaseClassName(String strClassName)
+ {
+ // strip out the class name part after the $ sign; return
+ // the original value if the dollar sign wasn't found
+ String strResult = strClassName;
+
+ int iDollarIdx = strResult.indexOf("$");
+ if (iDollarIdx != -1) strResult = strResult.substring(0, iDollarIdx);
+
+ return (strResult);
+ }
+
+
+ /**
+ * Makes sure that the supplied string is no longer than provided length.
+ */
+ public static String ensureStringLength(String str, int iLength) {
+ if (str.length() > iLength) str = str.substring(0, iLength) + " (...)";
+ return (str);
+ }
+
+ /**
+ * Makes sure that the supplied string doesn't have any lines (separated by HTML line break tag) longer
+ * than specified; assumes that there are no line breaks in the source line.
+ *
+ * @param str The string to work with.
+ * @param iLineLength Desired length of each line.
+ * @param bIgnoreBrokenWords True if line breaks are to be inserted exactly each <code>iLineLength</code>
+ * symbols (which will most likely cause broken words); false to insert line breaks
+ * at the first space after <code>iLineLength</code> symbols since last line break.
+ * @return New string with inserted HTML line breaks.
+ */
+ public static String ensureLineLengthWithinString(String str, int iLineLength, boolean bIgnoreBrokenWords)
+ {
+ StringBuilder out = new StringBuilder(str);
+
+ // keep inserting line breaks from end of the line till the beginning until all done
+ int iLineBreakPosition = 0;
+ while (iLineBreakPosition >= 0 && iLineBreakPosition < out.length())
+ {
+ // insert line break either exactly at calculated position or
+ iLineBreakPosition += iLineLength;
+ iLineBreakPosition = (bIgnoreBrokenWords ?
+ iLineBreakPosition :
+ out.indexOf(" ", iLineBreakPosition));
+
+ if (iLineBreakPosition > 0 && iLineBreakPosition < out.length()) {
+ out.insert(iLineBreakPosition, "<br>");
+ iLineBreakPosition += 4; // -- four is the length of "<br>"
+ }
+ }
+
+ return (out.toString());
+ }
+
+
+ /**
+ * This is a convenience method for calling
+ * {@link Util#pluraliseNoun(String, long, boolean)}
+ * with <code>false</code> as a value for third parameter.
+ */
+ public static String pluraliseNoun(String noun, long count) {
+ return (pluraliseNoun(noun, count, false));
+ }
+
+ /**
+ * Performs naive pluralisation of the supplied noun.
+ *
+ * @param noun Noun in a singular form.
+ * @param count Number of occurrences of the item, for which the noun is provided.
+ * @param forceAppendingSByDefault <code>true</code> to make sure that "y" -> "ies"
+ * substitution is <b>not made</b>, but instead "s" is appended
+ * to unmodified root of the noun.
+ * @return Pluralised <code>noun</code>: with appended -s or -y replaced with -ies.
+ */
+ public static String pluraliseNoun(String noun, long count, boolean forceAppendingSByDefault)
+ {
+ if (count % 10 != 1 || count == 11) {
+ if (!forceAppendingSByDefault && noun.endsWith("y")) {
+ return (noun.substring(0, noun.length() - 1) + "ies"); // e.g. ENTRY -> ENTRIES
+ }
+ else {
+ return (noun + "s"); // e.g. SHIP -> SHIPS
+ }
+ }
+ else {
+ // no need to pluralise - count is of the type 21, 31, etc..
+ return noun;
+ }
+ }
+
+
+ /**
+ * Calculates time difference between two {@link Calendar} instances.
+ *
+ * @param earlier The "earlier" date.
+ * @param later The "later" date.
+ * @param maxDifferenceMillis The maximum allowed time difference between the two
+ * {@link Calendar} instances, in milliseconds. If the calculated
+ * difference will exceed <code>maxDifferenceMillis</code>,
+ * <code>null</code> will be returned. If this parameter has
+ * a value <code>less or equal to zero</code>, any time difference
+ * between the {@link Calendar} instances will be permitted.
+ * @return String in the form "XX seconds|minutes|hours|days ago". Proper pluralisation will
+ * be performed on the name of the time unit. <code>null</code> will be returned in
+ * cases where one of the {@link Calendar} instances is <code>null</code>, time
+ * difference between the provided instances is greater than <code>maxDifferenceMillis</code>
+ * or <code>earlier</code> date is not really earlier than <code>later</code> one.
+ */
+ public static String getAgoString(Calendar earlier, Calendar later, long maxDifferenceMillis)
+ {
+ // one of the dates is missing
+ if (earlier == null || later == null) {
+ return null;
+ }
+
+ if (earlier.before(later)) {
+ long differenceMillis = later.getTimeInMillis() - earlier.getTimeInMillis();
+
+ if (maxDifferenceMillis <= 0 || (maxDifferenceMillis > 0 && differenceMillis <= maxDifferenceMillis))
+ {
+ long result = 0;
+ String unitName = "";
+
+ if (differenceMillis < 60 * 1000) {
+ result = differenceMillis / 1000;
+ unitName = "second";
+ }
+ else if (differenceMillis < 60 * 60 * 1000) {
+ result = differenceMillis / (60 * 1000);
+ unitName = "minute";
+ }
+ else if (differenceMillis < 24 * 60 * 60 * 1000) {
+ result = differenceMillis / (60 * 60 * 1000);
+ unitName = "hour";
+ }
+ else {
+ result = differenceMillis / (24 * 60 * 60 * 1000);
+ unitName = "day";
+ }
+
+ return (result + " " + Util.pluraliseNoun(unitName, result, true) + " ago");
+ }
+ else {
+ // the difference is too large - larger than the supplied threshold
+ return null;
+ }
+ }
+ else {
+ // the "later" date is not really later than the "earlier" one
+ return null;
+ }
+ }
+
+
+ /**
+ * Joins the set of tokens in the provided list into a single string.
+ * This method is a shorthand for {@link Util#join(List, String, String, String)}.
+ *
+ * @param tokens List of strings to join.
+ * @param separator Separator to insert between individual strings.
+ * @return String of the form <code>[token1][separator][token2][separator]...[tokenN]</code>
+ */
+ public static String join(List<String> tokens, String separator) {
+ return (join(tokens, null, null, separator));
+ }
+
+ /**
+ * Joins the set of tokens in the provided list into a single string.
+ *
+ * Any empty strings or <code>null</code> entries in the <code>tokens</code> list
+ * will be removed to achieve a better resulting joined string.
+ *
+ * @param tokens List of strings to join.
+ * @param prefix String to prepend to each token.
+ * @param suffix String to append to each token.
+ * @param separator Separator to insert between individual strings.
+ * @return String of the form <code>[prefix][token1][suffix][separator][prefix][token2][suffix][separator]...[prefix][tokenN][suffix]</code>
+ * <br/><br/>
+ * Example: call <code>join(["cat","sat","on","the","mat"], "[", "]", ", ")</code> results in the following output:
+ * <code>"[cat], [sat], [on], [the], [mat]"</code>
+ */
+ public static String join(List<String> tokens, String prefix, String suffix, String separator)
+ {
+ if (tokens == null) {
+ // nothing to join
+ return (null);
+ }
+
+ // list of strings is not empty, but some pre-processing is necessary
+ // to remove any empty strings that may be there
+ for (int i = tokens.size() - 1; i >= 0; i--) {
+ if (tokens.get(i) == null || tokens.get(i).length() == 0) {
+ tokens.remove(i);
+ }
+ }
+
+ // now start the actual processing, but it may be the case that all strings
+ // were empty and we now have an empty list
+ if (tokens.isEmpty()) {
+ // nothing to join - just return an empty string
+ return ("");
+ }
+ else {
+ // there are some tokens -- perform the joining
+ String effectivePrefix = (prefix == null ? "" : prefix);
+ String effectiveSuffix = (suffix == null ? "" : suffix);
+ String effectiveSeparator = (separator == null ? "" : separator);
+
+ StringBuilder result = new StringBuilder();
+ for (int i = 0; i < tokens.size(); i++) {
+ result.append(effectivePrefix + tokens.get(i) + effectiveSuffix);
+ result.append(i == tokens.size() - 1 ? "" : effectiveSeparator);
+ }
+
+ return (result.toString());
+ }
+ }
+
+ /**
+ * Determines whether the plugin is running as a standalone JFrame or inside Taverna Workbench.
+ * This is a naive test, based only on the fact that Taverna uses Raven ApplicationRuntime.
+ */
+ public static boolean isRunningInTaverna()
+ {
+ try {
+ // ApplicationRuntime class is defined within Taverna API. If this is available,
+ // it should mean that the plugin runs within Taverna.
+ ApplicationRuntime.getInstance();
+ return true;
+ }
+ catch (NoClassDefFoundError e) {
+ return false;
+ }
+ }
+
+
+ // === STRIPPING OUT HTML FROM STRINGS ===
+
+ public static String prepareStringForComponent(String source) {
+ return "<html>" + StringEscapeUtils.escapeHtml(source) + "</html>";
+ }
+
+
+ /*
+ * === The following section is providing URL handling methods. ===
+ */
+
+ /**
+ * See: {@link Util#appendStringBeforeParametersOfURL(String, String, boolean)}
+ *
+ * Assumes the last parameter as false, so that the URL encoding will be done.
+ */
+ public static String appendStringBeforeParametersOfURL(String url, String strToAppend) {
+ return (appendStringBeforeParametersOfURL(url, strToAppend, false));
+ }
+
+ /**
+ * Tiny helper to strip out all HTML tags. This will not leave any HTML tags
+ * at all (so that the content can be displayed in DialogTextArea - and the
+ * like - components. This helps to present HTML content inside JAVA easier.
+ */
+ public static String stripAllHTML(String source) {
+ // don't do anything if not string is provided
+ if (source == null)
+ return ("");
+
+ // need to preserve at least all line breaks
+ // (ending and starting paragraph also make a line break)
+ source = source.replaceAll("</p>[\r\n]*<p>", "<br/>");
+ source = source.replaceAll("[\\s]+", " ");
+ source = source.replaceAll("\\<br/?\\>", "\n");
+ source = source.replaceAll("\n ", "\n");
+
+ // strip all HTML
+ source = source.replaceAll("\\<.*?\\>", ""); // any HTML tags
+ source = source.replaceAll("&\\w{1,4};", ""); // this is for things like " ", ">", etc
+
+ return (source);
+ }
+
+
+ /**
+ * Appends given string at the end of the provided URL just before the list of parameters in the url.
+ *
+ * For example, appending ".xml" to URL "http://www.sandbox.biocatalogue.org/services?tag=blast" will
+ * yield "http://www.sandbox.biocatalogue.org/services.xml?tag=blast".
+ *
+ * No duplication checking is made - if the URL is already ending (before parameters) with the value of
+ * the string to append, that string will still be appended.
+ *
+ * @param url URL to append the string to.
+ * @param strToAppend The string to append. The value will be url-encode before appending.
+ * @return New string containing modified <code>url</code> with the <code>strToAppend</code> appended
+ * before the "query string" of the URL.
+ */
+ public static String appendStringBeforeParametersOfURL(String url, String strToAppend, boolean ignoreURLEncoding)
+ {
+ StringBuilder modifiedURL = new StringBuilder(url);
+
+ int iPositionToInsertProvidedString = modifiedURL.indexOf("?");
+ if (iPositionToInsertProvidedString == -1) iPositionToInsertProvidedString = modifiedURL.length();
+
+ String stringToInsert = (ignoreURLEncoding ? strToAppend : Util.urlEncodeQuery(strToAppend));
+ modifiedURL.insert(iPositionToInsertProvidedString, stringToInsert);
+
+ return (modifiedURL.toString());
+ }
+
+
+ /**
+ * This method takes a collection of name-value pairs in the form of a map.
+ * It then adds all parameters from this map to the provided URL.
+ *
+ * If any parameter has the same name as was already present in the URL, the new value
+ * will replace the existing one.
+ *
+ * The implementation of this method is not particularly efficient - it makes a
+ * lot of overhead, but it's fine for non-intensive usage.
+ *
+ * @param url The URL to add a new parameter to.
+ * @param Map of parameters to add to the URL. Keys and values of the map are the names and values for URL parameters.
+ * @return New string which is the original <code>url</code> with all provided
+ * parameters (in the form <code>name</code>=<code>value</code> pair) added to it.
+ */
+ public static String appendAllURLParameters(String url, Map<String,String> parameterMap)
+ {
+ if (parameterMap == null || parameterMap.size() == 0) {
+ // nothing to add, return the same URL
+ return (url);
+ }
+ else {
+ // just call an overloaded method which has the main logic
+ // to do this action for each name-value pair in the map
+ String out = url;
+ for (Map.Entry<String,String> anotherParameter : parameterMap.entrySet()) {
+ out = appendURLParameter(out, anotherParameter);
+ }
+ return (out);
+ }
+ }
+
+
+
+ /**
+ * This method takes a string representation of a URL and a name-value pair
+ * of strings - in the form of Map.Entry instance to add to the URL as a new parameter.
+ *
+ * If parameter with the same name was already present in the URL, the new value
+ * will replace the existing one.
+ *
+ * @param url The URL to add a new parameter to.
+ * @param Map.Entry instance containing the name & the value for the parameter to add.
+ * @return New string which is the original <code>url</code> with the desired
+ * parameter (<code>name</code>=<code>value</code> pair) added to it.
+ */
+ public static String appendURLParameter(String url, Map.Entry<String,String> parameter)
+ {
+ if (parameter == null) {
+ // nothing to add, return the same URL
+ return (url);
+ }
+ else {
+ // just call an overloaded method which has the main logic to do this action
+ return (appendURLParameter(url, parameter.getKey(), parameter.getValue()));
+ }
+ }
+
+
+ /**
+ * This method takes a string representation of a URL and a name-value pair
+ * of strings to add to the URL as a new parameter.
+ *
+ * If parameter with the same name was already present in the URL, the new value
+ * will replace the existing one.
+ *
+ * @param url The URL to add a new parameter to.
+ * @param parameter String array with 2 elements - first element is the name
+ * of the parameter to add, second - the value of the parameter.
+ * @return New string which is the original <code>url</code> with the desired
+ * parameter (<code>name</code>=<code>value</code> pair) added to it.
+ */
+ public static String appendURLParameter(String url, String[] parameter)
+ {
+ if (parameter == null || parameter.length != 2) {
+ // nothing to add, return the same URL
+ return (url);
+ }
+ else {
+ // just call an overloaded method which has the main logic to do this action
+ return (appendURLParameter(url, parameter[0], parameter[1]));
+ }
+ }
+
+
+ /**
+ * This method takes a string representation of a URL and a name-value pair
+ * of strings to add to the URL as a new parameter.
+ *
+ * If parameter with the same name was already present in the URL, the new value
+ * will replace the existing one.
+ *
+ * @param url The URL to add a new parameter to.
+ * @param name Name of the parameter to add.
+ * @param value Value of the parameter to add.
+ * @return New string which is the original <code>url</code> with the desired
+ * parameter (<code>name</code>=<code>value</code> pair) added to it.
+ */
+ public static String appendURLParameter(String url, String name, String value)
+ {
+ // if name of the parameter is not given, ignore this request
+ // (makes sense to return the same URL as the input in this case -
+ // as appending "nothing" wouldn't make it any different)
+ if (name == null || name.length() == 0) {
+ return (url);
+ }
+
+ // do everything in the protected block
+ try
+ {
+ // parse the parameters of the given URL
+ Map<String,String> urlParameters = extractURLParameters(url);
+ if (urlParameters == null) {
+ // there were no parameters in the original URL, create new map
+ urlParameters = new HashMap<String,String>();
+ }
+
+ // add the new parameter (this will replace a parameter with identical
+ // name if it was already present in the map)
+ urlParameters.put(name, value);
+
+ // parse the URL string into the URL object to extract original query string
+ URL theURL = new URL(url);
+ String originalQueryString = theURL.getQuery();
+
+ // prepare the basis for the new URL to return
+ String newUrl = null;
+ if (originalQueryString != null) {
+ // replace the original query string with empty space to
+ // give way for appending the new query string
+ newUrl = url.replace(originalQueryString, "");
+ }
+ else {
+ // there were no parameters in the original URL
+ newUrl = url + "?";
+ }
+
+ // append the new query string
+ newUrl += constructURLQueryString(urlParameters);
+
+ return (newUrl);
+ }
+ catch (Exception e)
+ {
+ logger.error("\nCouldn't append parameter ('" + name + "', '" + value + "') to the URL: " + url, e);
+ return (null);
+ }
+ }
+
+
+ /**
+ * Extracts a value of a specific parameter from the supplied URL.
+ *
+ * @param url The URL to extract the parameter from.
+ * @param parameterName Name of the URL parameter to extract the value for.
+ * @return Value of the parameter with <code>parameterName</code> in the given <code>url</code>.
+ * If the parameter with specified name is not found in the given <code>url</code>,
+ * <code>null</code> is returned instead.
+ */
+ public static String extractURLParameter(String url, String parameterName)
+ {
+ // both URL and the name of the required parameter must be supplied
+ if (url == null || url.length() == 0 || parameterName == null || parameterName.length() == 0) return null;
+
+ Map<String,String> urlParameters = extractURLParameters(url);
+ if (urlParameters != null) {
+ // the URL has some parameters; check what's the value of the desired parameter
+ return (urlParameters.get(parameterName));
+ }
+ else {
+ // the URL doesn't contain any parameters
+ return (null);
+ }
+ }
+
+
+ /**
+ * Extracts the query string from the provided URL. Parses this query string into
+ * a map of parameters.
+ *
+ * All parameters (both names and values) will have special characters unescaped
+ * (i.e. decoded from the standard url-encoding) and can be used directly.
+ *
+ * @param url The string representation of the URL to parse.
+ */
+ public static Map<String,String> extractURLParameters(String url)
+ {
+ try {
+ // extract the query part of the supplied URL
+ URL theURL = new URL(url);
+ String queryString = theURL.getQuery();
+
+ // prepare storage for output
+ Map<String,String> parameterMap = null;
+
+ // extract each name-value pair from query string (if any are specified in the URL)
+ if (queryString != null && queryString.length() > 0)
+ {
+ // only initialise if there are some parameters
+ parameterMap = new HashMap<String,String>();
+
+ for (String parameter : queryString.split("&")) {
+ String[] nameValueArr = parameter.split("=");
+
+ String name = nameValueArr[0]; // parameter name must always be present
+ String value = (nameValueArr.length == 2 ? nameValueArr[1] : null); // could be that parameter value is not set (e.g. "q=") - insert null then
+
+ // decode possible special characters
+ name = urlDecodeQuery(name);
+ if (value != null) value = urlDecodeQuery(value);
+
+ parameterMap.put(name, value);
+ }
+ }
+
+ return (parameterMap);
+ }
+ catch (MalformedURLException e)
+ {
+ // some problem occurred - report it; can't return any data in this case
+ logger.error("Couldn't parse parameters of a URL: " + url + "; details below:", e);
+ return null;
+ }
+ }
+
+
+ /**
+ * This method is the opposite for <code>extractURLParameters(String url)</code>.
+ * It takes a map of parameters, performs URL-encoding of each and assembles them
+ * into a query string.
+ *
+ * The query string then can be added to the <code>URL</code> object by using standard
+ * Java API.
+ *
+ * @param urlParameters Map of parameters to use in query string construction.
+ * @return URL-encoded query string.
+ */
+ public static String constructURLQueryString(Map<String,String> urlParameters)
+ {
+ if (urlParameters != null) {
+ StringBuilder queryString = new StringBuilder();
+
+ // iterate through all parameters and reconstruct the query string
+ for (Map.Entry<String,String> parameter : urlParameters.entrySet())
+ {
+ if (queryString.length() > 0) queryString.append("&"); // parameter separator
+ queryString.append(urlEncodeQuery(parameter.getKey()) + "=" + urlEncodeQuery(parameter.getValue()));
+ }
+
+ return (queryString.toString());
+ }
+ else {
+ return (null);
+ }
+ }
+
+
+ /**
+ * Prepares the string to serve as a part of url query to the server.
+ * @param query The string that needs URL encoding.
+ * @return URL encoded string that can be inserted into the request URL.
+ */
+ public static String urlEncodeQuery(String query)
+ {
+ // "fast exit" - if null supplied, just return an empty string;
+ // this is because in the URLs we have "q=", rather than "q=null" - this will cater for such cases
+ if (query == null) return ("");
+
+ // encode the query
+ String strRes = "";
+ try {
+ strRes = URLEncoder.encode(query, "UTF-8");
+ }
+ catch (UnsupportedEncodingException e) {
+ // do nothing
+ }
+
+ return (strRes);
+ }
+
+
+ /**
+ * Decodes a string which came as a part of of URL (e.g. a URL parameter). This converts
+ * codes of escaped special characters back into those special characters.
+ *
+ * @param query The string that needs URL decoded.
+ * @return Decoded string that will contain all the special characters.
+ */
+ public static String urlDecodeQuery(String query)
+ {
+ String strRes = "";
+
+ try {
+ strRes = URLDecoder.decode(query, "UTF-8");
+ }
+ catch (UnsupportedEncodingException e) {
+ // do nothing
+ }
+
+ return (strRes);
+ }
+
+
+ /**
+ * This method is "clones" an object supplied as an argument. It uses
+ * serialisation to achieve this (as opposed to manually implementing deep
+ * copying of all referenced objects in the graph of the provided object).
+ * This technique is used to make sure that the new object will be exact
+ * replica, but totally independent of the original one.
+ *
+ * Note that this code works ~100 times slower than it would do if deep copying
+ * was implemented. However, this will not be used in tight loops (and in loops
+ * at all), so for one-off tasks it is fine.
+ *
+ * @author Dave Miller<br/>
+ * Original version of the code in this method is taken from
+ * <a href="http://www.javaworld.com/javaworld/javatips/jw-javatip76.html?page=2">
+ * http://www.javaworld.com/javaworld/javatips/jw-javatip76.html?page=2
+ * </a> [accessed on 25/Feb/2010].
+ * <br/><br/>
+ *
+ * @author Subhajit Dasgupta<br/>
+ * Example of using an alternative class loader during object de-serialisation
+ * was taken from
+ * <a href="http://blogs.sun.com/adventures/entry/desrializing_objects_custom_class_loaders">
+ * http://blogs.sun.com/adventures/entry/desrializing_objects_custom_class_loaders
+ * </a> [accessed on 29/Mar/2010].
+ *
+ * @return Deep copy of the provided object. If deep copying doesn't succeed,
+ * <code>null</code> is returned.
+ */
+ public static Object deepCopy(Object objectToCopy)
+ {
+ // a "safety net" - a class loader of BioCatalogue perspective may be used in
+ // de-serialisation process to make sure that all classes are recognised
+ // (system class loader may not be able to "see" all BioCatalogue plugin's files,
+ // but just those in Taverna's /lib folder)
+ final ClassLoader[] customClassLoaders = new ClassLoader[] { BioCataloguePerspective.class.getClassLoader() };
+
+ try
+ {
+ ObjectOutputStream oos = null;
+ ObjectInputStream ois = null;
+ try
+ {
+ ByteArrayOutputStream bos = new ByteArrayOutputStream();
+ oos = new ObjectOutputStream(bos);
+
+ // serialise and pass the object
+ oos.writeObject(objectToCopy);
+ oos.flush();
+
+ // read and return the new object
+ ByteArrayInputStream bin = new ByteArrayInputStream(bos.toByteArray());
+ ois = new ObjectInputStream(bin) {
+ /**
+ * <code>resolveClass()</code> method is overridden to make use of
+ * custom ClassLoader in the de-serialisation process.
+ * <br/>
+ * This is needed to make sure that the ClassLoader of the BioCatalogue
+ * perspective is used as opposed to the system ClassLoader which will
+ * only be able to see classes from Taverna's /lib folder.
+ */
+ protected Class<?> resolveClass(ObjectStreamClass desc) throws IOException, ClassNotFoundException
+ {
+ String className = desc.getName();
+ try {
+ // attempt to use default class loader
+ return Class.forName(className);
+ }
+ catch (ClassNotFoundException exc)
+ {
+ // default class loader was unable to locate a required class -
+ // attempt to use one of the provided class loaders
+ for (ClassLoader cl : customClassLoaders) {
+ try {
+ return cl.loadClass(className);
+ }
+ catch (ClassNotFoundException e) {
+ /* do nothing here - there may be other class loaders to try */
+ }
+ }
+ // none of the class loaders was able to recognise the currently
+ // de-serialised class, so it's indeed an exception
+ throw new ClassNotFoundException(className +
+ " -- neither system, nor alternative class loaders were able to load this class");
+ }
+ }
+ };
+ return ois.readObject();
+ }
+ catch(Exception e)
+ {
+ logger.error("Could not perform deep copy of " + objectToCopy.getClass() + " instance", e);
+ }
+ finally
+ {
+ oos.close();
+ ois.close();
+ }
+ }
+ catch (Exception e) {
+ logger.error("Could not close object streams during deep copy of " + objectToCopy.getClass() + " instance");
+ }
+
+ // Error occurred - couldn't produce the deep copy...
+ return null;
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/BeanForPOSTToFilteredIndex.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/BeanForPOSTToFilteredIndex.java
new file mode 100644
index 0000000..d879377
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/BeanForPOSTToFilteredIndex.java
@@ -0,0 +1,12 @@
+package net.sf.taverna.biocatalogue.model.connectivity;
+
+import java.util.Map;
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class BeanForPOSTToFilteredIndex
+{
+ public Map<String, String[]> filters;
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/BeansForJSONLiteAPI.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/BeansForJSONLiteAPI.java
new file mode 100644
index 0000000..ea3b391
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/BeansForJSONLiteAPI.java
@@ -0,0 +1,84 @@
+package net.sf.taverna.biocatalogue.model.connectivity;
+
+
+/**
+ * Binding beans for GSON library to instantiate objects
+ * from JSON data obtained from the 'Lite' version of the
+ * BioCatalogue JSON API.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class BeansForJSONLiteAPI
+{
+
+ public static abstract class ResourceIndex
+ {
+ public ResourceIndex() { }
+ public abstract ResourceLinkWithName[] getResources();
+ }
+
+
+ public static class SOAPOperationsIndex extends ResourceIndex {
+ public SOAPOperationsIndex() { }
+ public ResourceLinkWithName[] soap_operations;
+
+ public ResourceLinkWithName[] getResources() {
+ return soap_operations;
+ }
+ }
+
+ public static class RESTMethodsIndex extends ResourceIndex {
+ public RESTMethodsIndex() { }
+ public ResourceLinkWithName[] rest_methods;
+
+ public ResourceLinkWithName[] getResources() {
+ return rest_methods;
+ }
+ }
+
+ public static class ServicesIndex extends ResourceIndex {
+ public ServicesIndex() { }
+ public ResourceLinkWithName[] services;
+
+ public ResourceLinkWithName[] getResources() {
+ return services;
+ }
+ }
+
+ public static class ServiceProvidersIndex extends ResourceIndex {
+ public ServiceProvidersIndex() { }
+ public ResourceLinkWithName[] service_providers;
+
+ public ResourceLinkWithName[] getResources() {
+ return service_providers;
+ }
+ }
+
+ public static class UsersIndex extends ResourceIndex {
+ public UsersIndex() { }
+ public ResourceLinkWithName[] users;
+
+ public ResourceLinkWithName[] getResources() {
+ return users;
+ }
+ }
+
+
+
+ public static class ResourceLinkWithName
+ {
+ private ResourceLinkWithName() { }
+
+ private String resource;
+ private String name;
+
+ public String getURL() {
+ return (this.resource);
+ }
+
+ public String getName() {
+ return (this.name);
+ }
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/BioCatalogueAPIRequest.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/BioCatalogueAPIRequest.java
new file mode 100644
index 0000000..ea55a77
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/BioCatalogueAPIRequest.java
@@ -0,0 +1,47 @@
+package net.sf.taverna.biocatalogue.model.connectivity;
+
+/**
+ * A class to wrap BioCatalogue API requests - will include
+ * the type (GET, POST, etc), URL and the data to send
+ * if that's a POST / PUT request.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class BioCatalogueAPIRequest
+{
+ public static enum TYPE {
+ GET,
+ POST,
+ PUT,
+ DELETE
+ }
+
+
+ private TYPE requestType;
+ private String url;
+ private String data;
+
+
+ public BioCatalogueAPIRequest(TYPE requestType, String url, String data) {
+ this.requestType = requestType;
+ this.url = url;
+ this.data = data;
+ }
+
+
+ public TYPE getRequestType() {
+ return requestType;
+ }
+
+ public String getURL(){
+ return url;
+ }
+ public void setURL(String url) {
+ this.url = url;
+ }
+
+ public String getData(){
+ return data;
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/BioCatalogueClient.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/BioCatalogueClient.java
new file mode 100644
index 0000000..0e033cc
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/BioCatalogueClient.java
@@ -0,0 +1,785 @@
+package net.sf.taverna.biocatalogue.model.connectivity;
+
+import java.io.*;
+import java.net.*;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import net.sf.taverna.biocatalogue.model.BioCataloguePluginConstants;
+import net.sf.taverna.biocatalogue.model.Pair;
+import net.sf.taverna.biocatalogue.model.Resource.TYPE;
+import net.sf.taverna.biocatalogue.model.SoapOperationIdentity;
+import net.sf.taverna.biocatalogue.model.SoapOperationPortIdentity;
+import net.sf.taverna.biocatalogue.model.Util;
+import net.sf.taverna.biocatalogue.model.connectivity.BeansForJSONLiteAPI.ResourceIndex;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.config.BioCataloguePluginConfiguration;
+
+import org.apache.log4j.Logger;
+import org.biocatalogue.x2009.xml.rest.Annotations;
+import org.biocatalogue.x2009.xml.rest.AnnotationsDocument;
+import org.biocatalogue.x2009.xml.rest.CollectionCoreStatistics;
+import org.biocatalogue.x2009.xml.rest.Filters;
+import org.biocatalogue.x2009.xml.rest.FiltersDocument;
+import org.biocatalogue.x2009.xml.rest.ResourceLink;
+import org.biocatalogue.x2009.xml.rest.RestMethod;
+import org.biocatalogue.x2009.xml.rest.RestMethodDocument;
+import org.biocatalogue.x2009.xml.rest.RestMethods;
+import org.biocatalogue.x2009.xml.rest.RestMethodsDocument;
+import org.biocatalogue.x2009.xml.rest.Search;
+import org.biocatalogue.x2009.xml.rest.SearchDocument;
+import org.biocatalogue.x2009.xml.rest.Service;
+import org.biocatalogue.x2009.xml.rest.ServiceDocument;
+import org.biocatalogue.x2009.xml.rest.ServiceProvider;
+import org.biocatalogue.x2009.xml.rest.ServiceProviderDocument;
+import org.biocatalogue.x2009.xml.rest.ServiceProviders;
+import org.biocatalogue.x2009.xml.rest.ServiceProvidersDocument;
+import org.biocatalogue.x2009.xml.rest.Services;
+import org.biocatalogue.x2009.xml.rest.ServicesDocument;
+import org.biocatalogue.x2009.xml.rest.SoapInput;
+import org.biocatalogue.x2009.xml.rest.SoapInputDocument;
+import org.biocatalogue.x2009.xml.rest.SoapOperation;
+import org.biocatalogue.x2009.xml.rest.SoapOperationDocument;
+import org.biocatalogue.x2009.xml.rest.SoapOperations;
+import org.biocatalogue.x2009.xml.rest.SoapOperationsDocument;
+import org.biocatalogue.x2009.xml.rest.SoapOutput;
+import org.biocatalogue.x2009.xml.rest.SoapOutputDocument;
+import org.biocatalogue.x2009.xml.rest.SoapService;
+import org.biocatalogue.x2009.xml.rest.SoapServiceDocument;
+import org.biocatalogue.x2009.xml.rest.Tag;
+import org.biocatalogue.x2009.xml.rest.TagDocument;
+import org.biocatalogue.x2009.xml.rest.Tags;
+import org.biocatalogue.x2009.xml.rest.TagsDocument;
+import org.biocatalogue.x2009.xml.rest.User;
+import org.biocatalogue.x2009.xml.rest.UserDocument;
+import org.biocatalogue.x2009.xml.rest.Users;
+import org.biocatalogue.x2009.xml.rest.UsersDocument;
+
+import com.google.gson.Gson;
+
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class BioCatalogueClient
+{
+ // ******* CONSTANTS *******
+ // plugin details
+ public static final String PLUGIN_VERSION = "0.1.1";
+ public static final String PLUGIN_USER_AGENT = "Taverna2-ServiceCatalogue-plugin/" +
+ PLUGIN_VERSION +
+ " Java/" + System.getProperty("java.version");
+
+ public static final String XML_MIME_TYPE = "application/xml";
+ public static final String JSON_MIME_TYPE = "application/json";
+ public static final String LITE_JSON_MIME_TYPE = "application/biocat-lite+json";
+
+ public static final String XML_DATA_FORMAT = ".xml";
+ public static final String JSON_DATA_FORMAT = ".json";
+ public static final String LITE_JSON_DATA_FORMAT = ".bljson";
+
+
+
+ // API URLs
+ public static final String DEFAULT_API_SANDBOX_BASE_URL = "http://sandbox.biocatalogue.org";
+ public static final String DEFAULT_API_TEST_SERVER_BASE_URL = "http://test.biocatalogue.org";
+ public static final String DEFAULT_API_LIVE_SERVER_BASE_URL = "http://www.biocatalogue.org";
+
+ private static String BASE_URL; // BioCatalogue base URL to use (can be updated at runtime)
+
+ public static String API_REGISTRIES_URL;
+ public static String API_SERVICE_PROVIDERS_URL;
+ public static String API_USERS_URL;
+ public static String API_USER_FILTERS_URL;
+ public static String API_SERVICES_URL;
+ public static String API_SERVICE_FILTERS_URL;
+ public static String API_SOAP_OPERATIONS_URL;
+ public static String API_SOAP_OPERATION_FILTERS_URL;
+ public static String API_REST_METHODS_URL;
+ public static String API_REST_METHOD_FILTERS_URL;
+ public static String API_TAG_CLOUD_URL;
+ public static String API_SEARCH_URL;
+ public static String API_LOOKUP_URL;
+
+ // URL modifiers
+ public static final Map<String,String> API_INCLUDE_SUMMARY = Collections.singletonMap("include","summary"); // for fetching Service
+ public static final Map<String,String> API_INCLUDE_ANCESTORS = Collections.singletonMap("include", "ancestors,inputs,outputs"); // for fetching SOAP Operations and REST Methods
+ public static final String[] API_SORT_BY_NAME = {"sort","name"}; // for tag cloud
+ public static final String[] API_SORT_BY_COUNTS = {"sort","counts"}; // for tag cloud
+ public static final String[] API_ALSO_INPUTS_OUTPUTS = {"also","inputs,outputs"}; // for annotations on SOAP operation
+
+ public static final String API_PER_PAGE_PARAMETER = "per_page";
+ public static final String API_PAGE_PARAMETER = "page";
+ public static final String API_LIMIT_PARAMETER = "limit";
+ public static final String API_SERVICE_MONITORING_URL_SUFFIX = "/monitoring";
+ public static final String API_FILTERED_INDEX_SUFFIX = "/filtered_index";
+
+ // API Request scope
+ public static final String API_SCOPE_PARAMETER = "scope";
+ public static final String API_SCOPE_SOAP_OPERATIONS = "soap_operations";
+ public static final String API_SCOPE_REST_METHODS = "rest_methods";
+ public static final String API_SCOPE_SERVICES = "services";
+ public static final String API_SCOPE_SERVICE_PROVIDERS = "service_providers";
+ public static final String API_SCOPE_REGISTRIES = "registries";
+ public static final String API_SCOPE_USERS = "users";
+
+ public static final String API_TAG_PARAMETER = "tag";
+
+ public static final String API_LOOKUP_WSDL_LOCATION_PARAMETER = "wsdl_location";
+ public static final String API_LOOKUP_OPERATION_NAME_PARAMETER = "operation_name";
+ public static final String API_LOOKUP_SOAP_INPUT_NAME_PARAMETER = "input_name";
+ public static final String API_LOOKUP_SOAP_OUTPUT_NAME_PARAMETER = "output_name";
+
+
+ // *************************
+
+ // universal date formatters
+ private static final DateFormat DATE_FORMATTER = new SimpleDateFormat("EEE MMM dd HH:mm:ss Z yyyy");
+ private static final DateFormat SHORT_DATE_FORMATTER = new SimpleDateFormat("HH:mm 'on' dd/MM/yyyy");
+ private static final DateFormat API_LOGGING_TIMESTAMP_FORMATTER = DateFormat.getDateTimeInstance();
+
+
+ // SETTINGS
+ private Properties iniSettings; // settings that are read/stored from/to INI file
+
+ private File fAPIOperationLog;
+ private PrintWriter pwAPILogWriter;
+
+ // the logger
+ private Logger logger = Logger.getLogger(BioCatalogueClient.class);
+
+ private static BioCatalogueClient INSTANCE;
+
+ // default constructor
+ private BioCatalogueClient()
+ {
+ // TODO: load any config settings (if necessary)
+
+ // load the BioCatalogue API base URL from the plugin's configuration settings
+ this.setBaseURL(BioCataloguePluginConfiguration.getInstance().
+ getProperty(BioCataloguePluginConfiguration.SERVICE_CATALOGUE_BASE_URL));
+
+ // open API operation log file, if necessary
+ if (BioCataloguePluginConstants.PERFORM_API_RESPONSE_TIME_LOGGING ||
+ BioCataloguePluginConstants.PERFORM_API_XML_DATA_BINDING_TIME_LOGGING )
+ {
+ try {
+ BioCataloguePluginConstants.LOG_FILE_FOLDER.mkdirs(); // just in case this log file was never written - create the folder as well
+ fAPIOperationLog = new File(BioCataloguePluginConstants.LOG_FILE_FOLDER,
+ BioCataloguePluginConstants.API_OPERATION_LOG_FILENAME);
+ pwAPILogWriter = new PrintWriter(new FileOutputStream(fAPIOperationLog, true), true); // auto-flush makes sure that even if app crashes, log will not be lost
+ }
+ catch (NullPointerException e) {
+ pwAPILogWriter = new PrintWriter(System.out, true);
+ logger.error("ERROR: Folder to log API operation details is unknown (using System.out instead)... Details:", e);
+ }
+ catch (FileNotFoundException e) {
+ logger.error("ERROR: Couldn't open API operation log file... Details:", e);
+ }
+ }
+ }
+
+ public static synchronized BioCatalogueClient getInstance() {
+ if (INSTANCE == null) {
+ INSTANCE = new BioCatalogueClient();
+ }
+ return INSTANCE;
+ }
+
+
+ public String getBaseURL() {
+ return this.BASE_URL;
+ }
+
+ /**
+ * Updates the base API URL and also
+ * updates derived URLs of sub-URLs
+ * (e.g. BASE_URL + /services, etc)
+ *
+ * @param baseURL The new value for the BioCatalogue API base URL.
+ */
+ public void setBaseURL(String baseURL)
+ {
+ // make sure the base URL doesn't have a slash at the end
+ // (otherwise double slashes may occur during URL manipulation)
+ while (baseURL.endsWith("/")) { baseURL = baseURL.substring(0, baseURL.length() - 1); }
+
+ this.BASE_URL = baseURL;
+
+ API_REGISTRIES_URL = BASE_URL + "/registries";
+ API_SERVICE_PROVIDERS_URL = BASE_URL + "/service_providers";
+ API_USERS_URL = BASE_URL + "/users";
+ API_USER_FILTERS_URL = API_USERS_URL + "/filters";
+ API_SERVICES_URL = BASE_URL + "/services";
+ API_SERVICE_FILTERS_URL = API_SERVICES_URL + "/filters";
+ API_SOAP_OPERATIONS_URL = BASE_URL + "/soap_operations";
+ API_SOAP_OPERATION_FILTERS_URL = API_SOAP_OPERATIONS_URL + "/filters";
+ API_REST_METHODS_URL = BASE_URL + "/rest_methods";
+ API_REST_METHOD_FILTERS_URL = API_REST_METHODS_URL + "/filters";
+ API_TAG_CLOUD_URL = BASE_URL + "/tags";
+ API_SEARCH_URL = BASE_URL + "/search";
+ API_LOOKUP_URL = BASE_URL + "/lookup";
+ }
+
+ public File getAPIOperationLog() {
+ return fAPIOperationLog;
+ }
+
+ public PrintWriter getAPILogWriter() {
+ return pwAPILogWriter;
+ }
+
+
+ // ************ METHODS FOR RETRIEVAL OF SPECIALISED OBJECT FROM THE API VIA XML ************
+
+ public Annotations getBioCatalogueAnnotations(String strAnnotationsURL) throws Exception {
+ return (parseAPIResponseStream(Annotations.class, doBioCatalogueGET(strAnnotationsURL)));
+ }
+
+ public Filters getBioCatalogueFilters(String strURL) throws Exception {
+ return (parseAPIResponseStream(Filters.class, doBioCatalogueGET(strURL)));
+ }
+
+ public Services getBioCatalogueServices(String strURL) throws Exception {
+ return (parseAPIResponseStream(Services.class, doBioCatalogueGET(strURL)));
+ }
+
+ public Service getBioCatalogueService(String serviceURL) throws Exception {
+ return (parseAPIResponseStream(Service.class, doBioCatalogueGET(serviceURL)));
+ }
+
+ public Service getBioCatalogueServiceSummary(String serviceURL) throws Exception {
+ return (parseAPIResponseStream(Service.class, doBioCatalogueGET(Util.appendAllURLParameters(serviceURL, API_INCLUDE_SUMMARY))));
+ }
+
+ public Service getBioCatalogueServiceMonitoringData(String serviceURL) throws Exception
+ {
+ return (parseAPIResponseStream(Service.class,
+ doBioCatalogueGET(serviceURL + API_SERVICE_MONITORING_URL_SUFFIX))
+ );
+ }
+
+ public SoapService getBioCatalogueSoapService(String soapServiceURL) throws Exception {
+ return (parseAPIResponseStream(SoapService.class, doBioCatalogueGET(soapServiceURL)));
+ }
+
+ public SoapOperation getBioCatalogueSoapOperation(String soapOperationURL) throws Exception {
+ return (parseAPIResponseStream(SoapOperation.class, doBioCatalogueGET(soapOperationURL)));
+ }
+
+ public RestMethod getBioCatalogueRestMethod(String restMethodURL) throws Exception {
+ return (parseAPIResponseStream(RestMethod.class, doBioCatalogueGET(restMethodURL)));
+ }
+
+ public Search getBioCatalogueSearchData(String searchURL) throws Exception {
+ return (parseAPIResponseStream(Search.class, doBioCatalogueGET(searchURL)));
+ }
+
+ public Tag getBioCatalogueTag(String searchByTagURL) throws Exception {
+ return (parseAPIResponseStream(Tag.class, doBioCatalogueGET(searchByTagURL)));
+ }
+
+ public Tags getBioCatalogueTags(String tagsURL) throws Exception {
+ return (parseAPIResponseStream(Tags.class, doBioCatalogueGET(tagsURL)));
+ }
+
+
+ public ResourceLink getBioCatalogueResource(Class<? extends ResourceLink> classOfResourceToFetch, String resourceURL) throws Exception {
+ return (parseAPIResponseStream(classOfResourceToFetch, doBioCatalogueGET(resourceURL)));
+ }
+
+
+ public <T extends ResourceLink> Pair<CollectionCoreStatistics, List<T>> getListOfItemsFromResourceCollectionIndex(
+ Class<T> classOfCollectionOfRequiredReturnedObjects, BioCatalogueAPIRequest filteringRequest) throws Exception
+ {
+ ResourceLink matchingItems = null;
+ if (filteringRequest.getRequestType() == BioCatalogueAPIRequest.TYPE.GET) {
+ matchingItems = parseAPIResponseStream(classOfCollectionOfRequiredReturnedObjects, doBioCatalogueGET(filteringRequest.getURL()));
+ }
+ else {
+ matchingItems = parseAPIResponseStream(classOfCollectionOfRequiredReturnedObjects,
+ doBioCataloguePOST_SendJSON_AcceptXML(filteringRequest.getURL(), filteringRequest.getData()));
+ }
+
+ CollectionCoreStatistics statistics = null;
+
+ List<T> matchingItemList = new ArrayList<T>();
+
+ // SOAP Operations
+ if (classOfCollectionOfRequiredReturnedObjects.equals(SoapOperations.class)) {
+ SoapOperations soapOperations = (SoapOperations)matchingItems;
+ matchingItemList.addAll((Collection<? extends T>)(soapOperations.getResults().getSoapOperationList()));
+ statistics = soapOperations.getStatistics();
+ }
+
+ // REST Methods
+ else if (classOfCollectionOfRequiredReturnedObjects.equals(RestMethods.class)) {
+ RestMethods restMethods = (RestMethods)matchingItems;
+ matchingItemList.addAll((Collection<? extends T>)(restMethods.getResults().getRestMethodList()));
+ statistics = restMethods.getStatistics();
+ }
+
+ // Services
+ else if (classOfCollectionOfRequiredReturnedObjects.equals(Services.class)) {
+ Services services = (Services)matchingItems;
+ matchingItemList.addAll((Collection<? extends T>)(services.getResults().getServiceList()));
+ statistics = services.getStatistics();
+ }
+
+ // Service Providers
+ else if (classOfCollectionOfRequiredReturnedObjects.equals(ServiceProviders.class)) {
+ ServiceProviders serviceProviders = (ServiceProviders)matchingItems;
+ matchingItemList.addAll((Collection<? extends T>)(serviceProviders.getResults().getServiceProviderList()));
+ statistics = serviceProviders.getStatistics();
+ }
+
+ // Users
+ else if (classOfCollectionOfRequiredReturnedObjects.equals(Users.class)) {
+ Users users = (Users)matchingItems;
+ matchingItemList.addAll((Collection<? extends T>)(users.getResults().getUserList()));
+ statistics = users.getStatistics();
+ }
+
+ // no such option - error
+ else {
+ return null;
+ }
+
+ return new Pair<CollectionCoreStatistics, List<T>>(statistics, matchingItemList);
+ }
+
+
+
+
+ /**
+ * @param wsdlLocation
+ * @param operationName
+ * @return SoapOperation instance or <code>null</code> if nothing was found (or error occurred).
+ * @throws Exception
+ */
+ public SoapOperation lookupSoapOperation(SoapOperationIdentity soapOperationDetails) throws Exception
+ {
+ // first of all check for any problems with input data
+ if (soapOperationDetails == null || soapOperationDetails.hasError() ||
+ soapOperationDetails.getWsdlLocation() == null || soapOperationDetails.getWsdlLocation().length() == 0 ||
+ soapOperationDetails.getOperationName() == null || soapOperationDetails.getOperationName().length() == 0)
+ {
+ // something's not right - return null
+ return (null);
+ }
+
+ String lookupURL = Util.appendURLParameter(API_LOOKUP_URL, API_LOOKUP_WSDL_LOCATION_PARAMETER, soapOperationDetails.getWsdlLocation());
+ lookupURL = Util.appendURLParameter(lookupURL, API_LOOKUP_OPERATION_NAME_PARAMETER, soapOperationDetails.getOperationName());
+
+ ServerResponseStream lookupResponse = doBioCatalogueGET(lookupURL);
+ if (lookupResponse.getResponseCode() == HttpURLConnection.HTTP_NOT_FOUND) {
+ return null;
+ }
+ return (parseAPIResponseStream(SoapOperation.class, lookupResponse));
+ }
+
+
+ public <T extends ResourceLink> T lookupSoapOperationPort(Class<T> requiredResultClass, SoapOperationPortIdentity portDetails) throws Exception
+ {
+ // first of all check for any problems with port details
+ if (portDetails == null || portDetails.hasError() ||
+ portDetails.getWsdlLocation() == null || portDetails.getWsdlLocation().length() == 0 ||
+ portDetails.getOperationName() == null || portDetails.getOperationName().length() == 0 ||
+ portDetails.getPortName() == null || portDetails.getPortName().length() == 0)
+ {
+ // something's not right - return null
+ return (null);
+ }
+
+ // now check that specified class matches the port type
+ if (portDetails.isInput() && !requiredResultClass.equals(SoapInput.class) ||
+ !portDetails.isInput() && !requiredResultClass.equals(SoapOutput.class))
+ {
+ return (null);
+ }
+
+ String lookupURL = Util.appendURLParameter(API_LOOKUP_URL, API_LOOKUP_WSDL_LOCATION_PARAMETER, portDetails.getWsdlLocation());
+ lookupURL = Util.appendURLParameter(lookupURL, API_LOOKUP_OPERATION_NAME_PARAMETER, portDetails.getOperationName());
+ if (portDetails.isInput()) {
+ lookupURL = Util.appendURLParameter(lookupURL, API_LOOKUP_SOAP_INPUT_NAME_PARAMETER, portDetails.getPortName());
+ }
+ else {
+ lookupURL = Util.appendURLParameter(lookupURL, API_LOOKUP_SOAP_OUTPUT_NAME_PARAMETER, portDetails.getPortName());
+ }
+
+ ServerResponseStream lookupResponse = doBioCatalogueGET(lookupURL);
+ if (lookupResponse.getResponseCode() == HttpURLConnection.HTTP_NOT_FOUND) {
+ return null;
+ }
+ return (parseAPIResponseStream(requiredResultClass, lookupResponse));
+ }
+
+
+ public Service lookupParentService(SoapOperationIdentity soapOperationDetails) throws Exception
+ {
+ SoapOperation soapOperation = this.lookupSoapOperation(soapOperationDetails);
+ if (soapOperation != null) {
+ return (getBioCatalogueService(soapOperation.getAncestors().getService().getHref()));
+ }
+ else {
+ // lookup didn't find the SOAP operation or there
+ // was some problem with the input data
+ return (null);
+ }
+ }
+
+
+ public Service lookupParentServiceMonitoringData(SoapOperationIdentity soapOperationDetails) throws Exception
+ {
+ SoapOperation soapOperation = this.lookupSoapOperation(soapOperationDetails);
+ if (soapOperation != null) {
+ return (getBioCatalogueServiceMonitoringData(soapOperation.getAncestors().getService().getHref()));
+ }
+ else {
+ // lookup didn't find the SOAP operation or there
+ // was some problem with the input data
+ return (null);
+ }
+ }
+
+
+ // ************ METHODS FOR RETRIEVAL OF SPECIALISED OBJECT FROM THE API VIA LITE JSON ************
+
+ public BeansForJSONLiteAPI.ResourceIndex getBioCatalogueResourceLiteIndex(TYPE resourceType, String resourceIndexURL) throws Exception
+ {
+ ServerResponseStream response = doBioCatalogueGET_LITE_JSON(resourceIndexURL);
+
+ Gson gson = new Gson();
+ return (ResourceIndex)(gson.fromJson(new InputStreamReader(response.getResponseStream()), resourceType.getJsonLiteAPIBindingBeanClass()));
+ }
+
+
+ public BeansForJSONLiteAPI.ResourceIndex postBioCatalogueResourceLiteIndex(TYPE resourceType, String resourceIndexURL, String postData) throws Exception
+ {
+ ServerResponseStream response = doBioCataloguePOST_SendJSON_AcceptLITEJSON(resourceIndexURL, postData);
+
+ Gson gson = new Gson();
+ return (ResourceIndex)(gson.fromJson(new InputStreamReader(response.getResponseStream()), resourceType.getJsonLiteAPIBindingBeanClass()));
+ }
+
+
+ // ************ GENERIC API CONNECTIVITY METHODS ************
+
+ /**
+ * Generic method to issue GET requests to BioCatalogue server.
+ *
+ * This is a convenience method to be used instead of {@link BioCatalogueClient#doBioCatalogueGET_XML(String)}.
+ *
+ * @param strURL The URL on BioCatalogue to issue GET request to.
+ * @return TODO
+ * @throws Exception
+ */
+ public ServerResponseStream doBioCatalogueGET(String strURL) throws Exception {
+ return (doBioCatalogueGET_XML(strURL));
+ }
+
+ public ServerResponseStream doBioCatalogueGET_XML(String strURL) throws Exception {
+ return (doBioCatalogueGET(strURL, XML_MIME_TYPE, XML_DATA_FORMAT));
+ }
+
+ public ServerResponseStream doBioCatalogueGET_JSON(String strURL) throws Exception {
+ return (doBioCatalogueGET(strURL, JSON_MIME_TYPE, JSON_DATA_FORMAT));
+ }
+
+ public ServerResponseStream doBioCatalogueGET_LITE_JSON(String strURL) throws Exception {
+ return (doBioCatalogueGET(strURL, LITE_JSON_MIME_TYPE, LITE_JSON_DATA_FORMAT));
+ }
+
+
+ public ServerResponseStream doBioCatalogueGET(String strURL, String ACCEPT_HEADER, String REQUESTED_DATA_FORMAT) throws Exception
+ {
+ // TODO - HACK to speed up processing append .xml / .json / .bljson to all URLs to avoid LinkedData content negotiation
+ strURL = Util.appendStringBeforeParametersOfURL(strURL, REQUESTED_DATA_FORMAT);
+
+ // open server connection using provided URL (with no further modifications to it)
+ URL url = new URL(strURL);
+
+ Calendar requestStartedAt = Calendar.getInstance();
+ HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+ conn.setRequestProperty("User-Agent", PLUGIN_USER_AGENT);
+ conn.setRequestProperty("Accept", ACCEPT_HEADER);
+
+// if(LOGGED_IN) {
+// // if the user has "logged in", also add authentication details
+// conn.setRequestProperty("Authorization", "Basic " + AUTH_STRING);
+// }
+
+ // fetch server's response
+ ServerResponseStream serverResponse = doBioCatalogueReceiveServerResponse(conn, strURL, true);
+
+ if (BioCataloguePluginConstants.PERFORM_API_RESPONSE_TIME_LOGGING) {
+ logAPIOperation(requestStartedAt, "GET", serverResponse);
+ }
+ return (serverResponse);
+ }
+
+
+
+ public ServerResponseStream doBioCataloguePOST_SendJSON_AcceptXML(String strURL, String strDataBody) throws Exception {
+ return (doBioCataloguePOST(strURL, strDataBody, JSON_MIME_TYPE, XML_MIME_TYPE, XML_DATA_FORMAT));
+ }
+
+ public ServerResponseStream doBioCataloguePOST_SendJSON_AcceptLITEJSON(String strURL, String strDataBody) throws Exception {
+ return (doBioCataloguePOST(strURL, strDataBody, JSON_MIME_TYPE, LITE_JSON_MIME_TYPE, LITE_JSON_DATA_FORMAT));
+ }
+
+
+ /**
+ * Generic method to execute POST requests to BioCatalogue server.
+ *
+ * @param strURL The URL on BioCatalogue to POST to.
+ * @param strDataBody Body of the message to be POSTed to <code>strURL</code>.
+ * @return An object containing server's response body as an InputStream and
+ * a response code.
+ * @param CONTENT_TYPE_HEADER MIME type of the sent data.
+ * @param ACCEPT_HEADER MIME type of the data to be received.
+ * @param REQUESTED_DATA_FORMAT
+ * @throws Exception
+ */
+ public ServerResponseStream doBioCataloguePOST(String strURL, String strDataBody, String CONTENT_TYPE_HEADER,
+ String ACCEPT_HEADER, String REQUESTED_DATA_FORMAT) throws Exception
+ {
+ // TODO - HACK to speed up processing append .xml / .json / .bljson to all URLs to avoid LinkedData content negotiation
+ strURL = Util.appendStringBeforeParametersOfURL(strURL, REQUESTED_DATA_FORMAT);
+
+ // open server connection using provided URL (with no further modifications to it)
+ URL url = new URL (strURL);
+
+ Calendar requestStartedAt = Calendar.getInstance();
+ HttpURLConnection urlConn = (HttpURLConnection) url.openConnection();
+ urlConn.setRequestMethod("POST");
+ urlConn.setDoOutput(true);
+ urlConn.setRequestProperty("User-Agent", PLUGIN_USER_AGENT);
+ urlConn.setRequestProperty("Content-Type", CONTENT_TYPE_HEADER);
+ urlConn.setRequestProperty("Accept", ACCEPT_HEADER);
+
+ // prepare and POST XML data
+ OutputStreamWriter out = new OutputStreamWriter(urlConn.getOutputStream());
+ out.write(strDataBody);
+ out.close();
+
+
+ // fetch server's response
+ ServerResponseStream serverResponse = doBioCatalogueReceiveServerResponse(urlConn, strURL, false);
+
+ if (BioCataloguePluginConstants.PERFORM_API_RESPONSE_TIME_LOGGING) {
+ logAPIOperation(requestStartedAt, "POST", serverResponse);
+ }
+ return (serverResponse);
+ }
+
+
+ /**
+ * Generic method to execute DELETE requests to myExperiment server.
+ * This is only to be called when a user is logged in.
+ *
+ * @param strURL The URL on myExperiment to direct DELETE request to.
+ * @return An object containing XML Document with server's response body and
+ * a response code. Response body XML document might be null if there
+ * was an error or the user wasn't authorised to perform a certain action.
+ * Response code will always be set.
+ * @throws Exception
+ */
+ /*public ServerResponse doMyExperimentDELETE(String strURL) throws Exception
+ {
+ // open server connection using provided URL (with no modifications to it)
+ URL url = new URL(strURL);
+ HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+
+ // "tune" the connection
+ conn.setRequestMethod("DELETE");
+ conn.setRequestProperty("User-Agent", PLUGIN_USER_AGENT);
+ conn.setRequestProperty("Authorization", "Basic " + AUTH_STRING);
+
+ // check server's response
+ return (doMyExperimentReceiveServerResponse(conn, strURL, true));
+ }*/
+
+
+ /**
+ * A common method for retrieving BioCatalogue server's response for both
+ * GET and POST requests.
+ *
+ * @param conn Instance of the established URL connection to poll for server's response.
+ * @param strURL The URL on BioCatalogue with which the connection is established.
+ * @param bIsGetRequest Flag for identifying type of the request. True when the current
+ * connection executes GET request; false when it executes a POST / DELETE request.
+ * @return TODO
+ */
+ @SuppressWarnings("unchecked")
+ private ServerResponseStream doBioCatalogueReceiveServerResponse(HttpURLConnection conn, String strURL, boolean bIsGETRequest) throws Exception
+ {
+ int iResponseCode = conn.getResponseCode();
+
+ switch (iResponseCode)
+ {
+ case HttpURLConnection.HTTP_OK:
+ // regular operation path - simply return the reference to the data input stream
+ return (new ServerResponseStream(iResponseCode, conn.getInputStream(), strURL));
+
+ case HttpURLConnection.HTTP_BAD_REQUEST:
+ // this was a bad XML request - need full XML response to retrieve the error message from it;
+ // Java throws IOException if getInputStream() is used when non HTTP_OK response code was received -
+ // hence can use getErrorStream() straight away to fetch the error document
+ return (new ServerResponseStream(iResponseCode, conn.getErrorStream(), strURL));
+
+ case HttpURLConnection.HTTP_UNAUTHORIZED:
+ // this content is not authorised for current user
+ return (new ServerResponseStream(iResponseCode, null, strURL));
+
+ case HttpURLConnection.HTTP_NOT_FOUND:
+ // nothing was found at the provided URL
+ return (new ServerResponseStream(iResponseCode, conn.getErrorStream(), strURL));
+
+ default:
+ // unexpected response code - raise an exception
+ throw new IOException("Received unexpected HTTP response code (" + iResponseCode + ") while " +
+ (bIsGETRequest ? "fetching data at " : "posting data to ") + strURL);
+ }
+ }
+
+
+ /**
+ * This method is here to make sure that *all* parsing of received input stream data
+ * from the API is parsed ("bound") into Java objects in a central place - so it's
+ * possible to measure performance of XmlBeans for various inputs.
+ *
+ * NB! There is a serious limitation in Java's generics. Generic methods cannot
+ * access any of the static context of the classes of type parameters, because
+ * it wasn't designed for this. The only purpose of type parameters is compile-time
+ * type-checking.
+ * This means that even though all classes that could potentially be supplied as a
+ * type-parameter would have certain static functionality, it's not possible to access
+ * that through using the type-parameter like it's done in normal polymorhic situations.
+ * Therefore, some switching based on the class of the type-parameter for this method is
+ * done...
+ *
+ * @param <T>
+ * @param classOfRequiredReturnedObject Class of the object that the caller expects to receive
+ * after parsing provided server's response. For example,
+ * a call to /tags.xml return the <pre>[tags]...[/tags]</pre>
+ * document. <code>TagsDocument</code> should be used to access
+ * its static factory and parse the input stream - the return
+ * value will have type <code>Tags</code> -- <code>Tags.class</code>
+ * is the required input value for this parameter in this situation then.
+ * @param serverResponse This object should contain the input stream obtained from the API in return
+ * to the call on some URL.
+ * @return InputStream data parsed into the Java object of the supplied type [T].
+ * @throws Exception
+ */
+ @SuppressWarnings("unchecked")
+ private <T extends ResourceLink> T parseAPIResponseStream(Class<T> classOfRequiredReturnedObject, ServerResponseStream serverResponse) throws Exception
+ {
+ T parsedObject = null;
+ InputStream xmlInputStream = serverResponse.getResponseStream();
+
+ // choose a factory to parse the response and perform parsing
+ Calendar parsingStartedAt = Calendar.getInstance();
+ if (classOfRequiredReturnedObject.equals(Annotations.class)) {
+ parsedObject = (T)AnnotationsDocument.Factory.parse(xmlInputStream).getAnnotations();
+ }
+ else if (classOfRequiredReturnedObject.equals(Filters.class)) {
+ parsedObject = (T)FiltersDocument.Factory.parse(xmlInputStream).getFilters();
+ }
+ else if (classOfRequiredReturnedObject.equals(RestMethods.class)) {
+ parsedObject = (T)RestMethodsDocument.Factory.parse(xmlInputStream).getRestMethods();
+ }
+ else if (classOfRequiredReturnedObject.equals(RestMethod.class)) {
+ parsedObject = (T)RestMethodDocument.Factory.parse(xmlInputStream).getRestMethod();
+ }
+ else if (classOfRequiredReturnedObject.equals(Search.class)) {
+ parsedObject = (T)SearchDocument.Factory.parse(xmlInputStream).getSearch();
+ }
+ else if (classOfRequiredReturnedObject.equals(Services.class)) {
+ parsedObject = (T)ServicesDocument.Factory.parse(xmlInputStream).getServices();
+ }
+ else if (classOfRequiredReturnedObject.equals(Service.class)) {
+ parsedObject = (T)ServiceDocument.Factory.parse(xmlInputStream).getService();
+ }
+ else if (classOfRequiredReturnedObject.equals(ServiceProviders.class)) {
+ parsedObject = (T)ServiceProvidersDocument.Factory.parse(xmlInputStream).getServiceProviders();
+ }
+ else if (classOfRequiredReturnedObject.equals(ServiceProvider.class)) {
+ parsedObject = (T)ServiceProviderDocument.Factory.parse(xmlInputStream).getServiceProvider();
+ }
+ else if (classOfRequiredReturnedObject.equals(SoapOperations.class)) {
+ parsedObject = (T)SoapOperationsDocument.Factory.parse(xmlInputStream).getSoapOperations();
+ }
+ else if (classOfRequiredReturnedObject.equals(SoapOperation.class)) {
+ parsedObject = (T)SoapOperationDocument.Factory.parse(xmlInputStream).getSoapOperation();
+ }
+ else if (classOfRequiredReturnedObject.equals(SoapService.class)) {
+ parsedObject = (T)SoapServiceDocument.Factory.parse(xmlInputStream).getSoapService();
+ }
+ else if (classOfRequiredReturnedObject.equals(SoapInput.class)) {
+ parsedObject = (T)SoapInputDocument.Factory.parse(xmlInputStream).getSoapInput();
+ }
+ else if (classOfRequiredReturnedObject.equals(SoapOutput.class)) {
+ parsedObject = (T)SoapOutputDocument.Factory.parse(xmlInputStream).getSoapOutput();
+ }
+ else if (classOfRequiredReturnedObject.equals(Tags.class)) {
+ parsedObject = (T)TagsDocument.Factory.parse(xmlInputStream).getTags();
+ }
+ else if (classOfRequiredReturnedObject.equals(Tag.class)) {
+ parsedObject = (T)TagDocument.Factory.parse(xmlInputStream).getTag();
+ }
+ else if (classOfRequiredReturnedObject.equals(Users.class)) {
+ parsedObject = (T)UsersDocument.Factory.parse(xmlInputStream).getUsers();
+ }
+ else if (classOfRequiredReturnedObject.equals(User.class)) {
+ parsedObject = (T)UserDocument.Factory.parse(xmlInputStream).getUser();
+ }
+
+
+ // log the operation if necessary
+ if (BioCataloguePluginConstants.PERFORM_API_XML_DATA_BINDING_TIME_LOGGING) {
+ logAPIOperation(parsingStartedAt, null, serverResponse);
+ }
+
+ return (parsedObject);
+ }
+
+
+ // ************ HELPERS ************
+
+ public static DateFormat getDateFormatter() {
+ return(BioCatalogueClient.DATE_FORMATTER);
+ }
+
+ public static DateFormat getShortDateFormatter() {
+ return(BioCatalogueClient.SHORT_DATE_FORMATTER);
+ }
+
+
+ /**
+ * This is a helper to facilitate performance monitoring of the API usage.
+ *
+ * @param opearationStartedAt Instance of Calendar initialised with the date/time value of
+ * when the logged operation was started.
+ * @param requestType "GET" or "POST" to indicate that this was the actual URL connection with the BioCatalogue server
+ * to fetch some data; <code>null</code> to indicate an xml-binding operation using XmlBeans.
+ * @param serverResponse Will be used to extract the request URL.
+ */
+ private void logAPIOperation(Calendar opearationStartedAt, String requestType, ServerResponseStream serverResponse)
+ {
+ // just in case check that the writer was initialised
+ if (pwAPILogWriter != null) {
+ pwAPILogWriter.println(API_LOGGING_TIMESTAMP_FORMATTER.format(opearationStartedAt.getTime()) + ", " +
+ (System.currentTimeMillis() - opearationStartedAt.getTimeInMillis()) + ", " +
+ (requestType == null ? "xml_parsing" : requestType) + ", " +
+ serverResponse.getRequestURL());
+ }
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/ServerResponse.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/ServerResponse.java
new file mode 100644
index 0000000..d79235d
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/ServerResponse.java
@@ -0,0 +1,40 @@
+package net.sf.taverna.biocatalogue.model.connectivity;
+
+import net.sf.taverna.biocatalogue.model.Util;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public abstract class ServerResponse
+{
+ // this code is to be used when a local failure is encountered and the
+ // server response is a blank / invalid one
+ public static int LOCAL_FAILURE_CODE = -1;
+
+ // server response code - in theory should correspond to HTTP response codes
+ private int iResponseCode;
+
+ // URL that was used to make the request
+ private String requestURL;
+
+
+ public ServerResponse() {
+ // do nothing - empty constructor
+ }
+
+ public ServerResponse(int responseCode, String requestURL) {
+ super();
+ this.iResponseCode = responseCode;
+ this.requestURL = Util.urlDecodeQuery(requestURL);
+ }
+
+
+ public int getResponseCode() {
+ return (this.iResponseCode);
+ }
+
+ public String getRequestURL() {
+ return requestURL;
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/ServerResponseStream.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/ServerResponseStream.java
new file mode 100644
index 0000000..d4ebb56
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/connectivity/ServerResponseStream.java
@@ -0,0 +1,30 @@
+package net.sf.taverna.biocatalogue.model.connectivity;
+
+import java.io.InputStream;
+
+/**
+ * This class is a custom version of ServerResponse which contains the
+ * InputStream with the the actual server response data.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class ServerResponseStream extends ServerResponse
+{
+ private InputStream responseStream;
+
+ public ServerResponseStream(int responseCode, InputStream serverResponseStream, String requestURL)
+ {
+ super(responseCode, requestURL);
+ this.setResponseStream(serverResponseStream);
+ }
+
+ public void setResponseStream(InputStream responseStream)
+ {
+ this.responseStream = responseStream;
+ }
+
+ public InputStream getResponseStream()
+ {
+ return responseStream;
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchEngine.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchEngine.java
new file mode 100644
index 0000000..0c4018a
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchEngine.java
@@ -0,0 +1,221 @@
+package net.sf.taverna.biocatalogue.model.search;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.CountDownLatch;
+
+//import javax.annotation.Resource;
+
+import org.apache.log4j.Logger;
+import org.biocatalogue.x2009.xml.rest.CollectionCoreStatistics;
+import org.biocatalogue.x2009.xml.rest.ResourceLink;
+
+import com.google.gson.Gson;
+
+import net.sf.taverna.biocatalogue.model.Pair;
+import net.sf.taverna.biocatalogue.model.Tag;
+import net.sf.taverna.biocatalogue.model.Util;
+import net.sf.taverna.biocatalogue.model.connectivity.BeanForPOSTToFilteredIndex;
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueAPIRequest;
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
+import net.sf.taverna.biocatalogue.model.connectivity.BeansForJSONLiteAPI.ResourceIndex;
+import net.sf.taverna.biocatalogue.model.search.SearchInstance.TYPE;
+import net.sf.taverna.biocatalogue.ui.search_results.SearchResultsRenderer;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentFactory;
+
+import net.sf.taverna.biocatalogue.model.Resource;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class SearchEngine
+{
+ private static Logger logger = Logger.getLogger(SearchEngine.class);
+
+ protected SearchInstance searchInstance;
+ protected final BioCatalogueClient client;
+ protected final SearchInstanceTracker activeSearchInstanceTracker;
+ protected final CountDownLatch doneSignal;
+ protected final SearchResultsRenderer renderer;
+
+
+ public SearchEngine(SearchInstance searchInstance,
+ SearchInstanceTracker activeSearchInstanceTracker,
+ CountDownLatch doneSignal,
+ SearchResultsRenderer renderer)
+ {
+
+ this.searchInstance = searchInstance;
+ this.client = BioCatalogueClient.getInstance();
+ this.activeSearchInstanceTracker = activeSearchInstanceTracker;
+ this.doneSignal = doneSignal;
+ this.renderer = renderer;
+ }
+
+
+
+ /**
+ * @return <code>true</code> if the thread launched by this search engine is still
+ * the one treated as 'active' in the context of the user actions in the plugin;<br/>
+ * <code>false</code> - otherwise.
+ */
+ protected boolean isCurrentSearch() {
+ return (activeSearchInstanceTracker.isCurrentSearchInstance(
+ this.searchInstance.getResourceTypeToSearchFor(), searchInstance));
+ }
+
+
+
+ /**
+ * Primary API request is the one that is *generated* when the search is first executed --
+ * for further requests (like fetching more data) it won't be fully generated, but rather
+ * will be derived from this primary one.
+ */
+ protected BioCatalogueAPIRequest generateSearchRequest() {
+ return (generateSearchRequest(searchInstance.getSearchType()));
+ }
+
+ protected BioCatalogueAPIRequest generateSearchRequest(TYPE searchType)
+ {
+ // construct search request to execute on BioCatalogue server
+ BioCatalogueAPIRequest.TYPE requestType = BioCatalogueAPIRequest.TYPE.GET;
+ String requestURL = null;
+ String requestData = null;
+
+ switch (searchType) {
+ case QuerySearch:
+ requestURL = Util.appendURLParameter(searchInstance.getResourceTypeToSearchFor().getAPIResourceCollectionIndex(), "q", searchInstance.getSearchString());
+ break;
+
+ case TagSearch:
+ List<String> tags = new ArrayList<String>();
+ for (Tag t : searchInstance.getSearchTags()) {
+ tags.add(t.getFullTagName());
+ }
+ String tagParamValue = Util.join(tags, "[", "]", ",");
+ requestURL = Util.appendURLParameter(searchInstance.getResourceTypeToSearchFor().getAPIResourceCollectionIndex(), "tag", tagParamValue);
+ break;
+
+ case Filtering:
+ requestType = BioCatalogueAPIRequest.TYPE.POST;
+
+ // get search URL for the 'base' search upon which the filtering is based
+ requestURL = generateSearchRequest(searchInstance.getServiceFilteringBasedOn()).getURL();
+ requestURL = Util.appendStringBeforeParametersOfURL(requestURL, BioCatalogueClient.API_FILTERED_INDEX_SUFFIX, true);
+
+ // the base URL was prepared, now prepare filtering parameters as POST data
+ BeanForPOSTToFilteredIndex dataBean = new BeanForPOSTToFilteredIndex();
+ dataBean.filters = searchInstance.getFilteringSettings().getFilteringURLParameters();
+ Gson gson = new Gson();
+ requestData = gson.toJson(dataBean);
+ break;
+ }
+
+ // make sure that the URL was generated
+ if (requestURL == null) {
+ logger.error("Primary search URL couldn't be generated; Search engine must have encountered " +
+ "an unexpected search instance type: " + searchInstance.getSearchType());
+ return (null);
+ }
+
+ // Sort by name (for REST and SOAP only at the moment. Parent Web services do not have the sort by name facility yet.)
+// if (!searchInstance.getResourceTypeToSearchFor().equals(net.sf.taverna.biocatalogue.model.Resource.TYPE.Service)){
+ requestURL = Util.appendURLParameter(requestURL, "sort_by", "name");
+ requestURL = Util.appendURLParameter(requestURL, "sort_order", "asc");
+ requestURL = Util.appendURLParameter(requestURL, "include", "ancestors");
+// }
+ logger.info("Service Catalogue Plugin: Request URL for search: " + requestURL);
+
+ // append some search-type-independent parameters and return the URL
+ requestURL = Util.appendAllURLParameters(requestURL, searchInstance.getResourceTypeToSearchFor().getAPIResourceCollectionIndexAdditionalParameters());
+ return (new BioCatalogueAPIRequest(requestType, requestURL, requestData));
+ }
+
+
+
+ public void startNewSearch()
+ {
+ // construct API request for this search
+ BioCatalogueAPIRequest searchRequest = generateSearchRequest();
+
+ // perform the actual search operation
+ try
+ {
+ ResourceIndex resourceIndex = null;
+ if (searchRequest.getRequestType() == BioCatalogueAPIRequest.TYPE.GET) {
+ resourceIndex = client.getBioCatalogueResourceLiteIndex(searchInstance.getResourceTypeToSearchFor(), searchRequest.getURL());
+ }
+ else {
+ // can only be POST then!
+ resourceIndex = client.postBioCatalogueResourceLiteIndex(searchInstance.getResourceTypeToSearchFor(), searchRequest.getURL(), searchRequest.getData());
+ }
+ SearchResults searchResults = new SearchResults(searchInstance.getResourceTypeToSearchFor(), resourceIndex);
+
+ // only update search results of the associated search instance if the caller thread of
+ // this operation is still active - synchronisation helps to make sure that the results
+ // will definitely only be rendered if the current search instance is definitely active:
+ // this way searches finishing in quick succession will 'flash' the results for a short
+ // while before being updated, but that will happen in the correct order
+ synchronized (activeSearchInstanceTracker) {
+ if (isCurrentSearch()) {
+ searchInstance.setSearchResults(searchResults);
+ renderer.renderInitialResults(searchInstance);
+ }
+ }
+ }
+ catch (Exception e) {
+ logger.error("ERROR: Couldn't execute initial phase of a search by query, details below:", e);
+ }
+
+ // no matter if search was completed or interrupted by a new search, notify the caller // FIXME - is this needed?
+ searchCompleteNotifyCaller();
+ }
+
+
+ @SuppressWarnings("unchecked")
+ public void fetchMoreResults(int resultPageNumber)
+ {
+ if (resultPageNumber < 1 || resultPageNumber > searchInstance.getSearchResults().getTotalResultPageNumber()) {
+ logger.error("Prevented attempt to fetch an invalid result page: " + resultPageNumber + ". Returning...");
+ return;
+ }
+
+ // construct search URL to hit on BioCatalogue server --
+ // it is exactly as the one for the initial search, but with a page number
+ // parameter being added
+ BioCatalogueAPIRequest searchRequest = generateSearchRequest();
+ searchRequest.setURL(Util.appendURLParameter(searchRequest.getURL(), BioCatalogueClient.API_PAGE_PARAMETER, ""+resultPageNumber));
+
+ // fetch required result page
+ try
+ {
+ Pair<CollectionCoreStatistics,List<ResourceLink>> newResultBatch = client.getListOfItemsFromResourceCollectionIndex(
+ searchInstance.getResourceTypeToSearchFor().getXmlBeansGeneratedCollectionClass(), searchRequest);
+
+ int firstNewEntryIndex = searchInstance.getSearchResults().getFirstItemIndexOn(resultPageNumber);
+ searchInstance.getSearchResults().addSearchResults(newResultBatch.getSecondObject(), firstNewEntryIndex);
+
+ // only update search results of the associated search instance if the caller thread of
+ // this operation is still active
+ if (isCurrentSearch()) {
+ renderer.renderFurtherResults(searchInstance, firstNewEntryIndex, searchInstance.getResourceTypeToSearchFor().getApiResourceCountPerIndexPage());
+ }
+ }
+ catch (Exception e) {
+ // FIXME
+ }
+
+
+ // no matter if search was completed or interrupted by a new search, notify the caller // FIXME - is this needed?
+ searchCompleteNotifyCaller();
+ }
+
+
+ /**
+ * This method is used for notifying the object that has started the
+ * search of this particular search operation being complete.
+ */
+ protected void searchCompleteNotifyCaller() {
+ this.doneSignal.countDown();
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchInstance.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchInstance.java
new file mode 100644
index 0000000..fa43632
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchInstance.java
@@ -0,0 +1,490 @@
+package net.sf.taverna.biocatalogue.model.search;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.concurrent.CountDownLatch;
+
+import javax.swing.Icon;
+
+import net.sf.taverna.biocatalogue.model.Resource;
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.biocatalogue.model.Tag;
+import net.sf.taverna.biocatalogue.model.Util;
+import net.sf.taverna.biocatalogue.ui.search_results.SearchResultsRenderer;
+
+
+/**
+ * Class to hold settings for search instance. Objects of this type will
+ * be used to re-run a search instance at a later time -- or to apply
+ * filtering onto a previously executed search.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class SearchInstance implements Comparable<SearchInstance>, Serializable
+{
+ private static final long serialVersionUID = -5236966374301885370L;
+
+ // CONSTANTS
+ public static enum TYPE
+ {
+ QuerySearch(ResourceManager.getImageIcon(ResourceManager.SEARCH_ICON)),
+ TagSearch(ResourceManager.getImageIcon(ResourceManager.TAG_ICON)),
+ Filtering(ResourceManager.getImageIcon(ResourceManager.FILTER_ICON));
+
+ private Icon icon;
+
+ /**
+ * @param icon Icon to represent search instances in different listings
+ * - for example in search history.
+ */
+ TYPE(Icon icon) {
+ this.icon = icon;
+ }
+
+ /**
+ * @return An icon that is most suitable to display search instance of this type in a UI component.
+ */
+ public Icon getIcon() {
+ return this.icon;
+ }
+ }
+
+
+
+ // SEARCH SETTINGS - for either search by query or search by tag
+ private TYPE searchType;
+ private final TYPE serviceFilteringBasedOn; // service filtering may be based on {@link TYPE.QuerySearch} or {@link TYPE.TagSearch}
+ private final Resource.TYPE resourceTypeToSearchFor;
+
+ private final String searchString;
+ private final List<Tag> searchTags;
+
+
+ // SERVICE FILTERING settings
+ private ServiceFilteringSettings filteringSettings;
+
+ // SEARCH RESULTS
+ private transient SearchResults searchResults; // don't want to store search results when serialising...
+
+
+
+ /**
+ * Constructs a query search instance for finding instance of a specific resource type.
+ *
+ * @param searchString
+ * @param resourceTypeToSearchFor
+ */
+ public SearchInstance(String searchString, Resource.TYPE resourceTypeToSearchFor)
+ {
+ this.searchType = TYPE.QuerySearch;
+ this.serviceFilteringBasedOn = null;
+
+ this.resourceTypeToSearchFor = resourceTypeToSearchFor;
+
+ this.searchString = searchString;
+ this.searchTags = null;
+ }
+
+
+
+ /**
+ * Constructing a search instance for finding instance of a specific resource type by a single tag.
+ *
+ * @param searchTag
+ * @param resourceTypeToSearchFor
+ */
+ public SearchInstance(Tag searchTag, Resource.TYPE resourceTypeToSearchFor)
+ {
+ this.searchType = TYPE.TagSearch;
+ this.serviceFilteringBasedOn = null;
+
+ this.resourceTypeToSearchFor = resourceTypeToSearchFor;
+
+ this.searchTags = Collections.singletonList(searchTag);
+ this.searchString = null;
+ }
+
+
+ /**
+ * Constructing a search instance for finding instance of a specific resource type by a list of tags.
+ *
+ * @param searchTags
+ * @param resourceTypeToSearchFor
+ */
+ public SearchInstance(List<Tag> searchTags, Resource.TYPE resourceTypeToSearchFor)
+ {
+ this.searchType = TYPE.TagSearch;
+ this.serviceFilteringBasedOn = null;
+
+ this.resourceTypeToSearchFor = resourceTypeToSearchFor;
+
+ this.searchTags = searchTags;
+ this.searchString = null;
+ }
+
+
+
+ /**
+ * Constructing service filtering search instance.
+ *
+ * @param si SearchInstance to base the current on.
+ * Can be either {@link TYPE#TagSearch} or {@link TYPE#QuerySearch} type of SearchInstance.
+ * @param filteringSettings Filtering settings associated with this search instance.
+ */
+ public SearchInstance(SearchInstance si, ServiceFilteringSettings filteringSettings) throws IllegalArgumentException
+ {
+ if (!si.isTagSearch() && !si.isQuerySearch()) {
+ throw new IllegalArgumentException("Cannot create Service Filtering search instance - " +
+ "supplied base search instance must be either QuerySearch or TagSearch");
+ }
+
+ this.searchType = TYPE.Filtering;
+ this.serviceFilteringBasedOn = si.searchType;
+
+ this.resourceTypeToSearchFor = si.resourceTypeToSearchFor;
+
+ // this search instance inherits search term (i.e. search query or the tag) from the supplied search instance
+ this.searchString = si.isQuerySearch() ? si.searchString : null;
+ this.searchTags = si.isTagSearch() ? si.searchTags : null;
+
+ // also, store the filtering settings that are to be applied to the newly
+ // created search instance
+ this.filteringSettings = filteringSettings;
+ }
+
+
+ /**
+ * Determines whether the two search instances are identical.
+ */
+ // TODO - fix the equals() method
+ public boolean equals(Object other)
+ {
+ if (other instanceof SearchInstance)
+ {
+ SearchInstance s = (SearchInstance)other;
+
+ boolean bSearchTypesMatch = (this.searchType == s.getSearchType());
+ if (bSearchTypesMatch) {
+ switch (this.searchType) {
+ case QuerySearch: bSearchTypesMatch = this.searchString.equals(s.getSearchString()); break;
+
+ case TagSearch: bSearchTypesMatch = this.searchTags.equals(s.getSearchTags()); break;
+
+ case Filtering: bSearchTypesMatch = this.serviceFilteringBasedOn == s.getServiceFilteringBasedOn();
+ if (bSearchTypesMatch) {
+ if (this.serviceFilteringBasedOn == TYPE.QuerySearch) {
+ bSearchTypesMatch = this.searchString.equals(s.getSearchString());
+ }
+ else {
+ bSearchTypesMatch = this.searchTags.equals(s.getSearchTags());
+ }
+ }
+ if (bSearchTypesMatch) {
+ if (this.filteringSettings != null) {
+ bSearchTypesMatch = this.filteringSettings.equals(s.getFilteringSettings());
+ }
+ else if (s.filteringSettings != null) {
+ // other isn't null, this one is - so 'false'
+ bSearchTypesMatch = false;
+ }
+ else {
+ // both could be null
+ bSearchTypesMatch = (this.filteringSettings == s.getFilteringSettings());
+ }
+ }
+ break;
+ default: bSearchTypesMatch = false;
+ }
+ }
+
+ return (bSearchTypesMatch &&
+ /* TODO re-enable this when limits are implemented -- this.iResultCountLimit == s.getResultCountLimit() && */
+ this.resourceTypeToSearchFor == s.getResourceTypeToSearchFor());
+ }
+ else
+ return (false);
+ }
+
+
+ public int compareTo(SearchInstance other)
+ {
+ if (this.equals(other)) return(0);
+ else
+ {
+ // this will return results in the descending order - which is
+ // fine, because the way this collection will be rendered will
+ // eventually traverse it from the rear end first; so results
+ // will be shown alphabetically
+ return (-1 * this.toString().compareTo(other.toString()));
+ }
+ }
+
+
+ /**
+ * See {@link SearchInstance#getDescriptionStringForSearchStatus(SearchInstance)}
+ */
+ public String getDescriptionStringForSearchStatus() {
+ return (getDescriptionStringForSearchStatus(this));
+ }
+
+
+ /**
+ * @param si {@link SearchInstance} for which the method is executed.
+ * @return String that can be used as a description of the provided {@link SearchInstance}
+ * in the search status label. Returned strings may look like: <br/>
+ * - <code>empty search string</code><br/>
+ * - <code>query "[search_query]"</code><br/>
+ * - <code>tag "[search_tag]"</code><br/>
+ * - <code>tags "[tag1]", "[tag2]", "[tag3]"</code><br/>
+ * - <code>query "[search_query]" and X filter(s)</code><br/>
+ * - <code>tag "[search_tag]" and X filter(s)</code><br/>
+ * - <code>tags "[tag1]", "[tag2]", "[tag3]" and X filter(s)</code><br/>
+ */
+ public static String getDescriptionStringForSearchStatus(SearchInstance si)
+ {
+ switch (si.searchType)
+ {
+ case QuerySearch: String searchQuery = si.getSearchTerm();
+ return (searchQuery.length() == 0 ?
+ "empty search string" :
+ "query " + si.getSearchTerm());
+
+ case TagSearch: return (Util.pluraliseNoun("tag", si.getSearchTags().size()) + " " + si.getSearchTerm());
+
+ case Filtering: int filterNumber = si.getFilteringSettings().getNumberOfFilteringCriteria();
+
+ SearchInstance tempBaseSI = si.deepCopy();
+ tempBaseSI.searchType = si.getServiceFilteringBasedOn();
+ return getDescriptionStringForSearchStatus(tempBaseSI) + " and " + filterNumber + " " + Util.pluraliseNoun("filter", filterNumber);
+
+ default: return ("unexpected type of search");
+ }
+ }
+
+
+ public String toString()
+ {
+ String out = "<html>";
+
+ if (this.isQuerySearch() || this.isTagSearch()) {
+ out += (this.isTagSearch() ? "Tag s" : "S") + "earch: '" + getSearchTerm() + "' [" + this.detailsAsString() + "]";
+ }
+ else if (this.isServiceFilteringSearch()) {
+ out += "Filter:<br>" +
+ (getSearchTerm().length() > 0 ? ("- based on " + (this.isQuerySearch() ? "term" : "tag") + " '" + getSearchTerm() + "'<br>") : "") +
+ "- scope: " + detailsAsString() + "<br>" +
+ "- " + this.filteringSettings.detailsAsString();
+ }
+
+ out += "</html>";
+
+ return (out);
+ }
+
+
+ /**
+ * @return A string representation of search settings held in this object;
+ * actual search value (string/tag) are ignored - this only affects
+ * types to search and the number of objects to fetch.
+ */
+ public String detailsAsString()
+ {
+ // include the name of the resource type collection that is to be / was searched for
+ String str = this.getResourceTypeToSearchFor().getCollectionName();
+
+ // add the rest to the string representation of the search instance
+ str = str /* TODO re-enable when limits are implemented -- "; limit: " + this.iResultCountLimit +*/;
+
+ return (str);
+ }
+
+
+
+ // ***** Getters for all fields *****
+
+ /**
+ * @return Type of this search instance.
+ */
+ public TYPE getSearchType() {
+ return (this.searchType);
+ }
+
+
+ /**
+ * @return True if this search settings instance describes a search by tag.
+ */
+ public boolean isTagSearch() {
+ return (this.searchType == TYPE.TagSearch);
+ }
+
+
+ /**
+ * @return True if this search settings instance describes a search by query.
+ */
+ public boolean isQuerySearch() {
+ return (this.searchType == TYPE.QuerySearch);
+ }
+
+
+ /**
+ * @return True if this search settings instance describes service filtering operation.
+ */
+ public boolean isServiceFilteringSearch() {
+ return (this.searchType == TYPE.Filtering);
+ }
+
+
+ /**
+ * Allows to test which type of search this filtering operation is based on -- any filtering
+ * operation can be:
+ * <li>derived from an initial search by tag(s) or by free-text query</li>
+ * <li>or can be just a standalone filtering operation, where filtering criteria are
+ * applied to all resources of the specified type, without prior search.</li>
+ *
+ * @return Value {@link TYPE#QuerySearch} or {@link TYPE#TagSearch} if this filtering operation has a known "parent",<br/>
+ * <code>null</code> if this is a proper search (not a filtering!) operation, or
+ * if this filtering operation was not based on any search.
+ */
+ public TYPE getServiceFilteringBasedOn() {
+ return serviceFilteringBasedOn;
+ }
+
+
+ public Resource.TYPE getResourceTypeToSearchFor() {
+ return this.resourceTypeToSearchFor;
+ }
+
+
+ /**
+ * @return Search string; only valid when SearchSettings object holds data about a search by query, not a tag search.
+ */
+ public String getSearchString() {
+ return searchString;
+ }
+
+ public List<Tag> getSearchTags() {
+ return searchTags;
+ }
+
+ /**
+ * This method is to be used when the type of search is not checked - in
+ * case of query search the method returns the search string, otherwise
+ * the tag(s) that is to be searched.
+ *
+ * @return The value will be returned in double quotes.
+ */
+ public String getSearchTerm()
+ {
+ if (this.searchType == TYPE.QuerySearch || this.serviceFilteringBasedOn == TYPE.QuerySearch) {
+ return (this.searchString.length() == 0 ?
+ "" :
+ "\"" + this.searchString + "\"");
+ }
+ else {
+ List<String> tagDisplayNames = new ArrayList<String>();
+ for (Tag t : this.searchTags) {
+ tagDisplayNames.add(t.getTagDisplayName());
+ }
+ return (Util.join(tagDisplayNames, "\"", "\"", ", "));
+ }
+ }
+
+
+ public ServiceFilteringSettings getFilteringSettings() {
+ return filteringSettings;
+ }
+ public void setFilteringSettings(ServiceFilteringSettings filteringSettings) {
+ this.filteringSettings = filteringSettings;
+ }
+
+
+ public SearchResults getSearchResults() {
+ return searchResults;
+ }
+ public void setSearchResults(SearchResults searchResults) {
+ this.searchResults = searchResults;
+ }
+
+ /**
+ * @return True if search results are available;
+ * False if no search results are available - probably search hasn't been carried out yet.
+ */
+ public boolean hasSearchResults() {
+ return (searchResults != null);
+ }
+
+ /**
+ * @return True if this is a new search; false otherwise.
+ * (Search is currently treated as new if there are no search results available yet.)
+ */
+ public boolean isNewSearch() {
+ return (!hasSearchResults());
+ }
+
+ /**
+ * Removes any previous search results; after execution of
+ * this method this search instance is treated as "new search".
+ */
+ public void clearSearchResults() {
+ this.searchResults = null;
+ }
+
+
+
+
+ // *** Methods that call SearchEngine in order to start new / resume result fetching for a previous search ***
+ //
+ // They are used to relay external calls to these methods to the underlying instance
+ // of SearchEngine which will perform the actual search operations for this search instance.
+
+ /**
+ * @param activeSearchInstanceTracker Tracker of current search instances for different resource types -
+ * aids in early termination of older searches.
+ * @param doneSignal Means of notifying the parentSeachThread of completing the requested search operation.
+ * The parent thread will block until doneSignal is activated.
+ * @param renderer {@link SearchResultsRenderer} that will render results of this search.
+ */
+ public void startNewSearch(SearchInstanceTracker activeSearchInstanceTracker,
+ CountDownLatch doneSignal, SearchResultsRenderer renderer)
+ {
+ new SearchEngine(this, activeSearchInstanceTracker, doneSignal, renderer).startNewSearch();
+ }
+
+
+ /**
+ * @param activeSearchInstanceTracker Tracker of current search instances for different resource types -
+ * aids in early termination of older searches.
+ * @param doneSignal Means of notifying the parentSeachThread of completing the requested search operation.
+ * The parent thread will block until doneSignal is activated.
+ * @param renderer {@link SearchResultsRenderer} that will render results of this search.
+ * @param resultPageNumber
+ */
+ public void fetchMoreResults(SearchInstanceTracker activeSearchInstanceTracker,
+ CountDownLatch doneSignal, SearchResultsRenderer renderer, int resultPageNumber)
+ {
+ new SearchEngine(this, activeSearchInstanceTracker, doneSignal, renderer).fetchMoreResults(resultPageNumber);
+ }
+
+
+
+
+ /**
+ * Used in the plugin, for example, to transfer search results from Search tab to
+ * Filtering tab. This way both tabs will remain completely independent.
+ *
+ * @return Deep copy of this SearchInstance object. If deep copying doesn't succeed,
+ * <code>null</code> is returned.
+ */
+ public SearchInstance deepCopy() {
+ return (SearchInstance)Util.deepCopy(this);
+ }
+
+ public boolean isEmptySearch() {
+ return ((searchString == null) || searchString.isEmpty()) &&
+ ((searchTags == null) || searchTags.isEmpty()) &&
+ ((filteringSettings == null) || (filteringSettings.getNumberOfFilteringCriteria() == 0));
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchInstanceTracker.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchInstanceTracker.java
new file mode 100644
index 0000000..906ded1
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchInstanceTracker.java
@@ -0,0 +1,57 @@
+package net.sf.taverna.biocatalogue.model.search;
+
+import net.sf.taverna.biocatalogue.model.Resource;
+
+/**
+ * Implementations of this interface will keep track of
+ * current search instances for different resource types
+ * (under assumption that {@link SearchInstance} classes
+ * can only deal with one resource type per instance).
+ *
+ * In the BioCatalogue plugin it is one of the UI components
+ * that needs to keep track of active search instances. This
+ * interface helps to decouple the search engine model from the
+ * UI.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public interface SearchInstanceTracker
+{
+ /**
+ * Clears all records of previous search instances.
+ */
+ public void clearPreviousSearchInstances();
+
+ /**
+ * Registers an instance of {@link SearchInstance} class
+ * as a current one for a specific resource type.
+ *
+ * Repeated calls to this method with the same parameter
+ * should overwrite old values.
+ *
+ * @param searchType Resource type to associate the registered
+ * {@link SearchInstance} with.
+ */
+ public void registerSearchInstance(Resource.TYPE searchType, SearchInstance searchInstance);
+
+
+ /**
+ * Tests if provided {@link SearchInstance} is registered as the
+ * current one.
+ *
+ * @param searchType Resource type to perform the test for.
+ * @param searchInstance {@link SearchInstance} object that is expected to be
+ * the current search instance for the specified resource type.
+ * @return <code>true</code> - if the provided <code>searchInstance</code> is indeed
+ * currently registered as the active one for the given resouce type;<br/>
+ * <code>false</code> - otherwise.
+ */
+ public boolean isCurrentSearchInstance(Resource.TYPE searchType, SearchInstance searchInstance);
+
+
+ /**
+ * @param searchType
+ * @return Currently active {@link SearchInstance} object for the specified resource type.
+ */
+ public SearchInstance getCurrentSearchInstance(Resource.TYPE searchType);
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchOptions.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchOptions.java
new file mode 100644
index 0000000..cf5e7db
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchOptions.java
@@ -0,0 +1,70 @@
+package net.sf.taverna.biocatalogue.model.search;
+
+import java.util.Collections;
+import java.util.List;
+
+import net.sf.taverna.biocatalogue.model.Tag;
+import net.sf.taverna.biocatalogue.model.Resource.TYPE;
+import net.sf.taverna.biocatalogue.ui.SearchOptionsPanel;
+
+/**
+ * Instances of this class can store the state of the
+ * {@link SearchOptionsPanel} / {@link TagSelectionDialog} in
+ * order to help instantiate {@link SearchInstance} objects.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class SearchOptions
+{
+ private SearchInstance preconfiguredSearchInstance;
+ private SearchInstance.TYPE searchType;
+ private String searchString;
+ private List<Tag> searchTags;
+ private List<TYPE> resourceTypesToSearchFor;
+
+ public SearchOptions(String searchString, List<TYPE> searchTypes) {
+ this.preconfiguredSearchInstance = null;
+ this.searchType = SearchInstance.TYPE.QuerySearch;
+ this.searchString = searchString;
+ this.searchTags = null;
+ this.resourceTypesToSearchFor = searchTypes;
+ }
+
+ public SearchOptions(List<Tag> searchTags, List<TYPE> searchTypes) {
+ this.preconfiguredSearchInstance = null;
+ this.searchType = SearchInstance.TYPE.TagSearch;
+ this.searchString = null;
+ this.searchTags = searchTags;
+ this.resourceTypesToSearchFor = searchTypes;
+ }
+
+ public SearchOptions(SearchInstance preconfiguredSearchInstance) {
+ this.preconfiguredSearchInstance = preconfiguredSearchInstance;
+ this.searchType = preconfiguredSearchInstance.getSearchType();
+ this.searchString = preconfiguredSearchInstance.getSearchString();
+ this.searchTags = preconfiguredSearchInstance.getSearchTags();
+ this.resourceTypesToSearchFor = Collections.singletonList(preconfiguredSearchInstance.getResourceTypeToSearchFor());
+ }
+
+
+ public SearchInstance getPreconfiguredSearchInstance() {
+ return preconfiguredSearchInstance;
+ }
+
+ public SearchInstance.TYPE getSearchType() {
+ return searchType;
+ }
+
+ public String getSearchString() {
+ return searchString;
+ }
+
+ public List<Tag> getSearchTags() {
+ return searchTags;
+ }
+
+ public List<TYPE> getResourceTypesToSearchFor() {
+ return resourceTypesToSearchFor;
+ }
+
+}
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchResults.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchResults.java
new file mode 100644
index 0000000..d18076c
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/SearchResults.java
@@ -0,0 +1,214 @@
+package net.sf.taverna.biocatalogue.model.search;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import net.sf.taverna.biocatalogue.model.LoadingResource;
+import net.sf.taverna.biocatalogue.model.Resource.TYPE;
+import net.sf.taverna.biocatalogue.model.connectivity.BeansForJSONLiteAPI;
+import net.sf.taverna.biocatalogue.model.connectivity.BeansForJSONLiteAPI.ResourceIndex;
+import net.sf.taverna.biocatalogue.model.connectivity.BeansForJSONLiteAPI.ResourceLinkWithName;
+
+import org.apache.log4j.Logger;
+
+import org.biocatalogue.x2009.xml.rest.ResourceLink;
+
+
+/**
+ * Generic class for any kinds of search results.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class SearchResults implements Serializable
+{
+ private static final long serialVersionUID = 6994685875323246165L;
+
+ private transient Logger logger; // don't want to serialise the logger...
+
+ private final TYPE typeOfResourcesInTheResultSet;
+ private final int totalResultCount;
+
+ // Data store for found items
+ protected ArrayList<ResourceLink> foundItems;
+ private int fullyFetchedItemCount;
+
+
+
+ public SearchResults(TYPE typeOfResourcesInTheResultSet, BeansForJSONLiteAPI.ResourceIndex resourceIndex)
+ {
+ this.typeOfResourcesInTheResultSet = typeOfResourcesInTheResultSet;
+ this.totalResultCount = resourceIndex.getResources().length;
+ this.fullyFetchedItemCount = 0;
+
+ this.logger = Logger.getLogger(this.getClass());
+
+ initialiseSearchResultCollection(resourceIndex);
+ }
+
+
+ /**
+ * The collection of results is initialised to cater for the expected number of
+ * values - placeholder with just a name and URL for each of the expected result entries is stored.
+ *
+ * @param resourceIndex
+ */
+ protected void initialiseSearchResultCollection(ResourceIndex resourceIndex)
+ {
+ foundItems = new ArrayList<ResourceLink>();
+ foundItems.ensureCapacity(getTotalMatchingItemCount());
+
+ ResourceLinkWithName resourceLink = null;
+ for (int i = 0; i < getTotalMatchingItemCount(); i++) {
+ resourceLink = resourceIndex.getResources()[i];
+ this.foundItems.add(new LoadingResource(resourceLink.getURL(), resourceLink.getName()));
+ }
+ }
+
+
+ public synchronized void addSearchResults(List<ResourceLink> searchResultsData, int positionToStartAddingResults)
+ {
+ // only update a specific portion of results
+ for (int i = 0; i < searchResultsData.size(); i++) {
+ this.foundItems.set(i + positionToStartAddingResults, searchResultsData.get(i));
+ }
+
+ fullyFetchedItemCount += searchResultsData.size();
+ }
+
+
+ public TYPE getTypeOfResourcesInTheResultSet() {
+ return typeOfResourcesInTheResultSet;
+ }
+
+
+ /**
+ * @return List of resources that have matched the search query
+ * and/or specified filtering criteria.
+ */
+ public List<ResourceLink> getFoundItems() {
+ return (this.foundItems);
+ }
+
+
+ /**
+ * @return Number of resources that have matched the search query
+ * (and/or specified filtering criteria) that have already been
+ * fetched.
+ */
+ public int getFetchedItemCount() {
+ return (this.fullyFetchedItemCount);
+ }
+
+
+ /**
+ * @return Total number of resources that have matched the search query
+ * (and/or specified filtering criteria) - most of these will
+ * likely not be fetched yet.
+ */
+ public int getTotalMatchingItemCount() {
+ return (this.totalResultCount);
+ }
+
+
+ /**
+ * @return Total number of pages in the current result set.
+ */
+ public int getTotalResultPageNumber() {
+ int numberOfResourcesPerPageForThisResourceType = this.getTypeOfResourcesInTheResultSet().getApiResourceCountPerIndexPage();
+ return (int)(Math.ceil((double)getTotalMatchingItemCount() / numberOfResourcesPerPageForThisResourceType));
+ }
+
+
+ /**
+ * List of matching items will be partial and populated sequentially
+ * based on user actions. Therefore, this method helps to check
+ * which list entries are still not populated.
+ *
+ * @param startIndex Beginning of the range to check.
+ * @param endIndex End of the range to check.
+ * @return Zero-based index of the first entry in the list of
+ * matching resources that hasn't been fetched yet.
+ * Will return <code>-1</code> if the provided range
+ * parameters are incorrect or if all items in the
+ * specified range are already available.
+ */
+ public int getFirstMatchingItemIndexNotYetFetched(int startIndex, int endIndex)
+ {
+ // check the specified range is correct
+ if (startIndex < 0 || endIndex > getTotalMatchingItemCount() - 1) {
+ return (-1);
+ }
+
+ // go through the search results in the specified range
+ // in an attempt to find an item that hasn't been fetched
+ // just yet
+ for (int i = startIndex; i <= endIndex; i++) {
+ ResourceLink item = this.foundItems.get(i);
+ if (item != null && item instanceof LoadingResource && !((LoadingResource)item).isLoading()) {
+ return (i);
+ }
+ }
+
+ // apparently, all items in the provided range are fetched
+ return (-1);
+ }
+
+
+
+ /**
+ * @param matchingItemIndex Index of the matching item from search results.
+ * @return Index (starting from "1") of page in the search results, where
+ * the matching item with a specified index is located. If the
+ * <code>matchingItemIndex</code> is wrong, <code>-1</code> is returned.
+ */
+ public int getMatchingItemPageNumberFor(int matchingItemIndex)
+ {
+ // check the specified index is correct
+ if (matchingItemIndex < 0 || matchingItemIndex > getTotalMatchingItemCount() - 1) {
+ return (-1);
+ }
+
+ int resultsPerPageForThisType = this.getTypeOfResourcesInTheResultSet().getApiResourceCountPerIndexPage();
+ return (matchingItemIndex / resultsPerPageForThisType + 1);
+ }
+
+
+ /**
+ * @param resultPageNumber Number of the page, for which the calculations are to be done.
+ * @return Index of the first result entry on the specified result page. If <code>resultPageNumber</code>
+ * is less than <code>1</code> or greater than the total number of pages in the result set,
+ * a value of <code>-1</code> will be returned.
+ */
+ public int getFirstItemIndexOn(int resultPageNumber)
+ {
+ // page number must be in a valid range - starting with 1..onwards
+ if (resultPageNumber < 1 || resultPageNumber > getTotalResultPageNumber()) {
+ return (-1);
+ }
+
+ int numberOfResourcesPerPageForThisResourceType = this.getTypeOfResourcesInTheResultSet().getApiResourceCountPerIndexPage();
+ return ((resultPageNumber - 1) * numberOfResourcesPerPageForThisResourceType);
+ }
+
+
+
+ /**
+ * Mainly for testing - outputs number of search results per item type.
+ */
+ public String toString()
+ {
+ // FIXME
+
+// StringBuilder out = new StringBuilder("Breakdown of item counts by type:\n");
+// for (Map.Entry<Integer,String> itemTypeNamePair : Resource.ALL_SUPPORTED_RESOURCE_COLLECTION_NAMES.entrySet()) {
+// out.append(itemTypeNamePair.getValue() + ": " +getFetchedItemCount(itemTypeNamePair.getKey()) +
+// "/" + getTotalItemCount(itemTypeNamePair.getKey()) + "\n");
+// }
+//
+// return (out.toString());
+
+ return ("search results... not implemented!!!");
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/ServiceFilteringSettings.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/ServiceFilteringSettings.java
new file mode 100644
index 0000000..76d4eca
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/search/ServiceFilteringSettings.java
@@ -0,0 +1,184 @@
+package net.sf.taverna.biocatalogue.model.search;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.tree.TreePath;
+
+import net.sf.taverna.biocatalogue.model.Util;
+import net.sf.taverna.biocatalogue.ui.filtertree.FilterTreeNode;
+import net.sf.taverna.biocatalogue.ui.tristatetree.JTriStateTree;
+
+/**
+ * This class provides functionality to deal with service filtering settings.
+ * Particularly used to save the current state of the filtering tree as a
+ * favourite filter.
+ *
+ * Instances of this class hold all necessary information to restore the
+ * filtering state at a later point.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class ServiceFilteringSettings implements Comparable<ServiceFilteringSettings>, Serializable
+{
+ private static final long serialVersionUID = -5706169924295062628L;
+
+ private String filterName;
+ private int filteringCriteriaNumber;
+ private List<TreePath> filterTreeRootsOfCheckedPaths;
+
+
+
+ /**
+ * Stores current filtering selection in the provided JTriStateTree
+ * instance into the instance of this class.
+ *
+ * @param filterTree The JTriStateTree instance to get the current selection from.
+ */
+ public ServiceFilteringSettings(JTriStateTree filterTree)
+ {
+ this(null, filterTree);
+ }
+
+
+ /**
+ * Stores current filtering selection in the provided JTriStateTree
+ * instance into the instance of this class.
+ *
+ * @param filterName The name to associate with this filter.
+ * @param filterTree The JTriStateTree instance to get the current selection from.
+ */
+ @SuppressWarnings("unchecked")
+ public ServiceFilteringSettings(String filterName, JTriStateTree filterTree)
+ {
+ this.filterName = filterName;
+
+ this.filteringCriteriaNumber = filterTree.getLeavesOfCheckedPaths().size();
+
+ // a deep copy of the data from the filter tree is created, so that the data stored in this instance
+ // is fully independent of the filter tree itself; therefore local copy of this data may be modified
+ // as needed and will not affect the main filter (and vice versa)
+ this.filterTreeRootsOfCheckedPaths = (List<TreePath>)Util.deepCopy(filterTree.getRootsOfCheckedPaths());
+ }
+
+
+ /**
+ * Analyses the filter tree and produces part of the request URL containing settings regarding filters.
+ */
+ @SuppressWarnings("unchecked")
+ public Map<String,String[]> getFilteringURLParameters()
+ {
+ // analyse filter tree to get checked elements
+ Map<String,HashSet<String>> selections = new HashMap<String,HashSet<String>>();
+
+ // cycle through the deepest selected nodes;
+ // NB! the CheckboxTree acts in a way that if A contains B,C --
+ // 1) if only B is checked, tp.getLastPathComponent() will be B;
+ // 2) if both B,C are checked, tp.getLastPathComponent() will be A;
+ for (TreePath selectedRootNodePath : getFilterTreeRootsOfCheckedPaths()) {
+ FilterTreeNode selectedNode = (FilterTreeNode)selectedRootNodePath.getLastPathComponent();
+
+ // identify affected nodes
+ HashSet<FilterTreeNode> affectedNodes = new HashSet<FilterTreeNode>();
+ if (selectedNode.isFilterCategory()) {
+ // case as in example 2) -- need to "extract" nodes that are one level deeper
+ for (Enumeration children = selectedNode.children(); children.hasMoreElements(); ) {
+ affectedNodes.add((FilterTreeNode)children.nextElement());
+ }
+ }
+ else {
+ // case as in example 1)
+ affectedNodes.add(selectedNode);
+ }
+
+ // walk through the identified collection of nodes and build the data structure with URL values
+ for (FilterTreeNode node : affectedNodes) {
+ if (selections.containsKey(node.getType())) {
+ selections.get(node.getType()).add(node.getUrlValue());
+ }
+ else {
+ HashSet<String> newSet = new HashSet<String>();
+ newSet.add(node.getUrlValue());
+
+ selections.put(node.getType(), newSet);
+ }
+ }
+ }
+
+
+ // now use the constructed set of data to build the map of filtering URL parameters
+ Map<String,String[]> filterUrlParameters = new HashMap<String,String[]>();
+ for(String key : selections.keySet())
+ {
+ List<String> categoryValues = new ArrayList<String>();
+ for (String value : selections.get(key)) {
+ categoryValues.add(value);
+ }
+
+ filterUrlParameters.put(key, categoryValues.toArray(new String[0]));
+ }
+
+ return (filterUrlParameters);
+ }
+
+
+ // *** Getters ***
+
+ public String getFilterName() {
+ return (this.filterName == null || filterName.length() == 0 ? "untitled filter" : this.filterName);
+ }
+
+ public List<TreePath> getFilterTreeRootsOfCheckedPaths() {
+ return filterTreeRootsOfCheckedPaths;
+ }
+
+ /**
+ * @return Number of filtering criteria within the current filter.
+ */
+ public int getNumberOfFilteringCriteria() {
+ return filteringCriteriaNumber;
+ }
+
+ // *** End of getters ***
+
+
+ public boolean equals(Object other)
+ {
+ if (other instanceof ServiceFilteringSettings)
+ {
+ ServiceFilteringSettings o = (ServiceFilteringSettings)other;
+ return (this.filterName.equals(o.filterName) &&
+ this.filterTreeRootsOfCheckedPaths.equals(o.filterTreeRootsOfCheckedPaths));
+ }
+ else {
+ return false;
+ }
+ }
+
+
+ public int compareTo(ServiceFilteringSettings other)
+ {
+ int iOrdering = this.filterName.compareTo(other.filterName);
+ if (iOrdering == 0) {
+ iOrdering = this.getNumberOfFilteringCriteria() - other.getNumberOfFilteringCriteria();
+ }
+
+ // inverse order, as the traversal of lists in the favourite filters panel is
+ // done this way round
+ return (-1 * iOrdering);
+ }
+
+
+ public String toString() {
+ return ("Filter: '" + getFilterName() + "' [" + detailsAsString() + "]");
+ }
+
+ public String detailsAsString() {
+ return (getNumberOfFilteringCriteria() + " filtering criteria");
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/AnnotationBean.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/AnnotationBean.java
new file mode 100644
index 0000000..81ce849
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/AnnotationBean.java
@@ -0,0 +1,52 @@
+package net.sf.taverna.biocatalogue.test;
+
+
+public class AnnotationBean
+{
+ public AnnotationBean() { }
+
+ public String self;
+ private int version;
+ private String created;
+ public Annotatable annotatable;
+ private Source source;
+ private Attribute attribute;
+ private Value value;
+
+
+ public static class Annotatable
+ {
+ private Annotatable() { }
+
+ private String name;
+ public String resource;
+ private String type;
+ }
+
+ public static class Source
+ {
+ private Source() { }
+
+ private String name;
+ private String resource;
+ private String type;
+ }
+
+ public static class Attribute
+ {
+ private Attribute() { }
+
+ private String name;
+ private String resource;
+ private String identifier;
+ }
+
+ public static class Value
+ {
+ private Value() { }
+
+ private String resource;
+ private String type;
+ private String content;
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/DrawDefaultIconTest.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/DrawDefaultIconTest.java
new file mode 100644
index 0000000..1bec9e6
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/DrawDefaultIconTest.java
@@ -0,0 +1,38 @@
+package net.sf.taverna.biocatalogue.test;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.GraphicsConfiguration;
+import java.awt.GraphicsDevice;
+import java.awt.GraphicsEnvironment;
+import java.awt.image.BufferedImage;
+
+import javax.swing.ImageIcon;
+import javax.swing.JOptionPane;
+
+public class DrawDefaultIconTest {
+
+ /**
+ * @param args
+ */
+ public static void main(String[] args)
+ {
+ int w = 16;
+ int h = 16;
+ GraphicsEnvironment ge = GraphicsEnvironment.getLocalGraphicsEnvironment();
+ GraphicsDevice gd = ge.getDefaultScreenDevice();
+ GraphicsConfiguration gc = gd.getDefaultConfiguration();
+
+ BufferedImage image = gc.createCompatibleImage(w, h, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D g = image.createGraphics();
+ g.setColor(Color.RED);
+ g.setStroke(new BasicStroke(3, BasicStroke.CAP_SQUARE, BasicStroke.JOIN_MITER));
+ g.drawLine(4, 4, 12, 12);
+ g.drawLine(12, 4, 4, 12);
+ g.dispose();
+
+ JOptionPane.showMessageDialog(null, new ImageIcon(image));
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/GSONTest.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/GSONTest.java
new file mode 100644
index 0000000..eba01d6
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/GSONTest.java
@@ -0,0 +1,19 @@
+package net.sf.taverna.biocatalogue.test;
+
+import com.google.gson.Gson;
+
+public class GSONTest
+{
+
+ public static void main(String[] args) throws Exception
+ {
+ String json = "[{\"annotatable\":{\"name\":\"IndexerService\",\"resource\":\"http://sandbox.biocatalogue.org/services/2158\",\"type\":\"Service\"},\"self\":\"http://sandbox.biocatalogue.org/annotations/47473\",\"value\":{\"resource\":\"http://sandbox.biocatalogue.org/tags/indexing\",\"type\":\"Tag\",\"content\":\"indexing\"},\"version\":1,\"created\":\"2010-01-13T09:24:04Z\",\"source\":{\"name\":\"Marco Roos\",\"resource\":\"http://sandbox.biocatalogue.org/users/48\",\"type\":\"User\"},\"attribute\":{\"name\":\"Tag\",\"resource\":\"http://sandbox.biocatalogue.org/annotation_attributes/2\",\"identifier\":\"http://www.biocatalogue.org/attribute#Category\"}}]";
+
+ Gson gson = new Gson();
+ AnnotationBean[] a = gson.fromJson(json, AnnotationBean[].class);
+
+ System.out.println("Self URL: " + a[0].self);
+ System.out.println("Annotatable resource: " + a[0].annotatable.resource);
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/GSONTest_exportingJSON.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/GSONTest_exportingJSON.java
new file mode 100644
index 0000000..6e63ebb
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/GSONTest_exportingJSON.java
@@ -0,0 +1,30 @@
+package net.sf.taverna.biocatalogue.test;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import net.sf.taverna.biocatalogue.model.connectivity.BeanForPOSTToFilteredIndex;
+
+import com.google.gson.Gson;
+
+public class GSONTest_exportingJSON
+{
+
+ /**
+ * @param args
+ */
+ public static void main(String[] args)
+ {
+ Map<String, String[]> m = new HashMap<String, String[]>();
+ m.put("a", new String[] {"b","c"});
+ m.put("d", new String[] {"e","f"});
+
+ BeanForPOSTToFilteredIndex b = new BeanForPOSTToFilteredIndex();
+ b.filters = m;
+
+ Gson gson = new Gson();
+ System.out.println(gson.toJson(b));
+
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/GSONTest_forSoapOperationsIndex.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/GSONTest_forSoapOperationsIndex.java
new file mode 100644
index 0000000..30035f7
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/GSONTest_forSoapOperationsIndex.java
@@ -0,0 +1,27 @@
+package net.sf.taverna.biocatalogue.test;
+
+import net.sf.taverna.biocatalogue.model.Resource;
+import net.sf.taverna.biocatalogue.model.connectivity.BeansForJSONLiteAPI;
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
+
+public class GSONTest_forSoapOperationsIndex
+{
+
+ /**
+ * @param args
+ * @throws Exception
+ */
+ public static void main(String[] args) throws Exception
+ {
+ BioCatalogueClient client = BioCatalogueClient.getInstance();
+
+ String url = BioCatalogueClient.API_SOAP_OPERATIONS_URL;
+// url = Util.appendURLParameter(url, "q", "blast");
+ BeansForJSONLiteAPI.ResourceIndex soapOpIndex = client.getBioCatalogueResourceLiteIndex(Resource.TYPE.SOAPOperation, url);
+
+ System.out.println("result count: " + soapOpIndex.getResources().length + "\n\n");
+// System.out.println(soapOpIndex.soap_operations[1].getName() + "\n" + soapOpIndex.soap_operations[1].getURL() + "\n\n");
+
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/JWaitDialogTest.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/JWaitDialogTest.java
new file mode 100644
index 0000000..2aed586
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/JWaitDialogTest.java
@@ -0,0 +1,36 @@
+package net.sf.taverna.biocatalogue.test;
+
+import net.sf.taverna.biocatalogue.ui.JWaitDialog;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponent;
+
+public class JWaitDialogTest
+{
+
+ public static void main(String[] args)
+ {
+ System.out.println("start test");
+
+ final JWaitDialog jwd = new JWaitDialog(MainComponent.dummyOwnerJFrame, "Old title", "Please wait... Please wait... Please wait... Please wait...");
+
+ // NB! Background process must be started before the modal dialog box
+ // is made visible - otherwise processing freezes.
+ new Thread("testing delayed update of JWaitDialog")
+ {
+ public void run()
+ {
+ // wait for some time
+ try { Thread.sleep(3000); }
+ catch (InterruptedException e) { /* do nothing */ }
+
+ // update the dialog
+ jwd.setTitle("New title");
+ jwd.waitFinished("Great, all done!");
+
+ System.out.println("end test");
+ }
+ }.start();
+
+ jwd.setVisible(true);
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/LinkedListEqualsTest.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/LinkedListEqualsTest.java
new file mode 100644
index 0000000..6f252bd
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/LinkedListEqualsTest.java
@@ -0,0 +1,25 @@
+package net.sf.taverna.biocatalogue.test;
+
+import java.util.LinkedList;
+
+public class LinkedListEqualsTest
+{
+ public static void main(String[] args)
+ {
+ LinkedList l = new LinkedList();
+
+ String a = new String("test1");
+ String b = new String("test2");
+
+ System.out.println(a == b);
+ System.out.println(a.equals(b));
+
+ l.add(a);
+ l.add(b);
+
+ System.out.println(l);
+ System.out.println(l.indexOf(a));
+ System.out.println(l.indexOf(b));
+
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/TestAPICaller.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/TestAPICaller.java
new file mode 100644
index 0000000..a48a996
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/TestAPICaller.java
@@ -0,0 +1,241 @@
+package net.sf.taverna.biocatalogue.test;
+
+import javax.swing.JFrame;
+import java.awt.Dimension;
+import javax.swing.JPanel;
+import java.awt.BorderLayout;
+import javax.swing.JTextField;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JOptionPane;
+import javax.swing.JTextPane;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
+
+import java.awt.GridBagLayout;
+import java.awt.GridBagConstraints;
+import java.awt.Insets;
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class TestAPICaller extends JFrame implements ActionListener {
+
+ private JPanel jContentPane = null;
+ private JTextField tfURL = null;
+ private JButton bSubmitRequest = null;
+ private JButton bClear = null;
+ private JScrollPane spOutputPane = null;
+ private JTextPane tpOutputPane = null;
+
+ /**
+ * This method initializes
+ *
+ */
+ public TestAPICaller() {
+ super();
+ initialize();
+ }
+
+ /**
+ * This method initializes this
+ *
+ */
+ private void initialize() {
+ this.setSize(new Dimension(515, 321));
+ this.setTitle("Test Service Catalogue API Caller");
+ this.setContentPane(getJContentPane());
+
+ this.bSubmitRequest.setDefaultCapable(true);
+ this.getRootPane().setDefaultButton(bSubmitRequest);
+ }
+
+ /**
+ * This method initializes jContentPane
+ *
+ * @return javax.swing.JPanel
+ */
+ private JPanel getJContentPane() {
+ if (jContentPane == null) {
+ GridBagConstraints gridBagConstraints3 = new GridBagConstraints();
+ gridBagConstraints3.fill = GridBagConstraints.BOTH;
+ gridBagConstraints3.gridwidth = 2;
+ gridBagConstraints3.gridx = 0;
+ gridBagConstraints3.gridy = 2;
+ gridBagConstraints3.ipadx = 459;
+ gridBagConstraints3.ipady = 182;
+ gridBagConstraints3.weightx = 1.0;
+ gridBagConstraints3.weighty = 1.0;
+ gridBagConstraints3.insets = new Insets(4, 12, 9, 12);
+ GridBagConstraints gridBagConstraints2 = new GridBagConstraints();
+ gridBagConstraints2.fill = GridBagConstraints.HORIZONTAL;
+ gridBagConstraints2.gridy = 1;
+ gridBagConstraints2.ipadx = 0;
+ gridBagConstraints2.ipady = 0;
+ gridBagConstraints2.insets = new Insets(0, 5, 7, 12);
+ gridBagConstraints2.weightx = 0.5;
+ gridBagConstraints2.gridx = 1;
+ GridBagConstraints gridBagConstraints1 = new GridBagConstraints();
+ gridBagConstraints1.fill = GridBagConstraints.HORIZONTAL;
+ gridBagConstraints1.gridy = 1;
+ gridBagConstraints1.ipadx = 0;
+ gridBagConstraints1.ipady = 0;
+ gridBagConstraints1.insets = new Insets(0, 12, 7, 5);
+ gridBagConstraints1.weightx = 0.5;
+ gridBagConstraints1.gridx = 0;
+ GridBagConstraints gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.fill = GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.ipadx = 466;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.ipady = 3;
+ gridBagConstraints.insets = new Insets(13, 12, 8, 12);
+ jContentPane = new JPanel();
+ jContentPane.setLayout(new GridBagLayout());
+ jContentPane.add(getTfURL(), gridBagConstraints);
+ jContentPane.add(getBSubmitRequest(), gridBagConstraints1);
+ jContentPane.add(getBClear(), gridBagConstraints2);
+ jContentPane.add(getSpOutputPane(), gridBagConstraints3);
+ }
+ return jContentPane;
+ }
+
+ /**
+ * This method initializes tfURL
+ *
+ * @return javax.swing.JTextField
+ */
+ private JTextField getTfURL() {
+ if (tfURL == null) {
+ tfURL = new JTextField();
+ tfURL.setText(BioCatalogueClient.DEFAULT_API_SANDBOX_BASE_URL);
+ }
+ return tfURL;
+ }
+
+ /**
+ * This method initializes tfSubmitRequest
+ *
+ * @return javax.swing.JButton
+ */
+ private JButton getBSubmitRequest() {
+ if (bSubmitRequest == null) {
+ bSubmitRequest = new JButton();
+ bSubmitRequest.setText("Submit Request");
+ bSubmitRequest.addActionListener(this);
+ }
+ return bSubmitRequest;
+ }
+
+
+ /**
+ * This method initializes bClear
+ *
+ * @return javax.swing.JButton
+ */
+ private JButton getBClear() {
+ if (bClear == null) {
+ bClear = new JButton();
+ bClear.setText("Clear Output");
+ bClear.addActionListener(this);
+ }
+ return bClear;
+ }
+
+
+ /**
+ * This method initializes tpOutputPane
+ *
+ * @return javax.swing.JTextPane
+ */
+ private JTextPane getTpOutputPane() {
+ if (tpOutputPane == null) {
+ tpOutputPane = new JTextPane();
+ tpOutputPane.setContentType("text/plain");
+ }
+ return tpOutputPane;
+ }
+
+
+ /**
+ * This method initializes spOutputPane
+ *
+ * @return javax.swing.JScrollPane
+ */
+ private JScrollPane getSpOutputPane() {
+ if (spOutputPane == null) {
+ spOutputPane = new JScrollPane();
+ spOutputPane.setViewportView(getTpOutputPane());
+ }
+ return spOutputPane;
+ }
+
+
+ // ACTION LISTENER
+
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource().equals(bSubmitRequest)) {
+ tfURL.selectAll();
+
+ // call the actual test method
+ runBioCatalogueAPITest(tfURL.getText());
+ }
+ else if (e.getSource().equals(bClear)) {
+ this.tpOutputPane.setText("");
+ }
+
+ }
+
+
+ // ACTUAL TEST CLASS
+
+ private void runBioCatalogueAPITest(String url) {
+ final String urlFinal = url;
+ new Thread("making request") {
+ public void run() {
+ tpOutputPane.setText("Initialising Service Catalogue client...");
+ BioCatalogueClient client = null;
+ try {
+ client = BioCatalogueClient.getInstance();
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ final StringBuilder text = new StringBuilder();
+ try {
+ tpOutputPane.setText("Sending request...");
+ BufferedReader br = new BufferedReader(new InputStreamReader(client.doBioCatalogueGET(urlFinal).getResponseStream()));
+ String str = "";
+
+ while ((str = br.readLine()) != null) {
+ text.append(str + "\n");
+ }
+
+ br.close();
+ }
+ catch (Exception e) {
+ text.append(e);
+ }
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ tpOutputPane.setText(text.toString());
+ }
+ });
+ }
+ }.start();
+
+ }
+
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/TestDoubleUsageOfSameSwingElement.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/TestDoubleUsageOfSameSwingElement.java
new file mode 100644
index 0000000..e5ad39c
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/TestDoubleUsageOfSameSwingElement.java
@@ -0,0 +1,32 @@
+package net.sf.taverna.biocatalogue.test;
+
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JFrame;
+
+public class TestDoubleUsageOfSameSwingElement extends JFrame
+{
+ private String text = "abc";
+ boolean bLowerCase = true;
+
+ public TestDoubleUsageOfSameSwingElement()
+ {
+ final JButton bBtn = new JButton(text);
+ bBtn.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ bLowerCase = !bLowerCase;
+ bBtn.setText(bLowerCase ? text.toLowerCase() : text.toUpperCase());
+ }
+ });
+
+ this.setLayout(new BorderLayout());
+ this.add(bBtn, BorderLayout.WEST);
+ this.add(bBtn, BorderLayout.EAST);
+
+ this.pack();
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/TestUtilURLHandling.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/TestUtilURLHandling.java
new file mode 100644
index 0000000..71a6ca7
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/TestUtilURLHandling.java
@@ -0,0 +1,87 @@
+package net.sf.taverna.biocatalogue.test;
+
+import net.sf.taverna.biocatalogue.model.Util;
+
+public class TestUtilURLHandling
+{
+ public static void main(String[] args)
+ {
+ String url1 = "http://sandbox.biocatalogue.org/search";
+ String url2 = "http://sandbox.biocatalogue.org/search?";
+ String url3 = "http://sandbox.biocatalogue.org/search?q=";
+ String url4 = "http://sandbox.biocatalogue.org/search?q=franck";
+ String url5 = "http://sandbox.biocatalogue.org/services?tag=%5Bbiology%5D";
+ String url6 = "http://sandbox.biocatalogue.org/services?tag=%5B%3Chttp%3A%2F%2Fwww.mygrid.org.uk%2Fontology%23DDBJ%3E%5D";
+
+
+ System.out.println("----------------------------");
+ System.out.println("Extracting URL parameters:\n");
+
+
+ System.out.println(url1 + "\nParameter map:\n" + Util.extractURLParameters(url1));
+ System.out.println("Reconstructed query string from parameter map: " + Util.constructURLQueryString(Util.extractURLParameters(url1)) + "\n");
+
+
+ System.out.println(url2 + "\nParameter map:\n" + Util.extractURLParameters(url2));
+ System.out.println("Reconstructed query string from parameter map: " + Util.constructURLQueryString(Util.extractURLParameters(url2)) + "\n");
+
+
+ System.out.println(url3 + "\nParameter map:\n" + Util.extractURLParameters(url3));
+ System.out.println("Reconstructed query string from parameter map: " + Util.constructURLQueryString(Util.extractURLParameters(url3)) + "\n");
+
+
+ System.out.println(url4 + "\nParameter map:\n" + Util.extractURLParameters(url4));
+ System.out.println("Reconstructed query string from parameter map: " + Util.constructURLQueryString(Util.extractURLParameters(url4)) + "\n");
+
+
+ System.out.println(url5 + "\nParameter map:\n" + Util.extractURLParameters(url5));
+ System.out.println("Reconstructed query string from parameter map: " + Util.constructURLQueryString(Util.extractURLParameters(url5)) + "\n");
+
+
+ System.out.println("\n\n----------------------------");
+ System.out.println("Adding parameters:\n");
+
+ String newUrl = Util.appendURLParameter(url1, "testParam", "testValue");
+ System.out.println(url1 + "\n" + newUrl + "\n");
+
+ newUrl = Util.appendURLParameter(url2, "testParam", "testValue");
+ System.out.println(url2 + "\n" + newUrl + "\n");
+
+ newUrl = Util.appendURLParameter(url3, "testParam", "testValue");
+ System.out.println(url3 + "\n" + newUrl + "\n");
+
+ newUrl = Util.appendURLParameter(url4, "testParam", "testValue");
+ System.out.println(url4 + "\n" + newUrl + "\n");
+
+ newUrl = Util.appendURLParameter(url5, "testParam", "testValue");
+ System.out.println(url5 + "\n" + newUrl + "\n");
+
+
+ System.out.println("\n\n----------------------------");
+ System.out.println("Getting parameter values:\n");
+
+ System.out.println("Value of '" + "testParam" + "' in the URL: " + url1 + " -- " + Util.extractURLParameter(url1, "testParam"));
+ System.out.println("Value of '" + "testParam" + "' in the URL: " + url2 + " -- " + Util.extractURLParameter(url2, "testParam"));
+ System.out.println("Value of '" + "q" + "' in the URL: " + url3 + " -- " + Util.extractURLParameter(url3, "q"));
+ System.out.println("Value of '" + "q" + "' in the URL: " + url4 + " -- " + Util.extractURLParameter(url4, "q"));
+ System.out.println("Value of '" + "tag" + "' in the URL: " + url5 + " -- " + Util.extractURLParameter(url5, "tag"));
+
+
+ System.out.println("\n\n----------------------------");
+ System.out.println("URL decoding:\n");
+
+ System.out.println("Original URL: " + url6 + "\nDecoded URL: " + Util.urlDecodeQuery(url6));
+
+
+ System.out.println("\n\n----------------------------");
+ System.out.println("Appending a string before URL parameters:\n");
+
+ String strToAppend = ".xml";
+ System.out.println("Appending '" + strToAppend + "' in the URL: " + url1 + " -- " + Util.appendStringBeforeParametersOfURL(url1, strToAppend));
+ System.out.println("Appending '" + strToAppend + "' in the URL: " + url2 + " -- " + Util.appendStringBeforeParametersOfURL(url2, strToAppend));
+ System.out.println("Appending '" + strToAppend + "' in the URL: " + url3 + " -- " + Util.appendStringBeforeParametersOfURL(url3, strToAppend));
+ System.out.println("Appending '" + strToAppend + "' in the URL: " + url4 + " -- " + Util.appendStringBeforeParametersOfURL(url4, strToAppend));
+ System.out.println("Appending '" + strToAppend + "' in the URL: " + url5 + " -- " + Util.appendStringBeforeParametersOfURL(url5, strToAppend));
+ System.out.println("Appending '" + strToAppend + "' in the URL: " + url6 + " -- " + Util.appendStringBeforeParametersOfURL(url6, strToAppend));
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/TestXHTMLRenderer.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/TestXHTMLRenderer.java
new file mode 100644
index 0000000..a50254e
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/TestXHTMLRenderer.java
@@ -0,0 +1,42 @@
+package net.sf.taverna.biocatalogue.test;
+
+import java.awt.Container;
+import java.io.File;
+
+import javax.swing.JFrame;
+
+import org.xhtmlrenderer.simple.FSScrollPane;
+import org.xhtmlrenderer.simple.XHTMLPanel;
+
+public class TestXHTMLRenderer extends JFrame {
+ public TestXHTMLRenderer() {
+ try {
+ init();
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ public void init() throws Exception {
+ Container contentPane = this.getContentPane();
+
+ XHTMLPanel panel = new XHTMLPanel();
+ panel.getSharedContext().getTextRenderer().setSmoothingThreshold(0); // Anti-aliasing for all font sizes
+ panel.setDocument(new File("c:\\Temp\\MyExperiment\\T2 BioCatalogue Plugin\\BioCatalogue Plugin\\resources\\test.html"));
+
+ FSScrollPane scroll = new FSScrollPane(panel);
+ contentPane.add(scroll);
+
+ this.setTitle("XHTML rendered test");
+ this.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ this.pack();
+ this.setSize(1024, 768);
+ }
+
+
+ public static void main(String[] args) {
+ JFrame f = new TestXHTMLRenderer();
+ f.setVisible(true);
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/WrappableJLabelTest.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/WrappableJLabelTest.java
new file mode 100644
index 0000000..22afbd4
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/WrappableJLabelTest.java
@@ -0,0 +1,35 @@
+package net.sf.taverna.biocatalogue.test;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+public class WrappableJLabelTest extends JFrame
+{
+ public WrappableJLabelTest() {
+
+ // depending on the LayoutManager of the container, JLabel may
+ // be resized or simply "cut off" on the edges - e.g. FlowLayout
+ // cuts it off, BorderLayout does the resizing
+ JPanel jpTestPanel = new JPanel(new BorderLayout());
+ jpTestPanel.add(new JLabel("<html><span color=\"red\">a very long</span> text that <b>is just</b> " +
+ "showing how the whole thing looks - will it wrap text or not; this " +
+ "is the question</html>"), BorderLayout.CENTER);
+
+ this.getContentPane().add(jpTestPanel);
+
+ this.pack();
+ }
+
+ public static void main(String[] args)
+ {
+ WrappableJLabelTest f = new WrappableJLabelTest();
+ f.setLocationRelativeTo(null);
+ f.setPreferredSize(new Dimension(400, 300));
+ f.setVisible(true);
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/XStreamTest.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/XStreamTest.java
new file mode 100644
index 0000000..edc1d5a
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/test/XStreamTest.java
@@ -0,0 +1,32 @@
+package net.sf.taverna.biocatalogue.test;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import com.thoughtworks.xstream.XStream;
+import com.thoughtworks.xstream.io.xml.DomDriver;
+
+import net.sf.taverna.biocatalogue.model.SoapOperationIdentity;
+
+
+public class XStreamTest
+{
+
+ public static void main(String[] args)
+ {
+ List<SoapOperationIdentity> processors = new ArrayList<SoapOperationIdentity>();
+ processors.add(new SoapOperationIdentity("http://www.test.com/test.wsdl", "aa", null));
+ processors.add(new SoapOperationIdentity("http://www.example.com/example.wsdl", "bb", null));
+
+ XStream xstream = new XStream(new DomDriver());
+ String xml = xstream.toXML(processors);
+
+ System.out.println(xml);
+
+ List<SoapOperationIdentity> processorsFromXML = (List<SoapOperationIdentity>)xstream.fromXML(xml);
+ System.out.println("\n\n");
+ System.out.println(processorsFromXML.get(0).getWsdlLocation() + " - " + processorsFromXML.get(0).getOperationName());
+ System.out.println(processorsFromXML.get(1).getWsdlLocation() + " - " + processorsFromXML.get(1).getOperationName());
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/BioCatalogueExplorationTab.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/BioCatalogueExplorationTab.java
new file mode 100644
index 0000000..d3f452d
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/BioCatalogueExplorationTab.java
@@ -0,0 +1,131 @@
+package net.sf.taverna.biocatalogue.ui;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+
+import javax.swing.BorderFactory;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.LayoutFocusTraversalPolicy;
+
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
+import net.sf.taverna.biocatalogue.ui.search_results.SearchResultsMainPanel;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponent;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentFactory;
+
+import org.apache.log4j.Logger;
+
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public class BioCatalogueExplorationTab extends JPanel implements HasDefaultFocusCapability
+{
+ private final MainComponent pluginPerspectiveMainComponent;
+ private final BioCatalogueClient client;
+ private final Logger logger;
+
+
+ // COMPONENTS
+ private BioCatalogueExplorationTab thisPanel;
+
+ private SearchOptionsPanel searchOptionsPanel;
+ private SearchResultsMainPanel tabbedSearchResultsPanel;
+
+
+ public BioCatalogueExplorationTab()
+ {
+ this.thisPanel = this;
+
+ this.pluginPerspectiveMainComponent = MainComponentFactory.getSharedInstance();
+ this.client = BioCatalogueClient.getInstance();
+ this.logger = Logger.getLogger(this.getClass());
+
+ initialiseUI();
+
+ // this is to make sure that search will get focused when this tab is opened
+ // -- is a workaround to a bug in JVM
+ setFocusCycleRoot(true);
+ setFocusTraversalPolicy(new LayoutFocusTraversalPolicy() {
+ public Component getDefaultComponent(Container cont) {
+ return (thisPanel.getDefaultComponent());
+ }
+ });
+ }
+
+
+ private void initialiseUI()
+ {
+ this.tabbedSearchResultsPanel = new SearchResultsMainPanel();
+ this.searchOptionsPanel = new SearchOptionsPanel(tabbedSearchResultsPanel);
+
+
+ this.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.weightx = 0.0;
+ c.anchor = GridBagConstraints.WEST;
+ c.insets = new Insets(3,10,3,10);
+ String baseString= "<html><b>Using service catalogue at </b>" + client.getBaseURL() + "</html>";
+ this.add(new JLabel(baseString), c);
+
+
+ c.gridx = 1;
+ c.gridy = 0;
+ c.weightx = 0.1;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.anchor = GridBagConstraints.EAST;
+ c.insets = new Insets(3,30,3,10);
+
+ this.add(searchOptionsPanel, c);
+
+ c.insets = new Insets(0,0,0,0);
+ c.gridy++;
+ c.gridx = 0;
+ c.gridwidth = 2;
+ c.weightx = c.weighty = 1.0;
+ c.fill = GridBagConstraints.BOTH;
+ c.anchor = GridBagConstraints.CENTER;
+ this.add(tabbedSearchResultsPanel, c);
+
+ this.setBorder(BorderFactory.createEmptyBorder(20, 10, 10, 10));
+ }
+
+
+ public SearchResultsMainPanel getTabbedSearchResultsPanel() {
+ return tabbedSearchResultsPanel;
+ }
+
+
+
+ // *** Callbacks for HasDefaultFocusCapability interface ***
+
+ public void focusDefaultComponent() {
+ this.searchOptionsPanel.focusDefaultComponent();
+ }
+
+ public Component getDefaultComponent() {
+ return (this.searchOptionsPanel.getDefaultComponent());
+ }
+
+ // *********************************************************
+
+
+ public static void main(String[] args) {
+ JFrame f = new JFrame();
+ f.getContentPane().add(new BioCatalogueExplorationTab());
+ f.setSize(1000, 800);
+ f.setLocationRelativeTo(null);
+
+ f.setVisible(true);
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/HasDefaultFocusCapability.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/HasDefaultFocusCapability.java
new file mode 100644
index 0000000..d8915d5
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/HasDefaultFocusCapability.java
@@ -0,0 +1,15 @@
+package net.sf.taverna.biocatalogue.ui;
+
+import java.awt.Component;
+
+/**
+ * Indicates that the class which implements this interface will focus default
+ * component (as if the component represented by that class was activated).
+ *
+ * @author Sergejs Aleksejevs
+ */
+public interface HasDefaultFocusCapability
+{
+ public void focusDefaultComponent();
+ public Component getDefaultComponent();
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/JClickableLabel.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/JClickableLabel.java
new file mode 100644
index 0000000..0cc9246
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/JClickableLabel.java
@@ -0,0 +1,172 @@
+package net.sf.taverna.biocatalogue.ui;
+
+import java.awt.Color;
+import java.awt.Cursor;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.util.EventListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.Icon;
+import javax.swing.JLabel;
+import javax.swing.SwingUtilities;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public class JClickableLabel extends JLabel implements MouseListener
+{
+ /**
+ * Default height of the JClickableLabel - calculated based on 16-pixel
+ * standard square icon and 3-pixel thick padding on top / bottom of element.
+ */
+ public static final int DEFAULT_HEIGHT = 22;
+
+ public static final Color DEFAULT_REGULAR_FOREGROUND_COLOR = Color.BLUE;
+ public static final Color DEFAULT_HOVER_FOREGROUND_COLOR = new Color(133, 53, 53);
+
+
+ // This will hold the data which is relevant to processing the 'click' event on this label
+ private final String strData;
+
+ // This will hold a reference to ResourcePreviewBrowser instance that is supposed to process the clicks
+ // on JClickableLabels
+ private ActionListener clickHandler;
+
+
+ private Color REGULAR_FOREGROUND_COLOR = DEFAULT_REGULAR_FOREGROUND_COLOR;
+ private Color HOVER_FOREGROUND_COLOR = DEFAULT_HOVER_FOREGROUND_COLOR;
+
+
+ public JClickableLabel(String strLabel, String strDataForAction, EventListener eventHandler)
+ {
+ this(strLabel, strDataForAction, eventHandler, null);
+ }
+
+ public JClickableLabel(String strLabel, String strDataForAction, EventListener eventHandler, Icon icon)
+ {
+ this(strLabel, strDataForAction, eventHandler, icon, SwingUtilities.LEFT);
+ }
+
+ public JClickableLabel(String strLabel, String strDataForAction, EventListener eventHandler, Icon icon, int horizontalAlignment)
+ {
+ this(strLabel, strDataForAction, eventHandler, icon, horizontalAlignment, null);
+ }
+
+ /**
+ *
+ * @param strLabel Textual label that will be visible in the UI.
+ * @param strDataForAction Data that will be passed to eventHandler when click on the label is made.
+ * @param eventHandler ActionListener that will process clicks on this label.
+ * @param icon Icon to display in the label.
+ * @param horizontalAlignment This is one of SwingConstants: LEFT, CENTER, RIGHT, LEADING or TRAILING
+ * @param strTooltip Tooltip to show over the label - if none is provided (e.g. null value), the strLabel will be used as a tooltip.
+ */
+ public JClickableLabel(String strLabel, String strDataForAction, EventListener eventHandler, Icon icon, int horizontalAlignment, String strTooltip)
+ {
+ super(strLabel, icon, horizontalAlignment);
+
+ this.strData = strDataForAction;
+ this.clickHandler = (ActionListener)eventHandler;
+
+ // empty border at the top and bottom will simulate "line-spacing"
+ // (this is only needed when an icon is displayed)
+ if (icon != null) {
+ this.setBorder(BorderFactory.createEmptyBorder(3, 0, 3, 0));
+ }
+
+ // the tooltip for now only shows the full label text
+ this.setToolTipText(strTooltip == null ? strLabel : strTooltip);
+ this.setForeground(REGULAR_FOREGROUND_COLOR);
+ this.addMouseListener(this);
+ }
+
+
+ public void setRegularForegroundColor(Color regularForegroundColor)
+ {
+ REGULAR_FOREGROUND_COLOR = regularForegroundColor;
+
+ // apply the new foreground color immediately
+ this.setForeground(REGULAR_FOREGROUND_COLOR);
+ }
+
+ public Color getRegularForegroundColor() {
+ return REGULAR_FOREGROUND_COLOR;
+ }
+
+
+ public void setHoverForegroundColor(Color hoverForegroundColor)
+ {
+ // will be applied the next time mouse hovers over this label
+ HOVER_FOREGROUND_COLOR = hoverForegroundColor;
+ }
+
+ public Color getHoverForegroundColor() {
+ return HOVER_FOREGROUND_COLOR;
+ }
+
+
+ /**
+ * @return The "hidden" string value that is normally sent as an <code>ActionCommand</code>
+ * within <code>ActionEvent</code> when JClickableLabel is clicked.
+ */
+ public String getData() {
+ return (this.strData);
+ }
+
+
+ /**
+ * @return String value of the label that this JClickableLabel would have in the UI.
+ */
+ public String toString() {
+ return (this.getText());
+ }
+
+
+ /* This class extends JLabel, so it can't extend MouseAdapter;
+ * therefore, empty methods will be added for not useful callbacks
+ * from the MouseListener interface.
+ */
+ public void mouseClicked(MouseEvent e)
+ {
+ // call 'actionPerformed' method on the clickHandler instance that was supplied
+ // on creation of the JClickableLabel instance
+ this.clickHandler.actionPerformed(new ActionEvent(this, e.getID(), this.strData));
+ }
+
+ public void mouseEntered(MouseEvent e)
+ {
+ this.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR)) ;
+ this.setForeground(HOVER_FOREGROUND_COLOR);
+ }
+
+ public void mouseExited(MouseEvent e)
+ {
+ this.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)) ;
+ this.setForeground(REGULAR_FOREGROUND_COLOR);
+ }
+
+ public void mousePressed(MouseEvent e)
+ {
+ // do nothing
+ }
+
+ public void mouseReleased(MouseEvent e)
+ {
+ // do nothing
+ }
+
+
+ /**
+ * @return A dummy instance of JClickable label - only intended to
+ * represent an object of this class; doesn't have a click handler,
+ * so a click on it will result in a <code>NullPointerException</code>.
+ */
+ public static JClickableLabel getDummyInstance() {
+ return (new JClickableLabel("dummy", "", null));
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/JWaitDialog.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/JWaitDialog.java
new file mode 100644
index 0000000..526066b
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/JWaitDialog.java
@@ -0,0 +1,234 @@
+package net.sf.taverna.biocatalogue.ui;
+
+import java.awt.BorderLayout;
+//import java.awt.Dimension;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.util.Timer;
+import java.util.TimerTask;
+
+import javax.swing.BorderFactory;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.UIManager;
+
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.t2.workbench.MainWindow;
+
+/**
+ * Creates a modal non-resizable dialog window.
+ *
+ * Intended to be used for operations that consume some
+ * time, but the user must wait for them to complete before
+ * proceeding.
+ *
+ * Initially the dialog shows a specified string message or
+ * component and a "loader" bar - dynamic GIF image that
+ * displays "activity" going on. At this stage the window
+ * cannot be closed.
+ *
+ * When the operation completes, the caller notifies the dialog
+ * that it has finished, provides a new message / component to
+ * display and allows the dialog to be closed.
+ *
+ * If the operation doesn't complete within the specified time,
+ * a timeout occurs and the dialog windows lets to close itself.
+ *
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public class JWaitDialog extends JDialog
+{
+ private static final int DEFAULT_TIMEOUT = 10000;
+ private static final ImageIcon LOADER_ICON = ResourceManager.getImageIcon(ResourceManager.BAR_LOADER_ORANGE);
+
+ private JPanel jpInformationPanel;
+ private JLabel jlLoaderIcon;
+
+ private JButton bOK;
+ private JPanel jpOKButton;
+
+ private Timer timeoutTimer;
+ private boolean hasTimedOut;
+
+
+ /**
+ * Creates a new Wait Dialog with no parent and default timeout on
+ * operation - <code>JWaitDialog.DEFAULT_TIMEOUT</code>.
+ *
+ * @param dialogTitle Title to set for the dialog window.
+ * @param waitMessage Text to be displayed in the body of this dialog while
+ * the user waits.
+ */
+ public JWaitDialog(String dialogTitle, String waitMessage) {
+ this(null, dialogTitle, new JLabel(waitMessage, JLabel.CENTER), DEFAULT_TIMEOUT);
+ }
+
+
+ /**
+ * Creates a new Wait Dialog with specified parent and default timeout on
+ * operation - <code>JWaitDialog.DEFAULT_TIMEOUT</code>.
+ *
+ * @param owner Specified JFrame is set as an owner for this Wait Dialog.
+ * @param dialogTitle Title to set for the dialog window.
+ * @param waitMessage Text to be displayed in the body of this dialog while
+ * the user waits.
+ */
+ public JWaitDialog(JFrame owner, String dialogTitle, String waitMessage) {
+ this(owner, dialogTitle, new JLabel(waitMessage, JLabel.CENTER), DEFAULT_TIMEOUT);
+ }
+
+
+ /**
+ * Creates a new Wait Dialog with specified parent and timeout on
+ * operation.
+ *
+ * @param owner Specified JFrame is set as an owner for this Wait Dialog.
+ * @param dialogTitle Title to set for the dialog window.
+ * @param waitMessage Text to be displayed in the body of this dialog while
+ * the user waits.
+ * @param timeoutMillis Duration of the timeout on the operation - after this
+ * time has passed the window will notify of the timeout
+ * and allow to close itself. Value of 0 indicates that the timeout will never occur.
+ */
+ public JWaitDialog(JFrame owner, String dialogTitle, String waitMessage, int timeoutMillis) {
+ this(owner, dialogTitle, new JLabel(waitMessage, JLabel.CENTER), timeoutMillis);
+ }
+
+
+ /**
+ * Creates a new Wait Dialog with parent JFrame.
+ *
+ * @param owner Specified JFrame is set as an owner for this Wait Dialog.
+ * @param dialogTitle Title to set for the dialog window.
+ * @param waitInformationComponent Component to be shown in the body of this
+ * dialog windows while the user waits for an operation to complete.
+ * @param timeoutMillis Duration of the timeout on the operation - after this
+ * time has passed the window will notify of the timeout
+ * and allow to close itself. Value of 0 indicates that the timeout will never occur.
+ */
+ public JWaitDialog(JFrame owner, String dialogTitle, JComponent waitInformationComponent, int timeoutMillis)
+ {
+ super(owner);
+ this.setModal(true);
+ this.setTitle(dialogTitle);
+
+ // this will show the wait message to the user
+ jpInformationPanel = new JPanel(new GridLayout());
+ jpInformationPanel.add(waitInformationComponent);
+ jpInformationPanel.setBorder(BorderFactory.createEmptyBorder(20, 20, 10, 20));
+
+ // some graphical indication that the loading activity is going on
+ jlLoaderIcon = new JLabel(LOADER_ICON);
+ jlLoaderIcon.setBorder(BorderFactory.createEmptyBorder(0, 20, 20, 20));
+
+ // put components into the dialog box
+ this.getContentPane().setLayout(new BorderLayout());
+ this.getContentPane().add(jpInformationPanel, BorderLayout.CENTER);
+ this.getContentPane().add(jlLoaderIcon, BorderLayout.SOUTH);
+
+ this.pack();
+ // Set the height of the dialog not to be more than 500; the message is in the scroll pane so that should be OK
+ this.setSize(new Dimension(this.getPreferredSize().width, this.getPreferredSize().height > 500 ? 500 : this.getPreferredSize().height));
+ // this.setResizable(false);
+ this.setDefaultCloseOperation(JDialog.DO_NOTHING_ON_CLOSE);
+
+ // center this window within the main Taverna Workbench window
+ this.setLocationRelativeTo(MainWindow.getMainWindow());
+
+
+ // start the timer - on timeout it will produce the
+ // timeout message and allow to close the window
+ hasTimedOut = false;
+ if (timeoutMillis > 0)
+ {
+ timeoutTimer = new Timer();
+ timeoutTimer.schedule(
+ new TimerTask() {
+ public void run() {
+ waitFinished(new JLabel("<html><center>The operation did not complete within the " +
+ "allocated time.</center></html>",
+ UIManager.getIcon("OptionPane.warningIcon"), JLabel.CENTER));
+ hasTimedOut = true;
+ }
+ },
+ timeoutMillis);
+ }
+ }
+
+
+ public void waitFinished(String resultMessage) {
+ waitFinished(new JLabel(resultMessage, JLabel.CENTER));
+ }
+
+ public void waitFinished(JComponent resultInformationComponent)
+ {
+ // this prevents the real response to be set after the
+ // timeout message was already displayed
+ if (!hasTimedOut)
+ {
+ // first of all stop the timeout timer: if this
+ // method was called by the application explicitly, not on
+ // timeout, we don't want the timeout message to appear after that
+ if (timeoutTimer != null) { timeoutTimer.cancel(); }
+
+ // change the information component
+ jpInformationPanel.removeAll();
+ jpInformationPanel.add(resultInformationComponent);
+
+ // the OK button will allow closing the window
+ bOK = new JButton("OK");
+ //bOK.setPreferredSize(new Dimension(LOADER_ICON.getIconWidth(), (int) (1.5 * LOADER_ICON.getIconHeight())));
+ bOK.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ // just remove the window
+ dispose();
+ }
+ });
+ bOK.addKeyListener(new KeyAdapter() {
+ public void keyPressed(KeyEvent e) {
+ if (e.getKeyCode() == KeyEvent.VK_ENTER) {
+ // a fallback mechanism - default button doesn't work for some reason
+ // when the button is added into the dialog not in the constructor
+ bOK.doClick();
+ }
+ }
+ });
+ bOK.setDefaultCapable(true);
+ this.getRootPane().setDefaultButton(bOK);
+
+ // wrap OK button into a panel to add empty borders
+ jpOKButton = new JPanel(new FlowLayout(FlowLayout.CENTER, 0, 0));
+ jpOKButton.add(bOK);
+ jpOKButton.setBorder(BorderFactory.createEmptyBorder(0, 20, 20 - (bOK.getPreferredSize().height - LOADER_ICON.getIconHeight()), 20));
+
+
+ // add OK button instead of the loader icon
+ this.getContentPane().remove(jlLoaderIcon);
+ this.getContentPane().add(jpOKButton, BorderLayout.SOUTH);
+ this.bOK.requestFocusInWindow();
+
+ // re-enable (X) button in the title bar
+ this.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+
+ // update the size of this window - as the inner sizes of components have
+ // been likely to change; then center the dialog box within its parent
+ this.pack();
+ // Set the height of the dialog not to be more than 500; the message is in the scroll pane so that should be OK
+ this.setSize(new Dimension(this.getPreferredSize().width, this.getPreferredSize().height > 500 ? 500 : this.getPreferredSize().height));
+ this.setLocationRelativeTo(MainWindow.getMainWindow());
+ }
+ }
+
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/SearchOptionsPanel.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/SearchOptionsPanel.java
new file mode 100644
index 0000000..b0d9d26
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/SearchOptionsPanel.java
@@ -0,0 +1,167 @@
+package net.sf.taverna.biocatalogue.ui;
+
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.util.Arrays;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.event.CaretEvent;
+import javax.swing.event.CaretListener;
+
+import net.sf.taverna.biocatalogue.model.BioCataloguePluginConstants;
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.biocatalogue.model.Resource.TYPE;
+import net.sf.taverna.biocatalogue.model.search.SearchOptions;
+import net.sf.taverna.biocatalogue.ui.search_results.SearchResultsMainPanel;
+import net.sf.taverna.t2.lang.ui.DeselectingButton;
+
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public class SearchOptionsPanel extends JPanel implements HasDefaultFocusCapability
+{
+ // COMPONENTS
+ private SearchOptionsPanel thisPanel;
+
+private JTextField tfSearchQuery;
+ private JButton bSearch;
+
+ private final SearchResultsMainPanel tabbedSearchResultsPanel;
+
+
+ public SearchOptionsPanel(SearchResultsMainPanel tabbedSearchResultsPanel)
+ {
+ super();
+ this.thisPanel = this;
+ this.tabbedSearchResultsPanel = tabbedSearchResultsPanel;
+
+ this.initialiseUI();
+ }
+
+
+ private void initialiseUI()
+ {
+ this.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.weightx = 0.0;
+ c.fill = GridBagConstraints.NONE;
+
+
+ this.tfSearchQuery = new JTextField(30);
+ this.tfSearchQuery.setToolTipText(
+ "<html> Tips for creating search queries:<br>" +
+ " 1) Use wildcards to make more flexible queries. Asterisk (<b>*</b>) matches any zero or more<br>" +
+ " characters (e.g. <b><i>Seq*</i></b> would match <b><i>Sequence</i></b>), question mark (<b>?</b>) matches any single<br>" +
+ " character (e.g. <b><i>Bla?t</i></b> would match <b><i>Blast</i></b>).<br>" +
+ " 2) Enclose the <b><i>\"search query\"</i></b> in double quotes to make exact phrase matching, otherwise<br>" +
+ " items that contain any (or all) words in the <b><i>search query</i></b> will be found.</html>");
+
+ this.tfSearchQuery.addFocusListener(new FocusListener() {
+ public void focusGained(FocusEvent e) {
+ tfSearchQuery.selectAll();
+ }
+ public void focusLost(FocusEvent e) { /* do nothing */ }
+ });
+ this.tfSearchQuery.addKeyListener(new KeyAdapter() {
+ public void keyPressed(KeyEvent e) {
+ // ENTER pressed - start search by simulating "search" button click
+ // (only do this if the "search" button was active at that moment)
+ if (e.getKeyCode() == KeyEvent.VK_ENTER && bSearch.isEnabled()) {
+ bSearch.doClick();
+ }
+ }
+ });
+ JButton jbClearSearch = new DeselectingButton(new AbstractAction("Clear") {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ tfSearchQuery.setText("");
+ clearSearch();
+ }}, "");
+ jbClearSearch.setIcon(ResourceManager.getImageIcon(ResourceManager.CLEAR_ICON));
+
+ this.add(jbClearSearch, c);
+
+ c.gridx++;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 0.1;
+ this.add(tfSearchQuery, c);
+
+
+ // --- Search button ---
+
+ c.gridx++;
+ c.weightx = 0;
+ c.fill = GridBagConstraints.NONE;
+ c.anchor = GridBagConstraints.EAST;
+ this.bSearch = new DeselectingButton("Search",
+ new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ if (getSearchQuery().length() == 0) {
+ clearSearch();
+ }
+ else {
+ // search query available - collect data about the current search and execute it
+ tabbedSearchResultsPanel.startNewSearch(thisPanel.getState());
+ }
+ }
+ },
+ tfSearchQuery.getToolTipText());
+ this.bSearch.setIcon(ResourceManager.getImageIcon(ResourceManager.SEARCH_ICON));
+ this.add(bSearch, c);
+
+}
+
+ private void clearSearch() {
+ tabbedSearchResultsPanel.clearSearch();
+ thisPanel.focusDefaultComponent();
+ }
+
+ /**
+ * Saves the current state of the search options into a single {@link SearchOptions} object.
+ */
+ public SearchOptions getState() {
+ return (new SearchOptions(getSearchQuery(), Arrays.asList(TYPE.values())));
+ }
+
+
+ // *** GETTERS AND SETTERS ***
+
+ public String getSearchQuery() {
+ return (this.tfSearchQuery.getText().trim());
+ }
+ public void setSearchQuery(String strSearchQuery) {
+ this.tfSearchQuery.setText(strSearchQuery);
+ }
+
+
+ // *** Callbacks for HasDefaultFocusCapability interface ***
+
+ public void focusDefaultComponent() {
+ this.tfSearchQuery.selectAll();
+ this.tfSearchQuery.requestFocusInWindow();
+ }
+
+ public Component getDefaultComponent() {
+ return(this.tfSearchQuery);
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/filtertree/FilterTreeNode.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/filtertree/FilterTreeNode.java
new file mode 100644
index 0000000..fedd553
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/filtertree/FilterTreeNode.java
@@ -0,0 +1,91 @@
+package net.sf.taverna.biocatalogue.ui.filtertree;
+
+import net.sf.taverna.biocatalogue.ui.tristatetree.TriStateTreeNode;
+
+/**
+ * This class allows storing two pieces of data relevant to content filtering
+ * within the node of a tree. These values are kept hidden from the user and
+ * are only used when the filtering is about to happen.
+ *
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public class FilterTreeNode extends TriStateTreeNode
+{
+ private String type;
+ private String urlValue;
+ final private boolean isFilterCategory;
+
+
+ /**
+ * This constructor is useful for root nodes, which need not have filter type / value.
+ */
+ public FilterTreeNode(Object userObject) {
+ super(userObject);
+
+ this.isFilterCategory = true;
+ }
+
+
+ /**
+ * @param userObject As in the superclass (DefaultMutableTreeNode) - the object which represents the node in the UI
+ * @param filterType Type of the filter - e.g. 'Service Categories' --> "cat"; 'Service Types' --> "t"
+ * @param filterUrlValue Value that should be added to the URL to perform the filtering operation
+ */
+ public FilterTreeNode(Object userObject, String filterType, String filterUrlValue) {
+ super(userObject);
+
+ this.setType(filterType);
+ this.setUrlValue(filterUrlValue);
+ this.isFilterCategory = false;
+ }
+
+
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ public String getType() {
+ return type;
+ }
+
+ public void setUrlValue(String urlValue) {
+ this.urlValue = urlValue;
+ }
+
+
+ public String getUrlValue() {
+ return urlValue;
+ }
+
+ /**
+ * @return True if and only if this node is one of the "root" filter categories (not to be mixed with root of the filter tree).
+ */
+ public boolean isFilterCategory() {
+ return isFilterCategory;
+ }
+
+
+ /**
+ * @return <code>true</code> if the current {@link FilterTreeNode} represents a tag with a namespace
+ * (i.e. an ontological term), whose full tag name looks like:
+ * <code>< http://example.namespace.com#tag_display_name ></code>
+ */
+ public boolean isTagWithNamespaceNode() {
+ return (this.getType() != null && this.getType().contains("tag") && this.getUrlValue().contains("#") &&
+ this.getUrlValue().startsWith("<") && this.getUrlValue().endsWith(">"));
+ }
+
+
+ /**
+ * Static wrapper for {@link FilterTreeNode#isTagWithNamespaceNode()}
+ *
+ * @param filterType
+ * @param filterUrlValue
+ * @return
+ */
+ public static boolean isTagWithNamespaceNode(String filterType, String filterUrlValue) {
+ return (new FilterTreeNode("test_user_object", filterType, filterUrlValue).isTagWithNamespaceNode());
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/filtertree/FilterTreePane.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/filtertree/FilterTreePane.java
new file mode 100644
index 0000000..75a80ea
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/filtertree/FilterTreePane.java
@@ -0,0 +1,348 @@
+package net.sf.taverna.biocatalogue.ui.filtertree;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.BorderFactory;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JScrollPane;
+import javax.swing.JToolBar;
+import javax.swing.SwingUtilities;
+
+import net.sf.taverna.biocatalogue.model.BioCataloguePluginConstants;
+import net.sf.taverna.biocatalogue.model.Resource.TYPE;
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
+import net.sf.taverna.biocatalogue.model.search.SearchInstance;
+import net.sf.taverna.biocatalogue.model.search.ServiceFilteringSettings;
+import net.sf.taverna.biocatalogue.ui.tristatetree.JTriStateTree;
+import net.sf.taverna.biocatalogue.ui.tristatetree.TriStateTreeCheckingListener;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentFactory;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+
+import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.log4j.Logger;
+
+import org.biocatalogue.x2009.xml.rest.Filter;
+import org.biocatalogue.x2009.xml.rest.FilterGroup;
+import org.biocatalogue.x2009.xml.rest.FilterType;
+import org.biocatalogue.x2009.xml.rest.Filters;
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public class FilterTreePane extends JPanel implements TriStateTreeCheckingListener
+{
+ private TYPE resourceType;
+ private String filtersURL;
+ private BioCatalogueClient client;
+ private Logger logger;
+
+ private FilterTreePane thisPanel;
+
+ private JToolBar tbFilterTreeToolbar;
+
+ private JPanel jpFilters = null;
+ private JFilterTree filterTree; // tree component to display filter selections
+ private Filters filtersRoot; // last filters element which was received from the API
+
+
+
+ public FilterTreePane(TYPE resourceType)
+ {
+ this.thisPanel = this;
+
+ this.resourceType = resourceType;
+ this.filtersURL = resourceType.getAPIResourceCollectionFiltersURL();
+ this.client = BioCatalogueClient.getInstance();
+ this.logger = Logger.getLogger(this.getClass());
+
+ initialiseUI();
+ loadFiltersAndBuildTheTree();
+ }
+
+
+ private void initialiseUI()
+ {
+ jpFilters = new JPanel();
+ jpFilters.setBackground(Color.WHITE);
+
+ JScrollPane spFilters = new JScrollPane(jpFilters);
+ spFilters.setMinimumSize(new Dimension(235,0));
+ spFilters.setPreferredSize(new Dimension(300,0));
+ spFilters.getVerticalScrollBar().setUnitIncrement(BioCataloguePluginConstants.DEFAULT_SCROLL);
+
+
+ tbFilterTreeToolbar = createTreeActionToolbar();
+ resetTreeActionToolbar();
+
+ this.setLayout(new BorderLayout());
+ this.add(tbFilterTreeToolbar, BorderLayout.NORTH);
+ this.add(spFilters, BorderLayout.CENTER);
+ }
+
+
+ /**
+ * @return A toolbar that replicates all actions available in the contextual menu of
+ * the filtering tree - mainly: saving current filter, reloading filter tree,
+ * expanding/collapsing and selecting/deselecting everything in the tree.
+ */
+private JToolBar createTreeActionToolbar()
+ {
+
+
+ // the actual toolbar - no actions are added to it yet: done in a separate method
+ JToolBar tbTreeActions = new JToolBar(JToolBar.HORIZONTAL);
+ tbTreeActions.setAlignmentX(RIGHT_ALIGNMENT);
+ tbTreeActions.setBorderPainted(true);
+ tbTreeActions.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
+ tbTreeActions.setFloatable(false);
+ return (tbTreeActions);
+ }
+
+
+ /**
+ * Resets the action toolbar to the original state.
+ */
+ public void resetTreeActionToolbar()
+ {
+
+ tbFilterTreeToolbar.removeAll();
+ tbFilterTreeToolbar.repaint();
+ }
+
+
+ /**
+ * This method loads filter data from API and populates the view.
+ */
+ private void loadFiltersAndBuildTheTree()
+ {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run()
+ {
+ resetTreeActionToolbar();
+
+ jpFilters.removeAll();
+ jpFilters.setLayout(new BorderLayout());
+ jpFilters.add(new JLabel(" Loading filters..."), BorderLayout.NORTH);
+ jpFilters.add(new JLabel(ResourceManager.getImageIcon(ResourceManager.BAR_LOADER_ORANGE)), BorderLayout.CENTER);
+ thisPanel.validate();
+ thisPanel.repaint(); // validate and repaint this component to make sure that
+ // scroll bar around the filter tree placeholder panel disappears
+ }
+ });
+
+ new Thread("Load filters") {
+ public void run() {
+ try {
+ // load filter data
+ filtersRoot = client.getBioCatalogueFilters(filtersURL);
+
+ // Create root of the filter tree component
+ FilterTreeNode root = new FilterTreeNode("root");
+
+ // populate the tree via its root element
+ for (FilterGroup fgroup : filtersRoot.getGroupList())
+ {
+ // attach filter group directly to the root node
+ FilterTreeNode fgroupNode = new FilterTreeNode("<html><span style=\"color: black; font-weight: bold;\">" + StringEscapeUtils.escapeHtml(fgroup.getName().toString()) + "</span></html>");
+ root.add(fgroupNode);
+
+
+ // go through all filter types in this group and add them to the tree
+ for (FilterType ftype : fgroup.getTypeList())
+ {
+ // if there's more than one filter type in the group, add the type node as another level of nesting
+ // (otherwise, attach filters inside the single type directly to the group node)
+ FilterTreeNode filterTypeNode = fgroupNode;
+ if (fgroup.getTypeList().size() > 1) {
+ filterTypeNode = new FilterTreeNode("<html><span style=\"color: black; font-weight: bold;\">" + StringEscapeUtils.escapeHtml(ftype.getName().toString()) + "</span></html>");
+ fgroupNode.add(filterTypeNode);
+ }
+
+ // For some reason sorting the list of filters before inserting into tree
+ // messes up the tree nodes
+// Collections.sort(ftype.getFilterList(), new Comparator<Filter>(){
+// @Override
+// public int compare(Filter f1, Filter f2) {
+// return (f1.getName().compareToIgnoreCase(f2.getName()));
+// }
+// });
+ addFilterChildren(filterTypeNode, ftype.getUrlKey().toString(), ftype.getFilterList());
+ }
+ }
+
+ // Create the tree view with the populated root
+ filterTree = new JFilterTree(root);
+ filterTree.setRootVisible(false); // don't want the root to be visible; not a standard thing, so not implemented within JTriStateTree
+ filterTree.setLargeModel(true); // potentially can have many filters!
+ filterTree.addCheckingListener(thisPanel);
+
+
+ // insert the created tree view into the filters panel
+ jpFilters.removeAll();
+ jpFilters.setLayout(new GridLayout(0,1));
+ jpFilters.add(filterTree);
+ jpFilters.validate();
+
+
+ // add actions from the contextual menu of the filter tree into the toolbar
+ // that replicates those plus adds additional ones in this panel
+ tbFilterTreeToolbar.removeAll();
+ for (Action a : filterTree.getContextualMenuActions()) {
+ tbFilterTreeToolbar.add(a);
+ }
+
+
+ // enable all actions
+ filterTree.enableAllContextualMenuAction(true);
+ }
+ catch (Exception e) {
+ logger.error("Failed to load filter tree from the following URL: " + filtersURL, e);
+ }
+ }
+
+
+ /**
+ * Recursive method to populate a node of the filter tree with all
+ * sub-filters.
+ *
+ * Ontological terms will be underlined.
+ *
+ * @param root Tree node to add children to.
+ * @param filterList A list of Filters to add to "root" as children.
+ */
+ private void addFilterChildren(FilterTreeNode root, String filterCategory, List<Filter> filterList) {
+ for (Filter f : filterList) {
+
+ // Is this an ontological term?
+ String ontology = null;
+ if (FilterTreeNode.isTagWithNamespaceNode(filterCategory, f
+ .getUrlValue())) {
+ String nameAndNamespace = f.getUrlValue().substring(1,
+ f.getUrlValue().length() - 1);
+ String[] namePlusNamespace = nameAndNamespace
+ .split("#");
+ ontology = JFilterTree
+ .getOntologyFromNamespace(namePlusNamespace[0]);
+ }
+
+ FilterTreeNode fNode = new FilterTreeNode("<html><span color=\"black\"" /*(FilterTreeNode.isTagWithNamespaceNode(filterCategory, f.getUrlValue()) ? " style=\"text-decoration: underline;\"" : "") */ + ">" +
+ StringEscapeUtils.escapeHtml(f.getName()) + " (" + f.getCount() + ")" + "</span>" +
+ /*(FilterTreeNode.isTagWithNamespaceNode(filterCategory, f.getUrlValue()) ? "<span color=\"gray\"> ("+f.getCount().intValue()+")</span></html>" : "</html>"),*/
+ (ontology != null ? "<span color=\"#3090C7\"> <"+ ontology +"></span></html>" : "</html>"),
+ filterCategory, f.getUrlValue());
+ addFilterChildren(fNode, filterCategory, f.getFilterList());
+
+ // Insert the node into the (alphabetically) sorted children nodes
+ List<FilterTreeNode> children = Collections.list(root.children());
+ // Search for the index the new node should be inserted at
+ int index = Collections.binarySearch(children, fNode,
+ new Comparator<FilterTreeNode>() {
+ @Override
+ public int compare(FilterTreeNode o1,
+ FilterTreeNode o2) {
+ String str1 = ((String) o1.getUserObject())
+ .toString();
+ String str2 = ((String) o2.getUserObject())
+ .toString();
+ return (str1.compareToIgnoreCase(str2));
+ }
+ });
+
+ if (index < 0){ // not found - index will be equal to -insertion-point -1
+ index = -index - 1;
+ }// else node with the same name found in the array - insert it at that position
+ root.insert(fNode, index);
+
+ //root.add(fNode);
+ }
+ }
+ }.start();
+ }
+
+
+ /**
+ * @param si Uses this SearchInstance to restore the checking
+ * state of filtering criteria in the filter tree.
+ */
+ public void restoreFilteringSettings(SearchInstance si) {
+ this.filterTree.restoreFilterCheckingSettings(si.getFilteringSettings().getFilterTreeRootsOfCheckedPaths());
+ }
+
+
+ /**
+ * Clears any selections made in the filter tree -
+ * i.e. both clears checked nodes and removes all tree path selections.
+ */
+ public void clearSelection() {
+ // filter tree may not have been initialised yet, so perform a check
+ if (this.filterTree != null)
+ {
+ // remove, then restore self as a listener - this is to avoid
+ // receiving checking state change event
+ this.filterTree.removeCheckingListener(thisPanel);
+ this.filterTree.selectAllNodes(false);
+ this.filterTree.clearSelection();
+ this.filterTree.addCheckingListener(thisPanel);
+ }
+ }
+
+
+ /**
+ * Collapses all expanded nodes in the filter tree.
+ */
+ public void collapseAll() {
+ // filter tree may not have been initialised yet, so perform a check
+ if (this.filterTree != null) {
+ this.filterTree.collapseAll();
+ }
+ }
+
+ public void applyQueryString(final String queryString) {
+ this.filtersURL = resourceType.getAPIResourceCollectionFiltersURL() + "?q=" + queryString;
+ loadFiltersAndBuildTheTree();
+ }
+
+ /**
+ * Used for making preferred height of the search status label
+ * the same as the height of this toolbar.
+ *
+ * @return
+ */
+ public Dimension getTreeToolbarPreferredSize() {
+ return this.tbFilterTreeToolbar.getPreferredSize();
+ }
+
+
+ // *** Callback for TriStateTreeCheckingListener ***
+
+ /**
+ * We start a new search as soon as checking state of the filter tree changes.
+ */
+ public void triStateTreeCheckingChanged(JTriStateTree source)
+ {
+ MainComponentFactory.getSharedInstance().getBioCatalogueExplorationTab().getTabbedSearchResultsPanel().
+ startNewFiltering(resourceType, new ServiceFilteringSettings(filterTree));
+ }
+
+
+public void reset() {
+ this.filtersURL = resourceType.getAPIResourceCollectionFiltersURL();
+ loadFiltersAndBuildTheTree();
+}
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/filtertree/JFilterTree.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/filtertree/JFilterTree.java
new file mode 100644
index 0000000..a6cc111
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/filtertree/JFilterTree.java
@@ -0,0 +1,69 @@
+package net.sf.taverna.biocatalogue.ui.filtertree;
+
+import java.awt.event.MouseEvent;
+import java.util.HashMap;
+import java.util.Map;
+
+import net.sf.taverna.biocatalogue.ui.tristatetree.JTriStateTree;
+import net.sf.taverna.biocatalogue.ui.tristatetree.TriStateTreeNode;
+
+/**
+ * This subclass of {@link JTriStateTree} provides custom behaviour
+ * for tooltips: ontological terms will now always get a tooltip that
+ * displays the namespace for the tag, but plain text tags will still
+ * behave as before - the way it is defined in the superclass (so that
+ * the tooltip will only be shown if the tag does not fully fit into
+ * the visible part of the {@link FilterTreePane}.
+ *
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public class JFilterTree extends JTriStateTree
+{
+
+ private static Map<String, String> nameSpaceToOntologyMap = new HashMap<String, String>(){
+ {
+ put("http://www.mygrid.org.uk/ontology", "mygrid-domain-ontology");
+ put("http://www.mygrid.org.uk/mygrid-moby-service", "mygrid-service-ontology");
+ }
+ };
+
+
+ public JFilterTree(TriStateTreeNode root) {
+ super(root);
+ }
+
+
+ public String getToolTipText(MouseEvent e)
+ {
+ Object correspondingObject = super.getTreeNodeObject(e);
+ if (correspondingObject != null && correspondingObject instanceof FilterTreeNode) {
+ FilterTreeNode filterNode = (FilterTreeNode) correspondingObject;
+
+ if (filterNode.isTagWithNamespaceNode())
+ {
+ String nameAndNamespace = filterNode.getUrlValue().substring(1, filterNode.getUrlValue().length() - 1);
+ String[] namePlusNamespace = nameAndNamespace.split("#");
+
+ return ("<html>" + namePlusNamespace[1] + " (<b>Namespace: </b>" + namePlusNamespace[0] + ")</html>");
+ }
+ }
+
+ return super.getToolTipText(e);
+ }
+
+ public static String getOntologyFromNamespace(String namespace){
+ if (namespace == null){
+ return null;
+ }
+ else{
+ if (nameSpaceToOntologyMap.containsKey(namespace)){
+ return nameSpaceToOntologyMap.get(namespace);
+ }
+ else{
+ return null;
+ }
+ }
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/ExpandableOnDemandLoadedListCellRenderer.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/ExpandableOnDemandLoadedListCellRenderer.java
new file mode 100644
index 0000000..a223fc8
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/ExpandableOnDemandLoadedListCellRenderer.java
@@ -0,0 +1,220 @@
+package net.sf.taverna.biocatalogue.ui.search_results;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.BorderFactory;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.ListCellRenderer;
+import javax.swing.SwingUtilities;
+
+import net.sf.taverna.biocatalogue.model.LoadingResource;
+import net.sf.taverna.biocatalogue.model.Resource;
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.biocatalogue.model.Resource.TYPE;
+
+import org.biocatalogue.x2009.xml.rest.ResourceLink;
+
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public abstract class ExpandableOnDemandLoadedListCellRenderer extends JPanel implements ListCellRenderer
+{
+ protected static final int DESCRIPTION_MAX_LENGTH_COLLAPSED = 90;
+ protected static final int DESCRIPTION_MAX_LENGTH_EXPANDED = 500;
+
+ protected static final int LINE_LENGTH = 90;
+
+
+ protected static final int TOOLTIP_DESCRIPTION_LENGTH = 150;
+ protected static final int TOOLTIP_LINE_LENGTH = 60;
+
+ // list cells are not repainted by Swing by default - hence to use animated GIFs inside cells,
+ // need to have a special class that takes care of changing the frames as necessary
+ protected JLabel loaderBarAnimationOrange = new JLabel(ResourceManager.getImageIcon(ResourceManager.BAR_LOADER_ORANGE), JLabel.CENTER);
+ protected JLabel loaderBarAnimationGrey = new JLabel(ResourceManager.getImageIcon(ResourceManager.BAR_LOADER_GREY), JLabel.CENTER);
+ protected JLabel loaderBarAnimationGreyStill = new JLabel (ResourceManager.getImageIcon(ResourceManager.BAR_LOADER_GREY_STILL), JLabel.CENTER);
+
+
+ protected JPanel thisPanel;
+ private List<Class<? extends ResourceLink>> resourceClasses;
+
+
+ protected JLabel jlExpand;
+ protected static Rectangle expandRect;
+
+ public ExpandableOnDemandLoadedListCellRenderer()
+ {
+ this.thisPanel = this;
+
+ resourceClasses = new ArrayList<Class<? extends ResourceLink>>();
+ try {
+ for (Resource.TYPE resourceType : Resource.TYPE.values()) {
+ resourceClasses.add(resourceType.getXmlBeansGeneratedClass());
+ }
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ }
+
+
+ public static Rectangle getExpandRect() {
+ return (expandRect == null ? new Rectangle() : expandRect);
+ }
+
+
+ public Component getListCellRendererComponent(JList list, Object itemToRender, int itemIndex, boolean isSelected, boolean cellHasFocus)
+ {
+ // the same instance of the cell renderer is used for all cells, so
+ // need to remove everything from the current panel to ensure clean
+ // painting of the current cell
+ this.removeAll();
+
+ // GET THE DATA
+
+ // LoadingResource is a placeholder for the detailed data on the resource --
+ // it is being quickly fetched from the API and contanins just the name and the URL
+ // of the actual resource;
+ //
+ // these entries will be placed into the list when the initial part of the search
+ // is complete, further details will be loaded asynchronously and inserted into
+ // the same area
+ if (itemToRender instanceof LoadingResource) {
+ prepareInitiallyLoadingEntry(itemToRender);
+ }
+
+ // real data about some resource: details, but in the collapsed form
+ else if (isInstanceOfResourceType(itemToRender)) {
+ prepareLoadedEntry(itemToRender, isSelected);
+ }
+
+ // error case - unknown resource...
+ else {
+ prepareUnknownResourceTypeEntry();
+ }
+
+
+ // MAKE SURE CELL SELECTION WORKS AS DESIRED
+ if (shouldBeHidden(itemToRender)) {
+ this.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createMatteBorder(3, 4, 3, 4, list.getBackground()),
+ BorderFactory.createLineBorder(Color.DARK_GRAY)));
+ setBackground(list.getBackground());
+ setForeground(list.getBackground());
+ }
+ else if (isSelected) {
+ this.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createMatteBorder(3, 4, 3, 4, list.getBackground()),
+ BorderFactory.createLineBorder(Color.DARK_GRAY)));
+ setBackground(Color.decode("#BAE8FF")); // very light blue colour
+ setForeground(list.getSelectionForeground());
+ } else {
+ this.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createMatteBorder(3, 4, 3, 4, list.getBackground()),
+ BorderFactory.createLineBorder(Color.DARK_GRAY)));
+ setBackground(Color.WHITE);
+ setForeground(list.getForeground());
+ }
+
+ this.revalidate();
+
+ if (expandRect == null && jlExpand != null) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ expandRect = jlExpand.getBounds();
+ expandRect.x -= Math.abs(thisPanel.getBounds().x);
+ }
+ });
+ }
+
+ return (this);
+ }
+
+
+ /**
+ * This entry can be in one of two states:
+ * -- containing only the name of the resource and NOT loading further details;
+ * -- containing only the name of the resource and LOADING further details.
+ *
+ * @param itemToRender
+ * @return
+ */
+ protected abstract GridBagConstraints prepareInitiallyLoadingEntry(Object itemToRender);
+
+
+ /**
+ *
+ * @param itemToRender
+ * @param isSelected
+ * @param expandedView <code>true</code> to indicate that this method generates the top
+ * fragment of the expanded list entry for this SOAP operation / REST method.
+ * @return
+ */
+ protected abstract GridBagConstraints prepareLoadedEntry(Object itemToRender, boolean isSelected);
+
+
+ private void prepareUnknownResourceTypeEntry()
+ {
+ this.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+ c.anchor = GridBagConstraints.NORTHWEST;
+ c.fill = GridBagConstraints.HORIZONTAL;
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.weightx = 0;
+ c.insets = new Insets(8, 6, 6, 3);
+ this.add(new JLabel(ResourceManager.getImageIcon(ResourceManager.UNKNOWN_RESOURCE_TYPE_ICON)), c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.insets = new Insets(8, 3, 6, 3);
+ this.add(new JLabel("<html><font color=\"#FF0000\">ERROR: This item shoulnd't have been here...</font></html>"), c);
+
+ c.gridx = 1;
+ c.gridy++;
+ c.gridheight = 1;
+ c.weightx = 1.0;
+ c.weighty = 0;
+ c.insets = new Insets(3, 3, 3, 3);
+ this.add(new JLabel(" "), c);
+
+ c.gridy++;
+ c.insets = new Insets(3, 3, 8, 3);
+ this.add(new JLabel(" "), c);
+ }
+
+
+ private boolean isInstanceOfResourceType(Object itemToRender)
+ {
+ for (Class<? extends ResourceLink> resourceClass : resourceClasses) {
+ if (resourceClass.isInstance(itemToRender)) {
+ return (true);
+ }
+ }
+
+ return (false);
+ }
+
+ protected TYPE determineResourceType(Object itemToRender) {
+ if (itemToRender instanceof ResourceLink) {
+ return (Resource.getResourceTypeFromResourceURL(((ResourceLink)itemToRender).getHref()));
+ }
+ else {
+ return (null);
+ }
+ }
+
+ abstract boolean shouldBeHidden(Object itemToRender);
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/RESTMethodListCellRenderer.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/RESTMethodListCellRenderer.java
new file mode 100644
index 0000000..64bdfbf
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/RESTMethodListCellRenderer.java
@@ -0,0 +1,248 @@
+package net.sf.taverna.biocatalogue.ui.search_results;
+
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JLabel;
+
+import net.sf.taverna.biocatalogue.model.LoadingResource;
+import net.sf.taverna.biocatalogue.model.Resource;
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.biocatalogue.model.Util;
+import net.sf.taverna.t2.lang.ui.ReadOnlyTextArea;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check.ServiceMonitoringStatusInterpreter;
+
+import org.apache.commons.lang.StringEscapeUtils;
+import org.biocatalogue.x2009.xml.rest.RestMethod;
+import org.biocatalogue.x2009.xml.rest.RestParameter;
+import org.biocatalogue.x2009.xml.rest.RestRepresentation;
+import org.biocatalogue.x2009.xml.rest.Service;
+import org.biocatalogue.x2009.xml.rest.RestMethod.Ancestors;
+
+
+/**
+ *
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class RESTMethodListCellRenderer extends ExpandableOnDemandLoadedListCellRenderer
+{
+ private JLabel jlTypeIcon = new JLabel();
+ private JLabel jlItemStatus = new JLabel();
+ private JLabel jlItemTitle = new JLabel("X");
+ private JLabel jlPartOf = new JLabel("X");
+ private ReadOnlyTextArea jtDescription = new ReadOnlyTextArea(5, 80);
+ private JLabel jlMethodType = new JLabel("X");
+ private JLabel jlUrlTemplate = new JLabel("X");
+ private JLabel jlMethodParameters = new JLabel("X");
+ private JLabel jlInputRepresentations = new JLabel("X");
+ private JLabel jlOutputRepresentations = new JLabel("X");
+
+ private GridBagConstraints c;
+
+ private static Resource.TYPE resourceType = Resource.TYPE.RESTMethod;
+
+
+
+ public RESTMethodListCellRenderer() {
+ jlItemTitle.setFont(jlItemTitle.getFont().deriveFont(Font.PLAIN, jlItemTitle.getFont().getSize() + 2));
+ jtDescription.setOpaque(false);
+ jtDescription.setLineWrap(true);
+ jtDescription.setWrapStyleWord(true);
+ }
+
+
+
+ /**
+ * This entry can be in one of two states:
+ * -- containing only the name of the resource and NOT loading further details;
+ * -- containing only the name of the resource and LOADING further details.
+ *
+ * @param itemToRender
+ * @return
+ */
+ protected GridBagConstraints prepareInitiallyLoadingEntry(Object itemToRender)
+ {
+ LoadingResource resource = (LoadingResource)itemToRender;
+
+ jlTypeIcon.setIcon(resourceType.getIcon());
+ jlItemStatus.setIcon(ResourceManager.getImageIcon(ResourceManager.SERVICE_STATUS_UNCHECKED_ICON_LARGE));
+
+ jlItemTitle.setText("<html>" + StringEscapeUtils.escapeHtml(Resource.getDisplayNameForResource(resource)) + "<font color=\"gray\"><i>- fetching more information</i></font></html>");
+
+ jlPartOf.setText("");
+ jtDescription.setText(" ");
+ jlMethodType.setText(" ");
+ jlUrlTemplate.setText(" ");
+ jlMethodParameters.setText(" ");
+ jlInputRepresentations.setText(" ");
+ jlOutputRepresentations.setText(" ");
+
+ return (arrangeLayout());
+ }
+
+
+ /**
+ *
+ * @param itemToRender
+ * @param expandedView <code>true</code> to indicate that this method generates the top
+ * fragment of the expanded list entry for this SOAP operation / REST method.
+ * @return
+ */
+ protected GridBagConstraints prepareLoadedEntry(Object itemToRender, boolean selected)
+ {
+ RestMethod restMethod = (RestMethod)itemToRender;;
+
+ Ancestors ancestors = restMethod.getAncestors();
+ Service service = ancestors.getService();
+ String title = "<html>" + StringEscapeUtils.escapeHtml(Resource.getDisplayNameForResource(restMethod));
+
+ if (restMethod.isSetArchived() || service.isSetArchived()) {
+ jlTypeIcon.setIcon(ResourceManager.getImageIcon(ResourceManager.WARNING_ICON));
+ title = title + "<i> - this operation is archived and probably cannot be used</i></html>";
+ }
+ else {
+ jlTypeIcon.setIcon(resourceType.getIcon());
+ title = title + "</html>";
+ }
+
+ // service status
+ jlItemStatus.setIcon(ServiceMonitoringStatusInterpreter.getStatusIcon(service, false));
+ jlItemTitle.setText(title);
+
+ jlPartOf.setText("<html><b>Part of: </b>" + restMethod.getAncestors().getRestService().getResourceName() + "</html>");
+
+ String strDescription = (restMethod.getDescription() == null || restMethod.getDescription().length() == 0 ?
+ "No description" :
+ Util.stripAllHTML(restMethod.getDescription()));
+ jtDescription.setText(strDescription);
+
+ jlMethodType.setText("<html><b>HTTP Method: </b>" + StringEscapeUtils.escapeHtml(restMethod.getHttpMethodType().toString()) + "</html>");
+ jlUrlTemplate.setText("<html><b>URL Template: </b>" + StringEscapeUtils.escapeHtml(restMethod.getUrlTemplate()) + "</html>");
+
+ List<String> names = new ArrayList<String>();
+ for (RestParameter restParameter : restMethod.getInputs().getParameters().getRestParameterList()) {
+ names.add(restParameter.getName() + (restParameter.getIsOptional() ? " (optional)" : ""));
+ }
+
+ String methodParameters = "<b>" + names.size() + " " + Util.pluraliseNoun("Parameter", names.size()) + "</b>";
+ if(names.size() > 0) {
+ methodParameters += ": " + StringEscapeUtils.escapeHtml(Util.ensureLineLengthWithinString(Util.join(names, ", "), LINE_LENGTH, false));
+ }
+ methodParameters = "<html>" + methodParameters + "</html>";
+ jlMethodParameters.setText(methodParameters);
+
+ names.clear();
+ for (RestRepresentation restRepresentation : restMethod.getInputs().getRepresentations().getRestRepresentationList()) {
+ names.add(restRepresentation.getContentType());
+ }
+
+ String inputRepresentations = "<b>" + names.size() + " " + Util.pluraliseNoun("Input representation", names.size()) + "</b>";
+ if(names.size() > 0) {
+ inputRepresentations += ": " + StringEscapeUtils.escapeHtml(Util.ensureLineLengthWithinString(Util.join(names, ", "), LINE_LENGTH, false));
+ }
+ inputRepresentations = "<html>" + inputRepresentations + "</html>";
+
+ jlInputRepresentations.setText(inputRepresentations);
+
+ // output representations
+ names.clear();
+ for (RestRepresentation restRepresentation : restMethod.getOutputs().getRepresentations().getRestRepresentationList()) {
+ names.add(restRepresentation.getContentType());
+ }
+
+ String outputRepresentations = "<b>" + names.size() + " " + Util.pluraliseNoun("Output representation", names.size()) + "</b>";
+ if(names.size() > 0) {
+ outputRepresentations += ": " + StringEscapeUtils.escapeHtml(Util.ensureLineLengthWithinString(Util.join(names, ", "), LINE_LENGTH, false));
+ }
+ outputRepresentations = "<html>" + outputRepresentations + "</html>";
+
+ jlOutputRepresentations.setText(outputRepresentations);
+
+ return (arrangeLayout());
+ }
+
+
+ /**
+ * @return Final state of the {@link GridBagConstraints} instance
+ * that was used to lay out components in the panel.
+ */
+ private GridBagConstraints arrangeLayout()
+ {
+ // POPULATE PANEL WITH PREPARED COMPONENTS
+ this.setLayout(new GridBagLayout());
+ c = new GridBagConstraints();
+ c.anchor = GridBagConstraints.NORTHWEST;
+ c.fill = GridBagConstraints.HORIZONTAL;
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.weightx = 0;
+ c.insets = new Insets(8, 6, 6, 3);
+ this.add(jlTypeIcon, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.insets = new Insets(8, 3, 6, 3);
+ this.add(jlItemTitle, c);
+
+ c.gridx++;
+ c.gridheight = 8;
+ c.weightx = 0;
+ c.weighty = 1.0;
+ this.add(jlItemStatus, c);
+
+ c.gridx = 1;
+ c.gridy++;
+ c.gridheight = 1;
+ c.weightx = 1.0;
+ c.weighty = 0;
+ this.add(jlPartOf, c);
+
+ c.fill = GridBagConstraints.NONE;
+ c.gridy++;
+ this.add(jtDescription, c);
+
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.gridy++;
+ this.add(jlMethodType, c);
+
+ c.gridy++;
+ this.add(jlUrlTemplate, c);
+
+ c.gridy++;
+ this.add(jlMethodParameters, c);
+
+ c.gridy++;
+ this.add(jlInputRepresentations, c);
+
+ c.gridy++;
+ this.add(jlOutputRepresentations, c);
+ return (c);
+ }
+
+@Override
+boolean shouldBeHidden(Object itemToRender) {
+ if (!(itemToRender instanceof RestMethod)) {
+ return false;
+ }
+ RestMethod restMethod = (RestMethod)itemToRender;;
+
+ Ancestors ancestors = restMethod.getAncestors();
+ Service service = ancestors.getService();
+ String title = Resource.getDisplayNameForResource(restMethod);
+
+ if (restMethod.isSetArchived() || service.isSetArchived()) {
+ return true;
+ }
+ else {
+ return false;
+ }
+
+}
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/SOAPOperationListCellRenderer.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/SOAPOperationListCellRenderer.java
new file mode 100644
index 0000000..77939c7
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/SOAPOperationListCellRenderer.java
@@ -0,0 +1,257 @@
+package net.sf.taverna.biocatalogue.ui.search_results;
+
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+
+import net.sf.taverna.biocatalogue.model.LoadingExpandedResource;
+import net.sf.taverna.biocatalogue.model.LoadingResource;
+import net.sf.taverna.biocatalogue.model.Resource;
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.biocatalogue.model.Util;
+import net.sf.taverna.t2.lang.ui.ReadOnlyTextArea;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check.ServiceMonitoringStatusInterpreter;
+
+import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.commons.lang.StringUtils;
+import org.biocatalogue.x2009.xml.rest.Service;
+import org.biocatalogue.x2009.xml.rest.ServiceTechnologyType;
+import org.biocatalogue.x2009.xml.rest.SoapInput;
+import org.biocatalogue.x2009.xml.rest.SoapOperation;
+import org.biocatalogue.x2009.xml.rest.SoapOutput;
+import org.biocatalogue.x2009.xml.rest.SoapService;
+import org.biocatalogue.x2009.xml.rest.Service.ServiceTechnologyTypes;
+import org.biocatalogue.x2009.xml.rest.ServiceTechnologyType.Enum;
+import org.biocatalogue.x2009.xml.rest.SoapOperation.Ancestors;
+
+
+/**
+ *
+ *
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public class SOAPOperationListCellRenderer extends ExpandableOnDemandLoadedListCellRenderer
+{
+
+ private JLabel jlTypeIcon = new JLabel();
+ private JLabel jlItemStatus = new JLabel();
+ private JLabel jlItemTitle = new JLabel("X");
+ private JLabel jlPartOf = new JLabel("X");
+ private JLabel jlWsdlLocation = new JLabel("X");
+ private ReadOnlyTextArea jtDescription = new ReadOnlyTextArea(5,80);
+ private JLabel jlSoapInputs = new JLabel("X");
+ private JLabel jlSoapOutputs = new JLabel("X");
+
+ private GridBagConstraints c;
+
+ private static Resource.TYPE resourceType = Resource.TYPE.SOAPOperation;
+
+
+ public SOAPOperationListCellRenderer() {
+ jlItemTitle.setFont(jlItemTitle.getFont().deriveFont(Font.PLAIN, jlItemTitle.getFont().getSize() + 2));
+ jtDescription.setOpaque(false);
+ jtDescription.setLineWrap(true);
+ jtDescription.setWrapStyleWord(true);
+ }
+
+
+ /**
+ * This entry can be in one of two states:
+ * -- containing only the name of the resource and NOT loading further details;
+ * -- containing only the name of the resource and LOADING further details.
+ *
+ * @param itemToRender
+ * @return
+ */
+ protected GridBagConstraints prepareInitiallyLoadingEntry(Object itemToRender)
+ {
+ LoadingResource resource = (LoadingResource)itemToRender;
+
+ jlTypeIcon.setIcon(resourceType.getIcon());
+ jlItemStatus.setIcon(ResourceManager.getImageIcon(ResourceManager.SERVICE_STATUS_UNCHECKED_ICON_LARGE));
+
+ jlItemTitle.setText("<html>" + StringEscapeUtils.escapeHtml(Resource.getDisplayNameForResource(resource)) + "<font color=\"gray\"><i>- fetching more information</i></font></html>");
+
+ jlPartOf.setText(" ");
+ jlWsdlLocation.setText(" ");
+ jtDescription.setText("");
+ jlSoapInputs.setText(" ");
+ jlSoapOutputs.setText(" ");
+
+ return (arrangeLayout());
+ }
+
+
+ /**
+ *
+ * @param itemToRender
+ * @param selected
+ * @param expandedView <code>true</code> to indicate that this method generates the top
+ * fragment of the expanded list entry for this SOAP operation / REST method.
+ * @return
+ */
+ protected GridBagConstraints prepareLoadedEntry(Object itemToRender, boolean selected)
+ {
+ SoapOperation soapOp = (SoapOperation)itemToRender;
+
+ Ancestors ancestors = soapOp.getAncestors();
+ SoapService soapService = ancestors.getSoapService();
+ Service service = ancestors.getService();
+ String title = StringEscapeUtils.escapeHtml(Resource.getDisplayNameForResource(soapOp));
+
+ if (soapOp.isSetArchived() || service.isSetArchived()) {
+ jlTypeIcon.setIcon(ResourceManager.getImageIcon(ResourceManager.WARNING_ICON));
+ title = "<html>" + title + "<i> - this operation is archived and probably cannot be used</i></html>";
+ } else if (isSoapLab(service)) {
+ jlTypeIcon.setIcon(ResourceManager.getImageIcon(ResourceManager.WARNING_ICON));
+ title = "<html>" + title + "<i> - this operation can only be used as part of a SoapLab service</i></html>";
+ }
+ else {
+ jlTypeIcon.setIcon(resourceType.getIcon());
+ title = "<html>" + title + "</html>";
+ }
+
+ // service status
+ jlItemStatus.setIcon(ServiceMonitoringStatusInterpreter.getStatusIcon(service, false));
+ jlItemTitle.setText(title);
+
+ jlPartOf.setText("<html><b>Part of: </b>" + StringEscapeUtils.escapeHtml(soapOp.getAncestors().getSoapService().getResourceName()) + "</html>");
+
+ jlWsdlLocation.setText("<html><b>WSDL location: </b>" + soapService.getWsdlLocation() + "</html>");
+
+ String strDescription = (soapOp.getDescription() == null || soapOp.getDescription().length() == 0 ?
+ "No description" :
+ Util.stripAllHTML(soapOp.getDescription()));
+
+ jtDescription.setText(strDescription);
+
+ // add SOAP inputs
+ List<String> names = new ArrayList<String>();
+ for (SoapInput soapInput : soapOp.getInputs().getSoapInputList()) {
+ names.add(soapInput.getName());
+ }
+
+ String soapInputs = "<b>" + names.size() + " " + Util.pluraliseNoun("Input", names.size()) + "</b>";
+ if(names.size() > 0) {
+ soapInputs += ": " + StringEscapeUtils.escapeHtml(Util.ensureLineLengthWithinString(Util.join(names, ", "), LINE_LENGTH, false));
+ }
+ soapInputs = "<html>" + soapInputs + "</html>";
+ jlSoapInputs.setText(soapInputs);
+
+ c.gridy++;
+ this.add(jlSoapInputs, c);
+
+
+ // add SOAP outputs
+ names.clear();
+ for (SoapOutput soapOutput : soapOp.getOutputs().getSoapOutputList()) {
+ names.add(soapOutput.getName());
+ }
+
+ String soapOutputs = "<b>" + names.size() + " " + Util.pluraliseNoun("Output", names.size()) + "</b>";
+ if(names.size() > 0) {
+ soapOutputs += ": " + StringEscapeUtils.escapeHtml(Util.ensureLineLengthWithinString(Util.join(names, ", "), LINE_LENGTH, false));
+ }
+ soapOutputs = "<html>" + soapOutputs + "</html>";
+ jlSoapOutputs.setText(soapOutputs);
+
+ return (arrangeLayout());
+ }
+
+
+private boolean isSoapLab(Service service) {
+ boolean result = false;
+ ServiceTechnologyTypes serviceTechnologyTypes = service.getServiceTechnologyTypes();
+ if (serviceTechnologyTypes == null) {
+ return result;
+ }
+ List<Enum> typeList = serviceTechnologyTypes.getTypeList();
+ if (typeList == null) {
+ return result;
+ }
+ result = typeList.contains(ServiceTechnologyType.SOAPLAB);
+ return result;
+}
+
+
+ /**
+ * @return Final state of the {@link GridBagConstraints} instance
+ * that was used to lay out components in the panel.
+ */
+ private GridBagConstraints arrangeLayout()
+ {
+ // POPULATE PANEL WITH PREPARED COMPONENTS
+ this.setLayout(new GridBagLayout());
+ c = new GridBagConstraints();
+ c.anchor = GridBagConstraints.NORTHWEST;
+ c.fill = GridBagConstraints.HORIZONTAL;
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.weightx = 0;
+ c.insets = new Insets(8, 6, 6, 3);
+ this.add(jlTypeIcon, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.insets = new Insets(8, 3, 6, 3);
+ this.add(jlItemTitle, c);
+
+ c.gridx++;
+ c.gridheight = 7;
+ c.weightx = 0;
+ c.weighty = 1.0;
+ this.add(jlItemStatus, c);
+
+ c.gridx = 1;
+ c.gridy++;
+ c.gridheight = 1;
+ c.weightx = 0;
+ c.weighty = 0;
+ this.add(jlPartOf, c);
+
+ c.gridy++;
+ this.add(jlWsdlLocation, c);
+
+ c.fill = GridBagConstraints.NONE;
+ c.gridy++;
+ this.add(jtDescription, c);
+
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.gridy++;
+ this.add(jlSoapInputs, c);
+
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.gridy++;
+ this.add(jlSoapOutputs, c);
+
+ return (c);
+ }
+
+@Override
+boolean shouldBeHidden(Object itemToRender) {
+ if (!(itemToRender instanceof SoapOperation)) {
+ return false;
+ }
+ SoapOperation soapOp = (SoapOperation) itemToRender;
+ Ancestors ancestors = soapOp.getAncestors();
+ Service service = ancestors.getService();
+ if (soapOp.isSetArchived() || service.isSetArchived()) {
+ return true;
+ } else if (isSoapLab(service)) {
+ return true;
+ }
+ else {
+ return false;
+ }
+
+}
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/SearchResultsListingPanel.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/SearchResultsListingPanel.java
new file mode 100644
index 0000000..c88de40
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/SearchResultsListingPanel.java
@@ -0,0 +1,870 @@
+package net.sf.taverna.biocatalogue.ui.search_results;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Desktop;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.net.URI;
+import java.util.List;
+import java.util.concurrent.CountDownLatch;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.BorderFactory;
+import javax.swing.DefaultListModel;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JScrollPane;
+import javax.swing.JToolBar;
+import javax.swing.ListCellRenderer;
+import javax.swing.ListModel;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingUtilities;
+import javax.swing.event.ListDataListener;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+
+import net.sf.taverna.biocatalogue.model.BioCataloguePluginConstants;
+import net.sf.taverna.biocatalogue.model.LoadingExpandedResource;
+import net.sf.taverna.biocatalogue.model.LoadingResource;
+import net.sf.taverna.biocatalogue.model.Resource;
+import net.sf.taverna.biocatalogue.model.Resource.TYPE;
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.biocatalogue.model.Util;
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
+import net.sf.taverna.biocatalogue.model.search.SearchInstance;
+import net.sf.taverna.biocatalogue.ui.JWaitDialog;
+import net.sf.taverna.t2.lang.ui.ModelMap;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponent;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentFactory;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.Integration;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check.ServiceHealthChecker;
+import net.sf.taverna.t2.workbench.MainWindow;
+import net.sf.taverna.t2.workbench.ModelMapConstants;
+import net.sf.taverna.t2.workbench.ui.Workbench;
+import net.sf.taverna.t2.workbench.ui.zaria.PerspectiveSPI;
+
+import org.apache.log4j.Logger;
+import org.biocatalogue.x2009.xml.rest.ResourceLink;
+import org.biocatalogue.x2009.xml.rest.RestMethod;
+import org.biocatalogue.x2009.xml.rest.Service;
+import org.biocatalogue.x2009.xml.rest.ServiceTechnologyType;
+
+/**
+ * This class is responsible for producing search results listing panel. It only
+ * shows a single listing for a specified type. Multiple types are handled by
+ * having different tabs in {@link SearchResultsMainPanel} with instances of
+ * this class in each.
+ *
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public class SearchResultsListingPanel extends JPanel implements MouseListener,
+ SearchResultsRenderer, MouseMotionListener {
+ public static final int SEARCH_STATUS_TOOLTIP_LINE_LENGTH = 65;
+
+ private static final Logger logger = Logger.getLogger(SearchResultsListingPanel.class);
+ private final SearchResultsMainPanel parentMainSearchResultsPanel;
+
+ // currently displayed search results
+ SearchInstance searchInstance;
+
+ // main UI components
+ private SearchResultsListingPanel thisPanel;
+ private DefaultListModel resultsListingModel;
+ private JList jlResultsListing;
+ private JScrollPane spResultsListing;
+
+ // contextual menu
+ private JPopupMenu contextualMenu;
+ private Action addToServicePanelAction;
+ private Action addToWorkflowDiagramAction;
+ private Action openInBioCatalogueAction;
+ private Action doHealthCheckAction;
+ private Action addAllOperationsToServicePanelAction;
+
+ // search status and actions on selected items in the list
+ private JToolBar tbSelectedItemActions;
+ protected JPanel jpSearchStatus;
+ private JLabel jlSearchStatus;
+
+ // this is used for previewing items from the result listing through
+ // contextual menu -
+ // value will be updated by mouse event accordingly
+ private ResourceLink potentialObjectToPreview;
+ private final TYPE typeToPreview;
+
+ // Design perspective - some actions require switching to it
+ PerspectiveSPI designPerspective;
+
+ private ListCellRenderer listingCellRenderer;
+
+ /**
+ * @param typeToPreview
+ * Resource type that will be previewed in this panel.
+ * @param parentMainSearchResultsPanel
+ * Reference to a "parent" of this panel - this is needed to
+ * notify the main results panel with the
+ */
+ public SearchResultsListingPanel(TYPE typeToPreview,
+ SearchResultsMainPanel parentMainSearchResultsPanel) {
+ this.thisPanel = this;
+
+ this.typeToPreview = typeToPreview;
+ listingCellRenderer = this.typeToPreview
+ .getResultListingCellRenderer();
+ this.parentMainSearchResultsPanel = parentMainSearchResultsPanel;
+ MainComponentFactory
+ .getSharedInstance();
+
+ initialiseUI();
+
+ this.setPreferredSize(new Dimension(800, 400));
+ }
+
+ private void initialiseUI() {
+
+ this.addToServicePanelAction = new AbstractAction(
+ "Add to Service Panel",
+ ResourceManager
+ .getImageIcon(ResourceManager.ADD_PROCESSOR_AS_FAVOURITE_ICON)) {
+ // Tooltip
+ {
+ this.putValue(SHORT_DESCRIPTION, "Add selected "
+ + typeToPreview.getTypeName()
+ + " to the Service Panel");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ final JWaitDialog jwd = new JWaitDialog(
+ MainComponent.dummyOwnerJFrame,
+ "Service Catalogue Plugin - Adding "
+ + typeToPreview.getTypeName(),
+ "<html><center>Please wait for selected "
+ + typeToPreview.getTypeName()
+ + " details to be fetched from the Service Catalogue<br>"
+ + "and to be added into the Service Panel.</center></html>");
+
+ new Thread("Adding " + typeToPreview.getTypeName()
+ + " into Service Panel") {
+ public void run() {
+ // if it is the expanded that we are looking at, need to extract
+ // the 'associated' object
+ ResourceLink processorResourceToAdd = (potentialObjectToPreview instanceof LoadingExpandedResource ? ((LoadingExpandedResource) potentialObjectToPreview)
+ .getAssociatedObj()
+ : potentialObjectToPreview);
+
+ JComponent insertionOutcome = Integration
+ .insertProcesorIntoServicePanel(processorResourceToAdd);
+ jwd.waitFinished(insertionOutcome);
+
+ // Switch to Design Perspective
+ switchToDesignPerspective();
+ }
+ }.start();
+
+ // NB! The modal dialog window needs to be made visible after
+ // the background
+ // process (i.e. adding a processor) has already been started!
+ jwd.setVisible(true);
+ }
+ };
+
+ // For a parent Web service, action to add all operations to the Service Panel.
+ // Works for SOAP services at the moment.
+ this.addAllOperationsToServicePanelAction = new AbstractAction(
+ "Add all operations to Service Panel",
+ ResourceManager
+ .getImageIcon(ResourceManager.ADD_ALL_SERVICES_AS_FAVOURITE_ICON)) {
+ // Tooltip
+ {
+ this.putValue(SHORT_DESCRIPTION, "Add all associated services to the Service Panel");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ final JWaitDialog jwd = new JWaitDialog(
+ MainComponent.dummyOwnerJFrame,
+ "Service Catalogue Plugin - Adding "
+ + typeToPreview.getTypeName(),
+ "<html><center>Please wait for selected "
+ + typeToPreview.getTypeName()
+ + " details to be fetched from the Service Catalogue<br>"
+ + "and to be added into the Service Panel.</center></html>");
+
+ new Thread("Adding all operations of " + typeToPreview.getTypeName()
+ + " to the Service Panel") {
+ public void run() {
+ // if it is the expanded that we are looking at, need to extract
+ // the 'associated' object
+ ResourceLink resourceLink = (potentialObjectToPreview instanceof LoadingExpandedResource ? ((LoadingExpandedResource) potentialObjectToPreview)
+ .getAssociatedObj()
+ : potentialObjectToPreview);
+
+ JComponent insertionOutcome = Integration
+ .insertAllOperationsIntoServicePanel(resourceLink);
+ jwd.waitFinished(insertionOutcome);
+
+ // Switch to Design Perspective
+ switchToDesignPerspective();
+ }
+ }.start();
+
+ // NB! The modal dialog window needs to be made visible after
+ // the background
+ // process (i.e. adding a processor) has already been started!
+ jwd.setVisible(true);
+ }
+ };
+
+ this.addToWorkflowDiagramAction = new AbstractAction(
+ "Add to workflow",
+ ResourceManager
+ .getImageIcon(ResourceManager.ADD_PROCESSOR_TO_WORKFLOW_ICON)) {
+ // Tooltip
+ {
+ this.putValue(SHORT_DESCRIPTION, "<html>Insert selected "
+ + typeToPreview.getTypeName()
+ + " into the current workflow</html>");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ final JWaitDialog jwd = new JWaitDialog(
+ MainComponent.dummyOwnerJFrame,
+ "Service Catalogue Plugin - Adding "
+ + typeToPreview.getTypeName(),
+ "<html><center>Please wait for selected "
+ + typeToPreview.getTypeName()
+ + " details to be fetched from the Service Catalogue<br>"
+ + "and to be added into the current workflow.</center></html>");
+
+ new Thread("Adding " + typeToPreview.getTypeName()
+ + " into workflow") {
+ public void run() {
+ // if it is the expanded that we are looking at, need to extract
+ // the 'associated' object
+ ResourceLink processorResourceToAdd = (potentialObjectToPreview instanceof LoadingExpandedResource ? ((LoadingExpandedResource) potentialObjectToPreview)
+ .getAssociatedObj()
+ : potentialObjectToPreview);
+
+ JComponent insertionOutcome = Integration
+ .insertProcessorIntoCurrentWorkflow(processorResourceToAdd);
+ jwd.waitFinished(insertionOutcome);
+
+ // Switch to Design Perspective
+ switchToDesignPerspective();
+ }
+ }.start();
+
+ // NB! The modal dialog window needs to be made visible after
+ // the background
+ // process (i.e. adding a processor) has already been started!
+ jwd.setVisible(true);
+ }
+ };
+
+ this.openInBioCatalogueAction = new AbstractAction(
+ "Open in the Service Catalogue",
+ ResourceManager
+ .getImageIcon(ResourceManager.OPEN_IN_BIOCATALOGUE_ICON)) {
+ // Tooltip
+ {
+ this.putValue(SHORT_DESCRIPTION, "<html>View selected "
+ + typeToPreview.getTypeName()
+ + " on the Service Catalogue Web site.<br>"
+ + "This will open your standard Web browser.</html>");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ String hrefString = potentialObjectToPreview.getHref();
+ try {
+ Desktop.getDesktop().browse(new URI(hrefString));
+ }
+ catch (Exception ex) {
+ logger.error("Failed while trying to open the URL in a standard browser; URL was: " +
+ hrefString + "\nException was: " + ex + "\n" + ex.getStackTrace());
+ };
+ }
+ };
+
+ this.doHealthCheckAction = new AbstractAction(
+ "Check monitoring status",
+ ResourceManager
+ .getImageIcon(ResourceManager.EXECUTE_HEALTH_CHECK_ICON)) {
+ // Tooltip
+ {
+ this
+ .putValue(
+ SHORT_DESCRIPTION,
+ "<html>Fetch the latest monitoring data for selected "
+ + typeToPreview.getTypeName()
+ + ".<br>"
+ + "Data will be obtained from the Service Catalogue and displayed in a popup window.</html>");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ // if it is the expanded that we are looking at, need to extract
+ // the 'associated' object
+ ResourceLink resourceForHealthCheck = (potentialObjectToPreview instanceof LoadingExpandedResource ? ((LoadingExpandedResource) potentialObjectToPreview)
+ .getAssociatedObj()
+ : potentialObjectToPreview);
+
+ ServiceHealthChecker.checkResource(resourceForHealthCheck);
+ }
+ };
+
+ tbSelectedItemActions = new JToolBar(JToolBar.HORIZONTAL);
+ tbSelectedItemActions.setBorderPainted(true);
+ tbSelectedItemActions.setBorder(BorderFactory.createEmptyBorder(5, 5,
+ 5, 3));
+ tbSelectedItemActions.setFloatable(false);
+ if (typeToPreview.isSuitableForAddingToServicePanel()) {
+ tbSelectedItemActions.add(addToServicePanelAction);
+ }
+ if (typeToPreview.isSuitableForAddingAllToServicePanel()) {
+ tbSelectedItemActions.add(addAllOperationsToServicePanelAction);
+ }
+ if (typeToPreview.isSuitableForAddingToWorkflowDiagram()) {
+ tbSelectedItemActions.add(addToWorkflowDiagramAction);
+ }
+ if (typeToPreview.isSuitableForHealthCheck()) {
+ tbSelectedItemActions.add(doHealthCheckAction);
+ }
+ tbSelectedItemActions.add(openInBioCatalogueAction);
+
+ // *** Prepare search results status panel ***
+
+ GridBagConstraints c = new GridBagConstraints();
+ jpSearchStatus = new JPanel(new GridBagLayout());
+ c.anchor = GridBagConstraints.WEST;
+ c.weightx = 0;
+ jpSearchStatus.add(tbSelectedItemActions, c);
+
+ jlSearchStatus = new JLabel();
+ jlSearchStatus.setIconTextGap(20);
+ c.weightx = 1.0;
+ c.insets = new Insets(0, 20, 0, 0);
+ jpSearchStatus.add(jlSearchStatus, c);
+
+ if (parentMainSearchResultsPanel.getFilterTreePaneFor(typeToPreview) != null) {
+ Dimension preferredSize = new Dimension(200,
+ parentMainSearchResultsPanel.getFilterTreePaneFor(
+ typeToPreview).getTreeToolbarPreferredSize().height);
+
+ // HACK: due to concurrency issues, sometimes this doesn't work
+ // correctly -
+ // to rectify the problem using the hard-coded value that was
+ // correct at
+ // the time of coding...
+ if (preferredSize.height < 30) {
+ preferredSize.height = 33;
+ }
+
+ jpSearchStatus.setPreferredSize(preferredSize);
+ }
+
+ // *** Create list to hold search results and wrap it into a scroll pane
+ // ***
+ resultsListingModel = new DefaultListModel();
+ jlResultsListing = new JList(resultsListingModel);
+ jlResultsListing.setDoubleBuffered(true);
+ jlResultsListing.setCellRenderer(listingCellRenderer);
+ jlResultsListing.addMouseListener(this);
+ jlResultsListing.addMouseMotionListener(this);
+ jlResultsListing.setBackground(thisPanel.getBackground());
+
+ jlResultsListing.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ jlResultsListing.addListSelectionListener(new ListSelectionListener() {
+ public void valueChanged(ListSelectionEvent e) {
+ if (!e.getValueIsAdjusting()) {
+ // update value to be used in contextual menu click handler
+ // to act on the just-selected entry
+ potentialObjectToPreview = getResourceSelectedInJList();
+
+ if (potentialObjectToPreview != null) {
+
+ // only enable actions in the menu if the list entry
+ // that is being
+ // clicked on is beyond the initial 'loading' state
+ boolean shown = !isListEntryOnlyWithInitialDetails(potentialObjectToPreview);
+ boolean shownAndNotArchived = shown && !isArchived(potentialObjectToPreview);
+ addToServicePanelAction
+ .setEnabled(shownAndNotArchived);
+ addAllOperationsToServicePanelAction
+ .setEnabled(shownAndNotArchived && !(potentialObjectToPreview instanceof RestMethod));
+ addToWorkflowDiagramAction
+ .setEnabled(shownAndNotArchived);
+ openInBioCatalogueAction
+ .setEnabled(shown);
+ doHealthCheckAction
+ .setEnabled(shown);
+
+ return;
+ }
+ }
+
+ // disable actions if nothing is selected in the list or if
+ // selection is still "adjusting"
+ addToServicePanelAction.setEnabled(false);
+ addAllOperationsToServicePanelAction.setEnabled(false);
+ addToWorkflowDiagramAction.setEnabled(false);
+ openInBioCatalogueAction.setEnabled(false);
+ doHealthCheckAction.setEnabled(false);
+ }
+ });
+
+ spResultsListing = new JScrollPane(jlResultsListing);
+ spResultsListing.getVerticalScrollBar().addAdjustmentListener(
+ new AdjustmentListener() {
+ public void adjustmentValueChanged(AdjustmentEvent e) {
+ if (!e.getValueIsAdjusting()) {
+ // load missing details on adjusting the scroll bar
+ //
+ // only start loading more results in case if the
+ // value is "not adjusting" -
+ // this means that the mouse has been released and
+ // is not dragging the scroll bar
+ // any more, so effectively the user has stopped
+ // scrolling
+ checkAllEntriesInTheVisiblePartOfJListAreLoaded();
+ }
+ }
+ });
+
+ // tie components to the class panel itself
+ this.resetSearchResultsListing(true);
+
+ // *** Create CONTEXTUAL MENU ***
+
+ contextualMenu = new JPopupMenu();
+ if (typeToPreview.isSuitableForAddingToServicePanel()) {
+ contextualMenu.add(addToServicePanelAction);
+ contextualMenu.add(addAllOperationsToServicePanelAction);
+ }
+ if (typeToPreview.isSuitableForAddingToWorkflowDiagram()) {
+ contextualMenu.add(addToWorkflowDiagramAction);
+ }
+ if (typeToPreview.isSuitableForHealthCheck()) {
+ contextualMenu.add(doHealthCheckAction);
+ }
+ contextualMenu.add(openInBioCatalogueAction);
+ }
+
+ /**
+ * Allows to set the search status by supplying the message to display.
+ */
+ protected void setSearchStatusText(final String statusString,
+ final boolean spinnerActive) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ jlSearchStatus
+ .setIcon(spinnerActive ? ResourceManager
+ .getImageIcon(ResourceManager.BAR_LOADER_ORANGE)
+ : null);
+
+ jlSearchStatus.setText(statusString);
+ jlSearchStatus.setToolTipText("<html>"
+ + Util.ensureLineLengthWithinString(statusString,
+ SEARCH_STATUS_TOOLTIP_LINE_LENGTH, false)
+ + "</html>");
+ }
+ });
+ }
+
+ /**
+ * This helper method is used to initialise this panel. Also invoked when
+ * search results need to be cleared.
+ *
+ * @param showSuggestion
+ * <code>true</code> should be used on first load of the panel -
+ * in that case a suggestion would be displayed to perform a
+ * search, tag search or start directly with filtering;<br/>
+ * <code>false</code> to be used when resetting the panel after
+ * perfoming the search, but not finding any results.
+ */
+ public void resetSearchResultsListing(boolean showSuggestion) {
+ setSearchStatusText("No searches were made yet", false);
+
+ String labelText = "<html><center>"
+ + (showSuggestion ? "You can find "
+ + this.typeToPreview.getCollectionName()
+ + " by typing a search query."
+ + (this.typeToPreview.isSuitableForFiltering() ? "<br><br>Alternatively, you can select some filters from the tree on the left."
+ : "")
+ : "There are no "
+ + this.typeToPreview.getCollectionName()
+ + " that match your search criteria<br><br>"
+ + "Please try making the search query shorter or selecting fewer filters")
+ + "</center></html>";
+
+ JLabel jlMainLabel = new JLabel(labelText, JLabel.CENTER);
+ jlMainLabel.setFont(jlMainLabel.getFont().deriveFont(Font.PLAIN, 16));
+ jlMainLabel.setBorder(BorderFactory.createEtchedBorder());
+
+ this.removeAll();
+ this.setLayout(new BorderLayout(0, 0));
+ this.add(jpSearchStatus, BorderLayout.NORTH);
+ this.add(jlMainLabel, BorderLayout.CENTER);
+ this.validate();
+
+ // disable the toolbar actions
+ this.addToServicePanelAction.setEnabled(false);
+ this.addToWorkflowDiagramAction.setEnabled(false);
+ this.openInBioCatalogueAction.setEnabled(false);
+ this.doHealthCheckAction.setEnabled(false);
+ this.addAllOperationsToServicePanelAction.setEnabled(false);
+ }
+
+ /**
+ * Statistics will be rendered along with the collection of found items.
+ *
+ * @param searchInstance
+ * SearchInstance containing search results to render.
+ */
+ public void renderResults(SearchInstance searchInstance) {
+ // make the current search instance available globally within this class
+ this.searchInstance = searchInstance;
+
+ // stop spinner icon on the tab that is populated and add number of
+ // results
+ parentMainSearchResultsPanel.setDefaultIconForTab(typeToPreview);
+ parentMainSearchResultsPanel.setDefaultTitleForTabWithSuffix(
+ typeToPreview, " ("
+ + searchInstance.getSearchResults()
+ .getTotalMatchingItemCount() + ")");
+
+ // if nothing was found - display notification and finish result
+ // processing
+ if (searchInstance.getSearchResults().getTotalMatchingItemCount() == 0) {
+ resetSearchResultsListing(false);
+
+ // must happen after resetting the listing, as it replaces the
+ // default status text
+ setSearchStatusText("No results found for "
+ + searchInstance.getDescriptionStringForSearchStatus(),
+ false);
+ return;
+ }
+
+ // populate results
+ if (searchInstance.getSearchResults().getTotalMatchingItemCount() > 0) {
+ // populate the list box with users
+
+ List<? extends ResourceLink> foundItems = searchInstance
+ .getSearchResults().getFoundItems();
+ for (ResourceLink item : foundItems) {
+ resultsListingModel.addElement(item);
+ }
+ }
+
+ // update the UI once contents are ready
+ thisPanel.removeAll();
+ thisPanel.setLayout(new BorderLayout(0, 0));
+ thisPanel.add(jpSearchStatus, BorderLayout.NORTH);
+ thisPanel.add(spResultsListing, BorderLayout.CENTER);
+ thisPanel.repaint();
+
+ // automatically start loading details for the first section of result
+ // listing
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ checkAllEntriesInTheVisiblePartOfJListAreLoaded();
+ }
+ });
+
+ // *** Also update status text ***
+
+ setSearchStatusText("Search results for "
+ + searchInstance.getDescriptionStringForSearchStatus(), false);
+ }
+
+ /**
+ * Check if details are fetched for all result entries that are currently
+ * visible in the JList.
+ *
+ * If some are not yet loaded, identifies the page in the index of
+ * corresponding resources to fetch details.
+ *
+ * When done, recursively calls itself again to verify that no more entries
+ * need further details loaded.
+ */
+ private void checkAllEntriesInTheVisiblePartOfJListAreLoaded() {
+ int firstVisibleIndex = jlResultsListing.getFirstVisibleIndex();
+
+ if (firstVisibleIndex >= 0) {
+ int lastVisibleIndex = jlResultsListing.getLastVisibleIndex();
+
+ final int firstNotFetchedMatchingItemIndex = searchInstance
+ .getSearchResults().getFirstMatchingItemIndexNotYetFetched(
+ firstVisibleIndex, lastVisibleIndex);
+ final int pageToFetchNumber = searchInstance.getSearchResults()
+ .getMatchingItemPageNumberFor(
+ firstNotFetchedMatchingItemIndex);
+
+ // check if found a valid page to load
+ if (pageToFetchNumber != -1) {
+ int numberOfResourcesPerPageForThisResourceType = searchInstance
+ .getSearchResults().getTypeOfResourcesInTheResultSet()
+ .getApiResourceCountPerIndexPage();
+
+ int firstListIndexToLoad = searchInstance.getSearchResults()
+ .getFirstItemIndexOn(pageToFetchNumber); // first
+ // element
+ // on the
+ // page that
+ // is about
+ // to be
+ // loaded
+ int countToLoad = Math.min(
+ numberOfResourcesPerPageForThisResourceType, // if the
+ // last
+ // page
+ // isn't
+ // full,
+ // need
+ // to
+ // mark
+ // less
+ // items
+ // than
+ // the
+ // full
+ // page
+ resultsListingModel.getSize() - firstListIndexToLoad);
+
+ // mark the next "page" of items in the JList as "loading" -
+ // but also mark them in the SearchResults backing list, so
+ // that next calls to this listener are aware of the previous
+ // items that were marked as "loading"
+ for (int i = firstListIndexToLoad; i < firstListIndexToLoad
+ + countToLoad; i++) {
+ ((LoadingResource) searchInstance.getSearchResults()
+ .getFoundItems().get(i)).setLoading(true);
+ }
+
+ // update the UI to show 'loading' state on relevant entries
+ renderFurtherResults(searchInstance, firstListIndexToLoad,
+ countToLoad);
+
+ // now start loading data for the 'loading' entries
+ final CountDownLatch latch = new CountDownLatch(1);
+ new Thread("Search via the API") {
+ public void run() {
+ try {
+ searchInstance.fetchMoreResults(
+ parentMainSearchResultsPanel, latch,
+ thisPanel, pageToFetchNumber);
+ } catch (Exception e) {
+ logger.error("Error while searching via the Service Catalogue API", e);
+
+ }
+ }
+ }.start();
+
+ // wait for the previous portion of results to load, then fetch
+ // the next portion
+ new Thread(
+ "Fetch more another page of details for search results") {
+ public void run() {
+ try {
+ latch.await();
+ checkAllEntriesInTheVisiblePartOfJListAreLoaded();
+ } catch (InterruptedException e) {
+ logger
+ .error(
+ "Failed to wait for the previous page of results to load to check if "
+ + "another one needs loading as well. Details in the attache exception.",
+ e);
+ }
+ }
+ }.start();
+
+ }
+ }
+ }
+
+ /**
+ * Tests whether {@link ResourceLink} object corresponding to an entry in
+ * the search results list is in the state where only the first (initial)
+ * fragment of data was loaded (through BioCatalogue LITE JSON API) that
+ * contains just the title + URL of the resource.
+ *
+ * @param resource
+ * @return
+ */
+ private boolean isListEntryOnlyWithInitialDetails(ResourceLink resource) {
+ return (resource instanceof LoadingResource);
+ }
+
+ private boolean isArchived(ResourceLink resource) {
+ if (listingCellRenderer instanceof ExpandableOnDemandLoadedListCellRenderer) {
+ ExpandableOnDemandLoadedListCellRenderer r = (ExpandableOnDemandLoadedListCellRenderer) listingCellRenderer;
+ return r.shouldBeHidden(resource);
+ }
+ return false;
+ }
+
+
+ // ***** Callbacks for MouseListener *****
+
+ public void mouseClicked(MouseEvent e) {
+ }
+
+ public void mouseEntered(MouseEvent e) { /* NOT IN USE */
+ }
+
+ public void mouseExited(MouseEvent e) { /* NOT IN USE */
+ }
+
+ public void mousePressed(MouseEvent e) {
+ // checked in both mousePressed() & mouseReleased() for cross-platform
+ // operation
+ maybeShowPopupMenu(e);
+ }
+
+ public void mouseReleased(MouseEvent e) {
+ // checked in both mousePressed() & mouseReleased() for cross-platform
+ // operation
+ maybeShowPopupMenu(e);
+ }
+
+ // ***** Callbacks for MouseMotionListener *****
+
+ public void mouseMoved(MouseEvent e) {
+ }
+
+ public void mouseDragged(MouseEvent e) { /* do nothing */
+ }
+
+ /**
+ * Gets the selected object from the specified list. Used for previewing
+ * items through double-clicks and contextual menu.
+ *
+ * @return <code>null</code> if no selection in the list,
+ * <code>ResourceLink</code> object that is currently selected
+ * otherwise.
+ */
+ private ResourceLink getResourceSelectedInJList() {
+ return (jlResultsListing.getSelectedIndex() == -1 ? null
+ : (ResourceLink) jlResultsListing.getSelectedValue());
+ }
+
+ private void maybeShowPopupMenu(MouseEvent e) {
+ if (e.getSource().equals(jlResultsListing) && e.isPopupTrigger()
+ && jlResultsListing.locationToIndex(e.getPoint()) != -1) {
+ // select the entry in the list that triggered the event to show
+ // this popup menu
+ jlResultsListing.setSelectedIndex(jlResultsListing
+ .locationToIndex(e.getPoint()));
+
+ // update value to be used in contextual menu click handler to act
+ // on the just-selected entry
+ potentialObjectToPreview = getResourceSelectedInJList();
+
+ // show the contextual menu
+ this.contextualMenu.show(e.getComponent(), e.getX(), e.getY());
+ }
+ }
+
+ // *** Callbacks for SearchResultsRenderer ***
+
+ public void renderInitialResults(final SearchInstance si) {
+ // NB! critical to have UI update done within the invokeLater()
+ // method - this is to prevent UI from 'flashing' and to
+ // avoid concurrency-related errors
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // make sure to remove any old results from the list model!
+ resultsListingModel.clear();
+
+ // display the partial search results
+ logger.debug("Started rendering initial search results for "
+ + si.getResourceTypeToSearchFor().getCollectionName());
+ renderResults(si);
+ logger.debug("Finished rendering initial search results for "
+ + si.getResourceTypeToSearchFor().getCollectionName());
+ }
+ });
+ }
+
+ public void renderFurtherResults(SearchInstance si, int startIndex,
+ int count) {
+ renderFurtherResults(si, startIndex, count, false);
+ }
+
+ public void renderFurtherResults(final SearchInstance si,
+ final int startIndex, final int count,
+ final boolean disableListDataListeners) {
+ logger.debug("Started rendering further search results for "
+ + si.getResourceTypeToSearchFor().getCollectionName());
+
+ // NB! very important to remove all listeners here, so that the JList
+ // won't "freeze"
+ // on updating the components
+ ListDataListener[] listeners = null;
+ if (disableListDataListeners) {
+ listeners = resultsListingModel.getListDataListeners();
+ for (ListDataListener listener : listeners) {
+ resultsListingModel.removeListDataListener(listener);
+ }
+ }
+
+ for (int i = startIndex; i < startIndex + count
+ && i < resultsListingModel.getSize(); i++) {
+ resultsListingModel.set(i, searchInstance.getSearchResults()
+ .getFoundItems().get(i));
+ }
+
+ // reset all listeners in case they were removed
+ if (disableListDataListeners) {
+ for (ListDataListener listener : listeners) {
+ resultsListingModel.addListDataListener(listener);
+ }
+ }
+
+ // NB! critical to have UI update done within the invokeLater()
+ // method - this is to prevent UI from 'flashing' and to
+ // avoid some weird errors
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ jlResultsListing.validate();
+ jlResultsListing.repaint();
+
+ logger.debug("Finished rendering further search results for "
+ + si.getResourceTypeToSearchFor().getCollectionName());
+ }
+ });
+ }
+
+ private void switchToDesignPerspective() {
+ if (designPerspective == null) {
+ for (PerspectiveSPI perspective : Workbench.getInstance()
+ .getPerspectives().getPerspectives()) {
+ if (perspective.getText().equalsIgnoreCase("design")) {
+ designPerspective = perspective;
+ break;
+ }
+ }
+ }
+
+ if (designPerspective != null) {
+ ModelMap.getInstance().setModel(
+ ModelMapConstants.CURRENT_PERSPECTIVE, designPerspective);
+ }
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/SearchResultsMainPanel.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/SearchResultsMainPanel.java
new file mode 100644
index 0000000..a3fca27
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/SearchResultsMainPanel.java
@@ -0,0 +1,498 @@
+package net.sf.taverna.biocatalogue.ui.search_results;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.concurrent.CountDownLatch;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JToggleButton;
+
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.biocatalogue.model.Resource.TYPE;
+import net.sf.taverna.biocatalogue.model.search.SearchInstance;
+import net.sf.taverna.biocatalogue.model.search.SearchInstanceTracker;
+import net.sf.taverna.biocatalogue.model.search.SearchOptions;
+import net.sf.taverna.biocatalogue.model.search.ServiceFilteringSettings;
+import net.sf.taverna.biocatalogue.ui.filtertree.FilterTreePane;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentFactory;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class represents the main panel that deals with the status
+ * and results of the current search.
+ *
+ * It has a status label, spinner to depict search in progress,
+ * actual search results split into tabs by their type, a toolbar
+ * with search history, favourite searches settings, favourite filters,
+ * ability to restart last search, etc.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class SearchResultsMainPanel extends JPanel implements ActionListener, SearchInstanceTracker
+{
+ private final SearchResultsMainPanel instanceOfSelf;
+ private Logger logger;
+
+ private LinkedHashMap<TYPE, JComponent> searchResultTabs;
+ private Map<TYPE, SearchResultsListingPanel> searchResultListings;
+
+ // holds a reference to the instance of the search instances in the current context
+ // that should be active at the moment (will aid early termination of older searches
+ // when new ones are started)
+ private Map<TYPE, SearchInstance> currentSearchInstances;
+
+ // holds a map of references to the current instances of filter trees per resource type
+ private Map<TYPE, FilterTreePane> currentFilterPanes;
+
+
+ // COMPONENTS
+ private JTabbedPane tabbedSearchResultPanel;
+
+ protected JToggleButton bToggleSearchHistory;
+ protected JButton bRefreshLastSearch;
+ protected JButton bClearSearchResults;
+
+
+ public SearchResultsMainPanel()
+ {
+ this.instanceOfSelf = this;
+ MainComponentFactory.getSharedInstance();
+ this.logger = Logger.getLogger(SearchResultsMainPanel.class);
+
+ this.currentSearchInstances = new HashMap<TYPE,SearchInstance>();
+
+ this.searchResultListings = new HashMap<TYPE, SearchResultsListingPanel>();
+ this.currentFilterPanes = new HashMap<TYPE,FilterTreePane>();
+ this.searchResultTabs = new LinkedHashMap<TYPE, JComponent>(); // crucial to preserve the order -- so that these tabs always appear in the UI in the same order!
+ initialiseResultTabsMap();
+
+ initialiseUI();
+ }
+
+
+ private void initialiseUI()
+ {
+ // create a panel for tabbed listings of search results
+ this.tabbedSearchResultPanel = new JTabbedPane();
+ reloadResultTabsFromMap();
+
+ // pack all main components together
+ JPanel jpMainResultsPanel = new JPanel(new BorderLayout());
+ jpMainResultsPanel.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 3));
+
+ jpMainResultsPanel.add(tabbedSearchResultPanel, BorderLayout.CENTER);
+
+
+ // --- Put together all parts ---
+ // main components in the middle, toolbar on the right
+ this.setMinimumSize(new Dimension(450, 50));
+ this.setLayout(new BorderLayout());
+ this.add(jpMainResultsPanel, BorderLayout.CENTER);
+
+ // FIXME - add toolbar to the main window!
+// this.add(tbSearchActions, BorderLayout.EAST);
+ }
+
+
+
+ // ----- Hiding / Showing tabs for various search result types -----
+
+ /**
+ * Dynamically populates the map of resource types and components that represent these types
+ * in the tabbed pane -- this is only to be done once during the initialisation.
+ */
+ private void initialiseResultTabsMap()
+ {
+ for (TYPE t : TYPE.values()) {
+ toggleResultTabsInMap(t, t.isDefaultSearchType());
+ }
+ }
+
+
+ /**
+ * Adds or removes a tab for a specified type of resource.
+ *
+ * @param type Resource type for which the tab is to be added / removed.
+ * @param doShowTab Defines whether to add or remove tab for this resource type.
+ */
+ public void toggleResultTabsInMap(TYPE type, boolean doShowTab)
+ {
+ JPanel jpResultTabContent = null;
+
+ if (doShowTab)
+ {
+ jpResultTabContent = new JPanel(new GridLayout());
+
+ // decide if this resource type supports filtering
+ if (type.isSuitableForFiltering()) {
+ FilterTreePane filterTreePane = new FilterTreePane(type);
+ this.currentFilterPanes.put(type, filterTreePane);
+ }
+ else {
+ // not suitable for filtering - record this in a map
+ this.currentFilterPanes.put(type, null);
+ }
+
+
+ SearchResultsListingPanel resultsListingPanel = new SearchResultsListingPanel(type, this);
+ this.searchResultListings.put(type, resultsListingPanel);
+
+ if (this.currentFilterPanes.get(type) == null) {
+ jpResultTabContent.add(resultsListingPanel);
+ }
+ else {
+ JSplitPane spFiltersAndResultListing = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT);
+ spFiltersAndResultListing.setLeftComponent(this.currentFilterPanes.get(type));
+ spFiltersAndResultListing.setRightComponent(resultsListingPanel);
+ jpResultTabContent.add(spFiltersAndResultListing);
+ }
+ }
+ else {
+ // tab for this type is being hidden - just remove the references
+ // to the search result listing and to filter pane
+ this.searchResultListings.put(type, null);
+ this.currentFilterPanes.put(type, null);
+ }
+
+ this.searchResultTabs.put(type, jpResultTabContent);
+ }
+
+
+ /**
+ * (Re-)loads the user interface from the internal map.
+ */
+ public void reloadResultTabsFromMap()
+ {
+ Component selectedTabsComponent = tabbedSearchResultPanel.getSelectedComponent();
+ tabbedSearchResultPanel.removeAll();
+ for (TYPE type : this.searchResultTabs.keySet()) {
+ JComponent c = this.searchResultTabs.get(type);
+ if (c != null) {
+ tabbedSearchResultPanel.addTab(type.getCollectionName(), type.getIcon(), c, type.getCollectionTabTooltip());
+ }
+ }
+
+ // attempt to re-select the same tab that was open before reloading
+ try {
+ tabbedSearchResultPanel.setSelectedComponent(selectedTabsComponent);
+ }
+ catch (IllegalArgumentException e) {
+ // failed - probably previously selected tab got removed - select the first one
+ tabbedSearchResultPanel.setSelectedIndex(0);
+ }
+ }
+
+
+ /**
+ * @param resourceType Resource type to look for.
+ * @return Current index of the tab in the results tabbed pane view
+ * that holds a component showing search results for this type.
+ * Returns <code>-1</code> if requested type is not currently displayed.
+ */
+ protected int getTabIndexForResourceType(TYPE resourceType) {
+ return (tabbedSearchResultPanel.indexOfComponent(searchResultTabs.get(resourceType)));
+ }
+
+
+ // ----- ------
+
+
+ /**
+ * This method is intended to be called when filter options in one of the tabs change.
+ * It starts the new filtering operation.
+ *
+ * Effectively it sets the filtering parameters for the SearchInstance
+ * and then starts a new search with that {@link SearchInstance} wrapped into {@link SearchOptions}.
+ *
+ * @param resourceType Resource type for which the new filtering operation is started
+ * @param filteringSettings Filtering settings for the current filtering operation
+ * obtained from the filter tree (or favourite filters).
+ */
+ public void startNewFiltering(TYPE resourceType, ServiceFilteringSettings filteringSettings)
+ {
+ SearchInstance siPreviousSearchForThisType = getCurrentSearchInstance(resourceType);
+
+ // pass on the filtering parameters to the relevant search instance (this will overwrite the old ones if any were present!)
+ if (siPreviousSearchForThisType == null) {
+ // no filterings have been done earlier for this resource type;
+ // we'll need a new (blank) query search SearchInstance and
+ // wrap it into a service filtering SearchInstance
+ siPreviousSearchForThisType = new SearchInstance(new SearchInstance("", resourceType), filteringSettings);
+ }
+ else {
+ if (!siPreviousSearchForThisType.isServiceFilteringSearch()) {
+ // just wrap existing search instance that was (probably) transferred from the Search tab
+ // into another SearchInstance that explicitly deals with service filtering
+ siPreviousSearchForThisType = new SearchInstance(siPreviousSearchForThisType, filteringSettings);
+ }
+ else {
+ // previous search instance dealt with filtering -
+ // simply update the filtering settings (but before that
+ // run a 'deep copy' of the original search instance, so
+ // that the new one gets a new reference; this will aid
+ // in early termination of older filterings)
+ siPreviousSearchForThisType = siPreviousSearchForThisType.deepCopy();
+ siPreviousSearchForThisType.setFilteringSettings(filteringSettings);
+ }
+ }
+
+ // proceed with "search" as usual - it will treat this search instance differently
+ // from "ordinary" search
+ startNewSearch(new SearchOptions(siPreviousSearchForThisType));
+ }
+
+
+ /**
+ * Worker method responsible for starting a new search via the API.
+ *
+ * This method is to be used when a *new* search is started. It will
+ * mainly make updates to the UI and store the new search in the history.
+ */
+ public void startNewSearch(final SearchOptions searchOptions)
+ {
+ try
+ {
+ for (final TYPE resourceType : searchOptions.getResourceTypesToSearchFor())
+ {
+ SearchInstance si = null;
+ switch (searchOptions.getSearchType()) {
+ case QuerySearch: si = new SearchInstance(searchOptions.getSearchString(), resourceType);
+ resetAllFilterPanes(searchOptions.getSearchString());
+ break;
+
+ case TagSearch: if (resourceType.isSuitableForTagSearch()) {
+ si = new SearchInstance(searchOptions.getSearchTags(), resourceType);
+ resetAllFilterPanes(searchOptions.getSearchString());
+ }
+ else {
+ // FIXME implement this... - show "no results" in the appropriate tab
+ JOptionPane.showMessageDialog(null, "'" + resourceType.getTypeName() + "' resource type is not suitable for tag search");
+ }
+ break;
+
+ case Filtering: if (resourceType.isSuitableForFiltering()) {
+ si = searchOptions.getPreconfiguredSearchInstance();
+ }
+ else {
+ // FIXME implement this... - show "no results" in the appropriate tab
+ JOptionPane.showMessageDialog(null, "'" + resourceType.getTypeName() + "' resource type is not suitable for filtering");
+ }
+ break;
+ }
+
+ if (si.isEmptySearch()) {
+ clearListingPanels();
+ return;
+ }
+
+ // Record 'this' search instance and set it as the new "primary" one for
+ // this resource type;
+ // (this way it if a new search thread starts afterwards, it is possible to
+ // detect this and stop the 'older' search, because it is no longer relevant)
+ registerSearchInstance(resourceType, si);
+
+ // start spinner icon for this tab to indicate search in progress - also show status message
+ setSpinnerIconForTab(resourceType);
+ setDefaultTitleForTab(resourceType);
+ searchResultListings.get(resourceType).setSearchStatusText("Searching for " + si.getDescriptionStringForSearchStatus() + "...", true);
+
+
+ // start the actual search
+ final SearchInstance siToStart = si;
+ new Thread(searchOptions.getSearchType() + " of " + resourceType.getCollectionName() + " via the API") {
+ public void run() {
+ siToStart.startNewSearch(instanceOfSelf, new CountDownLatch(1), searchResultListings.get(resourceType)); // FIXME - the new countdown latch is never used...
+ }
+ }.start();
+ }
+ }
+ catch (Exception e) {
+ logger.error("Error while searching via the Service Catalogue API. Error details attached.", e);
+ }
+
+}
+
+
+
+ /**
+ * Clears selection of filtering criteria and collapses any expanded nodes
+ * in all filter tree panes.<br/><br/>
+ *
+ * To be used for resetting all filter panes when the new query / tag
+ * search starts.
+ * @param queryString
+ */
+ private void resetAllFilterPanes(String queryString) {
+ for (FilterTreePane filterTreePane : this.currentFilterPanes.values()) {
+ if (filterTreePane != null) {
+ filterTreePane.clearSelection();
+ filterTreePane.collapseAll();
+ if ((queryString != null) && !queryString.isEmpty()) {
+ filterTreePane.applyQueryString(queryString);
+ }
+ }
+ }
+ }
+
+
+ protected void setSpinnerIconForTab(TYPE resourceType) {
+ tabbedSearchResultPanel.setIconAt(getTabIndexForResourceType(resourceType), ResourceManager.getImageIcon(ResourceManager.SPINNER));
+ }
+
+ protected void setDefaultIconForTab(TYPE resourceType) {
+ this.tabbedSearchResultPanel.setIconAt(getTabIndexForResourceType(resourceType), resourceType.getIcon());
+ }
+
+
+ /**
+ * Same as {@link SearchResultsMainPanel#setDefaultTitleForTab(TYPE)},
+ * but allows to append a specified string at the end of the default title.
+ *
+ * @param resourceType
+ * @param suffix
+ */
+ protected void setDefaultTitleForTabWithSuffix(TYPE resourceType, String suffix) {
+ tabbedSearchResultPanel.setTitleAt(getTabIndexForResourceType(resourceType),
+ resourceType.getCollectionName() + (suffix == null ? "" : suffix) );
+ }
+
+
+ /**
+ * Sets default title for a tab that contains panel representing
+ * search results of the specified resource type. Default title
+ * is just a name of the collections of resources in that tab.
+ *
+ * @param resourceType
+ */
+ protected void setDefaultTitleForTab(TYPE resourceType) {
+ setDefaultTitleForTabWithSuffix(resourceType, null);
+ }
+
+
+ /**
+ * @param resourceType Resource type for which the search result listing panel is requested.
+ * @return Reference to the requested panel or <code>null</code> if a tab for the specified
+ * <code>resourceType</code> does not exist.
+ */
+ protected SearchResultsListingPanel getResultsListingFor(TYPE resourceType) {
+ return (this.searchResultListings.get(resourceType));
+ }
+
+
+ /**
+ * @param resourceType Resource type for which filter tree pane is to be returned.
+ * @return Reference to the requested filter tree pane or <code>null</code> if
+ * there is no search result tab for the specified <code>resourceType</code>
+ * (or if that <code>resourceType</code> does not support filtering).
+ */
+ protected FilterTreePane getFilterTreePaneFor(TYPE resourceType) {
+ return (this.currentFilterPanes.get(resourceType));
+ }
+
+
+ // *** Callback for ActionListener interface ***
+
+ public void actionPerformed(ActionEvent e)
+ {
+ // FIXME -- remove this...
+// if (e.getSource().equals(bRefreshLastSearch))
+// {
+// // restore state of the search options panel
+// pluginPerspectiveMainComponent.getSearchTab().restoreSearchOptions(siPreviousSearch);
+//
+// // completely re-run the previous search
+// startNewSearch(siPreviousSearch);
+// }
+// else if (e.getSource().equals(bClearSearchResults))
+// {
+// // manual request to clear results of previous search
+//
+// // if any search thread was running, deactivate it as well
+// if (isSearchThreadRunning()) {
+// vCurrentSearchThreadID.set(0, null);
+// }
+//
+// // changing both - spinner image and the status text simultaneously
+// setSearchStatusText("No searches were made yet", false);
+//
+// // removed the previous search, hence makes no sense to allow to clear "previous" results again
+// bClearSearchResults.setEnabled(false);
+//
+// // only remove data about previous search and disable refresh button
+// // if no search thread is currently running - otherwise keep the button
+// // enabled in case there is a need to re-start the search if it's frozen
+// if (!isSearchThreadRunning()) {
+// siPreviousSearch = null;
+// bRefreshLastSearch.setEnabled(false);
+// }
+//
+// // also notify tabbed results panel, so that it removes the actual search results
+// searchResultsPanel.clearPreviousSearchResults();
+// }
+// else if (e.getSource().equals(this.jclPreviewCurrentFilteringCriteria))
+// {
+// // open a preview window showing current filtering settings
+// SwingUtilities.invokeLater(new Runnable()
+// {
+// public void run() {
+// ServiceFilteringSettingsPreview p = new ServiceFilteringSettingsPreview(siPreviousSearch.getFilteringSettings());
+// p.setVisible(true);
+// }
+// });
+//
+// }
+ }
+
+
+ // *** Callbacks for SearchInstanceTracker interface ***
+
+ public synchronized void clearPreviousSearchInstances() {
+ this.currentSearchInstances.clear();
+ }
+
+ public synchronized boolean isCurrentSearchInstance(TYPE searchType, SearchInstance searchInstance) {
+ // NB! it is crucial to perform test by reference here (hence the use of "==", not equals()!)
+ return (this.currentSearchInstances.get(searchType) == searchInstance);
+ }
+
+ public synchronized void registerSearchInstance(TYPE searchType, SearchInstance searchInstance) {
+ this.currentSearchInstances.put(searchType, searchInstance);
+ }
+
+ public synchronized SearchInstance getCurrentSearchInstance(TYPE searchType) {
+ return this.currentSearchInstances.get(searchType);
+ }
+
+public void clearListingPanels() {
+ for (SearchResultsListingPanel listingPanel : searchResultListings.values()) {
+ listingPanel.resetSearchResultsListing(true);
+ }
+ for (TYPE t : searchResultListings.keySet()) {
+ setDefaultTitleForTab(t);
+ }
+
+}
+
+public void clearSearch() {
+ clearPreviousSearchInstances();
+ clearListingPanels();
+ for (FilterTreePane treePanel : currentFilterPanes.values()) {
+ treePanel.reset();
+ }
+}
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/SearchResultsRenderer.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/SearchResultsRenderer.java
new file mode 100644
index 0000000..58ee5fd
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/SearchResultsRenderer.java
@@ -0,0 +1,47 @@
+package net.sf.taverna.biocatalogue.ui.search_results;
+
+import net.sf.taverna.biocatalogue.model.search.SearchInstance;
+
+/**
+ * This interfaces avoids coupling of search engine classes
+ * directly with the UI classes.
+ *
+ * Search engines would send new chunks of search results
+ * to the <code>SearchResultsRenderer</code> as soon as
+ * they become available.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public interface SearchResultsRenderer
+{
+ /**
+ * Render initial fragment of search results. This includes
+ * creating a new <code>ListModel</code> in the results listing
+ * and populating it with the first chunk of results and placeholders
+ * for those results that haven't been fetched yet.
+ *
+// * @param searchThreadID This is the ID of the thread that initiated search // FIXME
+// * from within the UI component, rather than the ID of
+// * the real worker search engine's search thread.
+// * It is used to test whether that thread is still active -
+// * to determine whether the partial results need to be rendered.
+ * @param si The search instance containing partial search results to be rendered.
+ */
+ void renderInitialResults(SearchInstance si);
+
+
+ /**
+ * Update the results listing with a specific fragment of the collection
+ * of search results.
+ *
+ * @param si The search instance containing partial search results to be rendered.
+ * @param startIndex First index in the result collection to update.
+ * @param count Number of result listing entries to update.
+ * <br/>
+ * At most <code>count</code> results will be rendered - less can be rendered
+ * if end of result list is reached earlier. <code>count</code> is normally
+ * just a page size for a specific resource type.
+ */
+ void renderFurtherResults(SearchInstance si, int startIndex, int count);
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/ServiceListCellRenderer.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/ServiceListCellRenderer.java
new file mode 100644
index 0000000..eafe095
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/search_results/ServiceListCellRenderer.java
@@ -0,0 +1,291 @@
+package net.sf.taverna.biocatalogue.ui.search_results;
+
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+
+import org.apache.commons.lang.StringEscapeUtils;
+import org.biocatalogue.x2009.xml.rest.Location;
+import org.biocatalogue.x2009.xml.rest.ResourceLinkWithString;
+import org.biocatalogue.x2009.xml.rest.Service;
+import org.biocatalogue.x2009.xml.rest.ServiceSummary.Provider;
+
+import net.sf.taverna.biocatalogue.model.LoadingExpandedResource;
+import net.sf.taverna.biocatalogue.model.LoadingResource;
+import net.sf.taverna.biocatalogue.model.Resource;
+import net.sf.taverna.biocatalogue.model.Resource.TYPE;
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.biocatalogue.model.Util;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check.ServiceMonitoringStatusInterpreter;
+
+
+/**
+ * This list cell renderer is will display (web) Service items in the search results
+ * list box.
+ *
+ * In the collapsed state, four data items will be shown per service: status (as per monitoring data),
+ * service type (SOAP / REST), the name of the service and its description.
+ *
+ * In the expanded state, other details are added to the ones above: service categories, locations,
+ * endpoints and providers.
+ *
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public class ServiceListCellRenderer extends ExpandableOnDemandLoadedListCellRenderer
+{
+ private JLabel jlTypeIcon;
+ private JLabel jlItemStatus;
+ private JLabel jlItemTitle;
+ private JLabel jlDescription;
+
+ private GridBagConstraints c;
+
+
+ public ServiceListCellRenderer() {
+ /* do nothing */
+ }
+
+
+ /**
+ * This entry can be in one of two states:
+ * -- containing only the name of the resource and NOT loading further details;
+ * -- containing only the name of the resource and LOADING further details.
+ *
+ * @param itemToRender
+ * @return
+ */
+ protected GridBagConstraints prepareInitiallyLoadingEntry(Object itemToRender)
+ {
+ TYPE resourceType = determineResourceType(itemToRender);
+ LoadingResource resource = (LoadingResource)itemToRender;
+
+ jlTypeIcon = new JLabel(resourceType.getIcon());
+ jlItemStatus = new JLabel(ResourceManager.getImageIcon(ResourceManager.SERVICE_STATUS_UNKNOWN_ICON));
+
+ jlItemTitle = new JLabel(Resource.getDisplayNameForResource(resource), JLabel.LEFT);
+ jlItemTitle.setForeground(Color.decode("#AD0000")); // very dark red
+ jlItemTitle.setFont(jlItemTitle.getFont().deriveFont(Font.PLAIN, jlItemTitle.getFont().getSize() + 2));
+
+ jlDescription = resource.isLoading() ? loaderBarAnimationGrey : loaderBarAnimationGreyStill;
+
+ return (arrangeLayout(false));
+ }
+
+
+ /**
+ *
+ * @param itemToRender
+ * @param expandedView <code>true</code> to indicate that this method generates the top
+ * fragment of the expanded list entry for this SOAP operation / REST method.
+ * @return
+ */
+ protected GridBagConstraints prepareLoadedEntry(Object itemToRender, boolean selected)
+ {
+ TYPE resourceType = determineResourceType(itemToRender);
+ Service service = (Service)itemToRender;;
+
+ // service type
+ if (service.getServiceTechnologyTypes() != null && service.getServiceTechnologyTypes().getTypeList().size() > 0)
+ {
+ if (service.getServiceTechnologyTypes().getTypeList().size() > 1 &&
+ !(service.getServiceTechnologyTypes().getTypeList().get(0).toString().equalsIgnoreCase("SOAP")) &&
+ service.getServiceTechnologyTypes().getTypeList().get(1).toString().equalsIgnoreCase("SOAPLAB")
+ )
+ {
+ jlTypeIcon = new JLabel(ResourceManager.getImageIcon(ResourceManager.SERVICE_TYPE_MULTITYPE_ICON));
+ }
+ else if (service.getServiceTechnologyTypes().getTypeArray(0).toString().equalsIgnoreCase("SOAP")) {
+ jlTypeIcon = new JLabel(ResourceManager.getImageIcon(ResourceManager.SERVICE_TYPE_SOAP_ICON));
+ }
+ else if (service.getServiceTechnologyTypes().getTypeArray(0).toString().equalsIgnoreCase("REST")) {
+ jlTypeIcon = new JLabel(ResourceManager.getImageIcon(ResourceManager.SERVICE_TYPE_REST_ICON));
+ }
+ }
+ else {
+ // can't tell the type - just show as a service of no particular type
+ jlTypeIcon = new JLabel(resourceType.getIcon());
+ }
+
+
+ // service status
+ jlItemStatus = new JLabel(ServiceMonitoringStatusInterpreter.getStatusIcon(service, true));
+
+ jlItemTitle = new JLabel(Resource.getDisplayNameForResource(service), JLabel.LEFT);
+ jlItemTitle.setForeground(Color.decode("#AD0000")); // very dark red
+ jlItemTitle.setFont(jlItemTitle.getFont().deriveFont(Font.PLAIN, jlItemTitle.getFont().getSize() + 2));
+
+ int descriptionMaxLength = DESCRIPTION_MAX_LENGTH_EXPANDED;
+ String strDescription = Util.stripAllHTML(service.getDescription());
+ strDescription = (strDescription == null || strDescription.length() == 0 ?
+ "<font color=\"gray\">no description</font>" :
+ StringEscapeUtils.escapeHtml(Util.ensureLineLengthWithinString(strDescription, LINE_LENGTH, false)));
+
+ if (strDescription.length() > descriptionMaxLength) {
+ strDescription = strDescription.substring(0, descriptionMaxLength) + "<font color=\"gray\">(...)</font>";
+ }
+ strDescription = "<html><b>Description: </b>" + strDescription + "</html>";
+ jlDescription = new JLabel(strDescription);
+
+ return (arrangeLayout(true));
+ }
+
+
+ /**
+ * @return Final state of the {@link GridBagConstraints} instance
+ * that was used to lay out components in the panel.
+ */
+ private GridBagConstraints arrangeLayout(boolean showActionButtons)
+ {
+ // POPULATE PANEL WITH PREPARED COMPONENTS
+ this.setLayout(new GridBagLayout());
+ c = new GridBagConstraints();
+ c.anchor = GridBagConstraints.NORTHWEST;
+ c.fill = GridBagConstraints.HORIZONTAL;
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.weightx = 0;
+ c.insets = new Insets(10, 6, 6, 3);
+ this.add(jlTypeIcon, c);
+
+ c.gridx++;
+ c.insets = new Insets(10, 3, 6, 3);
+ this.add(jlItemStatus, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.insets = new Insets(10, 3, 6, 3);
+ this.add(jlItemTitle, c);
+
+ if (showActionButtons) {
+ c.gridx++;
+ c.gridheight = 3;
+ c.weightx = 0;
+ c.weighty = 1.0;
+ jlExpand = new JLabel(ResourceManager.getImageIcon(ResourceManager.FOLD_ICON));
+ this.add(jlExpand, c);
+ }
+
+ c.gridx = 2;
+ c.gridy++;
+ c.gridheight = 1;
+ c.weightx = 1.0;
+ c.weighty = 0;
+ c.insets = new Insets(3, 3, 3, 3);
+ this.add(jlDescription, c);
+
+ return (c);
+ }
+
+
+
+ protected void prepareLoadingExpandedEntry(Object itemToRender)
+ {
+ LoadingExpandedResource expandedResource = (LoadingExpandedResource) itemToRender;
+ GridBagConstraints c = prepareLoadedEntry(expandedResource.getAssociatedObj(), false);
+
+ if (expandedResource.isLoading())
+ {
+ c.gridx = 0;
+ c.gridy++;
+ c.gridwidth = 3;
+ c.anchor = GridBagConstraints.CENTER;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+ this.add(loaderBarAnimationOrange, c);
+ }
+ else
+ {
+ // *** additional data for this Web Service operations ***
+ Service service = (Service) expandedResource.getAssociatedObj();
+
+
+ // -- categories --
+ int categoryCount = service.getSummary().getCategoryList().size();
+ String categoryString = "";
+ if (categoryCount > 0) {
+ List<String> categoryNames = new ArrayList<String>();
+ for (ResourceLinkWithString category : service.getSummary().getCategoryList()) {
+ categoryNames.add(category.getStringValue());
+ }
+ categoryString = "<html><b>" + Util.pluraliseNoun("Category", categoryCount) + ": </b>" + StringEscapeUtils.escapeHtml(Util.join(categoryNames, ", ")) + "</html>";
+ }
+ else {
+ categoryString = "<html><b>Category: </b><font color=\"gray\">unknown</font></html>";
+ }
+
+ c.gridy++;
+ this.add(new JLabel(categoryString),c);
+
+
+ // -- endpoints --
+ int endpointCount = service.getSummary().getEndpointList().size();
+ String endpointString = "";
+ if (endpointCount > 0) {
+ endpointString = "<html><b>" + Util.pluraliseNoun("Endpoint", endpointCount) + ": </b>" +
+ StringEscapeUtils.escapeHtml(Util.join(service.getSummary().getEndpointList(), ", ")) + "</html>";
+ }
+ else {
+ endpointString = "<html><b>Endpoint: </b><font color=\"gray\">unknown</font></html>";
+ }
+
+ c.gridy++;
+ this.add(new JLabel(endpointString), c);
+
+
+ // -- providers --
+ int providerCount = service.getSummary().getProviderList().size();
+ String providerString = "";
+ if (providerCount > 0) {
+ List<String> providerNames = new ArrayList<String>();
+ for (Provider serviceProvider : service.getSummary().getProviderList()) {
+ providerNames.add(serviceProvider.getName());
+ }
+ providerString = "<html><b>" + Util.pluraliseNoun("Provider", providerCount) + ": </b>" + StringEscapeUtils.escapeHtml(Util.join(providerNames, ", ")) + "</html>";
+ }
+ else {
+ providerString = "<html><b>Provider: </b><font color=\"gray\">unknown</font></html>";
+ }
+
+ c.gridy++;
+ this.add(new JLabel(providerString),c);
+
+
+ // -- locations --
+ int locationCount = service.getSummary().getLocationList().size();
+ String locationString = "";
+ List<String> locations = new ArrayList<String>();
+ if (locationCount > 0) {
+ for (Location location : service.getSummary().getLocationList()) {
+ List<String> locationNameFragments = new ArrayList<String>();
+ locationNameFragments.add(location.getCity());
+ locationNameFragments.add(location.getCountry());
+ locations.add(Util.join(locationNameFragments, ", "));
+ }
+ }
+ locationString = "<html><b>" + Util.pluraliseNoun("Location", locations.size()) + ": </b>" +
+ (locations.size() > 0 ? StringEscapeUtils.escapeHtml(Util.join(locations, "; ")) : "<font color=\"gray\">unknown</font>") +
+ "</html>";
+
+ c.gridy++;
+ c.insets = new Insets(3, 3, 12, 3);
+ this.add(new JLabel(locationString),c);
+ }
+ }
+
+
+@Override
+boolean shouldBeHidden(Object itemToRender) {
+ return false;
+}
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/JTriStateTree.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/JTriStateTree.java
new file mode 100644
index 0000000..304e50a
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/JTriStateTree.java
@@ -0,0 +1,631 @@
+package net.sf.taverna.biocatalogue.ui.tristatetree;
+
+import java.awt.Component;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.JPopupMenu;
+import javax.swing.JTree;
+import javax.swing.SwingUtilities;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.DefaultTreeModel;
+import javax.swing.tree.MutableTreeNode;
+import javax.swing.tree.TreeNode;
+import javax.swing.tree.TreePath;
+
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public class JTriStateTree extends JTree
+{
+ // This is used to manage location and padding of tooltips on long items
+ // that don't fit into the visible part of this tree.
+ private static final int JCHECKBOX_WIDTH = 16;
+
+ private JTriStateTree instanceOfSelf;
+ private JPopupMenu contextualMenu;
+
+ private TriStateTreeNode root;
+
+ // will enable/disable checkboxes - when disabled the selection
+ // will remain, but will appear as read-only
+ private boolean bCheckingEnabled;
+
+ private List<Action> contextualMenuActions;
+ private Action expandAllAction;
+ private Action collapseAllAction;
+ private Action selectAllAction;
+ private Action deselectAllAction;
+
+ private Set<TriStateTreeCheckingListener> checkingListeners;
+
+
+ @SuppressWarnings("serial")
+public JTriStateTree(TriStateTreeNode root)
+ {
+ super(root);
+ this.root = root;
+ this.instanceOfSelf = this;
+
+ // by default checking is allowed
+ this.bCheckingEnabled = true;
+
+ // initially, no checking listeners
+ checkingListeners = new HashSet<TriStateTreeCheckingListener>();
+
+ // initially set to show the [+]/[-] icons for expanding collapsing top-level nodes
+ this.setShowsRootHandles(true);
+
+ // use the cell rendered which understands the three states of the
+ // nodes of this tree
+ this.setCellRenderer(new TriStateCheckBoxTreeCellRenderer());
+
+
+ // create all necessary actions for the popup menu: selecting/deselecting and expanding/collapsing all nodes
+ this.selectAllAction = new AbstractAction("Select all", ResourceManager.getImageIcon(ResourceManager.SELECT_ALL_ICON))
+ {
+ // Tooltip
+ { this.putValue(SHORT_DESCRIPTION, "Select all nodes in the tree"); }
+
+ public void actionPerformed(ActionEvent e) {
+ selectAllNodes(true);
+ }
+ };
+
+ // Use the Taverna untick icon
+ this.deselectAllAction = new AbstractAction("Deselect all", ResourceManager.getImageIcon(ResourceManager.UNCHECKED_ICON))
+ {
+ // Tooltip
+ { this.putValue(SHORT_DESCRIPTION, "Deselect all nodes in the tree"); }
+
+ public void actionPerformed(ActionEvent e) {
+ selectAllNodes(false);
+ }
+ };
+
+
+// this.expandAllAction = new AbstractAction("Expand all", ResourceManager.getImageIcon(ResourceManager.EXPAND_ALL_ICON))
+ // Use the standard Taverna plus icon
+ this.expandAllAction = new AbstractAction("Expand all", WorkbenchIcons.plusIcon)
+ {
+ // Tooltip
+ { this.putValue(SHORT_DESCRIPTION, "Expand all nodes in the tree"); }
+
+ public void actionPerformed(ActionEvent e) {
+ expandAll();
+ }
+ };
+
+// this.collapseAllAction = new AbstractAction("Collapse all", ResourceManager.getImageIcon(ResourceManager.COLLAPSE_ALL_ICON))
+ // Use the standard Taverna minus icon
+ this.collapseAllAction = new AbstractAction("Collapse all", WorkbenchIcons.minusIcon)
+ {
+ // Tooltip
+ { this.putValue(SHORT_DESCRIPTION, "Collapse all expanded nodes in the tree"); }
+
+ public void actionPerformed(ActionEvent e) {
+ collapseAll();
+ }
+ };
+
+
+ // populate the popup menu with created menu items
+ contextualMenuActions = Arrays.asList(new Action[] {expandAllAction, collapseAllAction, deselectAllAction});
+
+ contextualMenu = new JPopupMenu();
+ contextualMenu.add(expandAllAction);
+ contextualMenu.add(collapseAllAction);
+ contextualMenu.add(new JPopupMenu.Separator());
+ //contextualMenu.add(selectAllAction);
+ contextualMenu.add(deselectAllAction);
+
+
+ this.addMouseListener(new MouseAdapter() {
+ // use mousePressed, not mouseClicked to make sure that
+ // quick successive clicks get processed correctly, otherwise
+ // some clicks are disregarded
+ public void mousePressed(MouseEvent e)
+ {
+ // only listen to checkbox checking requests if this is
+ // a correct type of mouse event for this
+ if (!e.isPopupTrigger() && e.getButton() == MouseEvent.BUTTON1)
+ {
+ int clickedRow = instanceOfSelf.getRowForLocation(e.getX(), e.getY());
+
+ // only make changes to node selections if checking is enabled in the tree and
+ // it was a node which was clicked, not [+]/[-] or blank space
+ if (bCheckingEnabled && clickedRow != -1)
+ {
+ Object clickedObject = instanceOfSelf.getPathForRow(clickedRow).getLastPathComponent();
+ if (clickedObject instanceof TriStateTreeNode) {
+ TriStateTreeNode node = ((TriStateTreeNode)clickedObject);
+
+ // toggle state of the clicked node + propagate the changes to
+ // the checking state of all nodes
+ node.toggleState(true);
+
+ // repaint the whole tree
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ instanceOfSelf.repaint();
+ }
+ });
+
+ // notify all listeners
+ notifyCheckingListeners();
+ }
+ }
+ }
+ else {
+ // not a checking action - instead, bring up a popup menu
+ contextualMenu.show(instanceOfSelf, e.getX(), e.getY());
+ }
+ }
+
+ public void mouseReleased(MouseEvent e)
+ {
+ if (e.isPopupTrigger()) {
+ // another way a popup menu may be called on different systems
+ contextualMenu.show(instanceOfSelf, e.getX(), e.getY());
+ }
+ }
+
+
+ /**
+ * This method enables tooltips on this instance of JTriStateTree
+ * when mouse enters its bounds. Custom tooltips will be used, but
+ * this notifies ToolTipManager that tooltips must be shown on this
+ * tree.
+ */
+ public void mouseEntered(MouseEvent e) {
+ instanceOfSelf.setToolTipText("Filter tree");
+ }
+
+ /**
+ * Removes tooltips from this JTriStateTree when mouse leaves its bounds.
+ */
+ public void mouseExited(MouseEvent e) {
+ instanceOfSelf.setToolTipText(null);
+ }
+
+ });
+
+ }
+
+
+ /**
+ * This method is used to determine tooltip location.
+ *
+ * Helps to ensure that the tooltip appears directly over the
+ * text in the row over which the mouse currently hovers.
+ */
+ public Point getToolTipLocation(MouseEvent e)
+ {
+ int iRowIndex = this.getRowForLocation(e.getX(), e.getY());
+ if (iRowIndex != -1) {
+ // mouse hovers over one of the rows - make top-left corner of
+ // the tooltip to appear over the top-left corner of that row
+ Rectangle bounds = this.getRowBounds(iRowIndex);
+ return (new Point(bounds.x + JCHECKBOX_WIDTH, bounds.y));
+ }
+ else {
+ // let ToolTipManager determine where to show the tooltip (if it will be shown)
+ return null;
+ }
+ }
+
+
+ /**
+ * Supports dynamic tooltips for the contents of this JTriStateTree -
+ * the tooltips will only be shown for those tree nodes that don't
+ * fully fit within the visible bounds of the tree.
+ *
+ * For other nodes no tooltip will be shown.
+ */
+ public String getToolTipText(MouseEvent e)
+ {
+ String strTooltip = null;
+
+ Object correspondingObject = getTreeNodeObject(e);
+ if (correspondingObject != null) {
+ // mouse is hovering over some row in the tree, not a blank space --
+ // obtain a component that is identical to the one which is currently displayed at the identified row in the tree
+ Component rendering = this.getCellRenderer().getTreeCellRendererComponent(this, correspondingObject, false, false,
+ true, this.getRowForLocation(e.getX(), e.getY()), false);
+
+ if (rendering.getPreferredSize().width + getToolTipLocation(e).x - JCHECKBOX_WIDTH > this.getVisibleRect().width) {
+ // if the component is not fully visible, the tooltip will be displayed -
+ // tooltip text matches the one for this row in the tree, will just be shown in full
+ strTooltip = correspondingObject.toString();
+ }
+ }
+
+ // return either tooltip text or 'null' if no tooltip is currently required
+ return (strTooltip);
+ }
+
+
+ /**
+ * Check whether a {@link MouseEvent} happened in such a location
+ * in the {@link JTriStateTree} that corresponds to some node or a
+ * blank space.
+ *
+ * @param e
+ * @return Object contained in the tree node that corresponds to the
+ * location of specified {@link MouseEvent} <code>e</code>;
+ * or <code>null</code> if the event happened over a blank space.
+ */
+ public Object getTreeNodeObject(MouseEvent e)
+ {
+ int iRowIndex = this.getRowForLocation(e.getX(), e.getY());
+ if (iRowIndex != -1) {
+ // mouse is hovering over some row in the tree, not a blank space
+ return (this.getPathForRow(iRowIndex).getLastPathComponent());
+ }
+
+ return (null);
+ }
+
+
+ /**
+ * @return List of the highest-level nodes of the tree that have full (not partial) selection and,
+ * therefore, act as roots of checked paths.
+ */
+ public List<TreePath> getRootsOfCheckedPaths()
+ {
+ return getRootsOfCheckedPaths(this.root);
+ }
+
+ /**
+ * A recursive version of the getCheckedRootsOfCheckedPaths().
+ * Performs all the work for a given node and returns result to
+ * the caller.
+ *
+ * @param startNode Node to start with.
+ * @return
+ */
+ private List<TreePath> getRootsOfCheckedPaths(TriStateTreeNode startNode)
+ {
+ ArrayList<TreePath> pathsToRootsOfCheckings = new ArrayList<TreePath>();
+
+ Object currentNode = null;
+ for (Enumeration e = startNode.children(); e.hasMoreElements(); )
+ {
+ currentNode = e.nextElement();
+ if (currentNode instanceof TriStateTreeNode) {
+ TriStateTreeNode curTriStateNode = (TriStateTreeNode)currentNode;
+
+ if (curTriStateNode.getState().equals(TriStateCheckBox.State.CHECKED)) {
+ pathsToRootsOfCheckings.add(new TreePath(curTriStateNode.getPath()));
+ }
+ else if (curTriStateNode.getState().equals(TriStateCheckBox.State.PARTIAL)) {
+ pathsToRootsOfCheckings.addAll(getRootsOfCheckedPaths(curTriStateNode));
+ }
+ }
+ }
+
+ return (pathsToRootsOfCheckings);
+ }
+
+
+ /**
+ * @return List of TreePath objects, where the last component in each
+ * path is the root of an unchecked path in this tree. In other
+ * words each of those last components is either an unchecked
+ * leaf node or a node, none of whose children (and itself as
+ * well) are checked.
+ */
+ public List<TreePath> getRootsOfUncheckedPaths()
+ {
+ return (getRootsOfUncheckedPaths(this.root));
+ }
+
+
+ /**
+ * Recursive worker method for <code>getRootsOfUncheckedPaths()</code>.
+ */
+ private List<TreePath> getRootsOfUncheckedPaths(TreeNode startNode)
+ {
+ List<TreePath> rootNodesOfUncheckedPaths = new ArrayList<TreePath>();
+
+ Object currentNode = null;
+ for (Enumeration e = startNode.children(); e.hasMoreElements(); )
+ {
+ currentNode = e.nextElement();
+ if (!(currentNode instanceof TriStateTreeNode) ||
+ ((TriStateTreeNode)currentNode).getState().equals(TriStateCheckBox.State.UNCHECKED))
+ {
+ rootNodesOfUncheckedPaths.add(new TreePath(((DefaultMutableTreeNode)currentNode).getPath()));
+ }
+ else {
+ rootNodesOfUncheckedPaths.addAll(getRootsOfUncheckedPaths((TreeNode)currentNode));
+ }
+ }
+
+ return (rootNodesOfUncheckedPaths);
+ }
+
+
+ /**
+ * @return List of TreePath objects, that point to all "leaf"
+ * nodes in the tree that are checked - in other words
+ * this method returns a collection of paths to all "deepest"
+ * nodes in this tree that are checked and do not have any
+ * (checked) children.
+ */
+ public List<TreePath> getLeavesOfCheckedPaths() {
+ return (getLeavesOfCheckedPaths(this.root));
+ }
+
+
+ /**
+ * Recursive worker method for {@link JTriStateTree#getLeavesOfCheckedPaths()}
+ */
+ private List<TreePath> getLeavesOfCheckedPaths(TriStateTreeNode startNode)
+ {
+ List<TreePath> leavesOfCheckedPaths = new ArrayList<TreePath>();
+
+ // this node is only relevant if it is checked itself - if not,
+ // it must be the first-level child of another node that is checked
+ // and is only considered here on the recursive pass (but will be discarded)
+ if (startNode.getState().equals(TriStateCheckBox.State.CHECKED) ||
+ startNode.getState().equals(TriStateCheckBox.State.PARTIAL))
+ {
+ // "ask" all children to do the same...
+ Object currentNode = null;
+ for (Enumeration e = startNode.children(); e.hasMoreElements(); ) {
+ currentNode = e.nextElement();
+ if (currentNode instanceof TriStateTreeNode) {
+ leavesOfCheckedPaths.addAll(getLeavesOfCheckedPaths((TriStateTreeNode)currentNode));
+ }
+ }
+
+ // ...if we have a list of leaf nodes, then this node can't be a leaf;
+ // -> but alternatively, if the list is empty, it means that this node is
+ // itself a leaf node and must be added to the result
+ if (leavesOfCheckedPaths.isEmpty()) {
+ leavesOfCheckedPaths.add(new TreePath(startNode.getPath()));
+ }
+ }
+
+ return (leavesOfCheckedPaths);
+ }
+
+
+ /**
+ * @return List of all contextual menu actions that are available for this tree.
+ */
+ public List<Action> getContextualMenuActions() {
+ return this.contextualMenuActions;
+ }
+
+
+ /**
+ * Enables or disables all actions in the contextual menu
+ * @param actionsAreEnabled
+ */
+ public void enableAllContextualMenuAction(boolean actionsAreEnabled) {
+ for (Action a : getContextualMenuActions()) {
+ a.setEnabled(actionsAreEnabled);
+ }
+ }
+
+
+ /**
+ * Selects or deselects all nodes.
+ * @param selectAll True - to select all; false - to reset all selections.
+ */
+ public void selectAllNodes(boolean selectAll) {
+ root.setState(selectAll ? TriStateCheckBox.State.CHECKED : TriStateCheckBox.State.UNCHECKED);
+ root.updateStateOfRelatedNodes();
+ this.repaint();
+
+ // even though this isn't a click in the tree, the selection has changed -
+ // notify all listeners
+ notifyCheckingListeners();
+ }
+
+
+ /**
+ * TODO - this method doesn't take into account a possibility that the
+ * filter tree might have changed
+ *
+ * @param rootsOfCheckedPaths A list of TreePath objects which represent a checking state of
+ * the nodes in this tree (as returned by <code>getRootsOfCheckedPaths()</code>).
+ *
+ * The last node of each path is the one that should have <code>TriStateCheckBox.State.CHECKED</code>
+ * state (so that last node is a root of checked path that start at that node). Related partial
+ * checkings for the UI can be computed from that by the tree checking model.
+ *
+ * Therefore, a single "real" checking per provided TreePath from <code>rootsOfCheckedPaths</code> is
+ * made.
+ */
+ public void restoreFilterCheckingSettings(List<TreePath> rootsOfCheckedPaths)
+ {
+ // start with removing all selections
+ this.selectAllNodes(false);
+
+ for (TreePath p : rootsOfCheckedPaths) {
+ restoreTreePathCheckingSettings(this.root, p);
+ }
+ }
+
+ /**
+ * A worker method for <code>restoreFilterCheckingSettings(List<TreePath> rootsOfCheckedPaths)</code>.
+ * See that method for further details.
+ *
+ * @param startNode A node of this tree.
+ * @param pathFromStartNode A TreePath object from the stored filter, where the first node must be
+ * equals to <code>startNode</code> (based on the <code>userObject</code>,
+ * but not the checking state), should the traversal of the tree result in
+ * checking the last node of this TreePath eventually - which is the goal
+ * of this method.
+ * @return True if traversal of <code>pathFromStartNode</code> succeeded and a node in this tree was checked;
+ * false if traversal couldn't find a matching node in this tree, and so no checking was made.
+ */
+ private boolean restoreTreePathCheckingSettings(TriStateTreeNode startNode, TreePath pathFromStartNode)
+ {
+ if (startNode == null || pathFromStartNode == null || pathFromStartNode.getPathCount() == 0) {
+ // no match - no data to work with
+ return (false);
+ }
+
+ // compare the "roots" - provided start node and the root of the provided path
+ // (based on the 'user object', but not the selection state)
+ if (startNode.equals(pathFromStartNode.getPathComponent(0)))
+ {
+ if (pathFromStartNode.getPathCount() == 1) {
+ // provided startNode is equals to the only node in the provided tree path -
+ // so it is the node to mark as checked; also - make sure that this selection
+ // propagates through tree
+ startNode.setState(TriStateCheckBox.State.CHECKED, true);
+
+ // we've found the required node in this path - no further search needed,
+ // so terminate this method
+ return (true);
+ }
+ else {
+ // provided startNode is equals to the first node of the provided tree path -
+ // meaning that at this stage we need to traverse all children of the startNode
+ // and look for the child that would match the next element in the provided tree path
+ //
+ // to do this, produce a new tree path from the provided one that doesn't contain
+ // the first node - then proceed recursively
+ Object[] currentPathComponents = pathFromStartNode.getPath();
+ Object[] reducedPathComponents = new Object[currentPathComponents.length - 1];
+ System.arraycopy(currentPathComponents, 1, reducedPathComponents, 0, currentPathComponents.length - 1);
+
+ Enumeration children = startNode.children();
+ while (children.hasMoreElements()) {
+ TriStateTreeNode currentChild = (TriStateTreeNode)children.nextElement();
+
+ // if recursive call succeeds, no need to iterate any further
+ if (restoreTreePathCheckingSettings(currentChild, new TreePath(reducedPathComponents))) return (true);
+ }
+ }
+ }
+
+ // the startNode doesn't match the the first element in the provided tree path
+ // or no match could be found during recursive search for the node to "check"
+ return (false);
+ }
+
+
+ /**
+ * Expands all paths in this tree.
+ */
+ public void expandAll()
+ {
+ // this simply expands all tree nodes
+ // TODO - this actually "freezes" the UI if there are many nodes in the tree
+ // some better solution to be found (e.g. expand the nodes in the model, then update UI, or similar)
+ for (int i = 0; i < getRowCount(); i++) {
+ instanceOfSelf.expandRow(i);
+ }
+ }
+
+
+ /**
+ * Collapses all paths in this tree.
+ */
+ public void collapseAll()
+ {
+ // this simply collapses all expanded nodes - this is very quick, execute just as it is
+ for (int i = getRowCount() - 1; i >= 0; i--) {
+ instanceOfSelf.collapseRow(i);
+ }
+ }
+
+
+ /**
+ * Removes all nodes in this tree that are unchecked.
+ *
+ * It doesn't iterate through *all* nodes - if some node is
+ * indeed unchecked, it removes that node and any children that
+ * it has (because unchecked node is the root of an unchecked path).
+ */
+ public void removeAllUncheckedNodes()
+ {
+ // get the tree model first - will be used to remove the nodes
+ DefaultTreeModel theTreeModel = (DefaultTreeModel)this.treeModel;
+
+ // remove unchecked nodes
+ List<TreePath> allNodesToRemove = this.getRootsOfUncheckedPaths();
+ for (TreePath p : allNodesToRemove) {
+ theTreeModel.removeNodeFromParent((MutableTreeNode)p.getLastPathComponent());
+ }
+ }
+
+
+ /**
+ * Provides access to the contextual menu of this JTriStateTree.
+ *
+ * @return Reference to the contextual menu.
+ */
+ public JPopupMenu getContextualMenu() {
+ return contextualMenu;
+ }
+
+
+ public void setCheckingEnabled(boolean bCheckingEnabled) {
+ this.bCheckingEnabled = bCheckingEnabled;
+ }
+
+ /**
+ * @return True if the current state of this JTriStateTree
+ * allows making changes to checking of checkboxes
+ * in its nodes.
+ */
+ public boolean isCheckingEnabled() {
+ return bCheckingEnabled;
+ }
+
+
+ /**
+ * @param listener New tree checking listener to register for updates
+ * to tree node selections.
+ */
+ public void addCheckingListener(TriStateTreeCheckingListener listener) {
+ if (listener != null) {
+ this.checkingListeners.add(listener);
+ }
+ }
+
+
+ /**
+ * @param listener Tree checking listener to remove.
+ */
+ public void removeCheckingListener(TriStateTreeCheckingListener listener) {
+ if (listener != null) {
+ this.checkingListeners.remove(listener);
+ }
+ }
+
+
+ /**
+ * Sends a signal to all listeners to check the state of the tree,
+ * as it has changed.
+ */
+ private void notifyCheckingListeners() {
+ for (TriStateTreeCheckingListener listener : this.checkingListeners) {
+ listener.triStateTreeCheckingChanged(instanceOfSelf);
+ }
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/Swing - Tristate CheckBox.7z b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/Swing - Tristate CheckBox.7z
new file mode 100644
index 0000000..8c60d87
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/Swing - Tristate CheckBox.7z
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/Test.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/Test.java
new file mode 100644
index 0000000..6d58db3
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/Test.java
@@ -0,0 +1,67 @@
+package net.sf.taverna.biocatalogue.ui.tristatetree;
+
+import java.awt.BorderLayout;
+
+import javax.swing.JFrame;
+import javax.swing.JScrollPane;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class Test extends JFrame
+{
+ public Test() {
+ this.setLayout(new BorderLayout());
+
+ this.add(new TriStateCheckBox("LOL", TriStateCheckBox.State.PARTIAL), BorderLayout.NORTH);
+
+ TriStateTreeNode root = new TriStateTreeNode("root");
+ TriStateTreeNode c1 = new TriStateTreeNode("child 1");
+ TriStateTreeNode c2 = new TriStateTreeNode("child 2");
+ TriStateTreeNode c3 = new TriStateTreeNode("child 3");
+
+ TriStateTreeNode c1_1 = new TriStateTreeNode("child 1_1");
+ TriStateTreeNode c1_2 = new TriStateTreeNode("child 1_2");
+ TriStateTreeNode c1_3 = new TriStateTreeNode("child 1_3");
+
+ TriStateTreeNode c2_1 = new TriStateTreeNode("child 2_1");
+ TriStateTreeNode c2_2 = new TriStateTreeNode("child 2_2");
+ TriStateTreeNode c2_3 = new TriStateTreeNode("child 2_3");
+
+ TriStateTreeNode c3_1 = new TriStateTreeNode("child 3_1");
+ TriStateTreeNode c3_2 = new TriStateTreeNode("child 3_2");
+ TriStateTreeNode c3_3 = new TriStateTreeNode("child 3_3");
+
+ TriStateTreeNode c1_1_1 = new TriStateTreeNode("child 1_1_1");
+ TriStateTreeNode c1_1_2 = new TriStateTreeNode("child 1_1_2");
+ TriStateTreeNode c1_1_3 = new TriStateTreeNode("child 1_1_3");
+
+ // adding second level children
+ root.add(c1); root.add(c2); root.add(c3);
+
+ // adding third-level children
+ c1.add(c1_1); c1.add(c1_2); c1.add(c1_3);
+ c2.add(c2_1); c2.add(c2_2); c2.add(c2_3);
+ c3.add(c3_1); c3.add(c3_2); c3.add(c3_3);
+
+ // adding fourth-level children
+ c1_1.add(c1_1_1); c1_1.add(c1_1_2); c1_1.add(c1_1_3);
+
+
+ // NB! important to create the tree when 'root' is already populated with children
+ JTriStateTree tree = new JTriStateTree(root);
+ tree.setRootVisible(false);
+ tree.setShowsRootHandles(true);
+ this.add(new JScrollPane(tree), BorderLayout.CENTER);
+
+ this.setDefaultCloseOperation(EXIT_ON_CLOSE);
+ this.pack();
+ }
+
+
+ public static void main(String[] args) {
+ JFrame a = new Test();
+ a.setVisible(true);
+ }
+
+}
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/TriStateCheckBox.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/TriStateCheckBox.java
new file mode 100644
index 0000000..361dfc3
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/TriStateCheckBox.java
@@ -0,0 +1,172 @@
+package net.sf.taverna.biocatalogue.ui.tristatetree;
+
+/*
+ * Taken from: http://72.5.124.102/thread.jspa?threadID=721308&messageID=9955637
+ * Data webpage accessed: 07/February/2010
+ *
+ * Modified by Sergejs Aleksejevs
+ */
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.GradientPaint;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+
+import javax.swing.Icon;
+import javax.swing.JCheckBox;
+import javax.swing.JToggleButton;
+import javax.swing.UIManager;
+
+public class TriStateCheckBox extends JCheckBox
+{
+ private static final long serialVersionUID = 1L;
+
+ public static enum State {
+ CHECKED, UNCHECKED, PARTIAL
+ };
+
+
+ // these colors will be used for painting the 'partial' state of the checkbox -
+ // a gradient painting will be made from top-left to bottom-right
+ private Color partialStateTopLeftColor = Color.GREEN.darker().darker().darker();
+ private Color partialStateBottomRightColor = Color.GREEN.brighter().brighter().brighter();
+
+
+ /**
+ * Creates an initially unselected check box button with no text, no icon.
+ */
+ public TriStateCheckBox() {
+ this(null, State.UNCHECKED);
+ }
+
+ /**
+ * Creates a check box with text and icon, and specifies whether or not it is initially
+ * selected.
+ *
+ * @param text
+ * The text of the check box.
+ * @param initial
+ * The initial state
+ */
+ public TriStateCheckBox(String text, State initial) {
+ super.setText(text);
+ setModel(new TriStateModel(initial));
+ setIcon(new TriStateIcon(this));
+ // some UI settings
+ setRolloverEnabled(true);
+ }
+
+ /**
+ * Set the new state to either CHECKED, PARTIAL or UNCHECKED.
+ */
+ public void setState(State state) {
+ ((TriStateModel) model).setState(state);
+ }
+
+ /**
+ * Return the current state, which is determined by the selection status of the model.
+ */
+ public State getState() {
+ return ((TriStateModel) model).getState();
+ }
+
+ public void setSelected(boolean selected) {
+ ((TriStateModel) model).setSelected(selected);
+ }
+
+ /** The model for the button */
+ private static class TriStateModel extends JToggleButton.ToggleButtonModel {
+
+ private static final long serialVersionUID = 1L;
+ protected State state;
+
+ public TriStateModel(State state) {
+ this.state = state;
+ }
+
+ public boolean isSelected() {
+ return state == State.CHECKED;
+ }
+
+ public State getState() {
+ return state;
+ }
+
+ public void setState(State state) {
+ this.state = state;
+ fireStateChanged();
+ }
+
+ public void setPressed(boolean pressed) {
+ if (pressed) {
+ switch (state) {
+ case UNCHECKED:
+ state = State.CHECKED;
+ break;
+ case PARTIAL:
+ state = State.UNCHECKED;
+ break;
+ case CHECKED:
+ state = State.PARTIAL;
+ break;
+ }
+ }
+
+ }
+
+ public void setSelected(boolean selected) {
+ if (selected) {
+ this.state = State.CHECKED;
+ } else {
+ this.state = State.UNCHECKED;
+ }
+ }
+ }
+
+ private class TriStateIcon implements Icon
+ {
+ private Icon checkBoxIcon;
+ private TriStateCheckBox triStateCheckBox;
+ public TriStateIcon(TriStateCheckBox triStateCheckBox) {
+ this.triStateCheckBox = triStateCheckBox;
+ this.checkBoxIcon = UIManager.getIcon("CheckBox.icon");
+
+ return;
+ }
+
+ public final int getIconHeight() {
+ return this.checkBoxIcon.getIconHeight();
+
+ }
+
+ public final int getIconWidth() {
+ return this.checkBoxIcon.getIconWidth();
+
+ }
+
+
+ public void paintIcon(Component c, Graphics g, int x, int y)
+ {
+ checkBoxIcon.paintIcon(triStateCheckBox, g, x, y);
+ if (triStateCheckBox.getState().equals(TriStateCheckBox.State.PARTIAL))
+ {
+ // this is changed to create the gradient paint dynamically every time;
+ // this makes sure that the gradient is relative to the actual position of the checkbox,
+ // rather than in the absolute coordinates of the parent component
+ GradientPaint gradient = new GradientPaint(x, y, partialStateTopLeftColor, x + 8, y + 8, partialStateBottomRightColor, false);
+
+ Graphics2D g2d = (Graphics2D) g;
+ g2d.setPaint(gradient);
+ final int deltaX = 2;
+ final int deltaY = 2;
+ final int xNew = x + deltaX;
+ final int yNew = y + deltaY;
+ final int width = getIconWidth() - 2*deltaX;
+ final int height = getIconHeight() - 2*deltaY;
+ g2d.fillRect(xNew, yNew, width, height);
+ }
+ }
+
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/TriStateCheckBoxTreeCellRenderer.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/TriStateCheckBoxTreeCellRenderer.java
new file mode 100644
index 0000000..dd78bf7
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/TriStateCheckBoxTreeCellRenderer.java
@@ -0,0 +1,62 @@
+package net.sf.taverna.biocatalogue.ui.tristatetree;
+
+import java.awt.Color;
+import java.awt.Component;
+
+import javax.swing.JLabel;
+import javax.swing.JTree;
+import javax.swing.border.Border;
+import javax.swing.tree.DefaultTreeCellRenderer;
+
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+
+
+/**
+ * Provides a mechanism for rendering tri-state tree nodes.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class TriStateCheckBoxTreeCellRenderer extends DefaultTreeCellRenderer
+{
+ public Component getTreeCellRendererComponent(JTree tree, Object value,
+ boolean selected, boolean expanded, boolean leaf, int row,
+ boolean hasFocus)
+ {
+ Border treeNodePanelBorder = null; // will be obtained from default rendering and applied to the new one
+ Color backgroundColor = null; // likewise: will be applied to all constituents of the new rendering
+
+ // obtain the default rendering, we'll then customize it
+ Component defaultRendering = super.getTreeCellRendererComponent(tree, value, selected, expanded, leaf, row, hasFocus);
+
+ // it is most likely that the default rendering will be a JLabel, check just to be safe
+ if (defaultRendering instanceof JLabel)
+ {
+ JLabel defaultRenderedLabel = ((JLabel)defaultRendering);
+
+ // if this is not the case, it kind of undermines the whole purpose
+ // of using this tree cell renderer, but check just to be sure
+ if (value instanceof TriStateTreeNode) {
+ // a state value from within the TriStateTreeNode will be used to
+ // set the correct state in its rendering
+ switch (((TriStateTreeNode)value).getState()) {
+ case CHECKED:
+ if (((TriStateTreeNode)value).getPath().length > 2) {
+ // only allow CHECKED state icon for nodes that are deeper than second
+ // level in the tree - that is for any nodes that do not represent categories
+ // in the tree (root is not shown, so nodes that represent categories are
+ // effectively multiple category "roots" that have actual contents inside them)
+ defaultRenderedLabel.setIcon(ResourceManager.getImageIcon(ResourceManager.TRISTATE_CHECKBOX_CHECKED_ICON));
+ break;
+ }
+ // else -- 'fall through' to PARTIAL icon: this was a CHECKED state for the category node
+ case PARTIAL: defaultRenderedLabel.setIcon(ResourceManager.getImageIcon(ResourceManager.TRISTATE_CHECKBOX_PARTIAL_ICON)); break;
+ case UNCHECKED: defaultRenderedLabel.setIcon(ResourceManager.getImageIcon(ResourceManager.TRISTATE_CHECKBOX_UNCHECKED_ICON)); break;
+ default: defaultRenderedLabel.setIcon(null); break;
+ }
+ }
+ }
+
+ return (defaultRendering);
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/TriStateTreeCheckingListener.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/TriStateTreeCheckingListener.java
new file mode 100644
index 0000000..e612e54
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/TriStateTreeCheckingListener.java
@@ -0,0 +1,12 @@
+package net.sf.taverna.biocatalogue.ui.tristatetree;
+
+/**
+ * A simple interface to enable tracking tree checking
+ * changes.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public interface TriStateTreeCheckingListener
+{
+ public void triStateTreeCheckingChanged(JTriStateTree source);
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/TriStateTreeNode.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/TriStateTreeNode.java
new file mode 100644
index 0000000..248cdf8
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/ui/tristatetree/TriStateTreeNode.java
@@ -0,0 +1,246 @@
+package net.sf.taverna.biocatalogue.ui.tristatetree;
+
+import java.util.Enumeration;
+
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.TreeNode;
+
+/**
+ * This class models tri-state nodes in the tree. Effectively
+ * it associates a tri-state checkbox with each tree node.
+ *
+ * Useful for partial selections of hierarchical data -
+ * partial selection of a node indicates that some of the
+ * children of that node are selected.
+ *
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public class TriStateTreeNode extends DefaultMutableTreeNode
+{
+ private TriStateCheckBox.State state;
+
+ /**
+ * Creates a regular tree node; associated tri-state checkbox state is set to UNCHECKED.
+ *
+ * @param userObject The object this tree node will represent.
+ */
+ public TriStateTreeNode(Object userObject) {
+ this(userObject, TriStateCheckBox.State.UNCHECKED);
+ }
+
+ /**
+ * Creates a regular tree node; associated tri-state checkbox state is set to the provided <code>initialState</code> value.
+ *
+ * @param userObject The object this tree node will represent.
+ * @param initialState One of the enum values of <code>TriStateCheckBox.State</code>.
+ */
+ public TriStateTreeNode(Object userObject, TriStateCheckBox.State initialState) {
+ super(userObject);
+ this.state = initialState;
+ }
+
+
+ /**
+ * Compares based on the user object, not the state of this node.
+ */
+ public boolean equals(Object other) {
+ if (other instanceof TriStateTreeNode) {
+ return (this.userObject.equals(((TriStateTreeNode)other).userObject));
+ }
+ else {
+ return (false);
+ }
+ }
+
+
+ /**
+ * Sets the state of the current node and (optionally) propagates
+ * those changes through the tree.
+ *
+ * @param state The new state to set - value from <code>TriStateCheckBox.State</code> enum.
+ * @param propagateChangesToRelatedNodes True - to use the tree checking model to
+ * propagate changes of the state of the current tree node to the
+ * other related tree nodes (e.g. all descendants and ancestors) -
+ * up and down the tree hierarchy. False - to only update the current
+ * node and make no changes to the rest of the tree.
+ */
+ public void setState(TriStateCheckBox.State state, boolean propagateChangesToRelatedNodes)
+ {
+ this.state = state;
+
+ // check if the tree checking model should be activated
+ if (propagateChangesToRelatedNodes) {
+ updateStateOfRelatedNodes();
+ }
+ }
+
+
+ /**
+ * Sets the state of the current node.
+ *
+ * @param state The new state to set - value from <code>TriStateCheckBox.State</code> enum.
+ */
+ public void setState(TriStateCheckBox.State state) {
+ setState(state, false);
+ }
+
+
+ public TriStateCheckBox.State getState() {
+ return state;
+ }
+
+
+ /**
+ * Toggles the state of the associated tri-state checkbox.
+ * State transitions are as follows:</br>
+ * <code>
+ * TriStateCheckBox.State.CHECKED -> TriStateCheckBox.State.UNCHECKED
+ * TriStateCheckBox.State.PARTIAL -> TriStateCheckBox.State.UNCHECKED
+ * TriStateCheckBox.State.UNCHECKED -> TriStateCheckBox.State.CHECKED
+ * </code>
+ *
+ * @param propagateChangesToRelatedNodes True - to use the tree checking model to
+ * propagate changes of the state of the current tree node to the
+ * other related tree nodes (e.g. all descendants and ancestors) -
+ * up and down the tree hierarchy. False - to only update the current
+ * node and make no changes to the rest of the tree.
+ * @return The value of the new state.
+ */
+ public TriStateCheckBox.State toggleState(boolean propagateChangesToRelatedNodes)
+ {
+ if (state.equals(TriStateCheckBox.State.CHECKED) || state.equals(TriStateCheckBox.State.PARTIAL)) {
+ state = TriStateCheckBox.State.UNCHECKED;
+ }
+ else if (state.equals(TriStateCheckBox.State.UNCHECKED)) {
+ state = TriStateCheckBox.State.CHECKED;
+ }
+
+ // check if the tree checking model should be activated
+ if (propagateChangesToRelatedNodes) {
+ updateStateOfRelatedNodes();
+ }
+
+ return (state);
+ }
+
+
+ /*
+ * === The tree CHECKING MODEL ===
+ *
+ * Effectively, this defines the way the tree reacts to it's nodes
+ * being checked / unchecked. Only one model is implemented at the
+ * moment, therefore it's not extracted into a separate class, but
+ * remains to be a part of the TriStateTreeNode.
+ *
+ * Could possibly be better placed within the JTriStateTree, rather
+ * than TriStateTreeNode.
+ */
+
+ /**
+ * The entry point - must be invoked to traverse the tree and make
+ * changes to checking states of related tree nodes.
+ */
+ public void updateStateOfRelatedNodes()
+ {
+ updateStateOfAncestors(this.getParent());
+ updateStateOfDescendants(this);
+ }
+
+
+ /**
+ * Recursively visits all ancestors of the <code>parentNode</code>
+ * and decides on their checking states based on the states of their
+ * children nodes.
+ *
+ * @param parentNode Initially - parent node of the current node (i.e. the one,
+ * for which a state update has been made); then updated for
+ * recursive calls.
+ */
+ private void updateStateOfAncestors(TreeNode parentNode)
+ {
+ // reached root of the tree, do nothing - return
+ if (parentNode == null) {
+ return;
+ }
+
+ if (parentNode instanceof TriStateTreeNode) {
+ TriStateTreeNode parentTriStateNode = (TriStateTreeNode)parentNode;
+
+ // explicitly fetch children into a new enumeration - this is
+ // to make sure that we work with the same enumeration, rather
+ // than obtaining a fresh one with every reference to 'parentTriStateNode.children()'
+ Enumeration childNodes = parentTriStateNode.children();
+
+ // go through all the children and count the number of selected ones
+ int iChildrenCount = 0;
+ int iPartiallySelectedChildren = 0;
+ int iSelectedChildren = 0;
+
+ while(childNodes.hasMoreElements()) {
+ Object node = childNodes.nextElement();
+ if (node instanceof TriStateTreeNode) {
+ TriStateTreeNode currentNode = (TriStateTreeNode)node;
+ iChildrenCount++;
+ if (currentNode.getState().equals(TriStateCheckBox.State.CHECKED)) {
+ iSelectedChildren++;
+ }
+ else if (currentNode.getState().equals(TriStateCheckBox.State.PARTIAL)) {
+ iPartiallySelectedChildren++;
+ }
+ }
+ }
+
+
+ // decide on the state of the 'parentNode' based on the checking state of its children
+ if (iSelectedChildren == 0 && iPartiallySelectedChildren == 0) {
+ // no children are selected
+ parentTriStateNode.setState(TriStateCheckBox.State.UNCHECKED);
+ }
+ else if ((iSelectedChildren + iPartiallySelectedChildren) > 0 && iSelectedChildren < iChildrenCount) {
+ // some children are selected (either partially or fully)
+ parentTriStateNode.setState(TriStateCheckBox.State.PARTIAL);
+ }
+ else if (iSelectedChildren > 0 && iSelectedChildren == iChildrenCount) {
+ // all children are selected
+ parentTriStateNode.setState(TriStateCheckBox.State.CHECKED);
+ }
+
+
+ // repeat the same recursively up the hierarchy
+ updateStateOfAncestors(parentTriStateNode.getParent());
+ }
+ }
+
+ /**
+ * Recursively traverses all descendants of the <code>parentNode</code>
+ * to set their checking state to the value of the state of the <code>parentNode</code>.
+ *
+ * @param parentNode Initially - the tree node for which the state
+ * change was made; then updated for recursive calls.
+ */
+ private void updateStateOfDescendants(TriStateTreeNode parentNode)
+ {
+ // explicitly fetch children into a new enumeration - this is
+ // to make sure that we work with the same enumeration, rather
+ // than obtaining a fresh one with every reference to 'parentNode.children()'
+ Enumeration childNodes = parentNode.children();
+
+ // for all child nodes do 2 things:
+ // - set their state as that of the parent;
+ // - repeat the same recursively with their children
+ while(childNodes.hasMoreElements()) {
+ Object node = childNodes.nextElement();
+ if (node instanceof TriStateTreeNode) {
+ TriStateTreeNode currentNode = (TriStateTreeNode) node;
+ currentNode.setState(parentNode.getState());
+ currentNode.updateStateOfDescendants(currentNode);
+ }
+ }
+ }
+
+ /*
+ * === End of CHECKING MODEL implementation.
+ */
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/BioCataloguePerspective.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/BioCataloguePerspective.java
new file mode 100644
index 0000000..ac170dc
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/BioCataloguePerspective.java
@@ -0,0 +1,70 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue;
+
+import java.io.InputStream;
+import java.net.URL;
+
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.t2.workbench.ui.zaria.PerspectiveSPI;
+
+import org.jdom.Element;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class BioCataloguePerspective implements PerspectiveSPI
+{
+ private MainComponent perspectiveMainComponent;
+ private boolean visible = true;
+
+ public ImageIcon getButtonIcon()
+ {
+ return ResourceManager.getImageIcon(ResourceManager.FAVICON);
+ }
+
+ public InputStream getLayoutInputStream() {
+ return getClass().getResourceAsStream("biocatalogue-perspective.xml");
+ }
+
+ public String getText() {
+ return "Service Catalogue";
+ }
+
+ public boolean isVisible() {
+ return visible;
+ }
+
+ public int positionHint()
+ {
+ // this determines position of perspective in the
+ // bar with perspective buttons (currently makes it the last in
+ // the list)
+ return 40;
+ }
+
+ public void setVisible(boolean visible) {
+ this.visible = visible;
+
+ }
+
+ public void update(Element layoutElement) {
+ // TODO Auto-generated method stub
+
+ // Not sure what to do here
+ }
+
+ public void setMainComponent(MainComponent component)
+ {
+ this.perspectiveMainComponent = component;
+ }
+
+ /**
+ * Returns the instance of the main component of this perspective.
+ */
+ public MainComponent getMainComponent()
+ {
+ return this.perspectiveMainComponent;
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/MainComponent.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/MainComponent.java
new file mode 100644
index 0000000..eeb1cba
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/MainComponent.java
@@ -0,0 +1,285 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.GridLayout;
+
+import javax.swing.ImageIcon;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+import javax.swing.border.LineBorder;
+
+import net.sf.taverna.biocatalogue.model.BioCataloguePluginConstants;
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.biocatalogue.model.Util;
+import net.sf.taverna.biocatalogue.ui.BioCatalogueExplorationTab;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+import net.sf.taverna.t2.workbench.ui.zaria.UIComponentSPI;
+
+import org.apache.log4j.Logger;
+
+/*
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public final class MainComponent extends JPanel implements UIComponentSPI //, ChangeListener
+{
+// private static final String windowBaseTitle = "BioCatalogue API Demo";
+// private HashMap<String, String> windowTitleMap;
+
+ private MainComponent pluginPerspectiveMainComponent;
+ private final Logger logger = Logger.getLogger(MainComponent.class);
+
+ //private JTabbedPane tpMainTabs;
+ private BioCatalogueExplorationTab jpBioCatalogueExplorationTab;
+// private BioCataloguePluginAbout jpAboutTab;
+
+ public static JFrame dummyOwnerJFrame;
+ static {
+ // this is only to have a nice icon on all Dialog boxes - can be removed at any time
+ dummyOwnerJFrame = new JFrame();
+ dummyOwnerJFrame.setIconImage(ResourceManager.getImageIcon(ResourceManager.FAVICON).getImage());
+ }
+
+
+ /**
+ * This constructor is protected, and so is only available to the classes in its package -
+ * i.e. Taverna integration classes. Other parts of the plugin must use <code>MainComponentFactory.getSharedInstance()</code>
+ * to get the shared instance of this class.
+ */
+ protected MainComponent()
+ {
+ super();
+ initialiseEnvironment();
+ initialisePerspectiveUI();
+ }
+
+
+ // *** Methods implementing UIComponentSPI interface ***
+
+ public ImageIcon getIcon() {
+ return WorkbenchIcons.databaseIcon;
+ }
+
+ @Override
+ public String getName() {
+ return "Service Catalogue Perspective Main Component";
+ }
+
+ public void onDisplay() {
+ // TODO Auto-generated method stub
+ }
+
+ public void onDispose() {
+ // TODO Auto-generated method stub
+ }
+
+ // *** End of methods implementing UIComponentSPI interface ***
+
+
+ private void initialiseEnvironment()
+ {
+ // before anything else - store a reference to self for use during
+ // initialisation of other components
+ pluginPerspectiveMainComponent = this;
+
+
+ // pre-load classes for FlyingSaucer XHTML renderer - this will make sure
+ // that the first time it is used, there will be no delay while classes
+ // are loaded by Java
+ new Thread("class pre-loading") {
+ public void run() {
+ try {
+ Class.forName("org.xhtmlrenderer.simple.FSScrollPane");
+ Class.forName("org.xhtmlrenderer.simple.XHTMLPanel");
+ }
+ catch (ClassNotFoundException e) {
+ logger.error("Problem while pre-loading classes for FlyingSaucer XHTML renderer", e);
+ }
+ }
+ }.start();
+
+
+ // determine what folder is to be used for config files
+ if (!Util.isRunningInTaverna()) {
+ // running outside Taverna, place config file and log into the user's home directory
+ BioCataloguePluginConstants.CONFIG_FILE_FOLDER =
+ new java.io.File(System.getProperty("user.home"), BioCataloguePluginConstants.CONFIG_FILE_FOLDER_WHEN_RUNNING_STANDALONE);
+ BioCataloguePluginConstants.LOG_FILE_FOLDER =
+ new java.io.File(System.getProperty("user.home"), BioCataloguePluginConstants.CONFIG_FILE_FOLDER_WHEN_RUNNING_STANDALONE);
+ }
+
+
+ // this makes sure that tooltips will stay displayed for longer than default
+ ToolTipManager.sharedInstance().setDismissDelay(BioCataloguePluginConstants.DEFAULT_TOOLTIP_DURATION);
+
+ // these components must be accessed by all other components, hence need
+ // to be initialised before any other initialisation is done
+
+// windowTitleMap = new HashMap<String,String>();
+ }
+
+ private void initialisePerspectiveUI()
+ {
+ // set the loader icon to show that the perspective is loading
+ this.setLayout(new GridLayout(1,1));
+ this.add(new JLabel(ResourceManager.getImageIcon(ResourceManager.BAR_LOADER_ORANGE)));
+
+ new Thread("Initialise Service Catalogue Perspective UI")
+ {
+ public void run() {
+ // create all tabs prior to putting them inside the tabbed pane
+ jpBioCatalogueExplorationTab = new BioCatalogueExplorationTab();
+// jpServiceFilteringTab = new ServiceFilteringTab(pluginPerspectiveMainComponent, client, logger);
+// jpSearchTab = new SearchTab(pluginPerspectiveMainComponent, client, logger);
+// jpAboutTab = new BioCataloguePluginAbout(pluginPerspectiveMainComponent, client, logger);
+
+ // create main tabs
+// tpMainTabs = new JTabbedPane();
+// tpMainTabs.add("Explore BioCatalogue", jpBioCatalogueExplorationTab);
+// tpMainTabs.add("Search", jpSearchTab);
+// tpMainTabs.add("Filter Services", jpServiceFilteringTab);
+// tpMainTabs.add("About", jpAboutTab);
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run()
+ {
+ // add main tabs and the status bar into the perspective
+ pluginPerspectiveMainComponent.removeAll();
+ pluginPerspectiveMainComponent.setLayout(new BorderLayout());
+ pluginPerspectiveMainComponent.setBorder(new LineBorder(Color.BLACK));
+ pluginPerspectiveMainComponent.add(jpBioCatalogueExplorationTab, BorderLayout.CENTER);
+
+ // everything is prepared -- need to focus default component on the first tab
+ // (artificially generate change event on the tabbed pane to perform focus request)
+// tpMainTabs.setSelectedIndex(1);
+// tpMainTabs.addChangeListener(pluginPerspectiveMainComponent);
+// tpMainTabs.setSelectedIndex(0);
+ }
+ });
+ }
+ }.start();
+ }
+
+ /**
+ * Determines whether the specified tab is currently active in the main tabbed pane.
+ * @param strTabClassName Class name of the tab which is tested for being active.
+ * @return True if specified tab is currently active.
+ */
+/*
+ private boolean isTabActive(String strTabClassName)
+ {
+ if (tpMainTabs == null) return (false);
+
+ // if an anonymous thread within the main tab component class will call
+ // this method, we want to store the main tab's class, rather than
+ // the full class name of the anonymous worker thread
+ String strCurSelectedTabClassName = tpMainTabs.getSelectedComponent().getClass().getName();
+
+ // get the real class name to match
+ String strBaseClassName = Util.getBaseClassName(strTabClassName);
+
+ // compare the two class names
+ return (strBaseClassName.equals(strCurSelectedTabClassName));
+ }
+ */
+
+
+ /**
+ * This method "selects" the tab represented by the component provided as a parameter.
+ *
+ * @param c Component that represents one of the tabs in the main tabbed pane.
+ * If <code>c</code> is not found within the components of the tabbed pane, nothing will happen.
+ */
+/*
+ public void setTabActive(Component c)
+ {
+ try {
+ tpMainTabs.setSelectedComponent(c);
+ }
+ catch (IllegalArgumentException e) {
+ // do nothing, can't activate component which is not in the tabbed pane
+ }
+ }
+ */
+
+
+ /**
+ * Sets title of the main perspective window for a specified tab,
+ * thus supporting different window titles for different tabs;
+ * new title will only be displayed immediately if the specified tab.
+ *
+ * @param strTabClassName Class name of the tab, for which window title should be updated.
+ * @param strTitle New title to set.
+ */
+/*
+ public void setWindowTitle(String strTabClassName, String strTitle)
+ {
+ // if an anonymous thread within the main tab component class will call
+ // this method, we want to store the main tab's class, rather than
+ // the full class name of the anonymous worker thread
+ String strBaseClassName = Util.getBaseClassName(strTabClassName);
+
+ // store the new title for for the specified tab
+ windowTitleMap.put(strBaseClassName, strTitle);
+
+ // if the specified tab is active, update window title immediately
+ if (isTabActive(strBaseClassName)) displayWindowTitle(strBaseClassName);
+ }
+ */
+
+
+ /**
+ * Displays window title that corresponds to specified tab.
+ *
+ * @param strTabClassName Class name of the tab for which the window title is to be set.
+ */
+/*
+ public void displayWindowTitle(String strTabClassName)
+ {
+ // if an anonymous thread within the main tab component class will call
+ // this method, we want to store the main tab's class, rather than
+ // the full class name of the anonymous worker thread
+ String strBaseClassName = Util.getBaseClassName(strTabClassName);
+
+ if (windowTitleMap.containsKey(strBaseClassName)) {
+ // title for specified tab found - show it
+ // TODO - disabled until this info will be shown in the status bar
+ //this.setTitle(windowBaseTitle + " :: " + windowTitleMap.get(strBaseClassName));
+ }
+ else {
+ // tab not found - display standard title
+ // TODO - disabled until this info will be shown in the status bar
+ //this.setTitle(windowBaseTitle);
+ }
+ }
+ */
+
+ // *** Getters for various components ***
+
+ /**
+ * @return Reference to the component that represents the BioCatalogue Exploration
+ * tab in the BioCatalogue Perspective.
+ */
+ public BioCatalogueExplorationTab getBioCatalogueExplorationTab() {
+ return (this.jpBioCatalogueExplorationTab);
+ }
+
+ // *** Callbacks for ChangeListener interface ***
+
+/* public void stateChanged(ChangeEvent e)
+ {
+ if (e.getSource().equals(tpMainTabs)) {
+ // will get called when selected tab changes - need to focus default component in the active tab
+ // and also set a correct window title
+ if (tpMainTabs.getSelectedComponent() instanceof HasDefaultFocusCapability) {
+ ((HasDefaultFocusCapability)tpMainTabs.getSelectedComponent()).focusDefaultComponent();
+ this.displayWindowTitle(tpMainTabs.getSelectedComponent().getClass().getName());
+ }
+ }
+ }*/
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/MainComponentFactory.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/MainComponentFactory.java
new file mode 100644
index 0000000..c213600
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/MainComponentFactory.java
@@ -0,0 +1,46 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue;
+
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+import net.sf.taverna.t2.workbench.ui.zaria.UIComponentFactorySPI;
+import net.sf.taverna.t2.workbench.ui.zaria.UIComponentSPI;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class MainComponentFactory implements UIComponentFactorySPI
+{
+ // this is to ensure that the whole perspective is not re-created
+ // each time it is being activated in Taverna, rather it will only
+ // happen once during the execution
+ private static MainComponent mainPerspectiveComponent = null;
+
+ public static MainComponent getSharedInstance()
+ {
+ // double-check on existence of the 'mainPerspectiveComponent' ensures
+ // that it is really created only once
+ if (mainPerspectiveComponent == null) {
+ synchronized(MainComponentFactory.class) {
+ if (mainPerspectiveComponent == null) {
+ mainPerspectiveComponent = new MainComponent();
+ }
+ }
+ }
+ return (mainPerspectiveComponent);
+ }
+
+ public UIComponentSPI getComponent() {
+ return (getSharedInstance());
+ }
+
+
+ public ImageIcon getIcon() {
+ return WorkbenchIcons.databaseIcon;
+ }
+
+ public String getName() {
+ return "Service Catalogue Main Component Factory";
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/MainComponentShutdownHook.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/MainComponentShutdownHook.java
new file mode 100644
index 0000000..6c2e844
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/MainComponentShutdownHook.java
@@ -0,0 +1,49 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue;
+
+import com.thoughtworks.xstream.XStream;
+
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.config.BioCataloguePluginConfiguration;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.service_panel.BioCatalogueServiceProvider;
+import net.sf.taverna.t2.workbench.ShutdownSPI;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class MainComponentShutdownHook implements ShutdownSPI
+{
+ public int positionHint()
+ {
+ // all custom plugins are suggested to return a value of > 100;
+ // this affects when in the termination process will this plugin
+ // be shutdown;
+ return 100;
+ }
+
+ public boolean shutdown()
+ {
+ // Do not save service providers in BioCatalogue's conf file - they should be saved by Taverna together with
+ // other service providers
+
+// // store services that were added to the Service Panel - both REST and SOAP
+// XStream xstream = new XStream();
+//
+// BioCataloguePluginConfiguration configuration = BioCataloguePluginConfiguration.getInstance();
+//
+// configuration.setProperty(
+// BioCataloguePluginConfiguration.SOAP_OPERATIONS_IN_SERVICE_PANEL,
+// xstream.toXML(BioCatalogueServiceProvider.getRegisteredSOAPOperations()));
+// configuration.setProperty(
+// BioCataloguePluginConfiguration.REST_METHODS_IN_SERVICE_PANEL,
+// xstream.toXML(BioCatalogueServiceProvider.getRegisteredRESTMethods()));
+//
+// // save all the plugin's configuration
+// configuration.store();
+//
+//
+// // close API operation log
+// MainComponentFactory.getSharedInstance().getBioCatalogueClient().getAPILogWriter().close();
+//
+ return true;
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/TestJFrameForLocalLaunch.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/TestJFrameForLocalLaunch.java
new file mode 100644
index 0000000..28a52c7
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/TestJFrameForLocalLaunch.java
@@ -0,0 +1,68 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue;
+
+import java.awt.BorderLayout;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
+
+import javax.swing.JFrame;
+
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class TestJFrameForLocalLaunch extends JFrame implements ComponentListener
+{
+ private static final int DEFAULT_POSITION_X = 225;
+ private static final int DEFAULT_POSITION_Y = 150;
+
+ private static final int DEFAULT_WIDTH = 800;
+ private static final int DEFAULT_HEIGHT = 500;
+
+
+ private TestJFrameForLocalLaunch()
+ {
+ // set window title and icon
+ this.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ this.setTitle("Service Catalogue API Demo"/* TODO - windowBaseTitle */);
+ this.setIconImage(ResourceManager.getImageIcon(ResourceManager.FAVICON).getImage());
+ this.addComponentListener(this);
+
+ // get content pane
+ Container contentPane = this.getContentPane();
+ contentPane.setLayout(new BorderLayout());
+
+ // put main tabs into the content pane
+ contentPane.add(MainComponentFactory.getSharedInstance(), BorderLayout.CENTER);
+
+ this.pack();
+ }
+
+
+ // *** Callbacks for ComponentListener interface ***
+
+ public void componentResized(ComponentEvent e) { /* do nothing */ }
+ public void componentMoved(ComponentEvent e) { /* do nothing */ }
+ public void componentHidden(ComponentEvent e) { /* do nothing */ }
+ public void componentShown(ComponentEvent e) {
+ this.setLocation(DEFAULT_POSITION_X, DEFAULT_POSITION_Y);
+ }
+
+
+ /**
+ * This is a simple test class for launching BioCatalogue perspective
+ * from outside Taverna. At some point it will be not usable anymore,
+ * when proper integration of BioCatalogue plugin is made.
+ *
+ * @author Sergejs Aleksejevs
+ */
+ public static void main(String[] args)
+ {
+ TestJFrameForLocalLaunch standaloneFrame = new TestJFrameForLocalLaunch();
+ standaloneFrame.setMinimumSize(new Dimension(DEFAULT_WIDTH, DEFAULT_HEIGHT));
+ standaloneFrame.setVisible(true);
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/Integration.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/Integration.java
new file mode 100644
index 0000000..ec792d4
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/Integration.java
@@ -0,0 +1,518 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration;
+
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+
+import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.log4j.Logger;
+import org.biocatalogue.x2009.xml.rest.ResourceLink;
+import org.biocatalogue.x2009.xml.rest.RestMethod;
+import org.biocatalogue.x2009.xml.rest.RestService;
+import org.biocatalogue.x2009.xml.rest.Service;
+import org.biocatalogue.x2009.xml.rest.ServiceTechnologyType;
+import org.biocatalogue.x2009.xml.rest.SoapOperation;
+import org.biocatalogue.x2009.xml.rest.SoapService;
+import org.biocatalogue.x2009.xml.rest.Service.Variants;
+
+import net.sf.taverna.biocatalogue.model.HTTPMethodInterpreter;
+import net.sf.taverna.biocatalogue.model.HTTPMethodInterpreter.UnsupportedHTTPMethodException;
+import net.sf.taverna.biocatalogue.model.Resource;
+import net.sf.taverna.biocatalogue.model.Resource.TYPE;
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.biocatalogue.model.SoapOperationIdentity;
+import net.sf.taverna.biocatalogue.model.SoapOperationPortIdentity;
+import net.sf.taverna.biocatalogue.model.SoapProcessorIdentity;
+import net.sf.taverna.biocatalogue.model.Util;
+import net.sf.taverna.t2.activities.rest.RESTActivity;
+import net.sf.taverna.t2.activities.rest.RESTActivity.HTTP_METHOD;
+import net.sf.taverna.t2.activities.wsdl.WSDLActivity;
+import net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceDescription;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentFactory;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.service_panel.BioCatalogueRESTServiceProvider;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.service_panel.BioCatalogueWSDLOperationServiceProvider;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.service_panel.RESTFromBioCatalogueServiceDescription;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.service_panel.WSDLOperationFromBioCatalogueServiceDescription;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.workflowview.WorkflowView;
+import net.sf.taverna.t2.workflowmodel.Dataflow;
+import net.sf.taverna.t2.workflowmodel.Port;
+import net.sf.taverna.t2.workflowmodel.Processor;
+import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
+import net.sf.taverna.t2.workflowmodel.utils.Tools;
+
+/**
+ * This class contains helpers for deeper integration with Taverna UI.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class Integration
+{
+ private static final Logger logger = Logger.getLogger(Integration.class);
+
+
+ // deny instantiation of this class
+ private Integration() { }
+
+
+ /**
+ * Adds a processor to the current workflow.
+ * The processor is specified by WSDL location and the operation name.
+ *
+ * @param processorResource Resource to add to the current workflow.
+ * @return Outcome of inserting the processor into the current workflow as a
+ * HTML-formatted string (with no opening and closing HTML tags).
+ */
+ public static JComponent insertProcessorIntoCurrentWorkflow(ResourceLink processorResource)
+ {
+ // check if this type of resource can be added to workflow diagram
+ TYPE resourceType = Resource.getResourceTypeFromResourceURL(processorResource.getHref());
+ if (resourceType.isSuitableForAddingToWorkflowDiagram()) {
+ switch (resourceType) {
+ case SOAPOperation:
+ SoapOperation soapOp = (SoapOperation) processorResource;
+ try {
+ SoapService soapService = BioCatalogueClient.getInstance().
+ getBioCatalogueSoapService(soapOp.getAncestors().getSoapService().getHref());
+
+ try {
+ WSDLServiceDescription myServiceDescription = new WSDLServiceDescription();
+ myServiceDescription.setOperation(soapOp.getName());
+ myServiceDescription.setUse("literal"); // or "encoded"
+ myServiceDescription.setStyle("document"); // or "rpc"
+ myServiceDescription.setURI(new URI(soapService.getWsdlLocation()));
+ myServiceDescription.setDescription(StringEscapeUtils.escapeHtml(soapService.getDescription())); // TODO - not sure where this is used
+
+ if (WorkflowView.importServiceDescription(myServiceDescription, false) != null) {
+ return (new JLabel("Selected " + TYPE.SOAPOperation.getTypeName() + " was successfully added to the current workflow",
+ ResourceManager.getImageIcon(ResourceManager.TICK_ICON), JLabel.CENTER));
+ }
+ else {
+ return (new JLabel("<html><center>Taverna was unable to add selected " + TYPE.SOAPOperation.getTypeName() +
+ " as a service to the current workflow.<br>This could be because the service is currently not accessible.</center></html>",
+ ResourceManager.getImageIcon(ResourceManager.ERROR_ICON), JLabel.CENTER));
+ }
+ }
+ catch (URISyntaxException e)
+ {
+ logger.error("Couldn't add " + TYPE.SOAPOperation + " to the current workflow", e);
+ return (new JLabel("<html>Could not add the selected " + TYPE.SOAPOperation.getTypeName() + " to the current workflow.<br>" +
+ "Log file will containt additional details about this error.</html>",
+ ResourceManager.getImageIcon(ResourceManager.ERROR_ICON), JLabel.CENTER));
+ }
+
+ }
+ catch (Exception e) {
+ logger.error("Failed to fetch required details to add this " + TYPE.SOAPOperation + " into the current workflow.", e);
+ return (new JLabel("<html>Failed to fetch required details to add this<br>" +
+ TYPE.SOAPOperation.getTypeName() + " into the current workflow.</html>",
+ ResourceManager.getImageIcon(ResourceManager.ERROR_ICON), JLabel.CENTER));
+ }
+
+ case RESTMethod:
+ // received object may only contain limited data, therefore need to fetch full details first
+ try {
+ RestMethod restMethod = BioCatalogueClient.getInstance().
+ getBioCatalogueRestMethod(processorResource.getHref());
+
+ // actual import of the service into the workflow
+ RESTFromBioCatalogueServiceDescription restServiceDescription = createRESTServiceDescriptionFromRESTMethod(restMethod);
+ WorkflowView.importServiceDescription(restServiceDescription, false);
+
+ // prepare result of the operation to be shown in the the waiting dialog window
+ String warnings = extractWarningsFromRESTServiceDescription(restServiceDescription, false);
+ JLabel outcomes = new JLabel("<html>Selected " + TYPE.RESTMethod.getTypeName() + " was successfully added to the current workflow" + warnings + "</html>",
+ ResourceManager.getImageIcon(warnings.length() > 0 ? ResourceManager.WARNING_ICON : ResourceManager.TICK_ICON),
+ JLabel.CENTER);
+ outcomes.setIconTextGap(20);
+ return (outcomes);
+ }
+ catch (UnsupportedHTTPMethodException e) {
+ logger.error(e);
+ return (new JLabel(e.getMessage(), ResourceManager.getImageIcon(ResourceManager.ERROR_ICON), JLabel.CENTER));
+ }
+ catch (Exception e) {
+ logger.error("Failed to fetch required details to add this " + TYPE.RESTMethod + " as a service to the current workflow.", e);
+ return (new JLabel("<html>Failed to fetch required details to add this " + TYPE.RESTMethod.getTypeName() + "<br>" +
+ "as a service to the current workflow.</html>",
+ ResourceManager.getImageIcon(ResourceManager.ERROR_ICON), JLabel.CENTER));
+ }
+
+ // type not currently supported, but maybe in the future?
+ default: return (new JLabel("Adding " + resourceType.getCollectionName() + " to the current workflow is not yet possible",
+ ResourceManager.getImageIcon(ResourceManager.ERROR_ICON), JLabel.CENTER));
+ }
+ }
+
+ // definitely not supported type
+ return (new JLabel("<html>It is not possible to add resources of the provided type<br>" +
+ "into the current workflow.</html>",
+ ResourceManager.getImageIcon(ResourceManager.ERROR_ICON), JLabel.CENTER));
+ }
+
+
+ /**
+ *
+ * @param processorResource
+ * @return Outcome of inserting the processor into the current workflow as a
+ * HTML-formatted string (with no opening and closing HTML tags).
+ */
+ public static JComponent insertProcesorIntoServicePanel(ResourceLink processorResource)
+ {
+ // check if this type of resource can be added to Service Panel
+ TYPE resourceType = Resource.getResourceTypeFromResourceURL(processorResource.getHref());
+ if (resourceType.isSuitableForAddingToServicePanel()) {
+ switch (resourceType) {
+ case SOAPOperation:
+ SoapOperation soapOp = (SoapOperation) processorResource;
+ try {
+ SoapService soapService = BioCatalogueClient.getInstance().
+ getBioCatalogueSoapService(soapOp.getAncestors().getSoapService().getHref());
+ SoapOperationIdentity soapOpId = new SoapOperationIdentity(soapService.getWsdlLocation(), soapOp.getName(), StringEscapeUtils.escapeHtml(soapOp.getDescription()));
+ WSDLOperationFromBioCatalogueServiceDescription wsdlOperationDescription = new WSDLOperationFromBioCatalogueServiceDescription(soapOpId);
+ BioCatalogueWSDLOperationServiceProvider.registerWSDLOperation(wsdlOperationDescription, null);
+
+ return (new JLabel("Selected SOAP operation has been successfully added to the Service Panel.",
+ ResourceManager.getImageIcon(ResourceManager.TICK_ICON), JLabel.CENTER));
+ }
+ catch (Exception e) {
+ logger.error("Failed to fetch required details to add this SOAP service into the Service Panel.", e);
+ return (new JLabel("Failed to fetch required details to add this " +
+ "SOAP service into the Service Panel.", ResourceManager.getImageIcon(ResourceManager.ERROR_ICON), JLabel.CENTER));
+ }
+
+ case RESTMethod:
+ try {
+ // received object may only contain limited data, therefore need to fetch full details first
+ RestMethod restMethod = BioCatalogueClient.getInstance().
+ getBioCatalogueRestMethod(processorResource.getHref());
+ RESTFromBioCatalogueServiceDescription restServiceDescription = createRESTServiceDescriptionFromRESTMethod(restMethod);
+
+ // actual insertion of the REST method into Service Panel
+ BioCatalogueRESTServiceProvider.registerNewRESTMethod(restServiceDescription, null);
+
+ // prepare result of the operation to be shown in the the waiting dialog window
+ String warnings = extractWarningsFromRESTServiceDescription(restServiceDescription, true);
+ JLabel outcomes = new JLabel("<html>Selected REST method has been successfully added to the Service Panel" + warnings + "</html>",
+ ResourceManager.getImageIcon(warnings.length() > 0 ? ResourceManager.WARNING_ICON : ResourceManager.TICK_ICON),
+ JLabel.CENTER);
+ outcomes.setIconTextGap(20);
+ return (outcomes);
+ }
+ catch (UnsupportedHTTPMethodException e) {
+ logger.error(e);
+ return (new JLabel(e.getMessage(), ResourceManager.getImageIcon(ResourceManager.ERROR_ICON), JLabel.CENTER));
+ }
+ catch (Exception e) {
+ logger.error("Failed to fetch required details to add this REST service into the Service Panel.", e);
+ return (new JLabel("Failed to fetch required details to add this " +
+ "REST service into the Service Panel.", ResourceManager.getImageIcon(ResourceManager.ERROR_ICON), JLabel.CENTER));
+ }
+
+ // type not currently supported, but maybe in the future?
+ default: return (new JLabel("Adding " + resourceType.getCollectionName() + " to the Service Panel is not yet possible",
+ ResourceManager.getImageIcon(ResourceManager.ERROR_ICON), JLabel.CENTER));
+ }
+ }
+
+ // definitely not supported type
+ return (new JLabel("<html>It is not possible to add resources of the provided type<br>" +
+ "into the Service Panel.</html>",
+ ResourceManager.getImageIcon(ResourceManager.ERROR_ICON), JLabel.CENTER));
+ }
+
+ /**
+ * Inserts all operations of the given parent SOAP or REST Web service resource link
+ * into Service Panel. Works for SOAP operations only at the moment.
+ *
+ * @return Outcome of inserting operations into Service Panel as a
+ * HTML-formatted string (with no opening and closing HTML tags).
+ */
+ public static JComponent insertAllOperationsIntoServicePanel(ResourceLink serviceResource)
+ {
+ // Check if this type of resource is a parent SOAP Web service
+ // whose operations can be added to the Service Panel
+ TYPE resourceType = Resource
+ .getResourceTypeFromResourceURL(serviceResource.getHref());
+
+ Service service = null;
+ if (resourceType == TYPE.SOAPOperation) {
+ SoapService soapService = ((SoapOperation) serviceResource)
+ .getAncestors().getSoapService();
+
+ // Get the WSDL URL of the SOAP service
+ String wsdlURL = soapService.getWsdlLocation();
+
+ // Import this WSDL into Service panel - it will add all
+ // of
+ // its operations
+ if (BioCatalogueWSDLOperationServiceProvider.registerWSDLService(
+ wsdlURL, null)) {
+ return (new JLabel(
+ "Operation(s) of the SOAP service have been successfully added to the Service Panel.",
+ ResourceManager.getImageIcon(ResourceManager.TICK_ICON),
+ JLabel.CENTER));
+ } else {
+ return (new JLabel(
+ "Failed to insert the operations of the SOAP service "
+ + " to the Service Panel.", ResourceManager
+ .getImageIcon(ResourceManager.ERROR_ICON),
+ JLabel.CENTER));
+ }
+ } else if (resourceType == TYPE.RESTMethod) {
+ RestService restService = ((RestMethod) serviceResource)
+ .getAncestors().getRestService();
+ for (RestMethod method : restService.getMethods().getRestMethodList()) {
+
+ }
+ }
+
+ return (new JLabel(
+ "<html>It is not possible to add resources of the provided type<br>"
+ + "into the Service Panel.</html>", ResourceManager
+ .getImageIcon(ResourceManager.ERROR_ICON),
+ JLabel.CENTER));
+ }
+
+ /**
+ * Instantiates a {@link RESTFromBioCatalogueServiceDescription} object from the {@link RestMethod}
+ * XML data obtained from BioCatalogue API.
+ *
+ * @param restMethod
+ * @return
+ */
+ public static RESTFromBioCatalogueServiceDescription createRESTServiceDescriptionFromRESTMethod(RestMethod restMethod) throws UnsupportedHTTPMethodException
+ {
+ // if the type of the HTTP method is not supported, an exception will be throws
+ HTTP_METHOD httpMethod = HTTPMethodInterpreter.getHTTPMethodForRESTActivity(restMethod.getHttpMethodType());
+
+ RESTFromBioCatalogueServiceDescription restServiceDescription = new RESTFromBioCatalogueServiceDescription();
+ restServiceDescription.setServiceName(Resource.getDisplayNameForResource(restMethod));
+ restServiceDescription.setDescription(StringEscapeUtils.escapeHtml(restMethod.getDescription()));
+ restServiceDescription.setHttpMethod(httpMethod);
+ restServiceDescription.setURLSignature(restMethod.getUrlTemplate());
+
+ int outputRepresentationCount = restMethod.getOutputs().getRepresentations().getRestRepresentationList().size();
+ if (outputRepresentationCount > 0) {
+ if (outputRepresentationCount > 1) {
+ restServiceDescription.getDataWarnings().add(RESTFromBioCatalogueServiceDescription.AMBIGUOUS_ACCEPT_HEADER_VALUE);
+ }
+ restServiceDescription.setAcceptHeaderValue(restMethod.getOutputs().getRepresentations().getRestRepresentationList().get(0).getContentType());
+ }
+ else {
+ restServiceDescription.getDataWarnings().add(RESTFromBioCatalogueServiceDescription.DEFAULT_ACCEPT_HEADER_VALUE);
+ }
+
+ int inputRepresentationCount = restMethod.getInputs().getRepresentations().getRestRepresentationList().size();
+ if (inputRepresentationCount > 0) {
+ if (inputRepresentationCount > 1) {
+ restServiceDescription.getDataWarnings().add(RESTFromBioCatalogueServiceDescription.AMBIGUOUS_CONTENT_TYPE_HEADER_VALUE);
+ }
+ restServiceDescription.setOutgoingContentType(restMethod.getInputs().getRepresentations().getRestRepresentationList().get(0).getContentType());
+ }
+ else if (RESTActivity.hasMessageBodyInputPort(httpMethod)) {
+ restServiceDescription.getDataWarnings().add(RESTFromBioCatalogueServiceDescription.DEFAULT_CONTENT_TYPE_HEADER_VALUE);
+ }
+
+ return (restServiceDescription);
+ }
+
+
+ /**
+ * @param restServiceDescription {@link RESTFromBioCatalogueServiceDescription} to process.
+ * @param addingToServicePanel <code>true</code> indicates that the warning messages
+ * will assume that the processor is added to the service panel;
+ * <code>false</code> would mean that the processor is added to
+ * the current workflow.
+ * @return An HTML-formatted string (with no opening-closing HTML tags) that lists
+ * any warnings that have been recorded during the {@link RESTFromBioCatalogueServiceDescription}
+ * object creation. Empty string will be returned if there are no warnings.
+ */
+ public static String extractWarningsFromRESTServiceDescription(RESTFromBioCatalogueServiceDescription restServiceDescription,
+ boolean addingToServicePanel)
+ {
+ String messageSuffix = addingToServicePanel ?
+ " once you add it into the workflow" :
+ "";
+
+ String warnings = "";
+ if (restServiceDescription.getDataWarnings().contains(RESTFromBioCatalogueServiceDescription.AMBIGUOUS_ACCEPT_HEADER_VALUE)) {
+ warnings += "<br><br>Service Catalogue description of this REST method contains more than one<br>" +
+ "representation of the method's outputs - the first one was used.<br>" +
+ "Please check value of the 'Accept' header in the configuration<br>" +
+ "of the imported service" + messageSuffix + ".";
+ }
+ else if (restServiceDescription.getDataWarnings().contains(RESTFromBioCatalogueServiceDescription.DEFAULT_ACCEPT_HEADER_VALUE)) {
+ warnings += "<br><br>Service Catalogue description of this REST method does not contain any<br>" +
+ "representations of the method's outputs - default value was used.<br>" +
+ "Please check value of the 'Accept' header in the configuration<br>" +
+ "of the imported service" + messageSuffix + ".";
+ }
+
+ if (restServiceDescription.getDataWarnings().contains(RESTFromBioCatalogueServiceDescription.AMBIGUOUS_CONTENT_TYPE_HEADER_VALUE)) {
+ warnings += "<br><br>Service Catalogue description of this REST method contains more than one<br>" +
+ "representation of the method's input data - the first one was used.<br>" +
+ "Please check value of the 'Content-Type' header in the configuration<br>" +
+ "of the imported service" + messageSuffix + ".";
+ }
+ else if (restServiceDescription.getDataWarnings().contains(RESTFromBioCatalogueServiceDescription.DEFAULT_CONTENT_TYPE_HEADER_VALUE)) {
+ warnings += "<br><br>Service Catalogue description of this REST method does not contain any<br>" +
+ "representations of the method's input data - default value was used.<br>" +
+ "Please check value of the 'Content-Type' header in the configuration<br>" +
+ "of the imported service" + messageSuffix + ".";
+ }
+
+ if (warnings.length() > 0) {
+ warnings = "<br><br>WARNINGS:" + warnings;
+ }
+
+ return (warnings);
+ }
+
+
+
+ /**
+ * @param activityPort Probably comes from contextual selection - must be either
+ * ActivityInputPort or ActivityOutputPort.
+ * @return SOAP input / output port details (WSDL location, operation name, port name) from
+ * ActivityInputPort/ActivityOutputPort which is obtained from contextual selection in the Dataflow.
+ */
+ public static <T extends Port> SoapOperationPortIdentity extractSoapOperationPortDetailsFromActivityInputOutputPort(T activityPort)
+ {
+ // check that we have the correct instance of Port here - either ActivityInputPort or ActivityOutputPort
+ boolean hasInputPort;
+ if (activityPort instanceof ActivityInputPort) {
+ hasInputPort = true;
+ }
+ else if (activityPort instanceof ActivityOutputPort) {
+ hasInputPort = false;
+ }
+ else {
+ // ERROR - wrong type supplied
+ return new SoapOperationPortIdentity("Activity port from the contextual selection was not of correct type. Impossible to create preview.");
+ }
+
+ // get parent processor details
+ Dataflow currentDataflow = FileManager.getInstance().getCurrentDataflow();
+ Collection<Processor> processors = null;
+ if (hasInputPort) {
+ processors = Tools.getProcessorsWithActivityInputPort(currentDataflow, (ActivityInputPort)activityPort);
+ }
+ else {
+ processors = Tools.getProcessorsWithActivityOutputPort(currentDataflow, (ActivityOutputPort)activityPort);
+ }
+
+ // TODO - doesn't take into account that it's possible to have several
+ SoapOperationIdentity soapOperationDetails = extractSoapOperationDetailsFromProcessor(processors.toArray(new Processor[]{})[0]);
+
+ // if no error happened, add port details and return
+ if (!soapOperationDetails.hasError()) {
+ return (new SoapOperationPortIdentity(soapOperationDetails.getWsdlLocation(),
+ soapOperationDetails.getOperationName(),
+ activityPort.getName(), hasInputPort));
+ }
+ else {
+ // error...
+ return (new SoapOperationPortIdentity(soapOperationDetails.getErrorDetails()));
+ }
+ }
+
+
+ /**
+ * Uses contextual selection to extract WSDL location and operation name of the
+ * currently selected processor within the Design view of current workflow.
+ *
+ * @param contextualSelection Selection that was made in the Design view.
+ * @return Details of the SOAP operation that acts as a processor wrapped into
+ * this single instance. If any problems occurred while performing
+ * contextual selection analysis, these are also recorded into the same
+ * instance - before using the returned value the caller must check
+ * <code>SoapOperationIdentity.hasError()</code> value.
+ */
+ public static SoapOperationIdentity extractSoapOperationDetailsFromProcessorContextualSelection(ContextualSelection contextualSelection)
+ {
+ if (!(contextualSelection.getSelection() instanceof Processor)) {
+ return (new SoapOperationIdentity("ERROR: It is only possible to extract " +
+ "SOAP operation details from the service."));
+ }
+
+ // now we know it's a Processor
+ Processor processor = (Processor)contextualSelection.getSelection();
+ return (extractSoapOperationDetailsFromProcessor(processor));
+ }
+
+
+ /**
+ * Worker method for <code>extractSoapOperationDetailsFromProcessorContextualSelection()</code>.
+ *
+ * @param processor
+ * @return
+ */
+ public static SoapOperationIdentity extractSoapOperationDetailsFromProcessor(Processor processor)
+ {
+ List<? extends Activity> activityList = (List<? extends Activity>) processor.getActivityList();
+
+ if (activityList == null || activityList.size() == 0) {
+ return (new SoapOperationIdentity("ERROR: Selected processor doesn't have any activities - " +
+ "impossible to extract SOAP operation details."));
+ }
+ else {
+ // take only the first activity - TODO: figure out what should be done here...
+ Activity activity = activityList.get(0);
+ if (activity instanceof WSDLActivity) {
+ WSDLActivity a = (WSDLActivity)activity;
+ return (new SoapOperationIdentity(a.getConfiguration().getWsdl(), a.getConfiguration().getOperation(), null));
+ }
+ else {
+ return (new SoapOperationIdentity("Service Catalogue integration only works with WSDL Activities at the moment"));
+ }
+ }
+ }
+
+
+ /**
+ * @param contextualSelection
+ * @return A list of all WSDL activities (the only supported processors by BioCatalogue plugin for now).
+ */
+ public static List<SoapProcessorIdentity> extractSupportedProcessorsFromDataflow(ContextualSelection contextualSelection)
+ {
+ // check that there was a correct contextual selection
+ if (!(contextualSelection.getSelection() instanceof Dataflow)) {
+ logger.error("It is only possible to extract supported services from the workflow.");
+ return (new ArrayList<SoapProcessorIdentity>());
+ }
+
+ // first extract all processors
+ Dataflow dataflow = (Dataflow)contextualSelection.getSelection();
+ List<? extends Processor> allProcessors = dataflow.getEntities(Processor.class);
+
+ // now filter out any processors that are not WSDL activities
+ List<SoapProcessorIdentity> supportedProcessors = new ArrayList<SoapProcessorIdentity>();
+ for (Processor proc : allProcessors) {
+ List<? extends Activity> activityList = (List<? extends Activity>) proc.getActivityList();
+ if (activityList != null && activityList.size() > 0) {
+ // take only the first activity - TODO: figure out what should be done here...
+ Activity activity = activityList.get(0);
+ if (activity instanceof WSDLActivity) {
+ WSDLActivity a = (WSDLActivity)activity;
+ supportedProcessors.add(new SoapProcessorIdentity(a.getConfiguration().getWsdl(),
+ a.getConfiguration().getOperation(),
+ proc.getLocalName()));
+ }
+ }
+ }
+
+ // return all found processors
+ return (supportedProcessors);
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/config/BioCataloguePluginConfiguration.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/config/BioCataloguePluginConfiguration.java
new file mode 100644
index 0000000..3985ac5
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/config/BioCataloguePluginConfiguration.java
@@ -0,0 +1,68 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.config;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import uk.org.taverna.configuration.AbstractConfigurable;
+
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
+
+/**
+ *
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class BioCataloguePluginConfiguration extends AbstractConfigurable
+{
+ public static final String SERVICE_CATALOGUE_BASE_URL = "ServiceCatalogue_Base_URL";
+ public static final String SOAP_OPERATIONS_IN_SERVICE_PANEL = "SOAP_Operations_in_Service_Panel";
+ public static final String REST_METHODS_IN_SERVICE_PANEL = "REST_Methods_in_Service_Panel";
+
+
+ private static class Singleton {
+ private static BioCataloguePluginConfiguration instance = new BioCataloguePluginConfiguration();
+ }
+
+ // private static Logger logger = Logger.getLogger(MyExperimentConfiguration.class);
+
+ private Map<String, String> defaultPropertyMap;
+
+
+ public static BioCataloguePluginConfiguration getInstance() {
+ return Singleton.instance;
+ }
+
+ public String getCategory() {
+ return "general";
+ }
+
+ public Map<String,String> getDefaultPropertyMap() {
+ if (defaultPropertyMap == null) {
+ defaultPropertyMap = new HashMap<String,String>();
+ defaultPropertyMap.put(SERVICE_CATALOGUE_BASE_URL, BioCatalogueClient.DEFAULT_API_LIVE_SERVER_BASE_URL);
+ }
+ return defaultPropertyMap;
+ }
+
+ public String getDisplayName() {
+ return "Service catalogue";
+ }
+
+ public String getFilePrefix() {
+ return "ServiceCatalogue";
+ }
+
+ public String getUUID() {
+ return "4daac25c-bd56-4f90-b909-1e49babe5197";
+ }
+
+
+ /**
+ * Just a "proxy" method - {@link AbstractConfigurable#store()}
+ * is not visible to the users of instances of this class otherwise.
+ */
+ public void store() {
+ super.store();
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/config/BioCataloguePluginConfigurationPanel.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/config/BioCataloguePluginConfigurationPanel.java
new file mode 100644
index 0000000..a83a223
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/config/BioCataloguePluginConfigurationPanel.java
@@ -0,0 +1,448 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.config;
+
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.ProxySelector;
+import java.net.URL;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+
+import org.apache.http.HttpEntity;
+import org.apache.http.HttpResponse;
+import org.apache.http.auth.AuthScope;
+import org.apache.http.auth.UsernamePasswordCredentials;
+//import org.apache.http.client.HttpClient;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.DefaultHttpClient;
+import org.apache.http.impl.conn.ProxySelectorRoutePlanner;
+import org.apache.http.protocol.BasicHttpContext;
+import org.apache.http.protocol.HttpContext;
+import org.apache.log4j.Logger;
+import org.jdom.Attribute;
+import org.jdom.Document;
+import org.jdom.input.SAXBuilder;
+
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentFactory;
+
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public class BioCataloguePluginConfigurationPanel extends JPanel
+{
+ public static final String APPLICATION_XML_MIME_TYPE = "application/xml";
+
+ public static String PROXY_HOST = "http.proxyHost";
+ public static String PROXY_PORT = "http.proxyPort";
+ public static String PROXY_USERNAME = "http.proxyUser";
+ public static String PROXY_PASSWORD = "http.proxyPassword";
+
+ // 1.0.0b and higher until the first digit changes, as according to "Semantic Versioning"
+ // from http://www.biocatalogue.org/wiki/doku.php?id=public:api:changelog
+ // "Major version X (X.y.z | X > 0) MUST be incremented if any backwards
+ // incompatible changes are introduced to the public API. It MAY include minor and patch level changes."
+ public static String[] MIN_SUPPORTED_BIOCATALOGUE_API_VERSION = {"1", "1", "0"}; // major, minor and patch versions
+ public static String API_VERSION = "apiVersion";
+
+ private BioCataloguePluginConfiguration configuration =
+ BioCataloguePluginConfiguration.getInstance();
+
+
+ // UI elements
+ JTextField tfBioCatalogueAPIBaseURL;
+
+ private Logger logger = Logger.getLogger(BioCataloguePluginConfigurationPanel.class);
+
+ public BioCataloguePluginConfigurationPanel() {
+ initialiseUI();
+ resetFields();
+ }
+
+ private void initialiseUI()
+ {
+ this.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.anchor = GridBagConstraints.NORTHWEST;
+ c.weightx = 1.0;
+
+ c.gridx = 0;
+ c.gridy = 0;
+ JTextArea taDescription = new JTextArea("Configure the Service Catalogue integration functionality");
+ taDescription.setFont(taDescription.getFont().deriveFont(Font.PLAIN, 11));
+ taDescription.setLineWrap(true);
+ taDescription.setWrapStyleWord(true);
+ taDescription.setEditable(false);
+ taDescription.setFocusable(false);
+ taDescription.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
+ this.add(taDescription, c);
+
+
+ c.gridy++;
+ c.insets = new Insets(20, 0, 0, 0);
+ JLabel jlBioCatalogueAPIBaseURL = new JLabel("Base URL of the Service Catalogue instance to connect to:");
+ this.add(jlBioCatalogueAPIBaseURL, c);
+
+ c.gridy++;
+ c.insets = new Insets(0, 0, 0, 0);
+ tfBioCatalogueAPIBaseURL = new JTextField();
+ this.add(tfBioCatalogueAPIBaseURL, c);
+
+
+ c.gridy++;
+ c.insets = new Insets(30, 0, 0, 0);
+ // We are not removing BioCatalogue services from its config panel any more -
+ // they are being handled by the Taverna's Service Registry
+// JButton bForgetStoredServices = new JButton("Forget services added to Service Panel by BioCatalogue Plugin");
+// bForgetStoredServices.addActionListener(new ActionListener() {
+// public void actionPerformed(ActionEvent e)
+// {
+// int response = JOptionPane.showConfirmDialog(null, // no way T2ConfigurationFrame instance can be obtained to be used as a parent...
+// "Are you sure you want to clear all SOAP operations and REST methods\n" +
+// "that were added to the Service Panel by the BioCatalogue Plugin?\n\n" +
+// "This action is permanent is cannot be undone.\n\n" +
+// "Do you want to proceed?", "BioCatalogue Plugin", JOptionPane.YES_NO_OPTION);
+//
+// if (response == JOptionPane.YES_OPTION)
+// {
+// BioCatalogueServiceProvider.clearRegisteredServices();
+// JOptionPane.showMessageDialog(null, // no way T2ConfigurationFrame instance can be obtained to be used as a parent...
+// "Stored services have been successfully cleared, but will remain\n" +
+// "being shown in Service Panel during this session.\n\n" +
+// "They will not appear in the Service Panel after you restart Taverna.",
+// "BioCatalogue Plugin", JOptionPane.INFORMATION_MESSAGE);
+// }
+// }
+// });
+// this.add(bForgetStoredServices, c);
+
+
+ JButton bLoadDefaults = new JButton("Load Defaults");
+ bLoadDefaults.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ loadDefaults();
+ }
+ });
+
+ JButton bReset = new JButton("Reset");
+ bReset.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ resetFields();
+ }
+ });
+
+ JButton bApply = new JButton("Apply");
+ bApply.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ applyChanges();
+ }
+ });
+
+ JPanel jpActionButtons = new JPanel();
+ jpActionButtons.add(bLoadDefaults);
+ jpActionButtons.add(bReset);
+ jpActionButtons.add(bApply);
+ c.insets = new Insets(30, 0, 0, 0);
+ c.gridy++;
+ c.weighty = 1.0;
+ this.add(jpActionButtons, c);
+ }
+
+
+ /**
+ * Resets all fields to the last saved configuration.
+ */
+ private void resetFields() {
+ tfBioCatalogueAPIBaseURL.setText(configuration.getProperty(BioCataloguePluginConfiguration.SERVICE_CATALOGUE_BASE_URL));
+ }
+
+ /**
+ * Resets all fields to the default values.
+ */
+ private void loadDefaults() {
+ tfBioCatalogueAPIBaseURL.setText(configuration.getDefaultProperty(BioCataloguePluginConfiguration.SERVICE_CATALOGUE_BASE_URL));
+ }
+
+ /**
+ * Saves recent changes to the configuration parameter map.
+ * Some input validation is performed as well.
+ */
+ private void applyChanges() {
+ // --- BioCatalogue BASE URL ---
+
+ String candidateBaseURL = tfBioCatalogueAPIBaseURL.getText();
+ if (candidateBaseURL.length() == 0) {
+ JOptionPane.showMessageDialog(this,
+ "Service Catalogue base URL must not be blank",
+ "Service Catalogue Configuration", JOptionPane.WARNING_MESSAGE);
+ tfBioCatalogueAPIBaseURL.requestFocusInWindow();
+ return;
+ } else {
+ try {
+ new URL(candidateBaseURL);
+ } catch (MalformedURLException e) {
+ JOptionPane
+ .showMessageDialog(
+ this,
+ "Currently set Service Catalogue instance URL is not valid\n." +
+ "Please check the URL and try again.",
+ "Service Catalogue Configuration",
+ JOptionPane.WARNING_MESSAGE);
+ tfBioCatalogueAPIBaseURL.selectAll();
+ tfBioCatalogueAPIBaseURL.requestFocusInWindow();
+ return;
+ }
+
+ // check if the base URL has changed from the last saved state
+ if (!candidateBaseURL
+ .equals(configuration
+ .getProperty(BioCataloguePluginConfiguration.SERVICE_CATALOGUE_BASE_URL))) {
+ // Perform various checks on the new URL
+
+ // Do a GET with "Accept" header set to "application/xml"
+ // We are expecting a 200 OK and an XML doc in return that
+ // contains the BioCataogue version number element.
+ DefaultHttpClient httpClient = new DefaultHttpClient();
+
+ // Set the proxy settings, if any
+ if (System.getProperty(PROXY_HOST) != null
+ && !System.getProperty(PROXY_HOST).equals("")) {
+ // Instruct HttpClient to use the standard
+ // JRE proxy selector to obtain proxy information
+ ProxySelectorRoutePlanner routePlanner = new ProxySelectorRoutePlanner(
+ httpClient.getConnectionManager().getSchemeRegistry(), ProxySelector
+ .getDefault());
+ httpClient.setRoutePlanner(routePlanner);
+ // Do we need to authenticate the user to the proxy?
+ if (System.getProperty(PROXY_USERNAME) != null
+ && !System.getProperty(PROXY_USERNAME).equals("")) {
+ // Add the proxy username and password to the list of credentials
+ httpClient.getCredentialsProvider().setCredentials(
+ new AuthScope(System.getProperty(PROXY_HOST),Integer.parseInt(System.getProperty(PROXY_PORT))),
+ new UsernamePasswordCredentials(System.getProperty(PROXY_USERNAME), System.getProperty(PROXY_PASSWORD)));
+ }
+ }
+
+ HttpGet httpGet = new HttpGet(candidateBaseURL);
+ httpGet.setHeader("Accept", APPLICATION_XML_MIME_TYPE);
+
+ // Execute the request
+ HttpContext localContext = new BasicHttpContext();
+ HttpResponse httpResponse;
+ try {
+ httpResponse = httpClient.execute(httpGet, localContext);
+ } catch (Exception ex1) {
+ logger.error("Service Catalogue preferences configuration: Failed to do "
+ + httpGet.getRequestLine(), ex1);
+ // Warn the user
+ JOptionPane.showMessageDialog(this,
+ "Failed to connect to the URL of the Service Catalogue instance.\n"
+ + "Please check the URL and try again.",
+ "Service Catalogue Configuration",
+ JOptionPane.INFORMATION_MESSAGE);
+
+ // Release resource
+ httpClient.getConnectionManager().shutdown();
+
+ tfBioCatalogueAPIBaseURL.requestFocusInWindow();
+ return;
+ }
+
+ if (httpResponse.getStatusLine().getStatusCode() == HttpURLConnection.HTTP_OK) { // HTTP/1.1 200 OK
+ HttpEntity httpEntity = httpResponse.getEntity();
+ String contentType = httpEntity.getContentType().getValue()
+ .toLowerCase().trim();
+ logger
+ .info("Service Catalogue preferences configuration: Got 200 OK when testing the Service Catalogue instance by doing "
+ + httpResponse.getStatusLine()
+ + ". Content type of response "
+ + contentType);
+ if (contentType.startsWith(APPLICATION_XML_MIME_TYPE)) {
+ String value = null;
+ Document doc = null;
+ try {
+ value = readResponseBodyAsString(httpEntity)
+ .trim();
+ // Try to read this string into an XML document
+ SAXBuilder builder = new SAXBuilder();
+ byte[] bytes = value.getBytes("UTF-8");
+ doc = builder.build(new ByteArrayInputStream(bytes));
+ } catch (Exception ex2) {
+ logger.error("Service Catalogue preferences configuration: Failed to build an XML document from the response.", ex2);
+ // Warn the user
+ JOptionPane.showMessageDialog(this,
+ "Failed to get the expected response body when testing the Service Catalogue instance.\n"
+ + "The URL is probably wrong. Please check it and try again.",
+ "Service Catalogue Configuration",
+ JOptionPane.INFORMATION_MESSAGE);
+ tfBioCatalogueAPIBaseURL.requestFocusInWindow();
+ return;
+ }
+ finally{
+ // Release resource
+ httpClient.getConnectionManager().shutdown();
+ }
+ // Get the version element from the XML document
+ Attribute apiVersionAttribute = doc.getRootElement().getAttribute(API_VERSION);
+ if (apiVersionAttribute != null){
+ String apiVersion = apiVersionAttribute.getValue();
+ String versions[] = apiVersion.split("[.]");
+ String majorVersion = versions[0];
+ String minorVersion = versions[1];
+ try {
+ //String patchVersion = versions[2]; // we are not comparing the patch versions
+ String supportedMajorVersion = MIN_SUPPORTED_BIOCATALOGUE_API_VERSION[0];
+ String supportedMinorVersion = MIN_SUPPORTED_BIOCATALOGUE_API_VERSION[1];
+ Integer iSupportedMajorVersion = Integer.parseInt(supportedMajorVersion);
+ Integer iMajorVersion = Integer.parseInt(majorVersion);
+ Integer iSupportedMinorVersion = Integer.parseInt(supportedMinorVersion);
+ Integer iMinorVersion = Integer.parseInt(minorVersion);
+ if (!(iSupportedMajorVersion == iMajorVersion &&
+ iSupportedMinorVersion <= iMinorVersion)){
+ // Warn the user
+ JOptionPane
+ .showMessageDialog(
+ this,
+ "The version of the Service Catalogue instance you are trying to connect to is not supported.\n"
+ + "Please change the URL and try again.",
+ "Service Catalogue Configuration",
+ JOptionPane.INFORMATION_MESSAGE);
+ tfBioCatalogueAPIBaseURL.requestFocusInWindow();
+ return;
+ }
+ } catch (Exception e) {
+ logger.error(e);
+ }
+ } // if null - we'll try to do our best to connect to BioCatalogue anyway
+ } else {
+ logger
+ .error("Service Catalogue preferences configuration: Failed to get the expected response content type when testing the Service Catalogue instance. "
+ + httpGet.getRequestLine()
+ + " returned content type '"
+ + contentType
+ + "'; expected response content type is 'application/xml'.");
+ // Warn the user
+ JOptionPane
+ .showMessageDialog(
+ this,
+ "Failed to get the expected response content type when testing the Service Catalogue instance.\n"
+ + "The URL is probably wrong. Please check it and try again.",
+ "Service Catalogue Plugin",
+ JOptionPane.INFORMATION_MESSAGE);
+ tfBioCatalogueAPIBaseURL.requestFocusInWindow();
+ return;
+ }
+ }
+ else{
+ logger
+ .error("Service Catalogue preferences configuration: Failed to get the expected response status code when testing the Service Catalogue instance. "
+ + httpGet.getRequestLine()
+ + " returned the status code "
+ + httpResponse.getStatusLine()
+ .getStatusCode() + "; expected status code is 200 OK.");
+ // Warn the user
+ JOptionPane
+ .showMessageDialog(
+ this,
+ "Failed to get the expected response status code when testing the Service Catalogue instance.\n"
+ + "The URL is probably wrong. Please check it and try again.",
+ "Service Catalogue Configuration",
+ JOptionPane.INFORMATION_MESSAGE);
+ tfBioCatalogueAPIBaseURL.requestFocusInWindow();
+ return;
+ }
+
+ // Warn the user of the changes in the BioCatalogue base URL
+ JOptionPane
+ .showMessageDialog(
+ this,
+ "You have updated the Service Catalogue base URL.\n"
+ + "This does not take effect until you restart Taverna.",
+ "Service catalogue Configuration",
+ JOptionPane.INFORMATION_MESSAGE);
+
+ }
+
+ // the new base URL seems to be valid - can save it into config
+ // settings
+ configuration.setProperty(
+ BioCataloguePluginConfiguration.SERVICE_CATALOGUE_BASE_URL,
+ candidateBaseURL);
+
+/* // also update the base URL in the BioCatalogueClient
+ BioCatalogueClient.getInstance()
+ .setBaseURL(candidateBaseURL);*/
+ }
+
+ }
+
+
+ /**
+ * For testing only.
+ */
+ public static void main(String[] args) {
+ JFrame theFrame = new JFrame();
+ theFrame.add(new BioCataloguePluginConfigurationPanel());
+ theFrame.pack();
+ theFrame.setLocationRelativeTo(null);
+ theFrame.setVisible(true);
+ }
+
+ /**
+ * Worker method that extracts the content of the received HTTP message as a
+ * string. It also makes use of the charset that is specified in the
+ * Content-Type header of the received data to read it appropriately.
+ *
+ * @param entity
+ * @return
+ * @throws IOException
+ */
+ // Taken from HTTPRequestHandler in rest-activity by Sergejs Aleksejevs
+ private static String readResponseBodyAsString(HttpEntity entity)
+ throws IOException {
+ // get charset name
+ String charset = null;
+ String contentType = entity.getContentType().getValue().toLowerCase();
+
+ String[] contentTypeParts = contentType.split(";");
+ for (String contentTypePart : contentTypeParts) {
+ contentTypePart = contentTypePart.trim();
+ if (contentTypePart.startsWith("charset=")) {
+ charset = contentTypePart.substring("charset=".length());
+ }
+ }
+
+ // read the data line by line
+ StringBuilder responseBodyString = new StringBuilder();
+ BufferedReader reader = new BufferedReader(new InputStreamReader(entity
+ .getContent(), charset));
+
+ String str;
+ while ((str = reader.readLine()) != null) {
+ responseBodyString.append(str + "\n");
+ }
+
+ return (responseBodyString.toString());
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/config/BioCataloguePluginConfigurationUIFactory.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/config/BioCataloguePluginConfigurationUIFactory.java
new file mode 100644
index 0000000..f5baa70
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/config/BioCataloguePluginConfigurationUIFactory.java
@@ -0,0 +1,27 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.config;
+
+import javax.swing.JPanel;
+
+import uk.org.taverna.configuration.Configurable;
+import uk.org.taverna.configuration.ConfigurationUIFactory;
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class BioCataloguePluginConfigurationUIFactory implements ConfigurationUIFactory
+{
+
+ public boolean canHandle(String uuid) {
+ return uuid.equals(getConfigurable().getUUID());
+ }
+
+ public Configurable getConfigurable() {
+ return BioCataloguePluginConfiguration.getInstance();
+ }
+
+ public JPanel getConfigurationPanel() {
+ return new BioCataloguePluginConfigurationPanel();
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/BioCataloguePluginInputPortContextViewFactory.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/BioCataloguePluginInputPortContextViewFactory.java
new file mode 100644
index 0000000..d067cce
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/BioCataloguePluginInputPortContextViewFactory.java
@@ -0,0 +1,45 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.contextual_views;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import net.sf.taverna.biocatalogue.model.SoapOperationPortIdentity;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.Integration;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
+
+
+public class BioCataloguePluginInputPortContextViewFactory implements
+ ContextualViewFactory<ActivityInputPort> {
+
+ public boolean canHandle(Object selection)
+ {
+ // TODO - HACK: this would stop showing the contextual view in case of any error,
+ // not just in case of unsupported contextual selection; this needs to be
+ // changed, so that useful error messages are still displayed in the
+ // contextual view
+ if (selection instanceof ActivityInputPort)
+ {
+ SoapOperationPortIdentity portDetails = Integration.
+ extractSoapOperationPortDetailsFromActivityInputOutputPort((ActivityInputPort)selection);
+ boolean canHandleSelection = !portDetails.hasError();
+ if (!canHandleSelection) {
+ Logger.getLogger(BioCataloguePluginProcessorContextViewFactory.class).debug(
+ "Input port contextual view not shown due to some condition: " + portDetails.getErrorDetails());
+ }
+
+ return (canHandleSelection);
+ }
+ else {
+ return (false);
+ }
+ }
+
+ public List<ContextualView> getViews(ActivityInputPort selection) {
+ return Arrays.<ContextualView>asList(new ProcessorInputPortView(selection));
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/BioCataloguePluginOutputPortContextViewFactory.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/BioCataloguePluginOutputPortContextViewFactory.java
new file mode 100644
index 0000000..1014a54
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/BioCataloguePluginOutputPortContextViewFactory.java
@@ -0,0 +1,45 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.contextual_views;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import net.sf.taverna.biocatalogue.model.SoapOperationPortIdentity;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.Integration;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
+
+
+public class BioCataloguePluginOutputPortContextViewFactory implements
+ ContextualViewFactory<ActivityOutputPort> {
+
+ public boolean canHandle(Object selection)
+ {
+ // TODO - HACK: this would stop showing the contextual view in case of any error,
+ // not just in case of unsupported contextual selection; this needs to be
+ // changed, so that useful error messages are still displayed in the
+ // contextual view
+ if (selection instanceof ActivityOutputPort)
+ {
+ SoapOperationPortIdentity portDetails = Integration.
+ extractSoapOperationPortDetailsFromActivityInputOutputPort((ActivityOutputPort)selection);
+ boolean canHandleSelection = !portDetails.hasError();
+ if (!canHandleSelection) {
+ Logger.getLogger(BioCataloguePluginProcessorContextViewFactory.class).debug(
+ "Output port contextual view not shown due to some condition: " + portDetails.getErrorDetails());
+ }
+
+ return (canHandleSelection);
+ }
+ else {
+ return (false);
+ }
+ }
+
+ public List<ContextualView> getViews(ActivityOutputPort selection) {
+ return Arrays.<ContextualView>asList(new ProcessorOutputPortView(selection));
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/BioCataloguePluginProcessorContextViewFactory.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/BioCataloguePluginProcessorContextViewFactory.java
new file mode 100644
index 0000000..05380d3
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/BioCataloguePluginProcessorContextViewFactory.java
@@ -0,0 +1,43 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.contextual_views;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import net.sf.taverna.biocatalogue.model.SoapOperationIdentity;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.Integration;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+import net.sf.taverna.t2.workflowmodel.Processor;
+
+public class BioCataloguePluginProcessorContextViewFactory implements
+ ContextualViewFactory<Processor> {
+
+ public boolean canHandle(Object selection)
+ {
+ // TODO - HACK: this would stop showing the contextual view in case of any error,
+ // not just in case of unsupported contextual selection; this needs to be
+ // changed, so that useful error messages are still displayed in the
+ // contextual view
+ if (selection instanceof Processor)
+ {
+ SoapOperationIdentity opId = Integration.extractSoapOperationDetailsFromProcessor((Processor) selection);
+ boolean canHandleSelection = !opId.hasError();
+ if (!canHandleSelection) {
+ Logger.getLogger(BioCataloguePluginProcessorContextViewFactory.class).debug(
+ "Service's contextual view not shown due to some condition: " + opId.getErrorDetails());
+ }
+
+ return (canHandleSelection);
+ }
+ else {
+ return (false);
+ }
+ }
+
+ public List<ContextualView> getViews(Processor selection) {
+ return Arrays.<ContextualView>asList(new ProcessorView(selection));
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/ProcessorInputPortView.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/ProcessorInputPortView.java
new file mode 100644
index 0000000..4e307f1
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/ProcessorInputPortView.java
@@ -0,0 +1,52 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.contextual_views;
+
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+
+import net.sf.taverna.biocatalogue.model.BioCataloguePluginConstants;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
+
+
+public class ProcessorInputPortView extends ContextualView
+{
+ private final ActivityInputPort inputPort;
+ private JPanel jPanel;
+
+ public ProcessorInputPortView(ActivityInputPort inputPort) {
+ this.inputPort = inputPort;
+
+ jPanel = new JPanel();
+
+ // NB! This is required to have the body of this contextual
+ // view added to the main view; otherwise, body will be
+ // blank
+ initView();
+ }
+
+ @Override
+ public JComponent getMainFrame()
+ {
+ return jPanel;
+ }
+
+ @Override
+ public String getViewTitle() {
+ return "Service Catalogue Information";
+ }
+
+ @Override
+ public void refreshView()
+ {
+ // this actually causes the parent container to validate itself,
+ // which is what is needed here
+ this.revalidate();
+ this.repaint();
+ }
+
+ @Override
+ public int getPreferredPosition() {
+ return BioCataloguePluginConstants.CONTEXTUAL_VIEW_PREFERRED_POSITION;
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/ProcessorOutputPortView.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/ProcessorOutputPortView.java
new file mode 100644
index 0000000..feff0f4
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/ProcessorOutputPortView.java
@@ -0,0 +1,52 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.contextual_views;
+
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+
+import net.sf.taverna.biocatalogue.model.BioCataloguePluginConstants;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
+
+
+public class ProcessorOutputPortView extends ContextualView
+{
+ private final ActivityOutputPort outputPort;
+ private JPanel jPanel;
+
+ public ProcessorOutputPortView(ActivityOutputPort outputPort) {
+ this.outputPort = outputPort;
+
+ jPanel = new JPanel();
+
+ // NB! This is required to have the body of this contextual
+ // view added to the main view; otherwise, body will be
+ // blank
+ initView();
+ }
+
+ @Override
+ public JComponent getMainFrame()
+ {
+ return jPanel;
+ }
+
+ @Override
+ public String getViewTitle() {
+ return "Service Catalogue Information";
+ }
+
+ @Override
+ public void refreshView()
+ {
+ // this actually causes the parent container to validate itself,
+ // which is what is needed here
+ this.revalidate();
+ this.repaint();
+ }
+
+ @Override
+ public int getPreferredPosition() {
+ return BioCataloguePluginConstants.CONTEXTUAL_VIEW_PREFERRED_POSITION;
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/ProcessorView.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/ProcessorView.java
new file mode 100644
index 0000000..ea41805
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/ProcessorView.java
@@ -0,0 +1,229 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.contextual_views;
+
+import java.awt.Component;
+import java.awt.Desktop;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.net.URI;
+import java.rmi.activation.UnknownObjectException;
+
+import javax.swing.AbstractAction;
+import javax.swing.BorderFactory;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+import javax.swing.UIManager;
+
+import net.sf.taverna.biocatalogue.model.BioCataloguePluginConstants;
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.biocatalogue.model.SoapOperationIdentity;
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
+import net.sf.taverna.t2.lang.ui.DeselectingButton;
+import net.sf.taverna.t2.lang.ui.ReadOnlyTextArea;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentFactory;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.Integration;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check.ServiceHealthChecker;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check.ServiceMonitoringStatusInterpreter;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workflowmodel.Processor;
+
+import org.apache.log4j.Logger;
+import org.biocatalogue.x2009.xml.rest.Service;
+import org.biocatalogue.x2009.xml.rest.SoapOperation;
+
+
+public class ProcessorView extends ContextualView {
+ private final Processor processor;
+ private JPanel jPanel;
+
+ private static Logger logger = Logger.getLogger(ProcessorView.class);
+
+
+
+ public ProcessorView(Processor processor) {
+ this.processor = processor;
+
+ jPanel = new JPanel();
+
+ // this is required to have the body of this contextual
+ // view added to the main view; otherwise, body will be
+ // blank
+ initView();
+ }
+
+
+
+ @Override
+ public JComponent getMainFrame()
+ {
+ Thread t = new Thread("loading processor data") {
+ public void run() {
+ final SoapOperationIdentity operationDetails = Integration.extractSoapOperationDetailsFromProcessor(processor);
+
+ if (operationDetails.hasError()) {
+ SwingUtilities.invokeLater(new RefreshThread(new JLabel(operationDetails.getErrorDetails().toString(),
+ UIManager.getIcon("OptionPane.warningIcon"), JLabel.CENTER)));
+ return;
+ }
+ else {
+ BioCatalogueClient client = BioCatalogueClient.getInstance();
+
+ if (client != null) {
+ try {
+ final SoapOperation soapOperation = client.lookupSoapOperation(operationDetails);
+ if (soapOperation == null) {
+ SwingUtilities.invokeLater(new RefreshThread(new JLabel("This service is not registered in the Service Catalogue",
+ UIManager.getIcon("OptionPane.warningIcon"), JLabel.CENTER)));
+ return;
+ }
+
+ Service parentService = client.getBioCatalogueService(soapOperation.getAncestors().getService().getHref());
+ if (parentService == null) {
+ SwingUtilities.invokeLater(new RefreshThread(new JLabel("Problem while fetching monitoring data from the Service Catalogue",
+ UIManager.getIcon("OptionPane.warningIcon"), JLabel.CENTER)));
+ return;
+ }
+
+
+ // *** managed to get all necessary data successfully - present it ***
+
+ // create status update panel
+ JButton jclServiceStatus = new DeselectingButton(
+ new AbstractAction("Check monitoring status") {
+ public void actionPerformed(ActionEvent e) {
+ ServiceHealthChecker.checkWSDLProcessor(operationDetails);
+ }
+ });
+ jclServiceStatus.setAlignmentX(Component.LEFT_ALIGNMENT);
+ JLabel jlStatusMessage = new JLabel(parentService.getLatestMonitoringStatus().getMessage());
+ jlStatusMessage.setAlignmentX(Component.LEFT_ALIGNMENT);
+
+ // operation description
+ String operationDescription = (soapOperation.getDescription().length() > 0 ?
+ soapOperation.getDescription() :
+ "No description is available for this service");
+
+ ReadOnlyTextArea jlOperationDescription = new ReadOnlyTextArea(operationDescription);
+
+ jlOperationDescription.setAlignmentX(Component.LEFT_ALIGNMENT);
+
+ // a button to open preview of the service
+ JButton jbLaunchProcessorPreview = new DeselectingButton("Show on the Service Catalogue",
+ new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ if (!operationDetails.hasError()) {
+ String hrefString = soapOperation.getHref();
+ try {
+ Desktop.getDesktop().browse(new URI(hrefString));
+ }
+ catch (Exception ex) {
+ logger.error("Failed while trying to open the URL in a standard browser; URL was: " +
+ hrefString, ex);
+ };
+ }
+ else {
+ // this error message comes from Integration class extracting SOAP operation details from the contextual selection
+ JOptionPane.showMessageDialog(null, operationDetails.getErrorDetails(), "Service Catalogue Error", JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ },
+ "View this service on the Service Catalogue");
+
+ JPanel jpPreviewButtonPanel = new JPanel();
+ jpPreviewButtonPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
+ jbLaunchProcessorPreview.setAlignmentX(Component.LEFT_ALIGNMENT);
+ // jpPreviewButtonPanel.add(jbLaunchProcessorPreview);
+ // put everything together
+ JPanel jpInnerPane = new JPanel();
+ jpInnerPane.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
+ jpInnerPane.setLayout(new BoxLayout(jpInnerPane, BoxLayout.Y_AXIS));
+ jpInnerPane.add(jlOperationDescription);
+ jpInnerPane.add(Box.createVerticalStrut(10));
+ jpInnerPane.add(jlStatusMessage);
+ jpInnerPane.add(Box.createVerticalStrut(10));
+ jpInnerPane.add(jclServiceStatus);
+ jpInnerPane.add(Box.createVerticalStrut(10));
+ jpInnerPane.add(jbLaunchProcessorPreview);
+
+ JScrollPane spInnerPane = new JScrollPane(jpInnerPane);
+
+ SwingUtilities.invokeLater(new RefreshThread(spInnerPane));
+ return;
+ }
+ catch (UnknownObjectException e) {
+ SwingUtilities.invokeLater(new RefreshThread(new JLabel(e.getMessage(),
+ UIManager.getIcon("OptionPane.informationIcon"), JLabel.CENTER)));
+ return;
+ }
+ catch (Exception e) {
+ // a real error occurred while fetching data about selected processor
+ logger.error("ERROR: unexpected problem while trying to ", e);
+ SwingUtilities.invokeLater(new RefreshThread(new JLabel("An unknown problem has prevented Taverna from loading this preview",
+ UIManager.getIcon("OptionPane.errorIcon"), JLabel.CENTER)));
+ return;
+ }
+ }
+ else {
+ SwingUtilities.invokeLater(new RefreshThread(new JLabel("Service Catalogue integration has not initialised yet. Please wait and try again.",
+ UIManager.getIcon("OptionPane.warningIcon"), JLabel.CENTER)));
+ return;
+ }
+ }
+ }
+ };
+
+ jPanel.removeAll();
+ jPanel.setPreferredSize(new Dimension(200,200));
+ jPanel.setLayout(new GridLayout());
+ jPanel.add(new JLabel(ResourceManager.getImageIcon(ResourceManager.BAR_LOADER_ORANGE), JLabel.CENTER));
+ t.start();
+ return jPanel;
+ }
+
+ @Override
+ public String getViewTitle() {
+ return "Service Catalogue Information";
+ }
+
+ @Override
+ public void refreshView()
+ {
+ // this actually causes the parent container to validate itself,
+ // which is what is needed here
+ this.revalidate();
+ this.repaint();
+ }
+
+ @Override
+ public int getPreferredPosition() {
+ return BioCataloguePluginConstants.CONTEXTUAL_VIEW_PREFERRED_POSITION;
+ }
+
+ class RefreshThread extends Thread {
+ private final Component component;
+
+ public RefreshThread (Component component) {
+ this.component = component;
+ }
+
+ public void run() {
+ jPanel.removeAll();
+ if (component != null) {
+ jPanel.add(component);
+ }
+ refreshView();
+ }
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/BioCatalogueWSDLActivityHealthCheck.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/BioCatalogueWSDLActivityHealthCheck.java
new file mode 100644
index 0000000..2461c2c
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/BioCatalogueWSDLActivityHealthCheck.java
@@ -0,0 +1,40 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check;
+
+import net.sf.taverna.t2.visit.VisitKind;
+import net.sf.taverna.t2.visit.Visitor;
+
+/**
+ * A {@link BioCatalogueWSDLActivityHealthCheck} is a kind of visit that determines
+ * if the corresponding WSDL activity in a workflow will work during a workflow run -
+ * checks will be made based on the monitoring status held about that service in BioCatalogue.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class BioCatalogueWSDLActivityHealthCheck extends VisitKind
+{
+ // The following values indicate the type of results that can be associated
+ // with a VisitReport generated by a health-checking visitor.
+ public static final int MESSAGE_IN_VISIT_REPORT = 0;
+
+
+ // property names to be placed into VisitReport generated by BioCatalogueWSDLActivityHealthChecker
+ public static final String WSDL_LOCATION_PROPERTY = "wsdlLocation";
+ public static final String OPERATION_NAME_PROPERTY = "soapOperationName";
+ public static final String EXPLANATION_MSG_PROPERTY = "fullExplanationMessage";
+
+
+
+
+ @Override
+ public Class<? extends Visitor> getVisitorClass() {
+ return BioCatalogueWSDLActivityHealthChecker.class;
+ }
+
+ private static class Singleton {
+ private static BioCatalogueWSDLActivityHealthCheck instance = new BioCatalogueWSDLActivityHealthCheck();
+ }
+
+ public static BioCatalogueWSDLActivityHealthCheck getInstance() {
+ return Singleton.instance;
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/BioCatalogueWSDLActivityHealthCheckVisitExplainer.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/BioCatalogueWSDLActivityHealthCheckVisitExplainer.java
new file mode 100644
index 0000000..8bee663
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/BioCatalogueWSDLActivityHealthCheckVisitExplainer.java
@@ -0,0 +1,111 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check;
+
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+
+import net.sf.taverna.biocatalogue.model.SoapOperationIdentity;
+import net.sf.taverna.t2.lang.ui.ReadOnlyTextArea;
+import net.sf.taverna.t2.visit.VisitKind;
+import net.sf.taverna.t2.visit.VisitReport;
+import net.sf.taverna.t2.workbench.report.explainer.VisitExplainer;
+
+// import status constants
+import static net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check.BioCatalogueWSDLActivityHealthCheck.*;
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class BioCatalogueWSDLActivityHealthCheckVisitExplainer implements VisitExplainer
+{
+
+ public boolean canExplain(VisitKind vk, int resultId) {
+ return (vk instanceof BioCatalogueWSDLActivityHealthCheck);
+ }
+
+
+ /**
+ * This class only handles {@link VisitReport} instances that are of
+ * {@link BioCatalogueWSDLActivityHealthCheck} kind. Therefore, decisions on
+ * the explanations / solutions are made solely by visit result IDs.
+ */
+ public JComponent getExplanation(final VisitReport vr)
+ {
+ int resultId = vr.getResultId();
+ String explanation = null;
+
+ switch (resultId) {
+ case MESSAGE_IN_VISIT_REPORT:
+ explanation = (String) vr.getProperty(EXPLANATION_MSG_PROPERTY); break;
+
+ default:
+ explanation = "Unknown issue - no expalanation available"; break;
+ }
+
+
+ JButton bRunBioCatalogueHealthCheck = new JButton("View monitoring status details");
+ bRunBioCatalogueHealthCheck.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ SoapOperationIdentity soapOpIdentity =
+ new SoapOperationIdentity((String)vr.getProperty(BioCatalogueWSDLActivityHealthCheck.WSDL_LOCATION_PROPERTY),
+ (String)vr.getProperty(BioCatalogueWSDLActivityHealthCheck.OPERATION_NAME_PROPERTY), null);
+
+ ServiceHealthChecker.checkWSDLProcessor(soapOpIdentity);
+ }
+ });
+ JPanel jpButton = new JPanel();
+ jpButton.setBorder(BorderFactory.createEmptyBorder(10, 0, 0, 0));
+ jpButton.add(bRunBioCatalogueHealthCheck);
+ jpButton.setOpaque(false);
+
+ JPanel jpExplanation = new JPanel(new BorderLayout());
+ jpExplanation.add(new ReadOnlyTextArea(explanation), BorderLayout.CENTER);
+ jpExplanation.add(jpButton, BorderLayout.SOUTH);
+
+ return (jpExplanation);
+ }
+
+
+
+ /**
+ * This class only handles {@link VisitReport} instances that are of
+ * {@link BioCatalogueWSDLActivityHealthCheck} kind. Therefore, decisions on
+ * the explanations / solutions are made solely by visit result IDs.
+ */
+ public JComponent getSolution(VisitReport vr)
+ {
+ String explanation = null;
+
+ // instead of switching between possible health check resultIDs,
+ // simply choose from possible statuses: for all failures there's
+ // nothing specific that can be done, so no need to differentiate
+ // displayed messages
+ switch (vr.getStatus()) {
+ case OK:
+ explanation = "This WSDL service works fine - no change necessary"; break;
+
+ case WARNING:
+ case SEVERE:
+ explanation = "This remote WSDL service appears to have an internal problem. There is nothing " +
+ "specific that can be done to fix it locally.\n\n" +
+ "It is possible that the current state of the service will still allow to execute " +
+ "the workflow successfully. Also, the service may have already recovered since the " +
+ "last time it's monitoring status has been checked.\n\n" +
+ "If this problem does affect the current workflow, it may be resolved by the " +
+ "service provider. It may be worth contacting them to report the issue.";
+ break;
+
+ default:
+ explanation = "Unknown issue - no solution available"; break;
+ }
+
+ return (new ReadOnlyTextArea(explanation));
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/BioCatalogueWSDLActivityHealthChecker.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/BioCatalogueWSDLActivityHealthChecker.java
new file mode 100644
index 0000000..c30ec8f
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/BioCatalogueWSDLActivityHealthChecker.java
@@ -0,0 +1,199 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check;
+
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.List;
+
+import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.log4j.Logger;
+import org.biocatalogue.x2009.xml.rest.MonitoringStatusLabel;
+import org.biocatalogue.x2009.xml.rest.Service;
+import org.biocatalogue.x2009.xml.rest.ServiceTest;
+import org.biocatalogue.x2009.xml.rest.TestScript;
+
+import net.sf.taverna.biocatalogue.model.SoapOperationIdentity;
+import net.sf.taverna.biocatalogue.model.Util;
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
+import net.sf.taverna.t2.activities.wsdl.WSDLActivity;
+import net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentFactory;
+import net.sf.taverna.t2.visit.VisitReport;
+import net.sf.taverna.t2.visit.VisitReport.Status;
+import net.sf.taverna.t2.workflowmodel.health.HealthChecker;
+
+
+/**
+ * A {@link HealthChecker} for a {@link WSDLActivity}.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class BioCatalogueWSDLActivityHealthChecker implements HealthChecker<WSDLActivity>
+{
+ private static final int MILLIS_IN_THE_PAST_FOR_OLDEST_MONITORING_DATA = 48 * 60 * 60 * 1000; // 48hrs
+
+
+ private Logger logger;
+
+ public BioCatalogueWSDLActivityHealthChecker() {
+ logger = Logger.getLogger(BioCatalogueWSDLActivityHealthChecker.class);
+ }
+
+
+ public boolean canVisit(Object subject) {
+ return (subject instanceof WSDLActivity);
+ }
+
+
+ public VisitReport visit(WSDLActivity activity, List<Object> ancestors)
+ {
+ WSDLActivityConfigurationBean configBean = activity.getConfiguration();
+ SoapOperationIdentity soapOpIdentity = new SoapOperationIdentity(configBean.getWsdl(), configBean.getOperation(), null);
+
+ try {
+ // make BioCatalogue API request to fetch the data
+ Service serviceWithMonitoringData = BioCatalogueClient.getInstance().lookupParentServiceMonitoringData(soapOpIdentity);
+ MonitoringStatusLabel.Enum serviceStatusLabel = null;
+
+
+ VisitReport.Status status = null;
+ String visitReportLabel = null;
+ String visitReportExplanation = null;
+ List<VisitReport> subReports = new ArrayList<VisitReport>();
+
+
+ if (serviceWithMonitoringData == null) {
+ // BioCatalogue doesn't "know" about this service - it appears not to be registered;
+ // --> nothing to report to Taverna
+ return (null);
+ }
+ else if (serviceWithMonitoringData.getLatestMonitoringStatus() == null) {
+ // BioCatalogue "knows" this service, but for some reason there was no monitoring data available;
+ // possibly an API change? either way --> nothing to report to Taverna
+ return (null);
+ }
+ else
+ {
+ Calendar lastCheckedAt = serviceWithMonitoringData.getLatestMonitoringStatus().getLastChecked();
+ String agoString = Util.getAgoString(lastCheckedAt, Calendar.getInstance(), MILLIS_IN_THE_PAST_FOR_OLDEST_MONITORING_DATA);
+ if (agoString == null) {
+ return (null);
+ }
+
+ serviceStatusLabel = serviceWithMonitoringData.getLatestMonitoringStatus().getLabel();
+ switch (serviceStatusLabel.intValue()) {
+ case MonitoringStatusLabel.INT_PASSED:
+ visitReportLabel = "Service Catalogue: all tests passed " + agoString;
+ visitReportExplanation = "The Service Catalogue reports that all available tests for this WSDL service have " +
+ "been successful. They have been last executed " + agoString;
+ status = Status.OK;
+ break;
+
+ case MonitoringStatusLabel.INT_WARNING:
+ case MonitoringStatusLabel.INT_FAILED:
+ visitReportLabel = "Service Catalogue: some tests failed " + agoString;
+ visitReportExplanation = "Some test scripts for this WSDL service have failed";
+
+ // only extract data about failing test scripts
+ subReports = createTestScriptSubReportsForFailingService(activity, serviceWithMonitoringData);
+ if (subReports.size() == 0) {
+ // failing tests must have been for endpoint / WSDL location - but not for scripts;
+ // Taverna doesn't need to know about the former, as it replicates internal checks
+ return (null);
+ }
+ else {
+ // determine the worst status and report as the one of the collection of subreports
+ status = VisitReport.getWorstStatus(subReports);
+ }
+ break;
+
+ case MonitoringStatusLabel.INT_UNCHECKED:
+ // monitoring record states that the status of this service was not (yet) checked;
+ // possibly monitoring on BioCatalogue was switched off before this service was registered;
+ // --> nothing to report to Taverna
+ return (null);
+
+ default:
+ visitReportLabel = "Service Catalogue: unknown monitoring status received - \"" + serviceStatusLabel.toString() + "\"";
+ visitReportExplanation = "The Service Catalogue has returned a new monitoring status for this service: \"" +
+ serviceStatusLabel.toString() + "\"\n\n" +
+ "It has never been used before and probably indicates a change in the Service Catalogue API. " +
+ "Please report this issue to the Service Catalogue developers.";
+ status = Status.WARNING;
+ break;
+ }
+ }
+
+ // wrap determined values into a single VisitReport object; then attach data to identify
+ // this service in associated VisitExplainer
+ VisitReport report = new VisitReport(BioCatalogueWSDLActivityHealthCheck.getInstance(), activity,
+ visitReportLabel, BioCatalogueWSDLActivityHealthCheck.MESSAGE_IN_VISIT_REPORT, status, subReports);
+ report.setProperty(BioCatalogueWSDLActivityHealthCheck.WSDL_LOCATION_PROPERTY, soapOpIdentity.getWsdlLocation());
+ report.setProperty(BioCatalogueWSDLActivityHealthCheck.OPERATION_NAME_PROPERTY, soapOpIdentity.getOperationName());
+ report.setProperty(BioCatalogueWSDLActivityHealthCheck.EXPLANATION_MSG_PROPERTY, visitReportExplanation);
+
+ return (report);
+ }
+ catch (Exception e) {
+ // not sure what could have happened - it will be visible in the logs
+ logger.error("Unexpected error while performing health check for " +
+ soapOpIdentity.getWsdlLocation() + " service.", e);
+ return (null);
+ }
+ }
+
+
+ private List<VisitReport> createTestScriptSubReportsForFailingService(WSDLActivity activity, Service serviceWithMonitoringData)
+ {
+ List<VisitReport> subReports = new ArrayList<VisitReport>();
+
+ try {
+ List<ServiceTest> serviceTests = serviceWithMonitoringData.getMonitoring().getTests().getServiceTestList();
+ for (ServiceTest test : serviceTests)
+ {
+ if (test.getTestType().getTestScript() != null &&
+ test.getTestType().getTestScript()instanceof TestScript)
+ {
+ TestScript testScript = test.getTestType().getTestScript();
+
+ String agoString = Util.getAgoString(test.getLatestStatus().getLastChecked(), Calendar.getInstance(),
+ MILLIS_IN_THE_PAST_FOR_OLDEST_MONITORING_DATA);
+
+ // only proceed if this test wasn't run too long ago
+ if (agoString != null) {
+ String label = "Service Catalogue: \"" + testScript.getName() + "\" test script " + test.getLatestStatus().getLabel();
+ VisitReport report = new VisitReport(BioCatalogueWSDLActivityHealthCheck.getInstance(), activity,
+ label, BioCatalogueWSDLActivityHealthCheck.MESSAGE_IN_VISIT_REPORT,
+ ServiceMonitoringStatusInterpreter.translateBioCatalogueStatusForTaverna(test.getLatestStatus().getLabel()));
+ report.setProperty(BioCatalogueWSDLActivityHealthCheck.WSDL_LOCATION_PROPERTY, activity.getConfiguration().getWsdl());
+ report.setProperty(BioCatalogueWSDLActivityHealthCheck.OPERATION_NAME_PROPERTY, activity.getConfiguration().getOperation());
+ report.setProperty(BioCatalogueWSDLActivityHealthCheck.EXPLANATION_MSG_PROPERTY,
+ "This test was last executed " + agoString + "." +
+ "\n\n" + StringEscapeUtils.escapeHtml(test.getLatestStatus().getMessage()) +
+ "\n\n---- Test script description ----\n" + StringEscapeUtils.escapeHtml(testScript.getDescription()));
+
+ subReports.add(report);
+ }
+ }
+ }
+ }
+ catch (Exception e) {
+ // log the error, but do not terminate the method - maybe some sub reports were successfully
+ // generated, in which case at least partial result can be returned
+ logger.error("Encountered unexpected problem while trying to generate a collection of sub-reports " +
+ "for a failing service: " + activity.getConfiguration().getWsdl(), e);
+ }
+
+ return (subReports);
+ }
+
+
+ /**
+ * Health check for the WSDL activities involves fetching
+ * the monitoring status of each activity from BioCatalogue -
+ * this *may* be time consuming.
+ */
+ public boolean isTimeConsuming() {
+ return true;
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/ServiceHealthChecker.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/ServiceHealthChecker.java
new file mode 100644
index 0000000..8e85e61
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/ServiceHealthChecker.java
@@ -0,0 +1,280 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.List;
+
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+import javax.swing.UIManager;
+import javax.swing.border.EmptyBorder;
+
+import org.apache.log4j.Logger;
+import org.biocatalogue.x2009.xml.rest.ResourceLink;
+import org.biocatalogue.x2009.xml.rest.RestMethod;
+import org.biocatalogue.x2009.xml.rest.Service;
+import org.biocatalogue.x2009.xml.rest.ServiceTest;
+import org.biocatalogue.x2009.xml.rest.SoapOperation;
+
+import net.sf.taverna.biocatalogue.model.BioCataloguePluginConstants;
+import net.sf.taverna.biocatalogue.model.Resource;
+import net.sf.taverna.biocatalogue.model.Resource.TYPE;
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.biocatalogue.model.SoapOperationIdentity;
+import net.sf.taverna.biocatalogue.model.SoapProcessorIdentity;
+import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
+import net.sf.taverna.biocatalogue.ui.JClickableLabel;
+import net.sf.taverna.biocatalogue.ui.JWaitDialog;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponent;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentFactory;
+
+
+/**
+ * This class helps with "health checks" of individual Taverna processors
+ * (i.e. SOAP operations) and the workflows in general (by iterating through
+ * the processors).
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class ServiceHealthChecker
+{
+ private static Logger logger = Logger.getLogger(ServiceHealthChecker.class);
+
+ // deny creation of instances of this class
+ private ServiceHealthChecker() { };
+
+
+ // =====================================================================================================
+ // *** Health Check of Individual Service / Processor ***
+ // =====================================================================================================
+
+ /**
+ * @param serviceURL URL of SOAP service or REST service on BioCatalogue;
+ * URL should be of the
+ */
+ public static void checkServiceByURL(String serviceURL)
+ {
+ if (serviceURL != null) {
+ checkMonitoringStatusRoutine(serviceURL);
+ }
+ else {
+ // for some reason the URL of the service wasn't provided...
+ JOptionPane.showMessageDialog(null, "Cannot provide monitoring status for this service - " +
+ "unknown service URL", "Service Catalogue Error", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+
+ /**
+ * @param
+ */
+ public static void checkResource(ResourceLink serviceOrOperationOrMethod)
+ {
+ if (serviceOrOperationOrMethod != null) {
+ checkMonitoringStatusRoutine(serviceOrOperationOrMethod);
+ }
+ else {
+ // for some reason resource object wasn't provided...
+ JOptionPane.showMessageDialog(null, "Cannot provide monitoring status - " +
+ "null reference received", "Service Catalogue Error", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+
+ /**
+ * Used when invoked from the workflow diagram - e.g. when a URL of the specific
+ * resource on BioCatalogue is not known, but have enough of identifying data
+ * to proceed with health check.
+ *
+ * @param soapOperationDetails
+ */
+ public static void checkWSDLProcessor(SoapOperationIdentity soapOperationDetails)
+ {
+ if (!soapOperationDetails.hasError()) {
+ checkMonitoringStatusRoutine(soapOperationDetails);
+ }
+ else {
+ // this error message comes from Integration class extracting SOAP operation details from the contextual selection
+ JOptionPane.showMessageDialog(null, soapOperationDetails.getErrorDetails(), "Service Catalogue Error", JOptionPane.WARNING_MESSAGE);
+ }
+ }
+
+
+ /**
+ * @param serviceOrSoapOperationToCheck Instance of SoapOperationIdentity representing Taverna processor
+ * or String representing a URL of the service to check health for.
+ */
+ private static void checkMonitoringStatusRoutine(final Object serviceOrSoapOperationToCheck)
+ {
+ // helper variable to determine the kind of check to perform - the difference is minimal:
+ // wording in the status messages ("Web Service" | "processor" | "REST Service") and which method to call on
+ // the BioCatalogue client to fetch monitoring data
+ final boolean bCheckingService = (serviceOrSoapOperationToCheck instanceof String);
+ final boolean bCheckingWSDLProcessor = (serviceOrSoapOperationToCheck instanceof SoapOperationIdentity);
+ final boolean bCheckingResource = (serviceOrSoapOperationToCheck instanceof ResourceLink);
+
+ final StringBuilder itemToCheck = new StringBuilder();
+ if (bCheckingService) {
+ itemToCheck.append("service");
+ }
+ else if (bCheckingWSDLProcessor) {
+ itemToCheck.append("WSDL service");
+ }
+ else if (bCheckingResource) {
+ TYPE resourceType = Resource.getResourceTypeFromResourceURL(((ResourceLink)serviceOrSoapOperationToCheck).getHref());
+ itemToCheck.append(resourceType.getTypeName());
+ }
+
+ // create the wait dialog, but don't make it visible - first need to start the background processing thread
+ final JWaitDialog jwd = new JWaitDialog(MainComponent.dummyOwnerJFrame, "Checking "+itemToCheck+" status",
+ "Please wait while status of selected "+itemToCheck+" is being checked...");
+
+ new Thread(itemToCheck + " lookup and health check operation") {
+ public void run() {
+ try
+ {
+ BioCatalogueClient client = BioCatalogueClient.getInstance();
+ Service serviceMonitoringData = null;
+
+ // attempt to get monitoring data from BioCatalogue - for this need to identify what type of
+ // item was provided as a parameter
+ if (bCheckingService) {
+ serviceMonitoringData = client.getBioCatalogueServiceMonitoringData((String)serviceOrSoapOperationToCheck);
+ }
+ else if (bCheckingWSDLProcessor) {
+ serviceMonitoringData = client.lookupParentServiceMonitoringData((SoapOperationIdentity)serviceOrSoapOperationToCheck);
+ }
+ else if (bCheckingResource) {
+ String resourceURL = ((ResourceLink)serviceOrSoapOperationToCheck).getHref();
+ TYPE resourceType = Resource.getResourceTypeFromResourceURL(resourceURL);
+
+// if (resourceType == TYPE.Service) {
+// serviceMonitoringData = client.getBioCatalogueServiceMonitoringData(resourceURL);
+// }
+// else
+ if (resourceType == TYPE.SOAPOperation) {
+ String parentServiceURL = ((SoapOperation)serviceOrSoapOperationToCheck).getAncestors().getService().getHref();
+ serviceMonitoringData = client.getBioCatalogueServiceMonitoringData(parentServiceURL);
+ }
+ else if (resourceType == TYPE.RESTMethod) {
+ String parentServiceURL = ((RestMethod)serviceOrSoapOperationToCheck).getAncestors().getService().getHref();
+ serviceMonitoringData = client.getBioCatalogueServiceMonitoringData(parentServiceURL);
+ }
+ else {
+ JOptionPane.showMessageDialog(jwd, "Unexpected resource type - can't execute health check for this",
+ "Service Catalogue Error", JOptionPane.ERROR_MESSAGE);
+ logger.error("Service Catalogue: Could not perform health check for" + resourceType);
+ }
+ }
+
+
+ // need to make this assignment to make the variable final - otherwise unavailable inside the new thread...
+ final Service serviceWithMonitoringData = serviceMonitoringData;
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ if (serviceWithMonitoringData == null) {
+ jwd.setTitle("Service Catalogue - Information");
+ jwd.waitFinished(new JLabel("There is no information about this "+itemToCheck+" in the Service Catalogue",
+ UIManager.getIcon("OptionPane.informationIcon"), JLabel.CENTER));
+ }
+ else if (serviceWithMonitoringData.getLatestMonitoringStatus() == null) {
+ jwd.setTitle("Service Catalogue Warning");
+ jwd.waitFinished(new JLabel("This "+itemToCheck+" is known to the Service Catalogue, but no monitoring data was available.",
+ UIManager.getIcon("OptionPane.warningIcon"), JLabel.CENTER));
+ }
+ else
+ {
+ // set the overall status message
+ String overallStatusLabel = "<html><b>Overall status:</b><br>" +
+ serviceWithMonitoringData.getLatestMonitoringStatus().getMessage() + "<br>" +
+ "(last checked";
+ if (serviceWithMonitoringData.getLatestMonitoringStatus().getLastChecked() == null) {
+ overallStatusLabel += ": never";
+ }
+ else {
+ overallStatusLabel += " at " + BioCatalogueClient.getShortDateFormatter().format(
+ serviceWithMonitoringData.getLatestMonitoringStatus().getLastChecked().getTime());
+ }
+ overallStatusLabel += ")</html>";
+ JLabel jlOverallStatus = new JLabel(overallStatusLabel);
+
+ // create panel for additional status messages (e.g. endpoint, wsdl location, etc)
+ JPanel jpStatusMessages = new JPanel();
+ jpStatusMessages.setLayout(new BoxLayout(jpStatusMessages, BoxLayout.Y_AXIS));
+
+ for (ServiceTest test : serviceWithMonitoringData.getMonitoring().getTests().getServiceTestList())
+ {
+ // First get the service type
+ String testLabel = "<html><br><b>";
+ if (test.getTestType().getUrlMonitor() != null)
+ {
+ if (test.getTestType().getUrlMonitor().getUrl().endsWith("wsdl")) {
+ // WSDL location test
+ testLabel += "WSDL Location Availability:</b><br>" +
+ "URL: " + test.getTestType().getUrlMonitor().getUrl();
+ }
+ else {
+ // Endpoint availability test
+ testLabel += "Endpoint Availability:</b><br>" +
+ "URL: " + test.getTestType().getUrlMonitor().getUrl();
+ }
+ }
+ else if (test.getTestType().getTestScript() != null) {
+ // test script
+ testLabel += "Test Script: " + test.getTestType().getTestScript().getName() + "</b>";
+ }
+ else {
+ testLabel += "Unknown test type</b>";
+ }
+ testLabel += "<br>";
+
+ // Add service results
+ testLabel += test.getLatestStatus().getMessage() + "</html>";
+
+ // Add the current test into the test messages panel
+ jpStatusMessages.add(new JLabel(testLabel));
+ }
+
+ // either way add the overall status on top of everything
+ jpStatusMessages.add(jlOverallStatus, 0);
+ jpStatusMessages.setBorder(new EmptyBorder(10,10,10,10));
+ JScrollPane jspStatusMessages = new JScrollPane(jpStatusMessages);
+ jspStatusMessages.setBorder(BorderFactory.createEmptyBorder());
+
+ // *** Put everything together ***
+ JPanel jpHealthCheckStatus = new JPanel(new BorderLayout(15, 10));
+ jpHealthCheckStatus.add(new JLabel(ServiceMonitoringStatusInterpreter.getStatusIcon(serviceWithMonitoringData, false)),
+ BorderLayout.WEST);
+ jpHealthCheckStatus.add(jspStatusMessages, BorderLayout.CENTER);
+
+ jwd.setTitle("Service Catalogue - Monitoring Status");
+ jwd.waitFinished(jpHealthCheckStatus);
+ }
+ }
+ });
+ }
+ catch (Exception e) {
+ logger.error("Service Catalogue: Error occurred while checking status of selected", e);
+ jwd.setTitle("Service Catalogue - Error");
+ jwd.waitFinished(new JLabel("<html>An unexpected error occurred while checking status of selected " +
+ itemToCheck + "<br>Please see error log for details...",
+ UIManager.getIcon("OptionPane.errorIcon"), JLabel.CENTER));
+ }
+ }
+ }.start();
+
+ jwd.setVisible(true);
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/ServiceMonitoringStatusInterpreter.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/ServiceMonitoringStatusInterpreter.java
new file mode 100644
index 0000000..0742cef
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/health_check/ServiceMonitoringStatusInterpreter.java
@@ -0,0 +1,77 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check;
+
+import java.net.URL;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.t2.visit.VisitReport;
+import net.sf.taverna.t2.visit.VisitReport.Status;
+
+import org.biocatalogue.x2009.xml.rest.MonitoringStatus;
+import org.biocatalogue.x2009.xml.rest.MonitoringStatusLabel;
+import org.biocatalogue.x2009.xml.rest.Service;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class ServiceMonitoringStatusInterpreter
+{
+ // prevent instantiation of this class
+ private ServiceMonitoringStatusInterpreter() { /* do nothing */ }
+
+
+ /**
+ * @param serviceWithMonitoringData
+ * @param listingIconRequired True to get a small icon suitable for a JList entry;
+ * false to get a larger icon.
+ * @return
+ */
+ public static ImageIcon getStatusIcon(Service serviceWithMonitoringData, boolean listingIconRequired)
+ {
+ MonitoringStatus latestMonitoringStatus = serviceWithMonitoringData.getLatestMonitoringStatus();
+ if (latestMonitoringStatus == null) {
+ return ResourceManager.getImageIcon((listingIconRequired ?
+ ResourceManager.SERVICE_STATUS_UNCHECKED_ICON :
+ ResourceManager.SERVICE_STATUS_UNCHECKED_ICON_LARGE));
+ }
+ MonitoringStatusLabel.Enum serviceStatusLabel = latestMonitoringStatus.getLabel();
+
+ switch (serviceStatusLabel.intValue()) {
+ case MonitoringStatusLabel.INT_PASSED:
+ return ResourceManager.getImageIcon((listingIconRequired ?
+ ResourceManager.SERVICE_STATUS_PASSED_ICON :
+ ResourceManager.SERVICE_STATUS_PASSED_ICON_LARGE));
+ case MonitoringStatusLabel.INT_WARNING:
+ return ResourceManager.getImageIcon((listingIconRequired ?
+ ResourceManager.SERVICE_STATUS_WARNING_ICON :
+ ResourceManager.SERVICE_STATUS_WARNING_ICON_LARGE));
+ case MonitoringStatusLabel.INT_FAILED:
+ return ResourceManager.getImageIcon((listingIconRequired ?
+ ResourceManager.SERVICE_STATUS_FAILED_ICON :
+ ResourceManager.SERVICE_STATUS_FAILED_ICON_LARGE));
+ case MonitoringStatusLabel.INT_UNCHECKED:
+ return ResourceManager.getImageIcon((listingIconRequired ?
+ ResourceManager.SERVICE_STATUS_UNCHECKED_ICON :
+ ResourceManager.SERVICE_STATUS_UNCHECKED_ICON_LARGE));
+ default:
+ return (ResourceManager.getImageIcon(ResourceManager.SERVICE_STATUS_UNKNOWN_ICON));
+ }
+
+ }
+
+
+ public static VisitReport.Status translateBioCatalogueStatusForTaverna(MonitoringStatusLabel.Enum monitoringStatusLabelEnum)
+ {
+ switch (monitoringStatusLabelEnum.intValue()) {
+ case MonitoringStatusLabel.INT_PASSED: return Status.OK;
+ case MonitoringStatusLabel.INT_WARNING: return Status.WARNING;
+ case MonitoringStatusLabel.INT_FAILED: return Status.SEVERE;
+ case MonitoringStatusLabel.INT_UNCHECKED: return Status.OK; // not really OK, but Taverna isn't interested in missing data anyway
+ default: return Status.WARNING; // could be worth to pop up a warning in this case, as it may mean something has changed
+ }
+ }
+
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/menus/BioCatalogueContextualMenuSection.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/menus/BioCatalogueContextualMenuSection.java
new file mode 100644
index 0000000..a5fb7a8
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/menus/BioCatalogueContextualMenuSection.java
@@ -0,0 +1,62 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.menus;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import net.sf.taverna.biocatalogue.model.ResourceManager;
+import net.sf.taverna.t2.lang.ui.ShadedLabel;
+import net.sf.taverna.t2.ui.menu.AbstractMenuSection;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.ContextualSelection;
+import net.sf.taverna.t2.ui.menu.DefaultContextualMenu;
+import net.sf.taverna.t2.workflowmodel.Dataflow;
+import net.sf.taverna.t2.workflowmodel.InputPort;
+import net.sf.taverna.t2.workflowmodel.Processor;
+
+
+public class BioCatalogueContextualMenuSection extends AbstractMenuSection implements ContextualMenuComponent
+{
+ // TODO - this shouldn't be here, must reference this field in AbstractMenuSection!!
+ public static final String SECTION_COLOR = "sectionColor";
+
+
+ public static final URI BIOCATALOGUE_MENU_SECTION_ID = URI.create("http://biocatalogue.org/2010/contextMenu/biocatalogue_section");
+ private static final String SECTION_TITLE = "Service Catalogue";
+
+ private ContextualSelection contextualSelection;
+
+
+ public BioCatalogueContextualMenuSection() {
+ super(DefaultContextualMenu.DEFAULT_CONTEXT_MENU, 100000, BIOCATALOGUE_MENU_SECTION_ID);
+ }
+
+ public ContextualSelection getContextualSelection() {
+ return contextualSelection;
+ }
+
+ public void setContextualSelection(ContextualSelection contextualSelection) {
+ this.contextualSelection = contextualSelection;
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled()
+ && (getContextualSelection().getSelection() instanceof Dataflow ||
+ getContextualSelection().getSelection() instanceof Processor ||
+ getContextualSelection().getSelection() instanceof InputPort);
+ }
+
+ @SuppressWarnings("serial")
+ protected Action createAction()
+ {
+ Action action = new AbstractAction(SECTION_TITLE, ResourceManager.getImageIcon(ResourceManager.FAVICON)) {
+ public void actionPerformed(ActionEvent e) {
+ }
+ };
+ action.putValue(SECTION_COLOR, ShadedLabel.GREEN);
+ return (action);
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/menus/MenuActionInputPort.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/menus/MenuActionInputPort.java
new file mode 100644
index 0000000..f94b0e6
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/menus/MenuActionInputPort.java
@@ -0,0 +1,43 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.menus;
+
+import java.awt.event.ActionEvent;
+import java.net.URISyntaxException;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.JOptionPane;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+
+import net.sf.taverna.t2.workflowmodel.InputPort;
+
+
+/**
+ * This class currently won't be used, as an entry for it was removed from
+ * META-INF/services/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
+ *
+ * This is because no useful action is yet available for input/output ports.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class MenuActionInputPort extends AbstractContextualMenuAction {
+
+ public MenuActionInputPort() throws URISyntaxException {
+ super(BioCatalogueContextualMenuSection.BIOCATALOGUE_MENU_SECTION_ID, 15);
+ }
+
+ @Override
+ protected Action createAction() {
+ return new AbstractAction("InputPort") {
+ public void actionPerformed(ActionEvent e) {
+ JOptionPane.showMessageDialog(getContextualSelection().getRelativeToComponent(), "Hoho!");
+ }
+ };
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return (super.isEnabled() && getContextualSelection().getSelection() instanceof InputPort);
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/menus/MenuActionProcessorHealthCheck.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/menus/MenuActionProcessorHealthCheck.java
new file mode 100644
index 0000000..c66d72b
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/menus/MenuActionProcessorHealthCheck.java
@@ -0,0 +1,51 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.menus;
+
+import java.awt.event.ActionEvent;
+import java.net.URISyntaxException;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import net.sf.taverna.biocatalogue.model.SoapOperationIdentity;
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.Integration;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check.ServiceHealthChecker;
+import net.sf.taverna.t2.workflowmodel.Processor;
+
+
+public class MenuActionProcessorHealthCheck extends AbstractContextualMenuAction {
+
+ public MenuActionProcessorHealthCheck() throws URISyntaxException {
+ super(BioCatalogueContextualMenuSection.BIOCATALOGUE_MENU_SECTION_ID, 20);
+ }
+
+ @SuppressWarnings("serial")
+@Override
+ protected Action createAction()
+ {
+ Action action = new AbstractAction("Service Health Check") {
+ public void actionPerformed(ActionEvent e) {
+ SoapOperationIdentity soapOperationDetails = Integration.extractSoapOperationDetailsFromProcessorContextualSelection(getContextualSelection());
+ ServiceHealthChecker.checkWSDLProcessor(soapOperationDetails);
+ }
+ };
+ action.putValue(Action.SHORT_DESCRIPTION, "Check monitoring status of this service");
+ return (action);
+ }
+
+ @Override
+ public boolean isEnabled()
+ {
+ // FIXME - this will only work for SOAP processors for now..
+ boolean isEnabled = super.isEnabled() && getContextualSelection().getSelection() instanceof Processor;
+
+ if (isEnabled) {
+ SoapOperationIdentity soapOperationDetails = Integration.extractSoapOperationDetailsFromProcessorContextualSelection(getContextualSelection());
+ isEnabled = !soapOperationDetails.hasError();
+ }
+
+ return isEnabled;
+ }
+
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/BioCatalogueRESTServiceProvider.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/BioCatalogueRESTServiceProvider.java
new file mode 100644
index 0000000..3c39b1d
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/BioCatalogueRESTServiceProvider.java
@@ -0,0 +1,117 @@
+/*******************************************************************************
+ * Copyright (C) 2008-2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.service_panel;
+
+import java.net.URI;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.Icon;
+
+import org.apache.log4j.Logger;
+
+//import net.sf.taverna.t2.activities.rest.ui.servicedescription.RESTActivityIcon;
+import net.sf.taverna.t2.servicedescriptions.AbstractConfigurableServiceProvider;
+import net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl;
+
+/**
+ * Service provider for REST service added to the Service Panel through the
+ * BioCatalogue perspective.
+ *
+ * @author Alex Nenadic
+ */
+public class BioCatalogueRESTServiceProvider extends
+ AbstractConfigurableServiceProvider<RESTFromBioCatalogueServiceDescription> {
+
+ public static final String PROVIDER_NAME = "Service Catalogue - selected services";
+
+ private static final URI providerId = URI
+ .create("http://taverna.sf.net/2010/service-provider/servicecatalogue/rest");
+
+ private static Logger logger = Logger.getLogger(BioCatalogueRESTServiceProvider.class);
+
+ public BioCatalogueRESTServiceProvider(
+ RESTFromBioCatalogueServiceDescription restServiceDescription) {
+ super(restServiceDescription);
+ }
+
+ public BioCatalogueRESTServiceProvider() {
+ super(new RESTFromBioCatalogueServiceDescription());
+ }
+
+ @Override
+ protected List<? extends Object> getIdentifyingData() {
+ return getConfiguration().getIdentifyingData();
+ }
+
+ @Override
+ public void findServiceDescriptionsAsync(
+ FindServiceDescriptionsCallBack callBack) {
+ callBack.status("Starting Service Catalogue REST Service Provider");
+ registerNewRESTMethod(getConfiguration(), callBack);
+ }
+
+ @Override
+ public Icon getIcon() {
+// return RESTActivityIcon.getRESTActivityIcon();
+ return getConfiguration().getIcon();
+ }
+
+ @Override
+ public String getId() {
+ return providerId.toString();
+ }
+
+ @Override
+ public String getName() {
+ return "Service Catalogue REST";
+ }
+
+ @Override
+ public String toString() {
+ return "Service Catalogue REST service " + getConfiguration().getName();
+ }
+
+ public static boolean registerNewRESTMethod(
+ RESTFromBioCatalogueServiceDescription restServiceDescription,
+ FindServiceDescriptionsCallBack callBack) {
+ if (callBack == null) {
+ // We are not adding service through a callback and
+ // findServiceDescriptionsAsync() -
+ // we are adding directly from the BioCatalogue perspective.
+ ServiceDescriptionRegistryImpl serviceDescriptionRegistry = ServiceDescriptionRegistryImpl
+ .getInstance();
+ serviceDescriptionRegistry
+ .addServiceDescriptionProvider(new BioCatalogueRESTServiceProvider(
+ restServiceDescription));
+ return true;
+ } else {
+ {
+ // Add the REST method to the Service Panel through the callback
+ callBack.partialResults(Collections
+ .singletonList(restServiceDescription));
+ callBack.finished();
+ return (true);
+ }
+ }
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/BioCatalogueServiceProvider.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/BioCatalogueServiceProvider.java
new file mode 100644
index 0000000..87518c3
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/BioCatalogueServiceProvider.java
@@ -0,0 +1,274 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.service_panel;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.Icon;
+import javax.wsdl.Operation;
+import javax.wsdl.WSDLException;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.apache.log4j.Logger;
+import org.xml.sax.SAXException;
+
+import com.thoughtworks.xstream.XStream;
+import com.thoughtworks.xstream.io.xml.DomDriver;
+
+import net.sf.taverna.biocatalogue.model.SoapOperationIdentity;
+import net.sf.taverna.biocatalogue.model.Util;
+import net.sf.taverna.t2.activities.wsdl.WSDLActivityHealthChecker;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.BioCataloguePerspective;
+import net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.config.BioCataloguePluginConfiguration;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+import net.sf.taverna.wsdl.parser.WSDLParser;
+
+public class BioCatalogueServiceProvider implements ServiceDescriptionProvider
+{
+ public static final String PROVIDER_NAME = "Service Catalogue - selected services";
+
+ private static BioCatalogueServiceProvider instanceOfSelf = null;
+ private static FindServiceDescriptionsCallBack callBack;
+
+ private static List<SoapOperationIdentity> registeredSOAPOperations;
+ private static List<RESTFromBioCatalogueServiceDescription> registeredRESTMethods;
+
+ private static Logger logger = Logger.getLogger(BioCatalogueServiceProvider.class);
+
+
+ public BioCatalogueServiceProvider() {
+ BioCatalogueServiceProvider.instanceOfSelf = this;
+ }
+
+ @SuppressWarnings("unchecked")
+ public void findServiceDescriptionsAsync(FindServiceDescriptionsCallBack callBack)
+ {
+ BioCatalogueServiceProvider.callBack = callBack;
+ callBack.status("Starting Service Catalogue Service Provider");
+
+ // --- Initilise the service provider with stored services ---
+
+ // read stored settings
+ // NB! it's crucial to set the custom classloader, otherwise XStream would fail,
+ // as it would attempt to use the default one, which wouldn't know about the
+ // plugin's classes
+ logger.info("Starting to deserialise the list of services stored in the configuration file");
+ XStream xstream = new XStream(new DomDriver());
+ xstream.setClassLoader(BioCataloguePerspective.class.getClassLoader());
+
+ BioCataloguePluginConfiguration configuration = BioCataloguePluginConfiguration.getInstance();
+
+ // *** load stored SOAP operations ***
+ String loadedSOAPServicesXMLString = configuration.getProperty(BioCataloguePluginConfiguration.SOAP_OPERATIONS_IN_SERVICE_PANEL);
+
+ Object loadedSOAPServices = (loadedSOAPServicesXMLString == null ?
+ null :
+ xstream.fromXML(loadedSOAPServicesXMLString));
+
+ registeredSOAPOperations = (loadedSOAPServices == null || !(loadedSOAPServices instanceof List<?>) ?
+ new ArrayList<SoapOperationIdentity>() :
+ (List<SoapOperationIdentity>)loadedSOAPServices
+ );
+ logger.info("Deserialised " + registeredSOAPOperations.size() + Util.pluraliseNoun("SOAP operation", registeredSOAPOperations.size()));
+
+ // prepare the correct format of data for initialisation
+ List<ServiceDescription> results = new ArrayList<ServiceDescription>();
+ for (SoapOperationIdentity opId : registeredSOAPOperations) {
+ results.add(new WSDLOperationFromBioCatalogueServiceDescription(opId));
+ }
+
+
+ // *** load stored REST methods ***
+ String loadedRESTMethodsXMLString = configuration.getProperty(BioCataloguePluginConfiguration.REST_METHODS_IN_SERVICE_PANEL);
+
+ Object loadedRESTMethods = (loadedRESTMethodsXMLString == null ?
+ null :
+ xstream.fromXML(loadedRESTMethodsXMLString));
+
+ registeredRESTMethods = (loadedRESTMethods == null || !(loadedRESTMethods instanceof List<?>) ?
+ new ArrayList<RESTFromBioCatalogueServiceDescription>() :
+ (List<RESTFromBioCatalogueServiceDescription>)loadedRESTMethods);
+ logger.info("Deserialised " + registeredRESTMethods.size() + Util.pluraliseNoun("REST method", registeredRESTMethods.size()));
+
+ results.addAll(registeredRESTMethods);
+
+
+ // *** send the services to the Service Panel ***
+ callBack.partialResults(results);
+
+
+ // NB! This is to be called when it is known that no more items will be added -
+ // it's never true for this provider, as items may be added on user request
+ // at any time!
+ //
+ // callBack.finished();
+ }
+
+ public Icon getIcon() {
+ return null;
+ }
+
+ public String getName(){
+ // TODO - not sure where this is used
+ return "My dummy service";
+ }
+
+ public String getId() {
+ return "http://www.taverna.org.uk/2010/services/servicecatalogue";
+ }
+
+
+ /**
+ * Adds a new "processor" - i.e. a WSDL operation into the main Service Panel.
+ *
+ * @param wsdlLocation URL of the WSDL location of the operation to add.
+ * @param operationName Name of the operation within specified WSDL document.
+ * @return True if the operation was added;
+ * false if the service provided was not yet initiliased (unlikely) or
+ * when supplied strings were empty/null.
+ */
+ public static boolean registerNewWSDLOperation(SoapOperationIdentity soapOperationDetails)
+ {
+ if (BioCatalogueServiceProvider.instanceOfSelf == null || soapOperationDetails == null ||
+ soapOperationDetails.getWsdlLocation() == null || soapOperationDetails.getWsdlLocation().length() == 0 ||
+ soapOperationDetails.getOperationName() == null || soapOperationDetails.getOperationName().length() == 0)
+ {
+ // the service provider hasn't been initialised yet
+ // OR not all details available
+ return (false);
+ }
+ else
+ {
+ // record the newly added operation in the internal list
+ registeredSOAPOperations.add(soapOperationDetails);
+
+ // add the provided operation to the Service Panel
+ ServiceDescription service = new WSDLOperationFromBioCatalogueServiceDescription(soapOperationDetails);
+ BioCatalogueServiceProvider.callBack.partialResults(Collections.singletonList(service));
+ return (true);
+ }
+
+ }
+
+ /**
+ * Adds a SOAP/WSDL service and all of its operations into the Taverna's Service Panel.
+ */
+ public static boolean registerNewWSDLService(String wsdlURL)
+ {
+ if (BioCatalogueServiceProvider.instanceOfSelf == null || wsdlURL == null)
+ {
+ // the service provider hasn't been initialised yet
+ // OR not all details available
+ return (false);
+ }
+ else
+ {
+ // Do the same thing as in the WSDL service provider
+ callBack.status("Service Catalogue service provider: Parsing wsdl: " + wsdlURL);
+ WSDLParser parser = null;
+ try {
+ parser = new WSDLParser(wsdlURL);
+ List<Operation> operations = parser.getOperations();
+ callBack.status("Found " + operations.size() + " WSDL operations of service "
+ + wsdlURL);
+ List<WSDLOperationFromBioCatalogueServiceDescription> items = new ArrayList<WSDLOperationFromBioCatalogueServiceDescription>();
+ for (Operation operation : operations) {
+ WSDLOperationFromBioCatalogueServiceDescription item;
+ try {
+ String operationName = operation.getName();
+ String operationDesc = parser.getOperationDocumentation(operationName);
+ String use = parser.getUse(operationName);
+ String style = parser.getStyle();
+ if (!WSDLActivityHealthChecker.checkStyleAndUse(style, use)) {
+ logger.warn("Unsupported style and use combination " + style + "/" + use + " for operation " + operationName + " from " + wsdlURL);
+ continue;
+ }
+ item = new WSDLOperationFromBioCatalogueServiceDescription(wsdlURL, operationName, operationDesc);
+ items.add(item);
+
+ // Record the newly added operation in the internal list
+ SoapOperationIdentity soapOperationDetails = new SoapOperationIdentity(wsdlURL, operationName, operationDesc);
+ registeredSOAPOperations.add(soapOperationDetails);
+ } catch (UnknownOperationException e) {
+ String message = "Encountered an unexpected operation name:"
+ + operation.getName();
+ callBack.fail(message, e);
+ return false;
+ }
+ }
+ callBack.partialResults(items);
+ callBack.finished();
+ return true;
+ } catch (ParserConfigurationException e) {
+ String message = "Error configuring the WSDL parser";
+ callBack.fail(message, e);
+ return false;
+ } catch (WSDLException e) {
+ String message = "There was an error with the wsdl: " + wsdlURL;
+ callBack.fail(message, e);
+ return false;
+ } catch (IOException e) {
+ String message = "There was an IO error parsing the wsdl: " + wsdlURL
+ + " Possible reason: the wsdl location was incorrect.";
+ callBack.fail(message, e);
+ return false;
+ } catch (SAXException e) {
+ String message = "There was an error with the XML in the wsdl: "
+ + wsdlURL;
+ callBack.fail(message, e);
+ return false;
+ } catch (IllegalArgumentException e) { // a problem with the wsdl url
+ String message = "There was an error with the wsdl: " + wsdlURL + " "
+ + "Possible reason: the wsdl location was incorrect.";
+ callBack.fail(message, e);
+ return false;
+ } catch (Exception e) { // anything else we did not expect
+ String message = "There was an error with the wsdl: " + wsdlURL;
+ callBack.fail(message, e);
+ return false;
+ }
+ }
+
+ }
+
+
+ public static boolean registerNewRESTMethod(RESTFromBioCatalogueServiceDescription restServiceDescription)
+ {
+ if (restServiceDescription == null) {
+ return (false);
+ }
+ else
+ {
+ // record the newly added method in the internal list
+ registeredRESTMethods.add(restServiceDescription);
+
+ // add the provided method to the Service Panel
+ BioCatalogueServiceProvider.callBack.partialResults(Collections.singletonList(restServiceDescription));
+ return (true);
+ }
+ }
+
+
+ public static List<SoapOperationIdentity> getRegisteredSOAPOperations() {
+ return (registeredSOAPOperations);
+ }
+
+ public static List<RESTFromBioCatalogueServiceDescription> getRegisteredRESTMethods() {
+ return (registeredRESTMethods);
+ }
+
+
+ /**
+ * Clears internal lists of stored SOAP operations / REST methods.
+ * Therefore, once Taverna is restarted, the stored services will
+ * be effectively "forgotten".
+ */
+ public static void clearRegisteredServices() {
+ registeredRESTMethods.clear();
+ registeredSOAPOperations.clear();
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/BioCatalogueWSDLOperationServiceProvider.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/BioCatalogueWSDLOperationServiceProvider.java
new file mode 100644
index 0000000..62a39d7
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/BioCatalogueWSDLOperationServiceProvider.java
@@ -0,0 +1,215 @@
+/*******************************************************************************
+ * Copyright (C) 2008-2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.service_panel;
+
+import java.io.IOException;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.Icon;
+import javax.wsdl.Operation;
+import javax.wsdl.WSDLException;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.apache.log4j.Logger;
+import org.xml.sax.SAXException;
+
+import net.sf.taverna.biocatalogue.model.SoapOperationIdentity;
+import net.sf.taverna.t2.activities.wsdl.WSDLActivityHealthChecker;
+import net.sf.taverna.t2.servicedescriptions.AbstractConfigurableServiceProvider;
+import net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+import net.sf.taverna.wsdl.parser.WSDLParser;
+
+/**
+ * Service provider for WSDL operations added to the Service Panel through the
+ * BioCatalogue perspective.
+ *
+ * @author Alex Nenadic
+ */
+public class BioCatalogueWSDLOperationServiceProvider extends
+ AbstractConfigurableServiceProvider<WSDLOperationFromBioCatalogueServiceDescription> {
+
+ public BioCatalogueWSDLOperationServiceProvider(
+ WSDLOperationFromBioCatalogueServiceDescription wsdlOperationDescription) {
+ super(wsdlOperationDescription);
+ }
+
+ public BioCatalogueWSDLOperationServiceProvider() {
+ super(new WSDLOperationFromBioCatalogueServiceDescription(new SoapOperationIdentity("", "", "")));
+ }
+
+ public static final String PROVIDER_NAME = "Service Catalogue - selected services";
+
+ private static final URI providerId = URI
+ .create("http://taverna.sf.net/2010/service-provider/servicecatalogue/wsdl");
+
+ private static Logger logger = Logger.getLogger(BioCatalogueWSDLOperationServiceProvider.class);
+
+ @Override
+ protected List<? extends Object> getIdentifyingData() {
+ return getConfiguration().getIdentifyingData();
+ }
+
+ @Override
+ public void findServiceDescriptionsAsync(
+ FindServiceDescriptionsCallBack callBack) {
+ callBack.status("Starting Service Catalogue WSDL Service Provider");
+ registerWSDLOperation(getConfiguration(), callBack);
+ }
+
+ @Override
+ public Icon getIcon() {
+ return getConfiguration().getIcon();
+ }
+
+ @Override
+ public String getId() {
+ return providerId.toString();
+ }
+
+ @Override
+ public String getName() {
+ return "Service Catalogue WSDL";
+ }
+
+ @Override
+ public String toString() {
+ return "Service Catalogue WSDL service " + getConfiguration().getName();
+ }
+
+ public static boolean registerWSDLOperation(
+ WSDLOperationFromBioCatalogueServiceDescription wsdlOperationDescription,
+ FindServiceDescriptionsCallBack callBack) {
+
+ if (callBack == null) {
+ // We are not adding service through Taverna service registry's callback and
+ // findServiceDescriptionsAsync() -
+ // we are adding directly from the BioCatalogue perspective.
+ ServiceDescriptionRegistryImpl serviceDescriptionRegistry = ServiceDescriptionRegistryImpl
+ .getInstance();
+ serviceDescriptionRegistry
+ .addServiceDescriptionProvider(new BioCatalogueWSDLOperationServiceProvider(
+ wsdlOperationDescription));
+ return true;
+ } else {
+ // Add the WSDL operation to the Service Panel through the callback
+ callBack.partialResults(Collections
+ .singletonList(wsdlOperationDescription));
+ callBack.finished();
+ return (true);
+ }
+ }
+
+ /**
+ * Adds a SOAP/WSDL service and all of its operations into the Taverna's Service Panel.
+ */
+ public static boolean registerWSDLService(String wsdlURL, FindServiceDescriptionsCallBack callBack)
+ {
+ String errorMessage = null;
+ Exception ex = null;
+
+ List<Operation> operations = null;
+ List<WSDLOperationFromBioCatalogueServiceDescription> items = null;
+
+ // Do the same thing as in the WSDL service provider
+ WSDLParser parser = null;
+ try {
+ parser = new WSDLParser(wsdlURL);
+ operations = parser.getOperations();
+ items = new ArrayList<WSDLOperationFromBioCatalogueServiceDescription>();
+ for (Operation operation : operations) {
+ WSDLOperationFromBioCatalogueServiceDescription item;
+ try {
+ String operationName = operation.getName();
+ String operationDesc = parser.getOperationDocumentation(operationName);
+ String use = parser.getUse(operationName);
+ String style = parser.getStyle();
+ if (!WSDLActivityHealthChecker.checkStyleAndUse(style, use)) {
+ logger.warn("Unsupported style and use combination " + style + "/" + use + " for operation " + operationName + " from " + wsdlURL);
+ continue;
+ }
+ item = new WSDLOperationFromBioCatalogueServiceDescription(wsdlURL, operationName, operationDesc);
+ items.add(item);
+ } catch (UnknownOperationException e) {
+ errorMessage = "Encountered an unexpected operation name:"
+ + operation.getName();
+ ex = e;
+ }
+ }
+ } catch (ParserConfigurationException e) {
+ errorMessage = "Error configuring the WSDL parser";
+ ex = e;
+ } catch (WSDLException e) {
+ errorMessage = "There was an error with the wsdl: " + wsdlURL;
+ ex = e;
+ } catch (IOException e) {
+ errorMessage = "There was an IO error parsing the wsdl: " + wsdlURL
+ + " Possible reason: the wsdl location was incorrect.";
+ ex = e;
+ } catch (SAXException e) {
+ errorMessage = "There was an error with the XML in the wsdl: "
+ + wsdlURL;
+ ex = e;
+ } catch (IllegalArgumentException e) { // a problem with the wsdl url
+ errorMessage = "There was an error with the wsdl: " + wsdlURL + " "
+ + "Possible reason: the wsdl location was incorrect.";
+ ex = e;
+ } catch (Exception e) { // anything else we did not expect
+ errorMessage = "There was an error with the wsdl: " + wsdlURL;
+ ex = e;
+ }
+
+ if (callBack == null) {
+ if (errorMessage != null){
+ logger.error(errorMessage, ex);
+ return false;
+ }
+ else{
+ // We are not adding service through Taverna service registry's callback and
+ // findServiceDescriptionsAsync() -
+ // we are adding directly from the BioCatalogue perspective.
+ ServiceDescriptionRegistryImpl serviceDescriptionRegistry = ServiceDescriptionRegistryImpl
+ .getInstance();
+ for (WSDLOperationFromBioCatalogueServiceDescription item : items) {
+ serviceDescriptionRegistry
+ .addServiceDescriptionProvider(new BioCatalogueWSDLOperationServiceProvider(
+ item));
+ }
+ return true;
+ }
+ } else {
+ if (errorMessage != null){
+ callBack.fail(errorMessage, ex);
+ return false;
+ }
+ else{
+ callBack.status("Found " + operations.size() + " WSDL operations of service "
+ + wsdlURL);
+ callBack.partialResults(items);
+ callBack.finished();
+ return true;
+ }
+ }
+ }
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/RESTFromBioCatalogueServiceDescription.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/RESTFromBioCatalogueServiceDescription.java
new file mode 100644
index 0000000..1551294
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/RESTFromBioCatalogueServiceDescription.java
@@ -0,0 +1,194 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.service_panel;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.swing.Icon;
+
+import net.sf.taverna.t2.lang.beans.PropertyAnnotation;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
+
+import net.sf.taverna.t2.activities.rest.RESTActivity;
+import net.sf.taverna.t2.activities.rest.RESTActivity.DATA_FORMAT;
+import net.sf.taverna.t2.activities.rest.RESTActivity.HTTP_METHOD;
+import net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean;
+import net.sf.taverna.t2.activities.rest.ui.servicedescription.RESTActivityIcon;
+
+/**
+ * This class is solely intended to support import of REST services from BioCatalogue.
+ *
+ * @author Sergejs Aleksejevs
+ */
+/*******************************************************************************
+ * Copyright (C) 2008-2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+public class RESTFromBioCatalogueServiceDescription extends ServiceDescription<RESTActivityConfigurationBean>
+{
+ private static final int SHORT_DESCRIPTION_MAX_LENGTH = 200;
+
+ private static final String FULL_DESCRIPTION = "Full description";
+
+ public static final int AMBIGUOUS_ACCEPT_HEADER_VALUE = 100;
+ public static final int DEFAULT_ACCEPT_HEADER_VALUE = 110;
+ public static final int AMBIGUOUS_CONTENT_TYPE_HEADER_VALUE = 200;
+ public static final int DEFAULT_CONTENT_TYPE_HEADER_VALUE = 210;
+
+
+ private RESTActivityConfigurationBean serviceConfigBean;
+ private String serviceName;
+ private String description;
+
+ private List<Integer> dataWarnings;
+
+
+ /**
+ * Constructor instantiates config bean and pre-populates
+ * it with default values.
+ */
+ public RESTFromBioCatalogueServiceDescription()
+ {
+ // apply default name in case it won't be set manually later
+ this.serviceName = "REST Service";
+ this.serviceConfigBean = RESTActivityConfigurationBean.getDefaultInstance();
+ this.dataWarnings = new ArrayList<Integer>();
+ }
+
+ /**
+ * The subclass of Activity which should be instantiated when adding a service
+ * for this description.
+ */
+ @Override
+ public Class<? extends Activity<RESTActivityConfigurationBean>> getActivityClass() {
+ return RESTActivity.class;
+ }
+
+ /**
+ * The configuration bean which is to be used for configuring the instantiated activity.
+ *
+ * Values are to be set through individual setters provided in this class.
+ */
+ @Override
+ public RESTActivityConfigurationBean getActivityConfiguration() {
+ return serviceConfigBean;
+ }
+
+ /**
+ * An icon to represent this service type in the service palette.
+ */
+ @Override
+ public Icon getIcon() {
+ return RESTActivityIcon.getRESTActivityIcon();
+ }
+
+ /**
+ * The display name that will be shown in service palette and will
+ * be used as a template for processor name when added to workflow.
+ */
+ @Override
+ public String getName() {
+ return serviceName;
+ }
+
+
+ /**
+ * Truncates the description if necessary to {@link WSDLOperationFromBioCatalogueServiceDescription#SHORT_DESCRIPTION_MAX_LENGTH} --
+ * to get full description, use {@link WSDLOperationFromBioCatalogueServiceDescription#getFullDescription()}
+ */
+ public String getDescription() {
+ if (this.description != null && this.description.length() > SHORT_DESCRIPTION_MAX_LENGTH) {
+ return (this.description.substring(0, SHORT_DESCRIPTION_MAX_LENGTH) + "(...)");
+ }
+ else {
+ return this.description;
+ }
+ }
+
+ @PropertyAnnotation(displayName = FULL_DESCRIPTION)
+ public String getFullDescription() {
+ return this.description;
+ }
+
+
+ /**
+ * The path to this service description in the service palette. Folders
+ * will be created for each element of the returned path.
+ *
+ * (Shouldn't really be ever used, as instances of different type are
+ * added into the Service Panel).
+ */
+ @Override
+ public List<String> getPath() {
+ // For deeper paths you may return several strings
+ return Arrays.asList(BioCatalogueRESTServiceProvider.PROVIDER_NAME, "REST @ " + serviceConfigBean.getUrlSignature());
+ }
+
+ /**
+ * Return a list of data values uniquely identifying this service
+ * description (to avoid duplicates). Include only primary key like fields,
+ * ie. ignore descriptions, icons, etc.
+ */
+ @Override
+ protected List<? extends Object> getIdentifyingData() {
+ return Arrays.<Object>asList(serviceConfigBean.getUrlSignature(), serviceConfigBean.getHttpMethod());
+ }
+
+
+ public List<Integer> getDataWarnings() {
+ return dataWarnings;
+ }
+
+
+ public void setURLSignature(String urlSignature) {
+ this.serviceConfigBean.setUrlSignature(urlSignature);
+ }
+
+
+ public void setHttpMethod(HTTP_METHOD httpMethod) {
+ this.serviceConfigBean.setHttpMethod(httpMethod);
+ }
+
+
+ public void setAcceptHeaderValue(String acceptHeaderValue) {
+ this.serviceConfigBean.setAcceptsHeaderValue(acceptHeaderValue);
+ }
+
+
+ public void setOutgoingContentType(String outgoingContentType)
+ {
+ this.serviceConfigBean.setUrlSignature(outgoingContentType);
+
+ // automatically infer data format - string/binary from the content type
+ if (outgoingContentType.startsWith("text")) { this.serviceConfigBean.setOutgoingDataFormat(DATA_FORMAT.String); }
+ else { this.serviceConfigBean.setOutgoingDataFormat(DATA_FORMAT.Binary); }
+ }
+
+
+ public void setServiceName(String name) {
+ this.serviceName = name;
+ }
+
+
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/WSDLOperationFromBioCatalogueServiceDescription.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/WSDLOperationFromBioCatalogueServiceDescription.java
new file mode 100644
index 0000000..f5de088
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/service_panel/WSDLOperationFromBioCatalogueServiceDescription.java
@@ -0,0 +1,116 @@
+package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.service_panel;
+
+import java.util.Arrays;
+import java.util.List;
+
+import javax.swing.Icon;
+
+import net.sf.taverna.biocatalogue.model.SoapOperationIdentity;
+import net.sf.taverna.t2.activities.wsdl.WSDLActivity;
+import net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean;
+import net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLActivityIcon;
+import net.sf.taverna.t2.lang.beans.PropertyAnnotation;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+
+/*******************************************************************************
+ * Copyright (C) 2008-2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+public class WSDLOperationFromBioCatalogueServiceDescription extends ServiceDescription<WSDLActivityConfigurationBean>
+{
+ private static final int SHORT_DESCRIPTION_MAX_LENGTH = 200;
+
+ private static final String FULL_DESCRIPTION = "Full description";
+
+
+ private final String wsdlLocation;
+ private final String operationName;
+ private final String description;
+
+
+ public WSDLOperationFromBioCatalogueServiceDescription(String wsdlLocation, String operationName, String description)
+ {
+ this.wsdlLocation = wsdlLocation;
+ this.operationName = operationName;
+ this.description = description;
+ }
+
+ public WSDLOperationFromBioCatalogueServiceDescription(SoapOperationIdentity soapOpearationIdentity)
+ {
+ this.wsdlLocation = soapOpearationIdentity.getWsdlLocation();
+ this.operationName = soapOpearationIdentity.getOperationName();
+ this.description = soapOpearationIdentity.getDescription();
+ }
+
+
+ @Override
+ public Class getActivityClass() {
+ return WSDLActivity.class;
+ }
+
+ @Override
+ public WSDLActivityConfigurationBean getActivityConfiguration() {
+ WSDLActivityConfigurationBean bean = new WSDLActivityConfigurationBean();
+ bean.setOperation(operationName);
+ bean.setWsdl(wsdlLocation);
+ return bean;
+ }
+
+ @Override
+ public Icon getIcon() {
+ return WSDLActivityIcon.getWSDLIcon();
+ }
+
+ @Override
+ public String getName() {
+ return (this.operationName);
+ }
+
+ /**
+ * Truncates the description if necessary to {@link WSDLOperationFromBioCatalogueServiceDescription#SHORT_DESCRIPTION_MAX_LENGTH} --
+ * to get full description, use {@link WSDLOperationFromBioCatalogueServiceDescription#getFullDescription()}
+ */
+ public String getDescription() {
+ if (this.description != null && this.description.length() > SHORT_DESCRIPTION_MAX_LENGTH) {
+ return (this.description.substring(0, SHORT_DESCRIPTION_MAX_LENGTH) + "(...)");
+ }
+ else {
+ return this.description;
+ }
+ }
+
+ @PropertyAnnotation(displayName = FULL_DESCRIPTION)
+ public String getFullDescription() {
+ return this.description;
+ }
+
+ @Override
+ public List<String> getPath() {
+ return Arrays.asList(BioCatalogueWSDLOperationServiceProvider.PROVIDER_NAME, "WSDL @ " + this.wsdlLocation);
+ }
+
+ @Override
+ protected List<? extends Object> getIdentifyingData()
+ {
+ // This is important - Taverna won't add identical operations
+ // into the Service Panel. These tokens distinguish added items.
+ return Arrays.asList(wsdlLocation, operationName);
+ }
+
+}
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
new file mode 100644
index 0000000..44cf82b
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
@@ -0,0 +1,2 @@
+net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.service_panel.BioCatalogueWSDLOperationServiceProvider
+net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.service_panel.BioCatalogueRESTServiceProvider
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
new file mode 100644
index 0000000..8bdcfa5
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
@@ -0,0 +1,2 @@
+net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.menus.BioCatalogueContextualMenuSection
+net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.menus.MenuActionProcessorHealthCheck
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ShutdownSPI b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ShutdownSPI
new file mode 100644
index 0000000..b036654
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ShutdownSPI
@@ -0,0 +1 @@
+#net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentShutdownHook
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.configuration.ConfigurationUIFactory b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.configuration.ConfigurationUIFactory
new file mode 100644
index 0000000..bc9b362
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.configuration.ConfigurationUIFactory
@@ -0,0 +1 @@
+net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.config.BioCataloguePluginConfigurationUIFactory
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.report.explainer.VisitExplainer b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.report.explainer.VisitExplainer
new file mode 100644
index 0000000..5b64699
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.report.explainer.VisitExplainer
@@ -0,0 +1 @@
+net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check.BioCatalogueWSDLActivityHealthCheckVisitExplainer
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
new file mode 100644
index 0000000..a26e638
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
@@ -0,0 +1,3 @@
+net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.contextual_views.BioCataloguePluginProcessorContextViewFactory
+#net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.contextual_views.BioCataloguePluginInputPortContextViewFactory
+#net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.contextual_views.BioCataloguePluginOutputPortContextViewFactory
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.PerspectiveSPI b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.PerspectiveSPI
new file mode 100644
index 0000000..eb7f253
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.PerspectiveSPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.ui.perspectives.biocatalogue.BioCataloguePerspective
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.UIComponentFactorySPI b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.UIComponentFactorySPI
new file mode 100644
index 0000000..1c7d751
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.UIComponentFactorySPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentFactory
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.UIComponentSPI b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.UIComponentSPI
new file mode 100644
index 0000000..40b15c7
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.UIComponentSPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponent
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
new file mode 100644
index 0000000..f24a3dd
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
@@ -0,0 +1 @@
+net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.health_check.BioCatalogueWSDLActivityHealthChecker
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-grey-bert2-still.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-grey-bert2-still.png
new file mode 100644
index 0000000..12abdf6
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-grey-bert2-still.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-grey-bert2.gif b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-grey-bert2.gif
new file mode 100644
index 0000000..c4793ec
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-grey-bert2.gif
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-orange-bert2-still.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-orange-bert2-still.png
new file mode 100644
index 0000000..9b6784e
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-orange-bert2-still.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-orange-bert2.gif b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-orange-bert2.gif
new file mode 100644
index 0000000..c6745b9
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-orange-bert2.gif
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-still.gif b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-still.gif
new file mode 100644
index 0000000..b100470
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader-still.gif
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader.gif b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader.gif
new file mode 100644
index 0000000..078b55f
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/ajax-loader.gif
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/biocatalogue-perspective.xml b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/biocatalogue-perspective.xml
new file mode 100644
index 0000000..8145d87
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/biocatalogue-perspective.xml
@@ -0,0 +1,19 @@
+<basepane>
+ <child>
+ <znode classname="net.sf.taverna.zaria.ZRavenComponent">
+ <component scroll="false">
+ <raven>
+ <group>net.sf.taverna.t2.ui-exts</group>
+ <artifact>perspective-biocatalogue</artifact>
+ </raven>
+ <classname>
+ net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentFactory
+ </classname>
+ <interface>
+ net.sf.taverna.t2.workbench.ui.zaria.UIComponentFactorySPI
+ </interface>
+ </component>
+ </znode>
+ </child>
+ <namedcomponents />
+</basepane>
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/biocatalogue_styles.css b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/biocatalogue_styles.css
new file mode 100644
index 0000000..3f7246a
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/biocatalogue_styles.css
@@ -0,0 +1,2673 @@
+@charset "utf-8";
+/**
+ * BioCatalogue: app/public/stylesheets/styles.css
+ *
+ * Copyright (c) 2009, University of Manchester, The European Bioinformatics
+ * Institute (EMBL-EBI) and the University of Southampton.
+ * See license.txt for details
+ */
+
+/* CSS Document */
+
+/**
+ * NOTE: this relies on the Yahoo IU reset-fonts CSS to normalise styles for HTML elements and fonts
+ * ALl font sizes MUST be specified in %ages as per the table here: http://developer.yahoo.com/yui/fonts/
+ */
+
+/*
+** Markup free clearing
+** Details: http://www.positioniseverything.net/easyclearing.html
+*/
+.clear-block:after {
+ content: ".";
+ display: block;
+ height: 0;
+ clear: both;
+ visibility: hidden;
+}
+
+.clear-block {
+ display: inline-block;
+}
+
+/* Hides from IE-mac \*/
+* html .clear-block {
+ height: 1%;
+}
+.clear-block {
+ display: block;
+}
+/* End hide from IE-mac */
+
+
+
+/**
+ *
+ * This css is a variation of the Garland theme, for Drupal 5.0
+ *
+ * Credits to:
+ * Stefan Nagtegaal, iStyledThis [dot] nl
+ * Steven Wittens, acko [dot] net`
+ *
+ */
+
+/**
+ * Generic elements
+ */
+
+html {
+ background-color: #e9f7cc;
+}
+
+body {
+ margin: 0;
+ padding: 0;
+ background-color: #e9f7cc;
+ font-family: arial;
+ color: #333333;
+ min-width: 950px;
+}
+
+p {
+ font-family: arial;
+ margin: 1em 0;
+ padding: 0;
+ line-height: 1.5;
+}
+
+input {
+ color: #333333;
+ vertical-align: middle;
+}
+
+textarea, select {
+ color: #333333;
+}
+
+h1, h2, h3, h4, h5, h6 {
+ margin: 0;
+ padding: 0;
+ font-weight: bold;
+ font-family: arial;
+ line-height: 1.5;
+ color: #333333;
+}
+
+h1 {
+ font-size: 153.9%;
+ color: #000033;
+ margin: 0.5em 0;
+}
+
+h2 {
+ font-size: 138.5%;
+}
+
+h3 {
+ font-size: 123.1%;
+}
+
+h4 {
+ margin: 0.5em 0;
+}
+
+h5 {
+ margin: 0.8em 0 0.5em 0;
+ padding-bottom: 0.3em;
+ border-bottom: 1px solid #CCC;
+}
+
+h6 {
+}
+
+table {
+ margin: 0;
+ border-collapse: separate;
+}
+
+th,td {
+ text-align: left;
+ border: none;
+ vertical-align: top;
+}
+
+ul, quote, code, fieldset {
+ margin: 0.5em 0;
+}
+
+pre {
+ background-color: #EEEEEE;
+ padding: 1em;
+ font-size: 85%;
+}
+
+small {
+ line-height: 1.3;
+ color: #555555;
+}
+
+fieldset {
+ border: 1px solid #cdeb8b;
+ padding: 0.3em 1.3em 0.8em 1.3em;
+}
+
+legend {
+ padding: 0.3em 0.6em;
+ text-align: left;
+ font-weight: bold;
+ margin: 0;
+ margin-bottom: 0.2em;
+}
+
+strong {
+ font-weight: bold;
+}
+
+em {
+ font-style: italic;
+}
+
+a:link, a:visited {
+ color: #333333;
+ text-decoration: underline;
+}
+
+a:hover {
+ color: #ff7400;
+ text-decoration: underline;
+}
+
+a:active, a.active {
+ color: #ff7400;
+ text-decoration: underline;
+}
+
+a img {
+ text-decoration: none;
+}
+
+hr {
+ margin: 0.5em 0;
+ *margin: 0;
+ padding: 0;
+ border: none;
+ height: 1px;
+ background: #5294c1;
+}
+
+ul {
+ margin: 0;
+ padding: 0;
+}
+
+ul li {
+ margin: 0;
+ padding: 0;
+ line-height: 1.4;
+}
+
+img, a img {
+ border: none;
+}
+
+.center {
+ text-align: center;
+}
+
+.nomargin {
+ margin: 0;
+}
+
+.medium_linespaced {
+ line-height: 1.5;
+}
+
+.high_linespaced {
+ line-height: 2.0;
+}
+
+.inline-block {
+ display:-moz-inline-block;
+ display:-moz-inline-box;
+ display: inline-block;
+}
+
+.faded {
+ color: #999;
+}
+
+.faded_plus {
+ color: #AAA;
+}
+
+.faded_plus_plus {
+ color: #BBB;
+}
+
+.green_box {
+ border: 1px dotted #999999;
+ background-color: #e9f7cc;
+ padding: 2px;
+}
+
+.green_highlight {
+ background-color: #e9f7cc;
+ padding: 3px 5px 3px 5px;
+}
+
+.orange_highlight {
+ background-color: #ffbb7f;
+ padding: 4px 6px 4px 6px;
+}
+
+.yellow_highlight {
+ background-color: #FFC;
+ padding: 3px 5px 3px 5px;
+}
+
+.standout_link {
+ color: #333333;
+ border: 1px solid #EED799;
+ background: #FFC;
+ padding: 0.3em 0.5em;
+ line-height: 1.3;
+}
+
+.ago {
+ margin-left: 0.2em;
+ color: #666;
+}
+
+.container_middled * {
+ vertical-align: middle;
+}
+
+a:link.login, a:visited.login {
+ padding-left: 2px;
+ padding-right: 20px;
+ background: url(../images/login.gif) right no-repeat;
+ white-space: nowrap;
+}
+
+a:link.signup, a:visited.signup {
+ padding-left: 2px;
+ padding-right: 20px;
+ background: url(../images/pencil.gif) right no-repeat;
+ white-space: nowrap;
+}
+
+a:link.green_arrow, a:visited.green_arrow {
+ padding-left: 2px;
+ padding-right: 18px;
+ background: url(../images/green_arrow.gif) right no-repeat;
+ white-space: nowrap;
+}
+
+a:link.red_arrow, a:visited.red_arrow {
+ padding-left: 2px;
+ padding-right: 18px;
+ background: url(../images/red_arrow.gif) right no-repeat;
+ white-space: nowrap;
+}
+
+a:link.red_arrow_left, a:visited.red_arrow_left {
+ padding-right: 2px;
+ padding-left: 18px;
+ background: url(../images/red_arrow_left.gif) left no-repeat;
+ white-space: nowrap;
+}
+
+a:link.write_email, a:visited.write_email {
+ padding-left: 2px;
+ padding-right: 22px;
+ background: url(../images/write_email.gif) right no-repeat;
+ white-space: nowrap;
+}
+
+a:link.edit_profile, a:visited.edit_profile {
+ padding-right: 2px;
+ padding-left: 22px;
+ background: url(../images/user_edit.gif) left no-repeat;
+ white-space: nowrap;
+}
+
+a:link.change_pwd, a:visited.change_pwd {
+ padding-right: 2px;
+ padding-left: 22px;
+ background: url(../images/key.gif) left no-repeat;
+ white-space: nowrap;
+}
+
+a:hover.login {
+ background: url(../images/login_hover.gif) right no-repeat;
+ text-decoration: underline;
+}
+
+a:hover.signup {
+ background: url(../images/pencil_hover.gif) right no-repeat;
+ text-decoration: underline;
+}
+
+a:hover.green_arrow {
+ background: url(../images/green_arrow_hover.gif) right no-repeat;
+ text-decoration: underline;
+}
+
+a:hover.red_arrow {
+ background: url(../images/red_arrow_hover.gif) right no-repeat;
+ text-decoration: underline;
+}
+
+a:hover.red_arrow_left {
+ background: url(../images/red_arrow_left_hover.gif) left no-repeat;
+ text-decoration: underline;
+}
+
+a:hover.write_email {
+ background: url(../images/write_email_hover.gif) right no-repeat;
+ text-decoration: underline;
+}
+
+a:hover.edit_profile {
+ background: url(../images/user_edit_hover.gif) left no-repeat;
+ text-decoration: underline;
+}
+
+a:hover.change_pwd {
+ background: url(../images/key_hover.gif) left no-repeat;
+ text-decoration: underline;
+}
+
+#error_flash .rcontainer,
+#notice_flash .rcontainer {
+ padding: 0;
+ margin: auto;
+ margin-top: 0;
+ margin-bottom: 1em;
+ text-align: center;
+ max-width: 800px;
+ line-height: 1.3;
+}
+
+#error_flash .rcontain,
+#notice_flash .rcontain {
+ padding: 0.1em 0.5em;
+}
+
+#last_search_notice {
+ text-align: right;
+ line-height: 1.0;
+ padding: 0;
+ margin: 0 1em;
+}
+
+#last_search_notice * {
+ vertical-align: middle;
+}
+
+#last_search_notice_text {
+ display:-moz-inline-block;
+ display:-moz-inline-box;
+ display: inline-block;
+ color: #333333;
+ border: 1px solid #99CCFF;
+ background-color: #EEF6FF;
+ padding: 0.2em 0.4em;
+}
+
+.flash_header {
+ font-weight: bold;
+ font-size: 108%;
+ margin-top: 5px;
+ margin-bottom: 10px;
+}
+
+.flash_body {
+ margin-top: 5px;
+ margin-bottom: 10px;
+}
+
+/**
+ * Layout
+ */
+#header-region {
+ height: 0.75em;
+}
+
+#wrapper {
+ background: #e9f7cc url(../images/central_part_small.gif) repeat-x top center;
+}
+
+#wrapper #container {
+ margin: 0 auto;
+ padding: 0 20px;
+ max-width: 1270px;
+}
+
+#wrapper #container #header {
+ padding-top: 1.1em;
+ height: 5em;
+}
+
+#wrapper #container #header #logo-floater {
+ position: absolute;
+ /*padding-top: 8px;*/
+}
+
+/* With 2 columns, require a minimum width of 800px. */
+body.sidebar-right {
+ min-width: 850px;
+}
+
+/* We must define 100% width to avoid the body being too narrow for near-empty pages */
+#wrapper #container #center {
+ float: left;
+ width: 100%;
+}
+
+/* So we move the #center container over the sidebars to compensate */
+body.sidebar-right #center {
+ margin-right: -210px;
+}
+
+/* And add blanks right for the sidebars to fill */
+body.sidebar-right #squeeze {
+ margin-right: 210px;
+}
+
+/* We ensure the sidebars are still clickable using z-index */
+#wrapper #container .sidebar {
+ margin: 60px 0 5em;
+ width: 210px;
+ float: left;
+ z-index: 2;
+ position: relative;
+}
+
+/* Now we add the backgrounds for the main content shading */
+#wrapper #container #center #squeeze {
+ background: #fff url(../images/central_bar_big.png) repeat-x 50% 0;
+ position: relative;
+ /*min-width: 600px;*/
+ min-width: 900px;
+}
+
+#wrapper #container #center .right-corner {
+ background: transparent url(../images/right_corner.gif) no-repeat 100% 0;
+ position: relative;
+ /*left: 10px;*/
+ left: 5px;
+ /*border: 1px #ff0000 solid;*/
+ /*min-width: 600px;*/
+ min-width: 900px;
+}
+
+#wrapper #container #center .right-corner .left-corner {
+ padding: 50px 25px 3em 25px;
+ background: transparent url(../images/left_corner.gif) no-repeat 0 0;
+ margin-left: -10px;
+ position: relative;
+ /*left: 1px;*/
+ min-height: 400px;
+}
+
+#footer {
+ float: none;
+ clear: both;
+ text-align: center;
+ padding-top: 1em;
+ padding-bottom: 1em;
+ /*margin: 4em 0 -3em;*/
+ /*color: #898989;*/
+}
+
+body.sidebar-right #footer {
+ width: 75%;
+}
+
+#footer_links {
+ float:left;
+ position:relative;
+ left:50%;
+ text-align:left;
+}
+
+#footer_links ul {
+ list-style:none;
+ position:relative;
+ left:-50%;
+}
+
+#footer_links ul li {
+ list-style-type: none;
+ list-style-image: none;
+ margin: 0;
+ padding: 0;
+ float: left;
+ position:relative;
+}
+
+#footer_links ul li.separator {
+ border-left: 1px solid #333333;
+}
+
+#footer_links ul li a, #footer_links ul li a:link, #footer_links ul li a:visited {
+ display: block;
+ margin: 0 1em;
+ color: #333333;
+}
+
+#footer_links ul li a:hover, #footer_links ul li a.active {
+ color: #ff7400;
+}
+
+#footer .logos {
+ margin: 1.5em 0;
+ -moz-border-radius: 15px;
+ -webkit-border-radius: 15px;
+ border: 1px solid #DDD;
+ width: 950px;
+ color: #333;
+ background-color: #FFF;
+}
+
+#footer .logos * {
+ vertical-align: middle;
+}
+
+#footer .logos p {
+ text-align: center;
+}
+
+#footer .logos a {
+ margin: 0 0.8em;
+}
+
+#footer .copyright {
+ text-align: center;
+ font-weight: bold;
+ font-size: 93%;
+ margin-top: 1.5em;
+}
+
+#wrapper #container #content {
+ margin-top: 2em;
+}
+
+#wrapper #container #action_bar {
+ position: absolute;
+ top: 10px;
+ left: 30px;
+ z-index: 3;
+ font-size: 123.1%;
+ font-weight: bolder;
+ vertical-align: middle;
+}
+
+#wrapper #container #action_bar #action_links {
+ padding-left: 15px;
+}
+
+#wrapper #container #action_bar #action_links * {
+ vertical-align: middle;
+}
+
+#wrapper #container #action_bar #action_links a {
+ padding-left: 15px;
+ padding-right: 14px;
+ background: transparent url(../images/green_separator.gif) no-repeat left;
+ vertical-align: middle;
+ text-align: center;
+}
+
+#wrapper #container #action_icons {
+ position: absolute;
+ top: 14px;
+ right: 10px;
+ z-index: 3;
+ vertical-align: middle;
+}
+
+#wrapper #container #action_icons * {
+ vertical-align: middle;
+}
+
+#wrapper #container #action_icons a {
+ padding: 0 5px 0 10px;
+ background: transparent url(../images/green_separator.gif) no-repeat left;
+ vertical-align: middle;
+}
+
+#wrapper #container #action_bar img {
+ vertical-align: middle;
+}
+
+body.sidebar-right #footer {
+ margin-right: -210px;
+}
+
+/* BEGIN breadcrumbs */
+
+#breadcrumbs_bar {
+ z-index: 3;
+ font-size: 85%;
+ color: #666666;
+ margin: 3px -10px 0 -5px;
+}
+
+#breadcrumbs_bar table {
+ width: 100%;
+ padding: 0;
+ margin: 0;
+}
+
+#breadcrumbs_bar td {
+ text-align: left;
+ margin: 0;
+ padding: 0;
+ vertical-align: top;
+}
+
+#breadcrumbs_bar td * {
+ vertical-align: middle;
+}
+
+ul.breadcrumb_list {
+ list-style: none;
+ margin: 0;
+ padding: 0;
+ border: none;
+ vertical-align: middle;
+}
+
+ul.breadcrumb_list li {
+ display: inline;
+}
+
+/* END breadcrumbs */
+
+/**
+ * Primary navigation
+ */
+ul.primary-links {
+ margin: 0;
+ padding: 0;
+ float: right;
+ position: relative;
+ z-index: 4;
+ font-size: 108%;
+ font-weight: bold;
+}
+
+ul.primary-links li {
+ margin: 0;
+ padding: 0;
+ float: left;
+ list-style-type: none;
+ list-style-image: none;
+}
+
+ul.primary-links li.separator {
+ /*background: transparent url(../images/green_separator.gif) no-repeat bottom left;*/
+ border-left: 1px solid #999;
+}
+
+ul.primary-links li a, ul.primary-links li a:link, ul.primary-links li a:visited {
+ display: block;
+ margin: 0 1em;
+ /*padding: .75em 0 0;*/
+ color: #333333;
+ /*background: transparent url(images/bg-navigation-item.png) no-repeat 50% 0;*/
+}
+
+ul.primary-links li a:hover, ul.primary-links li a.active {
+ color: #ff7400;
+ /*background: transparent url(images/bg-navigation-item-hover.png) no-repeat 50% 0;*/
+}
+
+/**
+ * Secondary navigation
+ */
+ul.secondary-links {
+ margin: 0;
+ padding: 18px 0 0;
+ float: right;
+ clear: right;
+ position: relative;
+ z-index: 4;
+}
+
+ul.secondary-links li {
+ margin: 0;
+ padding: 0;
+ float: left;
+ background-image: none;
+}
+
+ul.secondary-links li a, ul.secondary-links li a:link, ul.secondary-links li a:visited {
+ display: block;
+ margin: 0 1em;
+ padding: .75em 0 0;
+ color: #cde3f1;
+ background: transparent;
+}
+
+ul.secondary-links li a:hover, ul.secondary-links li a.active {
+ color: #cde3f1;
+ background: transparent;
+}
+
+/**
+ * Local tasks
+ */
+ul.primary, ul.primary li, ul.secondary, ul.secondary li {
+ border: 0;
+ background: none;
+ margin: 0;
+ padding: 0;
+}
+
+#tabs-wrapper {
+ margin: 0 -26px 1em;
+ padding: 0 26px;
+ border-bottom: 1px solid #e9eff3;
+ position: relative;
+}
+ul.primary {
+ padding: 0.5em 0 10px;
+ float: left;
+}
+ul.secondary {
+ clear: both;
+ text-align: left;
+ border-bottom: 1px solid #e9eff3;
+ margin: -0.2em -26px 1em;
+ padding: 0 26px 0.6em;
+}
+h2.with-tabs {
+ float: left;
+ margin: 0 2em 0 0;
+ padding: 0;
+}
+
+ul.primary li a, ul.primary li.active a, ul.primary li a:hover, ul.primary li a:visited,
+ul.secondary li a, ul.secondary li.active a, ul.secondary li a:hover, ul.secondary li a:visited {
+ border: 0;
+ background: transparent;
+ padding: 4px 1em;
+ margin: 0 0 0 1px;
+ height: auto;
+ text-decoration: none;
+ position: relative;
+ top: -1px;
+}
+ul.primary li.active a, ul.primary li.active a:link, ul.primary li.active a:visited, ul.primary li a:hover,
+ul.secondary li.active a, ul.secondary li.active a:link, ul.secondary li.active a:visited, ul.secondary li a:hover {
+ background: url(images/bg-tab.png) repeat-x 0 50%;
+ color: #fff;
+}
+ul.primary li.active a,
+ul.secondary li.active a {
+ font-weight: bold;
+}
+
+/**
+ * CSS support
+ */
+span.clear {
+ display: block;
+ clear: both;
+ height: 1px;
+ line-height: 0px;
+ font-size: 0px;
+ margin-bottom: -1px;
+}
+
+/* BEGIN Login box styles */
+#wrapper #container #header #login_links {
+ clear: both;
+ float: right;
+ padding: 2.1em 0 0 0;
+ margin-bottom: 0;
+ position: relative;
+ z-index: 4;
+ color: #333;
+ font-size: 93%;
+}
+
+#wrapper #container #header #login_links .sep {
+ color: #999;
+ margin: 0 0.4em;
+}
+
+body.sidebar-right #wrapper #container #header #login_links {
+ margin-right: 210px;
+}
+
+#login_box {
+ position: absolute;
+ top: 3px;
+ right: 3px;
+ background-color: #e9f7cc;
+ border: 2px solid #CCC;
+ width: 320px;
+ height: auto;
+ margin: 0 0 auto auto;
+ z-index: 4;
+ padding: 7px;
+}
+
+body.sidebar-right #login_box {
+ margin-right: 210px;
+ top: 3px;
+ right: -15.6em;
+}
+
+#login_box form {
+ margin: 10px 0 1.5em 0;
+}
+
+#login_box span label {
+ float: left;
+ font-weight: bold;
+ padding-top: 0.2em;
+}
+
+#login_box span input.small_login {
+ clear: both;
+ float: right;
+ height: 1.4em;
+ line-height: 1.4;
+ width: 200px;
+ /*background-color: #feffcf;*/
+ margin-bottom: 5px;
+}
+
+#login_box input.small_submit_button {
+ clear: both;
+ float: right;
+ position: relative;
+ top: 5px;
+ width: 80px;
+}
+
+#login_box .rpx {
+ margin: 0;
+ padding: 0.8em 0;
+ border-top: 1px dotted #CCC;
+ text-align: center;
+ line-height: 1.8;
+}
+
+#login_box_other_links {
+ clear: both;
+ font-size: 93%;
+ width: 100%;
+ padding-top: 1.2em;
+ border-top: 1px dotted #CCC;
+ text-align: right;
+}
+
+#login_box_other_links li {
+ margin-bottom: 0.7em;
+}
+
+/* END Login box styles */
+
+/* BEGIN sidebar box styles */
+.sidebar_box {
+ border: solid 1px #cccccc;
+ width: 200px;
+ height: 270px;
+ margin-left: 1em;
+}
+
+.sidebar_box .box_title {
+ text-align: center;
+ font-weight: bold;
+ font-size: 123.1%;
+ height: 30px;
+ line-height: 28px;
+ background: url(../images/box_title_bkgd_green_14.gif) repeat-x;
+ /*color: #ff7400;*/
+ /*color: #ffffff;*/
+}
+
+.sidebar_box .box_body {
+ background-color: #fdfdfd;
+ height: 240px;
+ /*background: url(../images/green_body_bkgd2.gif) repeat-x;*/
+}
+
+.sidebar_box .box_body .box_text {
+ padding: 1em 1em 1em 1em;
+}
+
+.sidebar_box .box_body .separator {
+ border-bottom: 1px solid #cccccc;
+ height: 1px;
+ margin: 0 1em 0 1em;
+}
+
+.sidebar_box .box_body .box_subtitle {
+ text-align: center;
+ font-weight: bold;
+ font-size: 108%;
+ position: relative;
+}
+
+/* END sidebar box styles */
+
+/* BEGIN css tooltips/boxovers */
+
+.boxoverTooltipHeader {
+ z-index: 100000;
+ display: none;
+ border: 0;
+ height: 0;
+}
+
+.boxoverTooltipBody {
+ z-index: 100000;
+ border: solid 1px Gray;
+ color: #000000;
+ background-color: #FFFF66;
+ font-size: 93%;
+ font-weight: normal;
+ padding: 0.3em 0.6em;
+ max-width: 500px;
+ text-align: left;
+ line-height: 1.4;
+}
+
+.boxoverInfoHeader {
+ z-index: 100000;
+ display: none;
+ border: 0;
+ height: 0;
+}
+
+.boxoverInfoBody {
+ z-index: 100000;
+ border: solid 1px Gray;
+ color: #333333;
+ padding: 0.3em 0.6em;
+ background-color: #ebf3ff;
+ font-size: 93%;
+ text-align: left;
+ max-width: 500px;
+ line-height: 1.4;
+}
+
+/* END css tooltips/boxovers */
+
+/* BEGIN liquid round corners box styles */
+.liquid-round {
+ /*width: 70%;*/
+ margin: 25px auto;
+ background: url(../images/round_box_2_left.gif) repeat-y left top;
+}
+
+.liquid-round .top {
+ width: 100%;
+ height: 12px;
+ background: url(../images/round_box_2_top.gif) no-repeat left top;
+}
+
+.liquid-round .top span {
+ display: block;
+ position: relative;
+ height: 12px;
+ background: url(../images/round_box_2_top_right.gif) no-repeat right top;
+}
+
+.liquid-round .center-content {
+ position: relative;
+ background: #f8f8f8 url(../images/round_box_2_right.gif) repeat-y right top;
+ padding: 1px 15px 1px 15px;
+ margin-left: 3px;
+}
+
+.liquid-round .center-content img.round_box_title {
+ margin-top: -38px;
+}
+
+.liquid-round .center-content p {
+ margin-top: 0px;
+ text-align: justify;
+ *line-height: 1.5;
+}
+
+.liquid-round .bottom {
+ width: 100%;
+ height: 13px;
+ background: url(../images/round_box_2_bottom.gif) no-repeat left bottom;
+}
+
+.liquid-round .bottom span {
+ display: block;
+ position: relative;
+ height: 13px;
+ background: url(../images/round_box_2_bottom_right.gif) no-repeat right bottom;
+}
+/* END liquid round corners box styles */
+
+.step_text {
+ font-weight: bold;
+ margin-top: 2em;
+ color: #660000;
+ /* border-top: 1px dotted #CCC;
+ padding-top: 0.5em; */
+}
+
+.none_text {
+ font-style: italic;
+ color: #666;
+}
+
+.error_text {
+ color: red;
+ font-weight: bold;
+}
+
+.additional_info_text {
+ font-size: 93%;
+ color: #666666;
+ font-weight: normal;
+}
+
+.required {
+ color: red;
+ font-weight: bold;
+}
+
+.framed {
+ vertical-align: middle;
+ padding: 3px;
+ background-color: #FFF;
+ border: 1px solid #DDD;
+}
+
+.field {
+ border: 1px solid #EEE;
+ background-color: #FFF;
+ padding: 0.2em 0.5em;
+}
+
+.flag {
+ vertical-align: middle;
+}
+
+/* BEGIN pagination styles */
+
+.pagination {
+ background: white;
+ /* self-clearing method: */
+ }
+
+.pagination a,
+.pagination span {
+ padding: .2em .5em;
+ display: block;
+ float: left;
+ margin-right: 1px;
+}
+
+.pagination span.disabled {
+ color: #999;
+ border: 1px solid #DDD;
+}
+
+.pagination span.current {
+ font-weight: bold;
+ background: #E9F7CC;
+ color: #333333;
+ border: 1px solid #CDEB8B;
+}
+
+.pagination a {
+ text-decoration: none;
+ color: #333333;
+ border: 1px solid #CDEB8B;
+}
+
+.pagination a:hover,
+.pagination a:focus {
+ background: #E9F7CC;
+}
+
+.pagination .page_info {
+ background: #E9F7CC;
+ color: #333333;
+ padding: .4em .6em;
+ width: 25em;
+ margin-bottom: 0.5em;
+ text-align: center;
+}
+
+.pagination .page_info b {
+ color: #003;
+ padding: .1em .25em;
+}
+
+.pagination:after {
+ content: ".";
+ display: block;
+ height: 0;
+ clear: both;
+ visibility: hidden;
+}
+
+* html .pagination {
+ height: 1%;
+}
+
+*:first-child+html .pagination {
+ overflow: hidden;
+}
+
+/* END pagination styles
+
+/* BEGIN listing styles */
+
+.listings {
+ padding: 0;
+ margin: 0;
+}
+
+.listing_item {
+ margin-bottom: 1.5em;
+ padding: 0.6em 1em;
+ border-left: 1px solid #CCC;
+ border-top: 1px solid #CCC;
+ border-right: 2px solid #BBB;
+ border-bottom: 2px solid #BBB;
+ background-color: #F5F5F5;
+}
+
+.listing_item p {
+ margin: 0;
+}
+
+.listing_item p * {
+ vertical-align: middle;
+}
+
+.listing_item .name_section td {
+ vertical-align: middle;
+}
+
+.listing_item .name {
+ font-size: 138.5%;
+ font-weight: bold;
+ line-height: 1.8;
+}
+
+.listing_item .simple_listing .name {
+ font-size: 123.1%;
+ font-weight: bold;
+ line-height: 1.6;
+}
+
+.listing_item .desc {
+ color: #333333;
+ padding: 0.6em 1em;
+ margin: 1em 0;
+ background-color: #F3F3F3;
+ border: 1px dotted #DDD;
+}
+
+.listing_item .detail {
+ color: #333333;
+ font-size: 85%;
+ margin-top: 0.6em;
+}
+
+.listing_item .detail_simple {
+ color: #333333;
+ font-size: 93%;
+ margin-top: 0.6em;
+}
+
+.listing_item .detail_simple * {
+ vertical-align: baseline;
+}
+
+.listing_item .extra_detail_box {
+ color: #333333;
+ font-size: 85%;
+ margin-top: 1.2em;
+ padding-top: 0.8em;
+ border-top: 1px solid #DDD;
+}
+
+/* END listing styles */
+
+.submitter_info {
+ color: #666;
+ vertical-align: baseline;
+}
+
+.submitter_info * {
+ vertical-align: baseline;
+}
+
+a.service_type_badge {
+ font-size: 85%;
+ font-weight: bold;
+ background-color: #FFF;
+ border: 1px solid #DDD;
+ padding: 2px 3px;
+ text-decoration: none;
+ line-height: 1.0;
+}
+
+a.service_type_badge:hover {
+ color: #FFF;
+ background-color: #999;
+}
+
+.service_type_badge_special {
+ font-size: 85%;
+ font-weight: bold;
+ background-color: #FFEFEF;
+ border: 1px solid #DDD;
+ padding: 2px 3px;
+ text-decoration: none;
+ line-height: 1.0;
+}
+
+a.service_location_flag {
+ margin-left: 1em;
+ line-height: 1.0;
+ vertical-align: middle;
+ padding: 0px;
+ line-height: 1.0;
+}
+
+.operation_box {
+ margin: 2em 0;
+ line-height: 1.5;
+ padding-bottom: 1em;
+ border: 0px solid #DDD;
+ border-width: 2px 0 2px 0;
+}
+
+.operation_heading {
+ margin: 0;
+ padding: 1em 0;
+ font-size: 116%;
+}
+
+.operation_name {
+ background-color: #FFBB7F;
+ font-weight: bold;
+ padding: 0.3em 0.5em;
+}
+
+.port {
+ margin-bottom: 1.5em;
+ padding: 0.7em 0.7em 0.3em 0.7em;
+ border: 1px solid #DDE;
+ background-color: #F7F7F7;
+}
+
+.monitoring_section {
+ margin-bottom: 1em;
+ padding: 0.7em 1em;
+ border: 1px solid #DDE;
+ background-color: #F7F7F7;
+}
+
+ul.simple_list {
+ padding: 0;
+ margin: 0;
+}
+
+ul.simple_list li {
+ padding: 0;
+ margin: 0 0 0.5em 2em;
+ list-style: disc;
+}
+
+.home_heading {
+ font-weight: bold;
+ font-size: 153.9%;
+ line-height: 1.5;
+ text-align: center;
+ padding: 0;
+ margin: 0;
+ margin-top: 1em;
+}
+
+#home_content {
+ width: 950px;
+ /*padding-top: 1em;*/
+ margin: 1em auto auto auto;
+}
+
+#home_content em {
+ color: #ff7400;
+ font-weight: bold;
+}
+
+#key_points {
+ clear:both;
+ margin: 0 0 1em 0;
+}
+
+#key_points li {
+ margin-top: 5px;
+ padding-left: 20px;
+ background: url(../images/bullet_green2.gif) left top no-repeat;
+ /*list-style-type: circle;
+ list-style-image: url("../images/bullet_green2.gif");*/
+ font-size: 108%;
+ line-height: 1.5;
+}
+
+#key_points em {
+ color: #ff7400;
+ font-weight: bold;
+}
+
+div.search_widget {
+ text-align: center;
+}
+
+div.search_widget * {
+ vertical-align: middle;
+}
+
+/* BEGIN Tabber tab styles */
+
+/*--------------------------------------------------
+ REQUIRED to hide the non-active tab content.
+ But do not hide them in the print stylesheet!
+ --------------------------------------------------*/
+.tabberlive .tabbertabhide {
+ display: none;
+}
+
+/*--------------------------------------------------
+ .tabber = before the tabber interface is set up
+ .tabberlive = after the tabber interface is set up
+ --------------------------------------------------*/
+.tabber {
+}
+
+.tabberlive {
+ margin-top: 1em;
+}
+
+/*--------------------------------------------------
+ ul.tabbernav = the tab navigation list
+ li.tabberactive = the active tab
+ --------------------------------------------------*/
+ul.tabbernav
+{
+ margin: 0;
+ border-bottom: 1px solid #CCC;
+ font-weight: bold;
+ font-size: 123.1%;
+ line-height: 24px;
+ padding-bottom: 1px;
+}
+
+ul.tabbernav li
+{
+ list-style: none;
+ margin: 0;
+ display: inline;
+}
+
+ul.tabbernav li a
+{
+ padding: 3px 0.5em;
+ margin-right: 4px;
+ border: 1px solid #CCC;
+ border-bottom: none;
+ background: #E9F7CC;
+ text-decoration: none;
+}
+
+ul.tabbernav li a:link { color: #333; }
+
+ul.tabbernav li a:hover
+{
+ color: #000;
+ background: #BFE76F;
+ border-color: #CCC;
+}
+
+ul.tabbernav li.tabberactive a
+{
+ background-color: #fff;
+ border-bottom: 1px solid #fff;
+}
+
+ul.tabbernav li.tabberactive a:hover
+{
+ color: #000;
+ background: white;
+ border-bottom: 1px solid white;
+}
+
+/*--------------------------------------------------
+ .tabbertab = the tab content
+ Add style only after the tabber interface is set up (.tabberlive)
+ --------------------------------------------------*/
+.tabberlive .tabbertab {
+ padding: 1em;
+ border: 1px solid #CCC;
+ border-top: 0;
+
+ /* If you don't want the tab size changing whenever a tab is changed
+ you can set a fixed height */
+
+ /* height:200px; */
+
+ /* If you set a fix height set overflow to auto and you will get a
+ scrollbar when necessary */
+
+ /* overflow:auto; */
+}
+
+/* If desired, hide the heading since a heading is provided by the tab */
+.tabberlive .tabbertab h3 {
+ display: none;
+}
+.tabberlive .tabbertab h3 {
+ display:none;
+}
+
+/* Example of using an ID to set different styles for the tabs on the page */
+.tabberlive#tab1 {
+}
+.tabberlive#tab2 {
+}
+.tabberlive#tab2 .tabbertab {
+ height:200px;
+ overflow:auto;
+}
+
+/* END Tabber tab styles */
+
+.search_button {
+ border: none;
+ height: 31px;
+ width: 38px;
+ background: url('/images/go_button.png') 0 0 no-repeat;
+ cursor: pointer;
+}
+
+.search_button:hover { }
+
+/* BEGIN tables styles */
+.biocat_table {
+ border: 1px solid #cccccc;
+}
+
+.biocat_table th {
+ font-weight: bold;
+ white-space: nowrap;
+ vertical-align: middle;
+ color: #333333;
+ height: 1.8em;
+ background: url(../images/box_title_bkgd_green_14.gif) repeat-x;
+ background-position: bottom;
+ padding-left: 6px;
+ padding-right: 6px;
+ border-right: 1px solid #cccccc;
+}
+
+.biocat_table th.center {
+ text-align: center;
+}
+
+.biocat_table .small_center {
+ text-align: center;
+ width: 40px;
+}
+
+.biocat_table tr.odd {
+ background-color: #f2fbe1;
+}
+
+.biocat_table td {
+ white-space: nowrap;
+ padding: 3px 6px 3px 6px;
+ border-left: 1px solid #cccccc;
+ border-right: 1px solid #cccccc;
+}
+
+.biocat_table td.center {
+ text-align: center;
+}
+
+.biocat_table td.action_links a:link, .biocat_table td.action_links a:visited {
+ text-align: center;
+ text-decoration: underline;
+ font-size: 93%;
+}
+
+.biocat_table td.action_links a:hover {
+ background-color: #feffcf;
+}
+/* END tables styles */
+
+/* BEGIN ActiveRecord errors box */
+
+/*.fieldWithErrors {
+ padding: 2px;
+ background-color: #ffaaaa;
+ display: table;
+}*/
+
+.fieldWithErrors label {
+ padding: 2px;
+ background-color: #ffaaaa;
+}
+
+.fieldWithErrors input, .fieldWithErrors select {
+ padding: 2px;
+ background-color: #ffaaaa;
+}
+
+#errorExplanation {
+ width: 400px;
+ border: 2px solid #ffaaaa;
+ margin: 1.5em 0;
+ background-color: #f5f5f5;
+ padding-bottom: 1em;
+}
+
+#errorExplanation h2 {
+ text-align: center;
+ font-weight: bold;
+ padding: 0.5em;
+ font-size: 93%;
+ margin: 0;
+ background-image: none;
+ background-color: #ffaaaa;
+ border: none;
+}
+
+#errorExplanation p {
+ font-size: 93%;
+ margin-bottom: 0;
+ margin-top: 0.5em;
+ padding: 0.5em;
+}
+
+#errorExplanation ul {
+ padding-left: 2em;
+}
+
+#errorExplanation ul li {
+ font-size: 93%;
+ list-style: square;
+}
+
+/* END ActiveRecord errors box */
+
+.box_description {
+ padding: 0.9em 1.3em;
+ background-color: #F7F7F7;
+ border: 1px solid #DDD;
+ line-height: 1.4;
+}
+
+.box_info {
+ background: #E9F7CC;
+ color: #333333;
+ padding: 0.6em 1em;
+ margin: 0;
+ margin-bottom: 1em;
+ text-align: center;
+}
+
+.box_info_standout {
+ color: #333333;
+ border: 1px solid #DDD;
+ background: #FFFFCC;
+ padding: 0.3em 0.6em;
+ margin-bottom: 1em;
+ line-height: 1.5;
+}
+
+.box_indented_with_bar {
+ border: 0;
+ border-left: 4px solid #DDD;
+ padding: 1em 0 1em 1em;
+ margin-left: 1em;
+}
+
+.box_currentuser_specific {
+ padding: 1em 1.5em;
+ border: 1px solid #99CCFF;
+ background-color: #EEF6FF;
+}
+
+.box_currentuser_specific * {
+ vertical-align: middle;
+}
+
+.box_form {
+ margin: 1em 0;
+ border: 1px solid #CCC;
+ padding: 0.7em 1.2em;
+ background-color: #EEE;
+}
+
+.box_form fieldset {
+ border: 1px solid #cccccc;
+}
+
+.box_form fieldset legend {
+ font-size: 108%;
+ color: #660000;
+}
+
+.box_form hr {
+ background: #CCC;
+}
+
+/* BEGIN annotations styles */
+
+.annotations_container { }
+
+.annotations_container .inactive {
+ color: #BBB;
+ line-height: 1.0;
+ display:-moz-inline-block;
+ display:-moz-inline-box;
+ display: inline-block;
+}
+
+.annotations_container .active {
+ line-height: 1.0;
+ text-decoration: none;
+ color: #333;
+ display: none;
+}
+
+.annotations_container:hover .inactive {
+ display: none;
+}
+
+.annotations_container:hover .active {
+ display:-moz-inline-block;
+ display:-moz-inline-box;
+ display: inline-block;
+}
+
+.box_annotations {
+ padding: 0;
+ line-height: 1.4;
+}
+
+.box_annotations .rcontain {
+ padding: 2px;
+}
+
+.box_annotations div.text {
+ padding: 0.1em 0.5em 0.2em 0.5em;
+ overflow-x: auto;
+}
+
+.box_annotations div.text p {
+ margin: 0.5em 0;
+ line-height: 1.4;
+}
+
+.box_annotations div.other {
+ padding: 0.1em 0.5em 0.2em 0.5em;
+}
+
+.box_annotations .actions {
+ margin: 0.5em 0 0 0;
+ font-size: 85%;
+ color: #666;
+ text-align: right;
+}
+
+.annotations_container .add_box {
+ margin-top: 0.5em;
+ text-align: center;
+}
+
+.annotations_container .add_box form {
+ text-align: center;
+}
+
+.annotations_container .add_box form div {
+ width: 100%;
+ text-align: center;
+}
+.annotations_container .add_box form textarea {
+ width: 99%;
+}
+
+.annotations_container .add_box .submit_button_div {
+ margin-top: 0.4em;
+ text-align: right;
+}
+
+.annotations_container .add_box .submit_button_div input {
+ width: 80px;
+}
+
+.annotations_container .login_link_box {
+ text-align: right;
+ margin-top: 0.7em;
+}
+
+.annotation_source_text {
+ float: right;
+ color: #666;
+ background-color: #FFC;
+ font-size: 85%;
+ padding: 0.1em 0.5em;
+ line-height: 1.3;
+}
+
+.annotation_source_text * {
+ vertical-align: middle;
+}
+
+.annotation_source_text a {
+ font-weight: bold;
+}
+
+.annotation_source_provider {
+ background-color: #FFDFDF;
+}
+
+.annotation_source_member {
+ background-color: #FFEFBF;
+}
+
+.annotation_source_registry {
+ background-color: #DDFFDD;
+}
+
+.aliases {
+ font-size: 100%;
+ margin: 0.3em 0 0.2em 0;
+ margin-left: 1em;
+ line-height: 1.6;
+}
+
+.annotations_counts_outer_box {
+ display: -moz-inline-block;
+ display: -moz-inline-box;
+ display: -moz-inline-stack;
+ display: inline-block;
+ *display: inline;
+ vertical-align: top;
+ white-space: nowrap;
+ line-height: 1.0;
+ zoom: 1;
+}
+
+.annotations_counts_outer_box .rtop,
+.annotations_counts_outer_box .rbottom {
+ *display: none;
+}
+
+.annotations_counts_outer_box .rcontain {
+ padding: 0px 3px;
+ *padding: 6px 3px 4px 3px;
+}
+
+.annotations_counts_box {
+ font-weight: bold;
+ font-size: 93%;
+ color: #333333;
+ vertical-align: middle;
+ line-height: 22px;
+}
+
+.annotations_counts_box span {
+ padding: 4px 3px 4px 5px;
+ vertical-align: middle;
+}
+
+.annotations_counts_box img {
+ vertical-align: middle;
+ margin-left: 2px;
+ *margin-left: 0;
+}
+
+.annotations_counts_box span.total {
+ background-color: #DDD;
+}
+
+.annotations_counts_box img {
+ vertical-align: middle;
+}
+
+.annotations_counts_box span.end {
+}
+
+/* END annotations styles */
+
+/* BEGIN terms of use page styles */
+#terms_of_use ul, #terms_of_use ol {
+ padding-left: 3em;
+}
+
+#terms_of_use ul li {
+ padding-top: 1em;
+ list-style: square;
+}
+
+#terms_of_use ol li {
+ padding-top: 1em;
+ list-style: decimal;
+}
+/* END terms of use page styles */
+
+/* BEGIN generic horizontal buttons classes */
+/* Should be used with <ul> elements */
+
+.buttons {
+ margin: 2em 0;
+ font-weight: bold;
+ text-align: center;
+}
+
+.buttons li {
+ display:-moz-inline-block;
+ display:-moz-inline-box;
+ display: inline-block;
+ margin: 0;
+ margin-left: 8px;
+ line-height: 2.0;
+}
+
+.buttons li.first {
+ margin-left: 0;
+}
+
+.buttons li:hover {
+}
+
+.buttons li * {
+ vertical-align: middle;
+}
+
+.buttons li a {
+ width: 100%;
+ padding: 6px 0.5em;
+ line-height: 2.0;
+ font-weight: bold;
+ text-decoration: none;
+ border: 1px solid #BBBBBB;
+ background-image: url('/images/button_slim_bg.png');
+ background-position: top;
+ background-repeat: repeat-x;
+ background-color: #EEF6FF;
+}
+
+.buttons li a:hover {
+ background-image: none;
+ background-color: #0099FF;
+ color: #F5F5F5;
+}
+
+.buttons li a * {
+ vertical-align: middle;
+}
+
+a.button_slim {
+ font-weight: bold;
+ line-height: 1.6;
+ text-decoration: none;
+ border: 1px solid #BBBBBB;
+ background-image: url('/images/button_slim_bg.png');
+ background-position: top;
+ background-repeat: repeat-x;
+ background-color: #EEF6FF;
+ vertical-align: middle;
+ padding: 0.1em 0.5em;
+ display:-moz-inline-block;
+ display:-moz-inline-box;
+ display: inline-block;
+}
+
+a.button_slim:hover {
+ background-image: none;
+ background-color: #0099FF;
+ color: #F5F5F5;
+}
+
+a.button_slim * {
+ vertical-align: middle;
+}
+
+/* END generic horizontal buttons classes */
+
+/* BEGIN tag cloud styles */
+
+.tag_cloud {
+ text-align: center;
+ line-height: 1.7;
+}
+
+.tag_cloud ul {
+ margin: 0;
+ padding: 0;
+}
+
+.tag_cloud ul li {
+ display: inline;
+ text-decoration: none;
+ margin: 0 0.25em;
+}
+
+.tag_cloud li a {
+ color: #000099;
+ padding: 0.1em 0;
+ display:-moz-inline-block;
+ display:-moz-inline-box;
+ display: inline-block;
+}
+
+span.namespace,
+.tag_cloud li a.namespace {
+ color: #999;
+ font-size: 10px;
+}
+
+span.ontology_term,
+.tag_cloud li a.ontology_term {
+ color: #6600CC;
+}
+
+/* END tag cloud styles */
+
+/* BEGIN Section Boxes (usually for inner sidebars) */
+
+.box_section {
+ margin: 0;
+ text-align: center;
+ margin-bottom: 1em;
+}
+
+.box_section .content {
+ padding: 0.5em 0.8em;
+ border-top: none;
+ border-right: 1px solid #DDD;
+ border-bottom: none;
+ border-left: 1px solid #DDD;
+ background-image: url('/images/box-bg1.png');
+ background-position: top;
+ background-repeat: repeat-x;
+ background-color: #FFC;
+ overflow: hidden;
+ line-height: 1.5;
+}
+
+.box_section .xtop,
+.box_section .xbottom {
+ display: block;
+ background: transparent;
+ font-size: 1px;
+}
+
+.box_section .xb1,
+.box_section .xb2,
+.box_section .xb3,
+.box_section .xb4,
+.box_section .xb5,
+.box_section .xb6,
+.box_section .xb7 {
+ display: block;
+ overflow: hidden;
+}
+
+.box_section .xb1,
+.box_section .xb2,
+.box_section .xb3,
+.box_section .xb6,
+.box_section .xb7 {
+ height: 1px;
+}
+
+.box_section .xb2,
+.box_section .xb3,
+.box_section .xb4 {
+ background: #f4f0b0;
+ border-left: 1px solid #DDD;
+ border-right: 1px solid #DDD;
+}
+
+.box_section .xb5,
+.box_section .xb6,
+.box_section .xb7 {
+ background: #ffffcb;
+ border-left: 1px solid #DDD;
+ border-right: 1px solid #DDD;
+}
+
+.box_section .xb1 {
+ margin: 0 5px;
+ background: #DDD;
+}
+
+.box_section .xb2,
+.box_section .xb7 {
+ margin: 0 3px;
+ border-width: 0 2px;
+}
+
+.box_section .xb3,
+.box_section .xb6 {
+ margin: 0 2px;
+}
+
+.box_section .xb4,
+.box_section .xb5 {
+ height: 2px;
+ margin: 0 1px;
+}
+
+.box_section .heading {
+ font-size: 108%;
+ font-weight: bold;
+ line-height: 1.0;
+ margin-top: 0.2em;
+}
+
+.box_section .footer {
+ text-align: center;
+ margin-top: 1em;
+ border-top: 1px solid #DDD;
+ padding-top: 0.7em;
+}
+
+.box_section ul.items {
+ margin: 0 0 0.8em 1em;
+ text-align: left;
+}
+
+.box_section ul.items li {
+ list-style-type: none;
+ margin: 0.6em 0;
+ padding-left: 0.8em;
+ line-height: 1.1;
+ /*border-left: 3px solid #DDDDBB;*/
+ text-align: center;
+}
+
+.box_section ul.items li * {
+ vertical-align: middle;
+}
+
+/* END Section Boxes (usually for inner sidebars) */
+
+
+/* BEGIN ratings table styles */
+
+.ratings_table {
+ border: 1px solid #cccccc;
+ margin-bottom: 0.5em;
+ background-color: #FFC;
+ border-collapse: collapse;
+ font-size: 93%;
+}
+
+.ratings_table th {
+ font-weight: bold;
+ white-space: nowrap;
+ vertical-align: middle;
+ color: #333333;
+ height: 2em;
+ background: url(../images/box_title_bkgd_green_14.gif) repeat-x;
+ background-position: bottom;
+ padding-left: 6px;
+ padding-right: 6px;
+ border-right: 1px solid #cccccc;
+ text-align: center;
+}
+
+.ratings_table td {
+ white-space: nowrap;
+ padding: 4px 6px 4px 6px;
+ border-left: 1px solid #cccccc;
+ border-right: 1px solid #cccccc;
+ vertical-align: middle;
+ text-align: center;
+}
+
+.ratings_table tr:hover {
+ background-color: #F7F7F7;
+}
+
+.ratings_table .your_rating .delete_rating_faded {
+ width: 10px;
+ height: 10px;
+ margin-left: 0.5em;
+ vertical-align: middle;
+ display:-moz-inline-block;
+ display:-moz-inline-box;
+ display: inline-block;
+ background: url('/images/delete_faded.png') no-repeat center;
+}
+
+.ratings_table .your_rating .delete_rating a {
+ text-decoration: none;
+}
+
+.ratings_table .your_rating:hover .delete_rating {
+ background: url('/images/delete.png') no-repeat center;
+}
+
+/* END ratings table styles */
+
+/* BEGIN filtering styles */
+
+#filters_header {
+ width: auto;
+ color: #000;
+ line-height: 1.2;
+ padding: 0.5em 0;
+ text-align: center;
+ margin-bottom: 0.5em;
+}
+
+#filters_header .text {
+ font-size: 108%;
+ font-weight: bold;
+ vertical-align: middle;
+}
+
+div.filters {
+ padding: 0 0.3em;
+ line-height: 1.5;
+}
+
+div.filters p.type {
+ font-weight: bold;
+ text-align: center;
+ line-height: 1.2;
+ padding: 0;
+ margin: 0;
+ margin-bottom: 0.8em;
+ color: #555;
+}
+
+div.filters p.subtype {
+ font-size: 93%;
+ font-weight: bold;
+ text-align: center;
+ line-height: 1.2;
+ padding: 0;
+ margin: 0;
+ margin-top: 0.7em;
+ margin-bottom: 0.6em;
+ color: #666;
+ border-bottom: 1px dotted #DDD;
+ padding-bottom: 0.3em;
+}
+
+div.filters p.type_small {
+ font-size: 85%;
+ line-height: 1.2;
+ font-weight: bold;
+ margin: 0;
+ margin-bottom: 0.7em;
+ text-align: center;
+ color: #555;
+}
+
+div.filters div.filter_type_box {
+ margin-bottom: 1em;
+ padding: 0;
+}
+
+div.filters div.current_filters_box {
+ margin-bottom: 1em;
+ padding: 0;
+}
+
+div.filters div.current_filters_box .rcontain {
+ padding: 2px 3px;
+}
+
+div.filters div.current_filters_box .and {
+ font-weight: bold;
+ font-size: 100%;
+ text-align: center;
+ margin: 0;
+ padding-right: 12px;
+}
+
+div.filters div.selected_filters_type_box {
+ margin: 0 0.1em;
+ padding: 0;
+}
+
+div.filters div.selected_filters_type_box .or {
+ font-weight: bold;
+ font-size: 77%;
+ text-align: center;
+ margin: 2px 0;
+ padding-right: 12px;
+}
+
+div.filters ul.top_level {
+ font-size: 85%;
+}
+
+div.filters li {
+ list-style: none;
+ margin: 0;
+ padding: 0;
+}
+
+div.filters li .container {
+
+}
+
+div.filters li .container a {
+ display: block;
+ vertical-align: top;
+ margin-bottom: 0.3em;
+ padding: 1px 3px;
+ text-decoration: none;
+ border: 1px dotted transparent;
+ vertical-align: baseline;
+}
+
+div.filters li .container a * {
+ vertical-align: baseline;
+}
+
+div.filters li .container a:hover {
+ border: 1px dotted #CCC;
+ background-color: #DDE;
+}
+
+div.filters li .container a.selected {
+ border: 1px dotted #CCC;
+ background-color: #DDE;
+}
+
+div.filters li .container a:hover.selected { }
+
+div.filters li .container a span.text {
+ text-decoration: underline;
+}
+
+div.filters li .container a span.count {
+ margin-left: 0.2em;
+}
+
+div.filters li .container a span.deselect {
+ float: right;
+ width: 12px;
+ background: url('/images/delete_faded_darker.png') no-repeat left center;
+}
+
+div.filters li .container a:hover span.deselect {
+ background: url('/images/delete.png') no-repeat left center;
+}
+
+div.filters li.category_root .container a {
+ margin-bottom: 0.5em;
+}
+
+div.filters li.sub_category .container a {
+ /*border-left: 1px dotted #CCC;*/
+ margin-left: 0.2em;
+}
+
+/* END filtering styles */
+
+/* BEGIN autocomplete styles */
+
+
+div.auto_complete {
+ position: absolute;
+ background-color: white;
+ border: 1px solid #999;
+ margin-top: -2px;
+ padding: 0px;
+ z-index: 10000;
+ font-size: 85%;
+ font-weight: normal;
+}
+
+div.auto_complete * {
+ vertical-align: baseline;
+}
+
+div.auto_complete ul {
+ list-style-type: none;
+ margin: 0px;
+ padding: 0px;
+}
+
+div.auto_complete ul li.selected {
+ background-color: #ffb;
+}
+
+div.auto_complete ul li {
+ text-align: left;
+ list-style-type: none;
+ display: block;
+ margin: 0;
+ padding: 3px;
+ border-bottom: 1px solid #DDD;
+ cursor: pointer;
+ overflow: hidden;
+}
+
+div.auto_complete ul li.selected {
+ background-color: #ffb;
+}
+
+div.auto_complete ul strong.highlight {
+ color: #800;
+ margin: 0px;
+ padding: 0px;
+ font-weight: normal;
+}
+
+/* END autocomplete styles */
+
+/* BEGIN stats page styles */
+
+#stats_page {
+ margin: 0 2em;
+}
+
+#stats_page p {
+ margin: 0.6em 0;
+}
+
+#stats_page h4 {
+ padding: 0.2em 0.6em;
+ background-color: #EEE;
+ margin-top: 1.5em;
+}
+
+#stats_page .left_column {
+ float: left;
+ width: 80%;
+}
+
+#stats_page .right_column {
+ float: right;
+ width: 18%;
+}
+
+#stats_page .box_indented_with_bar {
+ padding: 0.5em 1.5em;
+}
+
+#stats_page .box_info_standout {
+ width: 550px;
+ font-size: 85%;
+}
+
+#stats_page .services {
+ margin: 0.5em 0 0.5em 1.5em;
+ line-height: 1.5;
+ font-size: 85%;
+}
+
+#stats_page ul.contents {
+ text-align: left;
+}
+
+#stats_page ul.contents li {
+ padding: 0.2em 0;
+}
+
+#stats_page ul.contents li ul {
+ margin-left: 1em;
+}
+
+/* END stats page styles */
+
+/* BEGIN styles for rounded corner boxes */
+
+.rcontain {
+ padding: 0 0.3em;
+}
+
+/* END styles for rounded corner boxes */
+
+p.more_less_links {
+ font-weight: bold;
+ text-align: right;
+ font-size: 85%;
+ margin: 0;
+}
+
+p.more_less_links a {
+ text-decoration: none;
+}
+
+.search_box .rcontain {
+ padding: 0.4em 1em;
+}
+
+.form_field_section {
+ margin-top: 1.5em;
+}
+
+.form_selected_values {
+ padding: 0.3em 0.5em;
+ border: 1px solid #DDD;
+ background-color: #FFF;
+ color: #333;
+}
+
+/* BEGIN categories styles */
+
+.categories_box {
+ font-size: 85%;
+ line-height: 16px;
+}
+
+ul.categories {
+ float: left;
+ overflow: hidden;
+ margin: 0;
+ padding: 0;
+ list-style-type: none;
+}
+
+ul.categories li {
+ display: inline;
+}
+
+ul.categories li span.main {
+ display:-moz-inline-block;
+ display:-moz-inline-box;
+ display: inline-block;
+ background-color: #FFC;
+ margin-bottom: 0.4em;
+ margin-right: 0.5em;
+ padding: 0 3px;
+ border-top: 1px solid #DEDEDE;
+ border-left: 1px solid #DEDEDE;
+ border-right: 1px solid #999;
+ border-bottom: 1px solid #999;
+}
+
+ul.categories li span.main a.category {
+ line-height: 1.6;
+ text-decoration: none;
+ vertical-align: middle;
+}
+
+ul.categories li span.main a.category:hover {
+ color: #000;
+}
+
+ul.categories li span.main:hover {
+ background-color: #F0E68C;
+}
+
+/* END categories styles */
+
+/* BEGIN stats bar styles */
+
+.stats_bar {
+ color: #555;
+ font-weight: bold;
+}
+
+.stats_bar * {
+ vertical-align: middle;
+}
+
+.stats_bar img {
+ margin-right: 0.3em;
+}
+
+.stats_bar .each {
+ margin-left: 1em;
+}
+
+/* END stats bar styles */
+
+#feedback_help {
+ margin: 1.5em;
+ font-size: 93%;
+ text-align: left;
+}
+
+#feedback_help ul {
+ margin-left: 1.5em;
+ margin-bottom: 1em;
+}
+
+#search_within {
+ margin-bottom: 1em;
+}
+
+#search_within .rcontain {
+ padding: 0 1.5em;
+ text-align: right;
+}
+
+.service_properties p,
+.service_properties .property {
+ margin: 0;
+ margin-top: 1.5em;
+}
+
+#filter_message {
+ text-align: left;
+ font-size: 93%;
+ margin-bottom: 0.8em;
+ color: #333333;
+ /**border: 1px solid #DDD;
+ background: #FFFFCC;
+ padding: 0.4em 0.6em; */
+ line-height: 1.5;
+}
+
+#filter_message .rcontain {
+ padding: 1px 0.8em;
+}
+
+#filter_message .rtop,
+#filter_message .contain,
+#filter_message .rbottom {
+ margin: 0;
+}
+
+#filter_message .rtop,
+#filter_message .rbottom {
+ height: 4px;
+ line-height: 1.0;
+}
+
+#filter_message * {
+ vertical-align: middle;
+}
+
+#subscribe_results_link {
+ float: right;
+ text-decoration: none;
+ vertical-align: middle;
+ font-weight: bold;
+ margin-left: 2em;
+}
+
+#subscribe_results_link img {
+ margin-right: 0.4em;
+}
+
+/* Style for default texts in inputs */
+.ex {
+ color: #999;
+}
+
+/* BEGIN login page styles */
+
+.login_form {
+ padding: 1.2em 0.8em;
+}
+
+.login_form label {
+ float: left;
+ font-weight: bold;
+ margin-bottom: 1em;
+}
+
+.login_form input.login_field {
+ clear: both;
+ float: right;
+ height: 1.4em;
+ line-height: 1.4;
+ width: 220px;
+ margin-bottom: 1em;
+}
+
+.login_form input.sign_in_button {
+ clear: both;
+ float: right;
+ width: 80px;
+}
+
+.login_form .other_links {
+ clear: both;
+ width: 100%;
+ padding-top: 1.2em;
+ border-top: 1px dotted #CCC;
+ text-align: right;
+}
+
+.login_form .other_links li {
+ margin-bottom: 0.7em;
+}
+
+/* END login page styles */
+
+img.account_provider_logo {
+ margin: 0 2px;
+}
+
+.side_link {
+ color: #999;
+ margin-left: 3em;
+ font-size: 85%;
+}
+
+.side_link a {
+ color: #999;
+}
+
+.toolbar {
+ float: right;
+}
+
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/blue-sphere-50.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/blue-sphere-50.png
new file mode 100644
index 0000000..0b3626d
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/blue-sphere-50.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/cross-sphere-35.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/cross-sphere-35.png
new file mode 100644
index 0000000..2553bd9
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/cross-sphere-35.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/cross-sphere-50.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/cross-sphere-50.png
new file mode 100644
index 0000000..2bcba73
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/cross-sphere-50.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/accept.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/accept.png
new file mode 100644
index 0000000..89c8129
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/accept.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/add - tick.pdn b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/add - tick.pdn
new file mode 100644
index 0000000..04ee9be
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/add - tick.pdn
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/add - tick.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/add - tick.png
new file mode 100644
index 0000000..5d2d4af
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/add - tick.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/add.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/add.png
new file mode 100644
index 0000000..6332fef
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/add.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/application_form_add.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/application_form_add.png
new file mode 100644
index 0000000..28c2175
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/application_form_add.png
Binary files differ
diff --git "a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/arrow_join \050flipped vertically\051.png" "b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/arrow_join \050flipped vertically\051.png"
new file mode 100644
index 0000000..7858d14
--- /dev/null
+++ "b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/arrow_join \050flipped vertically\051.png"
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/arrow_left.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/arrow_left.png
new file mode 100644
index 0000000..2bed329
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/arrow_left.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/arrow_refresh.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/arrow_refresh.png
new file mode 100644
index 0000000..0de2656
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/arrow_refresh.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/arrow_right.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/arrow_right.png
new file mode 100644
index 0000000..2cf15f1
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/arrow_right.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/chart_organisation.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/chart_organisation.png
new file mode 100644
index 0000000..c32d25c
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/chart_organisation.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/cross.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/cross.png
new file mode 100644
index 0000000..1514d51
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/cross.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/disk.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/disk.png
new file mode 100644
index 0000000..99d532e
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/disk.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/error.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/error.png
new file mode 100644
index 0000000..628cf2d
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/error.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/exclamation.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/exclamation.png
new file mode 100644
index 0000000..c37bd06
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/exclamation.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/external_link_listing_small.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/external_link_listing_small.png
new file mode 100644
index 0000000..a22b1f7
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/external_link_listing_small.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/folder_explore.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/folder_explore.png
new file mode 100644
index 0000000..0ba9391
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/folder_explore.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/grey_circle.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/grey_circle.png
new file mode 100644
index 0000000..69ede6c
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/grey_circle.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/help.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/help.png
new file mode 100644
index 0000000..5c87017
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/help.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/information.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/information.png
new file mode 100644
index 0000000..12cd1ae
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/information.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/lightbulb.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/lightbulb.png
new file mode 100644
index 0000000..d22fde8
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/lightbulb.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/lock.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/lock.png
new file mode 100644
index 0000000..2ebc4f6
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/lock.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/lock_open.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/lock_open.png
new file mode 100644
index 0000000..a471765
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/lock_open.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/magnifier.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/magnifier.png
new file mode 100644
index 0000000..cf3d97f
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/magnifier.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/multiple_star.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/multiple_star.png
new file mode 100644
index 0000000..c663d73
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/multiple_star.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/page_white_code.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/page_white_code.png
new file mode 100644
index 0000000..0c76bd1
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/page_white_code.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/plugin.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/plugin.png
new file mode 100644
index 0000000..6187b15
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/plugin.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/remote_resource.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/remote_resource.png
new file mode 100644
index 0000000..b8edc12
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/remote_resource.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/server.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/server.png
new file mode 100644
index 0000000..720a237
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/server.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/star.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/star.png
new file mode 100644
index 0000000..b88c857
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/star.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/style.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/style.png
new file mode 100644
index 0000000..81e41de
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/style.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/sum.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/sum.png
new file mode 100644
index 0000000..fd7b32e
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/sum.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/tag_blue.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/tag_blue.png
new file mode 100644
index 0000000..9757fc6
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/tag_blue.png
Binary files differ
diff --git "a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/text_linespacing \050collapse\051.png" "b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/text_linespacing \050collapse\051.png"
new file mode 100644
index 0000000..ff09e31
--- /dev/null
+++ "b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/text_linespacing \050collapse\051.png"
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/text_linespacing.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/text_linespacing.png
new file mode 100644
index 0000000..1a91cbd
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/text_linespacing.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/text_list_numbers.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/text_list_numbers.png
new file mode 100644
index 0000000..33b0b8d
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/text_list_numbers.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/tick.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/tick.png
new file mode 100644
index 0000000..a9925a0
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/tick.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/user.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/user.png
new file mode 100644
index 0000000..79f35cc
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/famfamfam_silk/user.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/favicon.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/favicon.png
new file mode 100644
index 0000000..1ac1bde
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/favicon.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/folds/fold.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/folds/fold.png
new file mode 100644
index 0000000..a13d280
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/folds/fold.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/folds/fold_16x16.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/folds/fold_16x16.png
new file mode 100644
index 0000000..5a37b67
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/folds/fold_16x16.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/folds/unfold.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/folds/unfold.png
new file mode 100644
index 0000000..589e2c9
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/folds/unfold.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/folds/unfold_16x16.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/folds/unfold_16x16.png
new file mode 100644
index 0000000..dd2396c
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/folds/unfold_16x16.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/info-sphere-35.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/info-sphere-35.png
new file mode 100644
index 0000000..cdbacd3
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/info-sphere-35.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/info-sphere-50.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/info-sphere-50.png
new file mode 100644
index 0000000..8e8ac21
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/info-sphere-50.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/open_in_BioCatalogue.pdn b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/open_in_BioCatalogue.pdn
new file mode 100644
index 0000000..3357714
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/open_in_BioCatalogue.pdn
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/open_in_BioCatalogue.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/open_in_BioCatalogue.png
new file mode 100644
index 0000000..897b2c1
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/open_in_BioCatalogue.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/pling-sphere-35.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/pling-sphere-35.png
new file mode 100644
index 0000000..3326aad
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/pling-sphere-35.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/pling-sphere-50.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/pling-sphere-50.png
new file mode 100644
index 0000000..1f47035
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/pling-sphere-50.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/query-sphere-35.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/query-sphere-35.png
new file mode 100644
index 0000000..8091ff3
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/query-sphere-35.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/query-sphere-50.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/query-sphere-50.png
new file mode 100644
index 0000000..443a868
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/query-sphere-50.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/service_type_multitype.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/service_type_multitype.png
new file mode 100644
index 0000000..1a8e9cf
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/service_type_multitype.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/service_type_rest.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/service_type_rest.png
new file mode 100644
index 0000000..a4276c2
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/service_type_rest.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/service_type_soap.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/service_type_soap.png
new file mode 100644
index 0000000..aa80209
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/service_type_soap.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/service_type_unknown.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/service_type_unknown.png
new file mode 100644
index 0000000..92638f1
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/service_type_unknown.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/soap_rest_multitype_unknown.pdn b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/soap_rest_multitype_unknown.pdn
new file mode 100644
index 0000000..cc7fcb9
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/service_icons/soap_rest_multitype_unknown.pdn
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/styles.css b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/styles.css
new file mode 100644
index 0000000..48bbdff
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/styles.css
@@ -0,0 +1,290 @@
+/* BEGIN service preview header styles */
+
+p.service_aka_names {
+ margin-top: 5px;
+ margin-bottom: 0;
+}
+
+span.service_aka_name {
+ font-weight: bold;
+ margin-right: 0.5em;
+}
+
+a.service_status_details {
+ text-decoration: none;
+}
+
+a.service_status_details:hover {
+ color: #ff7400;
+ text-decoration: underline;
+}
+
+h1.service_title {
+ border: 1px solid #D7EFA4;
+ background-color: #E9F7CC;
+ color: #000033;
+ text-align: center;
+ font-size: 180%;
+ margin: 0.2em 0 0 0;
+ padding: 0;
+}
+
+
+h2.soap_operation_name {
+ border: 1px solid #D7EFA4;
+ background-color: #E9F7CC;
+ color: #000033;
+ text-align: center;
+ font-size: 120%;
+ margin: 0.2em 0 0 0;
+ padding: 0;
+}
+
+h3.soap_operation_inputs_or_outputs_section {
+ background-color: #EEEEEE;
+ border: 1px solid #CCCCCC;
+ padding: 0.1em 0.6em;
+ font-size: 110%;
+ margin-top: 2em;
+}
+
+div.soap_input_or_output {
+ border: 1px solid #C6961D;
+ margin: 0.5em 1em;
+}
+
+div.soap_input_or_output p.name {
+ background-color: #FFC526;
+ border: 1px solid #C6961D;
+ padding: 0.2em 1em;
+ margin: 0;
+}
+
+div.soap_input_or_output p.body {
+ border: 1px solid #C6961D;
+ padding: 0.5em 1em;
+ margin: 0;
+}
+
+
+.orange_highlight {
+ background-color: #ffbb7f;
+ padding: 1px 5px 1px 5px;
+ margin: 0 2px;
+}
+
+.none_text {
+ font-weight: normal;
+ font-style: italic;
+ color: #777777;
+}
+
+.left_indented {
+ margin-left: 2em;
+}
+
+/* END service preview header styles */
+
+
+/* BEGIN service preview annotation styles */
+
+div.annotation {
+ margin: 1em;
+ font-size: 100%;
+}
+
+div.annotation p.key {
+ margin: 0;
+ padding: 0;
+ font-weight: bold;
+}
+
+div.annotation p.value {
+ margin: 0;
+ padding: 0 0.7em;
+}
+
+div.annotation p.value_with_submitter {
+ margin: 0.4em 0;
+ padding: 0.3em 0.7em;
+ background-color: #AAFFC1;
+ border: 1px solid #91D8A4;
+}
+
+div.annotation p.value_with_submitter span.submitter{
+ float: right;
+ font-size: 80%;
+ margin: 0 0.2em 0 1em;
+ padding: 2px 5px 1px 5px;
+ background-color: #D8FFE2;
+}
+
+div.annotation img.link_icon {
+ padding: 0 3px;
+ vertical-align: middle;
+}
+
+div.annotation a {
+ vertical-align: middle;
+ color: #000000;
+}
+
+div.annotation a:link, a:visited {
+ /*color: #333333;*/
+ text-decoration: underline;
+}
+
+div.annotation a:hover {
+ color: #ff7400;
+ text-decoration: underline;
+}
+
+div.annotation a:active {
+ color: #ff7400;
+ text-decoration: underline;
+}
+
+/* END service preview annotation styles */
+
+
+
+/* BEGIN service type styles */
+
+p.service_types {
+ margin-top: 0.5em;
+ margin-bottom: 0px;
+}
+
+a.service_type_badge {
+ font-size: 85%;
+ font-weight: bold;
+ background-color: #FFF;
+ border: 1px solid #DDD;
+ padding: 2px 3px;
+ text-decoration: none;
+ line-height: 1.0;
+}
+
+a.service_type_badge:hover {
+ color: #FFF;
+ background-color: #999;
+}
+
+/* END service type styles */
+
+
+/* BEGIN categories styles */
+
+.categories_box {
+ font-size: 90%;
+}
+
+ul.categories {
+ float: left;
+ overflow: hidden;
+ margin: 0;
+ padding: 0;
+ list-style-type: none;
+}
+
+ul.categories li {
+ display: inline;
+}
+
+ul.categories li span.title {
+ line-height: 1.6;
+ font-weight: bold;
+ margin-right: 0.7em;
+ vertical-align: middle;
+}
+
+ul.categories li span.main {
+ display:-moz-inline-block;
+ display:-moz-inline-box;
+ display: inline-block;
+ background-color: #FFC;
+ margin-bottom: 0.4em;
+ margin-right: 0.5em;
+ padding: 0;
+ border-top: 1px solid #DEDEDE;
+ border-left: 1px solid #DEDEDE;
+ border-right: 1px solid #999;
+ border-bottom: 1px solid #999;
+}
+
+ul.categories li span.main a.category {
+ line-height: 1.6;
+ text-decoration: none;
+ vertical-align: middle;
+ padding: 3px 5px 2px 5px;
+}
+
+ul.categories li span.main a.category:hover {
+ color: #000;
+ background-color: #F0E68C;
+}
+
+ul.categories li span.main:hover {
+ background-color: #F0E68C;
+}
+
+/* END categories styles */
+
+
+
+/* BEGIN tag cloud styles */
+
+div.tag_cloud a {
+ font-family:Arial,Helvetica,sans-serif;
+ color: #000099; /* font color as on BioCatalogue */
+ margin: 0 10px; /* vertical margin doesn't seem to work, so adding line-height to make sure that selection borders on different lines do not overlap */
+ line-height: 1.9em;
+ padding: 0 4px 2px 4px;
+ text-decoration: none;
+
+ vertical-align: middle;
+}
+
+div.tag_cloud a:hover {
+ color: orange;
+}
+
+div.tag_cloud a.unselected {
+ /*
+ * this style is used to make sure that equal space
+ * around anchor tags is taken by the transparent border
+ * even when the tag is not "selected"
+ */
+ border-style: solid;
+ border-width: 2px;
+ border-color: transparent;
+}
+
+div.tag_cloud a.unselected_ontological_term {
+ /*
+ * this style is used to make sure that equal space
+ * around anchor tags is taken by the transparent border
+ * even when the tag is not "selected"
+ */
+ border-style: solid solid double solid;
+ border-width: 2px 2px 3px 2px;
+ border-color: transparent transparent #000099 transparent;
+}
+
+#ontological_term{
+ color:#3090C7 ; /*Deep Sky Blue3*/
+}
+
+div.tag_cloud a.selected {
+ border-style: solid;
+ border-width: 2px;
+ background: #D6E9FF;
+}
+
+div.tag_cloud a.selected_ontological_term {
+ border-style: double double double double;
+ border-width: 3px 3px 3px 3px;
+ background: #D6E9FF;
+}
+
+/* END tag cloud styles */
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/test.html b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/test.html
new file mode 100644
index 0000000..e23f24c
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/test.html
@@ -0,0 +1,78 @@
+<html>
+ <head>
+ <link href="styles.css" media="screen" rel="stylesheet" type="text/css" />
+ </head>
+ <body>
+ <h1 class="service_title">
+ Service:
+ <span class="orange_highlight">Blast</span>
+ <a class="service_type_badge" style="margin-left: 1.5em" href="">SOAP</a>
+ </h1>
+ <p class="left_indented service_aka_names"><span class="none_text">aka</span><span class="service_aka_name"> BLAST(DDBJ)</span></p>
+
+ <div class="categories_box">
+ <ul class="categories">
+ <li>
+ <span class="title">
+ Categories:
+ </span>
+ </li>
+ <li>
+ <span class="main">
+ <a href="/services?cat=%5B18%5D" class="category">Nucleotide Sequence Similarity</a>
+ </span>
+ </li>
+ <li>
+ <span class="main">
+ <a href="/services?cat=%5B6%5D" class="category">Protein Sequence Similarity</a>
+ </span>
+ </li>
+ </ul>
+ </div>
+
+ <p style="border-top: 1px solid #000000; margin-top: 3em;"></p>
+
+ <div class="annotation">
+ <p class="key">Provider</p>
+ <p class="value"><a href="">xml.nig.ac.jp</a></p>
+ </div>
+
+ <div class="annotation">
+ <p class="key">Location</p>
+ <p class="value">Japan</p>
+ </div>
+
+ <div class="annotation">
+ <p class="key">Submitter / Source</p>
+ <p class="value">
+ <img src="famfamfam_silk/user.png" class="link_icon"/>
+ <a href="">Franck</a>
+ <span class="none_text" style="margin-left: 0.7em; vertical-align: middle;">(2009-01-01)</span>
+ </p>
+ </div>
+
+ <div class="annotation">
+ <p class="key">Endpoint</p>
+ <p class="value"><a href="">http://xml.nig.ac.jp/xddbj/Blast</a></p>
+ </div>
+
+ <div class="annotation">
+ <p class="key">WSDL Location</p>
+ <p class="value"><a href="">http://xml.nig.ac.jp/xddbj/Blast.wsdl</a></p>
+ </div>
+
+ <div class="annotation">
+ <p class="key">Documentation URL(s)</p>
+ <p class="value_with_submitter">
+ <span class="submitter">
+ <span style="vertical-align: middle;">by</span>
+ <img src="famfamfam_silk/remote_resource.png" class="link_icon"/>
+ <a href="">The EMBRACE Registry</a>
+ <span class="none_text" style="margin-left: 0.3em;">(2009-02-03)</span>
+ </span>
+ <a href="">http://xml.nig.ac.jp/index.html</a>
+ </p>
+ </div>
+
+ </body>
+</html>
\ No newline at end of file
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tick-sphere-35.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tick-sphere-35.png
new file mode 100644
index 0000000..3593666
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tick-sphere-35.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tick-sphere-50.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tick-sphere-50.png
new file mode 100644
index 0000000..f93f269
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tick-sphere-50.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/trash.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/trash.png
new file mode 100644
index 0000000..80f5624
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/trash.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tristate_checkbox/tristate_checkbox_checked.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tristate_checkbox/tristate_checkbox_checked.png
new file mode 100644
index 0000000..af679a2
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tristate_checkbox/tristate_checkbox_checked.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tristate_checkbox/tristate_checkbox_partial.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tristate_checkbox/tristate_checkbox_partial.png
new file mode 100644
index 0000000..9a61aa4
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tristate_checkbox/tristate_checkbox_partial.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tristate_checkbox/tristate_checkbox_partial_green.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tristate_checkbox/tristate_checkbox_partial_green.png
new file mode 100644
index 0000000..9d1eeea
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tristate_checkbox/tristate_checkbox_partial_green.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tristate_checkbox/tristate_checkbox_unchecked.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tristate_checkbox/tristate_checkbox_unchecked.png
new file mode 100644
index 0000000..d9b5c92
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/tristate_checkbox/tristate_checkbox_unchecked.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/unchecked.png b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/unchecked.png
new file mode 100644
index 0000000..c131d07
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/resources/net/sf/taverna/t2/ui/perspectives/biocatalogue/unchecked.png
Binary files differ
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/xsd/dc.xsd b/taverna-workbench-perspective-biocatalogue/src/main/xsd/dc.xsd
new file mode 100644
index 0000000..815d1a2
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/xsd/dc.xsd
@@ -0,0 +1,119 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
+ xmlns="http://purl.org/dc/elements/1.1/"
+ targetNamespace="http://purl.org/dc/elements/1.1/"
+ elementFormDefault="qualified"
+ attributeFormDefault="unqualified">
+
+ <xs:annotation>
+ <xs:documentation xml:lang="en">
+ Simplified XML Schema for http://purl.org/dc/elements/1.1/
+
+ Created 2007-06-28
+
+ Created by
+
+ Stian Soiland (ssoiland@cs.man.ac.uk)
+
+ This simplification removes SimpleLiteral and specifies dc:any as
+ an xs:string, except for dc:date which is specified as an
+ xs:dateTime. This makes the schema more usable for tools like
+ XMLBeans.
+
+
+
+ Based on
+ http://dublincore.org/schemas/xmls/qdc/2006/01/06/dc.xsd :
+
+
+ DCMES 1.1 XML Schema
+ XML Schema for http://purl.org/dc/elements/1.1/ namespace
+
+ Created 2003-04-02
+
+ Created by
+
+ Tim Cole (t-cole3@uiuc.edu)
+ Tom Habing (thabing@uiuc.edu)
+ Jane Hunter (jane@dstc.edu.au)
+ Pete Johnston (p.johnston@ukoln.ac.uk),
+ Carl Lagoze (lagoze@cs.cornell.edu)
+
+ This schema declares XML elements for the 15 DC elements from the
+ http://purl.org/dc/elements/1.1/ namespace.
+
+ It defines a complexType SimpleLiteral which permits mixed content
+ and makes the xml:lang attribute available. It disallows child elements by
+ use of minOcccurs/maxOccurs.
+
+ However, this complexType does permit the derivation of other complexTypes
+ which would permit child elements.
+
+ All elements are declared as substitutable for the abstract element any,
+ which means that the default type for all elements is dc:SimpleLiteral.
+
+ </xs:documentation>
+
+ </xs:annotation>
+
+
+ <xs:import namespace="http://www.w3.org/XML/1998/namespace"
+ schemaLocation="http://www.w3.org/2001/xml.xsd">
+
+ </xs:import>
+
+
+ <xs:element name="any" type="xs:string" abstract="true"/>
+
+ <xs:element name="title" substitutionGroup="any"/>
+ <xs:element name="creator" substitutionGroup="any"/>
+ <xs:element name="subject" substitutionGroup="any"/>
+ <xs:element name="description" substitutionGroup="any"/>
+ <xs:element name="publisher" substitutionGroup="any"/>
+
+ <xs:element name="contributor" substitutionGroup="any"/>
+ <xs:element name="date" type="xs:dateTime" />
+ <xs:element name="type" substitutionGroup="any"/>
+ <xs:element name="format" substitutionGroup="any"/>
+ <xs:element name="identifier" substitutionGroup="any"/>
+ <xs:element name="source" substitutionGroup="any"/>
+ <xs:element name="language" substitutionGroup="any"/>
+ <xs:element name="relation" substitutionGroup="any"/>
+ <xs:element name="coverage" substitutionGroup="any"/>
+
+ <xs:element name="rights" substitutionGroup="any"/>
+
+ <xs:group name="elementsGroup">
+ <xs:annotation>
+ <xs:documentation xml:lang="en">
+ This group is included as a convenience for schema authors
+ who need to refer to all the elements in the
+ http://purl.org/dc/elements/1.1/ namespace.
+ </xs:documentation>
+ </xs:annotation>
+
+ <xs:sequence>
+
+ <xs:choice minOccurs="0" maxOccurs="unbounded">
+ <xs:element ref="any"/>
+ </xs:choice>
+ </xs:sequence>
+ </xs:group>
+
+ <xs:complexType name="elementContainer">
+ <xs:annotation>
+ <xs:documentation xml:lang="en">
+
+ This complexType is included as a convenience for schema authors who need to define a root
+ or container element for all of the DC elements.
+ </xs:documentation>
+ </xs:annotation>
+
+ <xs:choice>
+ <xs:group ref="elementsGroup"/>
+ </xs:choice>
+ </xs:complexType>
+
+
+</xs:schema>
+
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/xsd/dcterms.xsd b/taverna-workbench-perspective-biocatalogue/src/main/xsd/dcterms.xsd
new file mode 100644
index 0000000..205bf48
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/xsd/dcterms.xsd
@@ -0,0 +1,137 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ targetNamespace="http://purl.org/dc/terms/"
+ xmlns="http://purl.org/dc/terms/"
+ elementFormDefault="qualified"
+ attributeFormDefault="unqualified">
+
+ <xs:annotation>
+ <xs:documentation xml:lang="en">
+ Simplified XML Schema for http://purl.org/dc/terms/
+
+ Created 2007-06-28
+
+ Created by
+
+ Stian Soiland (ssoiland@cs.man.ac.uk)
+
+ This simplification removes SimpleLiteral references
+ so that it can be used with the simplified dc.xsd.
+ This makes the schema more usable for tools like
+ XMLBeans.
+
+
+ Based on
+ http://dublincore.org/schemas/xmls/qdc/2006/01/06/dcterms.xsd :
+
+
+ DCterms XML Schema
+ XML Schema for http://purl.org/dc/terms/ namespace
+
+ Created 2006-01-06
+
+ Created by
+
+ Tim Cole (t-cole3@uiuc.edu)
+ Tom Habing (thabing@uiuc.edu)
+ Jane Hunter (jane@dstc.edu.au)
+ Pete Johnston (p.johnston@ukoln.ac.uk),
+ Carl Lagoze (lagoze@cs.cornell.edu)
+
+ This schema declares XML elements for the DC elements and
+ DC element refinements from the http://purl.org/dc/terms/ namespace.
+
+ It reuses the complexType dc:SimpleLiteral, imported from the dc.xsd
+ schema, which permits simple element content, and makes the xml:lang
+ attribute available.
+
+ This complexType permits the derivation of other complexTypes
+ which would permit child elements.
+
+ DC elements are declared as substitutable for the abstract element dc:any, and
+ DC element refinements are defined as substitutable for the base elements
+ which they refine.
+
+ This means that the default type for all XML elements (i.e. all DC elements and
+ element refinements) is dc:SimpleLiteral.
+
+ Encoding schemes are defined as complexTypes which are restrictions
+ of the dc:SimpleLiteral complexType. These complexTypes restrict
+ values to an appropriates syntax or format using data typing,
+ regular expressions, or enumerated lists.
+
+ In order to specify one of these encodings an xsi:type attribute must
+ be used in the instance document.
+
+ Also, note that one shortcoming of this approach is that any type can be
+ applied to any of the elements or refinements. There is no convenient way
+ to restrict types to specific elements using this approach.
+
+ </xs:documentation>
+
+ </xs:annotation>
+
+
+ <xs:import namespace="http://www.w3.org/XML/1998/namespace"
+ schemaLocation="http://www.w3.org/2001/xml.xsd">
+
+ </xs:import>
+
+ <xs:import namespace="http://purl.org/dc/elements/1.1/"
+ schemaLocation="dc.xsd"/>
+
+ <xs:element name="alternative" substitutionGroup="dc:title"/>
+
+ <xs:element name="tableOfContents" substitutionGroup="dc:description"/>
+ <xs:element name="abstract" substitutionGroup="dc:description"/>
+
+ <xs:element name="created" substitutionGroup="dc:date"/>
+ <xs:element name="valid" substitutionGroup="dc:date"/>
+
+ <xs:element name="available" substitutionGroup="dc:date"/>
+ <xs:element name="issued" substitutionGroup="dc:date"/>
+ <xs:element name="modified" substitutionGroup="dc:date"/>
+ <xs:element name="dateAccepted" substitutionGroup="dc:date"/>
+ <xs:element name="dateCopyrighted" substitutionGroup="dc:date"/>
+ <xs:element name="dateSubmitted" substitutionGroup="dc:date"/>
+
+ <xs:element name="extent" substitutionGroup="dc:format"/>
+ <xs:element name="medium" substitutionGroup="dc:format"/>
+
+ <xs:element name="isVersionOf" substitutionGroup="dc:relation"/>
+ <xs:element name="hasVersion" substitutionGroup="dc:relation"/>
+ <xs:element name="isReplacedBy" substitutionGroup="dc:relation"/>
+ <xs:element name="replaces" substitutionGroup="dc:relation"/>
+ <xs:element name="isRequiredBy" substitutionGroup="dc:relation"/>
+ <xs:element name="requires" substitutionGroup="dc:relation"/>
+ <xs:element name="isPartOf" substitutionGroup="dc:relation"/>
+ <xs:element name="hasPart" substitutionGroup="dc:relation"/>
+
+ <xs:element name="isReferencedBy" substitutionGroup="dc:relation"/>
+ <xs:element name="references" substitutionGroup="dc:relation"/>
+ <xs:element name="isFormatOf" substitutionGroup="dc:relation"/>
+ <xs:element name="hasFormat" substitutionGroup="dc:relation"/>
+ <xs:element name="conformsTo" substitutionGroup="dc:relation"/>
+
+ <xs:element name="spatial" substitutionGroup="dc:coverage"/>
+ <xs:element name="temporal" substitutionGroup="dc:coverage"/>
+
+ <xs:element name="audience" substitutionGroup="dc:any"/>
+
+ <xs:element name="accrualMethod" substitutionGroup="dc:any"/>
+ <xs:element name="accrualPeriodicity" substitutionGroup="dc:any"/>
+ <xs:element name="accrualPolicy" substitutionGroup="dc:any"/>
+ <xs:element name="instructionalMethod" substitutionGroup="dc:any"/>
+ <xs:element name="provenance" substitutionGroup="dc:any"/>
+ <xs:element name="rightsHolder" substitutionGroup="dc:any"/>
+
+ <xs:element name="mediator" substitutionGroup="audience"/>
+ <xs:element name="educationLevel" substitutionGroup="audience"/>
+
+ <xs:element name="accessRights" substitutionGroup="dc:rights"/>
+ <xs:element name="license" substitutionGroup="dc:rights"/>
+
+ <xs:element name="bibliographicCitation" substitutionGroup="dc:identifier"/>
+
+</xs:schema>
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/xsd/schema-v1.xsd b/taverna-workbench-perspective-biocatalogue/src/main/xsd/schema-v1.xsd
new file mode 100644
index 0000000..6e57dd1
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/xsd/schema-v1.xsd
@@ -0,0 +1,3557 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xsd:schema targetNamespace="http://www.biocatalogue.org/2009/xml/rest"
+ xml:lang="en" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="http://www.biocatalogue.org/2009/xml/rest"
+ elementFormDefault="qualified" xmlns:xlink="http://www.w3.org/1999/xlink"
+ xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/">
+
+ <xsd:import namespace="http://purl.org/dc/elements/1.1/"
+ schemaLocation="dc.xsd" />
+ <xsd:import namespace="http://purl.org/dc/terms/"
+ schemaLocation="dcterms.xsd" />
+ <xsd:import namespace="http://www.w3.org/1999/xlink"
+ schemaLocation="xlink.xsd" />
+
+ <xsd:simpleType name="SearchScopeUrlValue">
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="all"></xsd:enumeration>
+ <xsd:enumeration value="service_providers"></xsd:enumeration>
+
+ <xsd:enumeration value="services"></xsd:enumeration>
+ <xsd:enumeration value="users"></xsd:enumeration>
+ <xsd:enumeration value="registries"></xsd:enumeration>
+ <xsd:enumeration value="soap_operations"></xsd:enumeration>
+ <xsd:enumeration value="rest_methods"></xsd:enumeration>
+ </xsd:restriction>
+ </xsd:simpleType>
+
+ <xsd:element name="search" type="Search"></xsd:element>
+
+ <xsd:complexType name="Search">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" type="SearchParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="statistics" type="SearchStatistics"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="results" type="SearchResults"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" type="SearchRelatedLinks"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="SearchParameters">
+ <xsd:sequence>
+
+ <xsd:element name="query" type="SearchQueryParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="scope" type="SearchScopeParameter"
+ maxOccurs="unbounded" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="page" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="pageSize" maxOccurs="1" minOccurs="1"></xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="SearchStatistics">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics">
+ <xsd:sequence>
+ <xsd:element name="scopedResults" minOccurs="0"
+ maxOccurs="unbounded">
+ <xsd:complexType>
+
+ <xsd:simpleContent>
+ <xsd:extension base="xsd:nonNegativeInteger">
+ <xsd:attribute name="scope" type="SearchScopeName">
+ </xsd:attribute>
+ </xsd:extension>
+ </xsd:simpleContent>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:element name="biocatalogue" type="BioCatalogue" />
+
+ <xsd:complexType name="BioCatalogue">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+
+ <xsd:element name="documentation" maxOccurs="1"
+ minOccurs="1" type="ResourceLink">
+ </xsd:element>
+ <xsd:element name="collections" maxOccurs="1"
+ minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="agents"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="annotationAttributes"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="annotations"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="categories"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="registries"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="restMethods"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="restResources"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="restServices"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="search"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="serviceProviders"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="services"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="soapOperations"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="soapServices"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="tags"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="testResults"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="users"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="filters"
+ maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element
+ name="annotations" type="ResourceLink" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element
+ name="restMethods" type="ResourceLink" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="services"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element
+ name="soapOperations" type="ResourceLink" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+
+ </xsd:element>
+ </xsd:sequence>
+ <xsd:attribute name="version" type="xsd:string"
+ use="required">
+ </xsd:attribute>
+ <xsd:attribute name="apiVersion" type="xsd:string" use="required"></xsd:attribute>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="SearchRelatedLinks">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks">
+ <xsd:sequence>
+ <xsd:element name="searches" minOccurs="1" maxOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="scoped" type="ScopedSearch"
+ minOccurs="0" maxOccurs="unbounded">
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="CollectionCoreRelatedLinks">
+
+ <xsd:sequence>
+ <xsd:element name="previous" type="ResourceLink"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="next" type="ResourceLink" maxOccurs="1"
+ minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="ResourceLink">
+
+ <xsd:attribute ref="xlink:href" use="required"></xsd:attribute>
+ <xsd:attribute ref="xlink:title" use="optional"></xsd:attribute>
+ <xsd:attribute name="resourceType" type="ResourceType"
+ use="optional"></xsd:attribute>
+ <xsd:attribute name="resourceName" type="xsd:string"
+ use="optional">
+ </xsd:attribute>
+ </xsd:complexType>
+
+
+ <xsd:complexType name="ScopedSearch">
+ <xsd:complexContent>
+
+ <xsd:extension base="ResourceLink">
+ <xsd:attribute name="scope" type="SearchScopeName"></xsd:attribute>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:simpleType name="SearchScopeName">
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="All"></xsd:enumeration>
+
+ <xsd:enumeration value="Services"></xsd:enumeration>
+ <xsd:enumeration value="Service Providers"></xsd:enumeration>
+ <xsd:enumeration value="Users"></xsd:enumeration>
+ <xsd:enumeration value="Registries"></xsd:enumeration>
+ <xsd:enumeration value="SOAP Operations"></xsd:enumeration>
+ <xsd:enumeration value="REST Endpoints"></xsd:enumeration>
+ </xsd:restriction>
+ </xsd:simpleType>
+
+ <xsd:complexType name="SearchScopeParameter">
+ <xsd:simpleContent>
+ <xsd:extension base="SearchScopeName">
+ <xsd:attribute name="urlKey" type="xsd:string"></xsd:attribute>
+ <xsd:attribute name="urlValue" type="SearchScopeUrlValue"
+ use="required">
+ </xsd:attribute>
+ </xsd:extension>
+ </xsd:simpleContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="SearchResults">
+ <xsd:sequence>
+ <xsd:choice maxOccurs="unbounded" minOccurs="0">
+ <xsd:element name="service" type="Service"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="soapOperation" type="SoapOperation"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="serviceProvider"
+ type="ServiceProvider" maxOccurs="unbounded" minOccurs="0">
+
+ </xsd:element>
+ <xsd:element name="user" type="User"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="registry" type="Registry"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="restMethod" type="RestMethod"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:choice>
+
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:element name="service" type="Service"></xsd:element>
+
+ <xsd:complexType name="Service">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1"
+ minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="name" type="xsd:string"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ <xsd:element name="originalSubmitter"
+ type="ResourceLink" minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dc:description" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="serviceTechnologyTypes"
+ maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+
+ <xsd:sequence>
+ <xsd:element name="type"
+ type="ServiceTechnologyType" maxOccurs="unbounded"
+ minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="latestMonitoringStatus"
+ type="MonitoringStatus" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" minOccurs="1"
+ maxOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="archived" type="xsd:dateTime"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="summary" minOccurs="0"
+ maxOccurs="1" type="ServiceSummary">
+ </xsd:element>
+ <xsd:element name="deployments" minOccurs="0"
+ maxOccurs="1">
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+
+ <xsd:sequence>
+ <xsd:element
+ name="serviceDeployment" type="ServiceDeployment"
+ minOccurs="1" maxOccurs="unbounded">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="variants" minOccurs="0"
+ maxOccurs="1">
+
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:choice
+ maxOccurs="unbounded" minOccurs="1">
+ <xsd:element
+ name="soapService" type="SoapService" maxOccurs="unbounded"
+ minOccurs="0">
+ </xsd:element>
+ <xsd:element
+ name="restService" type="RestService" maxOccurs="unbounded"
+ minOccurs="0">
+ </xsd:element>
+
+ </xsd:choice>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="monitoring" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:complexContent>
+
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="tests"
+ maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element
+ name="serviceTest" type="ServiceTest"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="related"
+ type="ServiceRelatedLinks" minOccurs="0" maxOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="ServiceSummary">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="counts" minOccurs="1" maxOccurs="1">
+
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="deployments" type="xsd:positiveInteger"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ <xsd:element name="variants" type="xsd:positiveInteger"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ <xsd:element name="metadata" type="MetadataCount"
+ minOccurs="0" maxOccurs="unbounded">
+ </xsd:element>
+ <xsd:element name="favourites" type="xsd:nonNegativeInteger"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="views" type="xsd:nonNegativeInteger"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="alternativeName" minOccurs="0"
+ maxOccurs="unbounded" type="xsd:string">
+ </xsd:element>
+ <xsd:element name="category" minOccurs="0" maxOccurs="unbounded"
+ type="ResourceLinkWithString">
+
+ </xsd:element>
+ <xsd:element name="provider" minOccurs="1" maxOccurs="unbounded">
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="name" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="endpoint" minOccurs="1" maxOccurs="unbounded"
+ type="xsd:anyURI">
+ </xsd:element>
+ <xsd:element name="wsdl" minOccurs="0" maxOccurs="unbounded"
+ type="xsd:anyURI">
+ </xsd:element>
+ <xsd:element name="location" minOccurs="0" maxOccurs="unbounded"
+ type="Location">
+
+ </xsd:element>
+ <xsd:element name="documentationUrl" maxOccurs="unbounded"
+ minOccurs="0" type="xsd:string">
+ </xsd:element>
+ <xsd:element ref="dc:description" maxOccurs="unbounded"
+ minOccurs="0">
+ </xsd:element>
+ <xsd:element name="tag" minOccurs="0" maxOccurs="unbounded"
+ type="ResourceLinkWithString">
+ </xsd:element>
+ <xsd:element name="cost" maxOccurs="unbounded"
+ minOccurs="0" type="xsd:string">
+ </xsd:element>
+
+ <xsd:element name="license" type="xsd:string"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="usageCondition" maxOccurs="unbounded"
+ minOccurs="0" type="xsd:string">
+ </xsd:element>
+ <xsd:element name="contact" maxOccurs="unbounded"
+ minOccurs="0" type="xsd:string">
+ </xsd:element>
+ <xsd:element name="publication" maxOccurs="unbounded"
+ minOccurs="0" type="xsd:string">
+ </xsd:element>
+ <xsd:element name="citation" maxOccurs="unbounded"
+ minOccurs="0" type="xsd:string">
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:element name="serviceProvider" type="ServiceProvider"></xsd:element>
+
+ <xsd:complexType name="ServiceProvider">
+ <xsd:complexContent>
+
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="name" type="xsd:string" minOccurs="1"
+ maxOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dc:description" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="hostnames" maxOccurs="1" minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="hostname" type="xsd:string"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+
+ <xsd:element name="related" type="ServiceProviderRelatedLinks"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:element name="user" type="User"></xsd:element>
+
+ <xsd:complexType name="User">
+
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="name" type="xsd:string"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ <xsd:element name="affiliation" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="location" type="Location"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="publicEmail" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="joined" type="xsd:dateTime"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="savedSearches" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:complexContent>
+
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="savedSearch"
+ type="SavedSearch" maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+
+ <xsd:element name="related" type="UserRelatedLinks"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:element name="registry" type="Registry"></xsd:element>
+
+ <xsd:complexType name="Registry">
+
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="name" type="xsd:string" minOccurs="1"
+ maxOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dc:description" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="homepage" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" type="RegistryRelatedLinks"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+
+ </xsd:complexType>
+
+ <xsd:element name="services" type="Services"></xsd:element>
+
+ <xsd:complexType name="Services">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" type="ServicesParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="statistics" type="ServicesStatistics"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="results" type="ServicesResults"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" type="ServicesRelatedLinks"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+
+ </xsd:complexType>
+
+ <xsd:complexType name="ServicesParameters">
+ <xsd:sequence>
+ <xsd:element name="filters" maxOccurs="1" minOccurs="1"
+ type="FiltersParameters">
+
+ </xsd:element>
+ <xsd:element name="query" maxOccurs="1" minOccurs="1"
+ type="SearchQueryParameter">
+ </xsd:element>
+ <xsd:element ref="sortBy" maxOccurs="1" minOccurs="1"></xsd:element>
+
+ <xsd:element ref="sortOrder" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="page" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="pageSize" maxOccurs="1" minOccurs="1"></xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="FiltersParameters">
+ <xsd:sequence>
+ <xsd:element name="group" type="FilterGroupParameter"
+ minOccurs="0" maxOccurs="unbounded">
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="ServicesStatistics">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics">
+ </xsd:extension>
+ </xsd:complexContent>
+
+ </xsd:complexType>
+
+ <xsd:complexType name="ServicesResults">
+ <xsd:sequence>
+ <xsd:element name="service" type="Service" maxOccurs="unbounded"
+ minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="ServicesRelatedLinks">
+
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks">
+ <xsd:sequence>
+ <xsd:element name="filters" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="filtersOnCurrentResults" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="withSummaries" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="withDeployments" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="withVariants" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="withMonitoring" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="withAllSections" type="ResourceLink"
+ maxOccurs="1" minOccurs="1"></xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="Filters">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="group" type="FilterGroup" maxOccurs="unbounded"
+ minOccurs="0">
+ </xsd:element>
+
+ </xsd:sequence>
+ <xsd:attribute name="for" type="ResourceType" use="required"></xsd:attribute>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:element name="filters" type="Filters"></xsd:element>
+
+ <xsd:complexType name="FilterType">
+ <xsd:sequence>
+
+ <xsd:element name="filter" type="Filter" maxOccurs="unbounded"
+ minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ <xsd:attribute name="name" type="FilterTypeName" use="required">
+ </xsd:attribute>
+ <xsd:attribute name="urlKey" type="FilterTypeUrlKey"
+ use="required">
+ </xsd:attribute>
+ <xsd:attribute name="description" type="xsd:string" use="required"></xsd:attribute>
+ </xsd:complexType>
+
+ <xsd:simpleType name="FilterTypeName">
+ <xsd:restriction base="xsd:string">
+ </xsd:restriction>
+ </xsd:simpleType>
+
+ <xsd:simpleType name="FilterTypeUrlKey">
+ <xsd:restriction base="xsd:string">
+ </xsd:restriction>
+ </xsd:simpleType>
+
+ <xsd:complexType name="Filter">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="filter" type="Filter" maxOccurs="unbounded"
+ minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ <xsd:attribute name="urlValue" type="xsd:string" use="required">
+
+ </xsd:attribute>
+ <xsd:attribute name="name" type="xsd:string" use="required"></xsd:attribute>
+ <xsd:attribute name="count" type="xsd:nonNegativeInteger"
+ use="required">
+ </xsd:attribute>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="CollectionCoreStatistics">
+
+ <xsd:sequence>
+ <xsd:element name="pages" type="xsd:nonNegativeInteger"
+ maxOccurs="1" minOccurs="1">
+ <xsd:annotation>
+ <xsd:documentation>The total number of pages available for this
+ result set</xsd:documentation>
+ </xsd:annotation>
+ </xsd:element>
+ <xsd:element name="results" type="xsd:nonNegativeInteger"
+ maxOccurs="1" minOccurs="1">
+ <xsd:annotation>
+
+ <xsd:documentation>The total number of results available for this
+ result set</xsd:documentation>
+ </xsd:annotation>
+ </xsd:element>
+ <xsd:element name="total" type="xsd:nonNegativeInteger"
+ maxOccurs="1" minOccurs="0">
+ <xsd:annotation>
+ <xsd:documentation>When present, this gives the total number of
+ resources of the particular resource type that the result set is
+ referring to. Eg: for /services, this would be the total number of
+ services available regardless of how many are in the result set
+ (which may have been filtered down).</xsd:documentation>
+ </xsd:annotation>
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+
+
+
+ <xsd:simpleType name="SortBy">
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="created"></xsd:enumeration>
+ <xsd:enumeration value="activated"></xsd:enumeration>
+ <xsd:enumeration value="name"></xsd:enumeration>
+
+ <xsd:enumeration value="modified"></xsd:enumeration>
+ </xsd:restriction>
+ </xsd:simpleType>
+
+ <xsd:simpleType name="SortOrder">
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="asc"></xsd:enumeration>
+ <xsd:enumeration value="desc"></xsd:enumeration>
+ </xsd:restriction>
+
+ </xsd:simpleType>
+
+ <xsd:element name="tags" type="Tags"></xsd:element>
+
+ <xsd:complexType name="Tags">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" type="TagsParameters"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="statistics" type="TagsStatistics"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ <xsd:element name="results" type="TagsResults"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" type="TagsRelated"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+
+ </xsd:complexType>
+
+ <xsd:complexType name="TagsParameters">
+ <xsd:sequence>
+ <xsd:element name="sort" maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:simpleContent>
+ <xsd:extension base="xsd:string">
+ <xsd:attribute name="urlKey" use="required">
+
+ <xsd:simpleType>
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="sort">
+ </xsd:enumeration>
+ </xsd:restriction>
+ </xsd:simpleType>
+ </xsd:attribute>
+ <xsd:attribute name="urlValue">
+ <xsd:simpleType>
+
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="counts">
+ </xsd:enumeration>
+ <xsd:enumeration value="name">
+ </xsd:enumeration>
+ </xsd:restriction>
+ </xsd:simpleType>
+ </xsd:attribute>
+ </xsd:extension>
+
+ </xsd:simpleContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element ref="page" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="pageSize" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element name="limit" type="xsd:nonNegativeInteger"
+ maxOccurs="1" minOccurs="1" nillable="true"></xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="TagsStatistics">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics">
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="TagsResults">
+ <xsd:sequence>
+
+ <xsd:element name="tag" type="Tag" minOccurs="0"
+ maxOccurs="unbounded">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="TagsRelated">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks">
+ </xsd:extension>
+
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="Tag">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="name" type="xsd:string" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="displayName" type="xsd:string"
+ maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element name="totalItemsCount" type="xsd:nonNegativeInteger"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" type="TagRelatedLinks"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:simpleType name="SubmitterType">
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="User"></xsd:enumeration>
+ <xsd:enumeration value="Registry"></xsd:enumeration>
+ </xsd:restriction>
+ </xsd:simpleType>
+
+ <xsd:simpleType name="AnnotationSourceType">
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="User"></xsd:enumeration>
+ <xsd:enumeration value="ServiceProvider"></xsd:enumeration>
+ <xsd:enumeration value="Registry"></xsd:enumeration>
+ </xsd:restriction>
+ </xsd:simpleType>
+
+
+ <xsd:complexType name="ServiceDeployment">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="endpoint" type="xsd:anyURI"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ <xsd:element name="serviceProvider" type="ServiceProvider"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ <xsd:element name="location" minOccurs="1" maxOccurs="1"
+ type="Location">
+
+ </xsd:element>
+ <xsd:element name="submitter" type="ResourceLink"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="providedVariant" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:choice>
+ <xsd:element name="soapService" type="SoapService"
+ maxOccurs="1" minOccurs="0">
+
+ </xsd:element>
+ <xsd:element name="restService" type="RestService"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ </xsd:choice>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="ancestors" maxOccurs="1" minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+
+ <xsd:element name="service"
+ type="Service" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="related" maxOccurs="1" minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="annotations" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+
+ <xsd:simpleType name="ServiceTechnologyType">
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="SOAP"></xsd:enumeration>
+ <xsd:enumeration value="REST"></xsd:enumeration>
+ <xsd:enumeration value="Soaplab"></xsd:enumeration>
+ </xsd:restriction>
+ </xsd:simpleType>
+
+ <xsd:complexType name="Annotation">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="annotatable" type="ResourceLink"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="source" type="ResourceLink"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="version" type="xsd:positiveInteger"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="annotationAttribute" type="AnnotationAttribute"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ <xsd:element name="value" minOccurs="1" maxOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="resource" type="ResourceLink"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="type" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="content" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+
+ <xsd:element ref="dcterms:created" minOccurs="1"
+ maxOccurs="1">
+ </xsd:element>
+
+ <xsd:element ref="dcterms:modified" minOccurs="0"
+ maxOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" maxOccurs="1" minOccurs="0">
+ <xsd:complexType></xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+
+ </xsd:extension>
+ </xsd:complexContent>
+
+ </xsd:complexType>
+
+ <xsd:complexType name="AnnotationAttribute">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="name" type="xsd:string" maxOccurs="1"
+ minOccurs="1">
+
+ </xsd:element>
+ <xsd:element ref="dc:identifier" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" maxOccurs="1" minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="annotations" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+
+
+
+ <xsd:complexType name="ServiceRelatedLinks">
+ <xsd:sequence>
+ <xsd:element name="withSummary" type="ResourceLink"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ <xsd:element name="withMonitoring" type="ResourceLink"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ <xsd:element name="withAllSections" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="summary" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="deployments" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="variants" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="monitoring" type="ResourceLink"
+ maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element name="annotations" type="ResourceLink"
+ minOccurs="1" maxOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+
+ </xsd:complexType>
+
+ <xsd:simpleType name="MetadataBy">
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="all"></xsd:enumeration>
+ <xsd:enumeration value="users"></xsd:enumeration>
+ <xsd:enumeration value="providers"></xsd:enumeration>
+ <xsd:enumeration value="registries"></xsd:enumeration>
+ </xsd:restriction>
+
+ </xsd:simpleType>
+
+ <xsd:complexType name="MetadataCount">
+ <xsd:simpleContent>
+ <xsd:extension base="xsd:nonNegativeInteger">
+ <xsd:attribute name="by" type="MetadataBy"></xsd:attribute>
+ </xsd:extension>
+ </xsd:simpleContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="SearchQueryParameter">
+ <xsd:simpleContent>
+ <xsd:extension base="xsd:string">
+ <xsd:attribute name="urlKey" type="xsd:string" use="required">
+ </xsd:attribute>
+ </xsd:extension>
+ </xsd:simpleContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="PageParameter">
+ <xsd:simpleContent>
+ <xsd:extension base="xsd:nonNegativeInteger">
+ <xsd:attribute name="urlKey" use="required">
+ <xsd:simpleType>
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="page"></xsd:enumeration>
+ </xsd:restriction>
+
+ </xsd:simpleType>
+ </xsd:attribute>
+ </xsd:extension>
+ </xsd:simpleContent>
+ </xsd:complexType>
+
+
+
+
+ <xsd:complexType name="SortByParameter">
+ <xsd:simpleContent>
+
+ <xsd:extension base="xsd:string">
+ <xsd:attribute name="urlKey" use="required">
+ <xsd:simpleType>
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="sort_by"></xsd:enumeration>
+ </xsd:restriction>
+ </xsd:simpleType>
+ </xsd:attribute>
+ <xsd:attribute name="urlValue" type="SortBy" use="required">
+
+ </xsd:attribute>
+ </xsd:extension>
+ </xsd:simpleContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="SortOrderParameter">
+ <xsd:simpleContent>
+ <xsd:extension base="xsd:string">
+ <xsd:attribute name="urlKey" use="required">
+
+ <xsd:simpleType>
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="sort_order"></xsd:enumeration>
+ </xsd:restriction>
+ </xsd:simpleType>
+ </xsd:attribute>
+ <xsd:attribute name="urlValue" type="SortOrder" use="required"></xsd:attribute>
+ </xsd:extension>
+ </xsd:simpleContent>
+
+ </xsd:complexType>
+
+ <xsd:element name="categories" type="Categories"></xsd:element>
+
+ <xsd:element name="category" type="Category"></xsd:element>
+
+ <xsd:complexType name="Category">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+
+ <xsd:element ref="dc:title" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element name="name" type="xsd:string" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="totalItemsCount" type="xsd:nonNegativeInteger"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="broader" maxOccurs="1" minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="category" type="Category"
+ maxOccurs="unbounded" minOccurs="0">
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="narrower" maxOccurs="1" minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="category" type="Category"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="related" maxOccurs="1" minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="services" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="Categories">
+ <xsd:complexContent>
+
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" type="CategoriesParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="statistics" type="CategoriesStatistics"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="results" type="CategoriesResults"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" type="CategoriesRelatedLinks"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="CategoriesParameters">
+ <xsd:sequence>
+ <xsd:element name="rootsOnly" maxOccurs="1" minOccurs="1">
+
+ <xsd:complexType>
+ <xsd:simpleContent>
+ <xsd:extension base="xsd:boolean">
+ <xsd:attribute name="urlKey" type="xsd:string" use="required">
+ </xsd:attribute>
+ </xsd:extension>
+ </xsd:simpleContent>
+ </xsd:complexType>
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="CategoriesStatistics">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics">
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="CategoriesResults">
+ <xsd:sequence>
+ <xsd:element name="category" type="Category" maxOccurs="unbounded"
+ minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="CategoriesRelatedLinks">
+ <xsd:sequence>
+
+ <xsd:element name="serviceFilters" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="ResourceLinkWithString">
+ <xsd:simpleContent>
+ <xsd:extension base="xsd:string">
+ <xsd:attribute ref="xlink:href" use="required"></xsd:attribute>
+
+ <xsd:attribute ref="xlink:title" use="optional"></xsd:attribute>
+ <xsd:attribute name="resourceType" type="ResourceType"
+ use="optional"></xsd:attribute>
+ </xsd:extension>
+ </xsd:simpleContent>
+ </xsd:complexType>
+
+
+ <xsd:complexType name="MonitoringStatus">
+ <xsd:sequence>
+ <xsd:element name="label" maxOccurs="1" minOccurs="1"
+ type="MonitoringStatusLabel">
+
+ </xsd:element>
+ <xsd:element name="message" type="xsd:string" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="symbol" type="ResourceLink" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="smallSymbol" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="lastChecked" type="xsd:dateTime"
+ maxOccurs="1" minOccurs="1" nillable="true"></xsd:element>
+ </xsd:sequence>
+
+ </xsd:complexType>
+
+ <xsd:complexType name="TagRelatedLinks">
+ <xsd:sequence>
+ <xsd:element name="services" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="soapOperations" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="restMethods" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:element name="tag" type="Tag"></xsd:element>
+
+ <xsd:complexType name="PageSizeParameter">
+ <xsd:simpleContent>
+ <xsd:extension base="xsd:nonNegativeInteger">
+ <xsd:attribute name="urlKey" use="required">
+
+ <xsd:simpleType>
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="per_page"></xsd:enumeration>
+ </xsd:restriction>
+ </xsd:simpleType>
+ </xsd:attribute>
+ </xsd:extension>
+ </xsd:simpleContent>
+ </xsd:complexType>
+
+ <xsd:element name="serviceProviders" type="ServiceProviders"></xsd:element>
+
+ <xsd:complexType name="ServiceProviders">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" type="ServiceProvidersParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="statistics" type="ServiceProvidersStatistics"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="results" type="ServiceProvidersResults"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" type="ServiceProvidersRelatedLinks"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="ServiceProviderRelatedLinks">
+ <xsd:sequence>
+ <xsd:element name="annotations" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="annotationsBy" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="services" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="ServiceProvidersParameters">
+ <xsd:sequence>
+ <xsd:element name="filters" type="FiltersParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="query" type="SearchQueryParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element ref="sortBy" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="sortOrder" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="page" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="pageSize" maxOccurs="1" minOccurs="1"></xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="ServiceProvidersStatistics">
+ <xsd:complexContent>
+
+ <xsd:extension base="CollectionCoreStatistics">
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="ServiceProvidersResults">
+ <xsd:sequence>
+ <xsd:element name="serviceProvider" type="ServiceProvider"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="ServiceProvidersRelatedLinks">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks">
+ <xsd:sequence>
+ <xsd:element name="filters" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="filtersOnCurrentResults"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:element name="sortBy" type="SortByParameter"></xsd:element>
+
+ <xsd:element name="sortOrder" type="SortOrderParameter"></xsd:element>
+
+ <xsd:element name="page" type="PageParameter"></xsd:element>
+
+ <xsd:element name="pageSize" type="PageSizeParameter"></xsd:element>
+
+ <xsd:element name="soapService" type="SoapService"></xsd:element>
+
+ <xsd:complexType name="SoapService">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+
+ <xsd:element ref="dc:title" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="name" type="xsd:string" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="wsdlLocation" type="xsd:anyURI"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="submitter" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dc:description" maxOccurs="1"
+ minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="documentationUrl" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="deployments" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+
+ <xsd:sequence>
+ <xsd:element name="serviceDeployment" type="ServiceDeployment"
+ maxOccurs="unbounded" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="operations" maxOccurs="1" minOccurs="0">
+
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="soapOperation" type="SoapOperation"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="ancestors" maxOccurs="1" minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="service"
+ type="Service" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ </xsd:element>
+ <xsd:element name="related" maxOccurs="1" minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="deployments" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="operations" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="annotations" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+
+ <xsd:element name="restService" type="RestService"></xsd:element>
+
+ <xsd:complexType name="RestService">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="name" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="submitter" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dc:description" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="documentationUrl"
+ type="xsd:string" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="deployments" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element
+ name="serviceDeployment" type="ServiceDeployment"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="resources" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+
+ <xsd:element name="restResource"
+ type="RestResource" maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="methods" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="restMethod"
+ type="RestMethod" maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ </xsd:element>
+ <xsd:element name="ancestors" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="service"
+ type="Service" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+
+ <xsd:element name="related" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="deployments"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="resources"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="methods"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="annotations"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+
+ </xsd:complexType>
+
+
+ <xsd:element name="serviceDeployment" type="ServiceDeployment"></xsd:element>
+
+
+ <xsd:complexType name="FilterTypeParameter">
+ <xsd:sequence>
+ <xsd:element name="filter" type="FilterParameter"
+ maxOccurs="unbounded" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+
+ <xsd:attribute name="name" type="FilterTypeName" use="required">
+ </xsd:attribute>
+ <xsd:attribute name="urlKey" type="FilterTypeUrlKey"
+ use="required">
+ </xsd:attribute>
+ <xsd:attribute name="description" type="xsd:string" use="required"></xsd:attribute>
+ </xsd:complexType>
+
+ <xsd:complexType name="FilterParameter">
+ <xsd:simpleContent>
+
+ <xsd:extension base="xsd:string">
+ <xsd:attribute name="urlValue" type="xsd:string" use="required">
+ </xsd:attribute>
+ </xsd:extension>
+ </xsd:simpleContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="Location">
+ <xsd:sequence>
+
+ <xsd:element name="city" type="xsd:string" maxOccurs="1"
+ minOccurs="0">
+ </xsd:element>
+ <xsd:element name="country" type="xsd:string" maxOccurs="1"
+ minOccurs="0">
+ </xsd:element>
+ <xsd:element name="iso3166CountryCode" type="xsd:string"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="flag" type="ResourceLink" maxOccurs="1"
+ minOccurs="0"></xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:element name="users" type="Users"></xsd:element>
+
+ <xsd:complexType name="Users">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" type="UsersParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="statistics" type="UsersStatistics"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="results" type="UsersResults"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" type="UsersRelatedLinks"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="UsersParameters">
+ <xsd:sequence>
+ <xsd:element name="filters" type="FiltersParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="query" type="SearchQueryParameter" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="sortBy" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="sortOrder" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="page" maxOccurs="1" minOccurs="1"></xsd:element>
+
+ <xsd:element ref="pageSize" maxOccurs="1" minOccurs="1"></xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="UsersStatistics">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics">
+ </xsd:extension>
+ </xsd:complexContent>
+
+ </xsd:complexType>
+
+ <xsd:complexType name="UsersResults">
+ <xsd:sequence>
+ <xsd:element name="user" type="User" maxOccurs="unbounded"
+ minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="UsersRelatedLinks">
+
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks">
+ <xsd:sequence>
+ <xsd:element name="filters" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="filtersOnCurrentResults"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="UserRelatedLinks">
+ <xsd:sequence>
+ <xsd:element name="annotationsBy" type="ResourceLink"
+ maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element name="services" type="ResourceLink"
+ maxOccurs="1" minOccurs="1"></xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:element name="registries" type="Registries"></xsd:element>
+
+ <xsd:complexType name="Registries">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" type="RegistriesParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="statistics" type="RegistriesStatistics"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="results" type="RegistriesResults"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" type="RegistriesRelatedLinks"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="RegistriesParameters">
+ <xsd:sequence>
+ <xsd:element ref="sortBy" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="sortOrder" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="page" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="pageSize" maxOccurs="1" minOccurs="1"></xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="RegistriesStatistics">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics">
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="RegistriesResults">
+ <xsd:sequence>
+
+ <xsd:element name="registry" type="Registry" maxOccurs="unbounded"
+ minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="RegistriesRelatedLinks">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks"></xsd:extension>
+ </xsd:complexContent>
+
+ </xsd:complexType>
+
+ <xsd:complexType name="RegistryRelatedLinks">
+ <xsd:sequence>
+ <xsd:element name="annotationsBy" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="services" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+
+ </xsd:complexType>
+
+ <xsd:simpleType name="MonitoringStatusLabel">
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="PASSED"></xsd:enumeration>
+ <xsd:enumeration value="WARNING"></xsd:enumeration>
+ <xsd:enumeration value="FAILED"></xsd:enumeration>
+ <xsd:enumeration value="UNCHECKED"></xsd:enumeration>
+ </xsd:restriction>
+
+ </xsd:simpleType>
+
+
+ <xsd:complexType name="SoapOperation">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="name" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element ref="dc:description" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="parameterOrder" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="archived" type="xsd:dateTime"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+
+ <xsd:element name="inputs" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="soapInput"
+ type="SoapInput" maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="outputs" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="soapOutput"
+ type="SoapOutput" maxOccurs="unbounded" minOccurs="0">
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="ancestors" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+
+ <xsd:element name="service"
+ type="Service" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="soapService"
+ type="SoapService" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="related" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+
+ <xsd:sequence>
+ <xsd:element name="inputs"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="outputs"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="annotations"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="annotationsOnAll"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:element name="soapOperation" type="SoapOperation"></xsd:element>
+
+ <xsd:element name="soapInput" type="SoapInput"></xsd:element>
+
+ <xsd:complexType name="SoapInput">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="name" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element ref="dc:description" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="computationalType"
+ type="xsd:string" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="computationalTypeDetails"
+ type="xsd:string" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="archived" type="xsd:dateTime"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="ancestors" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="service"
+ type="Service" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="soapService"
+ type="SoapService" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="soapOperation"
+ type="SoapOperation" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="related" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="annotations"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:element name="soapOutput" type="SoapOutput"></xsd:element>
+
+ <xsd:complexType name="SoapOutput">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="name" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element ref="dc:description" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="computationalType"
+ type="xsd:string" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="computationalTypeDetails"
+ type="xsd:string" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="archived" type="xsd:dateTime"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="ancestors" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="service"
+ type="Service" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="soapService"
+ type="SoapService" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="soapOperation"
+ type="SoapOperation" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="related" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="annotations"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:simpleType name="ResourceType">
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="Annotation"></xsd:enumeration>
+ <xsd:enumeration value="AnnotationAttribute"></xsd:enumeration>
+ <xsd:enumeration value="Annotations"></xsd:enumeration>
+ <xsd:enumeration value="BioCatalogue"></xsd:enumeration>
+ <xsd:enumeration value="Categories"></xsd:enumeration>
+ <xsd:enumeration value="Category"></xsd:enumeration>
+
+ <xsd:enumeration value="Filters"></xsd:enumeration>
+ <xsd:enumeration value="Registries"></xsd:enumeration>
+ <xsd:enumeration value="Registry"></xsd:enumeration>
+ <xsd:enumeration value="RestService"></xsd:enumeration>
+ <xsd:enumeration value="Search"></xsd:enumeration>
+ <xsd:enumeration value="Service"></xsd:enumeration>
+ <xsd:enumeration value="ServiceDeployment"></xsd:enumeration>
+ <xsd:enumeration value="ServiceProvider"></xsd:enumeration>
+ <xsd:enumeration value="ServiceProviders"></xsd:enumeration>
+
+ <xsd:enumeration value="Services"></xsd:enumeration>
+ <xsd:enumeration value="SoapInput"></xsd:enumeration>
+ <xsd:enumeration value="SoapOperation"></xsd:enumeration>
+ <xsd:enumeration value="SoapOutput"></xsd:enumeration>
+ <xsd:enumeration value="SoapService"></xsd:enumeration>
+ <xsd:enumeration value="Tag"></xsd:enumeration>
+ <xsd:enumeration value="Tags"></xsd:enumeration>
+ <xsd:enumeration value="Tags"></xsd:enumeration>
+ <xsd:enumeration value="User"></xsd:enumeration>
+
+ <xsd:enumeration value="Users"></xsd:enumeration>
+ <xsd:enumeration value="Annotations"></xsd:enumeration>
+ <xsd:enumeration value="AnnotationAttributes"></xsd:enumeration>
+ <xsd:enumeration value="ServiceTest"></xsd:enumeration>
+ <xsd:enumeration value="TestResult"></xsd:enumeration>
+ <xsd:enumeration value="TestResults"></xsd:enumeration>
+ <xsd:enumeration value="UrlMonitor"></xsd:enumeration>
+ <xsd:enumeration value="TestScript"></xsd:enumeration>
+ <xsd:enumeration value="Errors"></xsd:enumeration>
+
+ <xsd:enumeration value="SearchByData"></xsd:enumeration>
+ <xsd:enumeration value="SoapOperations"></xsd:enumeration>
+ <xsd:enumeration value="Agent"></xsd:enumeration>
+ <xsd:enumeration value="Agents"></xsd:enumeration>
+ <xsd:enumeration value="RestMethod"></xsd:enumeration>
+ <xsd:enumeration value="RestParameter"></xsd:enumeration>
+ <xsd:enumeration value="RestRepresentation"></xsd:enumeration>
+ <xsd:enumeration value="RestMethods"></xsd:enumeration>
+ <xsd:enumeration value="SoapServices"></xsd:enumeration>
+
+ <xsd:enumeration value="RestServices"></xsd:enumeration>
+ <xsd:enumeration value="RestResources"></xsd:enumeration>
+ <xsd:enumeration value="RestResource"></xsd:enumeration>
+ <xsd:enumeration value="SavedSearch"></xsd:enumeration>
+ <xsd:enumeration value="WsdlLocations"></xsd:enumeration>
+ </xsd:restriction>
+ </xsd:simpleType>
+
+ <xsd:element name="annotationAttribute" type="AnnotationAttribute">
+
+ </xsd:element>
+
+ <xsd:element name="annotationAttributes" type="AnnotationAttributes">
+ </xsd:element>
+
+ <xsd:complexType name="AnnotationAttributes">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" type="AnnotationAttributesParameters"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="statistics" type="AnnotationAttributesStatistics"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="results" type="AnnotationAttributesResults"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" type="AnnotationAttributesRelatedLinks"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="AnnotationAttributesParameters">
+ <xsd:sequence>
+ <xsd:element ref="page" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="pageSize" maxOccurs="1" minOccurs="1"></xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="AnnotationAttributesStatistics">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics"></xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="AnnotationAttributesResults">
+ <xsd:sequence>
+ <xsd:element name="annotationAttribute" type="AnnotationAttribute"
+ maxOccurs="unbounded" minOccurs="0">
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="AnnotationAttributesRelatedLinks">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks"></xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:element name="annotations" type="Annotations"></xsd:element>
+
+ <xsd:complexType name="Annotations">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" type="AnnotationsParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="statistics" type="AnnotationsStatistics"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="results" type="AnnotationsResults"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" type="AnnotationsRelatedLinks"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="AnnotationsParameters">
+ <xsd:sequence>
+ <xsd:element name="filters" type="FiltersParameters"
+ maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="sortBy" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="sortOrder" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="page" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="pageSize" maxOccurs="1" minOccurs="1"></xsd:element>
+ </xsd:sequence>
+
+ </xsd:complexType>
+
+ <xsd:complexType name="AnnotationsStatistics">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics"></xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="AnnotationsResults">
+ <xsd:sequence>
+
+ <xsd:element name="annotation" type="Annotation"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="AnnotationsRelatedLinks">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks">
+ <xsd:sequence>
+
+ <xsd:element name="filters" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="filtersOnCurrentResults" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:element name="annotation" type="Annotation"></xsd:element>
+
+ <xsd:element name="testResult" type="TestResult"></xsd:element>
+
+ <xsd:complexType name="TestResult">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="testAction" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="resultCode" type="xsd:integer"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="status" type="MonitoringStatus"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="ancestors" maxOccurs="1" minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+
+ <xsd:element name="service"
+ type="Service" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="serviceTest"
+ type="ServiceTest" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="related" maxOccurs="1" minOccurs="0">
+ <xsd:complexType></xsd:complexType>
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:element name="testResults" type="TestResults"></xsd:element>
+
+ <xsd:complexType name="TestResults">
+ <xsd:complexContent>
+
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element ref="sortBy" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="sortOrder" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+
+ <xsd:element ref="page" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="pageSize" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="serviceTest" type="ResourceLink"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+
+ <xsd:element name="statistics" maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics">
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="results" maxOccurs="1" minOccurs="1">
+
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="testResult" type="TestResult"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="related" maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks">
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+
+ </xsd:complexType>
+
+ <xsd:element name="serviceTest" type="ServiceTest"></xsd:element>
+
+ <xsd:complexType name="ServiceTest">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="testType" maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+
+ <xsd:choice>
+ <xsd:element name="urlMonitor" type="UrlMonitor"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="testScript" type="TestScript"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:choice>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="latestStatus" type="MonitoringStatus"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="ancestors" maxOccurs="1" minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="service"
+ type="Service" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="related" maxOccurs="1" minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="results" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="UrlMonitor">
+ <xsd:sequence>
+ <xsd:element name="url" type="xsd:anyURI" maxOccurs="1"
+ minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="resource" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="TestScript">
+ <xsd:sequence>
+ <xsd:element name="name" type="xsd:string" maxOccurs="1"
+ minOccurs="1">
+
+ </xsd:element>
+ <xsd:element ref="dc:description" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="contentType" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="programmingLanguage" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="executableFilename" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="download" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="submitter" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="activatedAt" type="xsd:dateTime"
+ nillable="true" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+
+ </xsd:complexType>
+
+ <xsd:element name="errors" type="Errors"></xsd:element>
+
+ <xsd:complexType name="Errors">
+ <xsd:sequence>
+ <xsd:element name="error" type="xsd:string" maxOccurs="unbounded"
+ minOccurs="1"></xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:element name="searchByData" type="SearchByData"></xsd:element>
+
+ <xsd:complexType name="SearchByData">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+
+ <xsd:element name="data" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="searchType" maxOccurs="1"
+ minOccurs="1">
+ <xsd:simpleType>
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="input">
+ </xsd:enumeration>
+ <xsd:enumeration value="output">
+ </xsd:enumeration>
+
+ </xsd:restriction>
+ </xsd:simpleType>
+ </xsd:element>
+ <xsd:element name="limit" type="xsd:nonNegativeInteger"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="statistics" maxOccurs="1" minOccurs="1">
+
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics">
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="results" maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+
+ <xsd:sequence>
+ <xsd:element name="resultItem" maxOccurs="unbounded"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="service" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="soapOperation" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="port" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="annotation" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+
+ <xsd:element name="related" maxOccurs="1" minOccurs="1">
+ <xsd:complexType></xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+
+
+ <xsd:element name="soapOperations" type="SoapOperations"></xsd:element>
+
+ <xsd:complexType name="SoapOperations">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+
+ <xsd:element name="filters" maxOccurs="1" minOccurs="1"
+ type="FiltersParameters">
+ </xsd:element>
+ <xsd:element name="query" type="SearchQueryParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="sortBy" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="sortOrder" maxOccurs="1"
+ minOccurs="1"></xsd:element>
+ <xsd:element ref="page" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="pageSize" maxOccurs="1" minOccurs="1"></xsd:element>
+ </xsd:sequence>
+
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="statistics" maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics">
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ </xsd:element>
+ <xsd:element name="results" maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="soapOperation" type="SoapOperation"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+
+ <xsd:element name="related" maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks">
+ <xsd:sequence>
+ <xsd:element name="filters" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="filtersOnCurrentResults" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="FilterGroup">
+ <xsd:sequence>
+ <xsd:element name="type" type="FilterType" maxOccurs="unbounded"
+ minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ <xsd:attribute name="name" type="xsd:string" use="required"></xsd:attribute>
+ </xsd:complexType>
+
+ <xsd:complexType name="FilterGroupParameter">
+
+ <xsd:sequence>
+ <xsd:element name="type" type="FilterTypeParameter"
+ maxOccurs="unbounded" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ <xsd:attribute name="name" type="xsd:string" use="required"></xsd:attribute>
+ </xsd:complexType>
+
+ <xsd:element name="agents" type="Agents"></xsd:element>
+
+ <xsd:complexType name="Agents">
+
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" type="AgentsParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="statistics" type="AgentsStatistics"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="results" type="AgentsResults"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="related" type="AgentsRelatedLinks"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="AgentsParameters">
+ <xsd:sequence>
+
+ <xsd:element ref="sortBy" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="sortOrder" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="page" maxOccurs="1" minOccurs="1"></xsd:element>
+ <xsd:element ref="pageSize" maxOccurs="1" minOccurs="1"></xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="AgentsStatistics">
+ <xsd:complexContent>
+
+ <xsd:extension base="CollectionCoreStatistics">
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="AgentsResults">
+ <xsd:sequence>
+ <xsd:element name="agent" type="Agent" maxOccurs="unbounded"
+ minOccurs="0">
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="AgentsRelatedLinks">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks"></xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="AgentRelatedLinks">
+
+ <xsd:sequence>
+ <xsd:element name="annotationsBy" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:element name="agent" type="Agent"></xsd:element>
+
+ <xsd:complexType name="Agent">
+ <xsd:complexContent>
+
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="name" type="xsd:string" minOccurs="1"
+ maxOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dc:description" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="related" type="AgentRelatedLinks"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+
+
+ <xsd:element name="soapServices" type="SoapServices"></xsd:element>
+
+ <xsd:complexType name="SoapServices">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" type="SoapServicesParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="statistics" type="SoapServicesStatistics"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="results" type="SoapServicesResults"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" type="SoapServicesRelatedLinks"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="SoapServicesParameters">
+ <xsd:sequence>
+ <xsd:element name="sortBy" type="SortByParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="sortOrder" type="SortOrderParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="page" type="PageParameter" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="pageSize" type="PageSizeParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="SoapServicesStatistics">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics"></xsd:extension>
+ </xsd:complexContent>
+
+ </xsd:complexType>
+
+ <xsd:complexType name="SoapServicesResults">
+ <xsd:sequence>
+ <xsd:element name="soapService" type="SoapService"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="SoapServicesRelatedLinks">
+
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks"></xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+
+ <xsd:element name="restServices" type="RestServices"></xsd:element>
+
+ <xsd:complexType name="RestServices">
+ <xsd:complexContent>
+
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" type="RestServicesParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="statistics" type="RestServicesStatistics"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="results" type="RestServicesResults"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" type="RestServicesRelatedLinks"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="RestServicesParameters">
+ <xsd:sequence>
+ <xsd:element name="sortBy" type="SortByParameter"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="sortOrder" type="SortOrderParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="page" type="PageParameter" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="pageSize" type="PageSizeParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="RestServicesStatistics">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics"></xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="RestServicesResults">
+ <xsd:sequence>
+ <xsd:element name="restService" type="RestService"
+ maxOccurs="unbounded" minOccurs="0">
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="RestServicesRelatedLinks">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks"></xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+
+ <xsd:element name="restResources" type="RestResources"></xsd:element>
+
+ <xsd:complexType name="RestResources">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" type="RestResourcesParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="statistics" type="RestResourcesStatistics"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="results" type="RestResourcesResults"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="related" type="RestResourcesRelatedLinks"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+
+ </xsd:complexType>
+
+ <xsd:complexType name="RestResourcesParameters">
+ <xsd:sequence>
+ <xsd:element name="sortBy" type="SortByParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="sortOrder" type="SortOrderParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="page" type="PageParameter" maxOccurs="1"
+ minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="pageSize" type="PageSizeParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="RestResourcesStatistics">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics"></xsd:extension>
+
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="RestResourcesResults">
+ <xsd:sequence>
+ <xsd:element name="restResource" type="RestResource"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="RestResourcesRelatedLinks">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks"></xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+
+ <xsd:element name="restMethods" type="RestMethods"></xsd:element>
+
+ <xsd:complexType name="RestMethods">
+
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters" type="RestMethodsParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="statistics" type="RestMethodsStatistics"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="results" type="RestMethodsResults"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="related" type="RestMethodsRelatedLinks"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="RestMethodsParameters">
+ <xsd:sequence>
+
+ <xsd:element name="filters" type="FiltersParameters"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="query" type="SearchQueryParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="sortBy" type="SortByParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="sortOrder" type="SortOrderParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="page" type="PageParameter" maxOccurs="1"
+ minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="pageSize" type="PageSizeParameter"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="RestMethodsStatistics">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreStatistics"></xsd:extension>
+
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="RestMethodsResults">
+ <xsd:sequence>
+ <xsd:element name="restMethod" type="RestMethod"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="RestMethodsRelatedLinks">
+ <xsd:complexContent>
+ <xsd:extension base="CollectionCoreRelatedLinks">
+ <xsd:sequence>
+ <xsd:element name="filters" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="filtersOnCurrentResults"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="RestResource">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+
+ <xsd:element ref="dc:title" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="path" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="submitter" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="archived" type="xsd:dateTime" maxOccurs="1" minOccurs="0"></xsd:element>
+
+ <xsd:element name="methods" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="restMethod"
+ type="RestMethod" maxOccurs="unbounded" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="ancestors" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="service"
+ type="Service" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="restService"
+ type="RestService" maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="related" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="restMethods"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="annotations"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+
+ </xsd:complexType>
+
+ <xsd:complexType name="RestMethod">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="name" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="endpointLabel" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="httpMethodType" type="HttpVerb"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="urlTemplate" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dc:description" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="documentationUrl"
+ type="xsd:string" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="submitter" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="archived" type="xsd:dateTime"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="inputs" maxOccurs="1"
+ minOccurs="0">
+
+ <xsd:complexType>
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters"
+ maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element
+ name="restParameter" type="RestParameter"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element
+ name="representations" maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element
+ name="restRepresentation" type="RestRepresentation"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="outputs" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="parameters"
+ maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element
+ name="restParameter" type="RestParameter"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element
+ name="representations" maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element
+ name="restRepresentation" type="RestRepresentation"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="ancestors" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+
+ <xsd:element name="service"
+ type="Service" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="restService"
+ type="RestService" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="restResource"
+ type="RestResource" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+
+ <xsd:element name="related" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="inputs"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="outputs"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="annotations"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+
+ <xsd:element name="restResource" type="RestResource"></xsd:element>
+
+ <xsd:element name="restMethod" type="RestMethod"></xsd:element>
+
+ <xsd:element name="restParameter" type="RestParameter"></xsd:element>
+
+ <xsd:complexType name="RestParameter">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1"
+ minOccurs="1">
+
+ </xsd:element>
+ <xsd:element name="name" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dc:description" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="computationalType"
+ type="xsd:string" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="defaultValue" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="paramStyle"
+ type="RestParameterStyle" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="isOptional" type="xsd:boolean"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="constrainedValues" maxOccurs="1"
+ minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="value"
+ type="xsd:string" maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="submitter" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="archived" type="xsd:dateTime"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+
+ <xsd:element name="ancestors" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="service"
+ type="Service" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="restService"
+ type="RestService" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="restResources"
+ maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+
+ <xsd:sequence>
+ <xsd:element
+ name="restResource" type="RestResource"
+ maxOccurs="unbounded" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="restMethods"
+ maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+
+ <xsd:element
+ name="restMethod" type="RestMethod" maxOccurs="unbounded"
+ minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="related" maxOccurs="1"
+ minOccurs="0">
+
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="annotations"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:simpleType name="RestParameterStyle">
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="template"></xsd:enumeration>
+ <xsd:enumeration value="query"></xsd:enumeration>
+ <xsd:enumeration value="matrix"></xsd:enumeration>
+ <xsd:enumeration value="header"></xsd:enumeration>
+
+ </xsd:restriction>
+ </xsd:simpleType>
+
+ <xsd:element name="restRepresentation" type="RestRepresentation"></xsd:element>
+
+ <xsd:complexType name="RestRepresentation">
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1"
+ minOccurs="1">
+
+ </xsd:element>
+ <xsd:element ref="dc:description" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="contentType" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="submitter" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="archived" type="xsd:dateTime"
+ maxOccurs="1" minOccurs="0">
+ </xsd:element>
+ <xsd:element name="ancestors" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="service"
+ type="Service" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="restService"
+ type="RestService" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element name="restResources"
+ maxOccurs="1" minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element
+ name="restResource" type="RestResource"
+ maxOccurs="unbounded" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="restMethods"
+ maxOccurs="1" minOccurs="1">
+
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element
+ name="restMethod" type="RestMethod" maxOccurs="unbounded"
+ minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ </xsd:element>
+ <xsd:element name="related" maxOccurs="1"
+ minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="annotations"
+ type="ResourceLink" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+
+ <xsd:element name="savedSearch" type="SavedSearch"></xsd:element>
+
+ <xsd:complexType name="SavedSearch">
+ <xsd:complexContent>
+
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element ref="dc:title" maxOccurs="1"
+ minOccurs="1">
+ </xsd:element>
+ <xsd:element name="name" type="xsd:string"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="allScopes" type="xsd:boolean"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element name="query" type="xsd:string"
+ maxOccurs="1" minOccurs="1" nillable="true">
+
+ </xsd:element>
+ <xsd:element name="scopes" maxOccurs="1"
+ minOccurs="1">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="scope"
+ maxOccurs="unbounded" minOccurs="0">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element
+ name="scopeName" type="SearchScopeName" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+
+ <xsd:element
+ name="scopeUrlValue" type="SearchScopeUrlValue" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element
+ name="scopeResourceType" maxOccurs="1" minOccurs="1"
+ type="ResourceType">
+ </xsd:element>
+ <xsd:element name="filters"
+ type="FiltersParameters" maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="user" type="ResourceLink"
+ maxOccurs="1" minOccurs="1">
+ </xsd:element>
+ <xsd:element ref="dcterms:created" maxOccurs="1" minOccurs="1"></xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+
+ </xsd:complexType>
+
+ <xsd:simpleType name="HttpVerb">
+ <xsd:restriction base="xsd:string">
+ <xsd:enumeration value="OPTIONS"></xsd:enumeration>
+ <xsd:enumeration value="GET"></xsd:enumeration>
+ <xsd:enumeration value="HEAD"></xsd:enumeration>
+ <xsd:enumeration value="POST"></xsd:enumeration>
+ <xsd:enumeration value="PUT"></xsd:enumeration>
+
+ <xsd:enumeration value="DELETE"></xsd:enumeration>
+ <xsd:enumeration value="TRACE"></xsd:enumeration>
+ <xsd:enumeration value="CONNECT"></xsd:enumeration>
+ </xsd:restriction>
+ </xsd:simpleType>
+
+
+ <xsd:element name="wsdlLocations" type="WsdlLocations"></xsd:element>
+
+ <xsd:complexType name="WsdlLocations">
+
+ <xsd:complexContent>
+ <xsd:extension base="ResourceLink">
+ <xsd:sequence>
+ <xsd:element name="wsdlLocation" type="xsd:anyURI"
+ maxOccurs="unbounded" minOccurs="0">
+ </xsd:element>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+</xsd:schema>
diff --git a/taverna-workbench-perspective-biocatalogue/src/main/xsd/xlink.xsd b/taverna-workbench-perspective-biocatalogue/src/main/xsd/xlink.xsd
new file mode 100644
index 0000000..6c2034b
--- /dev/null
+++ b/taverna-workbench-perspective-biocatalogue/src/main/xsd/xlink.xsd
@@ -0,0 +1,83 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- METS XLink Schema, v. 2, Nov. 15, 2004 -->
+<!-- Downloaded from http://www.loc.gov/standards/mets/xlink.xsd at 2007-04-19 -->
+<!-- Downloaded from http://taverna.cvs.sf.net/viewvc/taverna/taverna-service/taverna-interface/src/main/resources/xlink.xsd?view=log at 2009-10-19 -->
+<schema targetNamespace="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2001/XMLSchema" xmlns:xlink="http://www.w3.org/1999/xlink" elementFormDefault="qualified">
+ <!-- global attributes -->
+ <attribute name="href" type="anyURI"/>
+ <attribute name="role" type="string"/>
+ <attribute name="arcrole" type="string"/>
+ <attribute name="title" type="string" />
+ <attribute name="show">
+ <simpleType>
+
+ <restriction base="string">
+ <enumeration value="new" />
+ <enumeration value="replace" />
+ <enumeration value="embed" />
+ <enumeration value="other" />
+ <enumeration value="none" />
+ </restriction>
+ </simpleType>
+ </attribute>
+ <attribute name="actuate">
+ <simpleType>
+
+ <restriction base="string">
+ <enumeration value="onLoad" />
+ <enumeration value="onRequest" />
+ <enumeration value="other" />
+ <enumeration value="none" />
+ </restriction>
+ </simpleType>
+ </attribute>
+ <attribute name="label" type="string" />
+ <attribute name="from" type="string" />
+ <attribute name="to" type="string" />
+ <attributeGroup name="simpleLink">
+
+ <attribute name="type" type="string" fixed="simple" form="qualified" />
+ <attribute ref="xlink:href" use="optional" />
+ <attribute ref="xlink:role" use="optional" />
+ <attribute ref="xlink:arcrole" use="optional" />
+ <attribute ref="xlink:title" use="optional" />
+ <attribute ref="xlink:show" use="optional" />
+ <attribute ref="xlink:actuate" use="optional" />
+ </attributeGroup>
+ <attributeGroup name="extendedLink">
+ <attribute name="type" type="string" fixed="extended" form="qualified" />
+ <attribute ref="xlink:role" use="optional" />
+ <attribute ref="xlink:title" use="optional" />
+ </attributeGroup>
+ <attributeGroup name="locatorLink">
+
+ <attribute name="type" type="string" fixed="locator" form="qualified" />
+ <attribute ref="xlink:href" use="required" />
+ <attribute ref="xlink:role" use="optional" />
+ <attribute ref="xlink:title" use="optional" />
+ <attribute ref="xlink:label" use="optional" />
+ </attributeGroup>
+ <attributeGroup name="arcLink">
+ <attribute name="type" type="string" fixed="arc" form="qualified" />
+ <attribute ref="xlink:arcrole" use="optional" />
+ <attribute ref="xlink:title" use="optional" />
+ <attribute ref="xlink:show" use="optional" />
+ <attribute ref="xlink:actuate" use="optional" />
+ <attribute ref="xlink:from" use="optional" />
+ <attribute ref="xlink:to" use="optional" />
+ </attributeGroup>
+
+ <attributeGroup name="resourceLink">
+ <attribute name="type" type="string" fixed="resource" form="qualified" />
+ <attribute ref="xlink:role" use="optional" />
+ <attribute ref="xlink:title" use="optional" />
+ <attribute ref="xlink:label" use="optional" />
+ </attributeGroup>
+ <attributeGroup name="titleLink">
+ <attribute name="type" type="string" fixed="title" form="qualified" />
+ </attributeGroup>
+ <attributeGroup name="emptyLink">
+ <attribute name="type" type="string" fixed="none" form="qualified" />
+ </attributeGroup>
+
+</schema>
diff --git a/taverna-workbench-perspective-myexperiment/pom.xml b/taverna-workbench-perspective-myexperiment/pom.xml
new file mode 100644
index 0000000..9406580
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/pom.xml
@@ -0,0 +1,85 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna.t2</groupId>
+ <artifactId>ui-exts</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>perspective-myexperiment</artifactId>
+ <name>myExperiment perspective</name>
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository</url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>
+ http://www.mygrid.org.uk/maven/snapshot-repository
+ </url>
+ </repository>
+
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>menu-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>workbench-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>file-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>dataflow-activity-ui</artifactId>
+ <version>${t2.ui.activities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.lang</groupId>
+ <artifactId>ui</artifactId>
+ <version>${t2.lang.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-configuration-api</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-app-configuration-api</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.jdom</groupId>
+ <artifactId>com.springsource.org.jdom</artifactId>
+ <version>${jdom.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.log4j</groupId>
+ <artifactId>com.springsource.org.apache.log4j</artifactId>
+ </dependency>
+ </dependencies>
+</project>
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/AddCommentDialog.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/AddCommentDialog.java
new file mode 100644
index 0000000..fc1a8e6
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/AddCommentDialog.java
@@ -0,0 +1,330 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.net.HttpURLConnection;
+
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JRootPane;
+import javax.swing.JScrollPane;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.WindowConstants;
+import javax.swing.event.CaretEvent;
+import javax.swing.event.CaretListener;
+
+import net.sf.taverna.t2.lang.ui.DialogTextArea;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.ServerResponse;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Util;
+import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author Sergejs Aleksejevs, Jiten Bhagat
+ */
+
+public class AddCommentDialog extends HelpEnabledDialog implements ActionListener, CaretListener, ComponentListener, KeyListener {
+ // components for accessing application's main elements
+ private MainComponent pluginMainComponent;
+ private MyExperimentClient myExperimentClient;
+ private Logger logger;
+
+ // COMPONENTS
+ private DialogTextArea taComment;
+ private JButton bPost;
+ private JButton bCancel;
+ private JLabel lStatusMessage;
+
+ // STORAGE
+ private Resource resource; // a resource for which the comment is being posted
+ private String strComment = null;
+ private boolean bPostingSuccessful = false;
+
+ public AddCommentDialog(JFrame owner, Resource resource, MainComponent component, MyExperimentClient client, Logger logger) {
+ super(owner, "Add comment for \"" + resource.getTitle() + "\" "
+ + resource.getItemTypeName(), true);
+
+ // set main variables to ensure access to myExperiment, logger and the parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+
+ // set the resource for which the comment is being added
+ this.resource = resource;
+
+ // set options of the 'add comment' dialog box
+ this.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+ //this.setIconImage(new ImageIcon(MyExperimentPerspective.getLocalResourceURL("myexp_icon")).getImage());
+
+ this.initialiseUI();
+ }
+
+ private void initialiseUI() {
+ // get content pane
+ Container contentPane = this.getContentPane();
+
+ // set up layout
+ contentPane.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ // add all components
+ JLabel lInfo = new JLabel("Please type in you comment:");
+ c.gridx = 0;
+ c.gridy = 0;
+ c.anchor = GridBagConstraints.WEST;
+ c.gridwidth = 2;
+ c.fill = GridBagConstraints.NONE;
+ c.insets = new Insets(10, 10, 5, 10);
+ contentPane.add(lInfo, c);
+
+ this.taComment = new DialogTextArea(5, 35);
+ this.taComment.setLineWrap(true);
+ this.taComment.setWrapStyleWord(true);
+ this.taComment.addKeyListener(this);
+ this.taComment.addCaretListener(this);
+
+ JScrollPane spComment = new JScrollPane(this.taComment);
+ c.gridy = 1;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.insets = new Insets(0, 10, 0, 10);
+ contentPane.add(spComment, c);
+
+ this.bPost = new JButton("Post Comment");
+ this.bPost.setEnabled(false);
+ this.bPost.setDefaultCapable(true);
+ this.getRootPane().setDefaultButton(this.bPost);
+ this.bPost.addActionListener(this);
+ this.bPost.addKeyListener(this);
+ c.gridy = 2;
+ c.anchor = GridBagConstraints.EAST;
+ c.gridwidth = 1;
+ c.fill = GridBagConstraints.NONE;
+ c.weightx = 0.5;
+ c.insets = new Insets(10, 5, 10, 5);
+ contentPane.add(bPost, c);
+
+ this.bCancel = new JButton("Cancel");
+ this.bCancel.setPreferredSize(this.bPost.getPreferredSize());
+ this.bCancel.addActionListener(this);
+ c.gridx = 1;
+ c.anchor = GridBagConstraints.WEST;
+ c.weightx = 0.5;
+ contentPane.add(bCancel, c);
+
+ this.pack();
+ this.setMinimumSize(this.getPreferredSize());
+ this.setMaximumSize(this.getPreferredSize());
+ this.addComponentListener(this);
+ }
+
+ /**
+ * Opens up a modal dialog where the user can enter the comment text.
+ *
+ * Window is simply closed if 'Cancel' button is pressed; on pressing 'Post
+ * Comment' button the window will turn into 'waiting' state, post the comment
+ * and return the resulting XML document (which would contain the newly added
+ * comment) back to the caller.
+ *
+ * @return String value of the non-empty comment text to be sent to
+ * myExperiment or null if action was cancelled.
+ */
+ public String launchAddCommentDialogAndPostCommentIfRequired() {
+ // makes the 'add comment' dialog visible, then waits until it is closed;
+ // control returns to this method when the dialog window is disposed
+ this.setVisible(true);
+ return (strComment);
+ }
+
+ // *** Callback for ActionListener interface ***
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource().equals(this.bPost)) {
+ // 'Post' button is not active when text in the comment field is blank,
+ // so if it was pressed, there should be some text typed in
+ this.strComment = this.taComment.getText();
+
+ // the window will stay visible, but should turn into 'waiting' state
+ final JRootPane rootPane = this.getRootPane();
+ final Container contentPane = this.getContentPane();
+ contentPane.remove(this.bPost);
+ contentPane.remove(this.bCancel);
+ if (this.lStatusMessage != null)
+ contentPane.remove(this.lStatusMessage);
+ this.taComment.setEditable(false);
+
+ final GridBagConstraints c = new GridBagConstraints();
+ c.gridx = 0;
+ c.gridy = 2;
+ c.gridwidth = 2;
+ c.anchor = GridBagConstraints.CENTER;
+ c.fill = GridBagConstraints.NONE;
+ c.insets = new Insets(10, 5, 10, 5);
+ lStatusMessage = new JLabel("Posting your comment...", new ImageIcon(MyExperimentPerspective.getLocalResourceURL("spinner")), SwingConstants.CENTER);
+ contentPane.add(lStatusMessage, c);
+
+ // disable the (X) button (ideally, would need to remove it, but there's no way to do this)
+ this.setDefaultCloseOperation(JDialog.DO_NOTHING_ON_CLOSE);
+
+ // revalidate the window
+ this.pack();
+ this.validate();
+ this.repaint();
+
+ new Thread("Posting comment") {
+ public void run() {
+ // *** POST THE COMMENT ***
+ final ServerResponse response = myExperimentClient.postComment(resource, Util.stripAllHTML(strComment));
+ bPostingSuccessful = (response.getResponseCode() == HttpURLConnection.HTTP_OK);
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // *** REACT TO POSTING RESULT ***
+ if (bPostingSuccessful) {
+ // comment posted successfully
+ setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+ taComment.setEnabled(false);
+ contentPane.remove(lStatusMessage);
+
+ c.insets = new Insets(10, 5, 5, 5);
+ lStatusMessage = new JLabel("Your comment was posted successfully", new ImageIcon(MyExperimentPerspective.getLocalResourceURL("success_icon")), SwingConstants.LEFT);
+ contentPane.add(lStatusMessage, c);
+
+ bCancel.setText("OK");
+ bCancel.setDefaultCapable(true);
+ rootPane.setDefaultButton(bCancel);
+ c.insets = new Insets(5, 5, 10, 5);
+ c.gridy += 1;
+ contentPane.add(bCancel, c);
+
+ pack();
+ bCancel.requestFocusInWindow();
+ } else {
+ // posting wasn't successful, notify the user
+ // and provide an option to close window or start again
+ setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+ taComment.setEditable(true);
+ contentPane.remove(lStatusMessage);
+
+ c.insets = new Insets(10, 5, 5, 5);
+ lStatusMessage = new JLabel("Error occurred while posting comment: "
+ + Util.retrieveReasonFromErrorXMLDocument(response.getResponseBody()), new ImageIcon(MyExperimentPerspective.getLocalResourceURL("failure_icon")), SwingConstants.LEFT);
+ contentPane.add(lStatusMessage, c);
+
+ bPost.setText("Try again");
+ bPost.setToolTipText("Please review your comment before trying to post it again");
+ c.anchor = GridBagConstraints.EAST;
+ c.insets = new Insets(5, 5, 10, 5);
+ c.gridwidth = 1;
+ c.weightx = 0.5;
+ c.gridx = 0;
+ c.gridy += 1;
+ contentPane.add(bPost, c);
+ rootPane.setDefaultButton(bPost);
+
+ c.anchor = GridBagConstraints.WEST;
+ c.gridx = 1;
+ bCancel.setPreferredSize(bPost.getPreferredSize());
+ contentPane.add(bCancel, c);
+
+ pack();
+ validate();
+ repaint();
+ }
+ }
+ });
+
+ }
+ }.start();
+ } else if (e.getSource().equals(this.bCancel)) {
+ // cleanup the comment if it wasn't posted successfully + simply close and destroy the window
+ if (!this.bPostingSuccessful)
+ this.strComment = null;
+ this.dispose();
+ }
+
+ }
+
+ // *** Callbacks for KeyListener interface ***
+ public void keyPressed(KeyEvent e) {
+ // if TAB was pressed in the text area, need to move keyboard focus
+ if (e.getSource().equals(this.taComment)
+ && e.getKeyCode() == KeyEvent.VK_TAB) {
+ if ((e.getModifiersEx() & KeyEvent.SHIFT_DOWN_MASK) == KeyEvent.SHIFT_DOWN_MASK) {
+ // SHIFT + TAB move focus backwards
+ ((Component) e.getSource()).transferFocusBackward();
+ } else {
+ // TAB moves focus forward
+ ((Component) e.getSource()).transferFocus();
+ }
+ e.consume();
+ }
+ }
+
+ public void keyReleased(KeyEvent e) {
+ // not in use
+ }
+
+ public void keyTyped(KeyEvent e) {
+ // not in use
+ }
+
+ // *** Callback for CaretListener interface ***
+ public void caretUpdate(CaretEvent e) {
+ // check whether the 'Post' button should be available or not
+ this.bPost.setEnabled(this.taComment.getText().length() > 0);
+ }
+
+ // *** Callbacks for ComponentListener interface ***
+ public void componentShown(ComponentEvent e) {
+ // center this dialog box within the preview browser window
+ Util.centerComponentWithinAnother(this.pluginMainComponent.getPreviewBrowser(), this);
+ }
+
+ public void componentHidden(ComponentEvent e) {
+ // not in use
+ }
+
+ public void componentMoved(ComponentEvent e) {
+ // not in use
+ }
+
+ public void componentResized(ComponentEvent e) {
+ // not in use
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/AddRemoveFavouriteDialog.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/AddRemoveFavouriteDialog.java
new file mode 100644
index 0000000..563d2b8
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/AddRemoveFavouriteDialog.java
@@ -0,0 +1,277 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.Container;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
+import java.net.HttpURLConnection;
+
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.WindowConstants;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.ServerResponse;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Util;
+import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class AddRemoveFavouriteDialog extends HelpEnabledDialog implements ActionListener, ComponentListener {
+ // CONSTANTS
+ protected static final int OPERATION_SUCCESSFUL = 1;
+ protected static final int OPERATION_CANCELLED = 0;
+ protected static final int OPERATION_FAILED = -1;
+
+ // components for accessing application's main elements
+ private final MainComponent pluginMainComponent;
+ private final MyExperimentClient myExperimentClient;
+ private final Logger logger;
+
+ // COMPONENTS
+ private JButton bAddRemoveFavourite;
+ private JButton bCancel;
+
+ // STORAGE
+ private final Resource resource; // a resource which is being favourited / removed from favourites
+ private final boolean bIsFavouriteBeingAdded;
+ private int iOperationStatus = OPERATION_CANCELLED;
+ private ServerResponse response = null;
+
+ public AddRemoveFavouriteDialog(JFrame owner, boolean isFavouriteAdded, Resource resource, MainComponent component, MyExperimentClient client, Logger logger) {
+ super(owner, isFavouriteAdded ? "Add to" : "Remove from"
+ + " favourites - \"" + resource.getTitle() + "\" "
+ + resource.getItemTypeName(), true);
+
+ // set main variables to ensure access to myExperiment, logger and the parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+
+ // parameters
+ this.bIsFavouriteBeingAdded = isFavouriteAdded;
+ this.resource = resource;
+
+ // set options of the 'add/remove favourite' dialog box
+ this.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+ //this.setIconImage(new ImageIcon(MyExperimentPerspective.getLocalResourceURL("myexp_icon")).getImage());
+
+ this.initialiseUI();
+ }
+
+ private void initialiseUI() {
+ // get content pane
+ Container contentPane = this.getContentPane();
+
+ // set up layout
+ contentPane.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ // add all components
+ JLabel lInfo = new JLabel("<html><center>You are about to "
+ + (this.bIsFavouriteBeingAdded ? "add" : "remove") + " \""
+ + resource.getTitle() + "\" " + resource.getItemTypeName()
+ + (this.bIsFavouriteBeingAdded ? " to" : " from")
+ + " your favourites.<br><br>"
+ + "Do you want to proceed?</center></html>");
+ c.gridx = 0;
+ c.gridy = 0;
+ c.anchor = GridBagConstraints.WEST;
+ c.gridwidth = 2;
+ c.fill = GridBagConstraints.NONE;
+ c.insets = new Insets(10, 10, 10, 10);
+ contentPane.add(lInfo, c);
+
+ if (this.bIsFavouriteBeingAdded) {
+ this.bAddRemoveFavourite = new JButton("Add to Favourites");
+ } else {
+ this.bAddRemoveFavourite = new JButton("Remove from Favourites");
+ }
+ this.bAddRemoveFavourite.setDefaultCapable(true);
+ this.bAddRemoveFavourite.addActionListener(this);
+
+ c.gridy = 1;
+ c.anchor = GridBagConstraints.EAST;
+ c.gridwidth = 1;
+ c.fill = GridBagConstraints.NONE;
+ c.weightx = 0.5;
+ c.insets = new Insets(5, 5, 10, 5);
+ contentPane.add(this.bAddRemoveFavourite, c);
+
+ this.bCancel = new JButton("Cancel");
+ this.bCancel.setPreferredSize(this.bAddRemoveFavourite.getPreferredSize());
+ this.bCancel.addActionListener(this);
+ c.gridx = 1;
+ c.anchor = GridBagConstraints.WEST;
+ contentPane.add(bCancel, c);
+
+ this.pack();
+ this.getRootPane().setDefaultButton(this.bAddRemoveFavourite);
+ this.setMinimumSize(this.getPreferredSize());
+ this.setMaximumSize(this.getPreferredSize());
+ this.addComponentListener(this);
+ }
+
+ /**
+ * Makes the dialog for adding / removing an item from favourites visible.
+ * Based on the user actions, it might execute the adding / removing
+ * operation.
+ *
+ * @return Returns an integer value which represents status of the operation:
+ * {@value #OPERATION_SUCCESSFUL} - favourite item was added / removed
+ * successfully; {@value #OPERATION_CANCELLED} - the user has
+ * cancelled operation; {@value #OPERATION_FAILED} - failed while
+ * adding / removing favourite item;
+ */
+ public int launchAddRemoveFavouriteDialogAndPerformNecessaryActionIfRequired() {
+ this.setVisible(true);
+ return (this.iOperationStatus);
+ }
+
+ // *** Callback for ActionListener interface ***
+ public void actionPerformed(ActionEvent e) {
+
+ if (e.getSource().equals(this.bAddRemoveFavourite)) {
+ // the window will stay visible, but should turn into 'waiting' state
+ final Container contentPane = this.getContentPane();
+ contentPane.removeAll();
+
+ final GridBagConstraints c = new GridBagConstraints();
+ c.gridx = 0;
+ c.gridy = 0;
+ c.gridwidth = 2;
+ c.anchor = GridBagConstraints.CENTER;
+ c.fill = GridBagConstraints.NONE;
+ c.insets = new Insets(10, 5, 10, 5);
+ JLabel lInfo = new JLabel(this.bIsFavouriteBeingAdded ? "Adding to favourites..." : "Removing from favourites...", new ImageIcon(MyExperimentPerspective.getLocalResourceURL("spinner")), SwingConstants.CENTER);
+ contentPane.add(lInfo, c);
+
+ // disable the (X) button (ideally, would need to remove it, but there's no way to do this)
+ this.setDefaultCloseOperation(JDialog.DO_NOTHING_ON_CLOSE);
+
+ // revalidate the window
+ this.pack();
+ this.validate();
+ this.repaint();
+
+ new Thread("Execute add / remove favourite operation") {
+ @Override
+ public void run() {
+ // *** DO THE REQUIRED ACTION ***
+ response = (bIsFavouriteBeingAdded ? myExperimentClient.addFavourite(resource) : myExperimentClient.deleteFavourite(resource));
+ iOperationStatus = (response.getResponseCode() == HttpURLConnection.HTTP_OK) ? OPERATION_SUCCESSFUL : OPERATION_FAILED;
+
+ if (iOperationStatus == OPERATION_SUCCESSFUL) {
+ // update local list of favourite items - no data sync with the API is required at this point
+ if (bIsFavouriteBeingAdded) {
+ myExperimentClient.getCurrentUser().getFavourites().add(resource);
+ } else {
+ myExperimentClient.getCurrentUser().getFavourites().remove(resource);
+ }
+ } else {
+ // operation has failed - this might have been due to outdated data which is stored locally;
+ // sync favourite data with the API so that the UI can show more relevant data
+ // (e.g. replace 'add to favourites' with 'remove from favourites' if this item is already
+ // added to favourites - probably via another interface: web or another instance of the plugin)
+ myExperimentClient.updateUserFavourites(myExperimentClient.getCurrentUser());
+ }
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // *** REACT TO RESULT ***
+ setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+ contentPane.removeAll();
+ c.insets = new Insets(10, 5, 5, 5);
+
+ if (iOperationStatus == OPERATION_SUCCESSFUL) {
+ // favourite was added / removed successfully
+ contentPane.add(new JLabel("Item has been successfully "
+ + (bIsFavouriteBeingAdded ? "added to" : "removed from")
+ + " your favourites", new ImageIcon(MyExperimentPerspective.getLocalResourceURL("success_icon")), SwingConstants.LEFT), c);
+ } else {
+ // favourite wasn't added / removed - operation failed;
+ // display error message
+ contentPane.add(new JLabel("<html><center>Error occurred while "
+ + (bIsFavouriteBeingAdded ? "adding" : "removing")
+ + " the item "
+ + (bIsFavouriteBeingAdded ? "to" : "from")
+ + " your favourites:<br>"
+ + Util.retrieveReasonFromErrorXMLDocument(response.getResponseBody())
+ + "</center></html>", new ImageIcon(MyExperimentPerspective.getLocalResourceURL("failure_icon")), SwingConstants.LEFT), c);
+ }
+
+ bCancel.setText("OK");
+ bCancel.setPreferredSize(null); // resets preferred size to the automatic one
+ bCancel.setDefaultCapable(true);
+ c.insets = new Insets(5, 5, 10, 5);
+ c.gridy += 1;
+ contentPane.add(bCancel, c);
+
+ pack();
+ repaint();
+
+ bCancel.requestFocusInWindow();
+ getRootPane().setDefaultButton(bCancel);
+ }
+ });
+ }
+ }.start();
+
+ } else if (e.getSource().equals(this.bCancel)) {
+ // simply close and destroy the window
+ this.dispose();
+ }
+ }
+
+ // *** Callbacks for ComponentListener interface ***
+ public void componentShown(ComponentEvent e) {
+ // center this dialog box within the preview browser window
+ Util.centerComponentWithinAnother(this.pluginMainComponent.getPreviewBrowser(), this);
+ }
+
+ public void componentHidden(ComponentEvent e) {
+ // not in use
+ }
+
+ public void componentMoved(ComponentEvent e) {
+ // not in use
+ }
+
+ public void componentResized(ComponentEvent e) {
+ // not in use
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ExampleWorkflowsPanel.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ExampleWorkflowsPanel.java
new file mode 100644
index 0000000..d3a58a0
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ExampleWorkflowsPanel.java
@@ -0,0 +1,153 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.BorderLayout;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.ChangeEvent;
+
+import org.apache.log4j.Logger;
+
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.ResourceListPanel;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Workflow;
+
+/**
+ * @author Sergejs Aleksejevs, Jiten Bhagat
+ */
+public class ExampleWorkflowsPanel extends JPanel implements ActionListener, ChangeListener {
+
+ private static final String ACTION_REFRESH = "refresh_example_workflows";
+
+ private MainComponent pluginMainComponent;
+ private MyExperimentClient myExperimentClient;
+ private Logger logger;
+
+ private JLabel statusLabel;
+ private JButton refreshButton;
+
+ private List<Workflow> workflows = new ArrayList<Workflow>();
+
+ private ResourceListPanel workflowsListPanel;
+
+ public ExampleWorkflowsPanel(MainComponent component, MyExperimentClient client, Logger logger) {
+ super();
+
+ // set main variables to ensure access to myExperiment, logger and the
+ // parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+
+ this.initialiseUI();
+ }
+
+ public void actionPerformed(ActionEvent event) {
+ if (ACTION_REFRESH.equals(event.getActionCommand())) {
+ this.refresh();
+ }
+ }
+
+ public void stateChanged(ChangeEvent event) {
+
+ }
+
+ public void clear() {
+ this.statusLabel.setText("");
+ this.workflowsListPanel.clear();
+ }
+
+ public void refresh() {
+ this.pluginMainComponent.getStatusBar().setStatus(this.getClass().getName(), "Fetching example workflows from myExperiment");
+ this.statusLabel.setText("");
+
+ // Make call to myExperiment API in a different thread
+ // (then use SwingUtilities.invokeLater to update the UI when ready).
+ new Thread("Refresh for ExampleWorkflowsPanel") {
+ public void run() {
+ logger.debug("Refreshing Example Workflows tab");
+
+ try {
+ workflows = myExperimentClient.getExampleWorkflows();
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ repopulate();
+ }
+ });
+ } catch (Exception ex) {
+ logger.error("Failed to refresh Example Workflows panel", ex);
+ }
+ }
+ }.start();
+
+ }
+
+ public void repopulate() {
+ logger.debug("Repopulating Example Workflows tab");
+
+ this.pluginMainComponent.getStatusBar().setStatus(this.getClass().getName(), null);
+ this.statusLabel.setText("This will contain example resources to"
+ + " help get you started in Taverna. Coming Soon.");
+ this.statusLabel.setText(this.workflows.size() + " example workflows found");
+
+ // cannot cast a list of subclass items into a list of superclass items -
+ // hence a new list is created
+ this.workflowsListPanel.setListItems(new ArrayList<Resource>(this.workflows));
+
+ this.revalidate();
+ }
+
+ private void initialiseUI() {
+ this.setLayout(new BorderLayout());
+
+ JPanel topPanel = new JPanel(new BorderLayout());
+ topPanel.setBorder(BorderFactory.createEtchedBorder());
+ this.statusLabel = new JLabel();
+ this.statusLabel.setBorder(BorderFactory.createEmptyBorder(0, 7, 0, 0));
+ topPanel.add(this.statusLabel, BorderLayout.CENTER);
+ this.refreshButton = new JButton("Refresh", WorkbenchIcons.refreshIcon);
+ this.refreshButton.setActionCommand(ACTION_REFRESH);
+ this.refreshButton.addActionListener(this);
+ this.refreshButton.setToolTipText("Click this button to refresh the Example Workflows list");
+ topPanel.add(this.refreshButton, BorderLayout.EAST);
+ this.add(topPanel, BorderLayout.NORTH);
+
+ this.workflowsListPanel = new ResourceListPanel(this.pluginMainComponent, this.myExperimentClient, this.logger);
+ JScrollPane spExampleWorkflowList = new JScrollPane(this.workflowsListPanel);
+ spExampleWorkflowList.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+
+ this.add(spExampleWorkflowList, BorderLayout.CENTER);
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/HistoryBrowserTabContentPanel.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/HistoryBrowserTabContentPanel.java
new file mode 100644
index 0000000..3dfd2db
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/HistoryBrowserTabContentPanel.java
@@ -0,0 +1,541 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.ScrollPaneConstants;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.border.Border;
+
+import net.sf.taverna.t2.lang.ui.ShadedLabel;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Base64;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Tag;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Util;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.SearchEngine.QuerySearchInstance;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author Sergejs Aleksejevs, Emmanuel Tagarira
+ */
+public class HistoryBrowserTabContentPanel extends JPanel implements ActionListener {
+ // CONSTANTS
+ public static final int DOWNLOADED_ITEMS_HISTORY_LENGTH = 50;
+ public static final int OPENED_ITEMS_HISTORY_LENGTH = 50;
+ public static final int UPLOADED_ITEMS_HISTORY_LENGTH = 50;
+ public static final int COMMENTED_ON_ITEMS_HISTORY_LENGTH = 50;
+
+ public static final int PREVIEWED_ITEMS_HISTORY = 0;
+ public static final int DOWNLOADED_ITEMS_HISTORY = 1;
+ public static final int OPENED_ITEMS_HISTORY = 2;
+ public static final int UPLOADED_ITEMS_HISTORY = 4;
+ public static final int COMMENTED_ON_ITEMS_HISTORY = 3;
+
+ private final MainComponent pluginMainComponent;
+ private final MyExperimentClient myExperimentClient;
+ private final Logger logger;
+
+ // STORAGE
+ private ArrayList<Resource> lDownloadedItems;
+ private ArrayList<Resource> lOpenedItems;
+ private ArrayList<Resource> lUploadedItems;
+ private ArrayList<Resource> lCommentedOnItems;
+
+ // COMPONENTS
+ private JPanel jpPreviewHistory;
+ private JPanel jpSearchHistory;
+ private JPanel jpTagSearchHistory;
+ private JPanel jpDownloadedItemsHistory;
+ private JPanel jpOpenedItemsHistory;
+ private JPanel jpUploadedItemsHistory;
+ private JPanel jpCommentedOnHistory;
+ private JSplitPane spMain;
+ private JClickableLabel jclPreviewHistory;
+ private JClickableLabel jclSearchHistory;
+ private JClickableLabel jclTagSearchHistory;
+ private JClickableLabel jclDownloadedItemsHistory;
+ private JClickableLabel jclOpenedItemsHistory;
+ private JClickableLabel jclUploadedItemsHistory;
+ private JClickableLabel jclCommentedOnHistory;
+ private JPanel jpPreviewHistoryBox;
+ private JPanel jpSearchHistoryBox;
+ private JPanel jpTagSearchHistoryBox;
+ private JPanel jpDownloadedItemsHistoryBox;
+ private JPanel jpOpenedItemsHistoryBox;
+ private JPanel jpUploadedItemsHistoryBox;
+ private JPanel jpCommentedOnHistoryBox;
+
+ @SuppressWarnings("unchecked")
+ public HistoryBrowserTabContentPanel(MainComponent component, MyExperimentClient client, Logger logger) {
+ super();
+
+ // set main variables to ensure access to myExperiment, logger and the parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+
+ // initialise downloaded items history
+ String strDownloadedItemsHistory = (String) myExperimentClient.getSettings().get(MyExperimentClient.INI_DOWNLOADED_ITEMS_HISTORY);
+ if (strDownloadedItemsHistory != null) {
+ Object oDownloadedItemsHistory = Base64.decodeToObject(strDownloadedItemsHistory);
+ this.lDownloadedItems = (ArrayList<Resource>) oDownloadedItemsHistory;
+ } else {
+ this.lDownloadedItems = new ArrayList<Resource>();
+ }
+
+ // initialise opened items history
+ String strOpenedItemsHistory = (String) myExperimentClient.getSettings().get(MyExperimentClient.INI_OPENED_ITEMS_HISTORY);
+ if (strOpenedItemsHistory != null) {
+ Object oOpenedItemsHistory = Base64.decodeToObject(strOpenedItemsHistory);
+ this.lOpenedItems = (ArrayList<Resource>) oOpenedItemsHistory;
+ } else {
+ this.lOpenedItems = new ArrayList<Resource>();
+ }
+
+ // initialise uploaded items history
+ String strUploadedItemsHistory = (String) myExperimentClient.getSettings().get(MyExperimentClient.INI_UPLOADED_ITEMS_HISTORY);
+ if (strUploadedItemsHistory != null) {
+ Object oUploadedItemsHistory = Base64.decodeToObject(strUploadedItemsHistory);
+ this.lUploadedItems = (ArrayList<Resource>) oUploadedItemsHistory;
+ } else {
+ this.lUploadedItems = new ArrayList<Resource>();
+ }
+
+ // initialise history of the items that were commented on
+ String strCommentedItemsHistory = (String) myExperimentClient.getSettings().get(MyExperimentClient.INI_COMMENTED_ITEMS_HISTORY);
+ if (strCommentedItemsHistory != null) {
+ Object oCommentedItemsHistory = Base64.decodeToObject(strCommentedItemsHistory);
+ this.lCommentedOnItems = (ArrayList<Resource>) oCommentedItemsHistory;
+ } else {
+ this.lCommentedOnItems = new ArrayList<Resource>();
+ }
+
+ this.initialiseUI();
+ this.refreshAllData();
+ }
+
+ private void confirmHistoryDelete(final int id, String strBoxTitle) {
+ if (JOptionPane.showConfirmDialog(null, "This will the "
+ + strBoxTitle.toLowerCase() + " list.\nDo you want to proceed?", "myExperiment Plugin - Confirmation Required", JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) {
+ switch (id) {
+ case 1:
+ pluginMainComponent.getPreviewBrowser().clearPreviewHistory();
+ break;
+ case 2:
+ pluginMainComponent.getSearchTab().getSearchHistory().clear();
+ pluginMainComponent.getSearchTab().updateSearchHistory();
+ break;
+ case 3:
+ pluginMainComponent.getTagBrowserTab().getTagSearchHistory().clear();
+ break;
+ case 4:
+ clearDownloadedItemsHistory();
+ break;
+ case 5:
+ clearOpenedItemsHistory();
+ break;
+ case 6:
+ clearCommentedOnItemsHistory();
+ break;
+ case 7:
+ clearUploadedItemsHistory();
+ break;
+ }
+ refreshAllData();
+ }
+ }
+
+ private JPanel addSpecifiedPanel(final int id, final String strBoxTitle, JPanel jPanel) {
+ JPanel jpTemp = new JPanel();
+ jpTemp.setLayout(new BorderLayout());
+ jpTemp.add(generateContentBox(strBoxTitle, jPanel), BorderLayout.CENTER);
+ JButton bClear = new JButton("Clear " + strBoxTitle, WorkbenchIcons.deleteIcon);
+ bClear.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ confirmHistoryDelete(id, strBoxTitle);
+ }
+ });
+
+ jpTemp.add(bClear, BorderLayout.SOUTH);
+ jpTemp.setMinimumSize(new Dimension(500, 0));
+ return jpTemp;
+ }
+
+ private void initialiseUI() {
+ // create helper text
+ ShadedLabel lHelper = new ShadedLabel("All history sections are local to myExperiment plugin usage."
+ + " Detailed history of your actions on myExperiment is available in your profile on myExperiment.", ShadedLabel.BLUE);
+
+ // create all individual content holder panels
+ this.jpPreviewHistory = new JPanel();
+ this.jpTagSearchHistory = new JPanel();
+ this.jpSearchHistory = new JPanel();
+ this.jpDownloadedItemsHistory = new JPanel();
+ this.jpOpenedItemsHistory = new JPanel();
+ this.jpUploadedItemsHistory = new JPanel();
+ this.jpCommentedOnHistory = new JPanel();
+
+ // create sidebar
+ JPanel jpSidebar = new JPanel();
+ jpSidebar.setLayout(new BoxLayout(jpSidebar, BoxLayout.Y_AXIS));
+ Border border = BorderFactory.createEmptyBorder(5, 3, 10, 3);
+ jclPreviewHistory = new JClickableLabel("Previewed Items", "preview_history", this, WorkbenchIcons.editIcon, SwingConstants.LEFT, "tooltip");
+ jclPreviewHistory.setBorder(border);
+ jpSidebar.add(jclPreviewHistory);
+
+ jclSearchHistory = new JClickableLabel("Search History", "search_history", this, WorkbenchIcons.editIcon, SwingConstants.LEFT, "tooltip");
+ jclSearchHistory.setBorder(border);
+ jpSidebar.add(jclSearchHistory);
+
+ jclTagSearchHistory = new JClickableLabel("Tag Searches Made", "tag_history", this, WorkbenchIcons.editIcon, SwingConstants.LEFT, "tooltip");
+ jclTagSearchHistory.setBorder(border);
+ jpSidebar.add(jclTagSearchHistory);
+
+ jclDownloadedItemsHistory = new JClickableLabel("Downloaded Items", "downloads_history", this, WorkbenchIcons.editIcon, SwingConstants.LEFT, "tooltip");
+ jclDownloadedItemsHistory.setBorder(border);
+ jpSidebar.add(jclDownloadedItemsHistory);
+
+ jclOpenedItemsHistory = new JClickableLabel("Opened Items", "opened_history", this, WorkbenchIcons.editIcon, SwingConstants.LEFT, "tooltip");
+ jclOpenedItemsHistory.setBorder(border);
+ jpSidebar.add(jclOpenedItemsHistory);
+
+ jclUploadedItemsHistory = new JClickableLabel("Updated Items", "uploaded_history", this, WorkbenchIcons.editIcon, SwingConstants.LEFT, "tooltip");
+ jclUploadedItemsHistory.setBorder(border);
+ jpSidebar.add(jclUploadedItemsHistory);
+
+ jclCommentedOnHistory = new JClickableLabel("Items Commented On", "comments_history", this, WorkbenchIcons.editIcon, SwingConstants.LEFT, "tooltip");
+ jclCommentedOnHistory.setBorder(border);
+ jpSidebar.add(jclCommentedOnHistory);
+
+ JPanel jpSidebarContainer = new JPanel();
+ jpSidebarContainer.add(jpSidebar, BorderLayout.NORTH);
+ JScrollPane spSidebar = new JScrollPane(jpSidebarContainer);
+ spSidebar.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+ spSidebar.setMinimumSize(new Dimension(245, 0));
+ spSidebar.setMaximumSize(new Dimension(300, 0));
+
+ // create standard boxes for each content holder panels
+ // only one of these will hold the right hand side of spMain at any given time
+ // arg 1: is the ID, which will be used by confirmHistoryDelete() to decide
+ // how to delete the history item
+ jpPreviewHistoryBox = addSpecifiedPanel(1, "Items you have previewed", jpPreviewHistory);
+ jpSearchHistoryBox = addSpecifiedPanel(2, "Terms you have searched for", jpSearchHistory);
+ jpTagSearchHistoryBox = addSpecifiedPanel(3, "Tags searches you have made", jpTagSearchHistory);
+ jpDownloadedItemsHistoryBox = addSpecifiedPanel(4, "Items you have downloaded", jpDownloadedItemsHistory);
+ jpOpenedItemsHistoryBox = addSpecifiedPanel(5, "Workflows you have opened in Taverna", jpOpenedItemsHistory);
+ jpCommentedOnHistoryBox = addSpecifiedPanel(6, "Items you have commented on in myExperiment", jpCommentedOnHistory);
+ jpUploadedItemsHistoryBox = addSpecifiedPanel(7, "Items you have updated on myExperiment", jpUploadedItemsHistory);
+
+ // put everything together
+ spMain = new JSplitPane();
+ spMain.setLeftComponent(spSidebar);
+ spMain.setRightComponent(jpPreviewHistoryBox);
+
+ spMain.setOneTouchExpandable(true);
+ spMain.setDividerLocation(247);
+ spMain.setDoubleBuffered(true);
+
+ // spMyStuff will be the only component in the Panel
+ this.setLayout(new BorderLayout());
+ this.add(spMain);
+ this.add(lHelper, BorderLayout.NORTH);
+
+ }
+
+ public ArrayList<Resource> getDownloadedItemsHistoryList() {
+ return (this.lDownloadedItems);
+ }
+
+ public void clearDownloadedItemsHistory() {
+ this.lDownloadedItems.clear();
+ }
+
+ public ArrayList<Resource> getOpenedItemsHistoryList() {
+ return (this.lOpenedItems);
+ }
+
+ public ArrayList<Resource> getUploadedItemsHistoryList() {
+ return (this.lUploadedItems);
+ }
+
+ public void clearOpenedItemsHistory() {
+ this.lOpenedItems.clear();
+ }
+
+ public void clearUploadedItemsHistory() {
+ this.lUploadedItems.clear();
+ }
+
+ public ArrayList<Resource> getCommentedOnItemsHistoryList() {
+ return (this.lCommentedOnItems);
+ }
+
+ public void clearCommentedOnItemsHistory() {
+ this.lCommentedOnItems.clear();
+ }
+
+ /**
+ * Used to refresh all boxes at a time (for example at launch time).
+ */
+ private void refreshAllData() {
+ this.refreshHistoryBox(PREVIEWED_ITEMS_HISTORY);
+ this.refreshHistoryBox(DOWNLOADED_ITEMS_HISTORY);
+ this.refreshHistoryBox(OPENED_ITEMS_HISTORY);
+ this.refreshHistoryBox(UPLOADED_ITEMS_HISTORY);
+ this.refreshHistoryBox(COMMENTED_ON_ITEMS_HISTORY);
+ this.refreshSearchHistory();
+ this.refreshTagSearchHistory();
+ }
+
+ /**
+ * This helper can be called externally to refresh the following history
+ * boxes: previewed items history, downloaded items history, opened items
+ * history and the history of items that were commented on.
+ *
+ * Is used inside ResourcePreviewBrowser and MainComponent every time a
+ * relevant action occurs. Also useful, when an option to 'clear preview
+ * history' is used in the Preferences window for. a particular history type.
+ */
+ public void refreshHistoryBox(int historyType) {
+ switch (historyType) {
+ case PREVIEWED_ITEMS_HISTORY:
+ this.jpPreviewHistory.removeAll();
+ populateHistoryBox(this.pluginMainComponent.getPreviewBrowser().getPreviewHistory(), this.jpPreviewHistory, "No items were previewed yet");
+ break;
+ case DOWNLOADED_ITEMS_HISTORY:
+ this.jpDownloadedItemsHistory.removeAll();
+ populateHistoryBox(this.lDownloadedItems, this.jpDownloadedItemsHistory, "No items were downloaded");
+ break;
+ case OPENED_ITEMS_HISTORY:
+ this.jpOpenedItemsHistory.removeAll();
+ populateHistoryBox(this.lOpenedItems, this.jpOpenedItemsHistory, "No items were opened");
+ break;
+ case UPLOADED_ITEMS_HISTORY:
+ this.jpUploadedItemsHistory.removeAll();
+ populateHistoryBox(this.lUploadedItems, this.jpUploadedItemsHistory, "No items were updated");
+ break;
+ case COMMENTED_ON_ITEMS_HISTORY:
+ this.jpCommentedOnHistory.removeAll();
+ populateHistoryBox(this.lCommentedOnItems, this.jpCommentedOnHistory, "You didn't comment on any items");
+ break;
+ }
+ }
+
+ /**
+ * Retrieves history data from a relevant list and populates the specified
+ * panel with it. All listed items will be resources that can be opened by
+ * Preview Browser.
+ */
+ private void populateHistoryBox(List<Resource> lHistory, JPanel jpPanelToPopulate, String strLabelIfNoItems) {
+ if (lHistory.size() > 0) {
+ for (int i = lHistory.size() - 1; i >= 0; i--) {
+ Resource r = lHistory.get(i);
+ if (r != null) {
+ JClickableLabel lResource = Util.generateClickableLabelFor(r, this.pluginMainComponent.getPreviewBrowser());
+ jpPanelToPopulate.add(lResource);
+ }
+ }
+ } else {
+ jpPanelToPopulate.add(Util.generateNoneTextLabel(strLabelIfNoItems));
+ }
+
+ // make sure that the component is updated after population
+ jpPanelToPopulate.revalidate();
+ jpPanelToPopulate.repaint();
+ }
+
+ /**
+ * This helper can be called externally to refresh the search history. Is used
+ * inside SearchTabContentPanel every time a new item is added to search
+ * history.
+ */
+ public void refreshSearchHistory() {
+ this.jpSearchHistory.removeAll();
+ populateSearchHistory();
+ }
+
+ /**
+ * Retrieves search history data from SearchTabContentPanel and populates the
+ * relevant panel.
+ */
+ private void populateSearchHistory() {
+ List<QuerySearchInstance> lSearchHistory = this.pluginMainComponent.getSearchTab().getSearchHistory();
+
+ // prepare layout
+ this.jpSearchHistory.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+ c.anchor = GridBagConstraints.NORTHWEST;
+
+ if (lSearchHistory.size() > 0) {
+ for (int i = lSearchHistory.size() - 1; i >= 0; i--) {
+ QuerySearchInstance qsiCurrent = lSearchHistory.get(i);
+ JClickableLabel jclCurrentEntryLabel = new JClickableLabel(qsiCurrent.getSearchQuery(), SearchTabContentPanel.SEARCH_FROM_HISTORY
+ + ":" + i, this, WorkbenchIcons.findIcon, SwingUtilities.LEFT, qsiCurrent.toString());
+ JLabel jlCurrentEntrySettings = new JLabel(qsiCurrent.detailsAsString());
+ jlCurrentEntrySettings.setBorder(BorderFactory.createEmptyBorder(3, 5, 0, 0));
+
+ JPanel jpCurrentSearchHistoryEntry = new JPanel();
+ jpCurrentSearchHistoryEntry.setLayout(new GridBagLayout());
+ c.gridx = 0;
+ c.gridy = 0;
+ c.weightx = 0;
+ jpCurrentSearchHistoryEntry.add(jclCurrentEntryLabel, c);
+ c.gridx = 1;
+ c.gridy = 0;
+ c.weightx = 1.0;
+ jpCurrentSearchHistoryEntry.add(jlCurrentEntrySettings, c);
+
+ c.gridy = lSearchHistory.size() - 1 - i;
+ if (i == 0)
+ c.weighty = 1.0;
+ this.jpSearchHistory.add(jpCurrentSearchHistoryEntry, c);
+ }
+ } else {
+ c.weightx = 1.0;
+ c.weighty = 1.0;
+ this.jpSearchHistory.add(Util.generateNoneTextLabel(SearchResultsPanel.NO_SEARCHES_STATUS), c);
+ }
+
+ // make sure that the component is updated after population
+ this.jpSearchHistory.revalidate();
+ this.jpSearchHistory.repaint();
+ }
+
+ /**
+ * This helper can be called externally to refresh the tag search history. Is
+ * used inside TagBrowserTabContentPanel every time a new tag is searched for.
+ */
+ public void refreshTagSearchHistory() {
+ this.jpTagSearchHistory.removeAll();
+ populateTagSearchHistory();
+ }
+
+ /**
+ * Retrieves tag search history data from Tag Browser and populates the
+ * relevant panel.
+ */
+ private void populateTagSearchHistory() {
+ List<Tag> lTagSearchHistory = this.pluginMainComponent.getTagBrowserTab().getTagSearchHistory();
+
+ if (lTagSearchHistory.size() > 0) {
+ for (int i = lTagSearchHistory.size() - 1; i >= 0; i--) {
+ Tag t = lTagSearchHistory.get(i);
+ JClickableLabel lTag = new JClickableLabel(t.getTagName(), "tag:"
+ + t.getTagName(), this, new ImageIcon(MyExperimentPerspective.getLocalIconURL(Resource.TAG)), // HACK: after deserialization t.getItemType() return "Unknown" type
+ SwingConstants.LEFT, "Tag: " + t.getTagName());
+ this.jpTagSearchHistory.add(lTag);
+ }
+ } else {
+ this.jpTagSearchHistory.add(Util.generateNoneTextLabel("No searches by tags have been made yet"));
+ }
+
+ // make sure that the component is updated after population
+ this.jpTagSearchHistory.revalidate();
+ this.jpTagSearchHistory.repaint();
+ }
+
+ /**
+ * @param strBoxTitle
+ * Title of the content box.
+ * @param jpContentPanel
+ * JPanel which will be populated with history listing.
+ * @return Prepared JPanel with a border, title and jpContentPanel wrapped
+ * into a scroll pane.
+ */
+ private static JPanel generateContentBox(String strBoxTitle, JPanel jpContentPanel) {
+ // set layout for the content panel
+ jpContentPanel.setLayout(new BoxLayout(jpContentPanel, BoxLayout.Y_AXIS));
+
+ // wrap content panel into a standard scroll pane
+ JScrollPane spContent = new JScrollPane(jpContentPanel);
+ spContent.setBorder(BorderFactory.createEmptyBorder(0, 5, 5, 5));
+ spContent.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
+ spContent.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+
+ // create the actual box stub with a border which will contain the scroll pane
+ JPanel jpBox = new JPanel();
+ jpBox.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createEmptyBorder(2, 2, 2, 2), BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), " "
+ + strBoxTitle + " ")));
+
+ jpBox.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+ c.anchor = GridBagConstraints.NORTHWEST;
+ c.fill = GridBagConstraints.BOTH;
+ c.weightx = 1.0;
+ c.weighty = 1.0;
+ jpBox.add(spContent, c);
+
+ return (jpBox);
+ }
+
+ // *** Callback for ActionListener interface ***
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource() instanceof JClickableLabel) {
+ if (e.getActionCommand().startsWith(SearchTabContentPanel.SEARCH_FROM_HISTORY)) {
+ // open search tab and start the chosen search
+ this.pluginMainComponent.getSearchTab().actionPerformed(e);
+ this.pluginMainComponent.getMainTabs().setSelectedComponent(this.pluginMainComponent.getSearchTab());
+ } else if (e.getActionCommand().startsWith("tag:")) {
+ // open tag browser tab and start the chosen tag search
+ this.pluginMainComponent.getTagBrowserTab().actionPerformed(e);
+ this.pluginMainComponent.getMainTabs().setSelectedComponent(this.pluginMainComponent.getTagBrowserTab());
+ } else if (e.getActionCommand().contains("history")) {
+ if (e.getActionCommand() == "preview_history")
+ spMain.setRightComponent(jpPreviewHistoryBox);
+ else if (e.getActionCommand() == "search_history")
+ spMain.setRightComponent(jpSearchHistoryBox);
+ else if (e.getActionCommand() == "tag_history")
+ spMain.setRightComponent(jpTagSearchHistoryBox);
+ else if (e.getActionCommand() == "downloads_history")
+ spMain.setRightComponent(jpDownloadedItemsHistoryBox);
+ else if (e.getActionCommand() == "opened_history")
+ spMain.setRightComponent(jpOpenedItemsHistoryBox);
+ else if (e.getActionCommand() == "uploaded_history")
+ spMain.setRightComponent(jpUploadedItemsHistoryBox);
+ else if (e.getActionCommand() == "comments_history")
+ spMain.setRightComponent(jpCommentedOnHistoryBox);
+ }
+ }
+
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/JClickableLabel.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/JClickableLabel.java
new file mode 100644
index 0000000..53f901f
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/JClickableLabel.java
@@ -0,0 +1,127 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.Color;
+import java.awt.Cursor;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.util.EventListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.Icon;
+import javax.swing.JLabel;
+import javax.swing.SwingUtilities;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Util;
+
+/**
+ * @author Sergejs Aleksejevs, Jiten Bhagat
+ */
+
+public class JClickableLabel extends JLabel implements MouseListener
+{
+ // This will hold the data which is relevant to processing the 'click' event on this label
+ private String strData;
+
+ // This will hold a reference to ResourcePreviewBrowser instance that is supposed to process the clicks
+ // on JClickableLabels
+ private ActionListener clickHandler;
+
+
+ public JClickableLabel(String strLabel, String strDataForAction, EventListener eventHandler)
+ {
+ this(strLabel, strDataForAction, eventHandler, null);
+ }
+
+ public JClickableLabel(String strLabel, String strDataForAction, EventListener eventHandler, Icon icon)
+ {
+ this(strLabel, strDataForAction, eventHandler, icon, SwingUtilities.LEFT);
+ }
+
+ public JClickableLabel(String strLabel, String strDataForAction, EventListener eventHandler, Icon icon, int horizontalAlignment)
+ {
+ this(strLabel, strDataForAction, eventHandler, icon, horizontalAlignment, null);
+ }
+
+ /**
+ *
+ * @param strLabel Textual label that will be visible in the UI.
+ * @param strDataForAction Data that will be passed to eventHandler when click on the label is made.
+ * @param eventHandler ActionListener that will process clicks on this label.
+ * @param icon Icon to display in the label.
+ * @param horizontalAlignment This is one of SwingConstants: LEFT, CENTER, RIGHT, LEADING or TRAILING
+ * @param strTooltip Tooltip to show over the label - if none is provided (e.g. null value), the strLabel will be used as a tooltip.
+ */
+ public JClickableLabel(String strLabel, String strDataForAction, EventListener eventHandler, Icon icon, int horizontalAlignment, String strTooltip)
+ {
+ super(strLabel, icon, horizontalAlignment);
+
+ this.strData = strDataForAction;
+ this.clickHandler = (ActionListener)eventHandler;
+
+ // empty border at the top and bottom will simulate "line-spacing"
+ // (this is only needed when an icon is displayed)
+ if (icon != null) {
+ this.setBorder(BorderFactory.createEmptyBorder(3, 0, 3, 0));
+ }
+
+ // the tooltip for now only shows the full label text
+ this.setToolTipText(strTooltip == null ? strLabel : strTooltip);
+ this.setForeground(Color.BLUE);
+ this.addMouseListener(this);
+ }
+
+
+ /* This class extends JLabel, so it can't extend MouseAdapter;
+ * therefore, empty methods will be added for not useful callbacks
+ * from the MouseListener interface.
+ */
+ public void mouseClicked(MouseEvent e)
+ {
+ // call 'actionPerfermed' method on the clickHandler instance that was supplied
+ // on creation of the JClickableLabel instance
+ this.clickHandler.actionPerformed(new ActionEvent(this, e.getID(), this.strData));
+ }
+
+ public void mouseEntered(MouseEvent e)
+ {
+ this.setCursor( Cursor.getPredefinedCursor( Cursor.HAND_CURSOR ) ) ;
+ }
+
+ public void mouseExited(MouseEvent e)
+ {
+ this.setCursor( Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR ) ) ;
+ }
+
+ public void mousePressed(MouseEvent e)
+ {
+ // do nothing
+ }
+
+ public void mouseReleased(MouseEvent e)
+ {
+ // do nothing
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MainComponent.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MainComponent.java
new file mode 100644
index 0000000..f4b6ace
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MainComponent.java
@@ -0,0 +1,645 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+/**
+ *
+ */
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.io.ByteArrayInputStream;
+import java.awt.Desktop;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.ImageIcon;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTabbedPane;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.text.html.HTMLEditorKit;
+import javax.swing.text.html.StyleSheet;
+
+import net.sf.taverna.t2.lang.ui.ShadedLabel;
+import net.sf.taverna.t2.ui.perspectives.PerspectiveRegistry;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Util;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Workflow;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.file.FileType;
+import net.sf.taverna.t2.workbench.file.exceptions.OpenException;
+import net.sf.taverna.t2.workbench.file.importworkflow.gui.ImportWorkflowWizard;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+import net.sf.taverna.t2.workbench.ui.zaria.PerspectiveSPI;
+import net.sf.taverna.t2.workbench.ui.zaria.UIComponentSPI;
+import net.sf.taverna.t2.workflowmodel.Dataflow;
+import net.sf.taverna.t2.workflowmodel.serialization.xml.impl.XMLSerializationConstants;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author Sergejs Aleksejevs, Emmanuel Tagarira, Jiten Bhagat
+ */
+public final class MainComponent extends JPanel implements UIComponentSPI, ChangeListener {
+ // myExperiment client, logger and the stylesheet will be made available
+ // throughout the whole perspective
+ private MyExperimentClient myExperimentClient;
+ private final Logger logger = Logger.getLogger(MainComponent.class);
+ private final StyleSheet css;
+ private final ResourcePreviewFactory previewFactory;
+ private final ResourcePreviewBrowser previewBrowser;
+
+ // components of the perspective
+ private JTabbedPane tpMainTabs;
+ private MyStuffTabContentPanel pMyStuffContainer;
+ private ExampleWorkflowsPanel pExampleWorkflows;
+ private TagBrowserTabContentPanel pTagBrowser;
+ private SearchTabContentPanel pSearchTab;
+ private HistoryBrowserTabContentPanel pHistoryBrowserTab;
+ private PluginStatusBar pStatusBar;
+ private PluginPreferencesDialog jdPreferences;
+
+ public static MainComponent MAIN_COMPONENT;
+ public static MyExperimentClient MY_EXPERIMENT_CLIENT;
+ public static Logger LOGGER;
+ private final EditManager editManager;
+ private final FileManager fileManager;
+
+ public MainComponent(EditManager editManager, FileManager fileManager) {
+ super();
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+
+ // create and initialise myExperiment client
+ try {
+ this.myExperimentClient = new MyExperimentClient(logger);
+ } catch (Exception e) {
+ this.logger.error("Couldn't initialise myExperiment client");
+ }
+
+ // x, y, z ARE NOT USED ANYWHERE ELSE
+ // HACK TO BE ABLE TO GET THE REFS FROM TAVERNA'S PREFERENCE PANEL
+ // TODO: refactor code for all the other classes to utilise the class
+ // vars
+ MainComponent x = this;
+ MAIN_COMPONENT = x;
+
+ MyExperimentClient y = this.myExperimentClient;
+ MY_EXPERIMENT_CLIENT = y;
+
+ Logger z = this.logger;
+ LOGGER = z;
+
+ // components to generate and display previews
+ previewFactory = new ResourcePreviewFactory(this, myExperimentClient, logger);
+ previewBrowser = new ResourcePreviewBrowser(this, myExperimentClient, logger, fileManager);
+
+ this.css = new StyleSheet();
+ this.css.importStyleSheet(MyExperimentPerspective.getLocalResourceURL("css_stylesheet"));
+ logger.debug("Stylesheet loaded: \n" + this.css.toString());
+
+ // check if values for default tabs are set, if not - set defaults;
+ // NB! This has to be done before initialising UI
+ if (myExperimentClient.getSettings().getProperty(
+ MyExperimentClient.INI_DEFAULT_ANONYMOUS_TAB) == null)
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_DEFAULT_ANONYMOUS_TAB, "3"); // SEARCH
+ if (myExperimentClient.getSettings().getProperty(
+ MyExperimentClient.INI_DEFAULT_LOGGED_IN_TAB) == null)
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_DEFAULT_LOGGED_IN_TAB, "0"); // STUFF
+
+ initialisePerspectiveUI();
+
+ // HACK for a weird stylesheet bug (where the first thing to use the
+ // stylesheet doesn't actually get the styles)
+ // NB! This has to be located after all ShadedLabels were initialized to
+ // prevent bad layout in them
+ HTMLEditorKit kit = new StyledHTMLEditorKit(this.css);
+
+ // determine which shutdown operations to use
+ if (Util.isRunningInTaverna()) {
+ // register the current instance of main component with the
+ // myExperiment
+ // perspective; this will be used later on when shutdown operation
+ // needs
+ // to be performed - e.g. this aids ShutdownSPI to find the running
+ // instance of the plugin
+ for (PerspectiveSPI perspective : PerspectiveRegistry.getInstance().getPerspectives()) {
+ if (perspective.getText().equals(MyExperimentPerspective.PERSPECTIVE_NAME)) {
+ ((MyExperimentPerspective) perspective).setMainComponent(this);
+ break;
+ }
+ }
+ }
+
+ // Do the rest in a separate thread to avoid hanging the GUI.
+ // Remember to use SwingUtilities.invokeLater to update the GUI
+ // directly.
+ new Thread("Data initialisation for Taverna 2 - myExperiment plugin") {
+ @Override
+ public void run() {
+ // load the data into the plugin
+ initialiseData();
+ }
+ }.start();
+
+ }
+
+ public ImageIcon getIcon() {
+ return WorkbenchIcons.databaseIcon;
+ }
+
+ @Override
+ public String getName() {
+ return "myExperiment Perspective Main Component";
+ }
+
+ public void onDisplay() {
+ }
+
+ public void onDispose() {
+ }
+
+ public MyExperimentClient getMyExperimentClient() {
+ return this.myExperimentClient;
+ }
+
+ public Logger getLogger() {
+ return this.logger;
+ }
+
+ public StyleSheet getStyleSheet() {
+ return this.css;
+ }
+
+ public PluginStatusBar getStatusBar() {
+ return this.pStatusBar;
+ }
+
+ public PluginPreferencesDialog getPreferencesDialog() {
+ return this.jdPreferences;
+ }
+
+ public ResourcePreviewFactory getPreviewFactory() {
+ return this.previewFactory;
+ }
+
+ public ResourcePreviewBrowser getPreviewBrowser() {
+ return this.previewBrowser;
+ }
+
+ public HistoryBrowserTabContentPanel getHistoryBrowser() {
+ return this.pHistoryBrowserTab;
+ }
+
+ public JTabbedPane getMainTabs() {
+ return (this.tpMainTabs);
+ }
+
+ public MyStuffTabContentPanel getMyStuffTab() {
+ return (this.pMyStuffContainer);
+ }
+
+ public ExampleWorkflowsPanel getExampleWorkflowsTab() {
+ return (this.pExampleWorkflows);
+ }
+
+ public TagBrowserTabContentPanel getTagBrowserTab() {
+ return (this.pTagBrowser);
+ }
+
+ public SearchTabContentPanel getSearchTab() {
+ return (this.pSearchTab);
+ }
+
+ private void initialisePerspectiveUI() {
+ // HACK: this is required to prevent some labels from having white
+ // non-transparent background
+ ShadedLabel testLabel = new ShadedLabel("test", ShadedLabel.BLUE);
+
+ // create instances of individual components
+ // (NB! Status bar needs to be initialised first, so that it is
+ // available to
+ // other components immediately!)
+ this.pStatusBar = new PluginStatusBar(this, myExperimentClient, logger);
+ this.pMyStuffContainer = new MyStuffTabContentPanel(this, myExperimentClient, logger, fileManager);
+ this.pExampleWorkflows = new ExampleWorkflowsPanel(this, myExperimentClient, logger);
+ this.pTagBrowser = new TagBrowserTabContentPanel(this, myExperimentClient, logger);
+ this.pSearchTab = new SearchTabContentPanel(this, myExperimentClient, logger);
+ this.pHistoryBrowserTab = new HistoryBrowserTabContentPanel(this, myExperimentClient,
+ logger);
+
+ // add the required ones into the main tabs
+ this.tpMainTabs = new JTabbedPane();
+ this.tpMainTabs.add("My Stuff", this.pMyStuffContainer);
+ // TODO: implement the starter pack
+ this.tpMainTabs.add("Starter Pack", this.pExampleWorkflows);
+ this.tpMainTabs.add("Tag Browser", this.pTagBrowser);
+ this.tpMainTabs.add("Search", this.pSearchTab);
+ this.tpMainTabs.add("Local History", this.pHistoryBrowserTab);
+
+ // add main tabs and the status bar into the perspective
+ this.setLayout(new BorderLayout());
+ this.add(this.tpMainTabs, BorderLayout.CENTER);
+ this.add(this.pStatusBar, BorderLayout.SOUTH);
+
+ // add listener to TabbedPane, so that the app "knows" when some tab was
+ // opened
+ this.tpMainTabs.addChangeListener(this);
+
+ // initialise the preferences dialog
+ /*
+ * NB! this has to be done after all tabs were created (Preview Browser
+ * is used as an owner of the preferences dialog because Preview Browser
+ * is the only JFrame in the application - in Java 1.5 it is only
+ * possible to set an icon to a JFrame and all 'children' dialog of it
+ * get the same icon - so essentially, this is only to set the
+ * myExperiment logo as an icon of preferences dialog.)
+ */
+ this.jdPreferences = new PluginPreferencesDialog(this.getPreviewBrowser(), this,
+ myExperimentClient, logger);
+ }
+
+ private void initialiseData() {
+ this.logger.debug("Initialising myExperiment Perspective data");
+
+ // check if 'auto-login' is required (NB! This requires the BASE_URL to
+ // be
+ // set correctly!)
+ Object oAutoLogin = this.myExperimentClient.getSettings().get(
+ MyExperimentClient.INI_AUTO_LOGIN);
+ if (oAutoLogin != null && oAutoLogin.equals("true")) {
+ this.getStatusBar().setStatus(this.getMyStuffTab().getClass().getName(),
+ "Performing autologin");
+ this.myExperimentClient.doLoginFromStoredCredentials();
+ this.getStatusBar().setStatus(this.getMyStuffTab().getClass().getName(),
+ "Autologin finished. Fetching user data");
+ }
+
+ // NB! This should only be done if the user is logged in -
+ // otherwise this component simply doesn't exist
+ // this.pMyStuffContainer.spMyStuff.setDividerLocation(0.3);
+
+ // load data into all tabs
+ this.pMyStuffContainer.createAndInitialiseInnerComponents();
+ if (this.myExperimentClient.isLoggedIn()) {
+ // set the default tab for logged in user (e.g. as a consequence of
+ // auto-login)
+ tpMainTabs.setSelectedIndex(Integer.parseInt(myExperimentClient.getSettings()
+ .getProperty(MyExperimentClient.INI_DEFAULT_LOGGED_IN_TAB)));
+
+ // auto-login was successful - can display user tags
+ // (no need to refresh this cloud on its own, because the whole tab
+ // is refreshed immediately after)
+ this.pTagBrowser.setMyTagsShown(true);
+ } else {
+ // set the default tab for anonymous user (auto-login failed or
+ // wasn't
+ // chosen)
+ tpMainTabs.setSelectedIndex(Integer.parseInt(myExperimentClient.getSettings()
+ .getProperty(MyExperimentClient.INI_DEFAULT_ANONYMOUS_TAB)));
+ }
+
+ this.pExampleWorkflows.refresh();
+ this.pTagBrowser.refresh();
+ }
+
+ public void stateChanged(ChangeEvent e) {
+ // invoked when a tab is opened
+ if (e.getSource().equals(this.tpMainTabs)) {
+ this.getStatusBar().displayStatus(
+ this.getMainTabs().getSelectedComponent().getClass().getName());
+ }
+ }
+
+ // ************** ACTIONS ***************
+ public class PreviewResourceAction extends AbstractAction {
+ private int iResourceType = Resource.UNKNOWN;
+ private String strResourceURI = "";
+
+ public PreviewResourceAction(int iResourceType, String strResourceURI) {
+ putValue(SMALL_ICON, WorkbenchIcons.zoomIcon);
+ putValue(NAME, "Preview");
+ putValue(SHORT_DESCRIPTION,
+ "Preview this " + Resource.getResourceTypeName(iResourceType).toLowerCase()
+ + " in the Preview Browser window");
+
+ this.iResourceType = iResourceType;
+ this.strResourceURI = strResourceURI;
+ }
+
+ public void actionPerformed(ActionEvent actionEvent) {
+ getPreviewBrowser()
+ .preview("preview:" + this.iResourceType + ":" + this.strResourceURI);
+ }
+ }
+
+ public class DownloadResourceAction extends AbstractAction {
+ private Resource resource = null;
+
+ public DownloadResourceAction(Resource resource) {
+ this(resource, true);
+ }
+
+ public DownloadResourceAction(Resource resource, boolean bShowButtonLabel) {
+ this.resource = resource;
+ String strResourceType = resource.getItemTypeName().toLowerCase();
+
+ // in either case the icon is the same; label might be displayed -
+ // based
+ // on the parameter
+ putValue(SMALL_ICON, WorkbenchIcons.saveIcon);
+ if (bShowButtonLabel)
+ putValue(NAME, "Download");
+
+ String strTooltip = "Downloading " + strResourceType + "s is currently not possible";
+ boolean bDownloadAllowed = false;
+ if (resource.isDownloadable()) {
+ if (resource.isDownloadAllowed()) {
+ strTooltip = "Download this " + strResourceType + " and store it locally";
+ bDownloadAllowed = true;
+ } else {
+ strTooltip = "You don't have permissions to download this " + strResourceType;
+ }
+ }
+
+ setEnabled(bDownloadAllowed);
+ putValue(SHORT_DESCRIPTION, strTooltip);
+ }
+
+ public void actionPerformed(ActionEvent actionEvent) {
+ try {
+ Desktop.getDesktop().browse(new URI(resource.getResource() + "/download"));
+
+ // update downloaded items history making sure that:
+ // - there's only one occurrence of this item in the history;
+ // - if this item was in the history before, it is moved to the
+ // 'top'
+ // now;
+ // - predefined history size is not exceeded
+ getHistoryBrowser().getDownloadedItemsHistoryList().remove(resource);
+ getHistoryBrowser().getDownloadedItemsHistoryList().add(resource);
+ if (getHistoryBrowser().getDownloadedItemsHistoryList().size() > HistoryBrowserTabContentPanel.DOWNLOADED_ITEMS_HISTORY_LENGTH) {
+ getHistoryBrowser().getDownloadedItemsHistoryList().remove(0);
+ }
+
+ // now update the downloaded items history panel in 'History'
+ // tab
+ if (getHistoryBrowser() != null) {
+ getHistoryBrowser().refreshHistoryBox(
+ HistoryBrowserTabContentPanel.DOWNLOADED_ITEMS_HISTORY);
+ }
+ } catch (Exception ex) {
+ logger.error("Failed while trying to open download URL in a standard browser; URL was: "
+ + resource.getURI() + "\nException was: " + ex);
+ }
+ }
+ }
+
+ public class LoadResourceInTavernaAction extends AbstractAction {
+ private final Resource resource;
+
+ public LoadResourceInTavernaAction(Resource resource) {
+ this(resource, true);
+ }
+
+ public LoadResourceInTavernaAction(Resource resource, boolean bShowButtonLabel) {
+ this.resource = resource;
+ String strResourceType = resource.getItemTypeName().toLowerCase();
+
+ putValue(SMALL_ICON, WorkbenchIcons.openIcon);
+ if (bShowButtonLabel)
+ putValue(NAME, "Open");
+
+ boolean bLoadingAllowed = false;
+ String strTooltip = "Loading " + strResourceType
+ + "s into Taverna Workbench is currently not possible";
+ if (resource.getItemType() == Resource.WORKFLOW) {
+ if (((Workflow) resource).isTavernaWorkflow()) {
+ if (resource.isDownloadAllowed()) {
+ // Taverna workflow and download allowed - can load in
+ // Taverna
+ bLoadingAllowed = true;
+ strTooltip = "Download and load this workflow in Design mode of Taverna Workbench";
+ } else {
+ strTooltip = "You don't have permissions to download this workflow, and thus to load into Taverna Workbench";
+ }
+ } else {
+ strTooltip = "Loading workflow of unsupported type into Taverna Workbench is not possible.";
+ }
+ }
+
+ setEnabled(bLoadingAllowed);
+ putValue(SHORT_DESCRIPTION, strTooltip);
+
+ }
+
+ public void actionPerformed(ActionEvent actionEvent) {
+ // if the preview browser window is opened, hide it beneath the main
+ // window
+ if (getPreviewBrowser().isActive())
+ getPreviewBrowser().toBack();
+
+ final String strCallerTabClassName = getMainTabs().getSelectedComponent().getClass()
+ .getName();
+ getStatusBar().setStatus(strCallerTabClassName, "Downloading and opening workflow...");
+ logger.debug("Downloading and opening workflow from URI: " + resource.getURI());
+
+ new Thread("Download and open workflow") {
+ @Override
+ public void run() {
+ try {
+ Workflow w = myExperimentClient.fetchWorkflowBinary(resource.getURI());
+ ByteArrayInputStream workflowDataInputStream = new ByteArrayInputStream(
+ w.getContent());
+
+ FileType fileTypeType = (w.isTaverna1Workflow() ? new ScuflFileType()
+ : new T2FlowFileType());
+ Dataflow openDataflow = fileManager.openDataflow(fileTypeType,
+ workflowDataInputStream);
+ } catch (Exception e) {
+ javax.swing.JOptionPane.showMessageDialog(null,
+ "An error has occurred while trying to load a workflow from myExperiment.\n\n"
+ + e, "Error", JOptionPane.ERROR_MESSAGE);
+ logger.error(
+ "Failed to open connection to URL to download and open workflow, from myExperiment.",
+ e);
+ }
+
+ getStatusBar().setStatus(strCallerTabClassName, null);
+
+ // update opened items history making sure that:
+ // - there's only one occurrence of this item in the
+ // history;
+ // - if this item was in the history before, it is moved to
+ // the 'top'
+ // now;
+ // - predefined history size is not exceeded
+ getHistoryBrowser().getOpenedItemsHistoryList().remove(resource);
+ getHistoryBrowser().getOpenedItemsHistoryList().add(resource);
+ if (getHistoryBrowser().getOpenedItemsHistoryList().size() > HistoryBrowserTabContentPanel.OPENED_ITEMS_HISTORY_LENGTH) {
+ getHistoryBrowser().getOpenedItemsHistoryList().remove(0);
+ }
+
+ // now update the opened items history panel in 'History'
+ // tab
+ if (getHistoryBrowser() != null) {
+ getHistoryBrowser().refreshHistoryBox(
+ HistoryBrowserTabContentPanel.OPENED_ITEMS_HISTORY);
+ }
+ }
+ }.start();
+ }
+ }
+
+ public class ImportIntoTavernaAction extends AbstractAction {
+ private final Resource resource;
+ private boolean importAsNesting;
+
+ public ImportIntoTavernaAction(Resource r) {
+ this.resource = r;
+
+ String strResourceType = resource.getItemTypeName().toLowerCase();
+
+ putValue(SMALL_ICON, WorkbenchIcons.importIcon);
+ putValue(NAME, "Import");
+
+ boolean bLoadingAllowed = false;
+ String strTooltip = "Loading " + strResourceType
+ + "s into Taverna Workbench is currently not possible";
+ if (resource.getItemType() == Resource.WORKFLOW) {
+ if (((Workflow) resource).isTavernaWorkflow()) {
+ if (resource.isDownloadAllowed()) {
+ // Taverna workflow and download allowed - can load in
+ // Taverna
+ bLoadingAllowed = true;
+ strTooltip = "Import this workflow into one that is currently open in the Design mode of Taverna Workbench";
+ } else {
+ strTooltip = "You don't have permissions to download this workflow, and thus to load into Taverna Workbench";
+ }
+ } else {
+ strTooltip = "Loading workflow of unsupported type into Taverna Workbench is not possible.";
+ }
+ }
+
+ setEnabled(bLoadingAllowed);
+ putValue(SHORT_DESCRIPTION, strTooltip);
+ }
+
+ public void actionPerformed(ActionEvent actionEvent) {
+ // if the preview browser window is opened, hide it beneath the main
+ // window
+ if (getPreviewBrowser().isActive())
+ getPreviewBrowser().toBack();
+
+ ImportWorkflowWizard importWorkflowDialog = new ImportWorkflowWizard(
+ getPreviewBrowser(), editManager, fileManager);
+
+ Workflow w;
+ try {
+ w = MY_EXPERIMENT_CLIENT.fetchWorkflowBinary(resource.getURI());
+ } catch (Exception e) {
+ JOptionPane.showMessageDialog(null, "An error has occurred "
+ + "while trying to load a " + "workflow from myExperiment.\n\n" + e,
+ "Error", JOptionPane.ERROR_MESSAGE);
+ LOGGER.error("Failed to open connection to URL to "
+ + "download and open workflow, from myExperiment.", e);
+ return;
+ }
+ ByteArrayInputStream workflowDataInputStream = new ByteArrayInputStream(w.getContent());
+ FileType fileTypeType = (w.isTaverna1Workflow() ? new MainComponent.ScuflFileType()
+ : new MainComponent.T2FlowFileType());
+ Dataflow toBeImported;
+ try {
+ toBeImported = fileManager.openDataflowSilently(fileTypeType,
+ workflowDataInputStream).getDataflow();
+ } catch (OpenException e) {
+ JOptionPane.showMessageDialog(null, "An error has occurred"
+ + " while trying to load a " + "workflow from myExperiment.\n\n" + e,
+ "Error", JOptionPane.ERROR_MESSAGE);
+ LOGGER.error("Failed to" + " open connection to URL "
+ + "to download and open workflow, from myExperiment.", e);
+ return;
+ }
+ importWorkflowDialog.setCustomSourceDataflow(toBeImported, "From myExperiment: "
+ + resource.getTitle());
+ importWorkflowDialog.setSourceEnabled(false);
+ importWorkflowDialog.setVisible(true);
+
+ // update opened items history making sure that:
+ // - there's only one occurrence of this item in the history;
+ // - if this item was in the history before, it is moved to the
+ // 'top' now;
+ // - predefined history size is not exceeded
+ getHistoryBrowser().getOpenedItemsHistoryList().remove(resource);
+ getHistoryBrowser().getOpenedItemsHistoryList().add(resource);
+ if (getHistoryBrowser().getOpenedItemsHistoryList().size() > HistoryBrowserTabContentPanel.OPENED_ITEMS_HISTORY_LENGTH) {
+ getHistoryBrowser().getOpenedItemsHistoryList().remove(0);
+ }
+
+ // now update the opened items history panel in 'History' tab
+ if (getHistoryBrowser() != null)
+ getHistoryBrowser().refreshHistoryBox(
+ HistoryBrowserTabContentPanel.OPENED_ITEMS_HISTORY);
+ }
+
+ }
+
+ // *** FileTypes for opening workflows inside Taverna
+
+ public static class ScuflFileType extends FileType {
+
+ @Override
+ public String getDescription() {
+ return "Taverna 1 SCUFL workflow";
+ }
+
+ @Override
+ public String getExtension() {
+ return "xml";
+ }
+
+ @Override
+ public String getMimeType() {
+ return "application/vnd.taverna.scufl+xml";
+ }
+ }
+
+ public static class T2FlowFileType extends FileType {
+ @Override
+ public String getDescription() {
+ return "Taverna 2 workflow";
+ }
+
+ @Override
+ public String getExtension() {
+ return "t2flow";
+ }
+
+ @Override
+ public String getMimeType() {
+ // "application/vnd.taverna.t2flow+xml";
+ return XMLSerializationConstants.WORKFLOW_DOCUMENT_MIMETYPE;
+ }
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MainComponentFactory.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MainComponentFactory.java
new file mode 100644
index 0000000..65f8875
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MainComponentFactory.java
@@ -0,0 +1,60 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+/**
+ * @author Sergejs Aleksejevs, Jiten Bhagat
+ */
+
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+import net.sf.taverna.t2.workbench.ui.zaria.UIComponentFactorySPI;
+import net.sf.taverna.t2.workbench.ui.zaria.UIComponentSPI;
+
+public class MainComponentFactory implements UIComponentFactorySPI {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+
+ public UIComponentSPI getComponent() {
+ return new MainComponent(editManager, fileManager);
+ }
+
+ public ImageIcon getIcon() {
+ return WorkbenchIcons.databaseIcon;
+ }
+
+ public String getName() {
+ return "myExperiment Main Component Factory";
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MainComponentShutdownHook.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MainComponentShutdownHook.java
new file mode 100644
index 0000000..2214d5e
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MainComponentShutdownHook.java
@@ -0,0 +1,84 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import net.sf.taverna.t2.ui.perspectives.PerspectiveRegistry;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.workbench.ShutdownSPI;
+import net.sf.taverna.t2.workbench.ui.zaria.PerspectiveSPI;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author Sergejs Aleksejevs, Jiten Bhagat
+ */
+
+public class MainComponentShutdownHook implements ShutdownSPI {
+ private MainComponent pluginMainComponent;
+ private MyExperimentClient myExperimentClient;
+ private Logger logger;
+
+ public int positionHint() {
+ // all custom plugins are suggested to return a value of > 100;
+ // this affects when in the termination process will this plugin
+ // be shutdown;
+ return 100;
+ }
+
+ public boolean shutdown() {
+ // find instance of main component of the running myExperiment perspective
+ MainComponent mainComponent = null;
+ for (PerspectiveSPI perspective : PerspectiveRegistry.getInstance().getPerspectives()) {
+ if (perspective instanceof MyExperimentPerspective) {
+ mainComponent = ((MyExperimentPerspective) perspective).getMainComponent();
+ break;
+ }
+ }
+
+ // if myExperiment perspective wasn't initialised, no shutdown operations are required / possible
+ if (mainComponent != null) {
+ this.setLinks(mainComponent, mainComponent.getMyExperimentClient(), mainComponent.getLogger());
+ logger.debug("Starting shutdown operations for myExperiment plugin");
+
+ try {
+ myExperimentClient.storeHistoryAndSettings();
+ } catch (Exception e) {
+ logger.error("Failed while serializing myExperiment plugin settings:\n"
+ + e);
+ }
+
+ logger.debug("myExperiment plugin shutdown is completed; terminated...");
+ }
+
+ // "true" means that shutdown operations are complete and Taverna can terminate
+ return true;
+ }
+
+ /**
+ * Sets up links of this class with the rest of the plugin.
+ */
+ public void setLinks(MainComponent component, MyExperimentClient client, Logger logger) {
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MyExperimentPerspective.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MyExperimentPerspective.java
new file mode 100644
index 0000000..1982b75
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MyExperimentPerspective.java
@@ -0,0 +1,190 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.io.InputStream;
+import java.net.URL;
+
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import net.sf.taverna.t2.workbench.ui.zaria.PerspectiveSPI;
+
+import org.jdom.Element;
+
+/**
+ * @author Sergejs Aleksejevs, Jiten Bhagat
+ */
+public class MyExperimentPerspective implements PerspectiveSPI {
+ // CONSTANTS
+ // this is where all icons, stylesheet, etc are located
+ private static final String BASE_RESOURCE_PATH = "/net/sf/taverna/t2/ui/perspectives/myexperiment/";
+ public static final String PERSPECTIVE_NAME = "myExperiment";
+ public static final String PLUGIN_VERSION = "0.2beta";
+
+ // COMPONENTS
+ private MainComponent perspectiveMainComponent;
+ private boolean visible = true;
+
+ public ImageIcon getButtonIcon() {
+ URL iconURL = MyExperimentPerspective.getLocalResourceURL("myexp_icon16x16");
+ if (iconURL == null) {
+ return null;
+ } else {
+ return new ImageIcon(iconURL);
+ }
+ }
+
+ public InputStream getLayoutInputStream() {
+ return getClass().getResourceAsStream("myexperiment-perspective.xml");
+ }
+
+ public String getText() {
+ return PERSPECTIVE_NAME;
+ }
+
+ public boolean isVisible() {
+ return visible;
+ }
+
+ public int positionHint() {
+ // this determines position of myExperiment perspective in the
+ // bar with perspective buttons (currently makes it the last in the
+ // list)
+ return 30;
+ }
+
+ public void setVisible(boolean visible) {
+ this.visible = visible;
+
+ }
+
+ public void update(Element layoutElement) {
+ // Not sure what to do here
+ }
+
+ public void setMainComponent(MainComponent component) {
+ this.perspectiveMainComponent = component;
+ }
+
+ /**
+ * Returns the instance of the main component of this perspective.
+ */
+ public MainComponent getMainComponent() {
+ return this.perspectiveMainComponent;
+ }
+
+ // a single point in the plugin where all resources are referenced
+ public static URL getLocalResourceURL(String strResourceName) {
+ String strResourcePath = MyExperimentPerspective.BASE_RESOURCE_PATH;
+
+ if (strResourceName.equals("not_authorized_icon"))
+ strResourcePath += "denied.png";
+ if (strResourceName.equals("failure_icon"))
+ strResourcePath += "denied.png";
+ else if (strResourceName.equals("success_icon"))
+ strResourcePath += "tick.png";
+ else if (strResourceName.equals("spinner"))
+ strResourcePath += "ajax-loader.gif";
+ else if (strResourceName.equals("spinner_stopped"))
+ strResourcePath += "ajax-loader-still.gif";
+ else if (strResourceName.equals("external_link_small_icon"))
+ strResourcePath += "external_link_listing_small.png";
+ else if (strResourceName.equals("back_icon"))
+ strResourcePath += "arrow_left.png";
+ else if (strResourceName.equals("forward_icon"))
+ strResourcePath += "arrow_right.png";
+ else if (strResourceName.equals("refresh_icon"))
+ strResourcePath += "arrow_refresh.png";
+ else if (strResourceName.equals("favourite_icon"))
+ strResourcePath += "star.png";
+ else if (strResourceName.equals("add_favourite_icon"))
+ strResourcePath += "favourite_add.png";
+ else if (strResourceName.equals("delete_favourite_icon"))
+ strResourcePath += "favourite_delete.png";
+ else if (strResourceName.equals("destroy_icon"))
+ strResourcePath += "cross.png";
+ else if (strResourceName.equals("add_comment_icon"))
+ strResourcePath += "comment_add.png";
+ else if (strResourceName.equals("myexp_icon"))
+ strResourcePath += "myexp_icon.png";
+ else if (strResourceName.equals("myexp_icon16x16"))
+ strResourcePath += "myexp_icon16x16.png";
+ else if (strResourceName.equals("open_in_my_experiment_icon"))
+ strResourcePath += "open_in_myExperiment.png";
+ else if (strResourceName.equals("login_icon"))
+ strResourcePath += "login.png";
+ else if (strResourceName.equals("logout_icon"))
+ strResourcePath += "logout.png";
+ else if (strResourceName.equals("css_stylesheet"))
+ strResourcePath += "styles.css";
+ else {
+ throw new java.lang.IllegalArgumentException(
+ "Unknown myExperiment plugin resource requested; requested resource name was: "
+ + strResourceName);
+ }
+
+ // no exception was thrown, therefore the supplied resource name was
+ // recognised;
+ // return the local URL of that resource
+ return (MyExperimentPerspective.class.getResource(strResourcePath));
+ }
+
+ // a single point in the plugin where all resources' icons are referenced
+ public static URL getLocalIconURL(int iResourceType) {
+ String strResourcePath = MyExperimentPerspective.BASE_RESOURCE_PATH;
+
+ switch (iResourceType) {
+ case Resource.WORKFLOW:
+ strResourcePath += "workflow.png";
+ break;
+ case Resource.FILE:
+ strResourcePath += "file.png";
+ break;
+ case Resource.PACK:
+ strResourcePath += "pack.png";
+ break;
+ case Resource.PACK_EXTERNAL_ITEM:
+ strResourcePath += "remote_resource.png";
+ break;
+ case Resource.USER:
+ strResourcePath += "user.png";
+ break;
+ case Resource.GROUP:
+ strResourcePath += "group.png";
+ break;
+ case Resource.TAG:
+ strResourcePath += "tag_blue.png";
+ break;
+ default:
+ throw new java.lang.IllegalArgumentException(
+ "Unknown myExperiment plugin resource requested; requested resource name was: "
+ + Resource.getResourceTypeName(iResourceType));
+ }
+
+ // no exception was thrown, therefore the supplied resource name was
+ // recognised;
+ // return the local URL of that resource
+ return (MyExperimentPerspective.class.getResource(strResourcePath));
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MyStuffContributionsPanel.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MyStuffContributionsPanel.java
new file mode 100644
index 0000000..e7ef972
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MyStuffContributionsPanel.java
@@ -0,0 +1,370 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.BorderFactory;
+import javax.swing.ImageIcon;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+
+import net.sf.taverna.t2.lang.ui.ShadedLabel;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.File;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Pack;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Workflow;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+
+
+/**
+ * @author Sergejs Aleksejevs, Emmanuel Tagarira, Jiten Bhagat
+ */
+public class MyStuffContributionsPanel extends JPanel implements ActionListener {
+ // CONSTANTS
+ private static final int SHADED_LABEL_HEIGHT = 20;
+ private static final int SECTION_VSPACING = 5;
+ private static final int SCROLL_PANE_PADDING = 3;
+ private static final int TOTAL_SECTION_VSPACING = SHADED_LABEL_HEIGHT
+ + SECTION_VSPACING + SCROLL_PANE_PADDING + 5; // the last literal is to cover all paddings / margins / etc
+
+ private MainComponent pluginMainComponent;
+ private MyExperimentClient myExperimentClient;
+ private Logger logger;
+
+ // MAIN COMPONENTS of the view
+ JPanel jpMyWorkflows;
+ JPanel jpMyFiles;
+ JPanel jpMyPacks;
+
+ // HELPER COMPONENTS
+ // these are the individual content listings for 'my workfows', 'my files' and 'my packs' ..
+ ResourceListPanel jpMyWorkflowsContent = null;
+ ResourceListPanel jpMyFilesContent = null;
+ ResourceListPanel jpMyPacksContent = null;
+
+ // .. these will be wrapped into individual scroll panes to ensure correct sizes
+ JScrollPane spMyWorkflowsContent = null;
+ JScrollPane spMyFilesContent = null;
+ JScrollPane spMyPacksContent = null;
+
+ // STORAGE
+ private ArrayList<JPanel> alVisiblePanels;
+ private ArrayList<JComponent[]> alVisiblePanelsWithHelperElements;
+
+ public MyStuffContributionsPanel(MainComponent component, MyExperimentClient client, Logger logger) {
+ super();
+
+ // set main variables to ensure access to myExperiment, logger and the parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+
+ alVisiblePanels = new ArrayList<JPanel>();
+ alVisiblePanelsWithHelperElements = new ArrayList<JComponent[]>();
+
+ // check that settings for this panel were set correctly in the INI file
+ // (if any record is missing - assume that this section is visible)
+ // (this will ensure that these values can be used with no further validity checks
+ // across the plugin; this is because this method will be executed at start of the plugin)
+ if (myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_MY_STUFF_WORKFLOWS) == null) {
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_MY_STUFF_WORKFLOWS, new Boolean(true).toString());
+ }
+ if (myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_MY_STUFF_FILES) == null) {
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_MY_STUFF_FILES, new Boolean(true).toString());
+ }
+ if (myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_MY_STUFF_PACKS) == null) {
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_MY_STUFF_PACKS, new Boolean(true).toString());
+ }
+
+ // create and initialise the UI of MyStuff tab
+ initialiseUI();
+ initialiseData();
+ }
+
+ private void initialiseUI() {
+ JPanel jpMyWorkflowsContainer = new JPanel();
+ jpMyWorkflowsContainer.setBorder(BorderFactory.createEmptyBorder());
+ if (Boolean.parseBoolean(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_MY_STUFF_WORKFLOWS))) {
+ // "My Workflows" panel
+ jpMyWorkflowsContainer.setBorder(BorderFactory.createEtchedBorder());
+ jpMyWorkflowsContainer.setLayout(new BorderLayout());
+
+ ShadedLabel l0 = new ShadedLabel("My Workflows", ShadedLabel.BLUE);
+ jpMyWorkflowsContainer.add(l0, BorderLayout.NORTH);
+
+ jpMyWorkflows = new JPanel();
+ jpMyWorkflows.setLayout(new BorderLayout());
+ jpMyWorkflows.setBackground(Color.WHITE);
+ jpMyWorkflows.setBorder(BorderFactory.createEmptyBorder(10, 0, 10, 0));
+ jpMyWorkflows.add(new JLabel("Loading...", new ImageIcon(MyExperimentPerspective.getLocalResourceURL("spinner")), SwingConstants.CENTER));
+
+ jpMyWorkflowsContainer.add(jpMyWorkflows, BorderLayout.CENTER);
+ alVisiblePanels.add(jpMyWorkflows);
+ }
+
+ JPanel jpMyFilesContainer = new JPanel();
+ if (Boolean.parseBoolean(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_MY_STUFF_FILES))) {
+ // "My Files" panel
+ jpMyFilesContainer.setBorder(BorderFactory.createEtchedBorder());
+ jpMyFilesContainer.setLayout(new BorderLayout());
+
+ ShadedLabel l1 = new ShadedLabel("My Files", ShadedLabel.BLUE);
+ jpMyFilesContainer.add(l1, BorderLayout.NORTH);
+
+ jpMyFiles = new JPanel();
+ jpMyFiles.setLayout(new BorderLayout());
+ jpMyFiles.setBackground(Color.WHITE);
+ jpMyFiles.setBorder(BorderFactory.createEmptyBorder(10, 0, 10, 0));
+ jpMyFiles.add(new JLabel("Loading...", new ImageIcon(MyExperimentPerspective.getLocalResourceURL("spinner")), SwingConstants.CENTER));
+
+ jpMyFilesContainer.add(jpMyFiles, BorderLayout.CENTER);
+ alVisiblePanels.add(jpMyFiles);
+ }
+
+ JPanel jpMyPacksContainer = new JPanel();
+ if (Boolean.parseBoolean(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_MY_STUFF_PACKS))) {
+ // "My Packs" panel
+ jpMyPacksContainer.setBorder(BorderFactory.createEtchedBorder());
+ jpMyPacksContainer.setLayout(new BorderLayout());
+
+ ShadedLabel l2 = new ShadedLabel("My Packs", ShadedLabel.BLUE);
+ jpMyPacksContainer.add(l2, BorderLayout.NORTH);
+
+ jpMyPacks = new JPanel();
+ jpMyPacks.setLayout(new BorderLayout());
+ jpMyPacks.setBackground(Color.WHITE);
+ jpMyPacks.setBorder(BorderFactory.createEmptyBorder(10, 0, 10, 0));
+ jpMyPacks.add(new JLabel("Loading...", new ImageIcon(MyExperimentPerspective.getLocalResourceURL("spinner")), SwingConstants.CENTER));
+
+ jpMyPacksContainer.add(jpMyPacks, BorderLayout.CENTER);
+ alVisiblePanels.add(jpMyPacks);
+ }
+
+ // ..putting everything together
+ JPanel jpEverything = new JPanel();
+ jpEverything.setLayout(new GridBagLayout());
+
+ GridBagConstraints gbConstraints = new GridBagConstraints();
+ gbConstraints.anchor = GridBagConstraints.NORTHWEST;
+ gbConstraints.fill = GridBagConstraints.BOTH;
+ gbConstraints.gridx = 0;
+ gbConstraints.weightx = 1;
+ gbConstraints.weighty = 1;
+ int index = 0;
+
+ gbConstraints.gridy = index++;
+ jpEverything.add(jpMyWorkflowsContainer, gbConstraints);
+
+ gbConstraints.gridy = index++;
+ jpEverything.add(jpMyFilesContainer, gbConstraints);
+
+ gbConstraints.gridy = index++;
+ jpEverything.add(jpMyPacksContainer, gbConstraints);
+
+ this.setLayout(new BorderLayout());
+ this.add(jpEverything, BorderLayout.NORTH);
+ }
+
+ private void initialiseData() {
+ // Make call to myExperiment API in a different thread
+ // (then use SwingUtilities.invokeLater to update the UI when ready).
+ new Thread("Loading data about contributions of current user.") {
+ @SuppressWarnings("unchecked")
+ public void run() {
+ logger.debug("Loading contributions data for current user");
+
+ try {
+ final ArrayList<Workflow> alWorkflowInstances = new ArrayList<Workflow>();
+ if (alVisiblePanels.contains(jpMyWorkflows)) {
+ boolean anyMore = true;
+ for (int page = 1; anyMore; page++) {
+ // fetch all user workflows
+ Document doc = myExperimentClient.getUserContributions(myExperimentClient.getCurrentUser(), Resource.WORKFLOW, Resource.REQUEST_SHORT_LISTING, page);
+ if (doc != null) {
+ List<Element> foundElements = doc.getRootElement().getChildren();
+ anyMore = !foundElements.isEmpty();
+ for (Element e : foundElements) {
+ Workflow wfCurrent = Workflow.buildFromXML(e, logger);
+ alWorkflowInstances.add(wfCurrent);
+ }
+ }
+ }
+ }
+
+ final ArrayList<File> alFileInstances = new ArrayList<File>();
+ if (alVisiblePanels.contains(jpMyFiles)) {
+ boolean anyMore = true;
+ for (int page = 1; anyMore; page++) {
+ // fetch all user files
+ Document doc = myExperimentClient.getUserContributions(myExperimentClient.getCurrentUser(), Resource.FILE, Resource.REQUEST_SHORT_LISTING, page);
+ if (doc != null) {
+ List<Element> foundElements = doc.getRootElement().getChildren();
+ anyMore = !foundElements.isEmpty();
+ for (Element e : foundElements) {
+ File fCurrent = File.buildFromXML(e, logger);
+ alFileInstances.add(fCurrent);
+ }
+ }
+ }
+ }
+
+ final ArrayList<Pack> alPackInstances = new ArrayList<Pack>();
+ if (alVisiblePanels.contains(jpMyPacks)) {
+ boolean anyMore = true;
+ for (int page = 1; anyMore; page++) {
+ // fetch all user packs
+ Document doc = myExperimentClient.getUserContributions(myExperimentClient.getCurrentUser(), Resource.PACK, Resource.REQUEST_SHORT_LISTING, page);
+ if (doc != null) {
+ List<Element> foundElements = doc.getRootElement().getChildren();
+ anyMore = !foundElements.isEmpty();
+ for (Element e : foundElements) {
+ Pack pCurrent = Pack.buildFromXML(e, myExperimentClient, logger);
+ alPackInstances.add(pCurrent);
+ }
+ }
+ }
+ }
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // now create views for all user contributions
+ if (alVisiblePanels.contains(jpMyWorkflows)) {
+ // .. workflows ..
+ jpMyWorkflowsContent = new ResourceListPanel(pluginMainComponent, myExperimentClient, logger);
+ jpMyWorkflowsContent.setFullSizeItemsList(false);
+ jpMyWorkflowsContent.setListItems(new ArrayList<Resource>(alWorkflowInstances));
+
+ spMyWorkflowsContent = new JScrollPane(jpMyWorkflowsContent);
+ spMyWorkflowsContent.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+
+ jpMyWorkflows.removeAll();
+ jpMyWorkflows.setBackground(null); // return background to default colour
+ jpMyWorkflows.setBorder(BorderFactory.createEmptyBorder()); // remove border that was added prior to loading
+ jpMyWorkflows.add(spMyWorkflowsContent);
+
+ alVisiblePanelsWithHelperElements.add(new JComponent[] { jpMyWorkflows, spMyWorkflowsContent, jpMyWorkflowsContent });
+ }
+
+ if (alVisiblePanels.contains(jpMyFiles)) {
+ // .. files ..
+ jpMyFilesContent = new ResourceListPanel(pluginMainComponent, myExperimentClient, logger);
+ jpMyFilesContent.setFullSizeItemsList(false);
+ jpMyFilesContent.setListItems(new ArrayList<Resource>(alFileInstances));
+
+ spMyFilesContent = new JScrollPane(jpMyFilesContent);
+ spMyFilesContent.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+
+ jpMyFiles.removeAll();
+ jpMyFiles.setBackground(null); // return background to default colour
+ jpMyFiles.setBorder(BorderFactory.createEmptyBorder()); // remove border that was added prior to loading
+ jpMyFiles.add(spMyFilesContent);
+
+ alVisiblePanelsWithHelperElements.add(new JComponent[] { jpMyFiles, spMyFilesContent, jpMyFilesContent });
+ }
+
+ if (alVisiblePanels.contains(jpMyPacks)) {
+ // .. packs ..
+ jpMyPacksContent = new ResourceListPanel(pluginMainComponent, myExperimentClient, logger);
+ jpMyPacksContent.setFullSizeItemsList(false);
+ jpMyPacksContent.setListItems(new ArrayList<Resource>(alPackInstances));
+
+ spMyPacksContent = new JScrollPane(jpMyPacksContent);
+ spMyPacksContent.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+
+ jpMyPacks.removeAll();
+ jpMyPacks.setBackground(null); // return background to default colour
+ jpMyPacks.setBorder(BorderFactory.createEmptyBorder()); // remove border that was added prior to loading
+ jpMyPacks.add(spMyPacksContent);
+
+ alVisiblePanelsWithHelperElements.add(new JComponent[] { jpMyPacks, spMyPacksContent, jpMyPacksContent });
+ }
+
+ // now work out correct sizes for each section - the goal is to maximize the usage of the space on the page
+
+ int iFullAvailableHeight = getSize().height;
+ ArrayList<Integer> alIndexesToScale = new ArrayList<Integer>();
+ for (int i = 0; i < alVisiblePanelsWithHelperElements.size(); i++) {
+ JScrollPane spContent = (JScrollPane) alVisiblePanelsWithHelperElements.get(i)[1];
+ JPanel jpContent = (JPanel) alVisiblePanelsWithHelperElements.get(i)[2];
+
+ if ((jpContent.getPreferredSize().height + TOTAL_SECTION_VSPACING) < (iFullAvailableHeight / alVisiblePanels.size())) {
+ Dimension d = jpContent.getPreferredSize();
+ d.height += SCROLL_PANE_PADDING;
+ spContent.setPreferredSize(d);
+
+ iFullAvailableHeight -= (jpContent.getPreferredSize().height)
+ + TOTAL_SECTION_VSPACING;
+ } else
+ alIndexesToScale.add(i);
+ }
+
+ if (alIndexesToScale.size() > 0) {
+ Dimension d = new Dimension();
+
+ for (Integer i : alIndexesToScale) {
+ d.height = (iFullAvailableHeight / alIndexesToScale.size())
+ - TOTAL_SECTION_VSPACING;
+ if (d.height > ((JPanel) alVisiblePanelsWithHelperElements.get(i)[2]).getPreferredSize().height
+ + SCROLL_PANE_PADDING)
+ d.height = ((JPanel) alVisiblePanelsWithHelperElements.get(i)[2]).getPreferredSize().height
+ + SCROLL_PANE_PADDING;
+
+ JScrollPane spCurrent = (JScrollPane) alVisiblePanelsWithHelperElements.get(i)[1];
+ spCurrent.setPreferredSize(d);
+ }
+ }
+
+ // report that this component has been loaded
+ pluginMainComponent.getMyStuffTab().cdlComponentLoadingDone.countDown();
+
+ validate();
+ repaint();
+ }
+ });
+ } catch (Exception ex) {
+ logger.error("Failed to populate some panel in My Stuff tab (User's files, workflows or packs)", ex);
+ }
+ }
+ }.start();
+ }
+
+ public void actionPerformed(ActionEvent arg0) {
+ javax.swing.JOptionPane.showMessageDialog(null, "button clicked");
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MyStuffSidebarPanel.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MyStuffSidebarPanel.java
new file mode 100644
index 0000000..79ef03c
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MyStuffSidebarPanel.java
@@ -0,0 +1,359 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.HashMap;
+import java.util.Iterator;
+
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.User;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Util;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author Sergejs Aleksejevs, Emmanuel Tagarira, Jiten Bhagat
+ */
+public class MyStuffSidebarPanel extends JPanel implements ActionListener {
+ private final MainComponent pluginMainComponent;
+ private final MyExperimentClient myExperimentClient;
+ private final Logger logger;
+
+ // main components of the SidebarPanel
+ private final JPanel jpMyProfileBox;
+ private final JPanel jpMyFriendsBox;
+ private final JPanel jpMyGroupsBox;
+ private final JPanel jpMyFavouritesBox;
+ private final JPanel jpMyTagsBox;
+ private JButton bLogout;
+ protected JButton bRefreshMyStuff;
+ private JButton bUpload;
+
+ // icons which are used in several places in the sidebar
+ private final ImageIcon iconUser;
+ private final ImageIcon iconLogout;
+ private final FileManager fileManager;
+
+ public MyStuffSidebarPanel(MainComponent component, MyExperimentClient client, Logger logger, FileManager fileManager) {
+ super();
+
+ // set main variables to ensure access to myExperiment, logger and the
+ // parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+ this.fileManager = fileManager;
+
+ // prepare icons
+ iconUser = new ImageIcon(MyExperimentPerspective.getLocalIconURL(Resource.USER));
+ iconLogout = new ImageIcon(MyExperimentPerspective.getLocalResourceURL("logout_icon"));
+
+ // add elements of the sidebar
+ this.setLayout(new GridBagLayout());
+ GridBagConstraints gbConstraints = new GridBagConstraints();
+ gbConstraints.anchor = GridBagConstraints.NORTHWEST;
+ gbConstraints.fill = GridBagConstraints.HORIZONTAL;
+ gbConstraints.weightx = 1;
+ gbConstraints.gridx = 0;
+
+ gbConstraints.gridy = 0;
+ jpMyProfileBox = createMyProfileBox();
+ this.add(jpMyProfileBox, gbConstraints);
+
+ gbConstraints.gridy = 1;
+ jpMyFriendsBox = createMyFriendsBox();
+ this.add(jpMyFriendsBox, gbConstraints);
+
+ gbConstraints.gridy = 2;
+ jpMyGroupsBox = createMyGroupsBox();
+ this.add(jpMyGroupsBox, gbConstraints);
+
+ gbConstraints.gridy = 3;
+ jpMyFavouritesBox = createMyFavouritesBox();
+ repopulateFavouritesBox();
+ this.add(jpMyFavouritesBox, gbConstraints);
+
+ gbConstraints.gridy = 4;
+ jpMyTagsBox = createMyTagsBox();
+ this.add(jpMyTagsBox, gbConstraints);
+
+ // report that this component has been loaded
+ pluginMainComponent.getMyStuffTab().cdlComponentLoadingDone.countDown();
+ }
+
+ // creates a JPanel displaying the currently logged in user, logout button,
+ // etc
+ private JPanel createMyProfileBox() {
+ // panel containing name and avatar
+ JPanel jpAvatar = new JPanel();
+ jpAvatar.setLayout(new BoxLayout(jpAvatar, BoxLayout.X_AXIS));
+
+ User currentUser = this.myExperimentClient.getCurrentUser();
+ ImageIcon userAvatar = currentUser.getAvatar();
+ JLabel jlUserAvatar = new JLabel("No Profile Picture Found");
+ if (userAvatar != null)
+ jlUserAvatar = new JLabel(Util.getResizedImageIcon(userAvatar, 80, 80));
+
+ jlUserAvatar.setAlignmentX(LEFT_ALIGNMENT);
+ jpAvatar.add(jlUserAvatar);
+
+ String name = "<html>";
+ for (int x = 0; x < currentUser.getName().split(" ").length; x++)
+ name += currentUser.getName().split(" ")[x] + "<br>";
+ name += "</html>";
+
+ JClickableLabel jclUserName = new JClickableLabel(name, "preview:"
+ + Resource.USER + ":" + currentUser.getURI(), pluginMainComponent.getPreviewBrowser(), this.iconUser);
+ jpAvatar.add(jclUserName);
+
+ // panel containing everything in the profile box
+ JPanel jpEverythingInProfileBox = new JPanel();
+ jpEverythingInProfileBox.setMaximumSize(new Dimension(1024, 0));
+ jpEverythingInProfileBox.setLayout(new BoxLayout(jpEverythingInProfileBox, BoxLayout.X_AXIS));
+
+ jpEverythingInProfileBox.add(jpAvatar);
+
+ // action buttons
+ bLogout = new JButton("Logout", iconLogout);
+ bLogout.addActionListener(this);
+
+ bRefreshMyStuff = new JButton("Refresh", WorkbenchIcons.refreshIcon);
+ bRefreshMyStuff.addActionListener(this.pluginMainComponent.getMyStuffTab());
+
+ bUpload = new JButton("Upload Workflow", WorkbenchIcons.upArrowIcon);
+ bUpload.addActionListener(this);
+
+ // panel for the buttons
+ JPanel jpButtons = new JPanel();
+ jpButtons.setLayout(new GridBagLayout());
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.gridwidth = 1;
+ gbc.gridy = 0;
+ gbc.anchor = GridBagConstraints.NORTH;
+ gbc.fill = GridBagConstraints.BOTH;
+ gbc.gridx = 0;
+
+ jpButtons.add(bUpload, gbc);
+ gbc.gridy++;
+ jpButtons.add(bRefreshMyStuff, gbc);
+ gbc.gridy++;
+ jpButtons.add(bLogout, gbc);
+
+ jpEverythingInProfileBox.add(jpButtons);
+
+ jpEverythingInProfileBox.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), " My Profile "), BorderFactory.createEmptyBorder(1, 8, 8, 5)));
+
+ return (jpEverythingInProfileBox);
+ }
+
+ // creates a JPanel that displays a list of all friends of the current user
+ private JPanel createMyFriendsBox() {
+ JPanel jpFriends = new JPanel();
+ jpFriends.setLayout(new BoxLayout(jpFriends, BoxLayout.Y_AXIS));
+
+ // iterate through all friends and add all to the panel
+ Iterator<HashMap<String, String>> iFriends = this.myExperimentClient.getCurrentUser().getFriends().iterator();
+ if (iFriends.hasNext()) {
+ while (iFriends.hasNext()) {
+ HashMap<String, String> hmCurFriend = iFriends.next();
+ jpFriends.add(new JClickableLabel(hmCurFriend.get("name"), "preview:"
+ + Resource.USER + ":" + hmCurFriend.get("uri"), pluginMainComponent.getPreviewBrowser(), this.iconUser));
+ }
+ } else {
+ // known not to have any friends
+ JLabel lNone = new JLabel("None");
+ lNone.setFont(lNone.getFont().deriveFont(Font.ITALIC));
+ lNone.setForeground(Color.GRAY);
+ jpFriends.add(lNone);
+ }
+
+ jpFriends.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), " My Friends "), BorderFactory.createEmptyBorder(1, 8, 8, 5)));
+
+ return (jpFriends);
+ }
+
+ // generates a JPanel that displays a list of groups for current user
+ // when they are logged in
+ private JPanel createMyGroupsBox() {
+ JPanel jpGroups = new JPanel();
+
+ jpGroups.setLayout(new BoxLayout(jpGroups, BoxLayout.Y_AXIS));
+
+ // prepare the icon for groups
+ ImageIcon iconGroup = new ImageIcon(MyExperimentPerspective.getLocalIconURL(Resource.GROUP));
+
+ // iterate through all groups and add all to the panel
+ Iterator<HashMap<String, String>> iGroups = this.myExperimentClient.getCurrentUser().getGroups().iterator();
+ if (iGroups.hasNext()) {
+ while (iGroups.hasNext()) {
+ HashMap<String, String> hmCurGroup = iGroups.next();
+ jpGroups.add(new JClickableLabel(hmCurGroup.get("name"), "preview:"
+ + Resource.GROUP + ":" + hmCurGroup.get("uri"), pluginMainComponent.getPreviewBrowser(), iconGroup));
+ }
+ } else {
+ // known not to have any groups
+ JLabel lNone = new JLabel("None");
+ lNone.setFont(lNone.getFont().deriveFont(Font.ITALIC));
+ lNone.setForeground(Color.GRAY);
+ jpGroups.add(lNone);
+ }
+
+ jpGroups.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), " My Groups "), BorderFactory.createEmptyBorder(1, 8, 8, 5)));
+
+ return (jpGroups);
+ }
+
+ // generates a JPanel that displays a list of favourite items for current user
+ // when they are logged in
+ private JPanel createMyFavouritesBox() {
+ JPanel jpFavourites = new JPanel();
+
+ jpFavourites.setLayout(new BoxLayout(jpFavourites, BoxLayout.Y_AXIS));
+ jpFavourites.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), " My Favourites "), BorderFactory.createEmptyBorder(1, 8, 8, 5)));
+
+ return (jpFavourites);
+ }
+
+ public void repopulateFavouritesBox() {
+ this.jpMyFavouritesBox.removeAll();
+
+ // iterate through all favourites and add all to the panel
+ Iterator<Resource> iFavourites = this.myExperimentClient.getCurrentUser().getFavourites().iterator();
+ if (iFavourites.hasNext()) {
+ while (iFavourites.hasNext()) {
+ Resource rFavourite = iFavourites.next();
+ this.jpMyFavouritesBox.add(new JClickableLabel(rFavourite.getTitle(), "preview:"
+ + rFavourite.getItemType() + ":" + rFavourite.getURI(), pluginMainComponent.getPreviewBrowser(), new ImageIcon(MyExperimentPerspective.getLocalIconURL(rFavourite.getItemType()))));
+ }
+ } else {
+ // known not to have any favourites
+ JLabel lNone = new JLabel("None");
+ lNone.setFont(lNone.getFont().deriveFont(Font.ITALIC));
+ lNone.setForeground(Color.GRAY);
+ this.jpMyFavouritesBox.add(lNone);
+ }
+ }
+
+ // creates a Panel that shows all tags of the current user
+ private JPanel createMyTagsBox() {
+ JPanel jpTags = new JPanel();
+ jpTags.setLayout(new BoxLayout(jpTags, BoxLayout.Y_AXIS));
+
+ // prepare the icon for tags
+ ImageIcon iconTag = new ImageIcon(MyExperimentPerspective.getLocalIconURL(Resource.TAG));
+
+ // iterate through all tags and add all to the panel
+ Iterator<HashMap<String, String>> iTags = this.myExperimentClient.getCurrentUser().getTags().iterator();
+ if (iTags.hasNext()) {
+ while (iTags.hasNext()) {
+ String strCurTag = iTags.next().get("name");
+ jpTags.add(new JClickableLabel(strCurTag, "tag:" + strCurTag, pluginMainComponent.getPreviewBrowser(), iconTag));
+ }
+ } else {
+ // known not to have any tags
+ JLabel lNone = new JLabel("None");
+ lNone.setFont(lNone.getFont().deriveFont(Font.ITALIC));
+ lNone.setForeground(Color.GRAY);
+ jpTags.add(lNone);
+ }
+
+ jpTags.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), " My Tags "), BorderFactory.createEmptyBorder(1, 8, 8, 5)));
+
+ return (jpTags);
+ }
+
+ public JPanel getMyProfileBox() {
+ return (this.jpMyProfileBox);
+ }
+
+ // listener of button clicks in the sidebar
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource().equals(bLogout)) {
+ // logout button was clicked
+
+ try {
+ // "forget" login details
+ this.myExperimentClient.doLogout();
+ } catch (Exception ex) {
+ logger.error("Error while trying to logout from myExperiment, exception:\n"
+ + ex);
+ }
+
+ // repaint "myStuff" tab to display the login box again
+ this.pluginMainComponent.getStatusBar().setStatus(this.pluginMainComponent.getMyStuffTab().getClass().getName(), "Logging out");
+ this.pluginMainComponent.getMyStuffTab().createAndInitialiseInnerComponents();
+ this.pluginMainComponent.getMyStuffTab().revalidate();
+ this.pluginMainComponent.getMyStuffTab().repaint();
+ this.pluginMainComponent.getStatusBar().setStatus(this.pluginMainComponent.getMyStuffTab().getClass().getName(), null);
+ this.pluginMainComponent.getStatusBar().setCurrentUser(null);
+
+ // remove "My Tags" from the tags browser tab and rerun last searches (tag
+ // & keyword)
+ // so that any "private" search results won't get shown anymore
+ this.pluginMainComponent.getTagBrowserTab().setMyTagsShown(false);
+ this.pluginMainComponent.getTagBrowserTab().getTagSearchResultPanel().clear();
+ this.pluginMainComponent.getTagBrowserTab().rerunLastTagSearch();
+
+ this.pluginMainComponent.getSearchTab().getSearchResultPanel().clear();
+ this.pluginMainComponent.getSearchTab().rerunLastSearch();
+
+ // TODO: also, update another tabs, so that they don't display any 'private' content?
+ } else if (e.getSource().equals(this.bUpload)) {
+ JFrame containingFrame = (JFrame) SwingUtilities.windowForComponent(this);
+ // UploadWorkflowDialog uploadWorkflowDialog = new UploadWorkflowDialog(containingFrame);
+
+ // File workflowFile = null;
+ // JFileChooser jfsSelectFile = new JFileChooser();
+ // if (jfsSelectFile.showOpenDialog(this) == JFileChooser.APPROVE_OPTION)
+ // workflowFile = jfsSelectFile.getSelectedFile();
+ // else
+ // return;
+
+ UploadWorkflowDialog uploadWorkflowDialog = new UploadWorkflowDialog(containingFrame, true, fileManager);
+
+ if (uploadWorkflowDialog.launchUploadDialogAndPostIfRequired())
+ // true was returned so refresh the whole of the mystuff content panel
+ this.actionPerformed(new ActionEvent(this.bRefreshMyStuff, 0, ""));
+
+ }
+
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MyStuffTabContentPanel.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MyStuffTabContentPanel.java
new file mode 100644
index 0000000..56e2dcf
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/MyStuffTabContentPanel.java
@@ -0,0 +1,342 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.util.concurrent.CountDownLatch;
+
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPasswordField;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+
+import net.sf.taverna.t2.lang.ui.ShadedLabel;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.workbench.file.FileManager;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author Sergejs Aleksejevs, Emmanuel Tagarira, Jiten Bhagat
+ */
+public class MyStuffTabContentPanel extends JPanel implements ActionListener, KeyListener {
+ private final MainComponent pluginMainComponent;
+ private final MyExperimentClient myExperimentClient;
+ private final Logger logger;
+
+ // components that should be accessible from anywhere in this class
+ private JButton bLogin;
+ private JCheckBox cbLoginAutomatically;
+ private MyStuffSidebarPanel jpSidebar;
+ public JSplitPane spMyStuff;
+
+ // synchronisation latch to let main thread know that all component-creation
+ // threads have been finished
+ protected CountDownLatch cdlComponentLoadingDone;
+ int NUMBER_OF_SUBCOMPONENTS = 2;
+
+ // "return to" type of thing, so that after a certain action has been done,
+ // it is possible to switch to another tab in this tabbed view
+ protected JComponent cTabContentComponentToSwitchToAfterLogin = null;
+ private final FileManager fileManager;
+
+ public MyStuffTabContentPanel(MainComponent component, MyExperimentClient client, Logger logger, FileManager fileManager) {
+ super();
+
+ // set main variables to ensure access to myExperiment, logger and the
+ // parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+ this.fileManager = fileManager;
+ }
+
+ public void createAndInitialiseInnerComponents() {
+ // if there are any components, these will be removed
+ this.removeAll();
+ cdlComponentLoadingDone = new CountDownLatch(NUMBER_OF_SUBCOMPONENTS);
+
+ // based on the current status (logged in / anonymous user), decide which
+ // components to create and display
+ if (this.myExperimentClient.isLoggedIn()) {
+ jpSidebar = new MyStuffSidebarPanel(pluginMainComponent, myExperimentClient, logger, fileManager);
+ JPanel jpSidebarContainer = new JPanel();
+ jpSidebarContainer.setLayout(new BorderLayout());
+ jpSidebarContainer.add(jpSidebar, BorderLayout.NORTH);
+ JScrollPane spSidebar = new JScrollPane(jpSidebarContainer);
+ spSidebar.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+ spSidebar.setMinimumSize(new Dimension(jpSidebar.getMyProfileBox().getPreferredSize().width + 30, 0)); // +30
+ // --> 10 for padding and 10 for vertical scroll bar + 10 extra current
+ // user is logged in to myExperiment, display all personal data
+
+ spMyStuff = new JSplitPane();
+ spMyStuff.setLeftComponent(spSidebar);
+ spMyStuff.setRightComponent(new MyStuffContributionsPanel(pluginMainComponent, myExperimentClient, logger));
+ this.pluginMainComponent.getStatusBar().setCurrentUser(myExperimentClient.getCurrentUser().getName());
+
+ // set proportional sizes of the two panes as 30/70 percents of the total
+ // width of the SplitPane
+ // this can only be done after the SplitPane is made visible - hence the
+ // need for the listener below
+ pluginMainComponent.addComponentListener(new ComponentAdapter() {
+ @Override
+ public void componentShown(ComponentEvent e) {
+ javax.swing.JOptionPane.showMessageDialog(null, "component shown");
+ // NB! This is only needed for use with test class, not when Taverna
+ // calls perspective!!
+ // the SplitPane wouldn't have loaded yet - wait until it does
+ try {
+ Thread.sleep(50);
+ } // 50ms is a tiny delay -- acceptable
+ catch (Exception ex) { /* do nothing */}
+
+ // set the proportions in the SplitPane
+ spMyStuff.setDividerLocation(400);
+ }
+ });
+
+ // make sure that both panes will grow/shrink at the same rate if the
+ // size of the whole SplitPane is changed by resizing the window
+ spMyStuff.setResizeWeight(0.3);
+ spMyStuff.setOneTouchExpandable(true);
+ spMyStuff.setDividerLocation(400);
+ spMyStuff.setDoubleBuffered(true);
+
+ // spMyStuff will be the only component in the Panel
+ this.setLayout(new BorderLayout());
+ this.add(spMyStuff);
+
+ // wait until two of the components finish loading and set the status to 'ready'
+ // (done in a new thread so that this doesn't freeze the plugin window)
+ new Thread("Waiting for myStuff data to load") {
+ @Override
+ public void run() {
+ try {
+ cdlComponentLoadingDone.await();
+ pluginMainComponent.getStatusBar().setStatus(this.getClass().getName(), null);
+ } catch (InterruptedException ex) { /* do nothing for now */
+ }
+ }
+ }.start();
+ } else { // NOT logged in
+ // reset status in case of unsuccessful autologin
+ this.pluginMainComponent.getStatusBar().setStatus(this.getClass().getName(), null);
+
+ // user isn't logged in, display login box only
+ JPanel jpLoginBoxContainer = new JPanel();
+ jpLoginBoxContainer.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+ jpLoginBoxContainer.add(createLoginBox(), c);
+
+ // put everything together (welcome banner + login box)
+ this.setLayout(new BorderLayout());
+ this.add(new ShadedLabel("Welcome to the myExperiment plugin. Please note that you can still use other tabs even "
+ + "if you don't have a user profile yet!", ShadedLabel.BLUE), BorderLayout.NORTH);
+ this.add(jpLoginBoxContainer, BorderLayout.CENTER);
+ }
+ }
+
+ // generates JPanel containing a login box
+ private JPanel createLoginBox() {
+ JPanel jpLoginBox = new JPanel();
+ jpLoginBox.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createEtchedBorder(), BorderFactory.createEmptyBorder(10, 10, 10, 10)));
+
+ jpLoginBox.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ // label "Login to myExp"
+ c.gridwidth = GridBagConstraints.REMAINDER;
+ c.insets = new Insets(0, 0, 15, 0);
+ c.gridx = 0;
+ c.gridy = 0;
+ JLabel jlHeader = new JLabel("<html><b>Log in to myExperiment</b></html>");
+ jlHeader.setFont(jlHeader.getFont().deriveFont((float) 13.0));
+ jpLoginBox.add(jlHeader, c);
+
+ // set values
+ c.weightx = 1;
+ c.gridwidth = 1;
+ c.anchor = GridBagConstraints.LINE_START;
+ c.insets = new Insets(0, 0, 3, 0);
+ c.ipadx = 10;
+
+ // autologin checkbox and label
+ c.gridy++;
+ c.insets = new Insets(0, 0, 0, 3);
+ cbLoginAutomatically = new JCheckBox("Log in automatically (next time)");
+ cbLoginAutomatically.setBorder(BorderFactory.createEmptyBorder()); // makes sure that this is aligned with text fields above
+ cbLoginAutomatically.addActionListener(this);
+ cbLoginAutomatically.addKeyListener(this);
+ jpLoginBox.add(cbLoginAutomatically, c);
+
+ // login button
+ c.gridy++;
+ c.gridx = 0;
+ c.anchor = GridBagConstraints.CENTER;
+ c.gridwidth = GridBagConstraints.REMAINDER;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.insets = new Insets(10, 0, 0, 0);
+ bLogin = new JButton("Login", new ImageIcon(MyExperimentPerspective.getLocalResourceURL("login_icon")));
+ bLogin.setDefaultCapable(true);
+ bLogin.addKeyListener(this);
+ bLogin.addActionListener(this);
+ jpLoginBox.add(bLogin, c);
+
+ // wrap contents into another panel to allow for some extra border around the contents
+ return (jpLoginBox);
+ }
+
+ public MyStuffSidebarPanel getSidebar() {
+ return (this.jpSidebar);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource().equals(this.bLogin)) {
+ // "Login" button clicked
+ pluginMainComponent.getStatusBar().setStatus(this.getClass().getName(), "Logging in");
+
+ // Make call to myExperiment API in a different thread
+ // (then use SwingUtilities.invokeLater to update the UI when ready).
+ new Thread("Login to myExperiment") {
+ @Override
+ public void run() {
+ logger.debug("Logging in to myExperiment");
+
+ try {
+ // do the actual "logging in"
+ boolean bLoginSuccessful = myExperimentClient.doLogin();
+
+ // check if need to store the login credentials and settings
+ if (bLoginSuccessful) {
+ // store the settings anyway (for instance, to clear stored login/password
+ // - when the 'remember me' tick is not checked anymore);
+ // however, need to check whether to store login details or not
+
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_AUTO_LOGIN, new Boolean(cbLoginAutomatically.isSelected()).toString());
+ myExperimentClient.storeHistoryAndSettings();
+
+ // if logging in was successful, set the status to the start of fetching the data
+ pluginMainComponent.getStatusBar().setStatus(this.getClass().getName(), "Fetching user data");
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ if (myExperimentClient.isLoggedIn()) {
+ // login successful, change view to "logged in" one
+ createAndInitialiseInnerComponents();
+
+ // ..also, load user's tag cloud
+ pluginMainComponent.getTagBrowserTab().setMyTagsShown(true);
+ pluginMainComponent.getTagBrowserTab().getMyTagPanel().refresh();
+
+ // ..also, refresh tag search results because these my include
+ // much more than
+ // during the previous search when the user was still not
+ // logged-in
+ pluginMainComponent.getTagBrowserTab().rerunLastTagSearch();
+
+ // ..also, refresh the keyword search results (as more items
+ // can now be found)
+ pluginMainComponent.getSearchTab().rerunLastSearch();
+
+ // if after logging it is needed to switch to other tab,
+ // that is done now
+ if (cTabContentComponentToSwitchToAfterLogin != null) {
+ pluginMainComponent.getMainTabs().setSelectedComponent(cTabContentComponentToSwitchToAfterLogin);
+ cTabContentComponentToSwitchToAfterLogin = null;
+ }
+
+ logger.debug("Logged in to myExperiment successfully");
+ } else {
+ // couldn't login - display error message
+ pluginMainComponent.getStatusBar().setStatus(this.getClass().getName(), null);
+ javax.swing.JOptionPane.showMessageDialog(null, "Unable to login to myExperiment - please check your login details", "myExperiment Plugin - Couldn't Login", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ });
+ }
+
+ } catch (Exception ex) {
+ logger.error("Exception on attempt to login to myExperiment:\n", ex);
+ }
+ }
+ }.start();
+
+ } else if (e.getSource().equals(this.jpSidebar.bRefreshMyStuff)) {
+ // this will re-fetch all user profile data and repopulate the whole of the 'My Stuff' tab
+ pluginMainComponent.getStatusBar().setStatus(this.getClass().getName(), "Refreshing user data");
+
+ new Thread("Refreshing myStuff tab data") {
+ @Override
+ public void run() {
+ // re-fetch user data first
+ myExperimentClient.setCurrentUser(myExperimentClient.fetchCurrentUser(myExperimentClient.getCurrentUser().getURI()));
+ createAndInitialiseInnerComponents();
+ revalidate();
+ }
+ }.start();
+ }
+ }
+
+ // *** Callbacks for KeyListener interface ***
+ public void keyPressed(KeyEvent e) {
+ // ENTER pressed - check which element is the source and determine what
+ // acion is to be taken
+ if (e.getKeyCode() == KeyEvent.VK_ENTER) {
+ if (e.getSource().equals(this.cbLoginAutomatically)
+ || e.getSource().equals(this.bLogin)) {
+ // ENTER pressed when focus was on the login button, one of checkboxes or the password field - do logging in
+ actionPerformed(new ActionEvent(this.bLogin, 0, ""));
+ }
+ }
+ }
+
+ public void keyReleased(KeyEvent e) {
+ // do nothing
+ }
+
+ public void keyTyped(KeyEvent e) {
+ // do nothing
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/PluginPreferencesDialog.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/PluginPreferencesDialog.java
new file mode 100644
index 0000000..2ad8a42
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/PluginPreferencesDialog.java
@@ -0,0 +1,372 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
+import java.util.ArrayList;
+
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Util;
+import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author Sergejs Aleksejevs, Emmanuel Tagarira
+ */
+public class PluginPreferencesDialog extends HelpEnabledDialog implements ComponentListener, ActionListener {
+ // CONSTANTS
+
+ // components for accessing application's main elements
+ private final MainComponent pluginMainComponent;
+ private final MyExperimentClient myExperimentClient;
+ private final Logger logger;
+
+ // COMPONENTS
+ private JTextField tfMyExperimentURL;
+ private JComboBox cbDefaultLoggedInTab;
+ private JComboBox cbDefaultNotLoggedInTab;
+ private JCheckBox cbMyStuffWorkflows;
+ private JCheckBox cbMyStuffFiles;
+ private JCheckBox cbMyStuffPacks;
+ private JButton bSave;
+ private JButton bCancel;
+ private JClickableLabel jclClearPreviewHistory;
+ private JClickableLabel jclClearSearchHistory;
+ private JClickableLabel jclClearFavouriteSearches;
+
+ // DATA STORAGE
+ private final Component[] pluginTabComponents;
+ private final ArrayList<String> alPluginTabComponentNames;
+
+ public PluginPreferencesDialog(JFrame owner, MainComponent component, MyExperimentClient client, Logger logger) {
+ super(owner, "Plugin preferences", true);
+
+ // set main variables to ensure access to myExperiment, logger and the parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+
+ // set options of the preview dialog box
+ this.addComponentListener(this);
+ //this.setIconImage(new ImageIcon(MyExperimentPerspective.getLocalResourceURL("myexp_icon")).getImage());
+
+ // prepare plugin tab names to display in the UI afterwards
+ this.alPluginTabComponentNames = new ArrayList<String>();
+ this.pluginTabComponents = this.pluginMainComponent.getMainTabs().getComponents();
+ for (int i = 0; i < this.pluginTabComponents.length; i++) {
+ alPluginTabComponentNames.add(this.pluginMainComponent.getMainTabs().getTitleAt(i));
+ }
+
+ this.initialiseUI();
+
+ // this is not computation-intensive method, so no need to run in a new thread
+ this.initialiseData();
+ }
+
+ private void initialiseUI() {
+ // this constraints instance will be shared among all components in the window
+ GridBagConstraints c = new GridBagConstraints();
+
+ // create the myExperiment API address box
+ JPanel jpApiLocation = new JPanel();
+ jpApiLocation.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), " myExperiment Location "), BorderFactory.createEmptyBorder(0, 5, 5, 5)));
+ jpApiLocation.setLayout(new GridBagLayout());
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.weightx = 1.0;
+ c.anchor = GridBagConstraints.WEST;
+ jpApiLocation.add(new JLabel("Base URL of myExperiment instance to connect to"), c);
+
+ c.gridy = 1;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ this.tfMyExperimentURL = new JTextField();
+ this.tfMyExperimentURL.setToolTipText("<html>Here you can specify the base URL of the myExperiment "
+ + "instance that you wish to connect to.<br>This allows the plugin to connect not only to the "
+ + "<b>main myExperiment website</b> (default value:<br><b>http://www.myexperiment.org</b>) but "
+ + "also to any other myExperiment instance that might<br>exist elsewhere.<br><br>It is recommended "
+ + "that you only change this setting if you are certain in your actions.</html>");
+ jpApiLocation.add(this.tfMyExperimentURL, c);
+
+ // create startup tab choice box
+ JPanel jpStartupTabChoice = new JPanel();
+ jpStartupTabChoice.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), " Plugin Start-up Settings "), BorderFactory.createEmptyBorder(0, 5, 5, 5)));
+ jpStartupTabChoice.setLayout(new GridBagLayout());
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.weightx = 0;
+ c.insets = new Insets(0, 0, 0, 10);
+ jpStartupTabChoice.add(new JLabel("Default startup tab for anonymous user"), c);
+
+ c.gridx = 1;
+ c.weightx = 1.0;
+ c.insets = new Insets(0, 0, 2, 0);
+ this.cbDefaultNotLoggedInTab = new JComboBox(this.alPluginTabComponentNames.toArray());
+ this.cbDefaultNotLoggedInTab.setToolTipText("<html>This tab will be automatically opened at plugin start up time if you are <b>not</b> logged id to myExperiment.</html>");
+ jpStartupTabChoice.add(this.cbDefaultNotLoggedInTab, c);
+
+ c.gridx = 0;
+ c.gridy = 1;
+ c.weightx = 0;
+ c.insets = new Insets(0, 0, 0, 10);
+ jpStartupTabChoice.add(new JLabel("Default startup tab after successful auto-login"), c);
+
+ c.gridx = 1;
+ c.weightx = 1.0;
+ c.insets = new Insets(2, 0, 0, 0);
+ this.cbDefaultLoggedInTab = new JComboBox(this.alPluginTabComponentNames.toArray());
+ this.cbDefaultLoggedInTab.setToolTipText("<html>This tab will be automatically opened at plugin start up time if you have chosen to use <b>auto logging in</b> to myExperiment.</html>");
+ jpStartupTabChoice.add(this.cbDefaultLoggedInTab, c);
+
+ // create 'my stuff' tab preference box
+ JPanel jpMyStuffPrefs = new JPanel();
+ jpMyStuffPrefs.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), " 'My Stuff' Tab Settings "), BorderFactory.createEmptyBorder(0, 5, 5, 5)));
+ jpMyStuffPrefs.setLayout(new GridBagLayout());
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.weightx = 0;
+ c.insets = new Insets(0, 0, 0, 0);
+ jpMyStuffPrefs.add(new JLabel("Sections to show in this tab:"), c);
+
+ c.gridx = 1;
+ c.gridy = 0;
+ c.weightx = 1.0;
+ c.insets = new Insets(0, 10, 0, 0);
+ this.cbMyStuffWorkflows = new JCheckBox("My Workflows");
+ jpMyStuffPrefs.add(this.cbMyStuffWorkflows, c);
+
+ c.gridy = 1;
+ this.cbMyStuffFiles = new JCheckBox("My Files");
+ jpMyStuffPrefs.add(this.cbMyStuffFiles, c);
+
+ c.gridy = 2;
+ this.cbMyStuffPacks = new JCheckBox("My Packs");
+ jpMyStuffPrefs.add(this.cbMyStuffPacks, c);
+
+ // create privacy settings box
+ JPanel jpPrivacySettings = new JPanel();
+ jpPrivacySettings.setLayout(new BoxLayout(jpPrivacySettings, BoxLayout.Y_AXIS));
+ jpPrivacySettings.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), " Privacy Settings "), BorderFactory.createEmptyBorder(0, 7, 5, 5)));
+
+ this.jclClearPreviewHistory = new JClickableLabel("Clear browsing history", "clear_preview_history", this);
+ jpPrivacySettings.add(this.jclClearPreviewHistory);
+
+ this.jclClearSearchHistory = new JClickableLabel("Clear search history", "clear_search_history", this);
+ this.jclClearSearchHistory.setBorder(BorderFactory.createEmptyBorder(3, 0, 3, 0));
+ jpPrivacySettings.add(this.jclClearSearchHistory);
+
+ this.jclClearFavouriteSearches = new JClickableLabel("Clear favourite searches", "clear_favourite_searches", this);
+ this.jclClearFavouriteSearches.setBorder(BorderFactory.createEmptyBorder(0, 0, 2, 0));
+ jpPrivacySettings.add(this.jclClearFavouriteSearches);
+
+ // create button panel
+ this.bSave = new JButton("Save");
+ this.bSave.addActionListener(this);
+
+ this.bCancel = new JButton("Cancel");
+ this.bCancel.addActionListener(this);
+
+ JPanel jpButtons = new JPanel();
+ jpButtons.setLayout(new GridBagLayout());
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.weightx = 0;
+ c.insets = new Insets(0, 0, 0, 2);
+ jpButtons.add(bSave, c);
+
+ c.gridx = 1;
+ c.insets = new Insets(0, 2, 0, 0);
+ jpButtons.add(bCancel, c);
+
+ // PUT EVERYTHING TOGETHER
+ this.setTitle("myExperiment Plugin Preferences");
+ BorderLayout layout = new BorderLayout();
+ JPanel jpEverything = new JPanel();
+ GridBagLayout jpEverythingLayout = new GridBagLayout();
+ jpEverything.setLayout(jpEverythingLayout);
+ this.getContentPane().setLayout(layout);
+
+ GridBagConstraints gbConstraints = new GridBagConstraints();
+ gbConstraints.fill = GridBagConstraints.BOTH;
+ gbConstraints.weightx = 1;
+ gbConstraints.gridx = 0;
+
+ gbConstraints.gridy = 0;
+ jpEverything.add(jpApiLocation, gbConstraints);
+
+ gbConstraints.gridy = 1;
+ jpEverything.add(jpStartupTabChoice, gbConstraints);
+
+ gbConstraints.gridy = 2;
+ jpEverything.add(jpMyStuffPrefs, gbConstraints);
+
+ gbConstraints.gridy = 3;
+ jpEverything.add(jpPrivacySettings, gbConstraints);
+
+ gbConstraints.gridy = 4;
+ jpEverything.add(jpButtons, gbConstraints);
+
+ this.add(jpEverything);
+ this.setResizable(false);
+
+ // pack() sets preferred size of the dialog box;
+ // after this, can set the minimum size to that value too
+ this.pack();
+ this.setMinimumSize(this.getPreferredSize());
+ }
+
+ private void initialiseData() {
+ // myExperiment Base URL
+ this.tfMyExperimentURL.setText(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_BASE_URL));
+
+ // default tabs
+ this.cbDefaultNotLoggedInTab.setSelectedIndex(Integer.parseInt(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_DEFAULT_ANONYMOUS_TAB)));
+ this.cbDefaultLoggedInTab.setSelectedIndex(Integer.parseInt(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_DEFAULT_LOGGED_IN_TAB)));
+
+ // components of "My Stuff" tab
+ this.cbMyStuffWorkflows.setSelected(Boolean.parseBoolean(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_MY_STUFF_WORKFLOWS)));
+ this.cbMyStuffFiles.setSelected(Boolean.parseBoolean(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_MY_STUFF_FILES)));
+ this.cbMyStuffPacks.setSelected(Boolean.parseBoolean(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_MY_STUFF_PACKS)));
+ }
+
+ // *** Callbacks for ComponentListener interface ***
+
+ public void componentShown(ComponentEvent e) {
+ // every time the settings window is shown, make sure that the dialog box appears
+ // centered horizontally and vertically relatively to the main component
+ Util.centerComponentWithinAnother(this.pluginMainComponent, this);
+
+ // also, need to make sure that correct settings get shown
+ // (e.g. especially relevant when this window was last closed with 'cancel',
+ // but some options were changed prior to that)
+ this.initialiseData();
+ }
+
+ public void componentHidden(ComponentEvent e) {
+ // do nothing
+ }
+
+ public void componentResized(ComponentEvent e) {
+ // do nothing
+ }
+
+ public void componentMoved(ComponentEvent e) {
+ // do nothing
+ }
+
+ // *** Callback for ActionListener interface ***
+
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource().equals(this.bSave)) {
+ // check if myExperiment address is present
+ String strNewMyExperimentURL = this.tfMyExperimentURL.getText().trim();
+ if (strNewMyExperimentURL.length() == 0) {
+ javax.swing.JOptionPane.showMessageDialog(null, "Please specify a base URL of myExperiment instance that you wish to connect to", "Error", JOptionPane.WARNING_MESSAGE);
+ this.tfMyExperimentURL.requestFocusInWindow();
+ return;
+ }
+
+ // check if at least one of the checkboxes (for sections in 'My Stuff' tab) is selected
+ if (!(this.cbMyStuffWorkflows.isSelected()
+ || this.cbMyStuffFiles.isSelected() || this.cbMyStuffPacks.isSelected())) {
+ javax.swing.JOptionPane.showMessageDialog(null, "Please choose at least one section to display in 'My Stuff' tab", "Error", JOptionPane.WARNING_MESSAGE);
+ this.cbMyStuffWorkflows.requestFocusInWindow();
+ return;
+ }
+
+ // NB! changed myExperiment location will not take action until the next application restart
+ if (!strNewMyExperimentURL.equals(myExperimentClient.getBaseURL())) {
+ // turn off auto-login
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_AUTO_LOGIN, new Boolean(false).toString());
+
+ javax.swing.JOptionPane.showMessageDialog(null, "You have selected a new Base URL for myExperiment. "
+ + "Your new setting has been saved,\nbut will not take effect until you restart Taverna.\n\n"
+ + "Auto-login feature has been switched off for you to check the login details at the next launch.", "myExperiment Plugin - Info", JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ // all values should be present - store these into Properties object
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_BASE_URL, strNewMyExperimentURL);
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_DEFAULT_ANONYMOUS_TAB, new Integer(cbDefaultNotLoggedInTab.getSelectedIndex()).toString());
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_DEFAULT_LOGGED_IN_TAB, new Integer(cbDefaultLoggedInTab.getSelectedIndex()).toString());
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_MY_STUFF_WORKFLOWS, new Boolean(cbMyStuffWorkflows.isSelected()).toString());
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_MY_STUFF_FILES, new Boolean(cbMyStuffFiles.isSelected()).toString());
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_MY_STUFF_PACKS, new Boolean(cbMyStuffPacks.isSelected()).toString());
+
+ // close the window eventually
+ setVisible(false);
+ } else if (e.getSource().equals(this.bCancel)) {
+ // simply close the preferences window
+ setVisible(false);
+ } else if (e.getSource().equals(this.jclClearPreviewHistory)) {
+ // request user confirmation and clear browsing history (preview history)
+ if (JOptionPane.showConfirmDialog(null, "This will delete the browsing history - the lists of previously previewed,\n"
+ + "downloaded, opened and commented on items will be emptied.\n\nDo you want to proceed?", "myExperiment Plugin - Confirmation Required", JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) {
+ pluginMainComponent.getPreviewBrowser().clearPreviewHistory();
+ pluginMainComponent.getHistoryBrowser().clearDownloadedItemsHistory();
+ pluginMainComponent.getHistoryBrowser().clearOpenedItemsHistory();
+ pluginMainComponent.getHistoryBrowser().clearCommentedOnItemsHistory();
+ pluginMainComponent.getHistoryBrowser().refreshHistoryBox(HistoryBrowserTabContentPanel.PREVIEWED_ITEMS_HISTORY);
+ pluginMainComponent.getHistoryBrowser().refreshHistoryBox(HistoryBrowserTabContentPanel.DOWNLOADED_ITEMS_HISTORY);
+ pluginMainComponent.getHistoryBrowser().refreshHistoryBox(HistoryBrowserTabContentPanel.OPENED_ITEMS_HISTORY);
+ pluginMainComponent.getHistoryBrowser().refreshHistoryBox(HistoryBrowserTabContentPanel.COMMENTED_ON_ITEMS_HISTORY);
+ }
+ } else if (e.getSource().equals(this.jclClearSearchHistory)) {
+ // request user confirmation and clear search history (tag search history + query search history)
+ if (JOptionPane.showConfirmDialog(null, "This will delete both query and tag search history.\nDo you want to proceed?", "myExperiment Plugin - Confirmation Required", JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) {
+ pluginMainComponent.getSearchTab().getSearchHistory().clear();
+ pluginMainComponent.getTagBrowserTab().getTagSearchHistory().clear();
+ pluginMainComponent.getSearchTab().updateSearchHistory();
+ pluginMainComponent.getHistoryBrowser().refreshSearchHistory();
+ pluginMainComponent.getHistoryBrowser().refreshTagSearchHistory();
+ }
+ } else if (e.getSource().equals(this.jclClearFavouriteSearches)) {
+ // request user confirmation and clear favourite searches
+ if (JOptionPane.showConfirmDialog(null, "This will delete all your favourite search settings.\nDo you want to proceed?", "myExperiment Plugin - Confirmation Required", JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) {
+ pluginMainComponent.getSearchTab().getSearchFavouritesList().clear();
+ pluginMainComponent.getSearchTab().updateFavouriteSearches();
+ }
+ }
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/PluginStatusBar.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/PluginStatusBar.java
new file mode 100644
index 0000000..0d68811
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/PluginStatusBar.java
@@ -0,0 +1,195 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import javax.swing.BorderFactory;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SwingConstants;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Util;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author Sergejs Aleksejevs, Emmanuel Tagarira
+ */
+public class PluginStatusBar extends JPanel implements ActionListener {
+ // CONSTANTS
+ private static final String STATUS_MESSAGE_READY = "Ready";
+
+ private MainComponent pluginMainComponent;
+ private MyExperimentClient myExperimentClient;
+ private Logger logger;
+
+ // all components that represent the status
+ private JLabel lSpinnerIcon;
+ private JLabel lStatusMsg;
+ private JLabel lCurrentUser;
+ // private JButton bPreferences;
+
+ // collections to keep the statuses for different tabs
+ ArrayList<String> alTabClassNames;
+ ArrayList<String> alTabStatuses;
+
+ // spinner icons
+ ImageIcon iconSpinner;
+ ImageIcon iconSpinnerStopped;
+
+ public PluginStatusBar(MainComponent component, MyExperimentClient client, Logger logger) {
+ super();
+
+ // set main variables to ensure access to myExperiment, logger and the
+ // parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+
+ // prepare status collections for different tabs
+ alTabClassNames = new ArrayList<String>();
+ alTabStatuses = new ArrayList<String>();
+
+ // load icons
+ this.iconSpinner = new ImageIcon(MyExperimentPerspective.getLocalResourceURL("spinner"));
+ this.iconSpinnerStopped = new ImageIcon(MyExperimentPerspective.getLocalResourceURL("spinner_stopped"));
+
+ // prepare main panel for the status bar
+ this.setLayout(new BorderLayout());
+ this.setBorder(BorderFactory.createEmptyBorder(1, 4, 1, 1)); // this will
+ // add a bit
+ // more spacing
+ // on the left
+ // - before the
+ // status
+ // message
+
+ // prepare status labels
+ this.lSpinnerIcon = new JLabel("", iconSpinnerStopped, SwingConstants.LEFT);
+ this.lStatusMsg = new JLabel("Ready");
+ this.lCurrentUser = new JLabel("Please log in to access your profile", SwingConstants.CENTER);
+
+ // 'Plugin Preferences' button
+ // this.bPreferences = new JButton("Plugin Preferences", WorkbenchIcons.configureIcon);
+ // this.bPreferences.addActionListener(this);
+
+ // put everything together
+ JPanel pWestStatusBarSection = new JPanel();
+ pWestStatusBarSection.add(lSpinnerIcon);
+ pWestStatusBarSection.add(lStatusMsg);
+
+ this.add(pWestStatusBarSection, BorderLayout.WEST);
+ this.add(this.lCurrentUser, BorderLayout.EAST);
+ // this.add(this.bPreferences, BorderLayout.EAST);
+ }
+
+ // updates the current user name in the middle of the status bar
+ public void setCurrentUser(String strUsername) {
+ // if "null" or "" is submitted as a parameter, the status will be set to
+ // "Ready"
+ if (strUsername == null || strUsername.length() == 0)
+ this.lCurrentUser.setText("Please log in to access your profile");
+ else
+ this.lCurrentUser.setText("<html>Logged in as <b>" + strUsername
+ + "</b></html>");
+ }
+
+ // sets the status message to the one that is relevant to the current tab
+ public void displayStatus(String strTabClassName) {
+ int iTabIdx = -1;
+ String strBaseClassName = Util.getBaseClassName(strTabClassName);
+
+ if ((iTabIdx = alTabClassNames.indexOf(strBaseClassName)) != -1) {
+ // tab found - show its status message
+ String strCurStatus = alTabStatuses.get(iTabIdx);
+ this.lStatusMsg.setText(strCurStatus);
+ startSpinner(!strCurStatus.equals(PluginStatusBar.STATUS_MESSAGE_READY));
+ } else {
+ // tab not found - assume no actions are happening
+ // (this will create the 'ready' status for the current tab,
+ // then return to display it)
+ setStatus(strBaseClassName, null);
+ }
+ }
+
+ // sets the status message for a particular tab;
+ // if this tab is currently active, the status will get displayed immediately
+ // (alternatively it will be displayed at the time when the tab becomes
+ // active)
+ public void setStatus(String strTabClassName, String strStatus) {
+ // PREPROCESSING - if "null" or "" is submitted as a parameter, the status
+ // will be set to "Ready"
+ if (strStatus == null || strStatus.length() == 0)
+ strStatus = PluginStatusBar.STATUS_MESSAGE_READY;
+ String strBaseClassName = Util.getBaseClassName(strTabClassName);
+
+ // STORING the status it in the collection
+ int iTabIdx = -1;
+ if ((iTabIdx = alTabClassNames.indexOf(strBaseClassName)) != -1) {
+ // only a change of status, already dealt with this tab before
+ alTabStatuses.set(iTabIdx, strStatus);
+ } else {
+ // never worked with this tab before, add new one
+ alTabClassNames.add(strBaseClassName);
+ alTabStatuses.add(strStatus);
+ }
+
+ // display the new status if the updated status is on the active tab
+ if (isTabActive(strBaseClassName))
+ displayStatus(strBaseClassName);
+ }
+
+ // helper to start / stop the spinner in the status bar that
+ // indicates that some action is currently in progress
+ // (action will be displayed by lStatusMsg label)
+ public void startSpinner(boolean bStart) {
+ this.lSpinnerIcon.setIcon(bStart ? this.iconSpinner : this.iconSpinnerStopped);
+ }
+
+ // Determine whether the tab in the parameter is currently active in the main
+ // tabbed pane.
+ private boolean isTabActive(String strTabClassName) {
+ // get the current active tab (this is a normal class name of the main tab
+ // content component)
+ String strCurSelectedTabClassName = this.pluginMainComponent.getMainTabs().getSelectedComponent().getClass().getName();
+
+ // get the real class name to match
+ String strBaseClassName = Util.getBaseClassName(strTabClassName);
+
+ // compare the two class names
+ return (strBaseClassName.equals(strCurSelectedTabClassName));
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ // if (e.getSource().equals(this.bPreferences)) {
+ // // open preferences dialog box
+ // pluginMainComponent.getPreferencesDialog().setVisible(true);
+ // }
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ResourceListPanel.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ResourceListPanel.java
new file mode 100644
index 0000000..d0b00a3
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ResourceListPanel.java
@@ -0,0 +1,182 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Desktop;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.net.URI;
+import java.util.List;
+
+import javax.swing.BorderFactory;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkListener;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import org.apache.log4j.Logger;
+
+/**
+ * @author Sergejs Aleksejevs, Emmanuel Tagarira, Jiten Bhagat
+ */
+public class ResourceListPanel extends JPanel implements HyperlinkListener {
+ // CONSTANTS
+ public final static int DESCRIPTION_TRUNCATE_LENGTH_FOR_SHORT_LIST_VIEW = 150;
+
+ public final static int THUMBNAIL_WIDTH_FOR_SHORT_LIST_VIEW = 60;
+ public final static int THUMBNAIL_HEIGHT_FOR_SHORT_LIST_VIEW = 45;
+
+ public final static int THUMBNAIL_WIDTH_FOR_FULL_LIST_VIEW = 90;
+ public final static int THUMBNAIL_HEIGHT_FOR_FULL_LIST_VIEW = 90;
+
+ private MainComponent pluginMainComponent;
+ private MyExperimentClient myExperimentClient;
+ private Logger logger;
+
+ private JPanel listPanel;
+ private GridBagConstraints gbConstraints;
+
+ private List<Resource> listItems;
+
+ // some of the components will not be shown in the item list if
+ // it's not of full size
+ private boolean bFullSizeItemsList = true;
+
+ public ResourceListPanel(MainComponent component, MyExperimentClient client, Logger logger) {
+ super();
+
+ // set main variables to ensure access to myExperiment, logger and the
+ // parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+
+ this.initialiseUI();
+ }
+
+ public boolean isFullSizeItemsList() {
+ return this.bFullSizeItemsList;
+ }
+
+ public void setFullSizeItemsList(boolean bFullSizeItemsList) {
+ this.bFullSizeItemsList = bFullSizeItemsList;
+ }
+
+ public void hyperlinkUpdate(HyperlinkEvent e) {
+ try {
+ if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+ String strAction = e.getDescription().toString();
+
+ if (strAction.startsWith("preview:")) {
+ this.pluginMainComponent.getPreviewBrowser().preview(strAction);
+ } else {
+ Desktop.getDesktop().browse(new URI(strAction));
+ }
+ }
+ } catch (Exception ex) {
+ logger.error("Error occurred whilst clicking a hyperlink", ex);
+ }
+ }
+
+ public void setListItems(List<Resource> items) {
+ this.listItems = items;
+
+ this.repopulate();
+ }
+
+ public void clear() {
+ this.listPanel.removeAll();
+ this.invalidate();
+ }
+
+ public void refresh() {
+ if (this.listItems != null) {
+ this.repopulate();
+ }
+ }
+
+ public void repopulate() {
+ if (this.listItems != null) {
+ this.clear();
+
+ if (this.listItems.size() > 0) {
+ Resource res = null;
+ for (int i = 0; i < this.listItems.size(); i++) {
+ try {
+ // this will make the layout manager to push all extra space in
+ // Y-axis
+ // to go to the last element in the panel; essentially, this will
+ // push
+ // all list items to the top of the list view panel
+ if (i == listItems.size() - 1)
+ gbConstraints.weighty = 1.0;
+
+ res = this.listItems.get(i);
+ this.listPanel.add(res.createListViewPanel(bFullSizeItemsList, pluginMainComponent, this, logger), gbConstraints);
+ logger.debug("Added entry in resource list panel for the resource (Type: "
+ + res.getItemTypeName() + ", URI: " + res.getURI() + ")");
+ } catch (Exception e) {
+ logger.error("Failed to add item entry to ResourceListPanel (Item Type : "
+ + res.getItemTypeName() + ", URI: " + res.getURI() + ")", e);
+ }
+ }
+ } else {
+ // no items in the list
+ JLabel lNone = new JLabel("None");
+ lNone.setBorder(BorderFactory.createEmptyBorder(0, 15, 0, 0));
+ lNone.setForeground(Color.GRAY);
+ lNone.setFont(lNone.getFont().deriveFont(Font.ITALIC));
+
+ gbConstraints.anchor = GridBagConstraints.WEST;
+ this.listPanel.add(lNone, gbConstraints);
+
+ this.listPanel.setPreferredSize(new Dimension(20, 40));
+ this.listPanel.setBackground(Color.WHITE);
+ }
+ }
+
+ this.validate();
+ this.repaint();
+ }
+
+ private void initialiseUI() {
+ this.listPanel = new JPanel();
+ this.listPanel.setBorder(BorderFactory.createEmptyBorder());
+
+ this.listPanel.setLayout(new GridBagLayout());
+ this.gbConstraints = new GridBagConstraints();
+ this.gbConstraints.anchor = GridBagConstraints.NORTH;
+ this.gbConstraints.fill = GridBagConstraints.HORIZONTAL;
+ this.gbConstraints.gridx = GridBagConstraints.REMAINDER;
+ this.gbConstraints.gridy = GridBagConstraints.RELATIVE;
+ this.gbConstraints.weightx = 1.0;
+ this.gbConstraints.weighty = 0;
+
+ this.setLayout(new BorderLayout());
+ this.add(this.listPanel, BorderLayout.CENTER);
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ResourcePreviewBrowser.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ResourcePreviewBrowser.java
new file mode 100644
index 0000000..bdef0e7
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ResourcePreviewBrowser.java
@@ -0,0 +1,711 @@
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.BorderLayout;
+import java.awt.Desktop;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.EventListener;
+import java.util.List;
+
+import javax.swing.BorderFactory;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkListener;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Base64;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author Sergejs Aleksejevs, Emmanuel Tagarira
+ */
+public class ResourcePreviewBrowser extends JFrame implements ActionListener, HyperlinkListener, ComponentListener {
+ // CONSTANTS
+ protected static final int PREFERRED_WIDTH = 750;
+ protected static final int PREFERRED_HEIGHT = 600;
+ protected static final int PREFERRED_SCROLL = 10;
+ protected static final int PREVIEW_HISTORY_LENGTH = 50;
+
+ // navigation data
+ private int iCurrentHistoryIdx; // index within the current history
+ private final ArrayList<String> alCurrentHistory; // current history - e.g. if one
+ // opens Page1, then Page2; goes back and opens Page3 - current preview would hold only [Page1, Page3]
+ private ArrayList<Resource> alFullHistory; // all resources that were
+ // previewed since application started (will be used by ResourcePreviewHistoryBrowser)
+
+ // components for accessing application's main elements
+ private final MainComponent pluginMainComponent;
+ private final MyExperimentClient myExperimentClient;
+ private final Logger logger;
+
+ // holder of the data about currently previewed item
+ private ResourcePreviewContent rpcContent;
+ private Resource resource;
+
+ // components of the preview window
+ private JPanel jpMain;
+ private JPanel jpStatusBar;
+ private JLabel lSpinnerIcon;
+ private JButton bBack;
+ private JButton bForward;
+ private JButton bRefresh;
+ private JButton bOpenInMyExp;
+ private JButton bDownload;
+ private JButton bOpenInTaverna;
+ private JButton bImportIntoTaverna;
+ private JButton bAddComment;
+ private JButton bAddRemoveFavourite;
+ private JButton bUpload;
+ private JButton bEditMetadata;
+ private JScrollPane spContentScroller;
+
+ // icons
+ private final ImageIcon iconOpenInMyExp = new ImageIcon(MyExperimentPerspective.getLocalResourceURL("open_in_my_experiment_icon"));
+ private final ImageIcon iconAddFavourite = new ImageIcon(MyExperimentPerspective.getLocalResourceURL("add_favourite_icon"));
+ private final ImageIcon iconDeleteFavourite = new ImageIcon(MyExperimentPerspective.getLocalResourceURL("delete_favourite_icon"));
+ private final ImageIcon iconAddComment = new ImageIcon(MyExperimentPerspective.getLocalResourceURL("add_comment_icon"));
+ private final ImageIcon iconSpinner = new ImageIcon(MyExperimentPerspective.getLocalResourceURL("spinner"));
+ private final ImageIcon iconSpinnerStopped = new ImageIcon(MyExperimentPerspective.getLocalResourceURL("spinner_stopped"));
+ private final FileManager fileManager;
+
+ public ResourcePreviewBrowser(MainComponent component, MyExperimentClient client, Logger logger, FileManager fileManager) {
+ super();
+
+ // set main variables to ensure access to myExperiment, logger and the
+ // parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+ this.fileManager = fileManager;
+
+ // initialise previewed items history
+ String strPreviewedItemsHistory = (String) myExperimentClient.getSettings().get(MyExperimentClient.INI_PREVIEWED_ITEMS_HISTORY);
+ if (strPreviewedItemsHistory != null) {
+ Object oPreviewedItemsHistory = Base64.decodeToObject(strPreviewedItemsHistory);
+ this.alFullHistory = (ArrayList<Resource>) oPreviewedItemsHistory;
+ } else {
+ this.alFullHistory = new ArrayList<Resource>();
+ }
+
+ // no navigation history at loading
+ this.iCurrentHistoryIdx = -1;
+ this.alCurrentHistory = new ArrayList<String>();
+
+ // set options of the preview dialog box
+ this.setIconImage(new ImageIcon(MyExperimentPerspective.getLocalResourceURL("myexp_icon")).getImage());
+ this.addComponentListener(this);
+
+ this.initialiseUI();
+ }
+
+ /**
+ * Accessor method for getting a full history of previewed resources as a
+ * list.
+ */
+ public ArrayList<Resource> getPreviewHistory() {
+ return (this.alFullHistory);
+ }
+
+ /**
+ * As opposed to getPreviewHistory() which returns full history of previewed
+ * resources, this helper method only retrieves the current history stack.
+ *
+ * Example: if a user was to view the following items - A -> B -> C B <- C B
+ * -> D, the full history would be [A,C,B,D]; current history stack would be
+ * [A,B,D] - note how item C was "forgotten" (this works the same way as all
+ * web browsers do)
+ */
+ public List<String> getCurrentPreviewHistory() {
+ return (this.alCurrentHistory);
+ }
+
+ /**
+ * Deletes both 'current history' (the latest preview history stack) and the
+ * 'full preview history'. Also, resets the index in the current history, so
+ * that the preview browser would not allow using Back-Forward buttons until
+ * some new previews are opened.
+ */
+ public void clearPreviewHistory() {
+ this.iCurrentHistoryIdx = -1;
+ this.alCurrentHistory.clear();
+ this.alFullHistory.clear();
+ }
+
+ /**
+ * This method is a launcher for the real worker method ('createPreview()')
+ * that does all the job.
+ *
+ * The purpose of having this method is to manage history. This method is to
+ * be called every time when a "new" preview is requested. This will add a new
+ * link to the CurrentHistory stack.
+ *
+ * Clicks on "Back" and "Forward" buttons will only need to advance the
+ * counter of the current position in the CurrentHistory. Therefore, these
+ * will directly call 'createPreview()'.
+ */
+ public void preview(String action) {
+ // *** History Update ***
+ // if this is not the "newest" page in current history, remove all newer
+ // ones
+ // (that is if the user went "back" and opened some new link from on of the
+ // older pages)
+ while (alCurrentHistory.size() > iCurrentHistoryIdx + 1) {
+ alCurrentHistory.remove(alCurrentHistory.size() - 1);
+ }
+
+ boolean bPreviewNotTheSameAsTheLastOne = true;
+ if (alCurrentHistory.size() > 0) {
+ // will add new page to the history only if it's not the same as the last
+ // one!
+ if (action.equals(alCurrentHistory.get(alCurrentHistory.size() - 1))) {
+ bPreviewNotTheSameAsTheLastOne = false;
+ }
+
+ // this is not the first page in the history, enable "Back" button (if
+ // only this isn't the same page as was the first one);
+ // (this, however, is the last page in the history now - so disable
+ // "Forward" button)
+ bBack.setEnabled(bPreviewNotTheSameAsTheLastOne
+ || alCurrentHistory.size() > 1);
+ bForward.setEnabled(false);
+ } else if (alCurrentHistory.size() == 0) {
+ // this is the first preview after application has loaded or since the
+ // preview history was cleared - disable both Back and Forward buttons
+ bBack.setEnabled(false);
+ bForward.setEnabled(false);
+ }
+
+ // add current preview URI to the history
+ if (bPreviewNotTheSameAsTheLastOne) {
+ iCurrentHistoryIdx++;
+ alCurrentHistory.add(action);
+ }
+
+ // *** Launch Preview ***
+ createPreview(action);
+ }
+
+ private void createPreview(String action) {
+ // JUST FOR TESTING THE CURRENT_HISTORY OPERATION
+ // javax.swing.JOptionPane.showMessageDialog(null, "History idx: " +
+ // this.iCurrentHistoryIdx + "\n" + alCurrentHistory.toString());
+
+ // show that loading is in progress
+ this.setTitle("Loading preview...");
+ this.lSpinnerIcon.setIcon(this.iconSpinner);
+
+ // disable all action buttons while loading is in progress
+ bOpenInMyExp.setEnabled(false);
+ bDownload.setEnabled(false);
+ bOpenInTaverna.setEnabled(false);
+ bImportIntoTaverna.setEnabled(false);
+ bAddRemoveFavourite.setEnabled(false);
+ bAddComment.setEnabled(false);
+ bUpload.setEnabled(false);
+ bEditMetadata.setEnabled(false);
+
+ // Make call to myExperiment API in a different thread
+ // (then use SwingUtilities.invokeLater to update the UI when ready).
+ final String strAction = action;
+ final EventListener self = this;
+
+ new Thread("Load myExperiment resource preview content") {
+ @Override
+ public void run() {
+ logger.debug("Starting to fetch the preview content data");
+
+ try {
+ // *** Fetch Data and Create Preview Content ***
+ rpcContent = pluginMainComponent.getPreviewFactory().createPreview(strAction, self);
+
+ // as all the details about the previewed resource are now known, can
+ // store this into full preview history
+ // (before that make sure that if the this item was viewed before,
+ // it's removed and re-added at the "top" of the list)
+ // (also make sure that the history size doesn't exceed the pre-set
+ // value)
+ alFullHistory.remove(rpcContent.getResource());
+ alFullHistory.add(rpcContent.getResource());
+ if (alFullHistory.size() > PREVIEW_HISTORY_LENGTH)
+ alFullHistory.remove(0);
+ pluginMainComponent.getHistoryBrowser().refreshHistoryBox(HistoryBrowserTabContentPanel.PREVIEWED_ITEMS_HISTORY);
+
+ // *** Update the Preview Dialog Box when everything is ready ***
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // 'stop' loading action in the status bar and window title
+ setTitle(Resource.getResourceTypeName(rpcContent.getResourceType())
+ + ": " + rpcContent.getResourceTitle());
+ lSpinnerIcon.setIcon(iconSpinnerStopped);
+
+ // update the state of action buttons in the button bar
+ updateButtonBarState(rpcContent);
+
+ // wrap received content into a ScrollPane
+ spContentScroller = new JScrollPane(rpcContent.getContent());
+ spContentScroller.setBorder(BorderFactory.createEmptyBorder());
+ spContentScroller.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+
+ // remove everything from the preview and re-add all components
+ // (NB! Removing only CENTER component didn't work properly)
+ jpMain.removeAll();
+ jpMain.add(redrawStatusBar(), BorderLayout.NORTH);
+ jpMain.add(spContentScroller, BorderLayout.CENTER);
+ validate();
+ repaint();
+ }
+ });
+ } catch (Exception ex) {
+ logger.error("Exception on attempt to login to myExperiment:\n", ex);
+ }
+ }
+ }.start();
+
+ // show the dialog box
+ this.setVisible(true);
+ }
+
+ private void initialiseUI() {
+ // create the STATUS BAR of the preview window
+ createButtonsForStatusBar();
+
+ // put everything together
+ jpMain = new JPanel();
+ jpMain.setOpaque(true);
+ jpMain.setLayout(new BorderLayout());
+ jpMain.add(redrawStatusBar(), BorderLayout.NORTH);
+
+ // add all content into the main dialog
+ this.getContentPane().add(jpMain);
+
+ }
+
+ private void createButtonsForStatusBar() {
+ // navigation buttons => far left of status bar
+ bBack = new JButton(new ImageIcon(MyExperimentPerspective.getLocalResourceURL("back_icon")));
+ bBack.setToolTipText("Back");
+ bBack.addActionListener(this);
+ bBack.setEnabled(false);
+
+ bForward = new JButton(new ImageIcon(MyExperimentPerspective.getLocalResourceURL("forward_icon")));
+ bForward.setToolTipText("Forward");
+ bForward.addActionListener(this);
+ bForward.setEnabled(false);
+
+ // refresh buttons => far right of status bar
+ bRefresh = new JButton(new ImageIcon(MyExperimentPerspective.getLocalResourceURL("refresh_icon")));
+ bRefresh.setToolTipText("Refresh");
+ bRefresh.addActionListener(this);
+
+ lSpinnerIcon = new JLabel(this.iconSpinner);
+
+ // ACTION BUTTONS
+ // 'open in myExperiment' button is the only one that is always available,
+ // still will be set available during loading of the preview for consistency of the UI
+
+ // myExperiment "webby" functions
+ bOpenInMyExp = new JButton(iconOpenInMyExp);
+ bOpenInMyExp.setEnabled(false);
+ bOpenInMyExp.addActionListener(this);
+
+ bAddRemoveFavourite = new JButton(iconAddFavourite);
+ bAddRemoveFavourite.setEnabled(false);
+ bAddRemoveFavourite.addActionListener(this);
+
+ bAddComment = new JButton(iconAddComment);
+ bAddComment.setEnabled(false);
+ bAddComment.addActionListener(this);
+
+ bEditMetadata = new JButton("Update", WorkbenchIcons.editIcon);
+ bEditMetadata.setEnabled(false);
+ bEditMetadata.addActionListener(this);
+
+ bUpload = new JButton("Upload", WorkbenchIcons.upArrowIcon);
+ bUpload.setEnabled(false);
+ bUpload.addActionListener(this);
+
+ // functions more specific to taverna
+ bOpenInTaverna = new JButton(WorkbenchIcons.openIcon);
+ bOpenInTaverna.setEnabled(false);
+ bOpenInTaverna.addActionListener(this);
+
+ bImportIntoTaverna = new JButton();
+ bImportIntoTaverna.setEnabled(false);
+ bImportIntoTaverna.addActionListener(this);
+
+ bDownload = new JButton(WorkbenchIcons.saveIcon);
+ bDownload.setEnabled(false);
+ bDownload.addActionListener(this);
+ }
+
+ private JPanel redrawStatusBar() {
+ // far left of button bar
+ JPanel jpNavigationButtons = new JPanel();
+ jpNavigationButtons.add(bBack);
+ jpNavigationButtons.add(bForward);
+
+ // far right of button bar
+ JPanel jpRefreshButtons = new JPanel();
+ jpRefreshButtons.add(bRefresh);
+ jpRefreshButtons.add(lSpinnerIcon);
+
+ // myExperiment buttons: second left of the button bar
+ JPanel jpMyExperimentButtons = new JPanel();
+ jpMyExperimentButtons.add(bOpenInMyExp);
+ jpMyExperimentButtons.add(bAddRemoveFavourite);
+ jpMyExperimentButtons.add(bAddComment);
+ jpMyExperimentButtons.add(bEditMetadata);
+ jpMyExperimentButtons.add(bUpload);
+
+ // taverna buttons: second right of the button bar
+ JPanel jpTavernaButtons = new JPanel();
+ jpTavernaButtons.add(bOpenInTaverna);
+ jpTavernaButtons.add(bImportIntoTaverna);
+ jpTavernaButtons.add(bDownload);
+
+ // put all action buttons into a button bar
+ JPanel jpStatusBar = new JPanel();
+ jpStatusBar.setLayout(new GridBagLayout());
+ int spaceBetweenSections = 40;
+
+ GridBagConstraints c = new GridBagConstraints();
+ c.insets = new Insets(0, spaceBetweenSections, 0, spaceBetweenSections / 2);
+ c.anchor = GridBagConstraints.WEST;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.gridx = 0;
+ c.gridy = 0;
+ jpStatusBar.add(jpNavigationButtons, c);
+
+ c.gridx++;
+ c.insets = new Insets(0, spaceBetweenSections / 2, 0, spaceBetweenSections / 2);
+ jpStatusBar.add(jpMyExperimentButtons, c);
+
+ c.gridx++;
+ jpStatusBar.add(jpTavernaButtons, c);
+
+ c.gridx++;
+ c.insets = new Insets(0, spaceBetweenSections / 2, 0, spaceBetweenSections);
+ jpStatusBar.add(jpRefreshButtons, c);
+
+ return jpStatusBar;
+
+ // // put all action buttons into a button bar
+ // JPanel jpActionButtons = new JPanel();
+ // jpActionButtons.setLayout(new GridBagLayout());
+ // GridBagConstraints c = new GridBagConstraints();
+ // double spacing = ResourcePreviewBrowser.PREFERRED_WIDTH * 0.1;
+ // c.insets = new Insets(0, (int) spacing, 0, (int) spacing / 2);
+ // c.gridx = 0;
+ // c.gridy = 0;
+ // jpActionButtons.add(jpMyExperimentButtons, c);
+ //
+ // c.gridx++;
+ // c.insets = new Insets(0, (int) spacing / 2, 0, (int) spacing);
+ // jpActionButtons.add(jpTavernaButtons, c);
+ //
+ // jpStatusBar = new JPanel();
+ // jpStatusBar.setLayout(new BorderLayout());
+ // jpStatusBar.add(jpNavigationButtons, BorderLayout.WEST);
+ // jpStatusBar.add(jpActionButtons, BorderLayout.CENTER);
+ // jpStatusBar.add(jpRefreshButtons, BorderLayout.EAST);
+ }
+
+ private void updateButtonBarState(ResourcePreviewContent content) {
+ // get the visible type name of the resource
+ Resource r = this.rpcContent.getResource();
+ String strResourceType = Resource.getResourceTypeName(r.getItemType()).toLowerCase();
+
+ // "Open in myExperiment" is always available for every item type
+ this.bOpenInMyExp.setEnabled(true);
+ this.bOpenInMyExp.setToolTipText("Open this " + strResourceType
+ + " in myExperiment");
+
+ // "edit metadata" to myExperiment is only available for logged in
+ // users who are the owners of the workflow
+ String strTooltip = "It is currently not possible to edit the metadata for this workflow";
+ boolean bUpdateMetaAvailable = false;
+
+ if (myExperimentClient.isLoggedIn()
+ && (myExperimentClient.getCurrentUser().equals(r.getUploader()))
+ && (r.getItemTypeName().equals("Workflow"))) {
+ strTooltip = "Update the metadata of this workflow.";
+ bUpdateMetaAvailable = true;
+ } else {
+ strTooltip = "Only the owners of workflows can change the metadata of workflows.";
+ }
+ this.bEditMetadata.setToolTipText(strTooltip);
+ this.bEditMetadata.setEnabled(bUpdateMetaAvailable);
+
+ // "upload new version" to myExperiment is only available for logged in
+ // users who are the owners of the workflow
+ strTooltip = "It is currently not possible to upload a new version of this workflow.";
+ boolean bUploadAvailable = false;
+
+ if (myExperimentClient.isLoggedIn()
+ && (myExperimentClient.getCurrentUser().equals(r.getUploader()))
+ && (r.getItemTypeName().equals("Workflow"))) {
+ strTooltip = "Upload a new version of this workflow.";
+ bUploadAvailable = true;
+ } else {
+ strTooltip = "Only the owners of workflows can upload new versions of workflows.";
+ }
+ this.bUpload.setToolTipText(strTooltip);
+ this.bUpload.setEnabled(bUploadAvailable);
+
+ // "Download" - only for selected types and based on current user's
+ // permissions (these conditions are checked within the action)
+ this.bDownload.setAction(pluginMainComponent.new DownloadResourceAction(r, false));
+
+ // "Open in Taverna" - only for Taverna workflows and when download is
+ // allowed for current user (these checks are carried out inside the action)
+ this.bOpenInTaverna.setAction(pluginMainComponent.new LoadResourceInTavernaAction(r, true));
+
+ // "Import into Taverna" - only for Taverna workflows and when download is
+ // allowed for current user (these checks are carried out inside the action)
+ // the import button
+ this.bImportIntoTaverna.setAction(pluginMainComponent.new ImportIntoTavernaAction(r));
+
+ // "Add to Favourites" - for all types, but only for logged in users
+ strTooltip = "It is currently not possible to add " + strResourceType
+ + "s to favourites";
+ boolean bFavouritingAvailable = false;
+ if (r.isFavouritable()) {
+ if (myExperimentClient.isLoggedIn()) {
+ if (r.isFavouritedBy(myExperimentClient.getCurrentUser())) {
+ strTooltip = "Remove this " + strResourceType
+ + " from your favourites";
+ this.bAddRemoveFavourite.setIcon(iconDeleteFavourite);
+ } else {
+ strTooltip = "Add this " + strResourceType + " to your favourites";
+ this.bAddRemoveFavourite.setIcon(iconAddFavourite);
+ }
+ bFavouritingAvailable = true;
+ } else {
+ // TODO should be changed to display login box first, then favouriting option
+ strTooltip = "Only logged in users can add items to favourites";
+ }
+ }
+ this.bAddRemoveFavourite.setToolTipText(strTooltip);
+ this.bAddRemoveFavourite.setEnabled(bFavouritingAvailable);
+
+ // "Add Comment" - for all types besides users and only for logged in users
+ strTooltip = "It is currently not possible to comment on "
+ + strResourceType + "s";
+ boolean bCommentingAvailable = false;
+ if (r.isCommentableOn()) {
+ if (myExperimentClient.isLoggedIn()) {
+ strTooltip = "Add a comment on this " + strResourceType;
+ bCommentingAvailable = true;
+ } else {
+ // TODO should be changed to display login box first, then commenting option
+ strTooltip = "Only logged in users can make comments";
+ }
+ }
+ this.bAddComment.setToolTipText(strTooltip);
+ this.bAddComment.setEnabled(bCommentingAvailable);
+ }
+
+ public void hyperlinkUpdate(HyperlinkEvent e) {
+ if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+ String strAction = e.getDescription().toString();
+
+ if (strAction.startsWith("preview:")) {
+ this.preview(strAction);
+ } else {
+ try {
+ Desktop.getDesktop().browse(new URI(strAction));
+ } catch (Exception ex) {
+ logger.error("Failed while trying to open the URL in a standard browser; URL was: "
+ + strAction + "\nException was: " + ex);
+ }
+ }
+ }
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource().equals(this.bBack)) {
+ // "Back" button clicked
+
+ // update position in the history
+ iCurrentHistoryIdx--;
+
+ // enable or disable "back"/"forward" buttons as appropriate
+ bBack.setEnabled(iCurrentHistoryIdx > 0);
+ bForward.setEnabled(iCurrentHistoryIdx < alCurrentHistory.size() - 1);
+
+ // open requested preview from the history
+ this.createPreview(alCurrentHistory.get(iCurrentHistoryIdx));
+ } else if (e.getSource().equals(this.bForward)) {
+ // "Forward" button clicked
+
+ // update position in the history
+ iCurrentHistoryIdx++;
+
+ // enable or disable "back"/"forward" buttons as appropriate
+ bBack.setEnabled(iCurrentHistoryIdx > 0);
+ bForward.setEnabled(iCurrentHistoryIdx < alCurrentHistory.size() - 1);
+
+ // open requested preview from the history
+ this.createPreview(alCurrentHistory.get(iCurrentHistoryIdx));
+ } else if (e.getSource().equals(this.bRefresh)) {
+ // "Refresh" button clicked
+
+ // simply reload the same preview
+ this.createPreview(alCurrentHistory.get(iCurrentHistoryIdx));
+ } else if (e.getSource().equals(this.bOpenInMyExp)) {
+ // "Open in myExperiment" button clicked
+ try {
+ Desktop.getDesktop().browse(new URI(this.rpcContent.getResourceURL()));
+ } catch (Exception ex) {
+ logger.error("Failed while trying to open the URL in a standard browser; URL was: "
+ + this.rpcContent.getResourceURL() + "\nException was: " + ex);
+ }
+ } else if (e.getSource().equals(this.bUpload)) {
+ /* ************************************************************************* */
+ Resource resource = this.rpcContent.getResource();
+ if (resource.getItemTypeName().equals("Workflow")) {
+ UploadWorkflowDialog uploadWorkflowDialog = new UploadWorkflowDialog(this, true, resource, fileManager);
+
+ if (uploadWorkflowDialog.launchUploadDialogAndPostIfRequired()) {
+ // "true" has been returned so update the resource
+ this.actionPerformed(new ActionEvent(this.bRefresh, 0, ""));
+ }
+ }
+ } else if (e.getSource().equals(this.bEditMetadata)) {
+ Resource resource = this.rpcContent.getResource();
+ if (resource.getItemTypeName().equals("Workflow")) {
+ UploadWorkflowDialog uploadWorkflowDialog = new UploadWorkflowDialog(this, false, resource, fileManager);
+
+ if (uploadWorkflowDialog.launchUploadDialogAndPostIfRequired()) {
+ // "true" has been returned so update the resource
+ this.actionPerformed(new ActionEvent(this.bRefresh, 0, ""));
+ }
+ }
+ /* ************************************************************************* */
+ } else if (e.getSource().equals(this.bAddComment)) {
+ // "Add Comment" button was clicked
+ String strComment = null;
+ AddCommentDialog commentDialog = new AddCommentDialog(this, this.rpcContent.getResource(), pluginMainComponent, myExperimentClient, logger);
+ if ((strComment = commentDialog.launchAddCommentDialogAndPostCommentIfRequired()) != null) {
+ // comment was added because return value is not null;
+ // a good option now would be to reload only the comments tab, but
+ // for now we refresh the whole of the preview
+ this.actionPerformed(new ActionEvent(this.bRefresh, 0, ""));
+
+ // update history of the items that were commented on, making sure that:
+ // - there's only one occurrence of this item in the history;
+ // - if this item was in the history before, it is moved to the 'top' now;
+ // - predefined history size is not exceeded
+ this.pluginMainComponent.getHistoryBrowser().getCommentedOnItemsHistoryList().remove(this.rpcContent.getResource());
+ this.pluginMainComponent.getHistoryBrowser().getCommentedOnItemsHistoryList().add(this.rpcContent.getResource());
+ if (this.pluginMainComponent.getHistoryBrowser().getCommentedOnItemsHistoryList().size() > HistoryBrowserTabContentPanel.COMMENTED_ON_ITEMS_HISTORY) {
+ this.pluginMainComponent.getHistoryBrowser().getCommentedOnItemsHistoryList().remove(0);
+ }
+
+ // now update the history of the items that were commented on in 'History' tab
+ if (this.pluginMainComponent.getHistoryBrowser() != null) {
+ this.pluginMainComponent.getHistoryBrowser().refreshHistoryBox(HistoryBrowserTabContentPanel.COMMENTED_ON_ITEMS_HISTORY);
+ }
+ }
+ } else if (e.getSource().equals(this.bAddRemoveFavourite)) {
+ boolean bItemIsFavourited = this.rpcContent.getResource().isFavouritedBy(this.myExperimentClient.getCurrentUser());
+
+ AddRemoveFavouriteDialog favouriteDialog = new AddRemoveFavouriteDialog(this, !bItemIsFavourited, this.rpcContent.getResource(), pluginMainComponent, myExperimentClient, logger);
+ int iFavouritingStatus = favouriteDialog.launchAddRemoveFavouriteDialogAndPerformNecessaryActionIfRequired();
+
+ // if the operation wasn't cancelled, update status of the
+ // "add/remove favourite" button and the list of favourites in the user profile
+ if (iFavouritingStatus != AddRemoveFavouriteDialog.OPERATION_CANCELLED) {
+ this.updateButtonBarState(this.rpcContent);
+ this.pluginMainComponent.getMyStuffTab().getSidebar().repopulateFavouritesBox();
+ this.pluginMainComponent.getMyStuffTab().getSidebar().revalidate();
+ }
+ } else if (e.getSource() instanceof JClickableLabel) {
+ // clicked somewhere on a JClickableLabel; if that's a 'preview' request - launch preview
+ if (e.getActionCommand().startsWith("preview:")) {
+ this.preview(e.getActionCommand());
+ } else if (e.getActionCommand().startsWith("tag:")) {
+ // pass this event onto the Tag Browser tab
+ this.pluginMainComponent.getTagBrowserTab().actionPerformed(e);
+ this.pluginMainComponent.getMainTabs().setSelectedComponent(this.pluginMainComponent.getTagBrowserTab());
+ } else {
+ // show the link otherwise
+ try {
+ Desktop.getDesktop().browse(new URI(e.getActionCommand()));
+ } catch (Exception ex) {
+ logger.error("Failed while trying to open the URL in a standard browser; URL was: "
+ + e.getActionCommand() + "\nException was: " + ex);
+ }
+ }
+ } else if (e.getSource() instanceof TagCloudPanel
+ && e.getActionCommand().startsWith("tag:")) {
+ // close the window and pass this event onto the Tag Browser tab
+ this.setVisible(false);
+ this.pluginMainComponent.getTagBrowserTab().actionPerformed(e);
+ this.pluginMainComponent.getMainTabs().setSelectedComponent(this.pluginMainComponent.getTagBrowserTab());
+ }
+ }
+
+ // *** Callbacks for ComponentListener interface ***
+
+ public void componentShown(ComponentEvent e) {
+ // every time the preview browser window is shown, it will start loading a preview
+ // - this state is set in the preview() method; (so this won't have to be done here)
+
+ // remove everything from the preview and re-add only the status bar
+ // (this is done so that newly opened preview window won't show the old
+ // preview)
+ jpMain.removeAll();
+ jpMain.add(redrawStatusBar(), BorderLayout.NORTH);
+ repaint();
+
+ // set the size of the dialog box (NB! Size needs to be set before the position!)
+ this.setSize(ResourcePreviewBrowser.PREFERRED_WIDTH, ResourcePreviewBrowser.PREFERRED_HEIGHT);
+ this.setMinimumSize(new Dimension(ResourcePreviewBrowser.PREFERRED_WIDTH, ResourcePreviewBrowser.PREFERRED_HEIGHT));
+
+ // make sure that the dialog box appears centered horizontally relatively to
+ // the main component; also, pad by 30px vertically from the top of the main component
+ int iMainComponentCenterX = (int) Math.round(this.pluginMainComponent.getLocationOnScreen().getX()
+ + (this.pluginMainComponent.getWidth() / 2));
+ int iPosX = iMainComponentCenterX - (this.getWidth() / 2);
+ int iPosY = ((int) this.pluginMainComponent.getLocationOnScreen().getY()) + 30;
+ this.setLocation(iPosX, iPosY);
+
+ myExperimentClient.storeHistoryAndSettings();
+ }
+
+ public void componentHidden(ComponentEvent e) {
+ myExperimentClient.storeHistoryAndSettings();
+ }
+
+ public void componentResized(ComponentEvent e) {
+ // do nothing
+ }
+
+ public void componentMoved(ComponentEvent e) {
+ // do nothing
+ }
+
+ public Resource getResource() {
+ return resource;
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ResourcePreviewContent.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ResourcePreviewContent.java
new file mode 100644
index 0000000..85b47c0
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ResourcePreviewContent.java
@@ -0,0 +1,78 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import javax.swing.JComponent;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+
+/**
+ * Helper class to hold all data about the generated preview.
+ *
+ * @author Sergejs Aleksejevs
+ *
+ */
+public class ResourcePreviewContent
+{
+ private Resource resource;
+ private JComponent jcContent;
+
+ public ResourcePreviewContent()
+ {
+ // empty constructor
+ }
+
+ public ResourcePreviewContent(Resource resource, JComponent content)
+ {
+ this.resource = resource;
+ this.jcContent = content;
+ }
+
+ public Resource getResource()
+ {
+ return(this.resource);
+ }
+
+ public int getResourceType()
+ {
+ return(this.resource.getItemType());
+ }
+
+ public String getResourceTitle()
+ {
+ return(this.resource.getTitle());
+ }
+
+ public String getResourceURL()
+ {
+ return(this.resource.getResource());
+ }
+
+ public String getResourceURI()
+ {
+ return(this.resource.getURI());
+ }
+
+ public JComponent getContent()
+ {
+ return(this.jcContent);
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ResourcePreviewFactory.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ResourcePreviewFactory.java
new file mode 100644
index 0000000..128cfd3
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/ResourcePreviewFactory.java
@@ -0,0 +1,1359 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.EventListener;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTable;
+import javax.swing.JTextPane;
+import javax.swing.ScrollPaneConstants;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.event.HyperlinkListener;
+import javax.swing.text.html.HTMLDocument;
+import javax.swing.text.html.HTMLEditorKit;
+
+import net.sf.taverna.t2.lang.ui.DialogTextArea;
+import net.sf.taverna.t2.lang.ui.ShadedLabel;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Comment;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.File;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Group;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Pack;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.PackItem;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Tag;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.User;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Util;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Workflow;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class ResourcePreviewFactory {
+ // CONSTANTS
+ private static final int PREFERRED_LOWER_TABBED_PANE_HEIGHT = 250; // used for
+ // all
+ // tabbed
+ // views
+ // inside
+ // preview
+ // for
+ // every
+ // resource
+ // type
+
+ private final MainComponent pluginMainComponent;
+ private final MyExperimentClient myExperimentClient;
+ private final Logger logger;
+
+ // icons which are used in several places in the preview factory
+ private final ImageIcon iconWorkflow;
+ private final ImageIcon iconFile;
+ private final ImageIcon iconPack;
+ private final ImageIcon iconUser;
+ private final ImageIcon iconGroup;
+
+ public ResourcePreviewFactory(MainComponent component, MyExperimentClient client, Logger logger) {
+ super();
+
+ // set main variables to ensure access to myExperiment, logger and the
+ // parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+
+ // set up the icons
+ iconWorkflow = new ImageIcon(MyExperimentPerspective.getLocalIconURL(Resource.WORKFLOW));
+ iconFile = new ImageIcon(MyExperimentPerspective.getLocalIconURL(Resource.FILE));
+ iconPack = new ImageIcon(MyExperimentPerspective.getLocalIconURL(Resource.PACK));
+ iconUser = new ImageIcon(MyExperimentPerspective.getLocalIconURL(Resource.USER));
+ iconGroup = new ImageIcon(MyExperimentPerspective.getLocalIconURL(Resource.GROUP));
+ }
+
+ // main worker method - generates the content to be shown in the preview;
+ // responsible for parsing the preview action request, fetching data and
+ // generating all the content (via helpers)
+ public ResourcePreviewContent createPreview(String action, EventListener eventHandler) {
+ JPanel panelToPopulate = new JPanel();
+
+ // === PREPROCESSING ===
+
+ // return error message if the action string isn't actually a request for
+ // preview
+ if (!action.startsWith("preview:")) {
+ this.logger.error("Bad preview request: \"" + action + "\"");
+ panelToPopulate.add(new JLabel("An error has occurred."));
+ Resource r = new Resource();
+ r.setItemType(Resource.UNEXPECTED_TYPE);
+ r.setTitle("Bad preview request");
+ r.setURI(action);
+ return (new ResourcePreviewContent(r, panelToPopulate));
+ }
+
+ // parse the action string - we are now sure that it starts with a
+ // 'preview:'
+ action = action.substring(action.indexOf(":") + 1); // remove "preview:"
+ int iType = Integer.parseInt(action.substring(0, action.indexOf(":"))); // get
+ // type
+ action = action.substring(action.indexOf(":") + 1); // remove type
+ String strURI = action; // get URI
+
+ // === FETCHING RESOURCE DATA ===
+ Document doc = null;
+ try {
+ // the resource type is known at this point, hence can use specialist
+ // method
+ // that only fetches required metadata for (individual for each resource
+ // type)
+ doc = this.myExperimentClient.getResource(iType, strURI, Resource.REQUEST_FULL_PREVIEW);
+ } catch (Exception e) {
+ logger.error("Error while fetching resource data from myExperiment to generate a preview.\nResource type: "
+ + Resource.getResourceTypeName(iType)
+ + "\nResource URI: "
+ + strURI
+ + "\nException: " + e);
+ }
+
+ // === GENERATING PREVIEW ===
+ Resource resource = null;
+ switch (iType) {
+ case Resource.WORKFLOW:
+ Workflow w = Workflow.buildFromXML(doc, this.logger);
+ resource = w;
+ this.generateWorkflowPreviewContent(w, panelToPopulate, eventHandler);
+ break;
+
+ case Resource.FILE:
+ File f = File.buildFromXML(doc, this.logger);
+ resource = f;
+ this.generateFilePreviewContent(f, panelToPopulate, eventHandler);
+ break;
+
+ case Resource.PACK:
+ Pack p = Pack.buildFromXML(doc, this.myExperimentClient, this.logger);
+ resource = p;
+ this.generatePackPreviewContent(p, panelToPopulate, eventHandler);
+ break;
+
+ case Resource.USER:
+ User u = User.buildFromXML(doc, logger);
+ resource = u;
+ this.generateUserPreviewContent(u, panelToPopulate, eventHandler);
+ break;
+
+ case Resource.GROUP:
+ Group g = Group.buildFromXML(doc, logger);
+ resource = g;
+ this.generateGroupPreviewContent(g, panelToPopulate, eventHandler);
+ break;
+
+ default:
+ // unexpected resource type - can't generate preview
+ this.logger.error("Failed generating preview. Reason: unknown resource type - \""
+ + Resource.getResourceTypeName(iType) + "\"");
+ panelToPopulate.add(new JLabel("Cannot generate preview for unknown resource types."));
+ Resource r = new Resource();
+ r.setItemType(iType);
+ r.setTitle("Error: unknown resource type");
+ r.setURI(strURI);
+ return (new ResourcePreviewContent(r, panelToPopulate));
+ }
+
+ // format output data
+ return (new ResourcePreviewContent(resource, panelToPopulate));
+ }
+
+ private void generateWorkflowPreviewContent(Workflow w, JPanel panelToPopulate, EventListener eventHandler) {
+ if (w != null) {
+ try {
+ StringBuffer content = new StringBuffer();
+ content.append("<div class='outer'>");
+ content.append("<div class='workflow'>");
+
+ content.append("<br>");
+
+ content.append("<p class='title'>");
+ content.append("Workflow Entry: <a href='preview:" + Resource.WORKFLOW
+ + ":" + w.getURI() + "'>" + w.getTitle() + "</a> (version "
+ + w.getVersion() + ")");
+ content.append("</p>");
+
+ content.append("<br>");
+
+ content.append("<p class='info'>");
+ content.append("<b>Type:</b> " + w.getVisibleType() + "<br><br>");
+ content.append("<b>Uploader:</b> <a href='preview:" + Resource.USER
+ + ":" + w.getUploader().getURI() + "'>" + w.getUploader().getName()
+ + "</a><br>");
+ content.append("<b>Created at: </b> " + w.getCreatedAt() + "<br>");
+ content.append("<b>License: </b> <a href='"
+ + w.getLicense().getLink()
+ + "'>"
+ + w.getLicense().getText()
+ + "</a>"
+ + " <img src='"
+ + MyExperimentPerspective.getLocalResourceURL("external_link_small_icon")
+ + "' />");
+ content.append("</p>");
+
+ content.append("<br>");
+
+ content.append("<a href='" + w.getPreview() + "'>");
+ content.append("<img class='preview' src='" + w.getThumbnailBig()
+ + "'></img>");
+ content.append("</a>");
+
+ content.append("<br>");
+ content.append("<br>");
+
+ if (!w.getDescription().equals("")) {
+ content.append("<p class='desc'>");
+ content.append("<br>");
+ content.append(Util.stripHTML(w.getDescription()));
+ content.append("<br>");
+ content.append("</p>");
+ } else {
+ content.append("<span class='none_text'>No description</span>");
+ }
+
+ content.append("<br>");
+ content.append("</div>");
+ content.append("</div>");
+
+ HTMLEditorKit kit = new StyledHTMLEditorKit(pluginMainComponent.getStyleSheet());
+ HTMLDocument doc = (HTMLDocument) (kit.createDefaultDocument());
+ doc.insertAfterStart(doc.getRootElements()[0].getElement(0), content.toString());
+
+ // === Now render user's items as Swing components ===
+ // .. TABS for components, tags, comments, credits, attributions ..
+ JScrollPane spComponentsTab = createWorkflowComponentPreviewTab(w);
+ JScrollPane spTagsTab = createTagPreviewTab(w.getTags());
+ JScrollPane spCommentsTab = createCommentsPreviewTab(w.getComments());
+ JScrollPane spCreditsTab = createCreditsPreviewTab(w.getCredits());
+ JScrollPane spAttributionsTab = createAttributionsPreviewTab(w.getAttributions());
+
+ // .. ASSEMBLE ALL TABS together
+ JTabbedPane tpTabbedView = new JTabbedPane();
+ tpTabbedView.add("Components", spComponentsTab);
+ tpTabbedView.add("Tags (" + w.getTags().size() + ")", spTagsTab);
+ tpTabbedView.add("Comments (" + w.getComments().size() + ")", spCommentsTab);
+ tpTabbedView.addTab("Credits (" + w.getCredits().size() + ")", spCreditsTab);
+ tpTabbedView.addTab("Attributions (" + w.getAttributions().size() + ")", spAttributionsTab);
+
+ // PUT EVERYTHING TOGETHER
+ JTextPane tpWorkflowPreview = new JTextPane();
+ tpWorkflowPreview.setEditable(false);
+ tpWorkflowPreview.setEditorKit(kit);
+ tpWorkflowPreview.setDocument(doc);
+ tpWorkflowPreview.addHyperlinkListener((HyperlinkListener) eventHandler);
+
+ JPanel jpFullWorkflowPreview = wrapTextPaneAndTabbedViewIntoFullPreview(tpWorkflowPreview, tpTabbedView);
+
+ // POPULATE THE GIVEN PANEL
+ panelToPopulate.setLayout(new BorderLayout());
+ panelToPopulate.add(jpFullWorkflowPreview, BorderLayout.CENTER);
+
+ // this.statusLabel.setText("Workflow information found. Last fetched: "
+ // + new Date().toString());
+
+ // this.clearButton.setEnabled(true);
+ // this.refreshButton.setEnabled(true);
+ // this.loadButton.setEnabled(true);
+ // this.importButton.setEnabled(true);
+ } catch (Exception e) {
+ logger.error("Failed to populate Workflow Preview pane", e);
+ }
+ } else {
+ // statusLabel.setText("Could not find information for workflow ID: " +
+ // currentWorkflowId);
+ // clearContentTextPane();
+ // disableButtons();
+ }
+ }
+
+ private void generateFilePreviewContent(File f, JPanel panelToPopulate, EventListener eventHandler) {
+ if (f != null) {
+ try {
+ StringBuffer content = new StringBuffer();
+ content.append("<div class='outer'>");
+ content.append("<div class='file'>");
+
+ content.append("<br>");
+
+ content.append("<p class='title'>");
+ content.append("File: <a href='preview:" + Resource.FILE + ":"
+ + f.getURI() + "'>" + f.getTitle() + "</a>");
+ content.append("</p>");
+
+ content.append("<br>");
+
+ content.append("<p class='info'>");
+ content.append("<b>Type:</b> " + f.getVisibleType() + "<br>");
+ content.append("<b>Filename:</b> " + f.getFilename() + "<br><br>");
+ content.append("<b>Uploader:</b> <a href='preview:" + Resource.USER
+ + ":" + f.getUploader().getURI() + "'>" + f.getUploader().getName()
+ + "</a><br>");
+ content.append("<b>Created at: </b> " + f.getCreatedAt() + "<br>");
+ content.append("<b>Last updated at: </b> " + f.getUpdatedAt() + "<br>");
+ content.append("<b>License: </b> <a href='"
+ + f.getLicense().getLink()
+ + "'>"
+ + f.getLicense().getText()
+ + "</a>"
+ + " <img src='"
+ + MyExperimentPerspective.getLocalResourceURL("external_link_small_icon")
+ + "' />");
+ content.append("</p>");
+
+ content.append("<br>");
+
+ if (!f.getDescription().equals("")) {
+ content.append("<p class='desc'>");
+ content.append("<br>");
+ content.append(Util.stripHTML(f.getDescription()));
+ content.append("<br>");
+ content.append("</p>");
+ } else {
+ content.append("<span class='none_text'>No description</span>");
+ }
+
+ content.append("<br>");
+ content.append("</div>");
+ content.append("</div>");
+
+ HTMLEditorKit kit = new StyledHTMLEditorKit(pluginMainComponent.getStyleSheet());
+ HTMLDocument doc = (HTMLDocument) (kit.createDefaultDocument());
+ doc.insertAfterStart(doc.getRootElements()[0].getElement(0), content.toString());
+
+ // === Now render group's items as Swing components ===
+ // TABS FOR file's tags, credits, etc
+ JScrollPane spTagsTab = createTagPreviewTab(f.getTags());
+ JScrollPane spCommentsTab = createCommentsPreviewTab(f.getComments());
+ JScrollPane spCreditsTab = createCreditsPreviewTab(f.getCredits());
+ JScrollPane spAttributionsTab = createAttributionsPreviewTab(f.getAttributions());
+
+ // ASSEMBLE tabs into tabbed view
+ JTabbedPane tpTabbedView = new JTabbedPane();
+ tpTabbedView.add("Tags (" + f.getTags().size() + ")", spTagsTab);
+ tpTabbedView.add("Comments (" + f.getComments().size() + ")", spCommentsTab);
+ tpTabbedView.add("Credits (" + f.getCredits().size() + ")", spCreditsTab);
+ tpTabbedView.add("Attributions (" + f.getAttributions().size() + ")", spAttributionsTab);
+
+ // PUT EVERYTHING TOGETHER
+ JTextPane tpFilePreview = new JTextPane();
+ tpFilePreview.setEditable(false);
+ tpFilePreview.setEditorKit(kit);
+ tpFilePreview.setDocument(doc);
+ tpFilePreview.addHyperlinkListener((HyperlinkListener) eventHandler);
+
+ JPanel jpFullFilePreview = new JPanel();
+ jpFullFilePreview.setBackground(Color.WHITE); // white background for
+ // the whole file preview
+ // panel
+ jpFullFilePreview.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ c.gridx = GridBagConstraints.REMAINDER;
+ c.gridy = 0;
+ c.weighty = 0; // will not change size when the window is resized
+ jpFullFilePreview.add(tpFilePreview, c);
+
+ c.gridx = GridBagConstraints.REMAINDER;
+ c.gridy = 1;
+ c.weighty = 1; // will grow in size when the window is resized..
+ c.fill = GridBagConstraints.VERTICAL; // ..and fill all available space
+ // vertically
+ c.insets = new Insets(20, 0, 5, 0); // a bit of margin at the top &
+ // bottom
+ jpFullFilePreview.add(tpTabbedView, c);
+
+ // POPULATE THE GIVEN PANEL
+ panelToPopulate.setLayout(new BorderLayout());
+ panelToPopulate.add(jpFullFilePreview, BorderLayout.CENTER);
+
+ // this.statusLabel.setText("File information found. Last fetched: " +
+ // new Date().toString());
+
+ // this.clearButton.setEnabled(true);
+ // this.refreshButton.setEnabled(true);
+ // this.loadButton.setEnabled(true);
+ // this.importButton.setEnabled(true);
+ } catch (Exception e) {
+ logger.error("Failed to populate File Preview pane", e);
+ }
+ } else {
+ // statusLabel.setText("Could not find information for file ID: " +
+ // currentFileId);
+ // clearContentTextPane();
+ // disableButtons();
+ }
+ }
+
+ private void generatePackPreviewContent(Pack p, JPanel panelToPopulate, EventListener eventHandler) {
+ if (p != null) {
+ try {
+ // === Render pack details in HTML format ===
+ StringBuffer content = new StringBuffer();
+ content.append("<div class='outer'>");
+ content.append("<div class='pack'>");
+
+ content.append("<br>");
+
+ content.append("<p class='title'>");
+ content.append("Pack: <a href='preview:" + Resource.PACK + ":"
+ + p.getURI() + "'>" + p.getTitle() + "</a>");
+ content.append("</p>");
+
+ content.append("<br>");
+
+ content.append("<p class='info'>");
+ content.append("<b>Creator:</b> <a href='preview:" + Resource.USER
+ + ":" + p.getCreator().getURI() + "'>" + p.getCreator().getName()
+ + "</a><br>");
+ content.append("<b>Created at: </b> " + p.getCreatedAt() + "<br>");
+ content.append("<b>Last updated at: </b> " + p.getUpdatedAt() + "<br>");
+ content.append("</p>");
+
+ content.append("<br>");
+
+ if (!p.getDescription().equals("")) {
+ content.append("<p class='desc'>");
+ content.append("<br>");
+ content.append(Util.stripHTML(p.getDescription()));
+ content.append("<br>");
+ content.append("<br>");
+ content.append("</p>");
+ } else {
+ content.append("<span class='none_text'>No description</span>");
+ }
+
+ content.append("<br>");
+ content.append("</div>");
+ content.append("</div>");
+
+ HTMLEditorKit kit = new StyledHTMLEditorKit(pluginMainComponent.getStyleSheet());
+ HTMLDocument doc = (HTMLDocument) (kit.createDefaultDocument());
+ doc.insertAfterStart(doc.getRootElements()[0].getElement(0), content.toString());
+
+ // === Now render group's items as Swing components ===
+ // TABS FOR pack items, tags, etc
+ JScrollPane spPackItemsTab = createPackItemPreviewTab(p);
+ JScrollPane spTagsTab = createTagPreviewTab(p.getTags());
+ JScrollPane spCommentsTab = createCommentsPreviewTab(p.getComments());
+
+ // ASSEMBLE tabs into tabbed view
+ JTabbedPane tpTabbedView = new JTabbedPane();
+ tpTabbedView.addTab("Pack Items (" + p.getItemCount() + ")", spPackItemsTab);
+ tpTabbedView.add("Tags (" + p.getTags().size() + ")", spTagsTab);
+ tpTabbedView.add("Comments (" + p.getComments().size() + ")", spCommentsTab);
+
+ // PUT EVERYTHING TOGETHER
+ JTextPane tpPackPreview = new JTextPane();
+ tpPackPreview.setEditable(false);
+ tpPackPreview.setEditorKit(kit);
+ tpPackPreview.setDocument(doc);
+ tpPackPreview.addHyperlinkListener((HyperlinkListener) eventHandler);
+
+ JPanel jpFullPackPreview = new JPanel();
+ jpFullPackPreview.setBackground(Color.WHITE); // white background for
+ // the whole pack preview
+ // panel
+ jpFullPackPreview.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ c.gridx = GridBagConstraints.REMAINDER;
+ c.gridy = 0;
+ c.weighty = 0; // will not change size when the window is resized
+ jpFullPackPreview.add(tpPackPreview, c);
+
+ c.gridx = GridBagConstraints.REMAINDER;
+ c.gridy = 1;
+ c.weighty = 1; // will grow in size when the window is resized..
+ c.fill = GridBagConstraints.VERTICAL; // ..and fill all available space
+ // vertically
+ c.insets = new Insets(20, 0, 5, 0); // a bit of margin at the top &
+ // bottom
+ jpFullPackPreview.add(tpTabbedView, c);
+
+ // POPULATE THE GIVEN PANEL
+ panelToPopulate.setLayout(new BorderLayout());
+ panelToPopulate.add(jpFullPackPreview, BorderLayout.CENTER);
+
+ // this.statusLabel.setText("Pack information found. Last fetched: " +
+ // new Date().toString());
+
+ // this.clearButton.setEnabled(true);
+ // this.refreshButton.setEnabled(true);
+ // this.loadButton.setEnabled(true);
+ // this.importButton.setEnabled(true);
+ } catch (Exception e) {
+ logger.error("Failed to populate Pack Preview pane", e);
+ }
+ } else {
+ // statusLabel.setText("Could not find information for pack ID: " +
+ // currentPackId);
+ // clearContentTextPane();
+ // disableButtons();
+ }
+ }
+
+ private void generateUserPreviewContent(User u, JPanel panelToPopulate, EventListener eventHandler) {
+ if (u != null) {
+ try {
+ // === Render user details in HTML format ===
+ StringBuffer content = new StringBuffer();
+ content.append("<div class='outer'>");
+ content.append("<div class='user'>");
+
+ content.append("<br>");
+
+ content.append("<p class='name'>");
+ content.append("User: <a href=preview:" + Resource.USER + ":"
+ + u.getURI() + "'>" + u.getName() + "</a>");
+ content.append("</p>");
+
+ content.append("<br>");
+
+ content.append("<p class='info'>");
+ String strLocation;
+ if (u.getCity().length() == 0 && u.getCountry().length() == 0)
+ strLocation = "<span class='none_text'>Not specified</span>";
+ else
+ strLocation = u.getCity()
+ + (u.getCity().length() == 0 || u.getCountry().length() == 0 ? "" : ", ")
+ + u.getCountry();
+ content.append("<b>Location:</b> " + strLocation + "<br>");
+ content.append("<b>Joined at: </b> " + u.getCreatedAt() + "<br>");
+ content.append("<b>Last seen at: </b> " + u.getUpdatedAt() + "<br>");
+ content.append("</p>");
+
+ content.append("<br>");
+
+ content.append("<a href='" + u.getAvatarResource() + "'>");
+ content.append("<img class='avatar' src='" + u.getAvatarResource()
+ + "'></img>");
+ content.append("</a>");
+
+ content.append("<br>");
+ content.append("<br>");
+
+ if (!u.getDescription().equals("")) {
+ // HACK: the way JAVA renders html causes styling not to be inherited;
+ // hence need to
+ // remove any nested <p> or <div> tags to get a proper layout
+ content.append("<p class='desc'>"
+ + Util.stripHTML(u.getDescription()) + "<br><br></p>");
+ } else {
+ content.append("<span class='none_text'>No description</span>");
+ }
+
+ content.append("<p class='contact_details_header'>Contact Details</p>");
+ content.append("<p class='contact_details'>");
+ content.append("<b>Email: </b>"
+ + (u.getEmail().length() == 0 ? "<span class='none_text'>Not specified</span>" : u.getEmail())
+ + "<br>");
+ content.append("<b>Website: </b>"
+ + (u.getWebsite().length() == 0 ? "<span class='none_text'>Not specified</span>" : u.getWebsite()));
+ content.append("</p>");
+
+ content.append("</div>");
+ content.append("</div>");
+
+ HTMLEditorKit kit = new StyledHTMLEditorKit(pluginMainComponent.getStyleSheet());
+ HTMLDocument doc = (HTMLDocument) (kit.createDefaultDocument());
+ doc.insertAfterStart(doc.getRootElements()[0].getElement(0), content.toString());
+
+ // === Now render user's items as Swing components ===
+ // .. WORKFLOWS ..
+ JPanel jpWorkflowsTabContent = new JPanel();
+ jpWorkflowsTabContent.setBorder(BorderFactory.createEmptyBorder(5, 10, 5, 10));
+ jpWorkflowsTabContent.setLayout(new BoxLayout(jpWorkflowsTabContent, BoxLayout.Y_AXIS));
+
+ // iterate through all workflows and add all to the panel
+ Iterator<HashMap<String, String>> iWorkflows = u.getWorkflows().iterator();
+ while (iWorkflows.hasNext()) {
+ HashMap<String, String> hmCurWF = iWorkflows.next();
+ jpWorkflowsTabContent.add(new JClickableLabel(hmCurWF.get("name"), "preview:"
+ + Resource.WORKFLOW + ":" + hmCurWF.get("uri"), pluginMainComponent.getPreviewBrowser(), this.iconWorkflow));
+ }
+
+ // .. FILES ..
+ JPanel jpFilesTabContent = new JPanel();
+ jpFilesTabContent.setBorder(BorderFactory.createEmptyBorder(5, 10, 5, 10));
+ jpFilesTabContent.setLayout(new BoxLayout(jpFilesTabContent, BoxLayout.Y_AXIS));
+
+ // iterate through all files and add all to the panel
+ Iterator<HashMap<String, String>> iFiles = u.getFiles().iterator();
+ while (iFiles.hasNext()) {
+ HashMap<String, String> hmCurFile = iFiles.next();
+ jpFilesTabContent.add(new JClickableLabel(hmCurFile.get("name"), "preview:"
+ + Resource.FILE + ":" + hmCurFile.get("uri"), pluginMainComponent.getPreviewBrowser(), this.iconFile));
+ }
+
+ // .. PACKS ..
+ JPanel jpPacksTabContent = new JPanel();
+ jpPacksTabContent.setBorder(BorderFactory.createEmptyBorder(5, 10, 5, 10));
+ jpPacksTabContent.setLayout(new BoxLayout(jpPacksTabContent, BoxLayout.Y_AXIS));
+
+ // iterate through all packs and add all to the panel
+ Iterator<HashMap<String, String>> iPacks = u.getPacks().iterator();
+ while (iPacks.hasNext()) {
+ HashMap<String, String> hmCurPack = iPacks.next();
+ jpPacksTabContent.add(new JClickableLabel(hmCurPack.get("name"), "preview:"
+ + Resource.PACK + ":" + hmCurPack.get("uri"), pluginMainComponent.getPreviewBrowser(), this.iconPack));
+ }
+
+ // .. FRIENDS ..
+ JPanel jpFriendsTabContent = new JPanel();
+ jpFriendsTabContent.setBorder(BorderFactory.createEmptyBorder(5, 10, 5, 10));
+ jpFriendsTabContent.setLayout(new BoxLayout(jpFriendsTabContent, BoxLayout.Y_AXIS));
+
+ // iterate through all friends and add all to the panel
+ Iterator<HashMap<String, String>> iFriends = u.getFriends().iterator();
+ while (iFriends.hasNext()) {
+ HashMap<String, String> hmCurFriend = iFriends.next();
+ jpFriendsTabContent.add(new JClickableLabel(hmCurFriend.get("name"), "preview:"
+ + Resource.USER + ":" + hmCurFriend.get("uri"), pluginMainComponent.getPreviewBrowser(), this.iconUser));
+ }
+
+ // .. GROUPS ..
+ JPanel jpGroupsTabContent = new JPanel();
+ jpGroupsTabContent.setBorder(BorderFactory.createEmptyBorder(5, 10, 5, 10));
+ jpGroupsTabContent.setLayout(new BoxLayout(jpGroupsTabContent, BoxLayout.Y_AXIS));
+
+ // iterate through all groups and add all to the panel
+ Iterator<HashMap<String, String>> iGroups = u.getGroups().iterator();
+ while (iGroups.hasNext()) {
+ HashMap<String, String> hmCurGroup = iGroups.next();
+ jpGroupsTabContent.add(new JClickableLabel(hmCurGroup.get("name"), "preview:"
+ + Resource.GROUP + ":" + hmCurGroup.get("uri"), pluginMainComponent.getPreviewBrowser(), this.iconGroup));
+ }
+
+ // .. WRAP EVERY TAB content into it's own scroll pane ..
+ Dimension dPreferredTabSize = new Dimension(ResourcePreviewBrowser.PREFERRED_WIDTH - 50, PREFERRED_LOWER_TABBED_PANE_HEIGHT);
+
+ JScrollPane spWorkflowsTab = new JScrollPane(jpWorkflowsTabContent);
+ spWorkflowsTab.setBorder(BorderFactory.createEmptyBorder());
+ spWorkflowsTab.setPreferredSize(dPreferredTabSize);
+ spWorkflowsTab.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+
+ JScrollPane spFilesTab = new JScrollPane(jpFilesTabContent);
+ spFilesTab.setBorder(BorderFactory.createEmptyBorder());
+ spFilesTab.setPreferredSize(dPreferredTabSize);
+ spFilesTab.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+
+ JScrollPane spPacksTab = new JScrollPane(jpPacksTabContent);
+ spPacksTab.setBorder(BorderFactory.createEmptyBorder());
+ spPacksTab.setPreferredSize(dPreferredTabSize);
+ spPacksTab.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+
+ JScrollPane spFriendsTab = new JScrollPane(jpFriendsTabContent);
+ spFriendsTab.setBorder(BorderFactory.createEmptyBorder());
+ spFriendsTab.setPreferredSize(dPreferredTabSize);
+ spFriendsTab.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+
+ JScrollPane spGroupsTab = new JScrollPane(jpGroupsTabContent);
+ spGroupsTab.setBorder(BorderFactory.createEmptyBorder());
+ spGroupsTab.setPreferredSize(dPreferredTabSize);
+ spGroupsTab.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+
+ // .. ASSEMBLE ALL TABS together
+ JTabbedPane tpTabbedItems = new JTabbedPane();
+ tpTabbedItems.addTab("Workflows (" + u.getWorkflows().size() + ")", spWorkflowsTab);
+ tpTabbedItems.addTab("Files (" + u.getFiles().size() + ")", spFilesTab);
+ tpTabbedItems.addTab("Packs (" + u.getPacks().size() + ")", spPacksTab);
+ tpTabbedItems.addTab("Friends (" + u.getFriends().size() + ")", spFriendsTab);
+ tpTabbedItems.addTab("Groups (" + u.getGroups().size() + ")", spGroupsTab);
+
+ // === PUT EVERYTHING TOGETHER ===
+ JTextPane tpUserPreview = new JTextPane();
+ tpUserPreview.setEditable(false);
+ tpUserPreview.setEditorKit(kit);
+ tpUserPreview.setDocument(doc);
+ tpUserPreview.addHyperlinkListener((HyperlinkListener) eventHandler);
+
+ JPanel jpFullUserPreview = new JPanel();
+ jpFullUserPreview.setBackground(Color.WHITE); // white background for
+ // the whole user preview
+ // panel
+ jpFullUserPreview.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ c.gridx = GridBagConstraints.REMAINDER;
+ c.gridy = 0;
+ c.weighty = 0; // will not change size when the window is resized
+ jpFullUserPreview.add(tpUserPreview, c);
+
+ c.gridx = GridBagConstraints.REMAINDER;
+ c.gridy = 1;
+ c.weighty = 1; // will grow in size when the window is resized..
+ c.fill = GridBagConstraints.VERTICAL; // ..and fill all available space
+ // vertically
+ c.insets = new Insets(20, 0, 5, 0); // a bit of margin at the top &
+ // bottom
+ jpFullUserPreview.add(tpTabbedItems, c);
+
+ // POPULATE THE GIVEN PANEL
+ panelToPopulate.setLayout(new BorderLayout());
+ panelToPopulate.add(jpFullUserPreview, BorderLayout.CENTER);
+
+ // this.statusLabel.setText("User information found. Last fetched: " +
+ // new Date().toString());
+
+ // this.clearButton.setEnabled(true);
+ // this.refreshButton.setEnabled(true);
+ // this.loadButton.setEnabled(true);
+ // this.importButton.setEnabled(true);
+ } catch (Exception e) {
+ logger.error("Failed to populate Workflow Preview pane", e);
+ }
+ } else {
+ // statusLabel.setText("Could not find information for workflow ID: " +
+ // currentWorkflowId);
+ // clearContentTextPane();
+ // disableButtons();
+ }
+ }
+
+ private void generateGroupPreviewContent(Group g, JPanel panelToPopulate, EventListener eventHandler) {
+ if (g != null) {
+ try {
+ // === Render group details in HTML format ===
+ StringBuffer content = new StringBuffer();
+ content.append("<div class='outer'>");
+ content.append("<div class='group'>");
+
+ content.append("<br>");
+
+ content.append("<p class='title'>");
+ content.append("Group: <a href='preview:" + Resource.GROUP + ":"
+ + g.getURI() + "'>" + g.getTitle() + "</a>");
+ content.append("</p>");
+
+ content.append("<br>");
+
+ content.append("<p class='info'>");
+ content.append("<b>Administrator:</b> <a href='preview:"
+ + Resource.USER + ":" + g.getAdmin().getURI() + "'>"
+ + g.getAdmin().getName() + "</a><br>");
+ content.append("<b>Created at: </b> " + g.getCreatedAt() + "<br>");
+ content.append("</p>");
+
+ content.append("<br>");
+
+ if (!g.getDescription().equals("")) {
+ content.append("<p class='desc'>");
+ content.append("<br>");
+ content.append(Util.stripHTML(g.getDescription()));
+ content.append("<br>");
+ content.append("</p>");
+ } else {
+ content.append("<span class='none_text'>No description</span>");
+ }
+
+ content.append("<br>");
+ content.append("</div>");
+ content.append("</div>");
+
+ HTMLEditorKit kit = new StyledHTMLEditorKit(pluginMainComponent.getStyleSheet());
+ HTMLDocument doc = (HTMLDocument) (kit.createDefaultDocument());
+ doc.insertAfterStart(doc.getRootElements()[0].getElement(0), content.toString());
+
+ // === Now render group's items as Swing components ===
+
+ // .. MEMBERS ..
+ JPanel jpMembersTabContent = createStandardTabContentPanel();
+
+ // iterate through all shared items and add all to the panel
+ Iterator<User> iMembers = g.getMembers().iterator();
+ while (iMembers.hasNext()) {
+ User uCurMember = iMembers.next();
+ jpMembersTabContent.add(new JClickableLabel(uCurMember.getName(), "preview:"
+ + uCurMember.getItemType() + ":" + uCurMember.getURI(), pluginMainComponent.getPreviewBrowser(), new ImageIcon(MyExperimentPerspective.getLocalIconURL(uCurMember.getItemType()))));
+ }
+
+ // wrap into a standard scroll pane
+ JScrollPane spMembersTabContent = wrapPreviewTabContentIntoScrollPane(jpMembersTabContent);
+
+ // .. SHARED ITEMS ..
+ JPanel jpSharedItemsTabContent = createStandardTabContentPanel();
+
+ // iterate through all shared items and add all to the panel
+ Iterator<Resource> iSharedItems = g.getSharedItems().iterator();
+ while (iSharedItems.hasNext()) {
+ Resource rCurItem = iSharedItems.next();
+ jpSharedItemsTabContent.add(new JClickableLabel(rCurItem.getTitle(), "preview:"
+ + rCurItem.getItemType() + ":" + rCurItem.getURI(), pluginMainComponent.getPreviewBrowser(), new ImageIcon(MyExperimentPerspective.getLocalIconURL(rCurItem.getItemType()))));
+ }
+
+ // wrap into a standard scroll pane
+ JScrollPane spSharedItemsTabContent = wrapPreviewTabContentIntoScrollPane(jpSharedItemsTabContent);
+
+ // .. TAGS, COMMENTS ..
+ JScrollPane spTagsTabContent = createTagPreviewTab(g.getTags());
+ JScrollPane spCommentsTab = createCommentsPreviewTab(g.getComments());
+
+ // ASSEMBLE tabs together
+ JTabbedPane tpTabbedItems = new JTabbedPane();
+ tpTabbedItems.addTab("Members (" + g.getMemberCount() + ")", spMembersTabContent);
+ tpTabbedItems.addTab("Shared Items (" + g.getSharedItemCount() + ")", spSharedItemsTabContent);
+ tpTabbedItems.addTab("Tags (" + g.getTags().size() + ")", spTagsTabContent);
+ tpTabbedItems.addTab("Comments (" + g.getComments().size() + ")", spCommentsTab);
+
+ // PUT EVERYTHING TOGETHER
+ JTextPane tpGroupPreview = new JTextPane();
+ tpGroupPreview.setEditable(false);
+ tpGroupPreview.setEditorKit(kit);
+ tpGroupPreview.setDocument(doc);
+ tpGroupPreview.addHyperlinkListener((HyperlinkListener) eventHandler);
+
+ JPanel jpFullGroupPreview = new JPanel();
+ jpFullGroupPreview.setBackground(Color.WHITE); // white background for
+ // the whole group
+ // preview panel
+ jpFullGroupPreview.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ c.gridx = GridBagConstraints.REMAINDER;
+ c.gridy = 0;
+ c.weighty = 0; // will not change size when the window is resized
+ jpFullGroupPreview.add(tpGroupPreview, c);
+
+ c.gridx = GridBagConstraints.REMAINDER;
+ c.gridy = 1;
+ c.weighty = 1; // will grow in size when the window is resized..
+ c.fill = GridBagConstraints.VERTICAL; // ..and fill all available space
+ // vertically
+ c.insets = new Insets(20, 0, 5, 0); // a bit of margin at the top &
+ // bottom
+ jpFullGroupPreview.add(tpTabbedItems, c);
+
+ // POPULATE THE GIVEN PANEL
+ panelToPopulate.setLayout(new BorderLayout());
+ panelToPopulate.add(jpFullGroupPreview, BorderLayout.CENTER);
+
+ // this.statusLabel.setText("Group information found. Last fetched: " +
+ // new Date().toString());
+
+ // this.clearButton.setEnabled(true);
+ // this.refreshButton.setEnabled(true);
+ // this.loadButton.setEnabled(true);
+ // this.importButton.setEnabled(true);
+ } catch (Exception e) {
+ logger.error("Failed to populate Group Preview pane", e);
+ }
+ } else {
+ // statusLabel.setText("Could not find information for group ID: " +
+ // currentGroupId);
+ // clearContentTextPane();
+ // disableButtons();
+ }
+ }
+
+ // *** Helper methods follow that generate particular reusable pieces of the
+ // previews ***
+
+ private JScrollPane createWorkflowComponentPreviewTab(Workflow w) {
+ final JPanel jpWorkflowComponentsTabContent = createStandardTabContentPanel();
+
+ if (!w.isTavernaWorkflow()) {
+ // can only display components for Taverna 1 workflows at the moment
+ JLabel lNotSupported = new JLabel("<html>This is a "
+ + w.getVisibleType()
+ + " workflow;<br>myExperiment can only display Taverna workflow components at the moment.</html>");
+ lNotSupported.setFont(lNotSupported.getFont().deriveFont(Font.ITALIC));
+ lNotSupported.setForeground(Color.GRAY);
+ jpWorkflowComponentsTabContent.add(lNotSupported);
+ } else if (!w.isDownloadAllowed()) {
+ // can display components for workflow of this type, but current user is
+ // not
+ // allowed to download this workflow - and, hence, to view its components
+ JLabel lNotAuthorized = new JLabel("You are not authorised to download this workflow, "
+ + "and hence component preview is not available.");
+ lNotAuthorized.setFont(lNotAuthorized.getFont().deriveFont(Font.ITALIC));
+ lNotAuthorized.setForeground(Color.GRAY);
+ jpWorkflowComponentsTabContent.add(lNotAuthorized);
+ } else {
+ // can display the components
+
+ // storage for table column names
+ Vector<String> vColumnNames = new Vector<String>();
+
+ // ** inputs **
+ vColumnNames.clear();
+ vColumnNames.addAll(Arrays.asList(new String[] { "Name", "Description" }));
+
+ Vector<Vector<String>> vInputsData = new Vector<Vector<String>>();
+ ArrayList<HashMap<String, String>> inputs = w.getComponents().get("inputs");
+ if (inputs != null) {
+ for (HashMap<String, String> curInput : inputs) {
+ Vector<String> vCurData = new Vector<String>();
+ vCurData.add(curInput.get("name"));
+ vCurData.add(curInput.get("description"));
+
+ vInputsData.add(vCurData);
+ }
+ }
+
+ JTable jtInputs = new JTable(vInputsData, vColumnNames);
+ jtInputs.getColumnModel().getColumn(0).setPreferredWidth(100);
+ jtInputs.getTableHeader().setFont(jtInputs.getTableHeader().getFont().deriveFont(Font.BOLD));
+ JPanel jpInputs = new JPanel();
+ jpInputs.setLayout(new BorderLayout());
+ jpInputs.add(jtInputs.getTableHeader(), BorderLayout.NORTH);
+ jpInputs.add(jtInputs, BorderLayout.CENTER);
+
+ JPanel jpInputsWithTitle = new JPanel();
+ jpInputsWithTitle.setBorder(BorderFactory.createEtchedBorder());
+ jpInputsWithTitle.setLayout(new BorderLayout());
+ jpInputsWithTitle.add(new ShadedLabel("Workflow input ports ("
+ + vInputsData.size() + ")", ShadedLabel.BLUE, true), BorderLayout.NORTH);
+ if (vInputsData.size() > 0) {
+ jpInputsWithTitle.add(jpInputs, BorderLayout.CENTER);
+ }
+
+ // ** processors **
+ vColumnNames.clear();
+ vColumnNames.addAll(Arrays.asList(new String[] { "Name", "Type", "Description" }));
+
+ Vector<Vector<String>> vProcessorsData = new Vector<Vector<String>>();
+ ArrayList<HashMap<String, String>> processors = w.getComponents().get("processors");
+ if (processors != null) {
+ for (HashMap<String, String> curProcessor : processors) {
+ Vector<String> vCurData = new Vector<String>();
+ vCurData.add(curProcessor.get("name"));
+ vCurData.add(curProcessor.get("type"));
+ vCurData.add(curProcessor.get("description"));
+
+ vProcessorsData.add(vCurData);
+ }
+ }
+
+ JTable jtProcessors = new JTable(vProcessorsData, vColumnNames);
+ jtProcessors.getTableHeader().setFont(jtProcessors.getTableHeader().getFont().deriveFont(Font.BOLD));
+ JPanel jpProcessors = new JPanel();
+ jpProcessors.setLayout(new BorderLayout());
+ jpProcessors.add(jtProcessors.getTableHeader(), BorderLayout.NORTH);
+ jpProcessors.add(jtProcessors, BorderLayout.CENTER);
+
+ JPanel jpProcessorsWithTitle = new JPanel();
+ jpProcessorsWithTitle.setBorder(BorderFactory.createEtchedBorder());
+ jpProcessorsWithTitle.setLayout(new BorderLayout());
+ jpProcessorsWithTitle.add(new ShadedLabel("Services ("
+ + vProcessorsData.size() + ")", ShadedLabel.BLUE, true), BorderLayout.NORTH);
+ if (vProcessorsData.size() > 0) {
+ jpProcessorsWithTitle.add(jpProcessors, BorderLayout.CENTER);
+ }
+
+ // ** links **
+ vColumnNames.clear();
+ vColumnNames.addAll(Arrays.asList(new String[] { "Source", "Sink" }));
+
+ Vector<Vector<String>> vLinksData = new Vector<Vector<String>>();
+ ArrayList<HashMap<String, String>> links = w.getComponents().get("links");
+ if (links != null) {
+ for (HashMap<String, String> curLink : links) {
+ Vector<String> vCurData = new Vector<String>();
+ vCurData.add(curLink.get("source"));
+ vCurData.add(curLink.get("sink"));
+
+ vLinksData.add(vCurData);
+ }
+ }
+
+ JTable jtLinks = new JTable(vLinksData, vColumnNames);
+ jtLinks.getColumnModel().getColumn(0).setPreferredWidth(100);
+ jtLinks.getTableHeader().setFont(jtLinks.getTableHeader().getFont().deriveFont(Font.BOLD));
+ JPanel jpLinks = new JPanel();
+ jpLinks.setLayout(new BorderLayout());
+ jpLinks.add(jtLinks.getTableHeader(), BorderLayout.NORTH);
+ jpLinks.add(jtLinks, BorderLayout.CENTER);
+
+ JPanel jpLinksWithTitle = new JPanel();
+ jpLinksWithTitle.setBorder(BorderFactory.createEtchedBorder());
+ jpLinksWithTitle.setLayout(new BorderLayout());
+ jpLinksWithTitle.add(new ShadedLabel("Links (" + vLinksData.size() + ")", ShadedLabel.BLUE, true), BorderLayout.NORTH);
+ if (vLinksData.size() > 0) {
+ jpLinksWithTitle.add(jpLinks, BorderLayout.CENTER);
+ }
+
+ // ** outputs **
+ vColumnNames.clear();
+ vColumnNames.addAll(Arrays.asList(new String[] { "Name", "Description" }));
+
+ Vector<Vector<String>> vOutputsData = new Vector<Vector<String>>();
+ ArrayList<HashMap<String, String>> outputs = w.getComponents().get("outputs");
+ if (outputs != null) {
+ for (HashMap<String, String> curOutput : outputs) {
+ Vector<String> vCurData = new Vector<String>();
+ vCurData.add(curOutput.get("name"));
+ vCurData.add(curOutput.get("description"));
+
+ vOutputsData.add(vCurData);
+ }
+ }
+
+ JTable jtOutputs = new JTable(vOutputsData, vColumnNames);
+ jtOutputs.getColumnModel().getColumn(0).setPreferredWidth(100);
+ jtOutputs.getTableHeader().setFont(jtOutputs.getTableHeader().getFont().deriveFont(Font.BOLD));
+ JPanel jpOutputs = new JPanel();
+ jpOutputs.setLayout(new BorderLayout());
+ jpOutputs.add(jtOutputs.getTableHeader(), BorderLayout.NORTH);
+ jpOutputs.add(jtOutputs, BorderLayout.CENTER);
+
+ JPanel jpOutputsWithTitle = new JPanel();
+ jpOutputsWithTitle.setBorder(BorderFactory.createEtchedBorder());
+ jpOutputsWithTitle.setLayout(new BorderLayout());
+ jpOutputsWithTitle.add(new ShadedLabel("Workflow output ports ("
+ + vOutputsData.size() + ")", ShadedLabel.BLUE, true), BorderLayout.NORTH);
+ if (vOutputsData.size() > 0) {
+ jpOutputsWithTitle.add(jpOutputs, BorderLayout.CENTER);
+ }
+
+ // PUT EVERYTHING TOGETHER
+ jpWorkflowComponentsTabContent.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ c.gridx = 0;
+ c.gridy = GridBagConstraints.RELATIVE;
+ c.weightx = 1.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.anchor = GridBagConstraints.NORTH;
+ jpWorkflowComponentsTabContent.add(jpInputsWithTitle, c);
+
+ c.insets = new Insets(10, 0, 0, 0);
+ jpWorkflowComponentsTabContent.add(jpProcessorsWithTitle, c);
+
+ jpWorkflowComponentsTabContent.add(jpLinksWithTitle, c);
+
+ c.weighty = 1.0; // ONLY FOR THE LAST ELEMENT
+ jpWorkflowComponentsTabContent.add(jpOutputsWithTitle, c);
+ }
+
+ return (wrapPreviewTabContentIntoScrollPane(jpWorkflowComponentsTabContent));
+ }
+
+ private JScrollPane createPackItemPreviewTab(Pack p) {
+ JPanel jpPackItemsTabContent = createStandardTabContentPanel();
+ GridBagConstraints c = new GridBagConstraints();
+ jpPackItemsTabContent.setLayout(new GridBagLayout());
+ c.anchor = GridBagConstraints.NORTHWEST;
+
+ // iterate through all internal and external items and add all to the panel
+ if (p.getItems().size() > 0) {
+ int iCnt = 0;
+ boolean bNoCommentForPrevItem = false;
+
+ for (PackItem piCurItem : p.getItems()) {
+ c.gridx = 0;
+ c.gridy = 3 * iCnt;
+ c.weightx = 1.0;
+ c.insets = (bNoCommentForPrevItem ? new Insets(7, 0, 0, 0) : new Insets(0, 0, 0, 0));
+ c.fill = GridBagConstraints.NONE;
+ // item data is stored differently whether the item is internal or
+ // external
+ if (piCurItem.isInternalItem()) {
+ jpPackItemsTabContent.add(new JClickableLabel(piCurItem.getItem().getTitle(), "preview:"
+ + piCurItem.getItem().getItemType()
+ + ":"
+ + piCurItem.getItem().getURI(), pluginMainComponent.getPreviewBrowser(), new ImageIcon(MyExperimentPerspective.getLocalIconURL(piCurItem.getItem().getItemType()))), c);
+ } else {
+ jpPackItemsTabContent.add(new JClickableLabel(piCurItem.getTitle(), piCurItem.getLink(), // link should open up directly in the web
+ // browser
+ pluginMainComponent.getPreviewBrowser(), new ImageIcon(MyExperimentPerspective.getLocalIconURL(piCurItem.getItemType())), SwingConstants.LEFT, piCurItem.getTitle()
+ + " (link: " + piCurItem.getLink() + ")"), c);
+ }
+
+ // prepare comment before populating the metadata
+ String strComment = Util.stripAllHTML(piCurItem.getComment());
+ bNoCommentForPrevItem = (strComment == null || strComment.length() == 0);
+
+ // add metadata to the item ..
+ // .. who and when added the item ..
+ JPanel jpWhoAddedTheItem = new JPanel();
+ jpWhoAddedTheItem.setLayout(new GridBagLayout());
+ GridBagConstraints c1 = new GridBagConstraints();
+ c1.anchor = GridBagConstraints.NORTHWEST;
+ jpWhoAddedTheItem.setBorder(BorderFactory.createEmptyBorder());
+ jpWhoAddedTheItem.add(new JLabel("Added by "), c1);
+ jpWhoAddedTheItem.add(new JClickableLabel(piCurItem.getUserWhoAddedTheItem().getName(), "preview:"
+ + Resource.USER + ":" + piCurItem.getUserWhoAddedTheItem().getURI(), pluginMainComponent.getPreviewBrowser()), c1);
+
+ String strAddedOnDate = MyExperimentClient.formatDate(piCurItem.getCreatedAt());
+ c1.weightx = 1.0;
+ jpWhoAddedTheItem.add(new JLabel(" [" + strAddedOnDate + "]"), c1);
+
+ c.gridx = 0;
+ c.gridy = 3 * iCnt + 1;
+ c.insets = new Insets(0, 25, 0, 0);
+ c.weightx = 1.0;
+ if (bNoCommentForPrevItem && (iCnt + 1 == p.getItems().size()))
+ c.weighty = 1.0;
+ jpPackItemsTabContent.add(jpWhoAddedTheItem, c);
+
+ // .. and the comment
+ if (!bNoCommentForPrevItem) {
+ c.gridx = 0;
+ c.gridy = 3 * iCnt + 2;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.insets = new Insets(0, 25, 7, 25);
+ c.weightx = 1.0;
+ if (iCnt + 1 == p.getItems().size())
+ c.weighty = 1.0; // only if this is the comment for the last item,
+ // shift all items to the top of the panel
+
+ DialogTextArea taCommentText = new DialogTextArea("Comment: "
+ + strComment);
+ taCommentText.setOpaque(false);
+ taCommentText.setEditable(false);
+ taCommentText.setLineWrap(true);
+ taCommentText.setWrapStyleWord(true);
+ jpPackItemsTabContent.add(taCommentText, c);
+ }
+
+ // update the item counter
+ iCnt++;
+ }
+ } else {
+ c.weighty = 1.0;
+ c.weightx = 1.0;
+ jpPackItemsTabContent.add(Util.generateNoneTextLabel("None"), c);
+ }
+
+ return (wrapPreviewTabContentIntoScrollPane(jpPackItemsTabContent));
+ }
+
+ private JScrollPane createTagPreviewTab(List<Tag> lTags) {
+ TagCloudPanel jpTagTabContent = new TagCloudPanel("Resource tag cloud", TagCloudPanel.TAGCLOUD_TYPE_RESOURCE_PREVIEW, pluginMainComponent.getPreviewBrowser(), pluginMainComponent, myExperimentClient, logger);
+ jpTagTabContent.getTagCloudData().clear();
+ jpTagTabContent.getTagCloudData().addAll(lTags);
+ jpTagTabContent.refresh();
+
+ // tag cloud panel itself already has a scroll pane in it; hence the outer
+ // scroll pane
+ // is only used for consistency across the user interface (contents of all
+ // tabs in the
+ // preview window are scroll panes); the preferred size of the tag cloud
+ // panel should
+ // still be adjusted accordingly to the preferred size of the outer scroll
+ // pane
+ JScrollPane spTagTabContent = wrapPreviewTabContentIntoScrollPane(jpTagTabContent);
+ spTagTabContent.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ spTagTabContent.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
+
+ jpTagTabContent.setPreferredSize(spTagTabContent.getPreferredSize());
+
+ return (spTagTabContent);
+ }
+
+ private JScrollPane createCommentsPreviewTab(List<Comment> comments) {
+ final List<Comment> lComments = comments;
+ final JPanel jpCommentsTabContent = createStandardTabContentPanel();
+
+ if (lComments.size() > 0) {
+ final GridBagConstraints c = new GridBagConstraints();
+ jpCommentsTabContent.setLayout(new GridBagLayout());
+ c.anchor = GridBagConstraints.NORTHWEST;
+
+ // a placeholder for comments while they are loading
+ JLabel lLoading = new JLabel("Loading comments...", new ImageIcon(MyExperimentPerspective.getLocalResourceURL("spinner")), SwingConstants.LEFT);
+ lLoading.setBorder(BorderFactory.createEmptyBorder(10, 5, 10, 10));
+ c.weightx = 1.0;
+ c.weighty = 1.0;
+ jpCommentsTabContent.add(lLoading, c);
+
+ new Thread("Load comments for preview") {
+ @Override
+ public void run() {
+ myExperimentClient.updateCommentListWithExtraData(lComments);
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // remove 'loading...' placeholder
+ jpCommentsTabContent.removeAll();
+
+ int iCnt = 0;
+ for (Comment comment : lComments) {
+ c.gridx = 0;
+ c.gridy = 2 * iCnt;
+ c.weightx = 0;
+ c.weighty = 0;
+ c.gridwidth = 1;
+ JClickableLabel lCommentAuthor = new JClickableLabel(comment.getUser().getName(), "preview:"
+ + comment.getUser().getItemType()
+ + ":"
+ + comment.getUser().getURI(), pluginMainComponent.getPreviewBrowser(), iconUser);
+ jpCommentsTabContent.add(lCommentAuthor, c);
+
+ c.gridx = 1;
+ c.gridy = 2 * iCnt;
+ c.weightx = 1.0;
+ String strCommentDate = MyExperimentClient.formatDate(comment.getCreatedAt());
+ JLabel lCommentDate = new JLabel(" - [" + strCommentDate + "]");
+ lCommentDate.setBorder(lCommentAuthor.getBorder());
+ jpCommentsTabContent.add(lCommentDate, c);
+
+ c.gridx = 0;
+ c.gridy = 2 * iCnt + 1;
+ c.weightx = 1.0;
+ c.gridwidth = 2;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ if (iCnt + 1 == lComments.size())
+ c.weighty = 1.0;
+
+ DialogTextArea taCommentText = new DialogTextArea(Util.stripAllHTML(comment.getComment()));
+ taCommentText.setBorder(BorderFactory.createEmptyBorder(0, 25, 10, 25));
+ taCommentText.setOpaque(false);
+ taCommentText.setEditable(false);
+ taCommentText.setLineWrap(true);
+ taCommentText.setWrapStyleWord(true);
+ jpCommentsTabContent.add(taCommentText, c);
+
+ iCnt++;
+ }
+
+ jpCommentsTabContent.validate();
+ jpCommentsTabContent.repaint();
+
+ // this will ensure that even if there are many comments,
+ // the comment panel is still shown starting at the top comment
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ jpCommentsTabContent.scrollRectToVisible(new Rectangle());
+ }
+ });
+ }
+ });
+ }
+ }.start();
+ } else {
+ jpCommentsTabContent.add(Util.generateNoneTextLabel("None"));
+ }
+
+ JScrollPane spCommentsTabContent = wrapPreviewTabContentIntoScrollPane(jpCommentsTabContent);
+ spCommentsTabContent.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
+ return (spCommentsTabContent);
+ }
+
+ private JScrollPane createCreditsPreviewTab(List<Resource> lCreditedUsersOrGroups) {
+ JPanel jpCreditsTabContent = createStandardTabContentPanel();
+
+ if (lCreditedUsersOrGroups.size() > 0) {
+ for (Resource r : lCreditedUsersOrGroups) {
+ jpCreditsTabContent.add(new JClickableLabel(r.getTitle(), "preview:"
+ + r.getItemType() + ":" + r.getURI(), pluginMainComponent.getPreviewBrowser(), new ImageIcon(MyExperimentPerspective.getLocalIconURL(r.getItemType()))));
+ }
+ } else {
+ jpCreditsTabContent.add(Util.generateNoneTextLabel("None"));
+ }
+
+ return (wrapPreviewTabContentIntoScrollPane(jpCreditsTabContent));
+ }
+
+ private JScrollPane createAttributionsPreviewTab(List<Resource> lAttributions) {
+ JPanel jpAttributionsTabContent = createStandardTabContentPanel();
+
+ if (lAttributions.size() > 0) {
+ for (Resource r : lAttributions) {
+ jpAttributionsTabContent.add(new JClickableLabel(r.getTitle(), "preview:"
+ + r.getItemType() + ":" + r.getURI(), pluginMainComponent.getPreviewBrowser(), new ImageIcon(MyExperimentPerspective.getLocalIconURL(r.getItemType()))));
+ }
+ } else {
+ jpAttributionsTabContent.add(Util.generateNoneTextLabel("None"));
+ }
+
+ return (wrapPreviewTabContentIntoScrollPane(jpAttributionsTabContent));
+ }
+
+ /**
+ * A standard starting point for all preview window tabs.
+ */
+ private JPanel createStandardTabContentPanel() {
+ JPanel jpTabContentPanel = new JPanel();
+ jpTabContentPanel.setBorder(BorderFactory.createEmptyBorder(5, 10, 5, 10));
+ jpTabContentPanel.setLayout(new BoxLayout(jpTabContentPanel, BoxLayout.Y_AXIS));
+
+ return (jpTabContentPanel);
+ }
+
+ private JScrollPane wrapPreviewTabContentIntoScrollPane(JPanel jpTabContentPanel) {
+ // WRAPS TAB CONTENT into it's own SCROLL PANE ..
+ Dimension dPreferredTabSize = new Dimension(ResourcePreviewBrowser.PREFERRED_WIDTH - 50, PREFERRED_LOWER_TABBED_PANE_HEIGHT);
+
+ JScrollPane spTabContent = new JScrollPane(jpTabContentPanel);
+ spTabContent.setBorder(BorderFactory.createEmptyBorder());
+ spTabContent.setPreferredSize(dPreferredTabSize);
+ spTabContent.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+
+ return (spTabContent);
+ }
+
+ private JPanel wrapTextPaneAndTabbedViewIntoFullPreview(JTextPane tpHTMLPreview, JTabbedPane tpTabbedView) {
+ // WRAPS HTML JTextPane PREVIEW AND A JTabbedPane WITH DETAILS INTO A SINGLE
+ // PREVIEW PANEL
+ JPanel jpFullPreview = new JPanel();
+ jpFullPreview.setBackground(Color.WHITE); // white background for the whole
+ // preview panel
+ jpFullPreview.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ c.gridx = GridBagConstraints.REMAINDER;
+ c.gridy = 0;
+ c.weighty = 0; // will not change size when the window is resized
+ jpFullPreview.add(tpHTMLPreview, c);
+
+ c.gridx = GridBagConstraints.REMAINDER;
+ c.gridy = 1;
+ c.weighty = 1; // will grow in size when the window is resized..
+ c.fill = GridBagConstraints.VERTICAL; // ..and fill all available space
+ // vertically
+ c.insets = new Insets(20, 0, 5, 0); // a bit of margin at the top & bottom
+ jpFullPreview.add(tpTabbedView, c);
+
+ return (jpFullPreview);
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/SearchOptionsPanel.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/SearchOptionsPanel.java
new file mode 100644
index 0000000..b2fd9f5
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/SearchOptionsPanel.java
@@ -0,0 +1,317 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JSpinner;
+import javax.swing.JTextField;
+import javax.swing.SpinnerNumberModel;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author Sergejs Aleksejevs, Emmanuel Tagarira
+ */
+public class SearchOptionsPanel extends JPanel implements ItemListener, KeyListener {
+ // CONSTANTS
+ protected static final int SEARCH_RESULT_LIMIT_MIN = 1;
+ protected static final int SEARCH_RESULT_LIMIT_INIT = 20;
+ protected static final int SEARCH_RESULT_LIMIT_MAX = 100;
+
+ private final MainComponent pluginMainComponent;
+ private final MyExperimentClient myExperimentClient;
+ private final Logger logger;
+ private final ActionListener clickHandler;
+
+ // COMPONENTS
+ protected JButton bSearch;
+ private JTextField tfSearchQuery;
+ private JCheckBox cbSearchAllTypes;
+ private JCheckBox cbWorkflows;
+ private JCheckBox cbFiles;
+ private JCheckBox cbPacks;
+ private JCheckBox cbUsers;
+ private JCheckBox cbGroups;
+ protected JSpinner jsResultLimit;
+ protected JTextField tfResultLimitTextField;
+
+ // Data
+ ArrayList<JCheckBox> alDataTypeCheckboxes;
+
+ public SearchOptionsPanel(ActionListener actionListener, MainComponent component, MyExperimentClient client, Logger logger) {
+ super();
+
+ // set main variables to ensure access to myExperiment, logger and the parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+ this.clickHandler = actionListener;
+
+ this.initialiseUI();
+
+ // this will hold the collection of all checkboxes that correspond to data types (will be used in item event handling)
+ alDataTypeCheckboxes = new ArrayList<JCheckBox>(Arrays.asList(new JCheckBox[] { cbWorkflows, cbFiles, cbPacks, cbUsers, cbGroups }));
+ }
+
+ private void initialiseUI() {
+ this.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), " Search Settings "), BorderFactory.createEmptyBorder(5, 5, 5, 5)));
+
+ this.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.anchor = GridBagConstraints.WEST;
+ this.add(new JLabel("Query"), c);
+
+ c.gridx = 0;
+ c.gridy = 1;
+ c.gridwidth = 4;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+ tfSearchQuery = new JTextField();
+ tfSearchQuery.setToolTipText("<html>Tips for creating search queries:<br>1) Use wildcards to make more "
+ + "flexible queries. Asterisk (<b>*</b>) matches any zero or more<br> characters (e.g. "
+ + "<b><i>Seq*</i></b> would match <b><i>Sequence</i></b>), question mark (<b>?</b>) matches any single<br>"
+ + " character (e.g. <b><i>Tave?na</i></b> would match <b><i>Taverna</i></b>).<br>"
+ + "2) Enclose the <b><i>\"search query\"</i></b> in double quotes to make exact phrase matching, otherwise<br>"
+ + " items that contain any (or all) words in the <b><i>search query</i></b> will be found.</html>");
+ tfSearchQuery.addKeyListener(this);
+ this.add(tfSearchQuery, c);
+
+ c.gridx = 4;
+ c.gridy = 1;
+ c.gridwidth = 1;
+ c.fill = GridBagConstraints.NONE;
+ c.weightx = 0;
+ c.insets = new Insets(0, 5, 0, 0);
+ bSearch = new JButton("Search", WorkbenchIcons.searchIcon);
+ bSearch.addActionListener(this.clickHandler);
+ bSearch.addKeyListener(this);
+ this.add(bSearch, c);
+
+ c.gridx = 0;
+ c.gridy = 2;
+ c.insets = new Insets(10, 0, 3, 0);
+ this.add(new JLabel("Search for..."), c);
+
+ c.gridx = 0;
+ c.gridy = 3;
+ c.gridwidth = 2;
+ c.insets = new Insets(0, 0, 0, 0);
+ cbSearchAllTypes = new JCheckBox("all resource types", true);
+ cbSearchAllTypes.addItemListener(this);
+ cbSearchAllTypes.addKeyListener(this);
+ this.add(cbSearchAllTypes, c);
+
+ c.gridx = 0;
+ c.gridy = 4;
+ c.gridwidth = 1;
+ c.ipady = 0;
+ cbWorkflows = new JCheckBox("workflows", true);
+ cbWorkflows.addItemListener(this);
+ cbWorkflows.addKeyListener(this);
+ this.add(cbWorkflows, c);
+
+ c.gridx = 0;
+ c.gridy = 5;
+ cbFiles = new JCheckBox("files", true);
+ cbFiles.addItemListener(this);
+ cbFiles.addKeyListener(this);
+ this.add(cbFiles, c);
+
+ c.gridx = 0;
+ c.gridy = 6;
+ cbPacks = new JCheckBox("packs", true);
+ cbPacks.addItemListener(this);
+ cbPacks.addKeyListener(this);
+ this.add(cbPacks, c);
+
+ c.gridx = 1;
+ c.gridy = 4;
+ cbUsers = new JCheckBox("users", true);
+ cbUsers.addItemListener(this);
+ cbUsers.addKeyListener(this);
+ this.add(cbUsers, c);
+
+ c.gridx = 1;
+ c.gridy = 5;
+ cbGroups = new JCheckBox("groups", true);
+ cbGroups.addItemListener(this);
+ cbGroups.addKeyListener(this);
+ this.add(cbGroups, c);
+
+ c.gridx = 3;
+ c.gridy = 2;
+ c.insets = new Insets(10, 25, 3, 0);
+ JLabel jlResultLimit = new JLabel("Result limit");
+ this.add(jlResultLimit, c);
+
+ c.gridx = 3;
+ c.gridy = 3;
+ c.insets = new Insets(0, 25, 0, 0);
+ jsResultLimit = new JSpinner(new SpinnerNumberModel(SEARCH_RESULT_LIMIT_INIT, SEARCH_RESULT_LIMIT_MIN, SEARCH_RESULT_LIMIT_MAX, 1));
+ jsResultLimit.setPreferredSize(new Dimension(jlResultLimit.getPreferredSize().width, jsResultLimit.getPreferredSize().height));
+ this.add(jsResultLimit, c);
+
+ // adding KeyListener to JSpinner directly doesn't make sense; need to attach KeyListener to the text field that is associated with spinner
+ tfResultLimitTextField = ((JSpinner.DefaultEditor) this.jsResultLimit.getEditor()).getTextField();
+ tfResultLimitTextField.addKeyListener(this);
+ }
+
+ public String getSearchQuery() {
+ return (this.tfSearchQuery.getText());
+ }
+
+ public void setSearchQuery(String strSearchQuery) {
+ this.tfSearchQuery.setText(strSearchQuery);
+ }
+
+ public void focusSearchQueryField() {
+ this.tfSearchQuery.selectAll();
+ this.tfSearchQuery.requestFocusInWindow();
+ }
+
+ public void setSearchAllResourceTypes(boolean bSearchAllTypes) {
+ this.cbSearchAllTypes.setSelected(bSearchAllTypes);
+ }
+
+ public boolean getSearchWorkflows() {
+ return (this.cbWorkflows.isSelected());
+ }
+
+ public void setSearchWorkflows(boolean bSearchWorkflows) {
+ this.cbWorkflows.setSelected(bSearchWorkflows);
+ }
+
+ public boolean getSearchFiles() {
+ return (this.cbFiles.isSelected());
+ }
+
+ public void setSearchFiles(boolean bSearchFiles) {
+ this.cbFiles.setSelected(bSearchFiles);
+ }
+
+ public boolean getSearchPacks() {
+ return (this.cbPacks.isSelected());
+ }
+
+ public void setSearchPacks(boolean bSearchPacks) {
+ this.cbPacks.setSelected(bSearchPacks);
+ }
+
+ public boolean getSearchUsers() {
+ return (this.cbUsers.isSelected());
+ }
+
+ public void setSearchUsers(boolean bSearchUsers) {
+ this.cbUsers.setSelected(bSearchUsers);
+ }
+
+ public boolean getSearchGroups() {
+ return (this.cbGroups.isSelected());
+ }
+
+ public void setSearchGroups(boolean bSearchGroups) {
+ this.cbGroups.setSelected(bSearchGroups);
+ }
+
+ public int getResultCountLimit() {
+ // JSpinner handles value validation itself, so there is no need to
+ // make our own validation too
+ return (Integer.parseInt(this.jsResultLimit.getValue().toString()));
+ }
+
+ public void setResultCountLimit(int iLimit) {
+ this.jsResultLimit.setValue(iLimit);
+ }
+
+ // this monitors all checkbox clicks and selects / deselects other checkboxes which are relevant
+ public void itemStateChanged(ItemEvent e) {
+ if (e.getItemSelectable().equals(this.cbSearchAllTypes)) {
+ // "all resource types" clicked - need to select / deselect all data type checkboxes accordingly
+ for (JCheckBox cb : this.alDataTypeCheckboxes) {
+ cb.removeItemListener(this);
+ cb.setSelected(this.cbSearchAllTypes.isSelected());
+ cb.addItemListener(this);
+ }
+
+ // also, enable / disable the search button
+ this.bSearch.setEnabled(this.cbSearchAllTypes.isSelected());
+ } else if (this.alDataTypeCheckboxes.contains(e.getItemSelectable())) {
+ // one of the checkboxes for data types was clicked (e.g. workflows, files, etc);
+ // need to calculate how many of those are currently selected
+ int iSelectedCnt = 0;
+ for (JCheckBox cb : this.alDataTypeCheckboxes) {
+ if (cb.isSelected())
+ iSelectedCnt++;
+ }
+
+ // if all are selected, tick "search all types" checkbox; uncheck otherwise
+ this.cbSearchAllTypes.removeItemListener(this);
+ this.cbSearchAllTypes.setSelected(iSelectedCnt == this.alDataTypeCheckboxes.size());
+ this.cbSearchAllTypes.addItemListener(this);
+
+ // enable search button if at least one data type is selected; disable otherwise
+ this.bSearch.setEnabled(iSelectedCnt > 0);
+ }
+ }
+
+ public void keyPressed(KeyEvent e) {
+ // ENTER pressed - start search by simulating "search" button click
+ // (only do this if the "search" button was active at that moment)
+ if (e.getKeyCode() == KeyEvent.VK_ENTER
+ && this.bSearch.isEnabled()
+ && (Arrays.asList(new JComponent[] { this.tfSearchQuery, this.bSearch, this.cbSearchAllTypes, this.tfResultLimitTextField }).contains(e.getSource()) || this.alDataTypeCheckboxes.contains(e.getSource()))) {
+ this.clickHandler.actionPerformed(new ActionEvent(this.bSearch, 0, ""));
+ }
+ }
+
+ public void keyReleased(KeyEvent e) {
+ // do nothing
+ }
+
+ public void keyTyped(KeyEvent e) {
+ // do nothing
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/SearchResultsPanel.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/SearchResultsPanel.java
new file mode 100644
index 0000000..dbc3b36
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/SearchResultsPanel.java
@@ -0,0 +1,201 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.BorderLayout;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class SearchResultsPanel extends JPanel
+{
+ // CONSTANTS
+ public static final String NO_SEARCHES_STATUS = "No searches have been done so far";
+
+
+ private MainComponent pluginMainComponent;
+ private MyExperimentClient myExperimentClient;
+ private Logger logger;
+
+ // COMPONENTS
+ private JLabel lStatusLabel;
+ public JButton bRefresh;
+ public JButton bClear;
+ private JPanel jpResultsBody;
+ private ActionListener alClickHandler;
+
+ // result data store
+ boolean bNoSearchesMadeYet;
+ String strCurrentSearchTerm;
+ HashMap<Integer, ArrayList<Resource>> hmSearchResults;
+
+
+ public SearchResultsPanel(ActionListener buttonClickHandler, MainComponent component, MyExperimentClient client, Logger logger)
+ {
+ super();
+
+ // set main variables to ensure access to myExperiment, logger and the parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+ this.alClickHandler = buttonClickHandler;
+
+ // initialise the result data collection to an empty one, just in case
+ // someone calls refresh() before setting the real result data
+ bNoSearchesMadeYet = true;
+ hmSearchResults = new HashMap<Integer, ArrayList<Resource>>();
+
+ this.initialiseUI();
+ }
+
+
+
+ private void initialiseUI()
+ {
+ // label to hold the status of search (e.g. result query + count, etc)
+ this.lStatusLabel = new JLabel(NO_SEARCHES_STATUS);
+ this.lStatusLabel.setBorder(BorderFactory.createEmptyBorder(0, 5, 0, 0)); // a bit of padding on the left
+
+ // control buttons for the search results panel
+ JPanel jpButtonsPanel = new JPanel();
+ jpButtonsPanel.setLayout(new BoxLayout(jpButtonsPanel, BoxLayout.LINE_AXIS));
+ this.bClear = new JButton("Clear", WorkbenchIcons.deleteIcon);
+ this.bClear.addActionListener(this.alClickHandler);
+ this.bClear.setToolTipText("Click this button to clear the search results");
+ this.bClear.setEnabled(false);
+ jpButtonsPanel.add(this.bClear);
+ this.bRefresh = new JButton("Refresh", WorkbenchIcons.refreshIcon);
+ this.bRefresh.addActionListener(this.alClickHandler);
+ this.bRefresh.setToolTipText("Click this button to refresh the search results");
+ this.bRefresh.setEnabled(false);
+ jpButtonsPanel.add(this.bRefresh);
+
+ // status panel containing the status label and control buttons
+ JPanel jpStatusPanel = new JPanel(new BorderLayout());
+ jpStatusPanel.setBorder(BorderFactory.createEtchedBorder());
+ jpStatusPanel.add(this.lStatusLabel, BorderLayout.CENTER);
+ jpStatusPanel.add(jpButtonsPanel, BorderLayout.EAST);
+
+ // create empty panel for the main search result content
+ this.jpResultsBody = new JPanel();
+ jpResultsBody.setLayout(new BorderLayout());
+
+ // PUT EVERYTHING TOGETHER
+ this.setLayout(new BorderLayout());
+ this.add(jpStatusPanel, BorderLayout.NORTH);
+ this.add(this.jpResultsBody, BorderLayout.CENTER);
+
+ // tabbed results view is missing from this method - this is
+ // because if no results will be found in a particular category,
+ // that tab will not be displayed (hence the results view will
+ // need to be generated every time dynamically)
+ }
+
+
+ public void setCurrentSearchTerm(String strSearchTerm)
+ {
+ this.strCurrentSearchTerm = strSearchTerm;
+ }
+
+ public String getCurrentSearchTerm()
+ {
+ return (this.strCurrentSearchTerm);
+ }
+
+
+ public void setSearchResultsData(HashMap<Integer, ArrayList<Resource>> hmResults)
+ {
+ this.bNoSearchesMadeYet = false;
+ this.hmSearchResults = hmResults;
+ }
+
+
+ public void setStatus(String status)
+ {
+ this.lStatusLabel.setText(status);
+ }
+
+ public void refresh()
+ {
+ // remove all items from the main results content panel
+ this.jpResultsBody.removeAll();
+
+ if (!this.bNoSearchesMadeYet) // this will be true if the result collection was never assigned to this result panel
+ {
+ ArrayList<Integer> alResourceTypes = new ArrayList<Integer>(this.hmSearchResults.keySet());
+ Collections.sort(alResourceTypes); // this will ensure that the tabs are always in the correct order
+ if(alResourceTypes.isEmpty()) {
+ this.jpResultsBody.add(new JLabel("No items to display"), BorderLayout.NORTH);
+ this.repaint();
+ }
+ else {
+ JTabbedPane tpResults = new JTabbedPane();
+
+ for(int iType : alResourceTypes)
+ {
+ // HACK: for now all item types are suitably turned into plural by simply appending "s"
+ String strTabLabel = Resource.getResourceTypeName(iType) + "s (" + this.hmSearchResults.get(iType).size() + ")";
+
+ ResourceListPanel jpTabContents = new ResourceListPanel(pluginMainComponent, myExperimentClient, logger);
+ jpTabContents.setListItems(this.hmSearchResults.get(iType));
+
+ JScrollPane spTabContents = new JScrollPane(jpTabContents);
+ spTabContents.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+
+ tpResults.add(strTabLabel, spTabContents);
+ }
+
+ this.jpResultsBody.add(tpResults, BorderLayout.CENTER);
+ this.bClear.setEnabled(true);
+ this.bRefresh.setEnabled(true);
+ }
+ }
+
+ this.revalidate();
+ }
+
+
+ public void clear()
+ {
+ // remove all items from the main results content panel
+ this.jpResultsBody.removeAll();
+ this.repaint();
+ this.revalidate();
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/SearchTabContentPanel.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/SearchTabContentPanel.java
new file mode 100644
index 0000000..b583491
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/SearchTabContentPanel.java
@@ -0,0 +1,450 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.text.ParseException;
+import java.util.Collections;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.BorderFactory;
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.SwingUtilities;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Base64;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.SearchEngine;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Util;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.SearchEngine.QuerySearchInstance;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class SearchTabContentPanel extends JPanel implements ActionListener {
+ // CONSTANTS
+ private final static int SEARCH_HISTORY_LENGTH = 50;
+ private final static int SEARCH_FAVOURITES_LENGTH = 30;
+ protected final static String SEARCH_FROM_FAVOURITES = "searchFromFavourites";
+ protected final static String SEARCH_FROM_HISTORY = "searchFromHistory";
+ protected final static String ADD_FAVOURITE_SEARCH_INSTANCE = "addFavouriteSearchInstance";
+ protected final static String REMOVE_FAVOURITE_SEARCH_INSTANCE = "removeFavouriteSearchInstance";
+
+ private final MainComponent pluginMainComponent;
+ private final MyExperimentClient myExperimentClient;
+ private final Logger logger;
+
+ // COMPONENTS
+ private JSplitPane spMainSplitPane;
+ private SearchOptionsPanel jpSearchOptions;
+ private JPanel jpFavouriteSearches;
+ private JPanel jpSearchHistory;
+ private SearchResultsPanel jpSearchResults;
+ private final ImageIcon iconFavourite = new ImageIcon(MyExperimentPerspective.getLocalResourceURL("favourite_icon"));
+ private final ImageIcon iconRemove = new ImageIcon(MyExperimentPerspective.getLocalResourceURL("destroy_icon"));
+
+ // Data storage
+ private QuerySearchInstance siPreviousSearch;
+ private LinkedList<QuerySearchInstance> llFavouriteSearches;
+ private LinkedList<QuerySearchInstance> llSearchHistory;
+
+ // Search components
+ private final SearchEngine searchEngine; // The search engine for executing keyword query searches
+ private final Vector<Long> vCurrentSearchThreadID; // This will keep ID of the current search thread (there will only be one such thread)
+
+ public SearchTabContentPanel(MainComponent component, MyExperimentClient client, Logger logger) {
+ super();
+
+ // set main variables to ensure access to myExperiment, logger and the parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+
+ // initialise the favourite searches
+ String strFavouriteSearches = (String) myExperimentClient.getSettings().get(MyExperimentClient.INI_FAVOURITE_SEARCHES);
+ if (strFavouriteSearches != null) {
+ Object oFavouriteSearches = Base64.decodeToObject(strFavouriteSearches);
+ this.llFavouriteSearches = (LinkedList<QuerySearchInstance>) oFavouriteSearches;
+ } else {
+ this.llFavouriteSearches = new LinkedList<QuerySearchInstance>();
+ }
+
+ // initialise the search history
+ String strSearchHistory = (String) myExperimentClient.getSettings().get(MyExperimentClient.INI_SEARCH_HISTORY);
+ if (strSearchHistory != null) {
+ Object oSearchHistory = Base64.decodeToObject(strSearchHistory);
+ this.llSearchHistory = (LinkedList<QuerySearchInstance>) oSearchHistory;
+ } else {
+ this.llSearchHistory = new LinkedList<QuerySearchInstance>();
+ }
+
+ this.initialiseUI();
+ this.updateFavouriteSearches();
+ this.updateSearchHistory();
+
+ // initialise the search engine
+ vCurrentSearchThreadID = new Vector<Long>(1);
+ vCurrentSearchThreadID.add(null); // this is just a placeholder, so that it's possible to update this value instead of adding new ones later
+ this.searchEngine = new SearchEngine(vCurrentSearchThreadID, false, jpSearchResults, pluginMainComponent, myExperimentClient, logger);
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // THIS MIGHT NOT BE NEEDED AS THE SEARCH OPTIONS BOX NOW
+ // SETS THE MINIMUM SIZE OF THE SIDEBAR PROPERLY
+ spMainSplitPane.setDividerLocation(390);
+ spMainSplitPane.setOneTouchExpandable(true);
+ spMainSplitPane.setDoubleBuffered(true);
+ }
+ });
+ }
+
+ private void initialiseUI() {
+ // create search options panel
+ jpSearchOptions = new SearchOptionsPanel(this, this.pluginMainComponent, this.myExperimentClient, this.logger);
+ jpSearchOptions.setMaximumSize(new Dimension(1024, 0)); // HACK: this is to make sure that search options box won't be stretched
+
+ // create favourite searches panel
+ jpFavouriteSearches = new JPanel();
+ jpFavouriteSearches.setMaximumSize(new Dimension(1024, 0)); // HACK: this is to make sure that favourite searches box won't be stretched
+ jpFavouriteSearches.setLayout(new GridBagLayout());
+ jpFavouriteSearches.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), " Favourite Searches "), BorderFactory.createEmptyBorder(0, 5, 5, 5)));
+
+ // create search history panel
+ jpSearchHistory = new JPanel();
+ jpSearchHistory.setMaximumSize(new Dimension(1024, 0)); // HACK: this is to make sure that search history box won't be stretched
+ jpSearchHistory.setLayout(new GridBagLayout());
+ jpSearchHistory.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), " Search History "), BorderFactory.createEmptyBorder(0, 5, 5, 5)));
+
+ // create the search sidebar
+ JPanel jpSearchSidebar = new JPanel();
+ jpSearchSidebar.setLayout(new GridBagLayout());
+
+ GridBagConstraints gbConstraints = new GridBagConstraints();
+ gbConstraints.anchor = GridBagConstraints.NORTHWEST;
+ gbConstraints.fill = GridBagConstraints.BOTH;
+ gbConstraints.weightx = 1;
+ gbConstraints.gridx = 0;
+
+ gbConstraints.gridy = 0;
+ jpSearchSidebar.add(jpSearchOptions, gbConstraints);
+
+ gbConstraints.gridy = 1;
+ jpSearchSidebar.add(jpFavouriteSearches, gbConstraints);
+
+ gbConstraints.gridy = 2;
+ jpSearchSidebar.add(jpSearchHistory, gbConstraints);
+
+ JPanel jpSidebarContainer = new JPanel();
+ jpSidebarContainer.setLayout(new BorderLayout());
+ jpSidebarContainer.add(jpSearchSidebar, BorderLayout.NORTH);
+
+ // wrap sidebar in a scroll pane
+ JScrollPane spSearchSidebar = new JScrollPane(jpSidebarContainer);
+ spSearchSidebar.getVerticalScrollBar().setUnitIncrement(ResourcePreviewBrowser.PREFERRED_SCROLL);
+ spSearchSidebar.setMinimumSize(new Dimension(jpSidebarContainer.getMinimumSize().width + 20, 0));
+
+ // create panel for search results
+ this.jpSearchResults = new SearchResultsPanel(this, pluginMainComponent, myExperimentClient, logger);
+
+ spMainSplitPane = new JSplitPane();
+ spMainSplitPane.setLeftComponent(spSearchSidebar);
+ spMainSplitPane.setRightComponent(jpSearchResults);
+
+ // PUT EVERYTHING TOGETHER
+ this.setLayout(new BorderLayout());
+ this.add(spMainSplitPane);
+ }
+
+ private void addToSearchListQueue(LinkedList<QuerySearchInstance> searchInstanceList, QuerySearchInstance searchInstanceToAdd, int queueSize) {
+ // check if such entry is already in the list
+ int iDuplicateIdx = searchInstanceList.indexOf(searchInstanceToAdd);
+
+ // only do the following if the new search instance list OR current instance is not the same
+ // as the last one in the list
+ if (searchInstanceList.size() == 0
+ || iDuplicateIdx != searchInstanceList.size() - 1) {
+ // if the current item is already in the list, remove it (then re-add at the end of the list)
+ if (iDuplicateIdx >= 0)
+ searchInstanceList.remove(iDuplicateIdx);
+
+ // we want to keep the history size constant, therefore when it reaches a certain
+ // size, oldest element needs to be removed
+ if (searchInstanceList.size() >= queueSize)
+ searchInstanceList.remove();
+
+ // in either case, add the new element to the tail of the search history
+ searchInstanceList.offer(searchInstanceToAdd);
+ }
+ }
+
+ private void addToFavouriteSearches(QuerySearchInstance searchInstance) {
+ this.addToSearchListQueue(this.llFavouriteSearches, searchInstance, SEARCH_FAVOURITES_LENGTH);
+ Collections.sort(this.llFavouriteSearches);
+ }
+
+ // the method to update search history listing
+ protected void updateFavouriteSearches() {
+ this.jpFavouriteSearches.removeAll();
+
+ if (this.llFavouriteSearches.size() == 0) {
+ GridBagConstraints c = new GridBagConstraints();
+ c.weightx = 1.0;
+ c.anchor = GridBagConstraints.WEST;
+ this.jpFavouriteSearches.add(Util.generateNoneTextLabel("No favourite searches"), c);
+ } else {
+ for (int i = this.llFavouriteSearches.size() - 1; i >= 0; i--) {
+ addEntryToSearchListingPanel(this.llFavouriteSearches, i, SEARCH_FROM_FAVOURITES, this.jpFavouriteSearches, this.iconRemove, REMOVE_FAVOURITE_SEARCH_INSTANCE, "<html>Click to remove from your local favourite searches.<br>"
+ + "(This will not affect your myExperiment profile settings.)</html>");
+ }
+ }
+
+ this.jpFavouriteSearches.repaint();
+ this.jpFavouriteSearches.revalidate();
+ }
+
+ private void addToSearchHistory(QuerySearchInstance searchInstance) {
+ this.addToSearchListQueue(this.llSearchHistory, searchInstance, SEARCH_HISTORY_LENGTH);
+ }
+
+ // the method to update search history listing
+ protected void updateSearchHistory() {
+ this.jpSearchHistory.removeAll();
+
+ if (this.llSearchHistory.size() == 0) {
+ GridBagConstraints c = new GridBagConstraints();
+ c.weightx = 1.0;
+ c.anchor = GridBagConstraints.WEST;
+ this.jpSearchHistory.add(Util.generateNoneTextLabel(SearchResultsPanel.NO_SEARCHES_STATUS), c);
+ } else {
+ for (int i = this.llSearchHistory.size() - 1; i >= 0; i--) {
+ addEntryToSearchListingPanel(this.llSearchHistory, i, SEARCH_FROM_HISTORY, this.jpSearchHistory, this.iconFavourite, ADD_FAVOURITE_SEARCH_INSTANCE, "<html>Click to add to your local favourite"
+ + " searches - these will be available every time you use Taverna.<br>(This will not affect your"
+ + " myExperiment profile settings.)</html>");
+ }
+ }
+
+ this.jpSearchHistory.repaint();
+ this.jpSearchHistory.revalidate();
+
+ // also update search history in History tab
+ if (this.pluginMainComponent.getHistoryBrowser() != null) {
+ this.pluginMainComponent.getHistoryBrowser().refreshSearchHistory();
+ }
+ }
+
+ private void addEntryToSearchListingPanel(List<QuerySearchInstance> searchInstanceList, int iIndex, String searchAction, JPanel panelToPopulate, ImageIcon entryIcon, String iconAction, String iconActionTooltip) {
+ // labels with search query and search settings
+ JClickableLabel jclCurrentEntryLabel = new JClickableLabel(searchInstanceList.get(iIndex).getSearchQuery(), searchAction
+ + ":" + iIndex, this, WorkbenchIcons.findIcon, SwingUtilities.LEFT, searchInstanceList.get(iIndex).toString());
+ JLabel jlCurrentEntrySettings = new JLabel(searchInstanceList.get(iIndex).detailsAsString());
+ jlCurrentEntrySettings.setBorder(BorderFactory.createEmptyBorder(0, 5, 0, 0));
+
+ // grouping search details and search settings together
+ JPanel jpCurentEntryDetails = new JPanel();
+ jpCurentEntryDetails.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ c.anchor = GridBagConstraints.WEST;
+ jpCurentEntryDetails.add(jclCurrentEntryLabel, c);
+ c.weightx = 1.0;
+ jpCurentEntryDetails.add(jlCurrentEntrySettings, c);
+
+ // creating a "button" to add current item to favourites
+ JClickableLabel jclFavourite = new JClickableLabel("", iconAction + ":"
+ + iIndex, this, entryIcon, SwingUtilities.LEFT, iconActionTooltip);
+ jclFavourite.setBorder(BorderFactory.createEmptyBorder(0, 5, 0, 0));
+
+ // putting all pieces of current item together
+ JPanel jpCurrentEntry = new JPanel();
+ jpCurrentEntry.setLayout(new GridBagLayout());
+
+ c.anchor = GridBagConstraints.WEST;
+ c.weightx = 1.0;
+ jpCurrentEntry.add(jpCurentEntryDetails, c);
+
+ c.anchor = GridBagConstraints.WEST;
+ c.weightx = 0;
+ jpCurrentEntry.add(jclFavourite, c);
+
+ // adding current item to the history list
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+ c.gridx = 0;
+ c.gridy = GridBagConstraints.RELATIVE;
+ panelToPopulate.add(jpCurrentEntry, c);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource().equals(this.jpSearchOptions.bSearch)) {
+ // "Search" button was clicked
+
+ // if no search query is specified, display error message
+ if (jpSearchOptions.getSearchQuery().length() == 0) {
+ javax.swing.JOptionPane.showMessageDialog(null, "Search query is empty. Please specify your search query and try again.", "Error", JOptionPane.WARNING_MESSAGE);
+ jpSearchOptions.focusSearchQueryField();
+ } else {
+ // will ensure that if the value in the search result limit editor
+ // is invalid, it is processed properly
+ try {
+ this.jpSearchOptions.jsResultLimit.commitEdit();
+ } catch (ParseException ex) {
+ JOptionPane.showMessageDialog(null, "Invalid search result limit value. This should be an\n"
+ + "integer in the range of "
+ + SearchOptionsPanel.SEARCH_RESULT_LIMIT_MIN
+ + ".."
+ + SearchOptionsPanel.SEARCH_RESULT_LIMIT_MAX, "MyExperiment Plugin - Error", JOptionPane.WARNING_MESSAGE);
+ this.jpSearchOptions.tfResultLimitTextField.selectAll();
+ this.jpSearchOptions.tfResultLimitTextField.requestFocusInWindow();
+ return;
+ }
+
+ // all fine, settings present - store the settings..
+ siPreviousSearch = new SearchEngine.QuerySearchInstance(jpSearchOptions.getSearchQuery(), jpSearchOptions.getResultCountLimit(), jpSearchOptions.getSearchWorkflows(), jpSearchOptions.getSearchFiles(), jpSearchOptions.getSearchPacks(), jpSearchOptions.getSearchUsers(), jpSearchOptions.getSearchGroups());
+
+ // .. and execute the query
+ this.jpSearchOptions.focusSearchQueryField();
+ this.runSearch();
+ }
+ } else if (e.getSource() instanceof JClickableLabel) {
+ if (e.getActionCommand().startsWith(SEARCH_FROM_HISTORY)
+ || e.getActionCommand().startsWith(SEARCH_FROM_FAVOURITES)) {
+ // the part of the action command that is following the prefix is the ID in the search history / favourites storage;
+ // this search instance is removed from history and will be re-added at the top of it when search is launched
+ int iEntryID = Integer.parseInt(e.getActionCommand().substring(e.getActionCommand().indexOf(":") + 1));
+ final QuerySearchInstance si = (e.getActionCommand().startsWith(SEARCH_FROM_HISTORY) ? this.llSearchHistory.remove(iEntryID) : this.llFavouriteSearches.get(iEntryID)); // in case of favourites, no need to remove the entry
+
+ // re-set search options in the settings box and re-run the search
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ jpSearchOptions.setSearchQuery(si.getSearchQuery());
+ jpSearchOptions.setSearchAllResourceTypes(false); // reset the 'all resource types'
+ jpSearchOptions.setSearchWorkflows(si.getSearchWorkflows());
+ jpSearchOptions.setSearchFiles(si.getSearchFiles());
+ jpSearchOptions.setSearchPacks(si.getSearchPacks());
+ jpSearchOptions.setSearchUsers(si.getSearchUsers());
+ jpSearchOptions.setSearchGroups(si.getSearchGroups());
+ jpSearchOptions.setResultCountLimit(si.getResultCountLimit());
+
+ // set this as the 'latest' search
+ siPreviousSearch = si;
+
+ // run the search (and update the search history)
+ runSearch();
+ }
+ });
+ } else if (e.getActionCommand().startsWith(ADD_FAVOURITE_SEARCH_INSTANCE)) {
+ // get the ID of the entry in the history listing first; then fetch the instance itself
+ int iHistID = Integer.parseInt(e.getActionCommand().substring(e.getActionCommand().indexOf(":") + 1));
+ final QuerySearchInstance si = this.llSearchHistory.get(iHistID);
+
+ // add item to favourites and re-draw the panel
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ addToFavouriteSearches(si);
+ updateFavouriteSearches();
+ }
+ });
+ } else if (e.getActionCommand().startsWith(REMOVE_FAVOURITE_SEARCH_INSTANCE)) {
+ // get the ID of the entry in the favourite searches listing first; then remove the instance with that ID from the list
+ int iFavouriteID = Integer.parseInt(e.getActionCommand().substring(e.getActionCommand().indexOf(":") + 1));
+ this.llFavouriteSearches.remove(iFavouriteID);
+
+ // item removed from favourites - re-draw the panel now
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ updateFavouriteSearches();
+ }
+ });
+ }
+ } else if (e.getSource().equals(this.jpSearchResults.bRefresh)) {
+ // "Refresh" button clicked; disable clearing results and re-run previous search
+ this.jpSearchResults.bClear.setEnabled(false);
+ this.rerunLastSearch();
+ } else if (e.getSource().equals(this.jpSearchResults.bClear)) {
+ // "Clear" button clicked - clear last search and disable re-running it
+ siPreviousSearch = null;
+ vCurrentSearchThreadID.set(0, null);
+ this.jpSearchResults.clear();
+ this.jpSearchResults.setStatus(SearchResultsPanel.NO_SEARCHES_STATUS);
+ this.jpSearchResults.bClear.setEnabled(false);
+ this.jpSearchResults.bRefresh.setEnabled(false);
+ }
+ }
+
+ // search history will get updated by default
+ private void runSearch() {
+ runSearch(true);
+ }
+
+ // makes preparations and runs the current search
+ // (has an option not to update the search history)
+ private void runSearch(boolean bUpdateHistory) {
+ if (bUpdateHistory) {
+ // add current search to search history ..
+ this.addToSearchHistory(siPreviousSearch);
+
+ // .. update the search history box ..
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ updateSearchHistory();
+ }
+ });
+ }
+
+ // ..and run the query
+ this.searchEngine.searchAndPopulateResults(siPreviousSearch);
+ }
+
+ // re-executes the search for the most recent query
+ // (if searches have already been done before or were not cleared)
+ public void rerunLastSearch() {
+ if (this.siPreviousSearch != null) {
+ runSearch();
+ }
+ }
+
+ public SearchResultsPanel getSearchResultPanel() {
+ return (this.jpSearchResults);
+ }
+
+ public LinkedList<QuerySearchInstance> getSearchFavouritesList() {
+ return (this.llFavouriteSearches);
+ }
+
+ public LinkedList<QuerySearchInstance> getSearchHistory() {
+ return (this.llSearchHistory);
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/StyledHTMLEditorKit.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/StyledHTMLEditorKit.java
new file mode 100644
index 0000000..2a2302a
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/StyledHTMLEditorKit.java
@@ -0,0 +1,19 @@
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import javax.swing.text.html.HTMLEditorKit;
+import javax.swing.text.html.StyleSheet;
+
+public class StyledHTMLEditorKit extends HTMLEditorKit {
+
+ private final StyleSheet styleSheet;
+
+ public StyledHTMLEditorKit(StyleSheet styleSheet) {
+ this.styleSheet = styleSheet;
+ }
+
+ @Override
+ public StyleSheet getStyleSheet() {
+ return styleSheet;
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/TagBrowserTabContentPanel.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/TagBrowserTabContentPanel.java
new file mode 100644
index 0000000..eca9ab0
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/TagBrowserTabContentPanel.java
@@ -0,0 +1,226 @@
+// Copyright (C) 2008 The University of Manchester, University of Southampton
+// and Cardiff University
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.BorderLayout;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.Vector;
+
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.SwingUtilities;
+
+import org.apache.log4j.Logger;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Base64;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.SearchEngine;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Tag;
+
+/*
+ * @author Jiten Bhagat
+ */
+public class TagBrowserTabContentPanel extends JPanel implements ActionListener {
+ // CONSTANTS
+ private static final double TAG_CLOUD_BALANCE = 0.35;
+ private static final double TAG_SIDEBAR_BALANCE = 0.4;
+ private static final int TAG_SEARCH_HISTORY_LENGTH = 50;
+
+ private MainComponent pluginMainComponent;
+ private MyExperimentClient myExperimentClient;
+ private Logger logger;
+
+ // COMPONENTS
+ private JSplitPane spMainSplitPane;
+ private JSplitPane spTagCloudSplitPane;
+ private TagCloudPanel jpMyTags;
+ private TagCloudPanel jpAllTags;
+ private SearchResultsPanel jpTagSearchResults;
+ private JButton bLoginToSeeMyTags;
+ private JPanel jpLoginToSeeMyTags;
+
+ // STORAGE
+ // last tag for which the search has been made
+ private String strCurrentTagCommand;
+ private ArrayList<Tag> lTagSearchHistory;
+
+ // Search components
+ private SearchEngine searchEngine; // The search engine for executing keyword
+ // query searches
+ private Vector<Long> vCurrentSearchThreadID; // This will keep ID of the
+
+ // current search thread (there
+ // will only be one such thread)
+
+ @SuppressWarnings("unchecked")
+ public TagBrowserTabContentPanel(MainComponent component, MyExperimentClient client, Logger logger) {
+ super();
+
+ // set main variables to ensure access to myExperiment, logger and the
+ // parent component
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+
+ // no tag searches have been done yet
+ this.strCurrentTagCommand = null;
+
+ // initialise the tag search history
+ String strTagSearchHistory = (String) myExperimentClient.getSettings().get(MyExperimentClient.INI_TAG_SEARCH_HISTORY);
+ if (strTagSearchHistory != null) {
+ Object oTagSearchHistory = Base64.decodeToObject(strTagSearchHistory);
+ this.lTagSearchHistory = (ArrayList<Tag>) oTagSearchHistory;
+ } else {
+ this.lTagSearchHistory = new ArrayList<Tag>();
+ }
+
+ this.initialiseUI();
+
+ // initialise the search engine
+ vCurrentSearchThreadID = new Vector<Long>(1);
+ vCurrentSearchThreadID.add(null); // this is just a placeholder, so that
+ // it's possible to update this value
+ // instead of adding new ones later
+ this.searchEngine = new SearchEngine(vCurrentSearchThreadID, true, jpTagSearchResults, pluginMainComponent, myExperimentClient, logger);
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ spTagCloudSplitPane.setDividerLocation(TAG_CLOUD_BALANCE);
+ spMainSplitPane.setDividerLocation(TAG_SIDEBAR_BALANCE);
+ spMainSplitPane.setOneTouchExpandable(true);
+ spMainSplitPane.setDoubleBuffered(true);
+ }
+ });
+ }
+
+ private void initialiseUI() {
+ // This panel will be used when the user is not logged in - i.e. when can't
+ // show "My Tags";
+ // log-in button will be shown instead
+ this.bLoginToSeeMyTags = new JButton("Login to see your tags", new ImageIcon(MyExperimentPerspective.getLocalResourceURL("login_icon")));
+ this.bLoginToSeeMyTags.addActionListener(this);
+
+ this.jpLoginToSeeMyTags = new JPanel();
+ this.jpLoginToSeeMyTags.setLayout(new GridBagLayout());
+ this.jpLoginToSeeMyTags.add(this.bLoginToSeeMyTags);
+
+ // Create the tag clouds
+ this.jpMyTags = new TagCloudPanel("My Tags", TagCloudPanel.TAGCLOUD_TYPE_USER, this, pluginMainComponent, myExperimentClient, logger);
+ this.jpAllTags = new TagCloudPanel("All Tags", TagCloudPanel.TAGCLOUD_TYPE_GENERAL, this, pluginMainComponent, myExperimentClient, logger);
+
+ // add the two tag clouds to the left-hand side sidebar
+ this.spTagCloudSplitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
+ this.spTagCloudSplitPane.setTopComponent(this.myExperimentClient.isLoggedIn() ? jpMyTags : jpLoginToSeeMyTags);
+ this.spTagCloudSplitPane.setBottomComponent(jpAllTags);
+
+ // create panel for tag search results
+ this.jpTagSearchResults = new SearchResultsPanel(this, pluginMainComponent, myExperimentClient, logger);
+
+ this.spMainSplitPane = new JSplitPane();
+ this.spMainSplitPane.setLeftComponent(spTagCloudSplitPane);
+ this.spMainSplitPane.setRightComponent(this.jpTagSearchResults);
+
+ this.setLayout(new BorderLayout());
+ this.add(this.spMainSplitPane, BorderLayout.CENTER);
+ }
+
+ // this helper is called when the user logs in / out to swap the
+ // view accordingly; 'refresh' on "My Tags" panel should be called
+ // immediately after changing the view
+ public void setMyTagsShown(boolean bShow) {
+ if (bShow) {
+ this.spTagCloudSplitPane.setTopComponent(this.jpMyTags);
+ } else {
+ this.spTagCloudSplitPane.setTopComponent(this.jpLoginToSeeMyTags);
+ }
+
+ // in either case apply element balance again
+ this.spTagCloudSplitPane.setDividerLocation(TAG_CLOUD_BALANCE);
+ }
+
+ public void refresh() {
+ if (this.myExperimentClient.isLoggedIn()) {
+ // "My Tags" are only accessible when the user has logged in
+ this.jpMyTags.refresh();
+ }
+ this.jpAllTags.refresh();
+ }
+
+ // re-executes the search for the most recent tag
+ // (if tag searches have already been done before)
+ public void rerunLastTagSearch() {
+ if (this.strCurrentTagCommand != null) {
+ this.actionPerformed(new ActionEvent(this.jpAllTags, 0, this.strCurrentTagCommand));
+ }
+ }
+
+ public TagCloudPanel getMyTagPanel() {
+ return (this.jpMyTags);
+ }
+
+ public TagCloudPanel getAllTagPanel() {
+ return (this.jpAllTags);
+ }
+
+ public SearchResultsPanel getTagSearchResultPanel() {
+ return (this.jpTagSearchResults);
+ }
+
+ public ArrayList<Tag> getTagSearchHistory() {
+ return (this.lTagSearchHistory);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource().equals(this.jpTagSearchResults.bRefresh)) {
+ // disable clearing results and re-run last tag search
+ this.getTagSearchResultPanel().bClear.setEnabled(false);
+ this.rerunLastTagSearch();
+ } else if (e.getSource().equals(this.jpTagSearchResults.bClear)) {
+ // clear last search and disable re-running it
+ this.strCurrentTagCommand = null;
+ vCurrentSearchThreadID.set(0, null);
+ this.getTagSearchResultPanel().clear();
+ this.getTagSearchResultPanel().setStatus(SearchResultsPanel.NO_SEARCHES_STATUS);
+ this.getTagSearchResultPanel().bClear.setEnabled(false);
+ this.getTagSearchResultPanel().bRefresh.setEnabled(false);
+ } else if (e.getSource() instanceof JClickableLabel
+ || e.getSource() instanceof TagCloudPanel) {
+ // one of the tags was clicked as a hyperlink in any TagCloudPanel
+ // (in Resource Preview Browser or in Tag Browser tab) or as a
+ // JClickableLabel
+ if (e.getActionCommand().startsWith("tag:")) {
+ // record the tag search command and run the search
+ this.strCurrentTagCommand = e.getActionCommand();
+ this.searchEngine.searchAndPopulateResults(strCurrentTagCommand);
+
+ // update tag search history making sure that:
+ // - there's only one occurrence of this tag in the history;
+ // - if this tag was in the history before, it is moved to the 'top'
+ // now;
+ // - predefined history size is not exceeded
+ Tag t = Tag.instantiateTagFromActionCommand(strCurrentTagCommand);
+ this.lTagSearchHistory.remove(t);
+ this.lTagSearchHistory.add(t);
+ if (this.lTagSearchHistory.size() > TAG_SEARCH_HISTORY_LENGTH)
+ this.lTagSearchHistory.remove(0);
+
+ // now update the tag search history panel in 'History' tab
+ if (this.pluginMainComponent.getHistoryBrowser() != null) {
+ this.pluginMainComponent.getHistoryBrowser().refreshTagSearchHistory();
+ }
+ }
+ } else if (e.getSource().equals(this.bLoginToSeeMyTags)) {
+ // set the return "link"
+ this.pluginMainComponent.getMyStuffTab().cTabContentComponentToSwitchToAfterLogin = this;
+
+ // switch to login tab
+ this.pluginMainComponent.getMainTabs().setSelectedComponent(this.pluginMainComponent.getMyStuffTab());
+ }
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/TagCloudPanel.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/TagCloudPanel.java
new file mode 100644
index 0000000..b03fd8f
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/TagCloudPanel.java
@@ -0,0 +1,342 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSlider;
+import javax.swing.JTextPane;
+import javax.swing.SwingUtilities;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkListener;
+import javax.swing.text.html.HTMLDocument;
+import javax.swing.text.html.HTMLEditorKit;
+
+import org.apache.log4j.Logger;
+
+import net.sf.taverna.t2.lang.ui.ShadedLabel;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Tag;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.TagCloud;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+
+/**
+ * @author Sergejs Aleksejevs, Jiten Bhagat
+ */
+public class TagCloudPanel extends JPanel implements ChangeListener, ItemListener, ActionListener, HyperlinkListener {
+ // CONSTANTS
+ private static final int TAGCLOUD_MAX_FONTSIZE = 36;
+ private static final int TAGCLOUD_MIN_FONTSIZE = 12;
+ private static final int TAGCLOUD_DEFAULT_MAX_SIZE = 350;
+ private static final int TAGCLOUD_DEFAULT_DISPLAY_SIZE = 50;
+
+ public static final int TAGCLOUD_TYPE_GENERAL = 0;
+ public static final int TAGCLOUD_TYPE_USER = 1;
+ public static final int TAGCLOUD_TYPE_RESOURCE_PREVIEW = 2;
+
+ private MainComponent pluginMainComponent;
+ private MyExperimentClient myExperimentClient;
+ private Logger logger;
+
+ // COMPONENTS
+ private String strTitle;
+ private int iType;
+ private ShadedLabel lCloudTitle;
+ private JSlider jsCloudSizeSlider;
+ private JCheckBox cbShowAllTags;
+ private JButton bRefresh;
+ private JTextPane tpTagCloudBody;
+
+ private ActionListener clickHandler;
+ private TagCloud tcData = new TagCloud();
+ private boolean bUserTagCloudSliderValueNeverSet = true;
+
+ public TagCloudPanel(String title, int iTagCloudType, ActionListener clickHandler, MainComponent component, MyExperimentClient client, Logger logger) {
+ super();
+
+ // set parameters and the main variables to ensure access to myExperiment,
+ // logger and the parent component
+ this.strTitle = title;
+ this.iType = iTagCloudType;
+ this.clickHandler = clickHandler;
+ this.pluginMainComponent = component;
+ this.myExperimentClient = client;
+ this.logger = logger;
+
+ initialiseUI();
+ }
+
+ private void initialiseUI() {
+ // set the title of the tag cloud
+ lCloudTitle = new ShadedLabel(this.strTitle, ShadedLabel.BLUE);
+
+ // create the tag cloud controls panel
+ // (all controls will be created anyway, but if that's a resource
+ // preview tag cloud, make sure that these controls are not displayed)
+ JPanel jpCloudControlsPanel = new JPanel();
+ jpCloudControlsPanel.setLayout(new BoxLayout(jpCloudControlsPanel, BoxLayout.LINE_AXIS));
+ this.jsCloudSizeSlider = new JSlider(1, TAGCLOUD_DEFAULT_MAX_SIZE, TAGCLOUD_DEFAULT_DISPLAY_SIZE);
+ this.cbShowAllTags = new JCheckBox("All tags", false);
+ this.bRefresh = new JButton("Refresh", WorkbenchIcons.refreshIcon);
+
+ if (this.iType != TagCloudPanel.TAGCLOUD_TYPE_RESOURCE_PREVIEW) {
+ this.jsCloudSizeSlider.addChangeListener(this);
+ this.jsCloudSizeSlider.setToolTipText("Drag the slider to select how big the tag cloud should be, or check the \"All tags\" box to get the full tag cloud.");
+ jpCloudControlsPanel.add(this.jsCloudSizeSlider);
+
+ this.cbShowAllTags.addItemListener(this);
+ jpCloudControlsPanel.add(this.cbShowAllTags);
+
+ this.bRefresh.addActionListener(this);
+ this.bRefresh.setToolTipText("Click this button to refresh the Tag Cloud");
+ jpCloudControlsPanel.add(this.bRefresh);
+ }
+
+ // tag cloud header panel which which contains controls
+ JPanel jpCloudHeader = new JPanel(new BorderLayout());
+ jpCloudHeader.add(jpCloudControlsPanel, BorderLayout.CENTER);
+ jpCloudHeader.setBorder(BorderFactory.createEtchedBorder());
+
+ // body of the tag cloud with the actual tags
+ this.tpTagCloudBody = new JTextPane();
+ this.tpTagCloudBody.setBorder(BorderFactory.createEmptyBorder());
+ this.tpTagCloudBody.setEditable(false);
+ this.tpTagCloudBody.setContentType("text/html");
+ this.tpTagCloudBody.addHyperlinkListener(this);
+
+ JScrollPane spTagCloudBody = new JScrollPane(this.tpTagCloudBody, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+ spTagCloudBody.setBorder(BorderFactory.createEmptyBorder());
+ spTagCloudBody.setOpaque(true);
+
+ // PUT EVERYTHING TOGETHER
+ JPanel jpTagCloudContentWithControls = new JPanel();
+ jpTagCloudContentWithControls.setLayout(new BorderLayout());
+ jpTagCloudContentWithControls.add(spTagCloudBody, BorderLayout.CENTER);
+ if (this.iType != TagCloudPanel.TAGCLOUD_TYPE_RESOURCE_PREVIEW) {
+ jpTagCloudContentWithControls.add(jpCloudHeader, BorderLayout.NORTH);
+ }
+
+ this.setLayout(new BorderLayout());
+ if (this.iType != TagCloudPanel.TAGCLOUD_TYPE_RESOURCE_PREVIEW) {
+ this.add(lCloudTitle, BorderLayout.NORTH);
+ }
+ this.add(jpTagCloudContentWithControls, BorderLayout.CENTER);
+ this.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createEmptyBorder(2, 2, 2, 2), BorderFactory.createEtchedBorder()));
+ }
+
+ public void refresh() {
+ this.lCloudTitle.setText(strTitle
+ + " <span style='color: gray;'>(Loading...)</span>");
+
+ // Make call to myExperiment API in a different thread
+ // (then use SwingUtilities.invokeLater to update the UI when ready).
+ new Thread("Get '" + this.strTitle + "' tag cloud data") {
+ public void run() {
+ logger.debug("Getting '" + strTitle + "' tag cloud data");
+
+ try {
+ int size = -1;
+ if (!cbShowAllTags.isSelected()) {
+ size = jsCloudSizeSlider.getValue();
+ }
+
+ // based on the type of the tag cloud, different data needs to be
+ // fetched
+ switch (iType) {
+ case TagCloudPanel.TAGCLOUD_TYPE_GENERAL:
+ tcData = myExperimentClient.getGeneralTagCloud(size);
+ break;
+
+ case TagCloudPanel.TAGCLOUD_TYPE_USER:
+ tcData = myExperimentClient.getUserTagCloud(myExperimentClient.getCurrentUser(), size);
+ break;
+
+ case TagCloudPanel.TAGCLOUD_TYPE_RESOURCE_PREVIEW:
+ // fetch tag counts for tags that are already pre-set
+ myExperimentClient.convertTagListIntoTagCloudData(tcData.getTags());
+ break;
+
+ default:
+ // unknown type of tag cloud; show no data
+ tcData = new TagCloud();
+ break;
+ }
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ repopulate();
+ }
+ });
+ } catch (Exception ex) {
+ logger.error("Failed to get tag cloud data from myExperiment", ex);
+ }
+ }
+ }.start();
+ }
+
+ public void repopulate() {
+ logger.debug("Building '" + this.strTitle + "' tag cloud...");
+
+ try {
+ this.jsCloudSizeSlider.removeChangeListener(this);
+ if (this.iType == TAGCLOUD_TYPE_USER) {
+ jsCloudSizeSlider.setMinimum(1);
+ jsCloudSizeSlider.setMaximum(myExperimentClient.getCurrentUser().getTags().size());
+ if (bUserTagCloudSliderValueNeverSet) {
+ // this is the first load of the cloud, show all user tags
+ jsCloudSizeSlider.setValue(jsCloudSizeSlider.getMaximum());
+ bUserTagCloudSliderValueNeverSet = false;
+ } else {
+ // not the first load, test if the position of the slider is still
+ // within the scope
+ // (put that back to maximum if exceeds)
+ if (jsCloudSizeSlider.getValue() > jsCloudSizeSlider.getMaximum()
+ || this.cbShowAllTags.isSelected())
+ jsCloudSizeSlider.setValue(jsCloudSizeSlider.getMaximum());
+ }
+ } else {
+ // if "All tags" check box is ticked, set the slider max to the max no
+ // of tags
+ // (this will be the total number of tags available from myExperiment);
+ // if "All tags" was never checked before, max position of the slider
+ // will
+ // stay at predefined default value (because the total number of tags is
+ // not known yet)
+ if (this.cbShowAllTags.isSelected()) {
+ int size = this.tcData.getTags().size();
+ this.jsCloudSizeSlider.setMaximum(size);
+ this.jsCloudSizeSlider.setValue(size);
+ }
+ }
+ this.jsCloudSizeSlider.addChangeListener(this);
+
+ // For tag cloud font size calculations
+ int iMaxCount = this.tcData.getMaxTagCount();
+
+ StringBuffer content = new StringBuffer();
+
+ if (this.tcData.getTags().size() > 0) {
+ content.append("<div class='outer'>");
+ content.append("<br>");
+ content.append("<div class='tag_cloud'>");
+
+ for (Tag t : this.tcData.getTags()) {
+ // Normalise count and use it to obtain a font size value.
+ // Also chops off based on min and max.
+ int fontSize = (int) (((double) t.getCount() / ((double) iMaxCount / 3)) * TAGCLOUD_MAX_FONTSIZE);
+ if (fontSize < TAGCLOUD_MIN_FONTSIZE) {
+ fontSize = TAGCLOUD_MIN_FONTSIZE;
+ }
+ if (fontSize > TAGCLOUD_MAX_FONTSIZE) {
+ fontSize = TAGCLOUD_MAX_FONTSIZE;
+ }
+
+ content.append("<a style='font-size: " + fontSize + "pt;' href='tag:"
+ + t.getTagName() + "'>" + t.getTagName() + "</a>");
+ content.append(" ");
+ }
+
+ content.append("<br>");
+ content.append("</div>");
+ content.append("</div>");
+ } else {
+ content.append("<br>");
+ content.append("<span style='color: gray; font-weight: italic;'> No tags to display</span>");
+ }
+
+ HTMLEditorKit kit = new StyledHTMLEditorKit(pluginMainComponent.getStyleSheet());
+ HTMLDocument doc = (HTMLDocument) (kit.createDefaultDocument());
+ doc.insertAfterStart(doc.getRootElements()[0].getElement(0), content.toString());
+
+ this.tpTagCloudBody.setEditorKit(kit);
+ this.tpTagCloudBody.setDocument(doc);
+ } catch (Exception e) {
+ logger.error("Failed to populate tag cloud", e);
+ }
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ lCloudTitle.setText(strTitle
+ + " <span style='color: gray;'>(currently showing "
+ + tcData.getTags().size() + ")</span>");
+ revalidate();
+ }
+ });
+ }
+
+ /**
+ * Helper method to get hold of the tag cloud data. Needed to be able to set
+ * tag cloud data when using this for resource preview (when tag fetching is
+ * not required).
+ */
+ public TagCloud getTagCloudData() {
+ return this.tcData;
+ }
+
+ public void stateChanged(ChangeEvent e) {
+ if (e.getSource().equals(this.jsCloudSizeSlider)) {
+ // cloud size slider was dragged to a new place and the drag event
+ // has finished; refresh the tag cloud with the newly selected tag count
+ if (!this.jsCloudSizeSlider.getValueIsAdjusting()) {
+ this.cbShowAllTags.removeItemListener(this);
+ this.cbShowAllTags.setSelected(false);
+ this.cbShowAllTags.addItemListener(this);
+
+ this.refresh();
+ }
+ }
+ }
+
+ public void itemStateChanged(ItemEvent e) {
+ if (e.getItemSelectable().equals(this.cbShowAllTags)) {
+ // "Show all" clicked - need to refresh with all tags being displayed
+ this.refresh();
+ }
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource().equals(this.bRefresh)) {
+ // refresh button clicked on the cloud controls panel -
+ // simply refresh the cloud with the same parameters
+ this.refresh();
+ }
+ }
+
+ public void hyperlinkUpdate(HyperlinkEvent e) {
+ if (e.getSource().equals(this.tpTagCloudBody)
+ && e.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+ // one of the tags was clicked, but click processing is off-loaded to
+ // 'clickHandler'
+ this.clickHandler.actionPerformed(new ActionEvent(this, (this.getClass().getName() + e.getDescription()).hashCode(), e.getDescription()));
+ }
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/TestJFrameForLocalLaunch.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/TestJFrameForLocalLaunch.java
new file mode 100644
index 0000000..15dd3a4
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/TestJFrameForLocalLaunch.java
@@ -0,0 +1,48 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.Dimension;
+import javax.swing.JFrame;
+
+public class TestJFrameForLocalLaunch {
+
+ /**
+ * This is a simple test class for launching myExperiment perspective
+ * from outside Taverna. At some point it will be not usable anymore,
+ * when proper integration of myExperiment plugin is made.
+ *
+ * @author Sergejs Aleksejevs
+ */
+ public static void main(String[] args)
+ {
+ JFrame frame = new JFrame("myExperiment Perspective Test");
+ frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+
+ frame.setMinimumSize(new Dimension(1000, 700));
+ frame.setLocation(300, 150);
+ frame.getContentPane().add(new net.sf.taverna.t2.ui.perspectives.myexperiment.MainComponent(null, null));
+
+ frame.pack();
+ frame.setVisible(true);
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/UploadWorkflowDialog.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/UploadWorkflowDialog.java
new file mode 100644
index 0000000..ed47183
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/UploadWorkflowDialog.java
@@ -0,0 +1,849 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment;
+
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.InputStream;
+import java.net.HttpURLConnection;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JDialog;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.JRootPane;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.event.CaretEvent;
+import javax.swing.event.CaretListener;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.License;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.ServerResponse;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Util;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Workflow;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.file.impl.actions.SaveWorkflowAsAction;
+import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+import net.sf.taverna.t2.workflowmodel.Dataflow;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author Emmanuel Tagarira, Sergejs Aleksejevs
+ */
+public class UploadWorkflowDialog extends HelpEnabledDialog implements ActionListener,
+ CaretListener, ComponentListener, KeyListener, FocusListener {
+ // components for accessing application's main elements
+ private final MainComponent pluginMainComponent = MainComponent.MAIN_COMPONENT;
+ private final MyExperimentClient myExperimentClient = MainComponent.MY_EXPERIMENT_CLIENT;
+ private final Logger logger = MainComponent.LOGGER;
+
+ // COMPONENTS
+ private JTextArea taDescription;
+ private JTextField tfTitle;
+ private JButton bUpload;
+ private JButton bCancel;
+ private JLabel lStatusMessage;
+ private JComboBox jcbLicences;
+ private JComboBox jcbSharingPermissions;
+ private String licence;
+ private String sharing;
+
+ // STORAGE
+ private File localWorkflowFile; // the local workflow file to be uploaded
+ private Resource updateResource; // the workflow resource that is to be
+ // updated
+ private File uploadFile; // THE UPLOAD FILE
+
+ private String strDescription = null;
+ private String strTitle = null;
+ private boolean bUploadingSuccessful = false;
+
+ // misc.
+ private int gridYPositionForStatusLabel;
+ private JRadioButton rbSelectLocalFile;
+ private JRadioButton rbSelectOpenWorkflow;
+ private JButton bSelectFile;
+ private JComboBox jcbOpenWorkflows;
+ private final JLabel selectedFileLabel = new JLabel("no wokflow file selected");
+ private boolean uploadWorkflowFromLocalFile;
+ JFileChooser jfsSelectFile = new JFileChooser();
+
+ private boolean userRequestedWorkflowUpload;
+ private final FileManager fileManager;
+
+ public UploadWorkflowDialog(JFrame parent, boolean doUpload, FileManager fileManager) {
+ super(parent, "Upload workflow to myExperiment", true);
+ this.fileManager = fileManager;
+ initVarsAndUI(doUpload, null);
+ }
+
+ public UploadWorkflowDialog(JFrame parent, boolean doUpload, Resource resource,
+ FileManager fileManager) {
+ super(parent, (doUpload ? "Upload new workflow version" : "Update workflow information"),
+ true);
+ this.fileManager = fileManager;
+ initVarsAndUI(doUpload, resource);
+ }
+
+ private void initVarsAndUI(boolean doUpload, Resource resource) {
+ // set the resource for which the comment is being added
+ this.updateResource = resource;
+ this.userRequestedWorkflowUpload = doUpload;
+
+ // set options of the 'add comment' dialog box
+ this.setDefaultCloseOperation(DISPOSE_ON_CLOSE);
+
+ initialiseUI();
+ this.setMinimumSize(new Dimension(525, 375));
+ }
+
+ private JPanel createSelectSource() {
+ // create radio buttons
+ ButtonGroup radioButtons = new ButtonGroup();
+ rbSelectOpenWorkflow = new JRadioButton("Already Opened Workflow");
+ rbSelectOpenWorkflow.addFocusListener(this);
+ rbSelectLocalFile = new JRadioButton("Select Local File");
+ rbSelectLocalFile.addFocusListener(this);
+ radioButtons.add(rbSelectOpenWorkflow);
+ rbSelectOpenWorkflow.setSelected(true);
+ radioButtons.add(rbSelectLocalFile);
+
+ // create the source panel and add items
+ JPanel source = new JPanel(new GridBagLayout());
+ source.setBorder(BorderFactory.createTitledBorder("Workflow source"));
+
+ GridBagConstraints c = new GridBagConstraints();
+ c.anchor = GridBagConstraints.NORTHWEST;
+ c.gridy = 0;
+ c.gridx = 0;
+ c.gridwidth = 1;
+ c.weightx = 1;
+ c.insets = new Insets(3, 0, 3, 0);
+ c.fill = GridBagConstraints.BOTH;
+
+ // add info label
+ // JLabel info = new
+ // JLabel("Upload a workflow you would like to upload:");
+ // source.add(info, c);
+
+ // add open workflow radio button
+ c.gridy++;
+ source.add(rbSelectOpenWorkflow, c);
+ c.gridx = 1;
+ c.gridwidth = 2;
+ createDropdown();
+ source.add(jcbOpenWorkflows, c);
+
+ // add local file radio button
+ c.gridwidth = 1;
+ c.gridy++;
+ c.gridx = 0;
+ source.add(rbSelectLocalFile, c);
+ c.gridx = 1;
+ source.add(selectedFileLabel, c);
+ bSelectFile = new JButton(WorkbenchIcons.openIcon);
+ bSelectFile.addActionListener(this);
+ bSelectFile.setToolTipText("Select the file you would like to upload to myExperiment");
+ c.gridx = 2;
+ source.add(bSelectFile, c);
+
+ return source;
+ }
+
+ private void createDropdown() {
+ List<DataflowSelection> openDataflows = new ArrayList<DataflowSelection>();
+
+ int currentlyOpenedIndex = 0;
+ boolean foundIndex = false;
+
+ for (Dataflow df : fileManager.getOpenDataflows()) {
+ Object source = fileManager.getDataflowSource(df);
+
+ String name = "";
+ boolean getLocalName = source instanceof InputStream;
+ if (source != null)
+ name = (getLocalName ? df.getLocalName() : source.toString());
+
+ if (df.equals(fileManager.getCurrentDataflow())) {
+ name = "<html><body>" + name + " - " + " <i>(current)</i></body></html>";
+ foundIndex = true;
+ }
+
+ openDataflows.add(new DataflowSelection(df, name));
+ if (!foundIndex)
+ currentlyOpenedIndex++;
+ }
+
+ jcbOpenWorkflows = new JComboBox(openDataflows.toArray());
+ jcbOpenWorkflows.setSelectedIndex(currentlyOpenedIndex);
+ }
+
+ private JPanel createMetadataPanel() {
+ Insets fieldInset = new Insets(0, 5, 4, 5);
+ Insets labelInset = new Insets(3, 5, 4, 5);
+
+ GridBagConstraints c = new GridBagConstraints();
+ c.gridx = 0;
+ c.weightx = 1;
+ c.gridy = 0;
+ c.anchor = GridBagConstraints.WEST;
+ c.gridwidth = 2;
+ c.fill = GridBagConstraints.HORIZONTAL;
+
+ JPanel metaPanel = new JPanel(new GridBagLayout());
+ metaPanel.setBorder(BorderFactory.createTitledBorder("Workflow information"));
+
+ // title
+ JLabel lTitle = new JLabel("Workflow title:");
+ c.insets = labelInset;
+ c.gridy++;
+ metaPanel.add(lTitle, c);
+
+ this.tfTitle = new JTextField();
+ if (this.updateResource != null)
+ this.tfTitle.setText(this.updateResource.getTitle());
+ c.gridy++;
+ c.insets = fieldInset;
+ metaPanel.add(this.tfTitle, c);
+
+ // description
+ JLabel lDescription = new JLabel("Workflow description:");
+ c.gridy++;
+ c.insets = labelInset;
+ metaPanel.add(lDescription, c);
+
+ this.taDescription = new JTextArea(5, 35);
+ this.taDescription.setLineWrap(true);
+ this.taDescription.setWrapStyleWord(true);
+ if (this.updateResource != null)
+ this.taDescription.setText(this.updateResource.getDescription());
+
+ JScrollPane spDescription = new JScrollPane(this.taDescription);
+ c.gridy++;
+ c.insets = fieldInset;
+ metaPanel.add(spDescription, c);
+
+ // licences
+ String[] licenseText = new String[License.SUPPORTED_TYPES.length];
+ for (int x = 0; x < License.SUPPORTED_TYPES.length; x++)
+ licenseText[x] = License.getInstance(License.SUPPORTED_TYPES[x]).getText();
+
+ jcbLicences = new JComboBox(licenseText);
+ String defaultLicenseText = License.getInstance(License.DEFAULT_LICENSE)
+ .getText();
+ jcbLicences.setSelectedItem(defaultLicenseText);
+
+ if (this.updateResource != null) { // adding a new workflow
+ Workflow wf = (Workflow) this.updateResource;
+ String wfText = wf.getLicense().getText();
+ for (int x = 0; x < licenseText.length; x++)
+ if (wfText.equals(licenseText[x])) {
+ jcbLicences.setSelectedIndex(x);
+ break;
+ }
+ }
+
+ jcbLicences.addActionListener(this);
+ jcbLicences.setEditable(false);
+
+ JLabel lLicense = new JLabel("Please select the licence to apply:");
+ c.gridy++;
+ c.insets = labelInset;
+ metaPanel.add(lLicense, c);
+
+ c.gridy++;
+ c.insets = fieldInset;
+ metaPanel.add(jcbLicences, c);
+
+ // sharing - options: private / view / download
+ String[] permissions = { "This workflow is private.",
+ "Anyone can view, but noone can download.",
+ "Anyone can view, and anyone can download" };
+
+ this.jcbSharingPermissions = new JComboBox(permissions);
+
+ jcbSharingPermissions.addActionListener(this);
+ jcbSharingPermissions.setEditable(false);
+
+ JLabel jSharing = new JLabel("Please select your sharing permissions:");
+ c.gridy++;
+ c.insets = labelInset;
+ metaPanel.add(jSharing, c);
+
+ c.gridy++;
+ c.insets = fieldInset;
+ metaPanel.add(jcbSharingPermissions, c);
+
+ return metaPanel;
+ }
+
+ private void initialiseUI() {
+ // get content pane
+ Container contentPane = this.getContentPane();
+
+ Insets fieldInset = new Insets(3, 5, 3, 5);
+
+ // set up layout
+ contentPane.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+ c.gridx = 0;
+ c.gridy = 0;
+ c.anchor = GridBagConstraints.NORTHWEST;
+ c.gridwidth = 2;
+ c.fill = GridBagConstraints.HORIZONTAL;
+
+ // ADD ALL COMPONENTS
+ // source for workflow to upload
+ if (userRequestedWorkflowUpload) {
+ c.insets = fieldInset;
+ contentPane.add(createSelectSource(), c);
+ c.gridy++;
+ }
+
+ // create metadata panel
+ contentPane.add(createMetadataPanel(), c);
+
+ // buttons
+ this.bUpload = new JButton(userRequestedWorkflowUpload ? "Upload Workflow"
+ : "Update Workflow");
+ this.bUpload.setDefaultCapable(true);
+ this.getRootPane().setDefaultButton(this.bUpload);
+ this.bUpload.addActionListener(this);
+ this.bUpload.addKeyListener(this);
+
+ c.gridy++;
+ c.anchor = GridBagConstraints.EAST;
+ c.gridwidth = 1;
+ c.fill = GridBagConstraints.NONE;
+ c.weightx = 0.5;
+ c.insets = new Insets(10, 5, 10, 5);
+ contentPane.add(bUpload, c);
+
+ this.bCancel = new JButton("Cancel");
+ this.bCancel.setPreferredSize(this.bUpload.getPreferredSize());
+ this.bCancel.addActionListener(this);
+ c.gridx = 1;
+ c.anchor = GridBagConstraints.WEST;
+ c.weightx = 0.5;
+ contentPane.add(bCancel, c);
+
+ this.pack();
+ this.addComponentListener(this);
+
+ gridYPositionForStatusLabel = c.gridy;
+ }
+
+ /**
+ * Opens up a modal dialog where the user can enter the comment text. Window
+ * is simply closed if 'Cancel' button is pressed; on pressing 'Post
+ * Comment' button the window will turn into 'waiting' state, post the
+ * comment and return the resulting XML document (which would contain the
+ * newly added comment) back to the caller.
+ *
+ * @return String value of the non-empty comment text to be sent to
+ * myExperiment or null if action was cancelled.
+ */
+ public boolean launchUploadDialogAndPostIfRequired() {
+ // makes the 'add comment' dialog visible, then waits until it is
+ // closed;
+ // control returns to this method when the dialog window is disposed
+ this.setVisible(true);
+ return (bUploadingSuccessful);
+ }
+
+ private File performSourceCheck() {
+ if (!rbSelectLocalFile.isSelected() && !rbSelectOpenWorkflow.isSelected()) { // it
+ // is
+ // logicall
+ // impossible
+ // to
+ // get
+ // this
+ // message,
+ // have
+ // it
+ // JUST
+ // IN
+ // CASE
+ JOptionPane.showConfirmDialog(this,
+ "You have not selected a source for you workflow.\n"
+ + "Please select a source and try again.", "Select Workflow Source",
+ JOptionPane.DEFAULT_OPTION, JOptionPane.ERROR_MESSAGE);
+ return null;
+ }
+
+ if (rbSelectOpenWorkflow.isSelected()) { // user requested to use a flow
+ // currently open in t2
+ Dataflow dataflowToUpload = ((DataflowSelection) jcbOpenWorkflows.getSelectedItem())
+ .getDataflow();
+ SaveWorkflowAsAction saveAction = new SaveWorkflowAsAction(fileManager);
+
+ boolean skipPrompt = false;
+ if (fileManager.isDataflowChanged(dataflowToUpload)) { // if flow
+ // has
+ // changed, prompt
+ // user to save
+ JOptionPane.showConfirmDialog(this, "The workflow you are trying to upload has\n"
+ + "changed since the last time it was saved.\n\n"
+ + "Please save your file to proceed...", "Save Workflow",
+ JOptionPane.DEFAULT_OPTION, JOptionPane.INFORMATION_MESSAGE);
+ saveAction.saveDataflow(this, dataflowToUpload);
+ skipPrompt = true;
+ }
+
+ File dataflowFile = (File) fileManager.getDataflowSource(dataflowToUpload);
+ if (dataflowFile == null && !skipPrompt) {
+ JOptionPane.showConfirmDialog(this, "You cannot upload an empty workflow.\n"
+ + "Please select a different workflow before\n"
+ + "you attempt the upload again.", "Upload Error",
+ JOptionPane.DEFAULT_OPTION, JOptionPane.ERROR_MESSAGE);
+ return null;
+ } else
+ return dataflowFile;
+
+ } else { // user wants to use local file
+ if (localWorkflowFile == null) {
+ JOptionPane.showConfirmDialog(this, "You have not selected a file to upload.\n"
+ + "Please select a file and try again.", "Select Workflow Source",
+ JOptionPane.DEFAULT_OPTION, JOptionPane.ERROR_MESSAGE);
+ return null;
+ }
+
+ return localWorkflowFile;
+ }
+ }
+
+ private void getMetadata() {
+ // get sharing permission
+ switch (this.jcbSharingPermissions.getSelectedIndex()) {
+ case 0:
+ this.sharing = "private";
+ break;
+ case 1:
+ this.sharing = "view";
+ break;
+ case 2:
+ this.sharing = "download";
+ break;
+ }
+
+ // get licence
+ this.licence = License.SUPPORTED_TYPES[this.jcbLicences.getSelectedIndex()];
+
+ // get title
+ this.strTitle = this.tfTitle.getText();
+ this.strTitle = this.strTitle.trim();
+
+ // get description
+ this.strDescription = this.taDescription.getText();
+ this.strDescription = this.strDescription.trim();
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource().equals(this.bUpload)) { // * *** *** *** * UPLOAD
+ // BUTTON *
+ // *** *** *** *
+ // perform source check returns a file if attaining the source was
+ // successful
+ if (userRequestedWorkflowUpload) {
+ uploadFile = performSourceCheck();
+ if (uploadFile == null)
+ return;
+ }
+
+ // collect and put the metadata values in their respectable vars
+ getMetadata();
+
+ // if the description or the title are empty, prompt the user to
+ // confirm
+ // the upload
+ boolean proceedWithUpload = false;
+ if ((this.strDescription.length() == 0) && (this.strTitle.length() == 0)) {
+ String strInfo = "The workflow 'title' field and the 'description' field\n"
+ + "(or both) are empty. Any metadata found within the\n"
+ + "workflow will be used instead. Do you wish to proceed?";
+ int confirm = JOptionPane.showConfirmDialog(this, strInfo, "Empty fields",
+ JOptionPane.YES_NO_OPTION, JOptionPane.INFORMATION_MESSAGE);
+ if (confirm == JOptionPane.YES_OPTION)
+ proceedWithUpload = true;
+ } else
+ proceedWithUpload = true;
+
+ if (proceedWithUpload) {
+ // the window will stay visible, but should turn into 'waiting'
+ // state
+ final JRootPane rootPane = this.getRootPane();
+ final Container contentPane = this.getContentPane();
+ contentPane.remove(this.bUpload);
+ contentPane.remove(this.bCancel);
+ if (this.lStatusMessage != null)
+ contentPane.remove(this.lStatusMessage);
+ this.taDescription.setEditable(false);
+
+ final GridBagConstraints c = new GridBagConstraints();
+ c.gridx = 0;
+ c.gridy = gridYPositionForStatusLabel;
+ c.gridwidth = 2;
+ c.anchor = GridBagConstraints.CENTER;
+ c.fill = GridBagConstraints.NONE;
+ c.insets = new Insets(10, 5, 10, 5);
+ lStatusMessage = new JLabel((updateResource == null ? "Uploading" : "Updating")
+ + " your workflow...", new ImageIcon(
+ MyExperimentPerspective.getLocalResourceURL("spinner")),
+ SwingConstants.CENTER);
+ contentPane.add(lStatusMessage, c);
+
+ // disable the (X) button (ideally, would need to remove it, but
+ // there's
+ // no way to do this)
+ this.setDefaultCloseOperation(JDialog.DO_NOTHING_ON_CLOSE);
+
+ // revalidate the window
+ this.pack();
+ this.validate();
+ this.repaint();
+
+ new Thread("Posting workflow") {
+ boolean formatRecognized = false;
+
+ @Override
+ public void run() {
+ String workflowFileContent = "";
+ if (userRequestedWorkflowUpload) {
+ if (uploadFile != null) {
+ try {
+ BufferedReader reader = new BufferedReader(new FileReader(
+ uploadFile));
+ String line;
+
+ String scuflSchemaDef = "xmlns:s=\"http://org.embl.ebi.escience/xscufl/0.1alpha\"";
+ String t2flowSchemaDef = "xmlns=\"http://taverna.sf.net/2008/xml/t2flow\"";
+
+ while ((line = reader.readLine()) != null) {
+ if (!formatRecognized
+ && (line.contains(scuflSchemaDef) || line
+ .contains(t2flowSchemaDef)))
+ formatRecognized = true;
+
+ workflowFileContent += line + "\n";
+ }
+ } catch (Exception e) {
+ lStatusMessage = new JLabel("Error occurred:" + e.getMessage(),
+ new ImageIcon(MyExperimentPerspective
+ .getLocalResourceURL("failure_icon")),
+ SwingConstants.LEFT);
+ logger.error(e.getCause() + "\n" + e.getMessage());
+ }
+ }
+ }
+
+ // *** POST THE WORKFLOW ***
+ final ServerResponse response;
+
+ if ((userRequestedWorkflowUpload && formatRecognized)
+ || !userRequestedWorkflowUpload) {
+ if (updateResource == null) // upload a new workflow
+ response = myExperimentClient.postWorkflow(workflowFileContent,
+ Util.stripAllHTML(strTitle),
+ Util.stripAllHTML(strDescription), licence, sharing);
+ else
+ // edit existing workflow
+ response = myExperimentClient.updateWorkflowVersionOrMetadata(
+ updateResource, workflowFileContent,
+ Util.stripAllHTML(strTitle),
+ Util.stripAllHTML(strDescription), licence, sharing);
+
+ bUploadingSuccessful = (response.getResponseCode() == HttpURLConnection.HTTP_OK);
+ } else {
+ bUploadingSuccessful = false;
+ response = null;
+ }
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // *** REACT TO POSTING RESULT ***
+ if (bUploadingSuccessful) {
+ // workflow uploaded successfully
+ setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+
+ // disable all fields in dialog
+ tfTitle.setEnabled(false);
+ taDescription.setEnabled(false);
+ jcbLicences.setEnabled(false);
+ jcbSharingPermissions.setEnabled(false);
+ if (userRequestedWorkflowUpload) {
+ rbSelectOpenWorkflow.setEnabled(false);
+ rbSelectLocalFile.setEnabled(false);
+ selectedFileLabel.setEnabled(false);
+ bSelectFile.setEnabled(false);
+ jcbOpenWorkflows.setEnabled(false);
+ }
+ contentPane.remove(lStatusMessage);
+
+ c.insets = new Insets(10, 5, 5, 5);
+ lStatusMessage = new JLabel("Your workflow was successfully "
+ + (updateResource == null ? "uploaded." : "updated."),
+ new ImageIcon(MyExperimentPerspective
+ .getLocalResourceURL("success_icon")),
+ SwingConstants.LEFT);
+ contentPane.add(lStatusMessage, c);
+
+ bCancel.setText("OK");
+ bCancel.setDefaultCapable(true);
+ rootPane.setDefaultButton(bCancel);
+ c.insets = new Insets(5, 5, 10, 5);
+ c.gridy++;
+ contentPane.add(bCancel, c);
+
+ pack();
+ bCancel.requestFocusInWindow();
+
+ // update uploaded items history making sure
+ // that:
+ // - there's only one occurrence of this
+ // item in the history;
+ // - if this item was in the history before,
+ // it is moved to
+ // the 'top' now;
+ // - predefined history size is not exceeded
+ MainComponent.MAIN_COMPONENT.getHistoryBrowser()
+ .getUploadedItemsHistoryList().remove(updateResource);
+ MainComponent.MAIN_COMPONENT.getHistoryBrowser()
+ .getUploadedItemsHistoryList().add(updateResource);
+ if (MainComponent.MAIN_COMPONENT.getHistoryBrowser()
+ .getUploadedItemsHistoryList().size() > HistoryBrowserTabContentPanel.UPLOADED_ITEMS_HISTORY_LENGTH) {
+ MainComponent.MAIN_COMPONENT.getHistoryBrowser()
+ .getUploadedItemsHistoryList().remove(0);
+ }
+
+ // now update the uploaded items history
+ // panel in 'History'
+ // tab
+ if (MainComponent.MAIN_COMPONENT.getHistoryBrowser() != null) {
+ MainComponent.MAIN_COMPONENT
+ .getHistoryBrowser()
+ .refreshHistoryBox(
+ HistoryBrowserTabContentPanel.UPLOADED_ITEMS_HISTORY);
+ }
+
+ } else {
+ // posting wasn't successful, notify the
+ // user
+ // and provide an option to close window or
+ // start again
+ setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+ taDescription.setEditable(true);
+ contentPane.remove(lStatusMessage);
+
+ c.insets = new Insets(10, 5, 5, 5);
+
+ String msg;
+ if (!formatRecognized)
+ msg = "Error occured: Invalid Taverna workflow.";
+ else
+ msg = "An error occured while processing your request.";
+
+ lStatusMessage = new JLabel(msg, new ImageIcon(
+ MyExperimentPerspective
+ .getLocalResourceURL("failure_icon")),
+ SwingConstants.LEFT);
+ contentPane.add(lStatusMessage, c);
+
+ bUpload.setText("Try again");
+ bUpload.setToolTipText("Please review your workflow or myExperiment base URL");
+ c.anchor = GridBagConstraints.EAST;
+ c.insets = new Insets(5, 5, 10, 5);
+ c.gridwidth = 1;
+ c.weightx = 0.5;
+ c.gridx = 0;
+ c.gridy++;
+ contentPane.add(bUpload, c);
+ rootPane.setDefaultButton(bUpload);
+
+ c.anchor = GridBagConstraints.WEST;
+ c.gridx = 1;
+ bCancel.setPreferredSize(bUpload.getPreferredSize());
+ contentPane.add(bCancel, c);
+
+ pack();
+ validate();
+ repaint();
+ }
+ }
+ });
+ }
+ }.start();
+ } // if proceedWithUpload
+ } else if (e.getSource().equals(this.bCancel)) { // * CANCEL BUTTON *
+ // cleanup the input fields if it wasn't posted successfully +
+ // simply
+ // close and destroy the window
+ if (!this.bUploadingSuccessful) {
+ this.strDescription = null;
+ this.tfTitle = null;
+ }
+ this.dispose();
+ } else if (e.getSource().equals(bSelectFile)) {// * SELECT FILE BUTTON *
+ // *
+ if (jfsSelectFile.showOpenDialog(this) == JFileChooser.APPROVE_OPTION) {
+ localWorkflowFile = jfsSelectFile.getSelectedFile();
+
+ if (localWorkflowFile != null) {
+ selectedFileLabel.setText(localWorkflowFile.getAbsolutePath());
+ selectedFileLabel.setEnabled(true);
+ }
+ pack();
+ }
+ }
+ }
+
+ public void keyPressed(KeyEvent e) {
+ // if TAB was pressed in the text field (title), need to move keyboard
+ // focus
+ if (e.getSource().equals(this.tfTitle) || e.getSource().equals(this.taDescription)) {
+ if (e.getKeyCode() == KeyEvent.VK_TAB) {
+ if ((e.getModifiersEx() & KeyEvent.SHIFT_DOWN_MASK) == KeyEvent.SHIFT_DOWN_MASK) {
+ // SHIFT + TAB move focus backwards
+ ((Component) e.getSource()).transferFocusBackward();
+ } else {
+ // TAB moves focus forward
+ ((Component) e.getSource()).transferFocus();
+ }
+ e.consume();
+ }
+ }
+ }
+
+ public void focusGained(FocusEvent e) {
+ if (e.getSource().equals(rbSelectLocalFile)) {
+ uploadWorkflowFromLocalFile = true;
+ bSelectFile.setEnabled(uploadWorkflowFromLocalFile);
+ jcbOpenWorkflows.setEnabled(!uploadWorkflowFromLocalFile);
+
+ if (localWorkflowFile != null) {
+ selectedFileLabel.setEnabled(uploadWorkflowFromLocalFile);
+ selectedFileLabel.setText(localWorkflowFile.getAbsolutePath());
+ pack();
+ } else
+ selectedFileLabel.setEnabled(!uploadWorkflowFromLocalFile);
+
+ } else if (e.getSource().equals(rbSelectOpenWorkflow)) {
+ uploadWorkflowFromLocalFile = false;
+ selectedFileLabel.setEnabled(uploadWorkflowFromLocalFile);
+ bSelectFile.setEnabled(uploadWorkflowFromLocalFile);
+ jcbOpenWorkflows.setEnabled(!uploadWorkflowFromLocalFile);
+ }
+ }
+
+ public void componentShown(ComponentEvent e) {
+ // center this dialog box within the preview browser window
+ if (updateResource == null) // upload has been pressed from the MAIN
+ // perspective window
+ Util.centerComponentWithinAnother(this.pluginMainComponent, this);
+ else
+ // upload pressed from resource preview window
+ Util.centerComponentWithinAnother(this.pluginMainComponent.getPreviewBrowser(), this);
+ }
+
+ public void focusLost(FocusEvent e) {
+ // not in use
+ }
+
+ public void caretUpdate(CaretEvent e) {
+ // not in use
+ }
+
+ public void componentHidden(ComponentEvent e) {
+ // not in use
+ }
+
+ public void componentMoved(ComponentEvent e) {
+ // not in use
+ }
+
+ public void keyReleased(KeyEvent e) {
+ // not in use
+ }
+
+ public void keyTyped(KeyEvent e) {
+ // not in use
+ }
+
+ public void componentResized(ComponentEvent e) {
+ // not in use
+ }
+
+ private class DataflowSelection {
+ private final Dataflow dataflow;
+ private final String name;
+
+ public DataflowSelection(Dataflow dataflow, String name) {
+ this.dataflow = dataflow;
+ this.name = name;
+ }
+
+ public Dataflow getDataflow() {
+ return dataflow;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ @Override
+ public String toString() {
+ return name;
+ }
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Base64$InputStream.class b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Base64$InputStream.class
new file mode 100644
index 0000000..a1a5f82
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Base64$InputStream.class
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Base64$OutputStream.class b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Base64$OutputStream.class
new file mode 100644
index 0000000..e754656
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Base64$OutputStream.class
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Base64.class b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Base64.class
new file mode 100644
index 0000000..84fcee9
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Base64.class
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Base64.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Base64.java
new file mode 100644
index 0000000..00af810
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Base64.java
@@ -0,0 +1,1813 @@
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import net.sf.taverna.t2.activities.dataflow.views.DataflowActivityConfigView;
+
+import org.apache.log4j.Logger;
+
+/**
+ * <p>Encodes and decodes to and from Base64 notation.</p>
+ * <p>Homepage: <a href="http://iharder.net/base64">http://iharder.net/base64</a>.</p>
+ *
+ * <p>The <tt>options</tt> parameter, which appears in a few places, is used to pass
+ * several pieces of information to the encoder. In the "higher level" methods such as
+ * encodeBytes( bytes, options ) the options parameter can be used to indicate such
+ * things as first gzipping the bytes before encoding them, not inserting linefeeds
+ * (though that breaks strict Base64 compatibility), and encoding using the URL-safe
+ * and Ordered dialects.</p>
+ *
+ * <p>The constants defined in Base64 can be OR-ed together to combine options, so you
+ * might make a call like this:</p>
+ *
+ * <code>String encoded = Base64.encodeBytes( mybytes, Base64.GZIP | Base64.DONT_BREAK_LINES );</code>
+ *
+ * <p>to compress the data before encoding it and then making the output have no newline characters.</p>
+ *
+ *
+ * <p>
+ * Change Log:
+ * </p>
+ * <ul>
+ * <li>v2.2.2 - Fixed encodeFileToFile and decodeFileToFile to use the
+ * Base64.InputStream class to encode and decode on the fly which uses
+ * less memory than encoding/decoding an entire file into memory before writing.</li>
+ * <li>v2.2.1 - Fixed bug using URL_SAFE and ORDERED encodings. Fixed bug
+ * when using very small files (~< 40 bytes).</li>
+ * <li>v2.2 - Added some helper methods for encoding/decoding directly from
+ * one file to the next. Also added a main() method to support command line
+ * encoding/decoding from one file to the next. Also added these Base64 dialects:
+ * <ol>
+ * <li>The default is RFC3548 format.</li>
+ * <li>Calling Base64.setFormat(Base64.BASE64_FORMAT.URLSAFE_FORMAT) generates
+ * URL and file name friendly format as described in Section 4 of RFC3548.
+ * http://www.faqs.org/rfcs/rfc3548.html</li>
+ * <li>Calling Base64.setFormat(Base64.BASE64_FORMAT.ORDERED_FORMAT) generates
+ * URL and file name friendly format that preserves lexical ordering as described
+ * in http://www.faqs.org/qa/rfcc-1940.html</li>
+ * </ol>
+ * Special thanks to Jim Kellerman at <a href="http://www.powerset.com/">http://www.powerset.com/</a>
+ * for contributing the new Base64 dialects.
+ * </li>
+ *
+ * <li>v2.1 - Cleaned up javadoc comments and unused variables and methods. Added
+ * some convenience methods for reading and writing to and from files.</li>
+ * <li>v2.0.2 - Now specifies UTF-8 encoding in places where the code fails on systems
+ * with other encodings (like EBCDIC).</li>
+ * <li>v2.0.1 - Fixed an error when decoding a single byte, that is, when the
+ * encoded data was a single byte.</li>
+ * <li>v2.0 - I got rid of methods that used booleans to set options.
+ * Now everything is more consolidated and cleaner. The code now detects
+ * when data that's being decoded is gzip-compressed and will decompress it
+ * automatically. Generally things are cleaner. You'll probably have to
+ * change some method calls that you were making to support the new
+ * options format (<tt>int</tt>s that you "OR" together).</li>
+ * <li>v1.5.1 - Fixed bug when decompressing and decoding to a
+ * byte[] using <tt>decode( String s, boolean gzipCompressed )</tt>.
+ * Added the ability to "suspend" encoding in the Output Stream so
+ * you can turn on and off the encoding if you need to embed base64
+ * data in an otherwise "normal" stream (like an XML file).</li>
+ * <li>v1.5 - Output stream pases on flush() command but doesn't do anything itself.
+ * This helps when using GZIP streams.
+ * Added the ability to GZip-compress objects before encoding them.</li>
+ * <li>v1.4 - Added helper methods to read/write files.</li>
+ * <li>v1.3.6 - Fixed OutputStream.flush() so that 'position' is reset.</li>
+ * <li>v1.3.5 - Added flag to turn on and off line breaks. Fixed bug in input stream
+ * where last buffer being read, if not completely full, was not returned.</li>
+ * <li>v1.3.4 - Fixed when "improperly padded stream" error was thrown at the wrong time.</li>
+ * <li>v1.3.3 - Fixed I/O streams which were totally messed up.</li>
+ * </ul>
+ *
+ * <p>
+ * I am placing this code in the Public Domain. Do with it as you will.
+ * This software comes with no guarantees or warranties but with
+ * plenty of well-wishing instead!
+ * Please visit <a href="http://iharder.net/base64">http://iharder.net/base64</a>
+ * periodically to check for updates or to contribute improvements.
+ * </p>
+ *
+ * @author Robert Harder
+ * @author rob@iharder.net
+ * @version 2.2.2
+ */
+public class Base64
+{
+
+ private static Logger logger = Logger
+ .getLogger(Base64.class);
+
+ /* ******** P U B L I C F I E L D S ******** */
+
+
+ /** No options specified. Value is zero. */
+ public final static int NO_OPTIONS = 0;
+
+ /** Specify encoding. */
+ public final static int ENCODE = 1;
+
+
+ /** Specify decoding. */
+ public final static int DECODE = 0;
+
+
+ /** Specify that data should be gzip-compressed. */
+ public final static int GZIP = 2;
+
+
+ /** Don't break lines when encoding (violates strict Base64 specification) */
+ public final static int DONT_BREAK_LINES = 8;
+
+ /**
+ * Encode using Base64-like encoding that is URL- and Filename-safe as described
+ * in Section 4 of RFC3548:
+ * <a href="http://www.faqs.org/rfcs/rfc3548.html">http://www.faqs.org/rfcs/rfc3548.html</a>.
+ * It is important to note that data encoded this way is <em>not</em> officially valid Base64,
+ * or at the very least should not be called Base64 without also specifying that is
+ * was encoded using the URL- and Filename-safe dialect.
+ */
+ public final static int URL_SAFE = 16;
+
+
+ /**
+ * Encode using the special "ordered" dialect of Base64 described here:
+ * <a href="http://www.faqs.org/qa/rfcc-1940.html">http://www.faqs.org/qa/rfcc-1940.html</a>.
+ */
+ public final static int ORDERED = 32;
+
+
+/* ******** P R I V A T E F I E L D S ******** */
+
+
+ /** Maximum line length (76) of Base64 output. */
+ private final static int MAX_LINE_LENGTH = 76;
+
+
+ /** The equals sign (=) as a byte. */
+ private final static byte EQUALS_SIGN = (byte)'=';
+
+
+ /** The new line character (\n) as a byte. */
+ private final static byte NEW_LINE = (byte)'\n';
+
+
+ /** Preferred encoding. */
+ private final static String PREFERRED_ENCODING = "UTF-8";
+
+
+ // I think I end up not using the BAD_ENCODING indicator.
+ //private final static byte BAD_ENCODING = -9; // Indicates error in encoding
+ private final static byte WHITE_SPACE_ENC = -5; // Indicates white space in encoding
+ private final static byte EQUALS_SIGN_ENC = -1; // Indicates equals sign in encoding
+
+
+/* ******** S T A N D A R D B A S E 6 4 A L P H A B E T ******** */
+
+ /** The 64 valid Base64 values. */
+ //private final static byte[] ALPHABET;
+ /* Host platform me be something funny like EBCDIC, so we hardcode these values. */
+ private final static byte[] _STANDARD_ALPHABET =
+ {
+ (byte)'A', (byte)'B', (byte)'C', (byte)'D', (byte)'E', (byte)'F', (byte)'G',
+ (byte)'H', (byte)'I', (byte)'J', (byte)'K', (byte)'L', (byte)'M', (byte)'N',
+ (byte)'O', (byte)'P', (byte)'Q', (byte)'R', (byte)'S', (byte)'T', (byte)'U',
+ (byte)'V', (byte)'W', (byte)'X', (byte)'Y', (byte)'Z',
+ (byte)'a', (byte)'b', (byte)'c', (byte)'d', (byte)'e', (byte)'f', (byte)'g',
+ (byte)'h', (byte)'i', (byte)'j', (byte)'k', (byte)'l', (byte)'m', (byte)'n',
+ (byte)'o', (byte)'p', (byte)'q', (byte)'r', (byte)'s', (byte)'t', (byte)'u',
+ (byte)'v', (byte)'w', (byte)'x', (byte)'y', (byte)'z',
+ (byte)'0', (byte)'1', (byte)'2', (byte)'3', (byte)'4', (byte)'5',
+ (byte)'6', (byte)'7', (byte)'8', (byte)'9', (byte)'+', (byte)'/'
+ };
+
+
+ /**
+ * Translates a Base64 value to either its 6-bit reconstruction value
+ * or a negative number indicating some other meaning.
+ **/
+ private final static byte[] _STANDARD_DECODABET =
+ {
+ -9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 0 - 8
+ -5,-5, // Whitespace: Tab and Linefeed
+ -9,-9, // Decimal 11 - 12
+ -5, // Whitespace: Carriage Return
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 14 - 26
+ -9,-9,-9,-9,-9, // Decimal 27 - 31
+ -5, // Whitespace: Space
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 33 - 42
+ 62, // Plus sign at decimal 43
+ -9,-9,-9, // Decimal 44 - 46
+ 63, // Slash at decimal 47
+ 52,53,54,55,56,57,58,59,60,61, // Numbers zero through nine
+ -9,-9,-9, // Decimal 58 - 60
+ -1, // Equals sign at decimal 61
+ -9,-9,-9, // Decimal 62 - 64
+ 0,1,2,3,4,5,6,7,8,9,10,11,12,13, // Letters 'A' through 'N'
+ 14,15,16,17,18,19,20,21,22,23,24,25, // Letters 'O' through 'Z'
+ -9,-9,-9,-9,-9,-9, // Decimal 91 - 96
+ 26,27,28,29,30,31,32,33,34,35,36,37,38, // Letters 'a' through 'm'
+ 39,40,41,42,43,44,45,46,47,48,49,50,51, // Letters 'n' through 'z'
+ -9,-9,-9,-9 // Decimal 123 - 126
+ /*,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 127 - 139
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 140 - 152
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 153 - 165
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 166 - 178
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 179 - 191
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 192 - 204
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 205 - 217
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 218 - 230
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 231 - 243
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9 // Decimal 244 - 255 */
+ };
+
+
+/* ******** U R L S A F E B A S E 6 4 A L P H A B E T ******** */
+
+ /**
+ * Used in the URL- and Filename-safe dialect described in Section 4 of RFC3548:
+ * <a href="http://www.faqs.org/rfcs/rfc3548.html">http://www.faqs.org/rfcs/rfc3548.html</a>.
+ * Notice that the last two bytes become "hyphen" and "underscore" instead of "plus" and "slash."
+ */
+ private final static byte[] _URL_SAFE_ALPHABET =
+ {
+ (byte)'A', (byte)'B', (byte)'C', (byte)'D', (byte)'E', (byte)'F', (byte)'G',
+ (byte)'H', (byte)'I', (byte)'J', (byte)'K', (byte)'L', (byte)'M', (byte)'N',
+ (byte)'O', (byte)'P', (byte)'Q', (byte)'R', (byte)'S', (byte)'T', (byte)'U',
+ (byte)'V', (byte)'W', (byte)'X', (byte)'Y', (byte)'Z',
+ (byte)'a', (byte)'b', (byte)'c', (byte)'d', (byte)'e', (byte)'f', (byte)'g',
+ (byte)'h', (byte)'i', (byte)'j', (byte)'k', (byte)'l', (byte)'m', (byte)'n',
+ (byte)'o', (byte)'p', (byte)'q', (byte)'r', (byte)'s', (byte)'t', (byte)'u',
+ (byte)'v', (byte)'w', (byte)'x', (byte)'y', (byte)'z',
+ (byte)'0', (byte)'1', (byte)'2', (byte)'3', (byte)'4', (byte)'5',
+ (byte)'6', (byte)'7', (byte)'8', (byte)'9', (byte)'-', (byte)'_'
+ };
+
+ /**
+ * Used in decoding URL- and Filename-safe dialects of Base64.
+ */
+ private final static byte[] _URL_SAFE_DECODABET =
+ {
+ -9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 0 - 8
+ -5,-5, // Whitespace: Tab and Linefeed
+ -9,-9, // Decimal 11 - 12
+ -5, // Whitespace: Carriage Return
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 14 - 26
+ -9,-9,-9,-9,-9, // Decimal 27 - 31
+ -5, // Whitespace: Space
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 33 - 42
+ -9, // Plus sign at decimal 43
+ -9, // Decimal 44
+ 62, // Minus sign at decimal 45
+ -9, // Decimal 46
+ -9, // Slash at decimal 47
+ 52,53,54,55,56,57,58,59,60,61, // Numbers zero through nine
+ -9,-9,-9, // Decimal 58 - 60
+ -1, // Equals sign at decimal 61
+ -9,-9,-9, // Decimal 62 - 64
+ 0,1,2,3,4,5,6,7,8,9,10,11,12,13, // Letters 'A' through 'N'
+ 14,15,16,17,18,19,20,21,22,23,24,25, // Letters 'O' through 'Z'
+ -9,-9,-9,-9, // Decimal 91 - 94
+ 63, // Underscore at decimal 95
+ -9, // Decimal 96
+ 26,27,28,29,30,31,32,33,34,35,36,37,38, // Letters 'a' through 'm'
+ 39,40,41,42,43,44,45,46,47,48,49,50,51, // Letters 'n' through 'z'
+ -9,-9,-9,-9 // Decimal 123 - 126
+ /*,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 127 - 139
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 140 - 152
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 153 - 165
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 166 - 178
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 179 - 191
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 192 - 204
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 205 - 217
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 218 - 230
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 231 - 243
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9 // Decimal 244 - 255 */
+ };
+
+
+
+/* ******** O R D E R E D B A S E 6 4 A L P H A B E T ******** */
+
+ /**
+ * I don't get the point of this technique, but it is described here:
+ * <a href="http://www.faqs.org/qa/rfcc-1940.html">http://www.faqs.org/qa/rfcc-1940.html</a>.
+ */
+ private final static byte[] _ORDERED_ALPHABET =
+ {
+ (byte)'-',
+ (byte)'0', (byte)'1', (byte)'2', (byte)'3', (byte)'4',
+ (byte)'5', (byte)'6', (byte)'7', (byte)'8', (byte)'9',
+ (byte)'A', (byte)'B', (byte)'C', (byte)'D', (byte)'E', (byte)'F', (byte)'G',
+ (byte)'H', (byte)'I', (byte)'J', (byte)'K', (byte)'L', (byte)'M', (byte)'N',
+ (byte)'O', (byte)'P', (byte)'Q', (byte)'R', (byte)'S', (byte)'T', (byte)'U',
+ (byte)'V', (byte)'W', (byte)'X', (byte)'Y', (byte)'Z',
+ (byte)'_',
+ (byte)'a', (byte)'b', (byte)'c', (byte)'d', (byte)'e', (byte)'f', (byte)'g',
+ (byte)'h', (byte)'i', (byte)'j', (byte)'k', (byte)'l', (byte)'m', (byte)'n',
+ (byte)'o', (byte)'p', (byte)'q', (byte)'r', (byte)'s', (byte)'t', (byte)'u',
+ (byte)'v', (byte)'w', (byte)'x', (byte)'y', (byte)'z'
+ };
+
+ /**
+ * Used in decoding the "ordered" dialect of Base64.
+ */
+ private final static byte[] _ORDERED_DECODABET =
+ {
+ -9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 0 - 8
+ -5,-5, // Whitespace: Tab and Linefeed
+ -9,-9, // Decimal 11 - 12
+ -5, // Whitespace: Carriage Return
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 14 - 26
+ -9,-9,-9,-9,-9, // Decimal 27 - 31
+ -5, // Whitespace: Space
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 33 - 42
+ -9, // Plus sign at decimal 43
+ -9, // Decimal 44
+ 0, // Minus sign at decimal 45
+ -9, // Decimal 46
+ -9, // Slash at decimal 47
+ 1,2,3,4,5,6,7,8,9,10, // Numbers zero through nine
+ -9,-9,-9, // Decimal 58 - 60
+ -1, // Equals sign at decimal 61
+ -9,-9,-9, // Decimal 62 - 64
+ 11,12,13,14,15,16,17,18,19,20,21,22,23, // Letters 'A' through 'M'
+ 24,25,26,27,28,29,30,31,32,33,34,35,36, // Letters 'N' through 'Z'
+ -9,-9,-9,-9, // Decimal 91 - 94
+ 37, // Underscore at decimal 95
+ -9, // Decimal 96
+ 38,39,40,41,42,43,44,45,46,47,48,49,50, // Letters 'a' through 'm'
+ 51,52,53,54,55,56,57,58,59,60,61,62,63, // Letters 'n' through 'z'
+ -9,-9,-9,-9 // Decimal 123 - 126
+ /*,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 127 - 139
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 140 - 152
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 153 - 165
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 166 - 178
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 179 - 191
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 192 - 204
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 205 - 217
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 218 - 230
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9, // Decimal 231 - 243
+ -9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9,-9 // Decimal 244 - 255 */
+ };
+
+
+/* ******** D E T E R M I N E W H I C H A L H A B E T ******** */
+
+
+ /**
+ * Returns one of the _SOMETHING_ALPHABET byte arrays depending on
+ * the options specified.
+ * It's possible, though silly, to specify ORDERED and URLSAFE
+ * in which case one of them will be picked, though there is
+ * no guarantee as to which one will be picked.
+ */
+ private final static byte[] getAlphabet( int options )
+ {
+ if( (options & URL_SAFE) == URL_SAFE ) return _URL_SAFE_ALPHABET;
+ else if( (options & ORDERED) == ORDERED ) return _ORDERED_ALPHABET;
+ else return _STANDARD_ALPHABET;
+
+ } // end getAlphabet
+
+
+ /**
+ * Returns one of the _SOMETHING_DECODABET byte arrays depending on
+ * the options specified.
+ * It's possible, though silly, to specify ORDERED and URL_SAFE
+ * in which case one of them will be picked, though there is
+ * no guarantee as to which one will be picked.
+ */
+ private final static byte[] getDecodabet( int options )
+ {
+ if( (options & URL_SAFE) == URL_SAFE ) return _URL_SAFE_DECODABET;
+ else if( (options & ORDERED) == ORDERED ) return _ORDERED_DECODABET;
+ else return _STANDARD_DECODABET;
+
+ } // end getAlphabet
+
+
+
+ /** Defeats instantiation. */
+ private Base64(){}
+
+
+ /**
+ * Encodes or decodes two files from the command line;
+ * <strong>feel free to delete this method (in fact you probably should)
+ * if you're embedding this code into a larger program.</strong>
+ */
+ public final static void main( String[] args )
+ {
+ if( args.length < 3 ){
+ usage("Not enough arguments.");
+ } // end if: args.length < 3
+ else {
+ String flag = args[0];
+ String infile = args[1];
+ String outfile = args[2];
+ if( flag.equals( "-e" ) ){
+ Base64.encodeFileToFile( infile, outfile );
+ } // end if: encode
+ else if( flag.equals( "-d" ) ) {
+ Base64.decodeFileToFile( infile, outfile );
+ } // end else if: decode
+ else {
+ usage( "Unknown flag: " + flag );
+ } // end else
+ } // end else
+ } // end main
+
+ /**
+ * Prints command line usage.
+ *
+ * @param msg A message to include with usage info.
+ */
+ private final static void usage( String msg )
+ {
+ logger.error( msg );
+ logger.error( "Usage: java Base64 -e|-d inputfile outputfile" );
+ } // end usage
+
+
+/* ******** E N C O D I N G M E T H O D S ******** */
+
+
+ /**
+ * Encodes up to the first three bytes of array <var>threeBytes</var>
+ * and returns a four-byte array in Base64 notation.
+ * The actual number of significant bytes in your array is
+ * given by <var>numSigBytes</var>.
+ * The array <var>threeBytes</var> needs only be as big as
+ * <var>numSigBytes</var>.
+ * Code can reuse a byte array by passing a four-byte array as <var>b4</var>.
+ *
+ * @param b4 A reusable byte array to reduce array instantiation
+ * @param threeBytes the array to convert
+ * @param numSigBytes the number of significant bytes in your array
+ * @return four byte array in Base64 notation.
+ * @since 1.5.1
+ */
+ private static byte[] encode3to4( byte[] b4, byte[] threeBytes, int numSigBytes, int options )
+ {
+ encode3to4( threeBytes, 0, numSigBytes, b4, 0, options );
+ return b4;
+ } // end encode3to4
+
+
+ /**
+ * <p>Encodes up to three bytes of the array <var>source</var>
+ * and writes the resulting four Base64 bytes to <var>destination</var>.
+ * The source and destination arrays can be manipulated
+ * anywhere along their length by specifying
+ * <var>srcOffset</var> and <var>destOffset</var>.
+ * This method does not check to make sure your arrays
+ * are large enough to accomodate <var>srcOffset</var> + 3 for
+ * the <var>source</var> array or <var>destOffset</var> + 4 for
+ * the <var>destination</var> array.
+ * The actual number of significant bytes in your array is
+ * given by <var>numSigBytes</var>.</p>
+ * <p>This is the lowest level of the encoding methods with
+ * all possible parameters.</p>
+ *
+ * @param source the array to convert
+ * @param srcOffset the index where conversion begins
+ * @param numSigBytes the number of significant bytes in your array
+ * @param destination the array to hold the conversion
+ * @param destOffset the index where output will be put
+ * @return the <var>destination</var> array
+ * @since 1.3
+ */
+ private static byte[] encode3to4(
+ byte[] source, int srcOffset, int numSigBytes,
+ byte[] destination, int destOffset, int options )
+ {
+ byte[] ALPHABET = getAlphabet( options );
+
+ // 1 2 3
+ // 01234567890123456789012345678901 Bit position
+ // --------000000001111111122222222 Array position from threeBytes
+ // --------| || || || | Six bit groups to index ALPHABET
+ // >>18 >>12 >> 6 >> 0 Right shift necessary
+ // 0x3f 0x3f 0x3f Additional AND
+
+ // Create buffer with zero-padding if there are only one or two
+ // significant bytes passed in the array.
+ // We have to shift left 24 in order to flush out the 1's that appear
+ // when Java treats a value as negative that is cast from a byte to an int.
+ int inBuff = ( numSigBytes > 0 ? ((source[ srcOffset ] << 24) >>> 8) : 0 )
+ | ( numSigBytes > 1 ? ((source[ srcOffset + 1 ] << 24) >>> 16) : 0 )
+ | ( numSigBytes > 2 ? ((source[ srcOffset + 2 ] << 24) >>> 24) : 0 );
+
+ switch( numSigBytes )
+ {
+ case 3:
+ destination[ destOffset ] = ALPHABET[ (inBuff >>> 18) ];
+ destination[ destOffset + 1 ] = ALPHABET[ (inBuff >>> 12) & 0x3f ];
+ destination[ destOffset + 2 ] = ALPHABET[ (inBuff >>> 6) & 0x3f ];
+ destination[ destOffset + 3 ] = ALPHABET[ (inBuff ) & 0x3f ];
+ return destination;
+
+ case 2:
+ destination[ destOffset ] = ALPHABET[ (inBuff >>> 18) ];
+ destination[ destOffset + 1 ] = ALPHABET[ (inBuff >>> 12) & 0x3f ];
+ destination[ destOffset + 2 ] = ALPHABET[ (inBuff >>> 6) & 0x3f ];
+ destination[ destOffset + 3 ] = EQUALS_SIGN;
+ return destination;
+
+ case 1:
+ destination[ destOffset ] = ALPHABET[ (inBuff >>> 18) ];
+ destination[ destOffset + 1 ] = ALPHABET[ (inBuff >>> 12) & 0x3f ];
+ destination[ destOffset + 2 ] = EQUALS_SIGN;
+ destination[ destOffset + 3 ] = EQUALS_SIGN;
+ return destination;
+
+ default:
+ return destination;
+ } // end switch
+ } // end encode3to4
+
+
+
+ /**
+ * Serializes an object and returns the Base64-encoded
+ * version of that serialized object. If the object
+ * cannot be serialized or there is another error,
+ * the method will return <tt>null</tt>.
+ * The object is not GZip-compressed before being encoded.
+ *
+ * @param serializableObject The object to encode
+ * @return The Base64-encoded object
+ * @since 1.4
+ */
+ public static String encodeObject( java.io.Serializable serializableObject )
+ {
+ return encodeObject( serializableObject, NO_OPTIONS );
+ } // end encodeObject
+
+
+
+ /**
+ * Serializes an object and returns the Base64-encoded
+ * version of that serialized object. If the object
+ * cannot be serialized or there is another error,
+ * the method will return <tt>null</tt>.
+ * <p>
+ * Valid options:<pre>
+ * GZIP: gzip-compresses object before encoding it.
+ * DONT_BREAK_LINES: don't break lines at 76 characters
+ * <i>Note: Technically, this makes your encoding non-compliant.</i>
+ * </pre>
+ * <p>
+ * Example: <code>encodeObject( myObj, Base64.GZIP )</code> or
+ * <p>
+ * Example: <code>encodeObject( myObj, Base64.GZIP | Base64.DONT_BREAK_LINES )</code>
+ *
+ * @param serializableObject The object to encode
+ * @param options Specified options
+ * @return The Base64-encoded object
+ * @see Base64#GZIP
+ * @see Base64#DONT_BREAK_LINES
+ * @since 2.0
+ */
+ public static String encodeObject( java.io.Serializable serializableObject, int options )
+ {
+ // Streams
+ java.io.ByteArrayOutputStream baos = null;
+ java.io.OutputStream b64os = null;
+ java.io.ObjectOutputStream oos = null;
+ java.util.zip.GZIPOutputStream gzos = null;
+
+ // Isolate options
+ int gzip = (options & GZIP);
+ int dontBreakLines = (options & DONT_BREAK_LINES);
+
+ try
+ {
+ // ObjectOutputStream -> (GZIP) -> Base64 -> ByteArrayOutputStream
+ baos = new java.io.ByteArrayOutputStream();
+ b64os = new Base64.OutputStream( baos, ENCODE | options );
+
+ // GZip?
+ if( gzip == GZIP )
+ {
+ gzos = new java.util.zip.GZIPOutputStream( b64os );
+ oos = new java.io.ObjectOutputStream( gzos );
+ } // end if: gzip
+ else
+ oos = new java.io.ObjectOutputStream( b64os );
+
+ oos.writeObject( serializableObject );
+ } // end try
+ catch( java.io.IOException e )
+ {
+ logger.error("Could not Base64 encode object");
+ return null;
+ } // end catch
+ finally
+ {
+ try{ oos.close(); } catch( Exception e ){logger.error("", e);}
+ } // end finally
+
+ // Return value according to relevant encoding.
+ try
+ {
+ return new String( baos.toByteArray(), PREFERRED_ENCODING );
+ } // end try
+ catch (java.io.UnsupportedEncodingException uue)
+ {
+ return new String( baos.toByteArray() );
+ } // end catch
+
+ } // end encode
+
+
+
+ /**
+ * Encodes a byte array into Base64 notation.
+ * Does not GZip-compress data.
+ *
+ * @param source The data to convert
+ * @since 1.4
+ */
+ public static String encodeBytes( byte[] source )
+ {
+ return encodeBytes( source, 0, source.length, NO_OPTIONS );
+ } // end encodeBytes
+
+
+
+ /**
+ * Encodes a byte array into Base64 notation.
+ * <p>
+ * Valid options:<pre>
+ * GZIP: gzip-compresses object before encoding it.
+ * DONT_BREAK_LINES: don't break lines at 76 characters
+ * <i>Note: Technically, this makes your encoding non-compliant.</i>
+ * </pre>
+ * <p>
+ * Example: <code>encodeBytes( myData, Base64.GZIP )</code> or
+ * <p>
+ * Example: <code>encodeBytes( myData, Base64.GZIP | Base64.DONT_BREAK_LINES )</code>
+ *
+ *
+ * @param source The data to convert
+ * @param options Specified options
+ * @see Base64#GZIP
+ * @see Base64#DONT_BREAK_LINES
+ * @since 2.0
+ */
+ public static String encodeBytes( byte[] source, int options )
+ {
+ return encodeBytes( source, 0, source.length, options );
+ } // end encodeBytes
+
+
+ /**
+ * Encodes a byte array into Base64 notation.
+ * Does not GZip-compress data.
+ *
+ * @param source The data to convert
+ * @param off Offset in array where conversion should begin
+ * @param len Length of data to convert
+ * @since 1.4
+ */
+ public static String encodeBytes( byte[] source, int off, int len )
+ {
+ return encodeBytes( source, off, len, NO_OPTIONS );
+ } // end encodeBytes
+
+
+
+ /**
+ * Encodes a byte array into Base64 notation.
+ * <p>
+ * Valid options:<pre>
+ * GZIP: gzip-compresses object before encoding it.
+ * DONT_BREAK_LINES: don't break lines at 76 characters
+ * <i>Note: Technically, this makes your encoding non-compliant.</i>
+ * </pre>
+ * <p>
+ * Example: <code>encodeBytes( myData, Base64.GZIP )</code> or
+ * <p>
+ * Example: <code>encodeBytes( myData, Base64.GZIP | Base64.DONT_BREAK_LINES )</code>
+ *
+ *
+ * @param source The data to convert
+ * @param off Offset in array where conversion should begin
+ * @param len Length of data to convert
+ * @param options Specified options
+ * @param options alphabet type is pulled from this (standard, url-safe, ordered)
+ * @see Base64#GZIP
+ * @see Base64#DONT_BREAK_LINES
+ * @since 2.0
+ */
+ public static String encodeBytes( byte[] source, int off, int len, int options )
+ {
+ // Isolate options
+ int dontBreakLines = ( options & DONT_BREAK_LINES );
+ int gzip = ( options & GZIP );
+
+ // Compress?
+ if( gzip == GZIP )
+ {
+ java.io.ByteArrayOutputStream baos = null;
+ java.util.zip.GZIPOutputStream gzos = null;
+ Base64.OutputStream b64os = null;
+
+
+ try
+ {
+ // GZip -> Base64 -> ByteArray
+ baos = new java.io.ByteArrayOutputStream();
+ b64os = new Base64.OutputStream( baos, ENCODE | options );
+ gzos = new java.util.zip.GZIPOutputStream( b64os );
+
+ gzos.write( source, off, len );
+ gzos.close();
+ } // end try
+ catch( java.io.IOException e )
+ {
+ logger.error("Could not encode bytes", e);
+ return null;
+ } // end catch
+ finally
+ {
+ try{ gzos.close(); } catch( Exception e ){logger.error("", e);}
+ try{ b64os.close(); } catch( Exception e ){logger.error("", e);}
+ try{ baos.close(); } catch( Exception e ){logger.error("", e);}
+ } // end finally
+
+ // Return value according to relevant encoding.
+ try
+ {
+ return new String( baos.toByteArray(), PREFERRED_ENCODING );
+ } // end try
+ catch (java.io.UnsupportedEncodingException uue)
+ {
+ return new String( baos.toByteArray() );
+ } // end catch
+ } // end if: compress
+
+ // Else, don't compress. Better not to use streams at all then.
+ else
+ {
+ // Convert option to boolean in way that code likes it.
+ boolean breakLines = dontBreakLines == 0;
+
+ int len43 = len * 4 / 3;
+ byte[] outBuff = new byte[ ( len43 ) // Main 4:3
+ + ( (len % 3) > 0 ? 4 : 0 ) // Account for padding
+ + (breakLines ? ( len43 / MAX_LINE_LENGTH ) : 0) ]; // New lines
+ int d = 0;
+ int e = 0;
+ int len2 = len - 2;
+ int lineLength = 0;
+ for( ; d < len2; d+=3, e+=4 )
+ {
+ encode3to4( source, d+off, 3, outBuff, e, options );
+
+ lineLength += 4;
+ if( breakLines && lineLength == MAX_LINE_LENGTH )
+ {
+ outBuff[e+4] = NEW_LINE;
+ e++;
+ lineLength = 0;
+ } // end if: end of line
+ } // en dfor: each piece of array
+
+ if( d < len )
+ {
+ encode3to4( source, d+off, len - d, outBuff, e, options );
+ e += 4;
+ } // end if: some padding needed
+
+
+ // Return value according to relevant encoding.
+ try
+ {
+ return new String( outBuff, 0, e, PREFERRED_ENCODING );
+ } // end try
+ catch (java.io.UnsupportedEncodingException uue)
+ {
+ return new String( outBuff, 0, e );
+ } // end catch
+
+ } // end else: don't compress
+
+ } // end encodeBytes
+
+
+
+
+
+/* ******** D E C O D I N G M E T H O D S ******** */
+
+
+ /**
+ * Decodes four bytes from array <var>source</var>
+ * and writes the resulting bytes (up to three of them)
+ * to <var>destination</var>.
+ * The source and destination arrays can be manipulated
+ * anywhere along their length by specifying
+ * <var>srcOffset</var> and <var>destOffset</var>.
+ * This method does not check to make sure your arrays
+ * are large enough to accomodate <var>srcOffset</var> + 4 for
+ * the <var>source</var> array or <var>destOffset</var> + 3 for
+ * the <var>destination</var> array.
+ * This method returns the actual number of bytes that
+ * were converted from the Base64 encoding.
+ * <p>This is the lowest level of the decoding methods with
+ * all possible parameters.</p>
+ *
+ *
+ * @param source the array to convert
+ * @param srcOffset the index where conversion begins
+ * @param destination the array to hold the conversion
+ * @param destOffset the index where output will be put
+ * @param options alphabet type is pulled from this (standard, url-safe, ordered)
+ * @return the number of decoded bytes converted
+ * @since 1.3
+ */
+ private static int decode4to3( byte[] source, int srcOffset, byte[] destination, int destOffset, int options )
+ {
+ byte[] DECODABET = getDecodabet( options );
+
+ // Example: Dk==
+ if( source[ srcOffset + 2] == EQUALS_SIGN )
+ {
+ // Two ways to do the same thing. Don't know which way I like best.
+ //int outBuff = ( ( DECODABET[ source[ srcOffset ] ] << 24 ) >>> 6 )
+ // | ( ( DECODABET[ source[ srcOffset + 1] ] << 24 ) >>> 12 );
+ int outBuff = ( ( DECODABET[ source[ srcOffset ] ] & 0xFF ) << 18 )
+ | ( ( DECODABET[ source[ srcOffset + 1] ] & 0xFF ) << 12 );
+
+ destination[ destOffset ] = (byte)( outBuff >>> 16 );
+ return 1;
+ }
+
+ // Example: DkL=
+ else if( source[ srcOffset + 3 ] == EQUALS_SIGN )
+ {
+ // Two ways to do the same thing. Don't know which way I like best.
+ //int outBuff = ( ( DECODABET[ source[ srcOffset ] ] << 24 ) >>> 6 )
+ // | ( ( DECODABET[ source[ srcOffset + 1 ] ] << 24 ) >>> 12 )
+ // | ( ( DECODABET[ source[ srcOffset + 2 ] ] << 24 ) >>> 18 );
+ int outBuff = ( ( DECODABET[ source[ srcOffset ] ] & 0xFF ) << 18 )
+ | ( ( DECODABET[ source[ srcOffset + 1 ] ] & 0xFF ) << 12 )
+ | ( ( DECODABET[ source[ srcOffset + 2 ] ] & 0xFF ) << 6 );
+
+ destination[ destOffset ] = (byte)( outBuff >>> 16 );
+ destination[ destOffset + 1 ] = (byte)( outBuff >>> 8 );
+ return 2;
+ }
+
+ // Example: DkLE
+ else
+ {
+ try{
+ // Two ways to do the same thing. Don't know which way I like best.
+ //int outBuff = ( ( DECODABET[ source[ srcOffset ] ] << 24 ) >>> 6 )
+ // | ( ( DECODABET[ source[ srcOffset + 1 ] ] << 24 ) >>> 12 )
+ // | ( ( DECODABET[ source[ srcOffset + 2 ] ] << 24 ) >>> 18 )
+ // | ( ( DECODABET[ source[ srcOffset + 3 ] ] << 24 ) >>> 24 );
+ int outBuff = ( ( DECODABET[ source[ srcOffset ] ] & 0xFF ) << 18 )
+ | ( ( DECODABET[ source[ srcOffset + 1 ] ] & 0xFF ) << 12 )
+ | ( ( DECODABET[ source[ srcOffset + 2 ] ] & 0xFF ) << 6)
+ | ( ( DECODABET[ source[ srcOffset + 3 ] ] & 0xFF ) );
+
+
+ destination[ destOffset ] = (byte)( outBuff >> 16 );
+ destination[ destOffset + 1 ] = (byte)( outBuff >> 8 );
+ destination[ destOffset + 2 ] = (byte)( outBuff );
+
+ return 3;
+ }catch( Exception e){
+ logger.error(""+source[srcOffset]+ ": " + ( DECODABET[ source[ srcOffset ] ] ) , e);
+ logger.error(""+source[srcOffset+1]+ ": " + ( DECODABET[ source[ srcOffset + 1 ] ] ), e);
+ logger.error(""+source[srcOffset+2]+ ": " + ( DECODABET[ source[ srcOffset + 2 ] ] ), e);
+ logger.error(""+source[srcOffset+3]+ ": " + ( DECODABET[ source[ srcOffset + 3 ] ] ), e);
+ return -1;
+ } // end catch
+ }
+ } // end decodeToBytes
+
+
+
+
+ /**
+ * Very low-level access to decoding ASCII characters in
+ * the form of a byte array. Does not support automatically
+ * gunzipping or any other "fancy" features.
+ *
+ * @param source The Base64 encoded data
+ * @param off The offset of where to begin decoding
+ * @param len The length of characters to decode
+ * @return decoded data
+ * @since 1.3
+ */
+ public static byte[] decode( byte[] source, int off, int len, int options )
+ {
+ byte[] DECODABET = getDecodabet( options );
+
+ int len34 = len * 3 / 4;
+ byte[] outBuff = new byte[ len34 ]; // Upper limit on size of output
+ int outBuffPosn = 0;
+
+ byte[] b4 = new byte[4];
+ int b4Posn = 0;
+ int i = 0;
+ byte sbiCrop = 0;
+ byte sbiDecode = 0;
+ for( i = off; i < off+len; i++ )
+ {
+ sbiCrop = (byte)(source[i] & 0x7f); // Only the low seven bits
+ sbiDecode = DECODABET[ sbiCrop ];
+
+ if( sbiDecode >= WHITE_SPACE_ENC ) // White space, Equals sign or better
+ {
+ if( sbiDecode >= EQUALS_SIGN_ENC )
+ {
+ b4[ b4Posn++ ] = sbiCrop;
+ if( b4Posn > 3 )
+ {
+ outBuffPosn += decode4to3( b4, 0, outBuff, outBuffPosn, options );
+ b4Posn = 0;
+
+ // If that was the equals sign, break out of 'for' loop
+ if( sbiCrop == EQUALS_SIGN )
+ break;
+ } // end if: quartet built
+
+ } // end if: equals sign or better
+
+ } // end if: white space, equals sign or better
+ else
+ {
+ logger.error( "Bad Base64 input character at " + i + ": " + source[i] + "(decimal)" );
+ return null;
+ } // end else:
+ } // each input character
+
+ byte[] out = new byte[ outBuffPosn ];
+ System.arraycopy( outBuff, 0, out, 0, outBuffPosn );
+ return out;
+ } // end decode
+
+
+
+
+ /**
+ * Decodes data from Base64 notation, automatically
+ * detecting gzip-compressed data and decompressing it.
+ *
+ * @param s the string to decode
+ * @return the decoded data
+ * @since 1.4
+ */
+ public static byte[] decode( String s )
+ {
+ return decode( s, NO_OPTIONS );
+ }
+
+
+ /**
+ * Decodes data from Base64 notation, automatically
+ * detecting gzip-compressed data and decompressing it.
+ *
+ * @param s the string to decode
+ * @param options encode options such as URL_SAFE
+ * @return the decoded data
+ * @since 1.4
+ */
+ public static byte[] decode( String s, int options )
+ {
+ byte[] bytes;
+ try
+ {
+ bytes = s.getBytes( PREFERRED_ENCODING );
+ } // end try
+ catch( java.io.UnsupportedEncodingException uee )
+ {
+ bytes = s.getBytes();
+ } // end catch
+ //</change>
+
+ // Decode
+ bytes = decode( bytes, 0, bytes.length, options );
+
+
+ // Check to see if it's gzip-compressed
+ // GZIP Magic Two-Byte Number: 0x8b1f (35615)
+ if( bytes != null && bytes.length >= 4 )
+ {
+
+ int head = ((int)bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
+ if( java.util.zip.GZIPInputStream.GZIP_MAGIC == head )
+ {
+ java.io.ByteArrayInputStream bais = null;
+ java.util.zip.GZIPInputStream gzis = null;
+ java.io.ByteArrayOutputStream baos = null;
+ byte[] buffer = new byte[2048];
+ int length = 0;
+
+ try
+ {
+ baos = new java.io.ByteArrayOutputStream();
+ bais = new java.io.ByteArrayInputStream( bytes );
+ gzis = new java.util.zip.GZIPInputStream( bais );
+
+ while( ( length = gzis.read( buffer ) ) >= 0 )
+ {
+ baos.write(buffer,0,length);
+ } // end while: reading input
+
+ // No error? Get new bytes.
+ bytes = baos.toByteArray();
+
+ } // end try
+ catch( java.io.IOException e )
+ {
+ // Just return originally-decoded bytes
+ } // end catch
+ finally
+ {
+ try{ baos.close(); } catch( Exception e ){logger.error("", e);}
+ try{ gzis.close(); } catch( Exception e ){logger.error("", e);}
+ try{ bais.close(); } catch( Exception e ){logger.error("", e);}
+ } // end finally
+
+ } // end if: gzipped
+ } // end if: bytes.length >= 2
+
+ return bytes;
+ } // end decode
+
+
+
+
+ /**
+ * Attempts to decode Base64 data and deserialize a Java
+ * Object within. Returns <tt>null</tt> if there was an error.
+ *
+ * @param encodedObject The Base64 data to decode
+ * @return The decoded and deserialized object
+ * @since 1.5
+ */
+ public static Object decodeToObject( String encodedObject )
+ {
+ // Decode and gunzip if necessary
+ byte[] objBytes = decode( encodedObject );
+
+ java.io.ByteArrayInputStream bais = null;
+ java.io.ObjectInputStream ois = null;
+ Object obj = null;
+
+ try
+ {
+ bais = new java.io.ByteArrayInputStream( objBytes );
+ ois = new java.io.ObjectInputStream( bais );
+
+ obj = ois.readObject();
+ } // end try
+ catch( java.io.IOException e )
+ {
+ logger.error("Could not decode Base64 object", e);
+ obj = null;
+ } // end catch
+ catch( java.lang.ClassNotFoundException e )
+ {
+ logger.error("Could not decode Base64 object", e);
+ obj = null;
+ } // end catch
+ finally
+ {
+ try{ bais.close(); } catch( Exception e ){logger.error("", e);}
+ try{ ois.close(); } catch( Exception e ){logger.error("", e);}
+ } // end finally
+
+ return obj;
+ } // end decodeObject
+
+
+
+ /**
+ * Convenience method for encoding data to a file.
+ *
+ * @param dataToEncode byte array of data to encode in base64 form
+ * @param filename Filename for saving encoded data
+ * @return <tt>true</tt> if successful, <tt>false</tt> otherwise
+ *
+ * @since 2.1
+ */
+ public static boolean encodeToFile( byte[] dataToEncode, String filename )
+ {
+ boolean success = false;
+ Base64.OutputStream bos = null;
+ try
+ {
+ bos = new Base64.OutputStream(
+ new java.io.FileOutputStream( filename ), Base64.ENCODE );
+ bos.write( dataToEncode );
+ success = true;
+ } // end try
+ catch( java.io.IOException e )
+ {
+
+ success = false;
+ } // end catch: IOException
+ finally
+ {
+ try{ bos.close(); } catch( Exception e ){logger.error("", e);}
+ } // end finally
+
+ return success;
+ } // end encodeToFile
+
+
+ /**
+ * Convenience method for decoding data to a file.
+ *
+ * @param dataToDecode Base64-encoded data as a string
+ * @param filename Filename for saving decoded data
+ * @return <tt>true</tt> if successful, <tt>false</tt> otherwise
+ *
+ * @since 2.1
+ */
+ public static boolean decodeToFile( String dataToDecode, String filename )
+ {
+ boolean success = false;
+ Base64.OutputStream bos = null;
+ try
+ {
+ bos = new Base64.OutputStream(
+ new java.io.FileOutputStream( filename ), Base64.DECODE );
+ bos.write( dataToDecode.getBytes( PREFERRED_ENCODING ) );
+ success = true;
+ } // end try
+ catch( java.io.IOException e )
+ {
+ success = false;
+ } // end catch: IOException
+ finally
+ {
+ try{ bos.close(); } catch( Exception e ){logger.error("", e);}
+ } // end finally
+
+ return success;
+ } // end decodeToFile
+
+
+
+
+ /**
+ * Convenience method for reading a base64-encoded
+ * file and decoding it.
+ *
+ * @param filename Filename for reading encoded data
+ * @return decoded byte array or null if unsuccessful
+ *
+ * @since 2.1
+ */
+ public static byte[] decodeFromFile( String filename )
+ {
+ byte[] decodedData = null;
+ Base64.InputStream bis = null;
+ try
+ {
+ // Set up some useful variables
+ java.io.File file = new java.io.File( filename );
+ byte[] buffer = null;
+ int length = 0;
+ int numBytes = 0;
+
+ // Check for size of file
+ if( file.length() > Integer.MAX_VALUE )
+ {
+ logger.error( "File is too big for this convenience method (" + file.length() + " bytes)." );
+ return null;
+ } // end if: file too big for int index
+ buffer = new byte[ (int)file.length() ];
+
+ // Open a stream
+ bis = new Base64.InputStream(
+ new java.io.BufferedInputStream(
+ new java.io.FileInputStream( file ) ), Base64.DECODE );
+
+ // Read until done
+ while( ( numBytes = bis.read( buffer, length, 4096 ) ) >= 0 )
+ length += numBytes;
+
+ // Save in a variable to return
+ decodedData = new byte[ length ];
+ System.arraycopy( buffer, 0, decodedData, 0, length );
+
+ } // end try
+ catch( java.io.IOException e )
+ {
+ logger.error( "Error decoding from file " + filename, e);
+ } // end catch: IOException
+ finally
+ {
+ try{ bis.close(); } catch( Exception e) {logger.error("", e);}
+ } // end finally
+
+ return decodedData;
+ } // end decodeFromFile
+
+
+
+ /**
+ * Convenience method for reading a binary file
+ * and base64-encoding it.
+ *
+ * @param filename Filename for reading binary data
+ * @return base64-encoded string or null if unsuccessful
+ *
+ * @since 2.1
+ */
+ public static String encodeFromFile( String filename )
+ {
+ String encodedData = null;
+ Base64.InputStream bis = null;
+ try
+ {
+ // Set up some useful variables
+ java.io.File file = new java.io.File( filename );
+ byte[] buffer = new byte[ Math.max((int)(file.length() * 1.4),40) ]; // Need max() for math on small files (v2.2.1)
+ int length = 0;
+ int numBytes = 0;
+
+ // Open a stream
+ bis = new Base64.InputStream(
+ new java.io.BufferedInputStream(
+ new java.io.FileInputStream( file ) ), Base64.ENCODE );
+
+ // Read until done
+ while( ( numBytes = bis.read( buffer, length, 4096 ) ) >= 0 )
+ length += numBytes;
+
+ // Save in a variable to return
+ encodedData = new String( buffer, 0, length, Base64.PREFERRED_ENCODING );
+
+ } // end try
+ catch( java.io.IOException e )
+ {
+ logger.error( "Error encoding from file " + filename, e);
+ } // end catch: IOException
+ finally
+ {
+ try{ bis.close(); } catch( Exception e) {logger.error("", e);}
+ } // end finally
+
+ return encodedData;
+ } // end encodeFromFile
+
+
+
+
+ /**
+ * Reads <tt>infile</tt> and encodes it to <tt>outfile</tt>.
+ *
+ * @param infile Input file
+ * @param outfile Output file
+ * @return true if the operation is successful
+ * @since 2.2
+ */
+ public static boolean encodeFileToFile( String infile, String outfile )
+ {
+ boolean success = false;
+ java.io.InputStream in = null;
+ java.io.OutputStream out = null;
+ try{
+ in = new Base64.InputStream(
+ new java.io.BufferedInputStream(
+ new java.io.FileInputStream( infile ) ),
+ Base64.ENCODE );
+ out = new java.io.BufferedOutputStream( new java.io.FileOutputStream( outfile ) );
+ byte[] buffer = new byte[65536]; // 64K
+ int read = -1;
+ while( ( read = in.read(buffer) ) >= 0 ){
+ out.write( buffer,0,read );
+ } // end while: through file
+ success = true;
+ } catch( java.io.IOException exc ){
+ logger.error("Could not encode Base64 file", exc);
+ } finally{
+ try{ in.close(); } catch( Exception exc ){logger.error("", exc);}
+ try{ out.close(); } catch( Exception exc ){logger.error("", exc);}
+ } // end finally
+
+ return success;
+ } // end encodeFileToFile
+
+
+
+ /**
+ * Reads <tt>infile</tt> and decodes it to <tt>outfile</tt>.
+ *
+ * @param infile Input file
+ * @param outfile Output file
+ * @return true if the operation is successful
+ * @since 2.2
+ */
+ public static boolean decodeFileToFile( String infile, String outfile )
+ {
+ boolean success = false;
+ java.io.InputStream in = null;
+ java.io.OutputStream out = null;
+ try{
+ in = new Base64.InputStream(
+ new java.io.BufferedInputStream(
+ new java.io.FileInputStream( infile ) ),
+ Base64.DECODE );
+ out = new java.io.BufferedOutputStream( new java.io.FileOutputStream( outfile ) );
+ byte[] buffer = new byte[65536]; // 64K
+ int read = -1;
+ while( ( read = in.read(buffer) ) >= 0 ){
+ out.write( buffer,0,read );
+ } // end while: through file
+ success = true;
+ } catch( java.io.IOException exc ){
+ logger.error("Could not decode Base64 file", exc);
+ } finally{
+ try{ in.close(); } catch( Exception exc ){logger.error("", exc);}
+ try{ out.close(); } catch( Exception exc ){logger.error("", exc);}
+ } // end finally
+
+ return success;
+ } // end decodeFileToFile
+
+
+ /* ******** I N N E R C L A S S I N P U T S T R E A M ******** */
+
+
+
+ /**
+ * A {@link Base64.InputStream} will read data from another
+ * <tt>java.io.InputStream</tt>, given in the constructor,
+ * and encode/decode to/from Base64 notation on the fly.
+ *
+ * @see Base64
+ * @since 1.3
+ */
+ public static class InputStream extends java.io.FilterInputStream
+ {
+ private boolean encode; // Encoding or decoding
+ private int position; // Current position in the buffer
+ private byte[] buffer; // Small buffer holding converted data
+ private int bufferLength; // Length of buffer (3 or 4)
+ private int numSigBytes; // Number of meaningful bytes in the buffer
+ private int lineLength;
+ private boolean breakLines; // Break lines at less than 80 characters
+ private int options; // Record options used to create the stream.
+ private byte[] alphabet; // Local copies to avoid extra method calls
+ private byte[] decodabet; // Local copies to avoid extra method calls
+
+
+ /**
+ * Constructs a {@link Base64.InputStream} in DECODE mode.
+ *
+ * @param in the <tt>java.io.InputStream</tt> from which to read data.
+ * @since 1.3
+ */
+ public InputStream( java.io.InputStream in )
+ {
+ this( in, DECODE );
+ } // end constructor
+
+
+ /**
+ * Constructs a {@link Base64.InputStream} in
+ * either ENCODE or DECODE mode.
+ * <p>
+ * Valid options:<pre>
+ * ENCODE or DECODE: Encode or Decode as data is read.
+ * DONT_BREAK_LINES: don't break lines at 76 characters
+ * (only meaningful when encoding)
+ * <i>Note: Technically, this makes your encoding non-compliant.</i>
+ * </pre>
+ * <p>
+ * Example: <code>new Base64.InputStream( in, Base64.DECODE )</code>
+ *
+ *
+ * @param in the <tt>java.io.InputStream</tt> from which to read data.
+ * @param options Specified options
+ * @see Base64#ENCODE
+ * @see Base64#DECODE
+ * @see Base64#DONT_BREAK_LINES
+ * @since 2.0
+ */
+ public InputStream( java.io.InputStream in, int options )
+ {
+ super( in );
+ this.breakLines = (options & DONT_BREAK_LINES) != DONT_BREAK_LINES;
+ this.encode = (options & ENCODE) == ENCODE;
+ this.bufferLength = encode ? 4 : 3;
+ this.buffer = new byte[ bufferLength ];
+ this.position = -1;
+ this.lineLength = 0;
+ this.options = options; // Record for later, mostly to determine which alphabet to use
+ this.alphabet = getAlphabet(options);
+ this.decodabet = getDecodabet(options);
+ } // end constructor
+
+ /**
+ * Reads enough of the input stream to convert
+ * to/from Base64 and returns the next byte.
+ *
+ * @return next byte
+ * @since 1.3
+ */
+ public int read() throws java.io.IOException
+ {
+ // Do we need to get data?
+ if( position < 0 )
+ {
+ if( encode )
+ {
+ byte[] b3 = new byte[3];
+ int numBinaryBytes = 0;
+ for( int i = 0; i < 3; i++ )
+ {
+ try
+ {
+ int b = in.read();
+
+ // If end of stream, b is -1.
+ if( b >= 0 )
+ {
+ b3[i] = (byte)b;
+ numBinaryBytes++;
+ } // end if: not end of stream
+
+ } // end try: read
+ catch( java.io.IOException e )
+ {
+ // Only a problem if we got no data at all.
+ if( i == 0 )
+ throw e;
+
+ } // end catch
+ } // end for: each needed input byte
+
+ if( numBinaryBytes > 0 )
+ {
+ encode3to4( b3, 0, numBinaryBytes, buffer, 0, options );
+ position = 0;
+ numSigBytes = 4;
+ } // end if: got data
+ else
+ {
+ return -1;
+ } // end else
+ } // end if: encoding
+
+ // Else decoding
+ else
+ {
+ byte[] b4 = new byte[4];
+ int i = 0;
+ for( i = 0; i < 4; i++ )
+ {
+ // Read four "meaningful" bytes:
+ int b = 0;
+ do{ b = in.read(); }
+ while( b >= 0 && decodabet[ b & 0x7f ] <= WHITE_SPACE_ENC );
+
+ if( b < 0 )
+ break; // Reads a -1 if end of stream
+
+ b4[i] = (byte)b;
+ } // end for: each needed input byte
+
+ if( i == 4 )
+ {
+ numSigBytes = decode4to3( b4, 0, buffer, 0, options );
+ position = 0;
+ } // end if: got four characters
+ else if( i == 0 ){
+ return -1;
+ } // end else if: also padded correctly
+ else
+ {
+ // Must have broken out from above.
+ throw new java.io.IOException( "Improperly padded Base64 input." );
+ } // end
+
+ } // end else: decode
+ } // end else: get data
+
+ // Got data?
+ if( position >= 0 )
+ {
+ // End of relevant data?
+ if( /*!encode &&*/ position >= numSigBytes )
+ return -1;
+
+ if( encode && breakLines && lineLength >= MAX_LINE_LENGTH )
+ {
+ lineLength = 0;
+ return '\n';
+ } // end if
+ else
+ {
+ lineLength++; // This isn't important when decoding
+ // but throwing an extra "if" seems
+ // just as wasteful.
+
+ int b = buffer[ position++ ];
+
+ if( position >= bufferLength )
+ position = -1;
+
+ return b & 0xFF; // This is how you "cast" a byte that's
+ // intended to be unsigned.
+ } // end else
+ } // end if: position >= 0
+
+ // Else error
+ else
+ {
+ // When JDK1.4 is more accepted, use an assertion here.
+ throw new java.io.IOException( "Error in Base64 code reading stream." );
+ } // end else
+ } // end read
+
+
+ /**
+ * Calls {@link #read()} repeatedly until the end of stream
+ * is reached or <var>len</var> bytes are read.
+ * Returns number of bytes read into array or -1 if
+ * end of stream is encountered.
+ *
+ * @param dest array to hold values
+ * @param off offset for array
+ * @param len max number of bytes to read into array
+ * @return bytes read into array or -1 if end of stream is encountered.
+ * @since 1.3
+ */
+ public int read( byte[] dest, int off, int len ) throws java.io.IOException
+ {
+ int i;
+ int b;
+ for( i = 0; i < len; i++ )
+ {
+ b = read();
+
+ //if( b < 0 && i == 0 )
+ // return -1;
+
+ if( b >= 0 )
+ dest[off + i] = (byte)b;
+ else if( i == 0 )
+ return -1;
+ else
+ break; // Out of 'for' loop
+ } // end for: each byte read
+ return i;
+ } // end read
+
+ } // end inner class InputStream
+
+
+
+
+
+
+ /* ******** I N N E R C L A S S O U T P U T S T R E A M ******** */
+
+
+
+ /**
+ * A {@link Base64.OutputStream} will write data to another
+ * <tt>java.io.OutputStream</tt>, given in the constructor,
+ * and encode/decode to/from Base64 notation on the fly.
+ *
+ * @see Base64
+ * @since 1.3
+ */
+ public static class OutputStream extends java.io.FilterOutputStream
+ {
+ private boolean encode;
+ private int position;
+ private byte[] buffer;
+ private int bufferLength;
+ private int lineLength;
+ private boolean breakLines;
+ private byte[] b4; // Scratch used in a few places
+ private boolean suspendEncoding;
+ private int options; // Record for later
+ private byte[] alphabet; // Local copies to avoid extra method calls
+ private byte[] decodabet; // Local copies to avoid extra method calls
+
+ /**
+ * Constructs a {@link Base64.OutputStream} in ENCODE mode.
+ *
+ * @param out the <tt>java.io.OutputStream</tt> to which data will be written.
+ * @since 1.3
+ */
+ public OutputStream( java.io.OutputStream out )
+ {
+ this( out, ENCODE );
+ } // end constructor
+
+
+ /**
+ * Constructs a {@link Base64.OutputStream} in
+ * either ENCODE or DECODE mode.
+ * <p>
+ * Valid options:<pre>
+ * ENCODE or DECODE: Encode or Decode as data is read.
+ * DONT_BREAK_LINES: don't break lines at 76 characters
+ * (only meaningful when encoding)
+ * <i>Note: Technically, this makes your encoding non-compliant.</i>
+ * </pre>
+ * <p>
+ * Example: <code>new Base64.OutputStream( out, Base64.ENCODE )</code>
+ *
+ * @param out the <tt>java.io.OutputStream</tt> to which data will be written.
+ * @param options Specified options.
+ * @see Base64#ENCODE
+ * @see Base64#DECODE
+ * @see Base64#DONT_BREAK_LINES
+ * @since 1.3
+ */
+ public OutputStream( java.io.OutputStream out, int options )
+ {
+ super( out );
+ this.breakLines = (options & DONT_BREAK_LINES) != DONT_BREAK_LINES;
+ this.encode = (options & ENCODE) == ENCODE;
+ this.bufferLength = encode ? 3 : 4;
+ this.buffer = new byte[ bufferLength ];
+ this.position = 0;
+ this.lineLength = 0;
+ this.suspendEncoding = false;
+ this.b4 = new byte[4];
+ this.options = options;
+ this.alphabet = getAlphabet(options);
+ this.decodabet = getDecodabet(options);
+ } // end constructor
+
+
+ /**
+ * Writes the byte to the output stream after
+ * converting to/from Base64 notation.
+ * When encoding, bytes are buffered three
+ * at a time before the output stream actually
+ * gets a write() call.
+ * When decoding, bytes are buffered four
+ * at a time.
+ *
+ * @param theByte the byte to write
+ * @since 1.3
+ */
+ public void write(int theByte) throws java.io.IOException
+ {
+ // Encoding suspended?
+ if( suspendEncoding )
+ {
+ super.out.write( theByte );
+ return;
+ } // end if: supsended
+
+ // Encode?
+ if( encode )
+ {
+ buffer[ position++ ] = (byte)theByte;
+ if( position >= bufferLength ) // Enough to encode.
+ {
+ out.write( encode3to4( b4, buffer, bufferLength, options ) );
+
+ lineLength += 4;
+ if( breakLines && lineLength >= MAX_LINE_LENGTH )
+ {
+ out.write( NEW_LINE );
+ lineLength = 0;
+ } // end if: end of line
+
+ position = 0;
+ } // end if: enough to output
+ } // end if: encoding
+
+ // Else, Decoding
+ else
+ {
+ // Meaningful Base64 character?
+ if( decodabet[ theByte & 0x7f ] > WHITE_SPACE_ENC )
+ {
+ buffer[ position++ ] = (byte)theByte;
+ if( position >= bufferLength ) // Enough to output.
+ {
+ int len = Base64.decode4to3( buffer, 0, b4, 0, options );
+ out.write( b4, 0, len );
+ //out.write( Base64.decode4to3( buffer ) );
+ position = 0;
+ } // end if: enough to output
+ } // end if: meaningful base64 character
+ else if( decodabet[ theByte & 0x7f ] != WHITE_SPACE_ENC )
+ {
+ throw new java.io.IOException( "Invalid character in Base64 data." );
+ } // end else: not white space either
+ } // end else: decoding
+ } // end write
+
+
+
+ /**
+ * Calls {@link #write(int)} repeatedly until <var>len</var>
+ * bytes are written.
+ *
+ * @param theBytes array from which to read bytes
+ * @param off offset for array
+ * @param len max number of bytes to read into array
+ * @since 1.3
+ */
+ public void write( byte[] theBytes, int off, int len ) throws java.io.IOException
+ {
+ // Encoding suspended?
+ if( suspendEncoding )
+ {
+ super.out.write( theBytes, off, len );
+ return;
+ } // end if: supsended
+
+ for( int i = 0; i < len; i++ )
+ {
+ write( theBytes[ off + i ] );
+ } // end for: each byte written
+
+ } // end write
+
+
+
+ /**
+ * Method added by PHIL. [Thanks, PHIL. -Rob]
+ * This pads the buffer without closing the stream.
+ */
+ public void flushBase64() throws java.io.IOException
+ {
+ if( position > 0 )
+ {
+ if( encode )
+ {
+ out.write( encode3to4( b4, buffer, position, options ) );
+ position = 0;
+ } // end if: encoding
+ else
+ {
+ throw new java.io.IOException( "Base64 input not properly padded." );
+ } // end else: decoding
+ } // end if: buffer partially full
+
+ } // end flush
+
+
+ /**
+ * Flushes and closes (I think, in the superclass) the stream.
+ *
+ * @since 1.3
+ */
+ public void close() throws java.io.IOException
+ {
+ // 1. Ensure that pending characters are written
+ flushBase64();
+
+ // 2. Actually close the stream
+ // Base class both flushes and closes.
+ super.close();
+
+ buffer = null;
+ out = null;
+ } // end close
+
+
+
+ /**
+ * Suspends encoding of the stream.
+ * May be helpful if you need to embed a piece of
+ * base640-encoded data in a stream.
+ *
+ * @since 1.5.1
+ */
+ public void suspendEncoding() throws java.io.IOException
+ {
+ flushBase64();
+ this.suspendEncoding = true;
+ } // end suspendEncoding
+
+
+ /**
+ * Resumes encoding of the stream.
+ * May be helpful if you need to embed a piece of
+ * base640-encoded data in a stream.
+ *
+ * @since 1.5.1
+ */
+ public void resumeEncoding()
+ {
+ this.suspendEncoding = false;
+ } // end resumeEncoding
+
+
+
+ } // end inner class OutputStream
+
+
+} // end class Base64
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Comment.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Comment.java
new file mode 100644
index 0000000..c5d9101
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Comment.java
@@ -0,0 +1,141 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import java.text.DateFormat;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class Comment extends Resource {
+ private User user;
+ private String comment;
+ private int typeOfCommentedResource;
+ private String uriOfCommetedResource;
+
+ public Comment() {
+ super();
+ this.setItemType(Resource.COMMENT);
+ }
+
+ public User getUser() {
+ return (this.user);
+ }
+
+ public void setUser(User user) {
+ this.user = user;
+ }
+
+ public String getComment() {
+ return (this.comment);
+ }
+
+ public void setComment(String comment) {
+ this.comment = comment;
+ }
+
+ public int getTypeOfCommentedResource() {
+ return (this.typeOfCommentedResource);
+ }
+
+ public void setTypeOfCommentedResource(int typeOfCommentedResource) {
+ this.typeOfCommentedResource = typeOfCommentedResource;
+ }
+
+ public String getURIOfCommentedResource() {
+ return (this.uriOfCommetedResource);
+ }
+
+ public void setURIOfCommentedResource(String uriOfCommetedResource) {
+ this.uriOfCommetedResource = uriOfCommetedResource;
+ }
+
+ /**
+ * A helper method to return a set of API elements that are needed to satisfy
+ * request of a particular type - e.g. creating a listing of resources or
+ * populating full preview, etc.
+ *
+ * @param iRequestType
+ * A constant value from Resource class.
+ * @return Comma-separated string containing values of required API elements.
+ */
+ public static String getRequiredAPIElements(int iRequestType) {
+ String strElements = "";
+
+ // cases higher up in the list are supersets of those that come below -
+ // hence no "break" statements are required, because 'falling through' the
+ // switch statement is the desired behaviour in this case
+ switch (iRequestType) {
+ case Resource.REQUEST_DEFAULT_FROM_API:
+ strElements += ""; // no change needed - defaults will be used
+ }
+
+ return (strElements);
+ }
+
+ //class method to build a comment instance from XML
+ public static Comment buildFromXML(Document doc, Logger logger) {
+ // if no XML was supplied, return null to indicate an error
+ if (doc == null)
+ return (null);
+
+ Comment c = new Comment();
+
+ try {
+ Element root = doc.getRootElement();
+
+ c.setResource(root.getAttributeValue("resource"));
+ c.setURI(root.getAttributeValue("uri"));
+
+ c.setTitle(root.getChildText("comment"));
+ c.setComment(root.getChildText("comment"));
+
+ Element commentedResourceElement = root.getChild("subject");
+ if (commentedResourceElement != null) {
+ c.setTypeOfCommentedResource(Resource.getResourceTypeFromVisibleName(commentedResourceElement.getName()));
+ c.setURIOfCommentedResource(commentedResourceElement.getAttributeValue("uri"));
+ }
+
+ Element userElement = root.getChild("author");
+ c.setUser(Util.instantiatePrimitiveUserFromElement(userElement));
+
+ String createdAt = root.getChildText("created-at");
+ if (createdAt != null && !createdAt.equals("")) {
+ c.setCreatedAt(MyExperimentClient.parseDate(createdAt));
+ }
+
+ logger.debug("Found information for comment with ID: " + c.getID()
+ + ", URI: " + c.getURI());
+ } catch (Exception e) {
+ logger.error("Failed midway through creating comment object from XML", e);
+ }
+
+ // return created comment instance
+ return (c);
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/File.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/File.java
new file mode 100644
index 0000000..83853ee
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/File.java
@@ -0,0 +1,237 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import java.text.DateFormat;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class File extends Resource {
+ private int accessType;
+
+ private User uploader;
+ private License license;
+ private String filename;
+ private String visibleType;
+ private String contentType;
+ private List<Tag> tags;
+ private List<Comment> comments;
+ private List<Resource> credits;
+ private List<Resource> attributions;
+
+ public File() {
+ super();
+ this.setItemType(Resource.FILE);
+ }
+
+ public int getAccessType() {
+ return this.accessType;
+ }
+
+ public void setAccessType(int accessType) {
+ this.accessType = accessType;
+ }
+
+ public List<Tag> getTags() {
+ return tags;
+ }
+
+ public User getUploader() {
+ return uploader;
+ }
+
+ public void setUploader(User uploader) {
+ this.uploader = uploader;
+ }
+
+ public License getLicense() {
+ return license;
+ }
+
+ public void setLicense(License license) {
+ this.license = license;
+ }
+
+ public String getFilename() {
+ return this.filename;
+ }
+
+ public void setFilename(String filename) {
+ this.filename = filename;
+ }
+
+ public String getContentType() {
+ return contentType;
+ }
+
+ public void setContentType(String contentType) {
+ this.contentType = contentType;
+ }
+
+ public String getVisibleType() {
+ return this.visibleType;
+ }
+
+ public void setVisibleType(String visibleType) {
+ this.visibleType = visibleType;
+ }
+
+ public List<Comment> getComments() {
+ return this.comments;
+ }
+
+ public List<Resource> getCredits() {
+ return this.credits;
+ }
+
+ public List<Resource> getAttributions() {
+ return this.attributions;
+ }
+
+ /**
+ * A helper method to return a set of API elements that are needed to satisfy
+ * request of a particular type - e.g. creating a listing of resources or
+ * populating full preview, etc.
+ *
+ * @param iRequestType
+ * A constant value from Resource class.
+ * @return Comma-separated string containing values of required API elements.
+ */
+ public static String getRequiredAPIElements(int iRequestType) {
+ String strElements = "";
+
+ // cases higher up in the list are supersets of those that come below -
+ // hence no "break" statements are required, because 'falling through' the
+ // switch statement is the desired behaviour in this case
+ switch (iRequestType) {
+ case Resource.REQUEST_FULL_PREVIEW:
+ strElements += "filename,content-type,created-at,updated-at,"
+ + "license-type,tags,comments,credits,attributions,";
+ case Resource.REQUEST_FULL_LISTING:
+ strElements += "uploader,type,";
+ case Resource.REQUEST_SHORT_LISTING:
+ strElements += "id,title,description,privileges";
+ }
+
+ return (strElements);
+ }
+
+ public static File buildFromXML(Document doc, Logger logger) {
+ // if no XML document was supplied, return NULL
+ if (doc == null)
+ return (null);
+
+ // call main method which parses XML document starting from root element
+ return (File.buildFromXML(doc.getRootElement(), logger));
+ }
+
+ //class method to build a file instance from XML
+ public static File buildFromXML(Element docRootElement, Logger logger) {
+ // return null to indicate an error if XML document contains no root element
+ if (docRootElement == null)
+ return (null);
+
+ File f = new File();
+
+ try {
+ // Access type
+ f.setAccessType(Util.getAccessTypeFromXMLElement(docRootElement.getChild("privileges")));
+
+ // URI
+ f.setURI(docRootElement.getAttributeValue("uri"));
+
+ // Resource URI
+ f.setResource(docRootElement.getAttributeValue("resource"));
+
+ // Id
+ String id = docRootElement.getChildText("id");
+ if (id == null || id.equals("")) {
+ id = "API Error - No file ID supplied";
+ logger.error("Error while parsing file XML data - no ID provided for file with title: \""
+ + docRootElement.getChildText("title") + "\"");
+ }
+ f.setID(id);
+
+ // Filename
+ f.setFilename(docRootElement.getChildText("filename"));
+
+ // Title
+ f.setTitle(docRootElement.getChildText("title"));
+
+ // Description
+ f.setDescription(docRootElement.getChildText("description"));
+
+ // Uploader
+ Element uploaderElement = docRootElement.getChild("uploader");
+ f.setUploader(Util.instantiatePrimitiveUserFromElement(uploaderElement));
+
+ // Created at
+ String createdAt = docRootElement.getChildText("created-at");
+ if (createdAt != null && !createdAt.equals("")) {
+ f.setCreatedAt(MyExperimentClient.parseDate(createdAt));
+ }
+
+ // Updated at
+ String updatedAt = docRootElement.getChildText("updated-at");
+ if (updatedAt != null && !updatedAt.equals("")) {
+ f.setUpdatedAt(MyExperimentClient.parseDate(updatedAt));
+ }
+
+ // License
+ f.setLicense(License.getInstance(docRootElement.getChildText("license-type")));
+
+ // Type and Content-Type
+ f.setVisibleType(docRootElement.getChildText("type"));
+ f.setContentType(docRootElement.getChildText("content-type"));
+
+ // Tags
+ f.tags = new ArrayList<Tag>();
+ f.getTags().addAll(Util.retrieveTags(docRootElement));
+
+ // Comments
+ f.comments = new ArrayList<Comment>();
+ f.getComments().addAll(Util.retrieveComments(docRootElement, f));
+
+ // Credits
+ f.credits = new ArrayList<Resource>();
+ f.getCredits().addAll(Util.retrieveCredits(docRootElement));
+
+ // Attributions
+ f.attributions = new ArrayList<Resource>();
+ f.getAttributions().addAll(Util.retrieveAttributions(docRootElement));
+
+ logger.debug("Found information for file with ID: " + f.getID()
+ + ", Title: " + f.getTitle());
+ } catch (Exception e) {
+ logger.error("Failed midway through creating file object from XML", e);
+ }
+
+ // return created file instance
+ return (f);
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Group.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Group.java
new file mode 100644
index 0000000..fa4ac87
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Group.java
@@ -0,0 +1,222 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import java.text.DateFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.User;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class Group extends Resource
+{
+ private User admin;
+
+ private List<Tag> tags;
+ private List<Comment> comments;
+ private List<User> members;
+ private List<Resource> sharedItems;
+
+
+ public Group()
+ {
+ super();
+ this.setItemType(Resource.GROUP);
+ }
+
+ public User getAdmin() {
+ return admin;
+ }
+
+ public void setAdmin(User admin) {
+ this.admin = admin;
+ }
+
+ public List<Tag> getTags() {
+ return this.tags;
+ }
+
+ public List<Comment> getComments()
+ {
+ return this.comments;
+ }
+
+ public int getSharedItemCount()
+ {
+ return this.sharedItems.size();
+ }
+
+ public int getMemberCount()
+ {
+ return this.members.size();
+ }
+
+ public List<Resource> getSharedItems()
+ {
+ return this.sharedItems;
+ }
+
+ public List<User> getMembers()
+ {
+ return this.members;
+ }
+
+
+ /**
+ * A helper method to return a set of API elements that are
+ * needed to satisfy request of a particular type - e.g. creating
+ * a listing of resources or populating full preview, etc.
+ *
+ * @param iRequestType A constant value from Resource class.
+ * @return Comma-separated string containing values of required API elements.
+ */
+ public static String getRequiredAPIElements(int iRequestType)
+ {
+ String strElements = "";
+
+ // cases higher up in the list are supersets of those that come below -
+ // hence no "break" statements are required, because 'falling through' the
+ // switch statement is the desired behaviour in this case
+ switch (iRequestType) {
+ case Resource.REQUEST_FULL_PREVIEW:
+ strElements += "created-at,updated-at,members,shared-items,tags,comments,";
+ case Resource.REQUEST_FULL_LISTING:
+ strElements += "owner,";
+ case Resource.REQUEST_SHORT_LISTING:
+ strElements += "id,title,description";
+ }
+
+ return (strElements);
+ }
+
+
+ public static Group buildFromXML(Document doc, Logger logger)
+ {
+ // if no XML document was supplied, return NULL
+ if(doc == null) return(null);
+
+ // call main method which parses XML document starting from root element
+ return (Group.buildFromXML(doc.getRootElement(), logger));
+ }
+
+
+ //class method to build a group instance from XML
+ @SuppressWarnings("unchecked")
+ public static Group buildFromXML(Element docRootElement, Logger logger)
+ {
+ // return null to indicate an error if XML document contains no root element
+ if(docRootElement == null) return(null);
+
+ Group g = new Group();
+
+ try {
+ // URI
+ g.setURI(docRootElement.getAttributeValue("uri"));
+
+ // Resource URI
+ g.setResource(docRootElement.getAttributeValue("resource"));
+
+ // Id
+ String id = docRootElement.getChildText("id");
+ if (id == null || id.equals("")) {
+ id = "API Error - No group ID supplied";
+ logger.error("Error while parsing group XML data - no ID provided for group with title: \"" + docRootElement.getChildText("title") + "\"");
+ }
+ g.setID(Integer.parseInt(id));
+
+ // Title
+ g.setTitle(docRootElement.getChildText("title"));
+
+ // Description
+ g.setDescription(docRootElement.getChildText("description"));
+
+ // Owner
+ Element ownerElement = docRootElement.getChild("owner");
+ g.setAdmin(Util.instantiatePrimitiveUserFromElement(ownerElement));
+
+ // Created at
+ String createdAt = docRootElement.getChildText("created-at");
+ if (createdAt != null && !createdAt.equals("")) {
+ g.setCreatedAt(MyExperimentClient.parseDate(createdAt));
+ }
+
+ // Updated at
+ String updatedAt = docRootElement.getChildText("updated-at");
+ if (updatedAt != null && !updatedAt.equals("")) {
+ g.setUpdatedAt(MyExperimentClient.parseDate(updatedAt));
+ }
+
+
+ // Tags
+ g.tags = new ArrayList<Tag>();
+ g.getTags().addAll(Util.retrieveTags(docRootElement));
+
+ // Comments
+ g.comments = new ArrayList<Comment>();
+ g.getComments().addAll(Util.retrieveComments(docRootElement, g));
+
+ // Members
+ g.members = new ArrayList<User>();
+
+ Element membersElement = docRootElement.getChild("members");
+ if (membersElement != null) {
+ List<Element> memberNodes = membersElement.getChildren();
+ for (Element e : memberNodes) {
+ g.getMembers().add(Util.instantiatePrimitiveUserFromElement(e));
+ }
+ }
+ // sort the items after all items have been added
+ Collections.sort(g.getMembers());
+
+
+ // Shared Items
+ g.sharedItems = new ArrayList<Resource>();
+
+ Element sharedItemsElement = docRootElement.getChild("shared-items");
+ if (sharedItemsElement != null) {
+ List<Element> itemsNodes = sharedItemsElement.getChildren();
+ for (Element e : itemsNodes) {
+ g.getSharedItems().add(Util.instantiatePrimitiveResourceFromElement(e));
+ }
+ }
+ // sort the items after all items have been added
+ Collections.sort(g.getSharedItems());
+
+
+ logger.debug("Found information for group with ID: " + g.getID() + ", Title: " + g.getTitle());
+ }
+ catch (Exception e) {
+ logger.error("Failed midway through creating group object from XML", e);
+ }
+
+ // return created group instance
+ return(g);
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/License.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/License.java
new file mode 100644
index 0000000..25b44ae
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/License.java
@@ -0,0 +1,62 @@
+// Copyright (C) 2008 The University of Manchester, University of Southampton
+// and Cardiff University
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import java.io.Serializable;
+
+/*
+ * @author Jiten Bhagat, Emmanuel Tagarira
+ */
+public class License implements Serializable {
+ private String type;
+
+ private String text;
+
+ private String link;
+
+ public static String[] SUPPORTED_TYPES = { "by-nd", "by", "by-sa", "by-nc-nd", "by-nc", "by-nc-sa" };
+ public static String DEFAULT_LICENSE = "by-sa";
+
+ private License() {
+
+ }
+
+ private License(String type, String text, String link) {
+ this.type = type;
+ this.text = text;
+ this.link = link;
+ }
+
+ public String getType() {
+ return type;
+ }
+
+ public String getText() {
+ return text;
+ }
+
+ public String getLink() {
+ return link;
+ }
+
+ public static License getInstance(String type) {
+ if (type == null)
+ return null;
+
+ if (type.equalsIgnoreCase("by-nd")) {
+ return new License(type, "Creative Commons Attribution-NoDerivs 3.0 License", "http://creativecommons.org/licenses/by-nd/3.0/");
+ } else if (type.equalsIgnoreCase("by")) {
+ return new License(type, "Creative Commons Attribution 3.0 License", "http://creativecommons.org/licenses/by/3.0/");
+ } else if (type.equalsIgnoreCase("by-sa")) {
+ return new License(type, "Creative Commons Attribution-Share Alike 3.0 License", "http://creativecommons.org/licenses/by-sa/3.0/");
+ } else if (type.equalsIgnoreCase("by-nc-nd")) {
+ return new License(type, "Creative Commons Attribution-Noncommercial-NoDerivs 3.0 License", "http://creativecommons.org/licenses/by-nc-nd/3.0/");
+ } else if (type.equalsIgnoreCase("by-nc")) {
+ return new License(type, "Creative Commons Attribution-Noncommercial 3.0 License", "http://creativecommons.org/licenses/by-nc/3.0/");
+ } else if (type.equalsIgnoreCase("by-nc-sa")) {
+ return new License(type, "Creative Commons Attribution-Noncommercial-Share Alike 3.0 License", "http://creativecommons.org/licenses/by-nc-sa/3.0/");
+ } else {
+ return null;
+ }
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/MyExperimentClient.class b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/MyExperimentClient.class
new file mode 100644
index 0000000..0f243ee
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/MyExperimentClient.class
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/MyExperimentClient.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/MyExperimentClient.java
new file mode 100644
index 0000000..6449e95
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/MyExperimentClient.java
@@ -0,0 +1,1218 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import java.io.BufferedReader;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.UnsupportedEncodingException;
+import java.net.HttpURLConnection;
+import java.net.URI;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.text.DateFormat;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Locale;
+import java.util.Properties;
+import java.util.Set;
+
+import javax.swing.ImageIcon;
+import javax.swing.JOptionPane;
+
+import net.sf.taverna.raven.appconfig.ApplicationRuntime;
+import net.sf.taverna.t2.security.credentialmanager.CMException;
+import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
+import net.sf.taverna.t2.security.credentialmanager.UsernamePassword;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.MainComponent;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.MyExperimentPerspective;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.SearchEngine.QuerySearchInstance;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.input.SAXBuilder;
+import org.xml.sax.InputSource;
+
+/**
+ * @author Sergejs Aleksejevs, Emmanuel Tagarira, Jiten Bhagat
+ */
+public class MyExperimentClient {
+ // CONSTANTS
+ public static final String DEFAULT_BASE_URL = "http://www.myexperiment.org";
+ public static final String PLUGIN_USER_AGENT = "Taverna2-myExperiment-plugin/"
+ + MyExperimentPerspective.PLUGIN_VERSION
+ + " Java/"
+ + System.getProperty("java.version");
+ private static final String INI_FILE_NAME = "myexperiment-plugin.ini";
+
+ private static final int EXAMPLE_WORKFLOWS_PACK_ID = 254;
+
+ public static final String INI_BASE_URL = "my_experiment_base_url";
+ public static final String INI_AUTO_LOGIN = "auto_login";
+ public static final String INI_FAVOURITE_SEARCHES = "favourite_searches";
+ public static final String INI_SEARCH_HISTORY = "search_history";
+ public static final String INI_TAG_SEARCH_HISTORY = "tag_search_history";
+ public static final String INI_PREVIEWED_ITEMS_HISTORY = "previewed_items_history";
+ public static final String INI_OPENED_ITEMS_HISTORY = "opened_items_history";
+ public static final String INI_UPLOADED_ITEMS_HISTORY = "uploaded_items_history";
+ public static final String INI_DOWNLOADED_ITEMS_HISTORY = "downloaded_items_history";
+ public static final String INI_COMMENTED_ITEMS_HISTORY = "commented_items_history";
+ public static final String INI_DEFAULT_LOGGED_IN_TAB = "default_tab_for_logged_in_users";
+ public static final String INI_DEFAULT_ANONYMOUS_TAB = "default_tab_for_anonymous_users";
+ public static final String INI_MY_STUFF_WORKFLOWS = "show_workflows_in_my_stuff";
+ public static final String INI_MY_STUFF_FILES = "show_files_in_my_stuff";
+ public static final String INI_MY_STUFF_PACKS = "show_packs_in_my_stuff";
+
+ private final String DO_PUT = "_DO_UPDATE_SIGNAL_";
+
+ public static boolean baseChangedSinceLastStart = false;
+
+ // old format
+ private static final DateFormat OLD_DATE_FORMATTER = new SimpleDateFormat(
+ "EEE MMM dd HH:mm:ss Z yyyy", Locale.ENGLISH);
+ private static final DateFormat OLD_SHORT_DATE_FORMATTER = new SimpleDateFormat(
+ "HH:mm 'on' dd/MM/yyyy", Locale.ENGLISH);
+
+ // universal date formatter
+ private static final DateFormat NEW_DATE_FORMATTER = new SimpleDateFormat(
+ "yyyy-MM-dd HH:mm:ss Z");
+
+ // SETTINGS
+ private String BASE_URL; // myExperiment base URL to use
+ private java.io.File fIniFileDir; // a folder, where the INI file will be
+ // stored
+ private Properties iniSettings; // settings that are read/stored from/to INI
+ // file
+
+ // the logger
+ private Logger logger;
+
+ // authentication settings (and the current user)
+ private boolean LOGGED_IN = false;
+ private String AUTH_STRING = "";
+ private User current_user = null;
+
+ // default constructor
+ public MyExperimentClient() {
+ }
+
+ public MyExperimentClient(Logger logger) {
+ this();
+
+ this.logger = logger;
+
+ // === Load INI settings ===
+ // but loading settings from INI file, determine what folder is to be used
+ // for INI file
+ if (Util.isRunningInTaverna()) {
+ // running inside Taverna - use its folder to place the config file
+ this.fIniFileDir = new java.io.File(ApplicationRuntime.getInstance()
+ .getApplicationHomeDir(), "conf");
+ } else {
+ // running outside Taverna, place config file into the user's home
+ // directory
+ this.fIniFileDir = new java.io.File(System.getProperty("user.home"),
+ ".Taverna2-myExperiment Plugin");
+ }
+
+ // load preferences if the INI file exists
+ this.iniSettings = new Properties();
+ this.loadSettings();
+
+ // === Check if defaults should be applied to override not sensible settings
+ // from INI file ===
+ // verify that myExperiment BASE URL was read - use default otherwise
+ if (BASE_URL == null || BASE_URL.length() == 0)
+ BASE_URL = DEFAULT_BASE_URL;
+ this.iniSettings.put(INI_BASE_URL, BASE_URL); // store this to settings (if
+ // no changes were made - same as before, alternatively default URL)
+ }
+
+ // getter for the current status
+ public boolean isLoggedIn() {
+ return (LOGGED_IN);
+ }
+
+ public String getBaseURL() {
+ return this.BASE_URL;
+ }
+
+ public void setBaseURL(String baseURL) {
+ this.BASE_URL = baseURL;
+ }
+
+ // getter for the current user, if one is logged in to myExperiment
+ public User getCurrentUser() {
+ return (this.current_user);
+ }
+
+ // setter for the current user (the one that has logged in to myExperiment)
+ public void setCurrentUser(User user) {
+ this.current_user = user;
+ }
+
+ public Properties getSettings() {
+ return this.iniSettings;
+ }
+
+ // loads all plugin settings from the INI file
+ public synchronized void loadSettings() {
+ try {
+ // === READ SETTINGS ===
+ FileInputStream fIniInputStream = new FileInputStream(new java.io.File(
+ this.fIniFileDir, this.INI_FILE_NAME));
+ this.iniSettings.load(fIniInputStream);
+ fIniInputStream.close();
+
+ // set BASE_URL if from INI settings
+ this.BASE_URL = this.iniSettings.getProperty(INI_BASE_URL);
+
+ } catch (FileNotFoundException e) {
+ this.logger
+ .debug("myExperiment plugin INI file was not found, defaults will be used.");
+
+ } catch (IOException e) {
+ this.logger.error("Error on reading settings from INI file:\n" + e);
+ }
+ }
+
+ // writes all plugin settings to the INI file
+ private void storeSettings() {
+
+ // === STORE THE SETTINGS ===
+ try {
+ this.fIniFileDir.mkdirs();
+ FileOutputStream fIniOutputStream = new FileOutputStream(
+ new java.io.File(this.fIniFileDir, this.INI_FILE_NAME));
+ this.iniSettings.store(fIniOutputStream, "Test comment");
+ fIniOutputStream.close();
+ } catch (IOException e) {
+ this.logger.error("Error while trying to store settings to INI file:\n"
+ + e);
+ }
+
+ }
+
+ public void storeHistoryAndSettings() {
+ this.iniSettings.put(MyExperimentClient.INI_FAVOURITE_SEARCHES, Base64
+ .encodeObject(MainComponent.MAIN_COMPONENT.getSearchTab()
+ .getSearchFavouritesList()));
+ this.iniSettings.put(MyExperimentClient.INI_SEARCH_HISTORY, Base64
+ .encodeObject(MainComponent.MAIN_COMPONENT.getSearchTab()
+ .getSearchHistory()));
+ this.iniSettings.put(MyExperimentClient.INI_TAG_SEARCH_HISTORY, Base64
+ .encodeObject(MainComponent.MAIN_COMPONENT.getTagBrowserTab()
+ .getTagSearchHistory()));
+ this.iniSettings.put(MyExperimentClient.INI_PREVIEWED_ITEMS_HISTORY, Base64
+ .encodeObject(MainComponent.MAIN_COMPONENT.getPreviewBrowser()
+ .getPreviewHistory()));
+ this.iniSettings.put(MyExperimentClient.INI_DOWNLOADED_ITEMS_HISTORY,
+ Base64.encodeObject(MainComponent.MAIN_COMPONENT.getHistoryBrowser()
+ .getDownloadedItemsHistoryList()));
+ this.iniSettings.put(MyExperimentClient.INI_OPENED_ITEMS_HISTORY, Base64
+ .encodeObject(MainComponent.MAIN_COMPONENT.getHistoryBrowser()
+ .getOpenedItemsHistoryList()));
+ this.iniSettings.put(MyExperimentClient.INI_UPLOADED_ITEMS_HISTORY, Base64
+ .encodeObject(MainComponent.MAIN_COMPONENT.getHistoryBrowser()
+ .getUploadedItemsHistoryList()));
+ this.iniSettings.put(MyExperimentClient.INI_COMMENTED_ITEMS_HISTORY, Base64
+ .encodeObject(MainComponent.MAIN_COMPONENT.getHistoryBrowser()
+ .getCommentedOnItemsHistoryList()));
+
+ storeSettings();
+ }
+
+ private UsernamePassword getUserPass(String urlString) {
+ try {
+ URI userpassUrl = URI.create(urlString);
+ final UsernamePassword userAndPass = CredentialManager.getInstance().getUsernameAndPasswordForService(userpassUrl, true, null);
+ return userAndPass;
+ } catch (CMException e) {
+ throw new RuntimeException("Error in Taverna Credential Manager", e);
+ }
+ }
+
+ public boolean doLogin() {
+
+ // check if the stored credentials are valid
+ ServerResponse response = null;
+ Document doc = null;
+ try {
+// CredentialManager.getInstance().getUsernameAndPasswordForService(new URI(this.BASE_URL), true, null);
+ response = this.doMyExperimentGET(this.BASE_URL + "/whoami.xml");
+ } catch (Exception e) {
+ this.logger
+ .error("Error while attempting to verify login credentials from INI file:\n"
+ + e);
+ }
+
+
+ if (response.getResponseCode() == HttpURLConnection.HTTP_UNAUTHORIZED) {
+ try {
+ List<String> toDelete = CredentialManager.getInstance().getServiceURLsforAllUsernameAndPasswordPairs();
+ for (String uri : toDelete) {
+ if (uri.startsWith(BASE_URL)) {
+ CredentialManager.getInstance().deleteUsernameAndPasswordForService(uri);
+ }
+ }
+// CredentialManager.getInstance().resetAuthCache();
+ doc = null;
+ } catch (Exception e) {
+ logger.error(e);
+ }
+ } else {
+ doc = response.getResponseBody();
+ }
+
+ // verify outcomes
+ if (doc == null) {
+ // login credentials were invalid - revert to not logged in state and
+ // disable autologin function;
+ // stored credentials will be kept to allow the user to verify and edit
+ // them
+ // (login screen will be displayed as usual + an error message box will
+ // appear)
+ this.LOGGED_IN = false;
+ this.AUTH_STRING = "";
+ this.iniSettings.put(MyExperimentClient.INI_AUTO_LOGIN,
+ new Boolean(false).toString());
+
+ javax.swing.JOptionPane.showMessageDialog(null,
+ "Your myExperiment login details appear to be incorrect.\n"
+ + "Please check your details.");
+ return false;
+ } else {
+ UsernamePassword userPass = getUserPass(this.BASE_URL + "/whoami.xml");
+
+ if (userPass == null) {
+ return false;
+ }
+
+ // set the system to the "logged in" state from INI file properties
+ this.LOGGED_IN = true;
+ this.AUTH_STRING = Base64.encodeBytes((userPass.getUsername() + ":" + userPass.getPasswordAsString())
+ .getBytes());
+
+ // login credentials were verified successfully; load current user
+ String strCurrentUserURI = doc.getRootElement().getAttributeValue("uri");
+ try {
+ this.current_user = this.fetchCurrentUser(strCurrentUserURI);
+ this.logger
+ .debug("Logged in to myExperiment successfully with credentials that were loaded from INI file.");
+ return true;
+ } catch (Exception e) {
+ // this is highly unlikely because the login credentials were validated
+ // successfully just before this
+ this.logger.error("Couldn't fetch user data from myExperiment ("
+ + strCurrentUserURI
+ + ")", e);
+ return false;
+ }
+ }
+ }
+
+ // Simulates a "logout" action. Logging in and out in the plugin is only an
+ // abstraction created for user convenience; it is a purely virtual concept,
+ // because the
+ // myExperiment API is completely stateless - hence, logging out simply
+ // consists of "forgetting"
+ // the authentication details and updating the state.
+ public void doLogout() throws Exception {
+ LOGGED_IN = false;
+ AUTH_STRING = "";
+ }
+
+ /**
+ * Generic method to execute GET requests to myExperiment server.
+ *
+ * @param strURL
+ * The URL on myExperiment to issue GET request to.
+ * @return An object containing XML Document with server's response body and a
+ * response code. Response body XML document might be null if there
+ * was an error or the user wasn't authorised to perform a certain
+ * action. Response code will always be set.
+ * @throws Exception
+ */
+ public ServerResponse doMyExperimentGET(String strURL) throws Exception {
+ // open server connection using provided URL (with no modifications to it)
+ URL url = new URL(strURL);
+ HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+ conn.setRequestProperty("User-Agent", PLUGIN_USER_AGENT);
+ if (LOGGED_IN) {
+ // if the user has "logged in", also add authentication details
+ conn.setRequestProperty("Authorization", "Basic " + AUTH_STRING);
+ }
+
+ // check server's response
+ return (doMyExperimentReceiveServerResponse(conn, strURL, true));
+ }
+
+ /**
+ * Generic method to execute GET requests to myExperiment server.
+ *
+ * @param strURL
+ * The URL on myExperiment to POST to.
+ * @param strXMLDataBody
+ * Body of the XML data to be POSTed to strURL.
+ * @return An object containing XML Document with server's response body and a
+ * response code. Response body XML document might be null if there
+ * was an error or the user wasn't authorised to perform a certain
+ * action. Response code will always be set.
+ * @throws Exception
+ */
+ public ServerResponse doMyExperimentPOST(String strURL, String strXMLDataBody)
+ throws Exception {
+ // POSTing to myExperiment is only allowed for authorised users
+ if (!LOGGED_IN) return (null);
+
+ // open server connection using provided URL (with no modifications to it)
+ URL url = new URL(strURL);
+ HttpURLConnection urlConn = (HttpURLConnection) url.openConnection();
+
+ // "tune" the connection
+ urlConn.setRequestMethod((strURL.contains(DO_PUT) ? "PUT" : "POST"));
+ strURL = strURL.replace(DO_PUT, "");
+ urlConn.setDoOutput(true);
+ urlConn.setRequestProperty("Content-Type", "application/xml");
+ urlConn.setRequestProperty("User-Agent", PLUGIN_USER_AGENT);
+ urlConn.setRequestProperty("Authorization", "Basic " + AUTH_STRING);
+ // the last line wouldn't be executed if the user wasn't logged in (see
+ // above code), so safe to run
+
+ // prepare and PUT/POST XML data
+ String strPOSTContent = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
+ + strXMLDataBody;
+ OutputStreamWriter out = new OutputStreamWriter(urlConn.getOutputStream());
+ out.write(strPOSTContent);
+ out.close();
+
+ // check server's response
+ return (doMyExperimentReceiveServerResponse(urlConn, strURL, false));
+ }
+
+ /**
+ * Generic method to execute DELETE requests to myExperiment server. This is
+ * only to be called when a user is logged in.
+ *
+ * @param strURL
+ * The URL on myExperiment to direct DELETE request to.
+ * @return An object containing XML Document with server's response body and a
+ * response code. Response body XML document might be null if there
+ * was an error or the user wasn't authorised to perform a certain
+ * action. Response code will always be set.
+ * @throws Exception
+ */
+ public ServerResponse doMyExperimentDELETE(String strURL) throws Exception {
+ // open server connection using provided URL (with no modifications to it)
+ URL url = new URL(strURL);
+ HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+
+ // "tune" the connection
+ conn.setRequestMethod("DELETE");
+ conn.setRequestProperty("User-Agent", PLUGIN_USER_AGENT);
+ conn.setRequestProperty("Authorization", "Basic " + AUTH_STRING);
+
+ // check server's response
+ return (doMyExperimentReceiveServerResponse(conn, strURL, true));
+ }
+
+ /**
+ * A common method for retrieving myExperiment server's response for both GET
+ * and POST requests.
+ *
+ * @param conn
+ * Instance of the established URL connection to poll for server's
+ * response.
+ * @param strURL
+ * The URL on myExperiment with which the connection is established.
+ * @param bIsGetRequest
+ * Flag for identifying type of the request. True when the current
+ * connection executes GET request; false when it executes a POST
+ * request.
+ * @return An object containing XML Document with server's response body and a
+ * response code. Response body XML document might be null if there
+ * was an error or the user wasn't authorised to perform a certain
+ * action. Response code will always be set.
+ */
+ private ServerResponse doMyExperimentReceiveServerResponse(
+ HttpURLConnection conn, String strURL, boolean bIsGETRequest)
+ throws Exception {
+ int iResponseCode = conn.getResponseCode();
+
+ switch (iResponseCode) {
+ case HttpURLConnection.HTTP_OK:
+ // data retrieval was successful - parse the response XML and return it
+ // along with response code
+ BufferedReader reader = new BufferedReader(new InputStreamReader(conn
+ .getInputStream()));
+ Document doc = new SAXBuilder().build(new InputSource(reader));
+ reader.close();
+
+ return (new ServerResponse(iResponseCode, doc));
+
+ case HttpURLConnection.HTTP_BAD_REQUEST:
+ // this was a bad XML request - need full XML response to retrieve the
+ // error message from it;
+ // Java throws IOException if getInputStream() is used when non HTTP_OK
+ // response code was received -
+ // hence can use getErrorStream() straight away to fetch the error
+ // document
+ BufferedReader errorReader = new BufferedReader(new InputStreamReader(
+ conn.getErrorStream()));
+ Document errorDoc = new SAXBuilder()
+ .build(new InputSource(errorReader));
+ errorReader.close();
+
+ return (new ServerResponse(iResponseCode, errorDoc));
+
+ case HttpURLConnection.HTTP_UNAUTHORIZED:
+ // this content is not authorised for current user
+ return (new ServerResponse(iResponseCode, null));
+
+ default:
+ // unexpected response code - raise an exception
+ throw new IOException("Received unexpected HTTP response code ("
+ + conn.getResponseCode() + ") while "
+ + (bIsGETRequest ? "fetching data at " : "posting data to ")
+ + strURL);
+ }
+ }
+
+ // a method to fetch a user instance with full details (including avatar
+ // image)
+ public User fetchCurrentUser(String uri) {
+ // fetch user data
+ User user = null;
+ try {
+ Document doc = this.getResource(Resource.USER, uri,
+ Resource.REQUEST_FULL_PREVIEW);
+ user = User.buildFromXML(doc, logger);
+ } catch (Exception ex) {
+ logger.error("Failed to fetch user data from myExperiment (" + uri
+ + "); exception:\n" + ex);
+ }
+
+ // fetch the avatar
+ try {
+ if (user.getAvatarURI() == null) {
+ ImageIcon icon = new ImageIcon(user.getAvatarResource());
+ user.setAvatar(icon);
+ } else {
+ Document doc = this.doMyExperimentGET(user.getAvatarURI())
+ .getResponseBody();
+ user.setAvatar(doc);
+ }
+ } catch (Exception ex) {
+ logger.error("Failed to fetch user's avatar from myExperiment ("
+ + user.getAvatarURI() + "); exception:\n" + ex);
+ }
+
+ return (user);
+ }
+
+ /**
+ * Fetches resource data and returns an XML document containing it.
+ *
+ * @param iResourceType
+ * Type of the resource for which the XML data is to be fetched. This
+ * implies which elements are required to be selected.
+ * @param strURI
+ * URI of the resource in myExperiment API.
+ * @param iRequestType
+ * Determines the level of detail of data to be fetched from the API;
+ * constants for using in this field are defined in Resource class.
+ */
+ public Document getResource(int iResourceType, String strURI, int iRequestType)
+ throws Exception {
+ if (iRequestType == Resource.REQUEST_ALL_DATA) {
+ // it doesn't matter what kind of resource this is if all available data
+ // is requested anyway
+ strURI += "&all_elements=yes";
+ } else {
+ // only required metadata is to be fetched; this depends on the type of
+ // the resource
+ switch (iResourceType) {
+ case Resource.WORKFLOW:
+ strURI += "&elements="
+ + Workflow.getRequiredAPIElements(iRequestType);
+ break;
+ case Resource.FILE:
+ strURI += "&elements=" + File.getRequiredAPIElements(iRequestType);
+ break;
+ case Resource.PACK:
+ strURI += "&elements=" + Pack.getRequiredAPIElements(iRequestType);
+ break;
+ case Resource.PACK_INTERNAL_ITEM:
+ strURI += "&all_elements=yes"; // TODO determine which are required
+ // elements
+ break;
+ case Resource.PACK_EXTERNAL_ITEM:
+ strURI += "&all_elements=yes"; // TODO determine which are required
+ // elements
+ break;
+ case Resource.USER:
+ strURI += "&elements=" + User.getRequiredAPIElements(iRequestType);
+ break;
+ case Resource.GROUP:
+ strURI += "&elements=" + Group.getRequiredAPIElements(iRequestType);
+ break;
+ case Resource.TAG:
+ // this should set no elements, because default is desired at the
+ // moment -
+ // but even having "&elements=" with and empty string at the end will
+ // still
+ // retrieve default fields from the API
+ strURI += "&elements=" + Tag.getRequiredAPIElements(iRequestType);
+ break;
+ case Resource.COMMENT:
+ // this should set no elements, because default is desired at the
+ // moment - but even having "&elements=" with and empty string at the
+ // end will
+ // still retrieve default fields from the API
+ strURI += "&elements=" + Comment.getRequiredAPIElements(iRequestType);
+ break;
+ }
+ }
+
+ return (this.doMyExperimentGET(strURI).getResponseBody());
+ }
+
+ /**
+ * Fetches workflow data from myExperiment.
+ *
+ * @param strWorkflowURI
+ * URI of the workflow to be opened.
+ * @return Workflow instance containing only workflow data and content type.
+ */
+ public Workflow fetchWorkflowBinary(String strWorkflowURI) throws Exception {
+ // fetch workflows data
+ Document doc = this.getResource(Resource.WORKFLOW, strWorkflowURI,
+ Resource.REQUEST_WORKFLOW_CONTENT_ONLY);
+
+ // verify that the type of the workflow data is correct
+ Element root = doc.getRootElement();
+ Workflow w = new Workflow();
+ w.setVisibleType(root.getChildText("type"));
+ w.setContentType(root.getChildText("content-type"));
+
+ if (!w.isTavernaWorkflow()) { throw new Exception(
+ "Unsupported workflow type. Details:\nWorkflow type: "
+ + w.getVisibleType() + "\nMime type: " + w.getContentType()); }
+
+ // check that content encoding is correct
+ String strEncoding = root.getChild("content").getAttributeValue("encoding");
+ String strDataFormat = root.getChild("content").getAttributeValue("type");
+ if (!strEncoding.toLowerCase().equals("base64")
+ || !strDataFormat.toLowerCase().equals("binary")) { throw new Exception(
+ "Unsupported workflow data format. Details:\nContent encoding: "
+ + strEncoding + "\nFormat: " + strDataFormat); }
+
+ // all checks seem to be fine, decode workflow data
+ byte[] arrWorkflowData = Base64.decode(root.getChildText("content"));
+ w.setContent(arrWorkflowData);
+
+ return (w);
+ }
+
+ @SuppressWarnings("unchecked")
+ public List<Workflow> getExampleWorkflows() {
+ List<Workflow> workflows = new ArrayList<Workflow>();
+
+ try {
+ String strExampleWorkflowsPackUrl = this.BASE_URL + "/pack.xml?id="
+ + EXAMPLE_WORKFLOWS_PACK_ID + "&elements=internal-pack-items";
+ Document doc = this.doMyExperimentGET(strExampleWorkflowsPackUrl)
+ .getResponseBody();
+
+ if (doc != null) {
+ List<Element> allInternalItems = doc.getRootElement().getChild(
+ "internal-pack-items").getChildren("workflow");
+ for (Element e : allInternalItems) {
+ String itemUri = e.getAttributeValue("uri");
+ Document itemDoc = this.doMyExperimentGET(itemUri).getResponseBody();
+ String workflowUri = itemDoc.getRootElement().getChild("item")
+ .getChild("workflow").getAttributeValue("uri");
+ Document docCurWorkflow = this.getResource(Resource.WORKFLOW,
+ workflowUri, Resource.REQUEST_FULL_LISTING);
+ workflows.add(Workflow.buildFromXML(docCurWorkflow, this.logger));
+ }
+ }
+ } catch (Exception e) {
+ this.logger.error("Failed to retrieve example workflows", e);
+ }
+
+ logger.debug(workflows.size()
+ + " example workflows retrieved from myExperiment");
+
+ return (workflows);
+ }
+
+ @SuppressWarnings("unchecked")
+ public TagCloud getGeneralTagCloud(int size) {
+ TagCloud tcCloud = new TagCloud();
+
+ try {
+ // assemble tag cloud URL and fetch the XML document
+ String strTagCloudURL = BASE_URL + "/tag-cloud.xml?num="
+ + (size > 0 ? ("" + size) : "all");
+ Document doc = this.doMyExperimentGET(strTagCloudURL).getResponseBody();
+
+ // process all tags and add them to the cloud
+ if (doc != null) {
+ List<Element> nodes = doc.getRootElement().getChildren("tag");
+ for (Element e : nodes) {
+ Tag t = new Tag();
+ t.setTitle(e.getText());
+ t.setTagName(e.getText());
+ t.setResource(e.getAttributeValue("resource"));
+ t.setURI(e.getAttributeValue("uri"));
+ t.setCount(Integer.parseInt(e.getAttributeValue("count")));
+
+ tcCloud.getTags().add(t);
+ }
+ }
+ } catch (Exception e) {
+ this.logger.error("ERROR: Failed to get tag cloud.\n", e);
+ }
+
+ logger.debug("Tag cloud retrieval successful; fetched "
+ + tcCloud.getTags().size() + " tags from myExperiment");
+ return (tcCloud);
+ }
+
+ public TagCloud getUserTagCloud(User user, int size) {
+ TagCloud tcCloud = new TagCloud();
+
+ // iterate through all tags that the user has applied;
+ // fetch the title and the number of times that this tag
+ // was applied across myExperiment (e.g. overall popularity)
+ try {
+ // update user tags first (this happens concurrently with the other
+ // threads
+ // during the load time, hence needs to be synchronised properly)
+ synchronized (user.getTags()) {
+ user.getTags().clear();
+ Document doc = this.getResource(Resource.USER, user.getURI(),
+ Resource.REQUEST_USER_APPLIED_TAGS_ONLY);
+ Iterator<Element> iNewUserTags = doc.getRootElement().getChild(
+ "tags-applied").getChildren().iterator();
+ Util.getResourceCollectionFromXMLIterator(iNewUserTags, user.getTags());
+ }
+
+ // fetch additional required data about the tags
+ Iterator<HashMap<String, String>> iTagsResourcesHashMaps = user.getTags()
+ .iterator();
+ while (iTagsResourcesHashMaps.hasNext()) {
+ // get the tag object uri in myExperiment API
+ String strCurTagURI = iTagsResourcesHashMaps.next().get("uri");
+
+ // fetch tag data from myExperiment (namely, number of times that this
+ // tag was applied)
+ Document doc = this.doMyExperimentGET(strCurTagURI).getResponseBody();
+ Element root = doc.getRootElement();
+
+ // create the tag
+ Tag t = new Tag();
+ t.setTagName(root.getChild("name").getText());
+ t.setCount(Integer.parseInt(root.getChild("count").getText()));
+
+ tcCloud.getTags().add(t);
+ }
+
+ // a little preprocessing before tag selection - if "size" is set to 0, -1
+ // or any negative number, assume the request is for ALL user tags
+ if (size <= 0) size = tcCloud.getTags().size();
+
+ // sort the collection by popularity..
+ Comparator<Tag> byPopularity = new Tag.ReversePopularityComparator();
+ Collections.sort(tcCloud.getTags(), byPopularity);
+
+ // ..take top "size" elements
+ int iSelectedTags = 0;
+ List<Tag> tagListOfRequiredSize = new ArrayList<Tag>();
+ Iterator<Tag> iTags = tcCloud.getTags().iterator();
+ while (iTags.hasNext() && iSelectedTags < size) {
+ tagListOfRequiredSize.add(iTags.next());
+ iSelectedTags++;
+ }
+
+ // purge the original tag collection; add only selected tags to it;
+ // then sort back in alphabetical order again
+ tcCloud.getTags().clear();
+ tcCloud.getTags().addAll(tagListOfRequiredSize);
+ Comparator<Tag> byAlphabet = new Tag.AlphanumericComparator();
+ Collections.sort(tcCloud.getTags(), byAlphabet);
+ } catch (Exception e) {
+ logger.error("Failed midway through fetching user tags for user ID = "
+ + user.getID() + "\n" + e);
+ }
+
+ return (tcCloud);
+ }
+
+ /**
+ * A helper to fetch workflows, files or packs of a specific user. This will
+ * only make *one* request to the API, therefore it's faster than getting all
+ * the items one by one.
+ *
+ * @param user
+ * User instance for which the items are to be fetched.
+ * @param iResourceType
+ * One of Resource.WORKFLOW, Resource.FILE, Resource.PACK
+ * @param iRequestType
+ * Type of the request - i.e. amount of data to fetch. One of
+ * Resource.REQUEST_SHORT_LISTING, Resource.REQUEST_FULL_LISTING,
+ * Resource.REQUEST_FULL_PREVIEW, Resource.REQUEST_ALL_DATA.
+ * @return An XML document containing data about all items in the amount that
+ * was specified.
+ */
+ public Document getUserContributions(User user, int iResourceType,
+ int iRequestType, int page) {
+ Document doc = null;
+ String strURL = BASE_URL;
+ String strElements = "&elements=";
+
+ try {
+ // determine query parameters
+ switch (iResourceType) {
+ case Resource.WORKFLOW:
+ strURL += "/workflows.xml?uploader=";
+ strElements += Workflow.getRequiredAPIElements(iRequestType);
+ break;
+ case Resource.FILE:
+ strURL += "/files.xml?uploader=";
+ strElements += File.getRequiredAPIElements(iRequestType);
+ break;
+ case Resource.PACK:
+ strURL += "/packs.xml?owner=";
+ strElements += Workflow.getRequiredAPIElements(iRequestType);
+ break;
+ }
+
+ if (page != 0) {
+ strElements += "&num=100&page=" + page;
+ }
+
+ // create final query URL and retrieve data
+ strURL += MyExperimentClient.urlEncodeQuery(user.getResource())
+ + strElements;
+ doc = this.doMyExperimentGET(strURL).getResponseBody();
+ } catch (Exception e) {
+ logger.error("ERROR: Failed to fetch user's contributions.");
+ }
+
+ return (doc);
+ }
+
+ /**
+ * Queries myExperiment API for all items that are tagged with particular
+ * type.
+ *
+ * @param strTag
+ * The tag to search for. This will be URL encoded before submitting
+ * the query.
+ * @return XML document containing search results.
+ */
+ public Document searchByTag(String strTag) {
+ Document doc = null;
+
+ try {
+ String strUrlEncodedTag = MyExperimentClient.urlEncodeQuery(strTag);
+ doc = this.doMyExperimentGET(
+ BASE_URL + "/tagged.xml?tag=" + strUrlEncodedTag
+ + Util.composeAPIQueryElements(null)).getResponseBody();
+ } catch (Exception e) {
+ logger
+ .error("ERROR: Failed to fetch tagged items from myExperiment. Query tag was '"
+ + strTag + "'\n" + e);
+ }
+
+ return (doc);
+ }
+
+ /**
+ * Converts a tag list into tag cloud data by fetching tag application count
+ * for each instance in the list.
+ *
+ * @param tags
+ * Tag list to work on.
+ */
+ public void convertTagListIntoTagCloudData(List<Tag> tags) {
+ try {
+ Document doc = null;
+
+ for (Tag t : tags) {
+ doc = this.getResource(Resource.TAG, t.getURI(),
+ Resource.REQUEST_ALL_DATA);
+ Element rootElement = doc.getRootElement();
+ t.setCount(Integer.parseInt(rootElement.getChild("count").getText()));
+ }
+ } catch (Exception e) {
+ logger
+ .error("Failed while getting tag application counts when turning tag list into tag cloud data", e);
+ }
+ }
+
+ /**
+ * Fetches the data about user's favourite items and updates the provided user
+ * instance with the latest data.
+ */
+ public void updateUserFavourites(User user) {
+ // fetch and update favourites data
+ try {
+ Document doc = this.getResource(Resource.USER, user.getURI(),
+ Resource.REQUEST_USER_FAVOURITES_ONLY);
+ List<Resource> newUserFavouritesList = Util.retrieveUserFavourites(doc
+ .getRootElement());
+
+ user.getFavourites().clear();
+ user.getFavourites().addAll(newUserFavouritesList);
+ } catch (Exception ex) {
+ logger
+ .error("Failed to fetch favourites data from myExperiment for a user (URI: "
+ + user.getURI() + "); exception:\n" + ex);
+ JOptionPane
+ .showMessageDialog(
+ null,
+ "Couldn't synchronise data about your favourite items with myExperiment.\n"
+ + "You might not be able to add / remove other items to your favourites and.\n"
+ + "Please refresh your profile data manually by clicking 'Refresh' button in 'My Stuff' tab.",
+ "myExperiment Plugin - Error", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+ /**
+ * For each comment in the list fetches the user which made the comment, the
+ * date when it was made, etc.
+ */
+ public void updateCommentListWithExtraData(List<Comment> comments) {
+ try {
+ Document doc = null;
+
+ for (Comment c : comments) {
+ doc = this.getResource(Resource.COMMENT, c.getURI(),
+ Resource.REQUEST_ALL_DATA);
+ Element rootElement = doc.getRootElement();
+
+ Element userElement = rootElement.getChild("author");
+ User u = new User();
+ u.setTitle(userElement.getText());
+ u.setName(userElement.getText());
+ u.setResource(userElement.getAttributeValue("resource"));
+ u.setURI(userElement.getAttributeValue("uri"));
+ c.setUser(u);
+
+ String createdAt = rootElement.getChildText("created-at");
+ if (createdAt != null && !createdAt.equals("")) {
+ c.setCreatedAt(MyExperimentClient.parseDate(createdAt));
+ }
+ }
+ } catch (Exception e) {
+ logger.error("Failed while updating comment list for preview", e);
+ }
+ }
+
+ public Document searchByQuery(QuerySearchInstance searchQuery) {
+ Document doc = null;
+ String strSearchURL = null;
+
+ try {
+ // this will URL encode the query so that it can be directly inserted into
+ // the search URL
+ String strUrlEncodedQuery = MyExperimentClient.urlEncodeQuery(searchQuery
+ .getSearchQuery());
+
+ // determine which types to include in the search URL
+ // (if none are added, any types will be searched for)
+ String strSearchFor = "";
+ if (searchQuery.getSearchWorkflows()) strSearchFor += "workflow";
+ if (searchQuery.getSearchFiles()) strSearchFor += ",file";
+ if (searchQuery.getSearchPacks()) strSearchFor += ",pack";
+ if (searchQuery.getSearchUsers()) strSearchFor += ",user";
+ if (searchQuery.getSearchGroups()) strSearchFor += ",group";
+ if (strSearchFor.length() != 0) {
+ // some types were added;
+ // remove leading comma (if it exists)
+ if (strSearchFor.startsWith(","))
+ strSearchFor = strSearchFor.replaceFirst(",", "");
+
+ // add parameter prefix
+ strSearchFor = "type=" + strSearchFor;
+ }
+
+ // assemble all search parameters together
+ // (we will definitely have the number of results)
+ String strParameters = strSearchFor;
+ if (strParameters.length() != 0) strParameters += "&";
+ strParameters += "num=" + searchQuery.getResultCountLimit();
+ strParameters += Util.composeAPIQueryElements(searchQuery);
+
+ // generate the search URL
+ strSearchURL = BASE_URL + "/search.xml?query=" + strUrlEncodedQuery + "&"
+ + strParameters;
+
+ // DEBUG
+ // javax.swing.JOptionPane.showMessageDialog(null, strSearchURL);
+
+ // execute the search on myExperiment
+ doc = this.doMyExperimentGET(strSearchURL).getResponseBody();
+ } catch (Exception e) {
+ logger
+ .error("ERROR: Failed to run search on myExperiment. Query URL was'"
+ + strSearchURL + "'\n" + e);
+ }
+
+ return (doc);
+ }
+
+ public ServerResponse postComment(Resource resource, String strComment) {
+ try {
+ String strCommentData = "<comment><subject resource=\""
+ + resource.getResource() + "\"/><comment>" + strComment
+ + "</comment></comment>";
+ ServerResponse response = this.doMyExperimentPOST(BASE_URL
+ + "/comment.xml", strCommentData);
+
+ if (response.getResponseCode() == HttpURLConnection.HTTP_OK) {
+ // XML response should contain the new comment that was posted
+ Comment cNew = Comment.buildFromXML(response.getResponseBody(), logger);
+
+ // this resource should be commentable on as the comment was posted
+ resource.getComments().add(cNew);
+ }
+
+ // will return the whole response object so that the application could
+ // decide
+ // on the next steps
+ return (response);
+ } catch (Exception e) {
+ logger.error("Failed while trying to post a comment for "
+ + resource.getURI() + "\n" + e);
+ return (new ServerResponse(ServerResponse.LOCAL_FAILURE, null));
+ }
+ }
+
+ private String prepareWorkflowPostContent(String workflowContent,
+ String title, String description, String license, String sharing) {
+ String strWorkflowData = "<workflow>";
+
+ if (title.length() > 0) strWorkflowData += "<title>" + title + "</title>";
+
+ if (description.length() > 0)
+ strWorkflowData += "<description>" + description + "</description>";
+
+ if (license.length() > 0)
+ strWorkflowData += "<license-type>" + license + "</license-type>";
+
+ if (sharing.length() > 0) {
+ if (sharing.contains("private")) strWorkflowData += "<permissions />";
+ else {
+ strWorkflowData += "<permissions><permission>"
+ + "<category>public</category>";
+ if (sharing.contains("view") || sharing.contains("download"))
+ strWorkflowData += "<privilege type=\"view\" />";
+ if (sharing.contains("download"))
+ strWorkflowData += "<privilege type=\"download\" />";
+ strWorkflowData += "</permission></permissions>";
+ }
+ }
+
+ String encodedWorkflow = "";
+
+ // check the format of the workflow
+ String scuflSchemaDef = "xmlns:s=\"http://org.embl.ebi.escience/xscufl/0.1alpha\"";
+ String t2flowSchemaDef = "xmlns=\"http://taverna.sf.net/2008/xml/t2flow\"";
+
+ if (workflowContent.length() > 0) {
+ String contentType;
+ if (workflowContent.contains(scuflSchemaDef)) contentType = "application/vnd.taverna.scufl+xml";
+ else if (workflowContent.contains(t2flowSchemaDef)) contentType = "application/vnd.taverna.t2flow+xml";
+ else contentType = "";
+
+ encodedWorkflow += "<content-type>" + contentType + "</content-type>"
+ + "<content encoding=\"base64\" type=\"binary\">"
+ + Base64.encodeBytes(workflowContent.getBytes()) + "</content>";
+ strWorkflowData += encodedWorkflow;
+ }
+
+ strWorkflowData += "</workflow>";
+
+ return (strWorkflowData);
+ }
+
+ private void afterMyExperimentPost(ServerResponse response) {
+ // if (response.getResponseCode() == HttpURLConnection.HTTP_OK) {
+ // // XML response should contain the new workflow that was posted
+ // Workflow newWorkflow = Workflow.buildFromXML(response.getResponseBody(),
+ // logger);
+ //
+ // System.out.println("* *** *** *** *" + response.getResponseBody()
+ // + "* *** *** *** *");
+ // }
+ }
+
+ public ServerResponse postWorkflow(String workflowContent, String title,
+ String description, String license, String sharing) {
+ try {
+ String strWorkflowData = prepareWorkflowPostContent(workflowContent,
+ title, description, license, sharing);
+
+ ServerResponse response = this.doMyExperimentPOST(BASE_URL
+ + "/workflow.xml", strWorkflowData);
+
+ afterMyExperimentPost(response);
+ // will return the whole response object so that the application could
+ // decide on the next steps
+ return (response);
+ } catch (Exception e) {
+ logger.error("Failed while trying to upload the workflow");
+ return (new ServerResponse(ServerResponse.LOCAL_FAILURE, null));
+ }
+ }
+
+ public ServerResponse updateWorkflowVersionOrMetadata(Resource resource,
+ String workflowContent, String title, String description, String license,
+ String sharing) {
+ try {
+ String strWorkflowData = prepareWorkflowPostContent(workflowContent,
+ title, description, license, sharing);
+
+ // if strWorkflowFileContent is empty; include version info for PUT (since
+ // workflow is being updated)
+ // a POST would require data, hence strWorkflowFileContent would not be
+ // empty
+ String doUpdateStatus = (workflowContent.length() == 0 ? DO_PUT : "");
+
+ ServerResponse response = this.doMyExperimentPOST(BASE_URL
+ + "/workflow.xml?id=" + resource.getID() + doUpdateStatus,
+ strWorkflowData);
+
+ afterMyExperimentPost(response);
+ // will return the whole response object so that the application could
+ // decide on the next steps
+ return (response);
+ } catch (Exception e) {
+ logger.error("Failed while trying to upload the workflow");
+ return (new ServerResponse(ServerResponse.LOCAL_FAILURE, null));
+ }
+ }
+
+ public ServerResponse addFavourite(Resource resource) {
+ try {
+ String strData = "<favourite><object resource=\""
+ + resource.getResource() + "\"/></favourite>";
+ ServerResponse response = this.doMyExperimentPOST(BASE_URL
+ + "/favourite.xml", strData);
+
+ // will return full server response
+ return (response);
+ } catch (Exception e) {
+ logger.error("Failed while trying to add an item (" + resource.getURI()
+ + ") to favourites4", e);
+ return (new ServerResponse(ServerResponse.LOCAL_FAILURE, null));
+ }
+ }
+
+ public ServerResponse deleteFavourite(Resource resource) {
+ try {
+ // deleting a favourite is a two-step process - first need to retrieve the
+ // the
+ // actual "favourite" object by current user's URL and favourited item's
+ // URL
+ String strGetFavouriteObjectURL = BASE_URL
+ + "/favourites.xml?user="
+ + MyExperimentClient.urlEncodeQuery(this.getCurrentUser()
+ .getResource()) + "&object="
+ + MyExperimentClient.urlEncodeQuery(resource.getResource());
+ ServerResponse response = this
+ .doMyExperimentGET(strGetFavouriteObjectURL);
+
+ // now retrieve this object's URI from server's response
+ Element root = response.getResponseBody().getRootElement();
+ String strFavouriteURI = root.getChild("favourite").getAttributeValue(
+ "uri");
+
+ // finally, delete the found object
+ response = this.doMyExperimentDELETE(strFavouriteURI);
+
+ // will return full server response
+ return (response);
+ } catch (Exception e) {
+ logger.error("Failed while trying to remove an item ("
+ + resource.getURI() + ") from favourites\n" + e);
+ return (new ServerResponse(ServerResponse.LOCAL_FAILURE, null));
+ }
+ }
+
+ public static Date parseDate(String date) {
+ Date result = null;
+ try {
+ result = OLD_DATE_FORMATTER.parse(date);
+ } catch (ParseException e) {
+ try {
+ result = OLD_SHORT_DATE_FORMATTER.parse(date);
+ }
+ catch (ParseException e1) {
+ try {
+ result = NEW_DATE_FORMATTER.parse(date);
+ } catch (ParseException e2) {
+ result = null;
+ }
+ }
+ }
+ return result;
+ }
+
+ public static String formatDate(Date date) {
+ return NEW_DATE_FORMATTER.format(date);
+ }
+
+ /**
+ * Prepares the string to serve as a part of url query to the server.
+ *
+ * @param query
+ * The string that needs URL encoding.
+ * @return URL encoded string that can be inserted into the request URL.
+ */
+ private static String urlEncodeQuery(String query) {
+ String strRes = "";
+
+ try {
+ strRes = URLEncoder.encode(query, "UTF-8");
+ } catch (UnsupportedEncodingException e) {
+ // do nothing
+ }
+
+ return (strRes);
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Pack.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Pack.java
new file mode 100644
index 0000000..d844fa6
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Pack.java
@@ -0,0 +1,232 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import java.text.DateFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.Resource;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.User;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class Pack extends Resource
+{
+ private int accessType;
+
+ private User creator;
+ private List<Tag> tags;
+ private List<Comment> comments;
+ private ArrayList<PackItem> items;
+
+
+ public Pack()
+ {
+ super();
+ this.setItemType(Resource.PACK);
+ }
+
+ public int getAccessType()
+ {
+ return this.accessType;
+ }
+
+ public void setAccessType(int accessType)
+ {
+ this.accessType = accessType;
+ }
+
+ public User getCreator() {
+ return creator;
+ }
+
+ public void setCreator(User creator) {
+ this.creator = creator;
+ }
+
+ public List<Tag> getTags()
+ {
+ return (this.tags);
+ }
+
+ public List<Comment> getComments()
+ {
+ return this.comments;
+ }
+
+ public int getItemCount()
+ {
+ return this.items.size();
+ }
+
+ public ArrayList<PackItem> getItems()
+ {
+ return this.items;
+ }
+
+
+ /**
+ * A helper method to return a set of API elements that are
+ * needed to satisfy request of a particular type - e.g. creating
+ * a listing of resources or populating full preview, etc.
+ *
+ * @param iRequestType A constant value from Resource class.
+ * @return Comma-separated string containing values of required API elements.
+ */
+ public static String getRequiredAPIElements(int iRequestType)
+ {
+ String strElements = "";
+
+ // cases higher up in the list are supersets of those that come below -
+ // hence no "break" statements are required, because 'falling through' the
+ // switch statement is the desired behaviour in this case
+ switch (iRequestType) {
+ case Resource.REQUEST_FULL_PREVIEW:
+ strElements += "created-at,updated-at,internal-pack-items,external-pack-items,tags,comments,";
+ case Resource.REQUEST_FULL_LISTING:
+ strElements += "owner,";
+ case Resource.REQUEST_SHORT_LISTING:
+ strElements += "id,title,description,privileges";
+ }
+
+ return (strElements);
+ }
+
+
+ public static Pack buildFromXML(Document doc, MyExperimentClient client, Logger logger)
+ {
+ // if no XML document was supplied, return NULL
+ if(doc == null) return(null);
+
+ // call main method which parses XML document starting from root element
+ return (Pack.buildFromXML(doc.getRootElement(), client, logger));
+ }
+
+
+ // class method to build a pack instance from XML
+ @SuppressWarnings("unchecked")
+ public static Pack buildFromXML(Element docRootElement, MyExperimentClient client, Logger logger)
+ {
+ // return null to indicate an error if XML document contains no root element
+ if(docRootElement == null) return(null);
+
+ Pack p = new Pack();
+
+ try {
+ // Access type
+ p.setAccessType(Util.getAccessTypeFromXMLElement(docRootElement.getChild("privileges")));
+
+ // URI
+ p.setURI(docRootElement.getAttributeValue("uri"));
+
+ // Resource URI
+ p.setResource(docRootElement.getAttributeValue("resource"));
+
+ // Id
+ String id = docRootElement.getChildText("id");
+ if (id == null || id.equals("")) {
+ id = "API Error - No pack ID supplied";
+ logger.error("Error while parsing pack XML data - no ID provided for pack with title: \"" + docRootElement.getChildText("title") + "\"");
+ }
+ p.setID(Integer.parseInt(id));
+
+ // Title
+ p.setTitle(docRootElement.getChildText("title"));
+
+ // Description
+ p.setDescription(docRootElement.getChildText("description"));
+
+ // Owner
+ Element ownerElement = docRootElement.getChild("owner");
+ p.setCreator(Util.instantiatePrimitiveUserFromElement(ownerElement));
+
+ // Created at
+ String createdAt = docRootElement.getChildText("created-at");
+ if (createdAt != null && !createdAt.equals("")) {
+ p.setCreatedAt(MyExperimentClient.parseDate(createdAt));
+ }
+
+ // Updated at
+ String updatedAt = docRootElement.getChildText("updated-at");
+ if (updatedAt != null && !updatedAt.equals("")) {
+ p.setUpdatedAt(MyExperimentClient.parseDate(updatedAt));
+ }
+
+ // Tags
+ p.tags = new ArrayList<Tag>();
+ p.getTags().addAll(Util.retrieveTags(docRootElement));
+
+ // Comments
+ p.comments = new ArrayList<Comment>();
+ p.getComments().addAll(Util.retrieveComments(docRootElement, p));
+
+
+ // === All items will be stored together in one array ===
+ p.items = new ArrayList<PackItem>();
+ int iCount = 0;
+
+ // adding internal items first
+ Element itemsElement = docRootElement.getChild("internal-pack-items");
+ if (itemsElement != null) {
+ List<Element> itemsNodes = itemsElement.getChildren();
+ for (Element e : itemsNodes) {
+ Document docCurrentItem = client.getResource(Resource.PACK_INTERNAL_ITEM, e.getAttributeValue("uri"), Resource.REQUEST_DEFAULT_FROM_API);
+ PackItem piCurrentItem = PackItem.buildFromXML(docCurrentItem, logger);
+
+ p.getItems().add(piCurrentItem);
+ iCount++;
+ }
+ }
+
+ // now adding external items
+ itemsElement = docRootElement.getChild("external-pack-items");
+ if (itemsElement != null) {
+ List<Element> itemsNodes = itemsElement.getChildren();
+ for (Element e : itemsNodes) {
+ Document docCurrentItem = client.getResource(Resource.PACK_EXTERNAL_ITEM, e.getAttributeValue("uri"), Resource.REQUEST_DEFAULT_FROM_API);
+ PackItem piCurrentItem = PackItem.buildFromXML(docCurrentItem, logger);
+
+ p.getItems().add(piCurrentItem);
+ iCount++;
+ }
+ }
+
+ // sort the items after all of those have been added
+ Collections.sort(p.getItems());
+
+
+ logger.debug("Found information for pack with ID: " + p.getID() + ", Title: " + p.getTitle());
+ }
+ catch (Exception e) {
+ logger.error("Failed midway through creating pack object from XML", e);
+ }
+
+ // return created pack instance
+ return(p);
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/PackItem.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/PackItem.java
new file mode 100644
index 0000000..d3f2773
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/PackItem.java
@@ -0,0 +1,186 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import java.text.DateFormat;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class PackItem extends Resource {
+ private int id;
+ private User userWhoAddedThisItem;
+ private String strComment;
+
+ private boolean bInternalItem;
+
+ private Resource item; // for internal items
+
+ private String strLink; // for external items
+ private String strAlternateLink; // for external items
+
+ public PackItem() {
+ super();
+ this.setItemType(Resource.UNKNOWN); // set to unknown originally; will be changed as soon as the type is known
+ }
+
+ public int getID() {
+ return id;
+ }
+
+ public void setID(int id) {
+ this.id = id;
+ }
+
+ public void setID(String id) {
+ this.id = Integer.parseInt(id);
+ }
+
+ public boolean isInternalItem() {
+ return this.bInternalItem;
+ }
+
+ public void setInternalItem(boolean bIsInternalItem) {
+ this.bInternalItem = bIsInternalItem;
+ }
+
+ public User getUserWhoAddedTheItem() {
+ return this.userWhoAddedThisItem;
+ }
+
+ public void setUserWhoAddedTheItem(User userWhoAddedTheItem) {
+ this.userWhoAddedThisItem = userWhoAddedTheItem;
+ }
+
+ public String getComment() {
+ return this.strComment;
+ }
+
+ public void setComment(String strComment) {
+ this.strComment = strComment;
+ }
+
+ public Resource getItem() {
+ return this.item;
+ }
+
+ public void setItem(Resource item) {
+ this.item = item;
+ }
+
+ public String getLink() {
+ return this.strLink;
+ }
+
+ public void setLink(String strLink) {
+ this.strLink = strLink;
+ }
+
+ public String getAlternateLink() {
+ return this.strAlternateLink;
+ }
+
+ public void setAlternateLink(String strAlternateLink) {
+ this.strAlternateLink = strAlternateLink;
+ }
+
+ public static PackItem buildFromXML(Document doc, Logger logger) {
+ // if no XML was supplied, return null to indicate an error
+ if (doc == null)
+ return (null);
+
+ PackItem p = new PackItem();
+
+ try {
+ Element root = doc.getRootElement();
+
+ // URI
+ p.setURI(root.getAttributeValue("uri"));
+
+ // Resource URI
+ p.setResource(root.getAttributeValue("resource"));
+
+ // Id
+ String strID = root.getChildText("id");
+ if (strID == null || strID.equals("")) {
+ strID = "API Error - No pack item ID supplied";
+ logger.error("Error while parsing pack item XML data - no ID provided for pack item with uri: \""
+ + p.getURI() + "\"");
+ } else {
+ p.setID(strID);
+ }
+
+ // User who added the item to the pack
+ Element ownerElement = root.getChild("owner");
+ p.setUserWhoAddedTheItem(Util.instantiatePrimitiveUserFromElement(ownerElement));
+
+ // Date when the item was added to the pack
+ String createdAt = root.getChildText("created-at");
+ if (createdAt != null && !createdAt.equals("")) {
+ p.setCreatedAt(MyExperimentClient.parseDate(createdAt));
+ }
+
+ // Comment
+ Element commentElement = root.getChild("comment");
+ if (commentElement != null) {
+ p.setComment(commentElement.getText());
+ }
+
+ // === UP TO THIS POINT EXTERNAL AND INTERNAL ITEMS HAD THE SAME DATA ===
+ if (root.getName().equals("internal-pack-item")) {
+ // record that this is internal item
+ p.setInternalItem(true);
+
+ // add a link to a resource for internal items
+ Element itemElement = (Element) root.getChild("item").getChildren().get(0);
+ if (itemElement != null) {
+ p.setItem(Util.instantiatePrimitiveResourceFromElement(itemElement));
+ }
+
+ // now need to replicate title and item type attributes to the pack item object
+ // itself - this is required to allow proper sorting of the items
+ p.setItemType(p.getItem().getItemType());
+ p.setTitle(p.getItem().getTitle());
+ } else {
+ // record that this is external item
+ p.setInternalItem(false);
+
+ // add links to the external resource for external items
+ p.setItemType(Resource.PACK_EXTERNAL_ITEM);
+ p.setTitle(root.getChildText("title"));
+ p.setLink(root.getChildText("uri"));
+ p.setAlternateLink(root.getChildText("alternate-uri"));
+ }
+
+ logger.debug("Found information for pack item with URI: " + p.getURI());
+ } catch (Exception e) {
+ logger.error("Failed midway through creating pack item object from XML", e);
+ }
+
+ // return created pack item instance
+ return (p);
+
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Resource.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Resource.java
new file mode 100644
index 0000000..3c1a36c
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Resource.java
@@ -0,0 +1,683 @@
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+// Copyright (C) 2008 The University of Manchester, University of Southampton
+// and Cardiff University
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.io.Serializable;
+import java.net.URI;
+import java.util.Date;
+import java.util.EventListener;
+import java.util.List;
+
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JPanel;
+import javax.swing.JTextPane;
+import javax.swing.event.HyperlinkListener;
+import javax.swing.text.html.HTMLDocument;
+import javax.swing.text.html.HTMLEditorKit;
+import javax.swing.text.html.StyleSheet;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.MainComponent;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.MyExperimentPerspective;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.ResourceListPanel;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.StyledHTMLEditorKit;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+
+/**
+ * @author Jiten Bhagat, Sergejs Aleksejevs
+ */
+public class Resource implements Comparable<Resource>, Serializable {
+ // CONSTANTS
+ // (integer resource types)
+ public static final int UNEXPECTED_TYPE = -1; // erroneous type
+ public static final int UNKNOWN = 0;
+ public static final int WORKFLOW = 10;
+ public static final int FILE = 11;
+ public static final int PACK = 12;
+ public static final int PACK_INTERNAL_ITEM = 14;
+ public static final int PACK_EXTERNAL_ITEM = 15;
+ public static final int USER = 20;
+ public static final int GROUP = 21;
+ public static final int TAG = 30;
+ public static final int COMMENT = 31;
+
+ // (string resource types)
+ public static final String WORKFLOW_VISIBLE_NAME = "Workflow";
+ public static final String FILE_VISIBLE_NAME = "File";
+ public static final String PACK_VISIBLE_NAME = "Pack";
+ public static final String USER_VISIBLE_NAME = "User";
+ public static final String GROUP_VISIBLE_NAME = "Group";
+ public static final String TAG_VISIBLE_NAME = "Tag";
+ public static final String COMMENT_VISIBLE_NAME = "Comment";
+ public static final String UNKWNOWN_VISIBLE_NAME = "Unknown";
+ public static final String UNEXPECTED_TYPE_VISIBLE_NAME = "ERROR: Unexpected unknown type!";
+
+ // (integer access types)
+ public static final int ACCESS_VIEWING = 1000;
+ public static final int ACCESS_DOWNLOADING = 1001;
+ public static final int ACCESS_EDITING = 1002;
+
+ // (categories for selecting required elements for every resource type for a particular purpose)
+ public static final int REQUEST_ALL_DATA = 5000; // essentially obtains all data that API provides
+ public static final int REQUEST_FULL_PREVIEW = 5005; // used to get all data for preview in a browser window
+ public static final int REQUEST_FULL_LISTING = 5010; // used for displaying results of searches by query / by tag
+ public static final int REQUEST_SHORT_LISTING = 5015; // used for displaying items in 'My Stuff' tab
+ public static final int REQUEST_USER_FAVOURITES_ONLY = 5050;
+ public static final int REQUEST_USER_APPLIED_TAGS_ONLY = 5051;
+ public static final int REQUEST_WORKFLOW_CONTENT_ONLY = 5055;
+ public static final int REQUEST_DEFAULT_FROM_API = 5100; // used when default fields that come from the API are acceptable
+
+ // instance variables
+ private int iID;
+ private String uri;
+ private String resource;
+ private String title;
+
+ private int itemType;
+
+ private Date createdAt;
+ private Date updatedAt;
+ private String description;
+
+ public Resource() {
+ // empty constructor
+ }
+
+ public int getID() {
+ return iID;
+ }
+
+ public void setID(int id) {
+ this.iID = id;
+ }
+
+ public void setID(String id) {
+ this.iID = Integer.parseInt(id);
+ }
+
+ public String getURI() {
+ return uri;
+ }
+
+ public String getResource() {
+ return resource;
+ }
+
+ public int getItemType() {
+ return itemType;
+ }
+
+ public String getItemTypeName() {
+ return Resource.getResourceTypeName(itemType);
+ }
+
+ public String getTitle() {
+ return title;
+ }
+
+ public String getDescription() {
+ return description;
+ }
+
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ public void setURI(String uri) {
+ this.uri = uri;
+ }
+
+ public void setResource(String resource) {
+ this.resource = resource;
+ }
+
+ public void setItemType(int type) {
+ this.itemType = type;
+ }
+
+ public void setItemType(String type) {
+ this.itemType = Resource.getResourceTypeFromVisibleName(type);
+ }
+
+ public void setTitle(String title) {
+ this.title = title;
+ }
+
+ public Date getCreatedAt() {
+ return createdAt;
+ }
+
+ public void setCreatedAt(Date createdAt) {
+ this.createdAt = createdAt;
+ }
+
+ public Date getUpdatedAt() {
+ return updatedAt;
+ }
+
+ public void setUpdatedAt(Date updatedAt) {
+ this.updatedAt = updatedAt;
+ }
+
+ @Override
+ public String toString() {
+ return ("(" + this.getItemTypeName() + ", " + this.getURI() + ","
+ + this.getTitle() + ")");
+ }
+
+ /**
+ * This method is needed to sort Resource instances.
+ */
+ public int compareTo(Resource other) {
+ int iTypesCompared = this.getItemType() - other.getItemType();
+
+ if (iTypesCompared == 0) {
+ // types are identical, compare by title
+ return (this.getTitle().compareTo(other.getTitle()));
+ } else {
+ // types are different - this is sufficient to order these two resources
+ // (NB! This presumes that type constants were set in a way that produces correct
+ // ordering of the types for sorting operations!)
+ return (iTypesCompared);
+ }
+ }
+
+ /**
+ * This makes sure that things like instanceOf() and remove() in List
+ * interface work properly - this way resources are treated to be the same if
+ * they store identical data, rather than they simply hold the same reference.
+ */
+ @Override
+ public boolean equals(Object other) {
+ // could only be equal to another Resource object, not anything else
+ if (!(other instanceof Resource))
+ return (false);
+
+ // 'other' object is a Resource; equality is based on the data stored
+ // in the current and 'other' Resource instances - the main data of the
+ // Resource: item type, URI in the API and resource URL on myExperiment
+ // (these fields will always be present in every Resource instance)
+ Resource otherRes = (Resource) other;
+ return (this.itemType == otherRes.itemType && this.uri.equals(otherRes.uri) && this.resource.equals(otherRes.resource));
+ }
+
+ /**
+ * Check if the current type of resource is supposed to have an uploader.
+ */
+ public boolean hasUploader() {
+ return (this.itemType == Resource.WORKFLOW || this.itemType == Resource.FILE);
+ }
+
+ /**
+ * Casts the resource to one of the specialist types to get the uploader.
+ */
+ public User getUploader() {
+ switch (this.itemType) {
+ case Resource.WORKFLOW:
+ return ((Workflow) this).getUploader();
+ case Resource.FILE:
+ return ((File) this).getUploader();
+ default:
+ return (null);
+ }
+ }
+
+ /**
+ * Check if the current type of resource is supposed to have a creator.
+ */
+ public boolean hasCreator() {
+ return (this.itemType == Resource.PACK);
+ }
+
+ /**
+ * Casts the resource to one of the specialist types to get the creator.
+ */
+ public User getCreator() {
+ switch (this.itemType) {
+ case Resource.PACK:
+ return ((Pack) this).getCreator();
+ default:
+ return (null);
+ }
+ }
+
+ /**
+ * Check if the current type of resource is supposed to have a administrator.
+ */
+ public boolean hasAdmin() {
+ return (this.itemType == Resource.GROUP);
+ }
+
+ /**
+ * Casts the resource to one of the specialist types to get the administrator.
+ */
+ public User getAdmin() {
+ switch (this.itemType) {
+ case Resource.GROUP:
+ return ((Group) this).getAdmin();
+ default:
+ return (null);
+ }
+ }
+
+ /**
+ * Determines whether the current type of resource can be favourited.
+ */
+ public boolean isFavouritable() {
+ switch (this.itemType) {
+ case Resource.WORKFLOW:
+ case Resource.FILE:
+ case Resource.PACK:
+ return (true);
+ default:
+ return (false);
+ }
+ }
+
+ /**
+ * Determines whether the current resource is favourited by specified user.
+ */
+ public boolean isFavouritedBy(User user) {
+ for (Resource r : user.getFavourites()) {
+ if (r.getURI().equals(this.getURI())) {
+ return (true);
+ }
+ }
+
+ return (false);
+ }
+
+ /**
+ * Determines whether the current type of resource can be commented on.
+ */
+ public boolean isCommentableOn() {
+ switch (this.itemType) {
+ case Resource.WORKFLOW:
+ case Resource.FILE:
+ case Resource.PACK:
+ case Resource.GROUP:
+ return (true);
+ default:
+ return (false);
+ }
+ }
+
+ /**
+ * Retrieves the collection of comments for the current resource.
+ */
+ public List<Comment> getComments() {
+ switch (this.itemType) {
+ case Resource.WORKFLOW:
+ return ((Workflow) this).getComments();
+ case Resource.FILE:
+ return ((File) this).getComments();
+ case Resource.PACK:
+ return ((Pack) this).getComments();
+ case Resource.GROUP:
+ return ((Group) this).getComments();
+ default:
+ return (null);
+ }
+ }
+
+ /**
+ * Determines whether the current type of resource can be downloaded in
+ * general.
+ */
+ public boolean isDownloadable() {
+ return (this.itemType == Resource.WORKFLOW
+ || this.itemType == Resource.FILE || this.itemType == Resource.PACK);
+ }
+
+ /**
+ * Determines whether the current resource instance can be downloaded by the
+ * current user.
+ */
+ public boolean isDownloadAllowed() {
+ int iAccessType = 0;
+
+ switch (this.itemType) {
+ case Resource.WORKFLOW:
+ iAccessType = ((Workflow) this).getAccessType();
+ break;
+ case Resource.FILE:
+ iAccessType = ((File) this).getAccessType();
+ break;
+ case Resource.PACK:
+ iAccessType = ((Pack) this).getAccessType();
+ break;
+ default:
+ iAccessType = 0;
+ }
+
+ return (iAccessType >= Resource.ACCESS_DOWNLOADING);
+ }
+
+ /**
+ * Only workflows (and files?) have visible types.
+ */
+ public boolean hasVisibleType() {
+ return (this.itemType == Resource.WORKFLOW || this.itemType == Resource.FILE);
+ }
+
+ public String getVisibleType() {
+ switch (this.itemType) {
+ case Resource.WORKFLOW:
+ return ((Workflow) this).getVisibleType();
+ case Resource.FILE:
+ return ((File) this).getVisibleType();
+ default:
+ return (null);
+ }
+ }
+
+ /**
+ * Will create a small preview panel for the instance of the resource that it
+ * holds. Shows reduced amount of information when "bCreateFullSizeView" is
+ * set to false.
+ *
+ * @return JPanel containing title, description and links to actions on this
+ * resource.
+ */
+ public JPanel createListViewPanel(boolean bCreateFullSizeView, MainComponent pluginMainComponent, EventListener eventHandler, Logger logger) {
+ try {
+ JPanel mainPanel = new JPanel(new BorderLayout());
+ mainPanel.setBorder(BorderFactory.createLineBorder(Color.LIGHT_GRAY));
+
+ JTextPane infoTextPane = new JTextPane();
+ infoTextPane.setBorder(BorderFactory.createEmptyBorder());
+ infoTextPane.setEditable(false);
+
+ StringBuffer content = new StringBuffer();
+ content.append("<div class='list_item_container'>");
+ content.append("<div class='list_item'>");
+
+ content.append("<p class='title'>");
+ content.append("<a href='preview:"
+ + this.getItemType()
+ + ":"
+ + this.getURI()
+ + "'>"
+ + this.getTitle()
+ + ((this.getItemType() == Resource.WORKFLOW) ? (" (version "
+ + ((Workflow) this).getVersion() + ")") : "") + "</a>");
+ content.append("</p>");
+
+ if (bCreateFullSizeView) {
+ // Uploader / Creator / Administrator
+ if (this.hasUploader()) {
+ content.append("<p class='uploader'>");
+ content.append("Uploader: <a href='preview:" + Resource.USER + ":"
+ + this.getUploader().getURI() + "'>"
+ + this.getUploader().getName() + "</a>");
+ content.append("</p>");
+ } else if (this.hasCreator()) {
+ content.append("<p class='uploader'>");
+ content.append("Creator: <a href='preview:" + Resource.USER + ":"
+ + this.getCreator().getURI() + "'>" + this.getCreator().getName()
+ + "</a>");
+ content.append("</p>");
+ } else if (this.hasAdmin()) {
+ content.append("<p class='uploader'>");
+ content.append("Administrator: <a href='preview:" + Resource.USER
+ + ":" + this.getAdmin().getURI() + "'>"
+ + this.getAdmin().getName() + "</a>");
+ content.append("</p>");
+ }
+
+ // Type
+ if (this.hasVisibleType()) {
+ content.append("<p class='uploader'>");
+ content.append("Type: " + this.getVisibleType());
+ content.append("</p>");
+ }
+ }
+
+ content.append("<div class='desc'>");
+ content.append("<table style='margin-top: 5px; margin-bottom: 5px;'>");
+ content.append("<tr>");
+
+ if (this.itemType == Resource.WORKFLOW || this.itemType == Resource.USER) {
+ boolean bManualResizeNeeded = false; // manual resize will be needed for user avatars (these don't have auto thumbnails)
+ URI previewURI = null;
+ if (this.itemType == Resource.WORKFLOW)
+ previewURI = ((Workflow) this).getThumbnail();
+ else if (this.itemType == Resource.USER
+ && ((User) this).getAvatarResource() != null) {
+ previewURI = new URI(((User) this).getAvatarResource());
+ bManualResizeNeeded = true;
+ }
+
+ // preview pictures are only shown for workflows
+ content.append("<td valign='top'>");
+ content.append("<a href='preview:" + this.itemType + ":"
+ + this.getURI() + "'>");
+
+ if (bCreateFullSizeView) {
+ if (!bManualResizeNeeded)
+ content.append("<img class='preview' src='" + previewURI
+ + "'></img>");
+ else {
+ String resizedImageURL = Util.getResizedImageIconTempFileURL(previewURI.toURL(), ResourceListPanel.THUMBNAIL_WIDTH_FOR_FULL_LIST_VIEW, ResourceListPanel.THUMBNAIL_HEIGHT_FOR_FULL_LIST_VIEW);
+ content.append("<img class='preview' src='" + resizedImageURL
+ + "'></img>");
+ }
+ } else {
+ String resizedImageURL = Util.getResizedImageIconTempFileURL(previewURI.toURL(), ResourceListPanel.THUMBNAIL_WIDTH_FOR_SHORT_LIST_VIEW, ResourceListPanel.THUMBNAIL_HEIGHT_FOR_SHORT_LIST_VIEW);
+ content.append("<img class='preview' src='" + resizedImageURL
+ + "'></img>");
+ }
+
+ content.append("</a>");
+ content.append("</td>");
+ }
+
+ content.append("<td>");
+ content.append(" ");
+ content.append("</td>");
+ content.append("<td valign='top' style='margin-bottom: 10px;'>");
+
+ if (this.getDescription() != null && this.getDescription().length() > 0) {
+ if (bCreateFullSizeView)
+ content.append(this.getDescription());
+ else {
+ String strTruncatedDescription = this.getDescription();
+ if (strTruncatedDescription.length() > ResourceListPanel.DESCRIPTION_TRUNCATE_LENGTH_FOR_SHORT_LIST_VIEW) {
+ strTruncatedDescription = strTruncatedDescription.substring(0, ResourceListPanel.DESCRIPTION_TRUNCATE_LENGTH_FOR_SHORT_LIST_VIEW);
+ strTruncatedDescription += " ...";
+ }
+ content.append(strTruncatedDescription);
+ }
+ } else {
+ content.append("<span class='none_text'>No description</span>");
+ }
+
+ content.append("</td>");
+ content.append("</tr>");
+ content.append("</table>");
+ content.append("</div>");
+
+ if (bCreateFullSizeView) {
+ content.append("<p style='text-align: left;'><b><a href='"
+ + this.getResource()
+ + "'>Open in myExperiment</a></b>"
+ + " <img style='border: 0px;' src='"
+ + MyExperimentPerspective.getLocalResourceURL("external_link_small_icon")
+ + "' /></p>");
+ }
+
+ content.append("</div>");
+ content.append("</div>");
+
+ HTMLEditorKit kit = new StyledHTMLEditorKit(pluginMainComponent.getStyleSheet());
+ HTMLDocument doc = (HTMLDocument) (kit.createDefaultDocument());
+
+ doc.insertAfterStart(doc.getRootElements()[0].getElement(0), content.toString());
+
+ infoTextPane.setEditorKit(kit);
+ infoTextPane.setDocument(doc);
+ infoTextPane.setContentType("text/html");
+ infoTextPane.addHyperlinkListener((HyperlinkListener) eventHandler);
+ infoTextPane.setBorder(BorderFactory.createEmptyBorder(0, 0, 7, 0)); // little bit of padding below the HTML preview pane
+
+ mainPanel.add(infoTextPane, BorderLayout.CENTER);
+
+ if (bCreateFullSizeView) {
+ JPanel jpButtonsPanel = new JPanel();
+ jpButtonsPanel.setLayout(new BoxLayout(jpButtonsPanel, BoxLayout.LINE_AXIS));
+
+ // "Preview" button
+ JButton previewButton = new JButton();
+ previewButton.setAction(pluginMainComponent.new PreviewResourceAction(this.getItemType(), this.getURI()));
+ jpButtonsPanel.add(previewButton);
+
+ // "Download" button
+ if (this.isDownloadable()) {
+ // will have a link to the actual resource on myExperiment
+ // (tests of different conditions are made inside the action)
+ JButton downloadButton = new JButton();
+ downloadButton.setAction(pluginMainComponent.new DownloadResourceAction(this));
+ jpButtonsPanel.add(downloadButton);
+ }
+
+ // "Load" button is only to be displayed for workflows
+ if (this.getItemType() == Resource.WORKFLOW) {
+ // (various checks apply to see if this can be done - these are made inside the action)
+ JButton loadButton = new JButton();
+ loadButton.setAction(pluginMainComponent.new LoadResourceInTavernaAction(this));
+ jpButtonsPanel.add(loadButton);
+ }
+
+ // "Import" button is only to be displayed for workflows
+ if (this.getItemType() == Resource.WORKFLOW) {
+ // (various checks apply to see if this can be done - these are made inside the action)
+ JButton importButton = new JButton();
+ importButton.setAction(pluginMainComponent.new ImportIntoTavernaAction(this));
+ jpButtonsPanel.add(importButton);
+ }
+
+ // setting look and feel for buttons
+ mainPanel.add(jpButtonsPanel, BorderLayout.SOUTH);
+ jpButtonsPanel.setBackground(new Color(247, 247, 247)); // grey background (lighter than main background of the frame)
+ jpButtonsPanel.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createLineBorder(new Color(235, 235, 235)), // subtle darker border around the button bar
+ BorderFactory.createEmptyBorder(3, 3, 3, 3) // a bit of padding around the buttons
+ ));
+ }
+
+ // setting border around one workflow entry
+ if (bCreateFullSizeView) {
+ mainPanel.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createEmptyBorder(5, 5, 0, 5), BorderFactory.createLineBorder(Color.GRAY)));
+ } else {
+ mainPanel.setBorder(BorderFactory.createMatteBorder(0, 0, 1, 0, Color.GRAY));
+ }
+
+ return (mainPanel);
+ } catch (Exception e) {
+ logger.error("Failed while creating " + this.getItemTypeName()
+ + " list view:\n" + e);
+ return (null);
+ }
+ }
+
+ /**
+ * Translates resource type codes into a textual representation.
+ *
+ * @param resourceTypeCode
+ * This code should be one of the resource type constants defined in
+ * Resource class.
+ * @return Textual translation of the resource type code.
+ */
+ public static String getResourceTypeName(int resourceTypeCode) {
+ switch (resourceTypeCode) {
+ case Resource.WORKFLOW:
+ return Resource.WORKFLOW_VISIBLE_NAME;
+ case Resource.FILE:
+ return Resource.FILE_VISIBLE_NAME;
+ case Resource.PACK:
+ return Resource.PACK_VISIBLE_NAME;
+ case Resource.USER:
+ return Resource.USER_VISIBLE_NAME;
+ case Resource.GROUP:
+ return Resource.GROUP_VISIBLE_NAME;
+ case Resource.TAG:
+ return Resource.TAG_VISIBLE_NAME;
+ case Resource.COMMENT:
+ return Resource.COMMENT_VISIBLE_NAME;
+ case Resource.UNKNOWN:
+ return Resource.UNKWNOWN_VISIBLE_NAME;
+ default:
+ return Resource.UNEXPECTED_TYPE_VISIBLE_NAME;
+ }
+ }
+
+ /**
+ * Translates resource visible name into the type codes.
+ */
+ public static int getResourceTypeFromVisibleName(String name) {
+ if (name.toLowerCase().equals(Resource.WORKFLOW_VISIBLE_NAME.toLowerCase()))
+ return (Resource.WORKFLOW);
+ else if (name.toLowerCase().equals(Resource.FILE_VISIBLE_NAME.toLowerCase()))
+ return (Resource.FILE);
+ else if (name.toLowerCase().equals(Resource.PACK_VISIBLE_NAME.toLowerCase()))
+ return (Resource.PACK);
+ else if (name.toLowerCase().equals(Resource.USER_VISIBLE_NAME.toLowerCase()))
+ return (Resource.USER);
+ else if (name.toLowerCase().equals(Resource.GROUP_VISIBLE_NAME.toLowerCase()))
+ return (Resource.GROUP);
+ else if (name.toLowerCase().equals(Resource.TAG_VISIBLE_NAME.toLowerCase()))
+ return (Resource.TAG);
+ else if (name.toLowerCase().equals(Resource.COMMENT_VISIBLE_NAME.toLowerCase()))
+ return (Resource.COMMENT);
+ else
+ return (Resource.UNKNOWN);
+ }
+
+ /**
+ * This method will act as dispatcher for local buildFromXML() methods for
+ * each of individual resource types. This way there's a generic way to turn
+ * XML content into a Resource instance.
+ */
+ public static Resource buildFromXML(Document resourceXMLDocument, MyExperimentClient client, Logger logger) {
+ Element root = resourceXMLDocument.getRootElement();
+ return (Resource.buildFromXML(root, client, logger));
+ }
+
+ /**
+ * This method will act as dispatcher for local buildFromXML() methods for
+ * each of individual resource types. This way there's a generic way to turn
+ * XML content into a Resource instance.
+ */
+ public static Resource buildFromXML(Element docRootElement, MyExperimentClient client, Logger logger) {
+ Resource res = null;
+ switch (Resource.getResourceTypeFromVisibleName(docRootElement.getName())) {
+ case Resource.WORKFLOW:
+ res = Workflow.buildFromXML(docRootElement, logger);
+ break;
+ case Resource.FILE:
+ res = File.buildFromXML(docRootElement, logger);
+ break;
+ case Resource.PACK:
+ res = Pack.buildFromXML(docRootElement, client, logger);
+ break;
+ case Resource.USER:
+ res = User.buildFromXML(docRootElement, logger);
+ break;
+ case Resource.GROUP:
+ res = Group.buildFromXML(docRootElement, logger);
+ break;
+ default:
+ // do nothing - will return 'null'
+ break;
+ }
+
+ return (res);
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/SearchEngine.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/SearchEngine.java
new file mode 100644
index 0000000..57b7a86
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/SearchEngine.java
@@ -0,0 +1,321 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JComponent;
+import javax.swing.SwingUtilities;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.MainComponent;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.SearchResultsPanel;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class SearchEngine {
+ // holds a reference to the instance of the search thread in the current context
+ // that should be active at the moment (will aid early termination of older searches
+ // when new ones are started)
+ private Vector<Long> vCurrentSearchThreadID;
+
+ private boolean bSearchByTag; // indicates what kind of search this is
+ private String strSearchQuery; // stores the actual query
+
+ private SearchResultsPanel jpResultsPanel;
+ private MainComponent pluginMainComponent;
+ private MyExperimentClient myExperimentClient;
+ private Logger logger;
+
+ /**
+ * Creates an instance of a search engine that is aware of the current context
+ * of the search.
+ */
+ public SearchEngine(Vector<Long> currentSearchThreadIDVector, boolean bSearchByTag, SearchResultsPanel resultsPanel, MainComponent pluginMainComponent, MyExperimentClient client, Logger logger) {
+ super();
+
+ this.vCurrentSearchThreadID = currentSearchThreadIDVector;
+ this.bSearchByTag = bSearchByTag;
+
+ this.jpResultsPanel = resultsPanel;
+ this.pluginMainComponent = pluginMainComponent;
+ this.myExperimentClient = client;
+ this.logger = logger;
+ }
+
+ public void searchAndPopulateResults(String tagQuery) {
+ this.strSearchQuery = tagQuery;
+
+ new Thread("Search by tag") {
+ public void run() {
+ // Record 'this' search thread and set it as the new "primary" one
+ // (this way it if a new search thread starts afterwards, it is possible to
+ // detect this and stop the 'older' search, because it is no longer relevant)
+ long lThisSearchThreadID = Thread.currentThread().getId();
+ vCurrentSearchThreadID.set(0, lThisSearchThreadID);
+
+ // set the status in the status bar
+ pluginMainComponent.getStatusBar().setStatus(pluginMainComponent.getTagBrowserTab().getClass().getName(), "Searching");
+
+ // get the search query (which is the tag name in this case)
+ strSearchQuery = Tag.instantiateTagFromActionCommand(strSearchQuery).getTagName();
+ jpResultsPanel.setCurrentSearchTerm(strSearchQuery);
+ jpResultsPanel.setStatus("Starting to search for a tag '"
+ + strSearchQuery + "'...");
+
+ // Execute the search query
+ Document doc = myExperimentClient.searchByTag(strSearchQuery);
+
+ if (doc == null) {
+ logger.error("Failed while fetching tagged items. See the error message above. Can't continue.");
+ javax.swing.JOptionPane.showMessageDialog(null, "An error occurred while searching for the results of your query. Please try again.", "Error", javax.swing.JOptionPane.ERROR_MESSAGE);
+ } else {
+ // search was successful, get tagged items' collection
+ Element root = doc.getRootElement();
+ processSearchResults(lThisSearchThreadID, root.getChildren());
+ }
+ }
+ }.start();
+ }
+
+ public void searchAndPopulateResults(QuerySearchInstance querySearchDetails) {
+ final QuerySearchInstance searchQuery = querySearchDetails;
+ this.strSearchQuery = searchQuery.getSearchQuery();
+
+ new Thread("Search by query") {
+ public void run() {
+ // Record 'this' search thread and set it as the new "primary" one
+ // (this way it if a new search thread starts afterwards, it is possible to
+ // detect this and stop the 'older' search, because it is no longer relevant)
+ long lThisSearchThreadID = Thread.currentThread().getId();
+ vCurrentSearchThreadID.set(0, lThisSearchThreadID);
+
+ // set the status in the status bar
+ pluginMainComponent.getStatusBar().setStatus(pluginMainComponent.getSearchTab().getClass().getName(), "Searching");
+
+ // strip out the leading "search:"
+ strSearchQuery = strSearchQuery.replaceFirst("search:", "");
+ jpResultsPanel.setCurrentSearchTerm(strSearchQuery);
+ jpResultsPanel.setStatus("Starting to search for '" + strSearchQuery
+ + "'...");
+
+ // Execute the search query
+ Document doc = myExperimentClient.searchByQuery(searchQuery);
+
+ if (doc == null) {
+ logger.error("Failed while fetching search result XML document. See the error message above. Can't continue.");
+ javax.swing.JOptionPane.showMessageDialog(null, "An error occurred while searching for the results of your query. Please try again.", "Error", javax.swing.JOptionPane.ERROR_MESSAGE);
+ } else {
+ // search was successful, get found items' collection
+ Element root = doc.getRootElement();
+ processSearchResults(lThisSearchThreadID, root.getChildren());
+ }
+ }
+ }.start();
+ }
+
+ /**
+ * Generic worker method to process search results from both search by tags
+ * and search by query.
+ *
+ * @param foundSearchItemElements
+ * List of Elements that comprise the search results.
+ */
+ private void processSearchResults(Long thisSearchThreadID, List<Element> foundSearchItemElements) {
+ // prepare variables
+ final Long lThisSearchThreadID = thisSearchThreadID;
+ final List<Element> lFoundSearchItemElements = foundSearchItemElements;
+ final HashMap<Integer, ArrayList<Resource>> hmClassifiedResults = new HashMap<Integer, ArrayList<Resource>>();
+
+ // iterate through all found items, fetch more data about each and classify
+ // the results by resource type
+ for (Element foundItem : foundSearchItemElements) {
+ // check if the current thread is still the active one (that is if a new search
+ // thread hasn't been started yet - if the new search has been started, the
+ // current one should terminate)
+ if (!lThisSearchThreadID.equals(vCurrentSearchThreadID.get(0)))
+ return;
+
+ // PROCESS THE NEXT ELEMENT
+ // data required for generating full listing preview was fetched along with the list of items -
+ // so now can build the item directly from the received data
+ Resource res = Resource.buildFromXML(foundItem, myExperimentClient, logger);
+
+ // check if this is a new type of resource - if so, create new ArrayList for these
+ if (!hmClassifiedResults.containsKey(res.getItemType())) {
+ hmClassifiedResults.put(res.getItemType(), new ArrayList<Resource>());
+ }
+
+ // add the resource into the result set
+ hmClassifiedResults.get(res.getItemType()).add(res);
+ }
+
+ // populate the results when everything's done
+ // (only make a final check to make sure that the "top" search thread is still the current one -
+ // otherwise, it's not necessary to make any rendering of unwanted results)
+ if (lThisSearchThreadID.equals(vCurrentSearchThreadID.get(0))) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ jpResultsPanel.setStatus(lFoundSearchItemElements.size()
+ + " items found " + (bSearchByTag ? "with tag '" : "by query '")
+ + jpResultsPanel.getCurrentSearchTerm() + "'");
+ jpResultsPanel.setSearchResultsData(hmClassifiedResults);
+ jpResultsPanel.refresh();
+
+ // if this search thread is displaying results, then this was the last search thread - can display
+ // "ready" status in the status bar now
+ JComponent jcTabForWhichToSetStatus = (bSearchByTag ? pluginMainComponent.getTagBrowserTab() : pluginMainComponent.getSearchTab());
+ pluginMainComponent.getStatusBar().setStatus(jcTabForWhichToSetStatus.getClass().getName(), null);
+ }
+ });
+ }
+ }
+
+ /**
+ * Class to hold settings for a query search. This will then be used to re-run
+ * a search instance at a later time.
+ */
+ public static class QuerySearchInstance implements Comparable<QuerySearchInstance>, Serializable {
+ private String strSearchQuery;
+ private int iResultCountLimit;
+ private boolean bSearchWorkflows;
+ private boolean bSearchFiles;
+ private boolean bSearchPacks;
+ private boolean bSearchUsers;
+ private boolean bSearchGroups;
+
+ // constructor
+ public QuerySearchInstance(String searchQuery, int resultCountLimit, boolean searchWorkflows, boolean searchFiles, boolean searchPacks, boolean searchUsers, boolean searchGroups) {
+ this.strSearchQuery = searchQuery;
+ this.iResultCountLimit = resultCountLimit;
+ this.bSearchWorkflows = searchWorkflows;
+ this.bSearchFiles = searchFiles;
+ this.bSearchPacks = searchPacks;
+ this.bSearchUsers = searchUsers;
+ this.bSearchGroups = searchGroups;
+ }
+
+ // determines whether the two search instances are identical
+ public boolean equals(Object other) {
+ if (other instanceof QuerySearchInstance) {
+ QuerySearchInstance si = (QuerySearchInstance) other;
+
+ return (this.strSearchQuery.equals(si.getSearchQuery())
+ && this.iResultCountLimit == si.getResultCountLimit()
+ && this.bSearchWorkflows == si.getSearchWorkflows()
+ && this.bSearchFiles == si.getSearchFiles()
+ && this.bSearchPacks == si.getSearchPacks()
+ && this.bSearchUsers == si.getSearchUsers() && this.bSearchGroups == si.getSearchGroups());
+ } else
+ return (false);
+ }
+
+ public int compareTo(QuerySearchInstance other) {
+ if (this.equals(other))
+ return (0);
+ else {
+ // this will return results in the descending order - which is
+ // fine, because the way this collection will be rendered will
+ // eventually traverse it from the rear end first; so results
+ // will be shown alphabetically
+ return (-1 * this.toString().compareTo(other.toString()));
+ }
+ }
+
+ public String toString() {
+ return ("Search: '" + this.strSearchQuery + "' " + this.detailsAsString());
+ }
+
+ public String detailsAsString() {
+ String str = "";
+
+ // output types that were searched for
+ int iCnt = 0;
+ if (this.bSearchWorkflows) {
+ str += "workflows, ";
+ iCnt++;
+ }
+ if (this.bSearchFiles) {
+ str += "files, ";
+ iCnt++;
+ }
+ if (this.bSearchPacks) {
+ str += "packs, ";
+ iCnt++;
+ }
+ if (this.bSearchUsers) {
+ str += "users, ";
+ iCnt++;
+ }
+ if (this.bSearchGroups) {
+ str += "groups, ";
+ iCnt++;
+ }
+
+ // if that's all types, have just the word 'all'
+ if (iCnt == 5)
+ str = "all";
+ else
+ str = str.substring(0, str.length() - 2); // remove trailing ", "
+
+ // add the rest to the string representation of the search instance
+ str = "[" + str + "; limit: " + this.iResultCountLimit + "]";
+
+ return (str);
+ }
+
+ public String getSearchQuery() {
+ return (this.strSearchQuery);
+ }
+
+ public int getResultCountLimit() {
+ return (this.iResultCountLimit);
+ }
+
+ public boolean getSearchWorkflows() {
+ return (this.bSearchWorkflows);
+ }
+
+ public boolean getSearchFiles() {
+ return (this.bSearchFiles);
+ }
+
+ public boolean getSearchPacks() {
+ return (this.bSearchPacks);
+ }
+
+ public boolean getSearchUsers() {
+ return (this.bSearchUsers);
+ }
+
+ public boolean getSearchGroups() {
+ return (this.bSearchGroups);
+ }
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/ServerResponse.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/ServerResponse.java
new file mode 100644
index 0000000..d3d5d94
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/ServerResponse.java
@@ -0,0 +1,59 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import org.jdom.Document;
+
+public class ServerResponse {
+ // CONSTANTS
+ public static int LOCAL_FAILURE = -1;
+
+ // STORAGE
+ private int iResponseCode;
+ private Document docResponseBody;
+
+ public ServerResponse() {
+ // do nothing - empty constructor
+ }
+
+ public ServerResponse(int responseCode, Document responseBody) {
+ super();
+
+ this.iResponseCode = responseCode;
+ this.docResponseBody = responseBody;
+ }
+
+ public int getResponseCode() {
+ return (this.iResponseCode);
+ }
+
+ public void setResponseCode(int responseCode) {
+ this.iResponseCode = responseCode;
+ }
+
+ public Document getResponseBody() {
+ return (this.docResponseBody);
+ }
+
+ public void setResponseBody(Document responseBody) {
+ this.docResponseBody = responseBody;
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Tag.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Tag.java
new file mode 100644
index 0000000..070dda1
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Tag.java
@@ -0,0 +1,125 @@
+// Copyright (C) 2008 The University of Manchester, University of Southampton
+// and Cardiff University
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import java.io.Serializable;
+import java.util.Comparator;
+
+/**
+ * @author Jiten Bhagat, Sergejs Aleksejevs
+ */
+public class Tag extends Resource implements Serializable {
+ private String tagName;
+ private int count;
+
+ public Tag() {
+ super();
+ this.setItemType(Resource.TAG);
+ }
+
+ public String getTagName() {
+ return tagName;
+ }
+
+ public void setTagName(String tagName) {
+ this.tagName = tagName;
+ }
+
+ public int getCount() {
+ return count;
+ }
+
+ public void setCount(int count) {
+ this.count = count;
+ }
+
+ public static class ReversePopularityComparator implements Comparator<Tag> {
+ public ReversePopularityComparator() {
+ super();
+ }
+
+ public int compare(Tag t1, Tag t2) {
+ if (t1.getCount() == t2.getCount()) {
+ // in case of the same popularity, compare by tag name
+ return (t1.getTagName().compareTo(t2.getTagName()));
+ } else {
+ // popularity isn't the same; arrange by popularity (more popular first)
+ return (t2.getCount() - t1.getCount());
+ }
+ }
+ }
+
+ public static class AlphanumericComparator implements Comparator<Tag> {
+ public AlphanumericComparator() {
+ super();
+ }
+
+ public int compare(Tag t1, Tag t2) {
+ return (t1.getTagName().compareTo(t2.getTagName()));
+ }
+ }
+
+ /**
+ * This makes sure that things like instanceOf() and remove() in List
+ * interface work properly - this way resources are treated to be the same if
+ * they store identical data, rather than they simply hold the same reference.
+ */
+ public boolean equals(Object other) {
+ // could only be equal to another Tag object, not anything else
+ if (!(other instanceof Tag))
+ return (false);
+
+ // 'other' object is a Tag; equality is based on the data stored
+ // in the current and 'other' Tag instances
+ Tag otherTag = (Tag) other;
+ return (this.count == otherTag.count && this.tagName.equals(otherTag.tagName));
+ }
+
+ public String toString() {
+ return ("Tag (" + this.tagName + ", " + this.count + ")");
+ }
+
+ /**
+ * A helper method to return a set of API elements that are needed to satisfy
+ * request of a particular type - e.g. creating a listing of resources or
+ * populating full preview, etc.
+ *
+ * @param iRequestType
+ * A constant value from Resource class.
+ * @return Comma-separated string containing values of required API elements.
+ */
+ public static String getRequiredAPIElements(int iRequestType) {
+ String strElements = "";
+
+ // cases higher up in the list are supersets of those that come below -
+ // hence no "break" statements are required, because 'falling through' the
+ // switch statement is the desired behaviour in this case
+ switch (iRequestType) {
+ case Resource.REQUEST_DEFAULT_FROM_API:
+ strElements += ""; // no change needed - defaults will be used
+ }
+
+ return (strElements);
+ }
+
+ /**
+ * Instantiates a Tag object from action command string that is used to
+ * trigger tag search events in the plugin. These action commands should look
+ * like "tag:<tag_name>".
+ *
+ * @param strActionCommand
+ * The action command to parse.
+ * @return A Tab object instance or null if action command was invalid.
+ */
+ public static Tag instantiateTagFromActionCommand(String strActionCommand) {
+ if (!strActionCommand.startsWith("tag:")) {
+ return (null);
+ } else {
+ // instantiate the Tag object, strip out the leading "tag:" and return result
+ Tag t = new Tag();
+ t.setTagName(strActionCommand.replaceFirst("tag:", ""));
+ return (t);
+ }
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/TagCloud.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/TagCloud.java
new file mode 100644
index 0000000..094d208
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/TagCloud.java
@@ -0,0 +1,47 @@
+// Copyright (C) 2008 The University of Manchester, University of Southampton
+// and Cardiff University
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * @author Jiten Bhagat
+ */
+public class TagCloud {
+
+ private List<Tag> tags = new ArrayList<Tag>();
+
+ public List<Tag> getTags() {
+ return this.tags;
+ }
+
+ /**
+ * Removes all tags from the current tag cloud.
+ */
+ public void clear() {
+ this.tags.clear();
+ }
+
+ /**
+ * Adds all tags from the supplied collection into the tag cloud.
+ */
+ public void addAll(List<Tag> newTags) {
+ this.tags.addAll(newTags);
+ }
+
+ /**
+ * @return Count of the occurrences of the most popular tag in the cloud data.
+ */
+ public int getMaxTagCount() {
+ int iMax = 0;
+
+ for (Tag t : tags) {
+ if (t.getCount() > iMax) {
+ iMax = t.getCount();
+ }
+ }
+
+ return (iMax);
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/User.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/User.java
new file mode 100644
index 0000000..719593d
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/User.java
@@ -0,0 +1,297 @@
+// Copyright (C) 2008 The University of Manchester, University of Southampton
+// and Cardiff University
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import java.text.DateFormat;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+
+import javax.swing.ImageIcon;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+
+/**
+ * @author Jiten Bhagat, Sergejs Aleksejevs
+ */
+public class User extends Resource {
+ private String name;
+ private String city;
+ private String country;
+ private String email;
+ private String website;
+
+ private ImageIcon avatar;
+ private String avatar_uri;
+ private String avatar_resource;
+
+ private ArrayList<HashMap<String, String>> workflows;
+ private ArrayList<HashMap<String, String>> files;
+ private ArrayList<HashMap<String, String>> packs;
+ private ArrayList<HashMap<String, String>> friends;
+ private ArrayList<HashMap<String, String>> groups;
+ private ArrayList<HashMap<String, String>> tags;
+ private ArrayList<Resource> favourites;
+
+ public User() {
+ super();
+ this.setItemType(Resource.USER);
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ this.setTitle(name); // this will allow to use name/title interchangeably
+ }
+
+ public String getCity() {
+ return city;
+ }
+
+ public void setCity(String city) {
+ this.city = city;
+ }
+
+ public String getCountry() {
+ return country;
+ }
+
+ public void setCountry(String country) {
+ this.country = country;
+ }
+
+ public String getEmail() {
+ return email;
+ }
+
+ public void setEmail(String email) {
+ this.email = email;
+ }
+
+ public String getWebsite() {
+ return website;
+ }
+
+ public void setWebsite(String website) {
+ this.website = website;
+ }
+
+ public String getAvatarURI() {
+ return avatar_uri;
+ }
+
+ public void setAvatarURI(String avatar_uri) {
+ this.avatar_uri = avatar_uri;
+ }
+
+ public ImageIcon getAvatar() {
+ return avatar;
+ }
+
+ // creates avatar from the XML of it
+ public void setAvatar(Document doc) {
+ Element root = doc.getRootElement();
+ String strAvatarData = root.getChild("data").getText();
+
+ this.avatar = new ImageIcon(Base64.decode(strAvatarData));
+ }
+
+ public void setAvatar(ImageIcon avatar) {
+ this.avatar = avatar;
+ }
+
+ public String getAvatarResource() {
+ return avatar_resource;
+ }
+
+ public void setAvatarResource(String avatar_resource) {
+ this.avatar_resource = avatar_resource;
+ }
+
+ public ArrayList<HashMap<String, String>> getWorkflows() {
+ return workflows;
+ }
+
+ public ArrayList<HashMap<String, String>> getFiles() {
+ return files;
+ }
+
+ public ArrayList<HashMap<String, String>> getPacks() {
+ return packs;
+ }
+
+ public ArrayList<HashMap<String, String>> getFriends() {
+ return friends;
+ }
+
+ public ArrayList<HashMap<String, String>> getGroups() {
+ return groups;
+ }
+
+ public ArrayList<Resource> getFavourites() {
+ return favourites;
+ }
+
+ public ArrayList<HashMap<String, String>> getTags() {
+ return this.tags;
+ }
+
+ /**
+ * A helper method to return a set of API elements that are needed to satisfy
+ * request of a particular type - e.g. creating a listing of resources or
+ * populating full preview, etc.
+ *
+ * @param iRequestType
+ * A constant value from Resource class.
+ * @return Comma-separated string containing values of required API elements.
+ */
+ public static String getRequiredAPIElements(int iRequestType) {
+ String strElements = "";
+
+ // cases higher up in the list are supersets of those that come below -
+ // hence no "break" statements are required, because 'falling through' the
+ // switch statement is the desired behaviour in this case;
+ //
+ // cases after first 'break' statement are separate ones and hence are treated
+ // individually
+ switch (iRequestType) {
+ case Resource.REQUEST_FULL_PREVIEW:
+ strElements += "created-at,updated-at,email,website,city,country,"
+ + "friends,groups,workflows,files,packs,favourited,tags-applied,";
+ case Resource.REQUEST_FULL_LISTING:
+ strElements += ""; // essentially the same as short listing
+ case Resource.REQUEST_SHORT_LISTING:
+ strElements += "id,name,description,avatar";
+ break;
+ case Resource.REQUEST_USER_FAVOURITES_ONLY:
+ strElements += "favourited";
+ break;
+ case Resource.REQUEST_USER_APPLIED_TAGS_ONLY:
+ strElements += "tags-applied";
+ break;
+ }
+
+ return (strElements);
+ }
+
+ public static User buildFromXML(Document doc, Logger logger) {
+ // if no XML document was supplied, return NULL
+ if (doc == null)
+ return (null);
+
+ // call main method which parses XML document starting from root element
+ return (User.buildFromXML(doc.getRootElement(), logger));
+ }
+
+ // class method to build a user instance from XML
+ @SuppressWarnings("unchecked")
+ public static User buildFromXML(Element docRootElement, Logger logger) {
+ // can't make any processing if root element is NULL
+ if (docRootElement == null)
+ return (null);
+
+ // create instance and parse the XML otherwise
+ User user = new User();
+
+ try {
+ // store all simple values
+ user.setURI(docRootElement.getAttributeValue("uri"));
+ user.setResource(docRootElement.getAttributeValue("resource"));
+ user.setID(docRootElement.getChildText("id"));
+ user.setName(docRootElement.getChildText("name"));
+ user.setTitle(user.getName()); // to allow generic handling of all resources - for users 'title' will replicate the 'name'
+ user.setDescription(docRootElement.getChild("description").getText());
+ user.setCity(docRootElement.getChildText("city"));
+ user.setCountry(docRootElement.getChildText("country"));
+ user.setEmail(docRootElement.getChildText("email"));
+ user.setWebsite(docRootElement.getChildText("website"));
+
+ // avatar URI in the API
+ Element avatarURIElement = docRootElement.getChild("avatar");
+ if (avatarURIElement != null) {
+ user.setAvatarURI(avatarURIElement.getAttributeValue("uri"));
+ }
+
+ // avatar resource on myExperiment
+ Element avatarElement = docRootElement.getChild("avatar");
+ if (avatarElement != null) {
+ user.setAvatarResource(avatarElement.getAttributeValue("resource"));
+ }
+
+ // Created at
+ String createdAt = docRootElement.getChildText("created-at");
+ if (createdAt != null && !createdAt.equals("")) {
+ user.setCreatedAt(MyExperimentClient.parseDate(createdAt));
+ }
+
+ // Updated at
+ String updatedAt = docRootElement.getChildText("updated-at");
+ if (updatedAt != null && !updatedAt.equals("")) {
+ user.setUpdatedAt(MyExperimentClient.parseDate(updatedAt));
+ }
+
+ // store workflows
+ user.workflows = new ArrayList<HashMap<String, String>>();
+ Element workflowsElement = docRootElement.getChild("workflows");
+ if (workflowsElement != null) {
+ Iterator<Element> iWorkflows = workflowsElement.getChildren().iterator();
+ Util.getResourceCollectionFromXMLIterator(iWorkflows, user.workflows);
+ }
+
+ // store files
+ user.files = new ArrayList<HashMap<String, String>>();
+ Element filesElement = docRootElement.getChild("files");
+ if (filesElement != null) {
+ Iterator<Element> iFiles = filesElement.getChildren().iterator();
+ Util.getResourceCollectionFromXMLIterator(iFiles, user.files);
+ }
+
+ // store packs
+ user.packs = new ArrayList<HashMap<String, String>>();
+ Element packsElement = docRootElement.getChild("packs");
+ if (packsElement != null) {
+ Iterator<Element> iPacks = packsElement.getChildren().iterator();
+ Util.getResourceCollectionFromXMLIterator(iPacks, user.packs);
+ }
+
+ // store friends
+ user.friends = new ArrayList<HashMap<String, String>>();
+ Element friendsElement = docRootElement.getChild("friends");
+ if (filesElement != null) {
+ Iterator<Element> iFriends = friendsElement.getChildren().iterator();
+ Util.getResourceCollectionFromXMLIterator(iFriends, user.friends);
+ }
+
+ // store groups
+ user.groups = new ArrayList<HashMap<String, String>>();
+ Element groupsElement = docRootElement.getChild("groups");
+ if (groupsElement != null) {
+ Iterator<Element> iGroups = groupsElement.getChildren().iterator();
+ Util.getResourceCollectionFromXMLIterator(iGroups, user.groups);
+ }
+
+ // store tags
+ user.tags = new ArrayList<HashMap<String, String>>();
+ Element tagsElement = docRootElement.getChild("tags-applied");
+ if (tagsElement != null) {
+ Iterator<Element> iTags = tagsElement.getChildren().iterator();
+ Util.getResourceCollectionFromXMLIterator(iTags, user.tags);
+ }
+
+ // store favourites
+ user.favourites = new ArrayList<Resource>();
+ user.favourites.addAll(Util.retrieveUserFavourites(docRootElement));
+
+ } catch (Exception e) {
+ logger.error("Failed midway through creating user object from XML", e);
+ }
+
+ return (user);
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Util.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Util.java
new file mode 100644
index 0000000..08f16e5
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Util.java
@@ -0,0 +1,624 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.RenderingHints;
+import java.awt.event.ActionListener;
+import java.awt.image.BufferedImage;
+import java.net.InetAddress;
+import java.net.URL;
+import java.net.UnknownHostException;
+import java.security.MessageDigest;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.TreeSet;
+
+import javax.crypto.Cipher;
+import javax.crypto.SecretKey;
+import javax.crypto.SecretKeyFactory;
+import javax.crypto.spec.PBEKeySpec;
+import javax.crypto.spec.PBEParameterSpec;
+import javax.imageio.ImageIO;
+import javax.swing.BorderFactory;
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+import javax.swing.SwingConstants;
+
+import net.sf.taverna.raven.appconfig.ApplicationRuntime;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.JClickableLabel;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.MyExperimentPerspective;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.SearchEngine.QuerySearchInstance;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class Util {
+ private static Logger logger = Logger.getLogger(Util.class);
+
+ // ******** DATA ENCRYPTION ********
+
+ private static final String PBE_PASSWORD = System.getProperty("user.home");
+ private static final String PBE_SALT;
+
+ static {
+ String host_name = "";
+ try {
+ host_name = InetAddress.getLocalHost().toString();
+ } catch (UnknownHostException e) {
+ host_name = "unknown_localhost";
+ }
+ PBE_SALT = host_name;
+ }
+
+ /**
+ * The following section (encrypt(), decrypt() and doEncryption() methods) is
+ * used to store user passwords in an encrypted way within the settings file.
+ */
+ public static byte[] encrypt(String str) {
+ return (doEncryption(str, Cipher.ENCRYPT_MODE));
+ }
+
+ public static byte[] decrypt(String str) {
+ return (doEncryption(str, Cipher.DECRYPT_MODE));
+ }
+
+ private static byte[] doEncryption(String str, int mode) {
+ // password-based encryption uses 2 parameters for processing:
+ // a *password*, which is then hashed with a *salt* to generate
+ // a strong key - these 2 are defined as class constants
+ try {
+ SecretKeyFactory keyFactory = SecretKeyFactory.getInstance("PBEWithMD5AndDES");
+ PBEKeySpec keySpec = new PBEKeySpec(Util.PBE_PASSWORD.toCharArray());
+ SecretKey key = keyFactory.generateSecret(keySpec);
+ MessageDigest md = MessageDigest.getInstance("MD5");
+ md.update(Util.PBE_SALT.getBytes());
+ byte[] digest = md.digest();
+ byte[] salt = new byte[8];
+ for (int i = 0; i < 8; ++i)
+ salt[i] = digest[i];
+ PBEParameterSpec paramSpec = new PBEParameterSpec(salt, 20);
+
+ Cipher cipher = Cipher.getInstance("PBEWithMD5AndDES");
+ cipher.init(mode, key, paramSpec);
+
+ byte[] encrypted = cipher.doFinal(str.getBytes());
+ return (encrypted);
+ } catch (Exception e) {
+ logger.error("Could not encrypt and store password");
+ logger.error(e.getCause() + "\n" + e.getMessage());
+ return (new byte[1]);
+ }
+
+ }
+
+ // ******** RESIZING OF IMAGES ********
+
+ /**
+ * The method will scale down the <b>sourceImageIcon</b> in a way that it will
+ * fit into the rectangle with dimensions <b>(iRequiredWidth,
+ * iRequiredHeight)</b> with the original aspect ratio being preserved.
+ *
+ * @param iRequiredWidth
+ * Maximum desired width of the resized image.
+ * @param iRequiredHeight
+ * Maximum desired height of the resized image.
+ */
+ public static ImageIcon getResizedImageIcon(ImageIcon sourceImageIcon, int iRequiredWidth, int iRequiredHeight) {
+ // *** calculate the desired width and height of the resized image ***
+ int iWidth = sourceImageIcon.getIconWidth();
+ int iHeight = sourceImageIcon.getIconHeight();
+
+ float fWidthResizeRatio = iWidth / (float) iRequiredWidth;
+ float fHeightResizeRatio = iHeight / (float) iRequiredHeight;
+
+ // the chosen resize ratio will be the greatest of the two -
+ // this way we will preserve aspect ratio of the sides of the
+ // original image
+ float fResizeRatio = Math.max(fWidthResizeRatio, fHeightResizeRatio);
+
+ // obtain the width and height of the new image
+ int iNewWidth = Math.round(iWidth / fResizeRatio);
+ int iNewHeight = Math.round(iHeight / fResizeRatio);
+
+ // *** make the actual resizing work ***
+ BufferedImage resizedImage = new BufferedImage(iNewWidth, iNewHeight, BufferedImage.TYPE_INT_RGB);
+ Graphics2D g2 = resizedImage.createGraphics();
+ g2.setRenderingHint(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BILINEAR);
+ g2.drawImage(sourceImageIcon.getImage(), 0, 0, iNewWidth, iNewHeight, null);
+ g2.dispose();
+ return (new ImageIcon(resizedImage, ""));
+ }
+
+ /**
+ * Loads an image from a remote URL, scales it down to the required size and
+ * stores in a temporary file for the duration of the current session (e.g.
+ * the temporary file will be destroyed on the application termination).
+ *
+ * @param sourceImageURL
+ * URL to fetch the source image from.
+ * @param iRequiredWidth
+ * Maximum desired width of the resized image.
+ * @param iRequiredHeight
+ * Maximum desired height of the resized image.
+ *
+ * @return Local file URL which can be directly used to fetch the resized
+ * image.
+ */
+ public static String getResizedImageIconTempFileURL(URL sourceImageURL, int iRequiredWidth, int iRequiredHeight) {
+ java.io.File fDestinationTempFile = null;
+
+ try {
+ // all resized images will be store in temporary files - these will be deleted on program termination
+ fDestinationTempFile = java.io.File.createTempFile("resized_image", "jpg");
+ fDestinationTempFile.deleteOnExit();
+
+ // resize the image icon
+ ImageIcon sourceImageIcon = new ImageIcon(sourceImageURL);
+ ImageIcon resizedImageIcon = Util.getResizedImageIcon(sourceImageIcon, iRequiredWidth, iRequiredHeight);
+
+ Image img = resizedImageIcon.getImage();
+ BufferedImage bi = new BufferedImage(img.getWidth(null), img.getHeight(null), BufferedImage.TYPE_INT_RGB);
+ Graphics2D g2 = bi.createGraphics();
+ // Draw img into bi so we can write it to file.
+ g2.drawImage(img, 0, 0, null);
+ g2.dispose();
+ // Now bi contains the img.
+ // Note: img may have transparent pixels in it; if so, okay.
+ // If not and you can use TYPE_INT_RGB you will get better
+ // performance with it in the jvm.
+ ImageIO.write(bi, "jpg", fDestinationTempFile);
+ } catch (Exception e) {
+
+ }
+
+ return ("file:///" + fDestinationTempFile.getAbsolutePath());
+ }
+
+ // ******** DATA RETRIEVAL FROM XML DOCUMENT FRAGMENTS ********
+
+ /**
+ * Instantiates primitive Resource object from XML element. This is very
+ * lightweight and completely generic - it only sets resource's type, title
+ * and URL on myExperiment / URI in the API.
+ */
+ public static Resource instantiatePrimitiveResourceFromElement(Element e) {
+ if (e != null) {
+ Resource r = new Resource();
+ r.setItemType(e.getName());
+ r.setTitle(e.getText());
+ r.setURI(e.getAttributeValue("uri"));
+ r.setResource(e.getAttributeValue("resource"));
+ return (r);
+ } else {
+ return (null);
+ }
+ }
+
+ /**
+ * Instantiates primitive User object from XML element. This is much more
+ * lightweight than User.buildFromXML() where full details of the user can be
+ * obtained from XML.
+ */
+ public static User instantiatePrimitiveUserFromElement(Element e) {
+ if (e != null) {
+ User u = new User();
+ u.setName(e.getText());
+ u.setTitle(e.getText());
+ u.setURI(e.getAttributeValue("uri"));
+ u.setResource(e.getAttributeValue("resource"));
+ return (u);
+ } else {
+ return (null);
+ }
+ }
+
+ /**
+ * Instantiates primitive Tag object from XML element. Very lightweight
+ * method.
+ */
+ public static Tag instantiatePrimitiveTagFromElement(Element e) {
+ if (e != null) {
+ Tag t = new Tag();
+ t.setTitle(e.getText());
+ t.setTagName(e.getText());
+ t.setResource(e.getAttributeValue("resource"));
+ t.setURI(e.getAttributeValue("uri"));
+ return (t);
+ } else {
+ return (null);
+ }
+ }
+
+ /**
+ * Instantiates primitive Comment object from XML element. Very lightweight
+ * method - faster and requires less data than Comment.buildFromXML().
+ *
+ * Can only be used if known which resource is being commented.
+ */
+ public static Comment instantiatePrimitiveCommentFromElement(Element e, Resource r) {
+ if (e != null) {
+ Comment c = new Comment();
+ c.setTitle(e.getText());
+ c.setComment(e.getText());
+ c.setTypeOfCommentedResource(r.getItemType());
+ c.setURIOfCommentedResource(r.getURI());
+ c.setResource(e.getAttributeValue("resource"));
+ c.setURI(e.getAttributeValue("uri"));
+ return (c);
+ } else {
+ return (null);
+ }
+ }
+
+ /**
+ * Generic method that accepts the iterator over a collection of resources in
+ * XML format (obtained from myExperiment API) and an ArrayList to store the
+ * processed results in.
+ *
+ * The method will extract 3 attributes for every item in the collection: 1)
+ * name of the item; 2) URI of the item (to access this item via the API); 3)
+ * URI of the item (to access via WEB);
+ *
+ * @return Returns the number of processed elements in the collection.
+ */
+ public static int getResourceCollectionFromXMLIterator(Iterator<Element> iterator, ArrayList<HashMap<String, String>> collection) {
+ int iCount = 0;
+
+ while (iterator.hasNext()) {
+ // get XML element for the next element in the collection
+ Element element = iterator.next();
+
+ // store all details of current group into a hash map
+ HashMap<String, String> itemDetails = new HashMap<String, String>();
+ itemDetails.put("name", element.getText());
+ itemDetails.put("uri", element.getAttributeValue("uri"));
+ itemDetails.put("resource", element.getAttributeValue("resource"));
+
+ // add current item to the complete list of items
+ collection.add(itemDetails);
+ iCount++;
+ }
+
+ return (iCount);
+ }
+
+ /**
+ * Takes XML Element instance with privilege listing for an item and returns
+ * an integer value for that access type.
+ */
+ public static int getAccessTypeFromXMLElement(Element privileges) {
+ // if the item for which the privileges are processed got received,
+ // there definitely is viewing access to it
+ int iAccessType = Resource.ACCESS_VIEWING;
+
+ // pick the highest allowed access type
+ Iterator<Element> iPrivileges = privileges.getChildren("privilege").iterator();
+ while (iPrivileges.hasNext()) {
+ Element privilege = iPrivileges.next();
+ String strValue = privilege.getAttributeValue("type");
+
+ int iCurrentPrivilege = Resource.ACCESS_VIEWING;
+ if (strValue.equals("download"))
+ iCurrentPrivilege = Resource.ACCESS_DOWNLOADING;
+ else if (strValue.equals("edit"))
+ iCurrentPrivilege = Resource.ACCESS_EDITING;
+
+ if (iCurrentPrivilege > iAccessType)
+ iAccessType = iCurrentPrivilege;
+ }
+
+ return (iAccessType);
+ }
+
+ /**
+ * Returns contents of the "reason" field of the error message.
+ */
+ public static String retrieveReasonFromErrorXMLDocument(Document doc) {
+ if (doc != null) {
+ Element root = doc.getRootElement();
+ return (root.getChildText("reason"));
+ } else {
+ return ("unknown reason");
+ }
+ }
+
+ /**
+ * Parses an XML document containing resources favourited by a User. These
+ * resources are instantiated with the basic data available in the XML
+ * document and collected into a single List object.
+ */
+ @SuppressWarnings("unchecked")
+ public static List<Resource> retrieveUserFavourites(Element docRootElement) {
+ List<Resource> favouritedItemList = new ArrayList<Resource>();
+
+ Element favouritesElement = docRootElement.getChild("favourited");
+ if (favouritesElement != null) {
+ Iterator<Element> iFavourites = favouritesElement.getChildren().iterator();
+ while (iFavourites.hasNext()) {
+ favouritedItemList.add(Util.instantiatePrimitiveResourceFromElement(iFavourites.next()));
+ }
+ }
+
+ return (favouritedItemList);
+ }
+
+ /**
+ * Returns a list of credits - can be applied to any XML document which
+ * contains "credits" element.
+ */
+ @SuppressWarnings("unchecked")
+ public static List<Resource> retrieveCredits(Element docRootElement) {
+ List<Resource> credits = new ArrayList<Resource>();
+
+ Element creditsElement = docRootElement.getChild("credits");
+ if (creditsElement != null) {
+ List<Element> creditsNodes = creditsElement.getChildren();
+ for (Element e : creditsNodes) {
+ credits.add(Util.instantiatePrimitiveResourceFromElement(e));
+ }
+ }
+
+ return (credits);
+ }
+
+ /**
+ * Returns a list of attributions - can be applied to any XML document which
+ * contains "attributions" element.
+ */
+ @SuppressWarnings("unchecked")
+ public static List<Resource> retrieveAttributions(Element docRootElement) {
+ List<Resource> attributions = new ArrayList<Resource>();
+
+ Element attributionsElement = docRootElement.getChild("attributions");
+ if (attributionsElement != null) {
+ List<Element> attributionsNodes = attributionsElement.getChildren();
+ for (Element e : attributionsNodes) {
+ attributions.add(Util.instantiatePrimitiveResourceFromElement(e));
+ }
+ }
+
+ return (attributions);
+ }
+
+ /**
+ * Returns a list of tags - can be applied to any XML document which contains
+ * "tags" element.
+ */
+ @SuppressWarnings("unchecked")
+ public static List<Tag> retrieveTags(Element docRootElement) {
+ List<Tag> tags = new ArrayList<Tag>();
+
+ Element tagsElement = docRootElement.getChild("tags");
+ if (tagsElement != null) {
+ List<Element> tagsNodes = tagsElement.getChildren();
+ for (Element e : tagsNodes) {
+ tags.add(Util.instantiatePrimitiveTagFromElement(e));
+ }
+ }
+
+ return (tags);
+ }
+
+ /**
+ * Returns a list of comments - can be applied to any XML document which
+ * contains "comments" element. This should be called when the Resource object
+ * (for which the list of comments is being obtained) is known.
+ */
+ @SuppressWarnings("unchecked")
+ public static List<Comment> retrieveComments(Element docRootElement, Resource r) {
+ List<Comment> comments = new ArrayList<Comment>();
+
+ Element tagsElement = docRootElement.getChild("comments");
+ if (tagsElement != null) {
+ List<Element> tagsNodes = tagsElement.getChildren();
+ for (Element e : tagsNodes) {
+ comments.add(Util.instantiatePrimitiveCommentFromElement(e, r));
+ }
+ }
+
+ return (comments);
+ }
+
+ // ******** STRIPPING OUT HTML FROM STRINGS ********
+
+ /**
+ * Tiny helper to strip out HTML tags. Basic HTML tags like and <br>
+ * are left in place, because these can be rendered by JLabel. This helps to
+ * present HTML content inside JAVA easier.
+ */
+ public static String stripHTML(String source) {
+ // don't do anything if not string is provided
+ if (source == null)
+ return ("");
+
+ // need to preserve at least all line breaks
+ // (ending and starting paragraph also make a line break)
+ source = source.replaceAll("</p>[\r\n]*<p>", "<br>");
+ source = source.replaceAll("\\<br/?\\>", "[-=BR=-]");
+
+ // strip all HTML
+ source = source.replaceAll("\\<.*?\\>", "");
+
+ // put the line breaks back
+ source = source.replaceAll("\\[-=BR=-\\]", "<br><br>");
+
+ return (source);
+ }
+
+ /**
+ * Tiny helper to strip out all HTML tags. This will not leave any HTML tags
+ * at all (so that the content can be displayed in DialogTextArea - and the
+ * like - components. This helps to present HTML content inside JAVA easier.
+ */
+ public static String stripAllHTML(String source) {
+ // don't do anything if not string is provided
+ if (source == null)
+ return ("");
+
+ // need to preserve at least all line breaks
+ // (ending and starting paragraph also make a line break)
+ source = source.replaceAll("</p>[\r\n]*<p>", "<br>");
+ source = source.replaceAll("\\<br/?\\>", "\n\n");
+
+ // strip all HTML
+ source = source.replaceAll("\\<.*?\\>", ""); // any HTML tags
+ source = source.replaceAll("&\\w{1,4};", ""); // this is for things like " ", ">", etc
+
+ return (source);
+ }
+
+ // ******** WINDOW OPERATIONS ********
+
+ /**
+ * Makes sure that one component (for example, a window) is centered
+ * horizontally and vertically relatively to the other component.
+ *
+ * This method is applicable when 'dependentComponent' fully fits within the
+ * 'mainComponent'. Otherwise behaviour is unpredictable.
+ */
+ public static void centerComponentWithinAnother(Component mainComponent, Component dependentComponent) {
+ int iMainComponentCenterX = (int) Math.round(mainComponent.getLocationOnScreen().getX()
+ + (mainComponent.getWidth() / 2));
+ int iPosX = iMainComponentCenterX - (dependentComponent.getWidth() / 2);
+ int iMainComponentCenterY = (int) Math.round(mainComponent.getLocationOnScreen().getY()
+ + (mainComponent.getHeight() / 2));
+ int iPosY = iMainComponentCenterY - (dependentComponent.getHeight() / 2);
+
+ dependentComponent.setLocation(iPosX, iPosY);
+ }
+
+ // ******** VARIOUS HELPERS ********
+
+ /**
+ * Generates a JClickableLabel instance for a supplied Resource object with a
+ * specified click handler.
+ */
+ public static JClickableLabel generateClickableLabelFor(Resource r, ActionListener clickHandler) {
+ return (new JClickableLabel(r.getTitle(), "preview:" + r.getItemType()
+ + ":" + r.getURI(), clickHandler, new ImageIcon(MyExperimentPerspective.getLocalIconURL(r.getItemType())), SwingConstants.LEFT, r.getItemTypeName()
+ + ": " + r.getTitle()));
+ }
+
+ /**
+ * Generates a JLabel with a "none-text" style.
+ */
+ public static JLabel generateNoneTextLabel(String strLabel) {
+ JLabel lNoneText = new JLabel(strLabel);
+ lNoneText.setFont(lNoneText.getFont().deriveFont(Font.ITALIC));
+ lNoneText.setForeground(Color.GRAY);
+ lNoneText.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
+ return (lNoneText);
+ }
+
+ /**
+ * A helper method to assemble part of the URL query for myExperiment API.
+ * This will produce a string in the form of
+ * "&elements=<element1>[,<element2>,...]
+ *
+ * @param queryInstance
+ * Instance of {@link QuerySearchInstance} that contains details on
+ * the current search by query or null value if search by tag is
+ * being made.
+ */
+ public static String composeAPIQueryElements(QuerySearchInstance queryInstance) {
+ // this will create one large comma-separated string of elements that
+ // are required for generating a FULL LISTING (which is used in search
+ // result presentation) for all various types
+ String strElements = "";
+ if (queryInstance == null || queryInstance.getSearchWorkflows()) {
+ strElements += Workflow.getRequiredAPIElements(Resource.REQUEST_FULL_LISTING)
+ + ",";
+ }
+ if (queryInstance == null || queryInstance.getSearchFiles()) {
+ strElements += File.getRequiredAPIElements(Resource.REQUEST_FULL_LISTING)
+ + ",";
+ }
+ if (queryInstance == null || queryInstance.getSearchPacks()) {
+ strElements += Pack.getRequiredAPIElements(Resource.REQUEST_FULL_LISTING)
+ + ",";
+ }
+ if (queryInstance == null || queryInstance.getSearchUsers()) {
+ strElements += User.getRequiredAPIElements(Resource.REQUEST_FULL_LISTING)
+ + ",";
+ }
+ if (queryInstance == null || queryInstance.getSearchGroups()) {
+ strElements += Group.getRequiredAPIElements(Resource.REQUEST_FULL_LISTING)
+ + ",";
+ }
+
+ // now need to make this list of elements to contain only unique tokens
+ TreeSet<String> elementSet = new TreeSet<String>(Arrays.asList(strElements.split(",")));
+ Iterator<String> elementSetIterator = elementSet.iterator();
+ strElements = "&elements=";
+ while (elementSetIterator.hasNext()) {
+ strElements += elementSetIterator.next();
+ if (elementSetIterator.hasNext())
+ strElements += ",";
+ }
+
+ return (strElements);
+ }
+
+ /**
+ * The parameter is the class name to be processed; class name is likely to be
+ * in the form <class_name>$<integer_value>, where the trailing part starting
+ * with the $ sign indicates the anonymous inner class within the base class.
+ * This will strip out that part of the class name to get the base class name.
+ */
+ public static String getBaseClassName(String strClassName) {
+ // strip out the class name part after the $ sign; return
+ // the original value if the dollar sign wasn't found
+ String strResult = strClassName;
+
+ int iDollarIdx = strResult.indexOf("$");
+ if (iDollarIdx != -1)
+ strResult = strResult.substring(0, iDollarIdx);
+
+ return (strResult);
+ }
+
+ /**
+ * Determines whether the plugin is running as a standalone JFrame or inside
+ * Taverna Workbench.
+ */
+ public static boolean isRunningInTaverna() {
+ try {
+ // ApplicationRuntime class is defined within Taverna API. If this is available,
+ // it should mean that the plugin runs within Taverna.
+ ApplicationRuntime.getInstance();
+ return true;
+ } catch (NoClassDefFoundError e) {
+ return false;
+ }
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Workflow.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Workflow.java
new file mode 100644
index 0000000..0b0e3d3
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/ui/perspectives/myexperiment/model/Workflow.java
@@ -0,0 +1,420 @@
+// Copyright (C) 2008 The University of Manchester, University of Southampton
+// and Cardiff University
+package net.sf.taverna.t2.ui.perspectives.myexperiment.model;
+
+import java.net.URI;
+import java.text.DateFormat;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+
+/**
+ * @author Jiten Bhagat, Sergejs Aleksejevs
+ */
+public class Workflow extends Resource {
+ // CONSTANTS
+ public static final String MIME_TYPE_TAVERNA_1 = "application/vnd.taverna.scufl+xml";
+ public static final String MIME_TYPE_TAVERNA_2 = "application/vnd.taverna.t2flow+xml";
+
+ private int accessType;
+
+ private int version;
+ private User uploader;
+ private URI preview;
+ private URI thumbnail;
+ private URI thumbnailBig;
+ private URI svg;
+ private License license;
+
+ private String visibleType;
+ private String contentType;
+ private URI contentUri;
+ byte[] content;
+
+ private List<Tag> tags;
+ private List<Comment> comments;
+ private List<Resource> credits;
+ private List<Resource> attributions;
+ private HashMap<String, ArrayList<HashMap<String, String>>> components;
+
+ public Workflow() {
+ super();
+ this.setItemType(Resource.WORKFLOW);
+ }
+
+ public int getAccessType() {
+ return this.accessType;
+ }
+
+ public void setAccessType(int accessType) {
+ this.accessType = accessType;
+ }
+
+ public int getVersion() {
+ return version;
+ }
+
+ public void setVersion(int version) {
+ this.version = version;
+ }
+
+ public User getUploader() {
+ return uploader;
+ }
+
+ public void setUploader(User uploader) {
+ this.uploader = uploader;
+ }
+
+ public URI getPreview() {
+ return preview;
+ }
+
+ public void setPreview(URI preview) {
+ this.preview = preview;
+ }
+
+ public URI getThumbnail() {
+ return thumbnail;
+ }
+
+ public void setThumbnail(URI thumbnail) {
+ this.thumbnail = thumbnail;
+ }
+
+ public URI getSvg() {
+ return svg;
+ }
+
+ public void setSvg(URI svg) {
+ this.svg = svg;
+ }
+
+ public License getLicense() {
+ return license;
+ }
+
+ public void setLicense(License license) {
+ this.license = license;
+ }
+
+ public URI getContentUri() {
+ return contentUri;
+ }
+
+ public void setContentUri(URI contentUri) {
+ this.contentUri = contentUri;
+ }
+
+ public String getVisibleType() {
+ return this.visibleType;
+ }
+
+ public void setVisibleType(String visibleType) {
+ this.visibleType = visibleType;
+ }
+
+ public String getContentType() {
+ return contentType;
+ }
+
+ public void setContentType(String contentType) {
+ this.contentType = contentType;
+ }
+
+ public byte[] getContent() {
+ return this.content;
+ }
+
+ public void setContent(byte[] content) {
+ this.content = content;
+ }
+
+ public List<Tag> getTags() {
+ return tags;
+ }
+
+ public List<Comment> getComments() {
+ return comments;
+ }
+
+ public List<Resource> getCredits() {
+ return credits;
+ }
+
+ public List<Resource> getAttributions() {
+ return this.attributions;
+ }
+
+ public HashMap<String, ArrayList<HashMap<String, String>>> getComponents() {
+ return this.components;
+ }
+
+ public URI getThumbnailBig() {
+ return thumbnailBig;
+ }
+
+ public void setThumbnailBig(URI thumbnailBig) {
+ this.thumbnailBig = thumbnailBig;
+ }
+
+ /**
+ * Determines whether the current instance of the workflow is a Taverna 1 or
+ * Taverna 2 workflow
+ */
+ public boolean isTavernaWorkflow() {
+ return (contentType.equals(Workflow.MIME_TYPE_TAVERNA_1) || contentType.equals(Workflow.MIME_TYPE_TAVERNA_2));
+ }
+
+ public boolean isTaverna1Workflow() {
+ return (contentType.equals(Workflow.MIME_TYPE_TAVERNA_1));
+ }
+
+ public boolean isTaverna2Workflow() {
+ return (contentType.equals(Workflow.MIME_TYPE_TAVERNA_2));
+ }
+
+ /**
+ * A helper method to return a set of API elements that are needed to satisfy
+ * request of a particular type - e.g. creating a listing of resources or
+ * populating full preview, etc.
+ *
+ * @param iRequestType
+ * A constant value from Resource class.
+ * @return Comma-separated string containing values of required API elements.
+ */
+ public static String getRequiredAPIElements(int iRequestType) {
+ String strElements = "";
+
+ // cases higher up in the list are supersets of those that come below -
+ // hence no "break" statements are required, because 'falling through' the
+ // switch statement is the desired behaviour in this case
+ //
+ // cases that follow after the first 'break' statement are to be treated
+ // separately - these require individual processing and have nothing to do
+ // with joining different elements for various listings / previews
+ switch (iRequestType) {
+ case Resource.REQUEST_FULL_PREVIEW:
+ strElements += "created-at,updated-at,preview,thumbnail-big,svg,license-type,content-uri,"
+ + "tags,comments,ratings,credits,attributions,components,";
+ case Resource.REQUEST_FULL_LISTING:
+ strElements += "uploader,type,";
+ case Resource.REQUEST_SHORT_LISTING:
+ strElements += "id,title,thumbnail,description,privileges,content-type";
+ break;
+ case Resource.REQUEST_WORKFLOW_CONTENT_ONLY:
+ strElements += "type,content-type,content";
+ break;
+ }
+
+ return (strElements);
+ }
+
+ public static Workflow buildFromXML(Document doc, Logger logger) {
+ // if no XML document was supplied, return NULL
+ if (doc == null)
+ return (null);
+
+ // call main method which parses XML document starting from root element
+ return (Workflow.buildFromXML(doc.getRootElement(), logger));
+ }
+
+ // class method to build a workflow instance from XML
+ @SuppressWarnings("unchecked")
+ public static Workflow buildFromXML(Element docRootElement, Logger logger) {
+ // return null to indicate an error if XML document contains no root element
+ if (docRootElement == null)
+ return (null);
+
+ Workflow w = new Workflow();
+
+ try {
+ // Access type
+ w.setAccessType(Util.getAccessTypeFromXMLElement(docRootElement.getChild("privileges")));
+
+ // URI
+ w.setURI(docRootElement.getAttributeValue("uri"));
+
+ // Resource URI
+ w.setResource(docRootElement.getAttributeValue("resource"));
+
+ // Version
+ String version = docRootElement.getAttributeValue("version");
+ if (version != null && !version.equals("")) {
+ w.setVersion(Integer.parseInt(version));
+ }
+
+ // Id
+ String id = docRootElement.getChildText("id");
+ if (id == null || id.equals("")) {
+ id = "API Error - No workflow ID supplied";
+ logger.error("Error while parsing workflow XML data - no ID provided for workflow with title: \""
+ + docRootElement.getChildText("title") + "\"");
+ }
+ w.setID(id);
+
+ // Title
+ w.setTitle(docRootElement.getChildText("title"));
+
+ // Description
+ w.setDescription(docRootElement.getChildText("description"));
+
+ // Uploader
+ Element uploaderElement = docRootElement.getChild("uploader");
+ w.setUploader(Util.instantiatePrimitiveUserFromElement(uploaderElement));
+
+ // Created at
+ String createdAt = docRootElement.getChildText("created-at");
+ if (createdAt != null && !createdAt.equals("")) {
+ w.setCreatedAt(MyExperimentClient.parseDate(createdAt));
+ }
+
+ // Updated at
+ String updatedAt = docRootElement.getChildText("updated-at");
+ if (updatedAt != null && !updatedAt.equals("")) {
+ w.setUpdatedAt(MyExperimentClient.parseDate(updatedAt));
+ }
+
+ // Preview
+ String preview = docRootElement.getChildText("preview");
+ if (preview != null && !preview.equals("")) {
+ w.setPreview(new URI(preview));
+ }
+
+ // Thumbnail
+ String thumbnail = docRootElement.getChildText("thumbnail");
+ if (thumbnail != null && !thumbnail.equals("")) {
+ w.setThumbnail(new URI(thumbnail));
+ }
+
+ // Thumbnail (big)
+ String thumbnailBig = docRootElement.getChildText("thumbnail-big");
+ if (thumbnailBig != null && !thumbnailBig.equals("")) {
+ w.setThumbnailBig(new URI(thumbnailBig));
+ }
+
+ // SVG
+ String svg = docRootElement.getChildText("svg");
+ if (svg != null && !svg.equals("")) {
+ w.setSvg(new URI(svg));
+ }
+
+ // License
+ w.setLicense(License.getInstance(docRootElement.getChildText("license-type")));
+
+ // Content URI
+ String contentUri = docRootElement.getChildText("content-uri");
+ if (contentUri != null && !contentUri.equals("")) {
+ w.setContentUri(new URI(contentUri));
+ }
+
+ // Type and Content-Type
+ w.setVisibleType(docRootElement.getChildText("type"));
+ w.setContentType(docRootElement.getChildText("content-type"));
+
+ // Tags
+ w.tags = new ArrayList<Tag>();
+ w.tags.addAll(Util.retrieveTags(docRootElement));
+
+ // Comments
+ w.comments = new ArrayList<Comment>();
+ w.getComments().addAll(Util.retrieveComments(docRootElement, w));
+
+ // Credits
+ w.credits = new ArrayList<Resource>();
+ w.getCredits().addAll(Util.retrieveCredits(docRootElement));
+
+ // Attributions
+ w.attributions = new ArrayList<Resource>();
+ w.getAttributions().addAll(Util.retrieveAttributions(docRootElement));
+
+ // Components
+ w.components = new HashMap<String, ArrayList<HashMap<String, String>>>();
+
+ Element componentsElement = docRootElement.getChild("components");
+ if (componentsElement != null) {
+ // ** inputs **
+ Element sourcesElement = componentsElement.getChild("sources");
+ if (sourcesElement != null) {
+ ArrayList<HashMap<String, String>> inputs = new ArrayList<HashMap<String, String>>();
+ List<Element> sourcesNodes = sourcesElement.getChildren();
+ for (Element e : sourcesNodes) {
+ HashMap<String, String> curInput = new HashMap<String, String>();
+ curInput.put("name", e.getChildText("name"));
+ curInput.put("description", e.getChildText("description"));
+ inputs.add(curInput);
+ }
+
+ // put all inputs that were found into the overall component collection
+ w.getComponents().put("inputs", inputs);
+ }
+
+ // ** outputs **
+ Element outputsElement = componentsElement.getChild("sinks");
+ if (outputsElement != null) {
+ ArrayList<HashMap<String, String>> sinks = new ArrayList<HashMap<String, String>>();
+ List<Element> outputsNodes = outputsElement.getChildren();
+ for (Element e : outputsNodes) {
+ HashMap<String, String> curOutput = new HashMap<String, String>();
+ curOutput.put("name", e.getChildText("name"));
+ curOutput.put("description", e.getChildText("description"));
+ sinks.add(curOutput);
+ }
+
+ // put all outputs that were found into the overall component collection
+ w.getComponents().put("outputs", sinks);
+ }
+
+ // ** processors **
+ Element processorsElement = componentsElement.getChild("processors");
+ if (processorsElement != null) {
+ ArrayList<HashMap<String, String>> processors = new ArrayList<HashMap<String, String>>();
+ List<Element> processorsNodes = processorsElement.getChildren();
+ for (Element e : processorsNodes) {
+ HashMap<String, String> curProcessor = new HashMap<String, String>();
+ curProcessor.put("name", e.getChildText("name"));
+ curProcessor.put("type", e.getChildText("type"));
+ curProcessor.put("description", e.getChildText("description"));
+ processors.add(curProcessor);
+ }
+
+ // put all processors that were found into the overall component collection
+ w.getComponents().put("processors", processors);
+ }
+
+ // ** links **
+ Element linksElement = componentsElement.getChild("links");
+ if (linksElement != null) {
+ ArrayList<HashMap<String, String>> links = new ArrayList<HashMap<String, String>>();
+ List<Element> linksNodes = linksElement.getChildren();
+ for (Element e : linksNodes) {
+ HashMap<String, String> curLink = new HashMap<String, String>();
+ String strSource = e.getChild("source").getChildText("node")
+ + (e.getChild("source").getChildText("port") == null ? "" : (":" + e.getChild("source").getChildText("port")));
+ curLink.put("source", strSource);
+ String strSink = e.getChild("sink").getChildText("node")
+ + (e.getChild("sink").getChildText("port") == null ? "" : (":" + e.getChild("sink").getChildText("port")));
+ curLink.put("sink", strSink);
+ links.add(curLink);
+ }
+
+ // put all links that were found into the overall component collection
+ w.getComponents().put("links", links);
+ }
+ }
+
+ logger.debug("Found information for worklow with ID: " + w.getID()
+ + ", Title: " + w.getTitle());
+ } catch (Exception e) {
+ logger.error("Failed midway through creating workflow object from XML", e);
+ }
+
+ // return created workflow instance
+ return (w);
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/workbench/myexperiment/config/MyExperimentConfiguration.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/workbench/myexperiment/config/MyExperimentConfiguration.java
new file mode 100644
index 0000000..6ae333b
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/workbench/myexperiment/config/MyExperimentConfiguration.java
@@ -0,0 +1,68 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.myexperiment.config;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import uk.org.taverna.configuration.AbstractConfigurable;
+//import org.apache.log4j.Logger;
+import uk.org.taverna.configuration.Configurable;
+
+/**
+ * @author Emmanuel Tagarira, Alan Williams
+ */
+public class MyExperimentConfiguration extends AbstractConfigurable {
+ private static class Singleton {
+ private static MyExperimentConfiguration instance = new MyExperimentConfiguration();
+ }
+
+ //private static Logger logger = Logger.getLogger(MyExperimentConfiguration.class);
+
+ private Map<String, String> defaultPropertyMap;
+
+ public String getCategory() {
+ return "general";
+ }
+
+ public Map<String, String> getDefaultPropertyMap() {
+ if (defaultPropertyMap == null) {
+ defaultPropertyMap = new HashMap<String, String>();
+ }
+ return defaultPropertyMap;
+ }
+
+ public String getDisplayName() {
+ return "myExperiment";
+ }
+
+ public String getFilePrefix() {
+ return "myExperiment";
+ }
+
+ public String getUUID() {
+ return "d25867g1-6078-22ee-bf27-1911311d0b77";
+ }
+
+ public static Configurable getInstance() {
+ return Singleton.instance;
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/workbench/myexperiment/config/MyExperimentConfigurationPanel.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/workbench/myexperiment/config/MyExperimentConfigurationPanel.java
new file mode 100644
index 0000000..656dfc1
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/workbench/myexperiment/config/MyExperimentConfigurationPanel.java
@@ -0,0 +1,305 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.myexperiment.config;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+import javax.swing.border.EmptyBorder;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.MainComponent;
+import net.sf.taverna.t2.ui.perspectives.myexperiment.model.MyExperimentClient;
+import net.sf.taverna.t2.workbench.helper.Helper;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+
+// import org.apache.log4j.Logger;
+
+/**
+ * @author Emmanuel Tagarira, Sergejs Aleksejevs, Alan Williams
+ */
+@SuppressWarnings("serial")
+public class MyExperimentConfigurationPanel extends JPanel implements ActionListener {
+ // CONSTANTS
+
+ // components for accessing application's main elements
+ private final MainComponent pluginMainComponent = MainComponent.MAIN_COMPONENT;
+ private final MyExperimentClient myExperimentClient = MainComponent.MY_EXPERIMENT_CLIENT;
+ //private final Logger logger = MainComponent.LOGGER;
+
+ // COMPONENTS
+ private JTextField tfMyExperimentURL;
+ private JComboBox cbDefaultLoggedInTab;
+ private JComboBox cbDefaultNotLoggedInTab;
+ private JCheckBox cbMyStuffWorkflows;
+ private JCheckBox cbMyStuffFiles;
+ private JCheckBox cbMyStuffPacks;
+ private JButton bApply;
+ private JButton bReset;
+ private JButton bHelp;
+
+ // DATA STORAGE
+ private final Component[] pluginTabComponents;
+ private final ArrayList<String> alPluginTabComponentNames;
+
+ public MyExperimentConfigurationPanel() {
+ super();
+
+ // prepare plugin tab names to display in the UI afterwards
+ this.alPluginTabComponentNames = new ArrayList<String>();
+ this.pluginTabComponents = pluginMainComponent.getMainTabs().getComponents();
+ for (int i = 0; i < this.pluginTabComponents.length; i++)
+ alPluginTabComponentNames.add(pluginMainComponent.getMainTabs().getTitleAt(i));
+
+ this.initialiseUI();
+ this.initialiseData();
+ }
+
+ private void initialiseUI() {
+ // this constraints instance will be shared among all components in the window
+ GridBagConstraints c = new GridBagConstraints();
+
+ // create the myExperiment API address box
+ JPanel jpApiLocation = new JPanel();
+ jpApiLocation.setLayout(new GridBagLayout());
+
+ Insets insLabel = new Insets(0, 0, 0, 10);
+ Insets insParam = new Insets(0, 3, 5, 3);
+
+ // Title describing what kind of settings we are configuring here
+ JTextArea descriptionText = new JTextArea("Configure the myExperiment integration functionality");
+ descriptionText.setLineWrap(true);
+ descriptionText.setWrapStyleWord(true);
+ descriptionText.setEditable(false);
+ descriptionText.setFocusable(false);
+ descriptionText.setBorder(new EmptyBorder(10, 10, 10, 10));
+ c.anchor = GridBagConstraints.WEST;
+ c.gridx = 0;
+ c.gridy = 0;
+ c.weightx = 1.0;
+ c.weighty = 0.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ jpApiLocation.add(descriptionText, c);
+
+ c.gridx = 0;
+ c.gridy = 1;
+ c.weightx = 1.0;
+ //c.insets = insLabel;
+ c.anchor = GridBagConstraints.WEST;
+ c.insets = new Insets(10, 0, 0, 10);
+ jpApiLocation.add(new JLabel("Base URL of myExperiment instance to connect to"), c);
+
+ c.gridy = 2;
+ //c.insets = insParam;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.insets = new Insets(0, 0, 0, 0);
+ this.tfMyExperimentURL = new JTextField();
+ this.tfMyExperimentURL.setToolTipText("<html>Here you can specify the base URL of the myExperiment "
+ + "instance that you wish to connect to.<br>This allows the plugin to connect not only to the "
+ + "<b>main myExperiment website</b> (default value:<br><b>http://www.myexperiment.org</b>) but "
+ + "also to any other myExperiment instance that might<br>exist elsewhere.<br><br>It is recommended "
+ + "that you only change this setting if you are certain in your actions.</html>");
+ jpApiLocation.add(this.tfMyExperimentURL, c);
+
+ // create startup tab choice box
+ JPanel jpStartupTabChoice = new JPanel();
+ jpStartupTabChoice.setLayout(new GridBagLayout());
+
+ c.gridy = 0;
+ c.insets = insLabel;
+ jpStartupTabChoice.add(new JLabel("Default startup tab for anonymous user"), c);
+
+ c.gridx = 1;
+ c.insets = insParam;
+ this.cbDefaultNotLoggedInTab = new JComboBox(this.alPluginTabComponentNames.toArray());
+ this.cbDefaultNotLoggedInTab.setToolTipText("<html>This tab will be automatically opened at plugin start up time if you are <b>not</b> logged id to myExperiment.</html>");
+ jpStartupTabChoice.add(this.cbDefaultNotLoggedInTab, c);
+
+ c.gridy = 1;
+ c.gridx = 0;
+ c.insets = insLabel;
+ jpStartupTabChoice.add(new JLabel("Default startup tab after successful auto-login"), c);
+
+ c.gridx = 1;
+ c.insets = insParam;
+ this.cbDefaultLoggedInTab = new JComboBox(this.alPluginTabComponentNames.toArray());
+ this.cbDefaultLoggedInTab.setToolTipText("<html>This tab will be automatically opened at plugin start up time if you have chosen to use <b>auto logging in</b> to myExperiment.</html>");
+ jpStartupTabChoice.add(this.cbDefaultLoggedInTab, c);
+
+ // create 'my stuff' tab preference box
+ JPanel jpMyStuffPrefs = new JPanel();
+ jpMyStuffPrefs.setLayout(new GridBagLayout());
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.insets = insLabel;
+ jpMyStuffPrefs.add(new JLabel("Sections to show in this tab:"), c);
+
+ c.gridx = 1;
+ c.gridy = 0;
+ c.weightx = 1.0;
+ c.insets = new Insets(insParam.top, 100, insParam.bottom / 3, insParam.right);
+ this.cbMyStuffWorkflows = new JCheckBox("My Workflows");
+ jpMyStuffPrefs.add(this.cbMyStuffWorkflows, c);
+
+ c.gridy = 1;
+ this.cbMyStuffFiles = new JCheckBox("My Files");
+ jpMyStuffPrefs.add(this.cbMyStuffFiles, c);
+
+ c.gridy = 2;
+ this.cbMyStuffPacks = new JCheckBox("My Packs");
+ jpMyStuffPrefs.add(this.cbMyStuffPacks, c);
+
+ // create button panel
+ this.bApply = new JButton("Apply");
+ this.bApply.addActionListener(this);
+
+ this.bReset = new JButton("Reset");
+ this.bReset.addActionListener(this);
+
+ this.bHelp = new JButton("Help");
+ this.bHelp.addActionListener(this);
+
+ JPanel jpButtons = new JPanel();
+ jpButtons.add(bHelp, c);
+ jpButtons.add(bReset, c);
+ jpButtons.add(bApply, c);
+
+ // PUT EVERYTHING TOGETHER
+ JPanel jpEverything = new JPanel();
+ GridBagLayout jpEverythingLayout = new GridBagLayout();
+ jpEverything.setLayout(jpEverythingLayout);
+
+ GridBagConstraints gbConstraints = new GridBagConstraints();
+ gbConstraints.fill = GridBagConstraints.BOTH;
+ c.anchor = GridBagConstraints.NORTHWEST;
+
+ gbConstraints.weightx = 1;
+ gbConstraints.gridx = 0;
+
+ gbConstraints.gridy = 0;
+ jpEverything.add(jpApiLocation, gbConstraints);
+
+ gbConstraints.gridy++;
+ jpEverything.add(jpStartupTabChoice, gbConstraints);
+
+ gbConstraints.gridy++;
+ jpEverything.add(jpMyStuffPrefs, gbConstraints);
+
+ gbConstraints.gridy++;
+ c.insets = new Insets(10, 0, 0, 0);
+ jpEverything.add(jpButtons, gbConstraints);
+
+ BorderLayout layout = new BorderLayout();
+ this.setLayout(layout);
+ this.add(jpEverything, BorderLayout.NORTH);
+
+ if (MyExperimentClient.baseChangedSinceLastStart) {
+ JPanel jpInfo = new JPanel();
+ jpInfo.setLayout(new BoxLayout(jpInfo, BoxLayout.Y_AXIS));
+ String info = "<html>Your myExperiment base url has been modified since Taverna was started;<br>"
+ + "this change will not take effect until you restart Taverna.</html>";
+ jpInfo.add(new JLabel(info, WorkbenchIcons.leafIcon, SwingConstants.LEFT));
+ this.add(jpInfo, BorderLayout.SOUTH);
+ }
+ }
+
+ private void initialiseData() {
+ // myExperiment Base URL
+ this.tfMyExperimentURL.setText(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_BASE_URL));
+
+ // default tabs
+ this.cbDefaultNotLoggedInTab.setSelectedIndex(Integer.parseInt(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_DEFAULT_ANONYMOUS_TAB)));
+ this.cbDefaultLoggedInTab.setSelectedIndex(Integer.parseInt(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_DEFAULT_LOGGED_IN_TAB)));
+
+ // components of "My Stuff" tab
+ this.cbMyStuffWorkflows.setSelected(Boolean.parseBoolean(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_MY_STUFF_WORKFLOWS)));
+ this.cbMyStuffFiles.setSelected(Boolean.parseBoolean(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_MY_STUFF_FILES)));
+ this.cbMyStuffPacks.setSelected(Boolean.parseBoolean(myExperimentClient.getSettings().getProperty(MyExperimentClient.INI_MY_STUFF_PACKS)));
+ }
+
+ // *** Callback for ActionListener interface ***
+
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource().equals(this.bApply)) {
+ // check if myExperiment address is present
+ String strNewMyExperimentURL = this.tfMyExperimentURL.getText().trim();
+ if (strNewMyExperimentURL.length() == 0) {
+ javax.swing.JOptionPane.showMessageDialog(null, "Please specify a base URL of myExperiment instance that you wish to connect to", "Error", JOptionPane.WARNING_MESSAGE);
+ this.tfMyExperimentURL.requestFocusInWindow();
+ return;
+ }
+
+ // check if at least one of the checkboxes (for sections in 'My Stuff' tab) is selected
+ if (!(this.cbMyStuffWorkflows.isSelected()
+ || this.cbMyStuffFiles.isSelected() || this.cbMyStuffPacks.isSelected())) {
+ javax.swing.JOptionPane.showMessageDialog(null, "Please choose at least one section to display in 'My Stuff' tab", "Error", JOptionPane.WARNING_MESSAGE);
+ this.cbMyStuffWorkflows.requestFocusInWindow();
+ return;
+ }
+
+ // all values should be present - store these into Properties object
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_BASE_URL, strNewMyExperimentURL);
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_DEFAULT_ANONYMOUS_TAB, new Integer(cbDefaultNotLoggedInTab.getSelectedIndex()).toString());
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_DEFAULT_LOGGED_IN_TAB, new Integer(cbDefaultLoggedInTab.getSelectedIndex()).toString());
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_MY_STUFF_WORKFLOWS, new Boolean(cbMyStuffWorkflows.isSelected()).toString());
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_MY_STUFF_FILES, new Boolean(cbMyStuffFiles.isSelected()).toString());
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_MY_STUFF_PACKS, new Boolean(cbMyStuffPacks.isSelected()).toString());
+
+ // NB! changed myExperiment location will not take action until the next application restart
+ if (MyExperimentClient.baseChangedSinceLastStart
+ || !strNewMyExperimentURL.equals(myExperimentClient.getBaseURL())) {
+ // turn off auto-login
+ myExperimentClient.getSettings().put(MyExperimentClient.INI_AUTO_LOGIN, new Boolean(false).toString());
+
+ javax.swing.JOptionPane.showMessageDialog(null, "You have selected a new Base URL for myExperiment.\n"
+ + "Your new setting has been saved, but will not take\n"
+ + "effect until you restart Taverna.\n\n"
+ + "The auto-login feature has been disabled for you to\n"
+ + "check the login details at the next launch.", "myExperiment Plugin - Info", JOptionPane.INFORMATION_MESSAGE);
+
+ MyExperimentClient.baseChangedSinceLastStart = true;
+ }
+
+ myExperimentClient.storeHistoryAndSettings();
+ // pluginMainComponent = new MainComponent();
+ } else if (e.getSource().equals(this.bHelp)) {
+ Helper.showHelp(this);
+ } else if (e.getSource().equals(this.bReset)) {
+ initialiseData();
+ }
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/workbench/myexperiment/config/MyExperimentConfigurationUIFactory.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/workbench/myexperiment/config/MyExperimentConfigurationUIFactory.java
new file mode 100644
index 0000000..3026edc
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/workbench/myexperiment/config/MyExperimentConfigurationUIFactory.java
@@ -0,0 +1,62 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.myexperiment.config;
+
+import javax.swing.JPanel;
+
+import uk.org.taverna.configuration.Configurable;
+import uk.org.taverna.configuration.ConfigurationUIFactory;
+
+import net.sf.taverna.t2.ui.perspectives.myexperiment.MainComponent;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+
+/**
+ * @author Emmanuel Tagarira, Alan Williams
+ */
+public class MyExperimentConfigurationUIFactory implements ConfigurationUIFactory {
+
+ private EditManager editManager;
+private FileManager fileManager;
+
+public boolean canHandle(String uuid) {
+ return uuid.equals(getConfigurable().getUUID());
+ }
+
+ public JPanel getConfigurationPanel() {
+ if (MainComponent.MAIN_COMPONENT == null)
+ MainComponent.MAIN_COMPONENT = new MainComponent(editManager, fileManager);
+ return new MyExperimentConfigurationPanel();
+ }
+
+ public Configurable getConfigurable() {
+ return MyExperimentConfiguration.getInstance();
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/workbench/myexperiment/config/TestJFrameForPreferencesLocalLaunch.java b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/workbench/myexperiment/config/TestJFrameForPreferencesLocalLaunch.java
new file mode 100644
index 0000000..2cdc111
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/java/net/sf/taverna/t2/workbench/myexperiment/config/TestJFrameForPreferencesLocalLaunch.java
@@ -0,0 +1,46 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.myexperiment.config;
+
+import java.awt.Dimension;
+
+import javax.swing.JFrame;
+
+/**
+ * This is a class to get a visual on what the preferences will look like when
+ * integrated into the main taverna preferences.
+ *
+ * @author Emmanuel Tagarira
+ */
+public class TestJFrameForPreferencesLocalLaunch {
+
+ public static void main(String[] args) {
+ JFrame frame = new JFrame("myExperiment Preferences Test");
+ frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+
+ frame.setMinimumSize(new Dimension(500, 300));
+ frame.setLocation(300, 150);
+ frame.getContentPane().add(new MyExperimentConfigurationPanel());
+
+ frame.pack();
+ frame.setVisible(true);
+ }
+}
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ShutdownSPI b/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ShutdownSPI
new file mode 100644
index 0000000..97e6981
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ShutdownSPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.ui.perspectives.myexperiment.MainComponentShutdownHook
\ No newline at end of file
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.configuration.ConfigurationUIFactory b/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.configuration.ConfigurationUIFactory
new file mode 100644
index 0000000..1391621
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.configuration.ConfigurationUIFactory
@@ -0,0 +1 @@
+net.sf.taverna.t2.workbench.myexperiment.config.MyExperimentConfigurationUIFactory
\ No newline at end of file
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.PerspectiveSPI b/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.PerspectiveSPI
new file mode 100644
index 0000000..62fd99e
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.PerspectiveSPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.ui.perspectives.myexperiment.MyExperimentPerspective
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.UIComponentFactorySPI b/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.UIComponentFactorySPI
new file mode 100644
index 0000000..9a7aa26
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.UIComponentFactorySPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.ui.perspectives.myexperiment.MainComponentFactory
\ No newline at end of file
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.UIComponentSPI b/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.UIComponentSPI
new file mode 100644
index 0000000..e9b6cee
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.zaria.UIComponentSPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.ui.perspectives.myexperiment.MainComponent
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/spring/perspective-myexperiment-context-osgi.xml b/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/spring/perspective-myexperiment-context-osgi.xml
new file mode 100644
index 0000000..0296415
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/spring/perspective-myexperiment-context-osgi.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="MyExperimentConfigurationUIFactory" interface="uk.org.taverna.configuration.ConfigurationUIFactory" />
+
+ <service ref="MainComponentFactory" interface="net.sf.taverna.t2.workbench.ui.zaria.UIComponentFactorySPI" />
+
+ <service ref="MyExperimentPerspective" interface="net.sf.taverna.t2.workbench.ui.zaria.PerspectiveSPI" />
+
+ <service ref="MainComponentShutdownHook" interface="net.sf.taverna.t2.workbench.ShutdownSPI" />
+
+ <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
+ <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
+
+</beans:beans>
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/spring/perspective-myexperiment-context.xml b/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/spring/perspective-myexperiment-context.xml
new file mode 100644
index 0000000..bfd031f
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/META-INF/spring/perspective-myexperiment-context.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="MyExperimentConfigurationUIFactory" class="net.sf.taverna.t2.workbench.myexperiment.config.MyExperimentConfigurationUIFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ </bean>
+
+ <bean id="MainComponentFactory" class="net.sf.taverna.t2.ui.perspectives.myexperiment.MainComponentFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ </bean>
+
+ <bean id="MyExperimentPerspective" class="net.sf.taverna.t2.ui.perspectives.myexperiment.MyExperimentPerspective" />
+
+ <bean id="MainComponentShutdownHook" class="net.sf.taverna.t2.ui.perspectives.myexperiment.MainComponentShutdownHook" />
+
+</beans>
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/ajax-loader-still.gif b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/ajax-loader-still.gif
new file mode 100644
index 0000000..b100470
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/ajax-loader-still.gif
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/ajax-loader.gif b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/ajax-loader.gif
new file mode 100644
index 0000000..078b55f
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/ajax-loader.gif
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/arrow_left.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/arrow_left.png
new file mode 100644
index 0000000..2bed329
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/arrow_left.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/arrow_refresh.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/arrow_refresh.png
new file mode 100644
index 0000000..0de2656
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/arrow_refresh.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/arrow_right.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/arrow_right.png
new file mode 100644
index 0000000..2cf15f1
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/arrow_right.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/comment_add.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/comment_add.png
new file mode 100644
index 0000000..75e78de
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/comment_add.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/comment_delete.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/comment_delete.png
new file mode 100644
index 0000000..643fdbe
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/comment_delete.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/cross.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/cross.png
new file mode 100644
index 0000000..1514d51
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/cross.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/denied.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/denied.png
new file mode 100644
index 0000000..c37bd06
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/denied.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/dummy-workflow.t2flow b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/dummy-workflow.t2flow
new file mode 100644
index 0000000..120c29d
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/dummy-workflow.t2flow
@@ -0,0 +1,157 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow">
+ <dataflow id="ec0991ba-275c-49ed-b1d6-38534180fb7c" role="top">
+ <name>simple_workflow_with_input</name>
+ <inputPorts>
+ <port>
+ <name>input</name>
+ <depth>0</depth>
+ <granularDepth>0</granularDepth>
+ </port>
+ </inputPorts>
+ <outputPorts>
+ <port>
+ <name>output</name>
+ </port>
+ </outputPorts>
+ <processors>
+ <processor>
+ <name>Concat_XXX</name>
+ <inputPorts>
+ <port>
+ <name>input</name>
+ <depth>0</depth>
+ </port>
+ </inputPorts>
+ <outputPorts>
+ <port>
+ <name>output</name>
+ <depth>0</depth>
+ <granularDepth>0</granularDepth>
+ </port>
+ </outputPorts>
+ <annotations />
+ <activities>
+ <activity>
+ <class>
+ net.sf.taverna.t2.activities.beanshell.BeanshellActivity
+ </class>
+ <inputMap>
+ <map from="input" to="input" />
+ </inputMap>
+ <outputMap>
+ <map from="output" to="output" />
+ </outputMap>
+ <configBean encoding="xstream">
+ <net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean
+ xmlns="">
+ <script>String output = input + "XXX";</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>input</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>output</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+ </net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean>
+ </configBean>
+ </activity>
+ </activities>
+ <dispatchStack>
+ <dispatchLayer>
+ <class>
+ net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
+ </class>
+ <configBean encoding="xstream">
+ <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
+ xmlns="">
+ <maxJobs>1</maxJobs>
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig>
+ </configBean>
+ </dispatchLayer>
+ <dispatchLayer>
+ <class>
+ net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce
+ </class>
+ <configBean encoding="xstream">
+ <null xmlns="" />
+ </configBean>
+ </dispatchLayer>
+ <dispatchLayer>
+ <class>
+ net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover
+ </class>
+ <configBean encoding="xstream">
+ <null xmlns="" />
+ </configBean>
+ </dispatchLayer>
+ <dispatchLayer>
+ <class>
+ net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
+ </class>
+ <configBean encoding="xstream">
+ <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
+ xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>0</initialDelay>
+ <maxDelay>0</maxDelay>
+ <maxRetries>0</maxRetries>
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig>
+ </configBean>
+ </dispatchLayer>
+ <dispatchLayer>
+ <class>
+ net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke
+ </class>
+ <configBean encoding="xstream">
+ <null xmlns="" />
+ </configBean>
+ </dispatchLayer>
+ </dispatchStack>
+ <iterationStrategyStack>
+ <iteration>
+ <strategy>
+ <port name="input" depth="0" />
+ </strategy>
+ </iteration>
+ </iterationStrategyStack>
+ </processor>
+ </processors>
+ <conditions />
+ <datalinks>
+ <datalink>
+ <sink type="processor">
+ <processor>Concat_XXX</processor>
+ <port>input</port>
+ </sink>
+ <source type="dataflow">
+ <port>input</port>
+ </source>
+ </datalink>
+ <datalink>
+ <sink type="dataflow">
+ <port>output</port>
+ </sink>
+ <source type="processor">
+ <processor>Concat_XXX</processor>
+ <port>output</port>
+ </source>
+ </datalink>
+ </datalinks>
+ </dataflow>
+</workflow>
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/external_link_listing_small.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/external_link_listing_small.png
new file mode 100644
index 0000000..a22b1f7
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/external_link_listing_small.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/favourite_add.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/favourite_add.png
new file mode 100644
index 0000000..e94a7b0
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/favourite_add.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/favourite_delete.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/favourite_delete.png
new file mode 100644
index 0000000..7d7c4f5
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/favourite_delete.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/file.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/file.png
new file mode 100644
index 0000000..336ea5d
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/file.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/group.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/group.png
new file mode 100644
index 0000000..7fb4e1f
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/group.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/login.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/login.png
new file mode 100644
index 0000000..41676a0
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/login.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/logout.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/logout.png
new file mode 100644
index 0000000..2541d2b
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/logout.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/myexp_icon.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/myexp_icon.png
new file mode 100644
index 0000000..6cc44a8
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/myexp_icon.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/myexp_icon16x16.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/myexp_icon16x16.png
new file mode 100644
index 0000000..1732b94
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/myexp_icon16x16.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/myexperiment-perspective.xml b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/myexperiment-perspective.xml
new file mode 100644
index 0000000..3f9a5e2
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/myexperiment-perspective.xml
@@ -0,0 +1,17 @@
+<basepane>
+ <child>
+ <znode classname="net.sf.taverna.zaria.ZRavenComponent">
+ <namedcomponent scroll="false">
+ <name>myExperiment Perspective</name>
+ </namedcomponent>
+ </znode>
+ </child>
+ <namedcomponents>
+ <namedcomponent>
+ <groupid>net.sf.taverna.t2.ui-exts</groupid>
+ <artifact>perspective-myexperiment</artifact>
+ <classname>net.sf.taverna.t2.ui.perspectives.myexperiment.MainComponentFactory</classname>
+ <name>myExperiment Perspective</name>
+ </namedcomponent>
+ </namedcomponents>
+</basepane>
\ No newline at end of file
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/open_in_myExperiment.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/open_in_myExperiment.png
new file mode 100644
index 0000000..c530a98
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/open_in_myExperiment.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/pack.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/pack.png
new file mode 100644
index 0000000..3f1fc42
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/pack.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/remote_resource.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/remote_resource.png
new file mode 100644
index 0000000..b8edc12
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/remote_resource.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/star.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/star.png
new file mode 100644
index 0000000..b88c857
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/star.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/styles.css b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/styles.css
new file mode 100644
index 0000000..4097415
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/styles.css
@@ -0,0 +1,380 @@
+body {
+ font-family: arial, helvetica, clean, sans-serif;
+ margin: 0;
+ padding: 0;
+ background: #FFFFFF;
+}
+
+div.outer {
+ padding-top: 0px;
+ padding-bottom: 0px;
+ padding-left: 10px;
+ padding-right: 10px;
+ background: #FFFFFF;
+}
+
+a {
+ color: #000099;
+ text-decoration: none;
+ overflow: auto;
+}
+
+div.list_item_container {
+ padding-left: 10px;
+ padding-right: 10px;
+ background: #FFFFFF;
+}
+
+div.list_item {
+ margin-top: 10px;
+}
+
+.list_item .title {
+ text-align: left;
+ line-height: 1.0;
+ font-size: 16pt;
+ font-weight: bold;
+ margin-bottom: 0;
+ margin-top: 0;
+ padding: 0;
+}
+
+.list_item .uploader {
+ font-weight: bold;
+ margin-bottom: 0;
+ margin-top: 0;
+ padding: 0;
+}
+
+.list_item .title a {
+ color: #990000;
+}
+
+.list_item .desc {
+ width: 400px;
+ font-size: 12pt;
+ padding-top: 0;
+ padding-bottom: 0;
+ padding-left: 15px;
+ padding-right: 5px;
+ margin-top: 6px;
+ margin-bottom: 0;
+ line-height: 1.4;
+}
+
+div.tag_cloud {
+ text-align: center;
+ line-height: 1.6;
+}
+
+div.tag_cloud a {
+ color: #990000;
+}
+
+div.workflow {
+ text-align: center;
+ margin: 6px;
+ border-width: 1px solid #333333;
+}
+
+.workflow .info {
+ text-align: center;
+ line-height: 1.6;
+ color: #333333;
+}
+
+.workflow .title {
+ text-align: center;
+ line-height: 1.0;
+ color: #333333;
+ font-size: 18pt;
+ font-weight: bold;
+ margin-bottom: 0;
+ margin-top; 0;
+ padding: 0;
+}
+
+.workflow img.preview {
+ padding: 5px;
+}
+
+.workflow .desc {
+ line-height: 1.4;
+ /*background-color: #EEEEEE;*/
+ text-align: left;
+ width: 400px;
+ font-size: 12pt;
+ padding-left: 12px;
+ padding-right: 12px;
+ padding-top: 0;
+ padding-bottom: 0;
+}
+
+.workflow .desc p {
+ padding: 0;
+}
+
+.workflow .tags {
+ text-align: center;
+ width: 400px;
+ line-height: 1.6;
+}
+
+.workflow .tags a {
+ color: #990000;
+}
+
+.workflow .credits {
+ text-align: center;
+ width: 400px;
+ line-height: 1.6;
+}
+
+
+div.file {
+ text-align: center;
+ margin: 6px;
+ border-width: 1px solid #333333;
+}
+
+.file .info {
+ text-align: center;
+ line-height: 1.6;
+ color: #333333;
+}
+
+.file .title {
+ text-align: center;
+ line-height: 1.0;
+ color: #333333;
+ font-size: 18pt;
+ font-weight: bold;
+ margin-bottom: 0;
+ margin-top: 0;
+ padding: 0;
+}
+
+.file img.preview {
+ padding: 5px;
+}
+
+.file .desc {
+ line-height: 1.4;
+ /*background-color: #EEEEEE;*/
+ text-align: left;
+ width: 400px;
+ font-size: 12pt;
+ padding-left: 12px;
+ padding-right: 12px;
+ padding-top: 0;
+ padding-bottom: 0;
+}
+
+.file .desc p {
+ padding: 0;
+}
+
+.file .tags {
+ text-align: center;
+ width: 400px;
+ line-height: 1.6;
+}
+
+.file .tags a {
+ color: #990000;
+}
+
+.file .credits {
+ text-align: center;
+ width: 400px;
+ line-height: 1.6;
+}
+
+
+div.pack {
+ text-align: center;
+ margin: 6px;
+ border-width: 1px solid #333333;
+}
+
+.pack .info {
+ text-align: center;
+ line-height: 1.6;
+ color: #333333;
+}
+
+.pack .title {
+ text-align: center;
+ line-height: 1.0;
+ color: #333333;
+ font-size: 18pt;
+ font-weight: bold;
+ margin-bottom: 0;
+ margin-top: 0;
+ padding: 0;
+}
+
+.pack img.preview {
+ padding: 5px;
+}
+
+.pack .desc {
+ line-height: 1.4;
+ text-align: left;
+ width: 400px;
+ font-size: 12pt;
+ padding-left: 12px;
+ padding-right: 12px;
+ padding-top: 0;
+ padding-bottom: 0;
+}
+
+.pack .desc p {
+ padding: 0;
+}
+
+.pack .tags {
+ text-align: center;
+ width: 400px;
+ line-height: 1.6;
+}
+
+.pack .tags a {
+ color: #990000;
+}
+
+.group .credits {
+ text-align: center;
+ width: 400px;
+ line-height: 1.6;
+}
+
+
+div.group {
+ text-align: center;
+ margin: 6px;
+ border-width: 1px solid #333333;
+}
+
+.group .info {
+ text-align: center;
+ line-height: 1.6;
+ color: #333333;
+}
+
+.group .title {
+ text-align: center;
+ line-height: 1.0;
+ color: #333333;
+ font-size: 18pt;
+ font-weight: bold;
+ margin-bottom: 0;
+ margin-top: 0;
+ padding: 0;
+}
+
+.group img.preview {
+ padding: 5px;
+}
+
+.group .desc {
+ line-height: 1.4;
+ text-align: left;
+ width: 400px;
+ font-size: 12pt;
+ padding-left: 12px;
+ padding-right: 12px;
+ padding-top: 0;
+ padding-bottom: 0;
+}
+
+.group .desc p {
+ padding: 0;
+}
+
+.group .tags {
+ text-align: center;
+ width: 400px;
+ line-height: 1.6;
+}
+
+.group .tags a {
+ color: #990000;
+}
+
+.group .credits {
+ text-align: center;
+ width: 400px;
+ line-height: 1.6;
+}
+
+
+div.user {
+ text-align: center;
+ margin: 6px;
+ border-width: 1px solid #333333;
+}
+
+.user .info {
+ text-align: center;
+ line-height: 1.6;
+ color: #333333;
+}
+
+.user .name {
+ text-align: center;
+ line-height: 1.0;
+ color: #333333;
+ font-size: 18pt;
+ font-weight: bold;
+ margin-bottom: 0;
+ margin-top: 0;
+ padding: 0;
+}
+
+.user img.avatar {
+ padding: 5px;
+}
+
+.user .desc {
+ line-height: 1.4;
+ text-align: left;
+ width: 400px;
+ font-size: 12pt;
+ padding-left: 12px;
+ padding-right: 12px;
+ padding-top: 0;
+ padding-bottom: 0;
+}
+
+.user .desc p {
+ padding: 0;
+ width: 400px;
+}
+
+.user .contact_details_header {
+ font-size: 12px;
+ font-weight: bold;
+ text-align: center;
+ margin-top: 12px;
+ margin-bottom: 6px;
+}
+
+.user .contact_details {
+ text-align: left;
+ margin-left: 100px;
+ line-height: 1.5;
+}
+
+.user .items_header {
+ font-size: 12px;
+ font-weight: bold;
+ text-align: center;
+ margin-top: 22px;
+ margin-bottom: 6px;
+}
+
+.none_text {
+ color: #666666;
+ font-style: italic;
+}
\ No newline at end of file
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/tag_blue.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/tag_blue.png
new file mode 100644
index 0000000..9757fc6
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/tag_blue.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/tick.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/tick.png
new file mode 100644
index 0000000..a9925a0
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/tick.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/transparent_icon.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/transparent_icon.png
new file mode 100644
index 0000000..39ede24
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/transparent_icon.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/user.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/user.png
new file mode 100644
index 0000000..79f35cc
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/user.png
Binary files differ
diff --git a/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/workflow.png b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/workflow.png
new file mode 100644
index 0000000..0be81b3
--- /dev/null
+++ b/taverna-workbench-perspective-myexperiment/src/main/resources/net/sf/taverna/t2/ui/perspectives/myexperiment/workflow.png
Binary files differ
diff --git a/taverna-workbench-renderers-exts/pom.xml b/taverna-workbench-renderers-exts/pom.xml
new file mode 100644
index 0000000..2060886
--- /dev/null
+++ b/taverna-workbench-renderers-exts/pom.xml
@@ -0,0 +1,62 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna.t2</groupId>
+ <artifactId>ui-exts</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>renderers-exts</artifactId>
+ <name>Renderers extensions</name>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>renderers-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>workbench-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.databundle</groupId>
+ <artifactId>databundle</artifactId>
+ <version>0.1.0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.mygrid.resources</groupId>
+ <artifactId>Jmol</artifactId>
+ <version>NO-VERSION</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.mygrid.resources</groupId>
+ <artifactId>seqvista-hacked</artifactId>
+ <version>NO-VERSION</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.xmlgraphics</groupId>
+ <artifactId>batik-swing</artifactId>
+ <version>${batik.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>com.springsource.org.apache.commons.io</artifactId>
+ <version>${commons.io.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.icepdf</groupId>
+ <artifactId>icepdf-viewer</artifactId>
+ <!-- <version>${org.icepdf.version}</version> -->
+ <version>4.1.1-taverna</version>
+ </dependency>
+
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+</project>
diff --git a/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/HTMLBrowserRenderer.java b/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/HTMLBrowserRenderer.java
new file mode 100644
index 0000000..048c728
--- /dev/null
+++ b/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/HTMLBrowserRenderer.java
@@ -0,0 +1,95 @@
+package net.sf.taverna.t2.renderers;
+
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+import java.awt.Desktop;
+import java.io.IOException;
+import java.net.URI;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardCopyOption;
+import java.util.regex.Pattern;
+
+import javax.swing.JComponent;
+import javax.swing.JEditorPane;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.databundle.DataBundles;
+
+/**
+ * Web browser renderer for MIME type text/html.
+ *
+ * @author Peter Li
+ */
+public class HTMLBrowserRenderer implements Renderer {
+ private Logger logger = Logger.getLogger(HTMLBrowserRenderer.class);
+ private Pattern pattern;
+
+ public HTMLBrowserRenderer() {
+ pattern = Pattern.compile(".*text/html.*");
+ }
+
+ @Override
+ public boolean canHandle(String mimeType) {
+ return pattern.matcher(mimeType).matches();
+ }
+
+ public boolean isTerminal() {
+ return true;
+ }
+
+ @Override
+ public String getType() {
+ return "HTML (in Web browser)";
+ }
+
+ @Override
+ public JComponent getComponent(Path path) throws RendererException {
+ URI uri = null;
+ try {
+ if (DataBundles.isValue(path)) {
+ Path tempFile = Files.createTempFile(null, ".html");
+ Files.copy(path, tempFile, StandardCopyOption.REPLACE_EXISTING);
+ uri = tempFile.toUri();
+ } else if (DataBundles.isReference(path)) {
+ uri = DataBundles.getReference(path);
+ }
+ } catch (IOException e) {
+ logger.error("Error fetching data value", e);
+ return new JEditorPane("text/html", "Error fetching data value\n"
+ + e.toString());
+ }
+
+ // Start Web browser
+ try {
+ Desktop.getDesktop().browse(uri);
+ } catch (IOException e) {
+ logger.error("Error attempting to launch Web browser", e);
+ return new JEditorPane("text/html", "Error attempting to launch Web browser\n"
+ + e.toString());
+
+ }
+
+ return new JEditorPane("text/plain", "Launching a Web browser ...");
+ }
+
+}
diff --git a/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/JMolRenderer.java b/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/JMolRenderer.java
new file mode 100644
index 0000000..e106a56
--- /dev/null
+++ b/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/JMolRenderer.java
@@ -0,0 +1,178 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.renderers;
+
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.Rectangle;
+import java.nio.file.Path;
+
+import javax.swing.JComponent;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
+
+import org.apache.log4j.Logger;
+import org.jmol.adapter.smarter.SmarterJmolAdapter;
+import org.jmol.api.JmolAdapter;
+import org.jmol.api.JmolSimpleViewer;
+import org.jmol.api.JmolViewer;
+import org.jmol.viewer.Viewer;
+
+import uk.org.taverna.databundle.DataBundles;
+
+/**
+ * Renders using the Jmol software for chemical structures
+ *
+ * @author Tom Oinn
+ * @author Ian Dunlop
+ * @author Alex Nenadic
+ */
+public class JMolRenderer implements Renderer {
+
+ private Logger logger = Logger.getLogger(JMolRenderer.class);
+
+ private int MEGABYTE = 1024 * 1024;
+
+ public boolean isTerminal() {
+ return true;
+ }
+
+ @Override
+ public boolean canHandle(String mimeType) {
+ if (mimeType.matches(".*chemical/x-pdb.*")
+ || mimeType.matches(".*chemical/x-mdl-molfile.*")
+ || mimeType.matches(".*chemical/x-cml.*")) {
+ return true;
+ }
+
+ return false;
+ }
+
+ static final String proteinScriptString = "wireframe off; spacefill off; select protein; cartoon; colour structure; select ligand; spacefill; colour cpk; select dna; spacefill 0.4; wireframe on; colour cpk;";
+
+ static final String scriptString = "select *; spacefill 0.4; wireframe 0.2; colour cpk;";
+
+ @Override
+ public String getType() {
+ return "Jmol";
+ }
+
+ @Override
+ public JComponent getComponent(Path path) throws RendererException {
+ if (DataBundles.isValue(path) || DataBundles.isReference(path)) {
+ long approximateSizeInBytes = 0;
+ try {
+ approximateSizeInBytes = RendererUtils.getSizeInBytes(path);
+ } catch (Exception ex) {
+ logger.error("Failed to get the size of the data", ex);
+ return new JTextArea(
+ "Failed to get the size of the data (see error log for more details): \n"
+ + ex.getMessage());
+ }
+
+ if (approximateSizeInBytes > MEGABYTE) {
+ int response = JOptionPane
+ .showConfirmDialog(
+ null,
+ "Result is approximately "
+ + bytesToMeg(approximateSizeInBytes)
+ + " MB in size, there could be issues with rendering this inside Taverna\nDo you want to continue?",
+ "Render using Jmol?", JOptionPane.YES_NO_OPTION);
+
+ if (response != JOptionPane.YES_OPTION) {
+ return new JTextArea(
+ "Rendering cancelled due to size of data. Try saving and viewing in an external application.");
+ }
+ }
+
+ String resolve = null;
+ try {
+ // Resolve it as a string
+ resolve = RendererUtils.getString(path);
+ } catch (Exception e) {
+ logger.error("Reference Service failed to render data as string", e);
+ return new JTextArea(
+ "Reference Service failed to render data as string (see error log for more details): \n"
+ + e.getMessage());
+ }
+ JmolPanel panel = new JmolPanel();
+ JmolSimpleViewer viewer = null;
+ try {
+ viewer = panel.getViewer();
+ viewer.openStringInline(resolve);
+ if (((JmolViewer) viewer).getAtomCount() > 300) {
+ viewer.evalString(proteinScriptString);
+ } else {
+ viewer.evalString(scriptString);
+ }
+ } catch (Exception e) {
+ logger.error("Failed to create Jmol renderer", e);
+ return new JTextArea(
+ "Failed to create Jmol renderer (see error log for more details): \n"
+ + e.getMessage());
+ }
+ return panel;
+ } else {
+ logger.error("Failed to obtain the data to render: data is not a value or reference");
+ return new JTextArea(
+ "Failed to obtain the data to render: data is not a value or reference");
+ }
+ }
+
+ class JmolPanel extends JPanel {
+ private static final long serialVersionUID = 1L;
+
+ JmolSimpleViewer viewer;
+ JmolAdapter adapter;
+
+ JmolPanel() {
+ adapter = new SmarterJmolAdapter(null);
+ viewer = Viewer.allocateJmolSimpleViewer(this, adapter);
+ // viewer = JmolSimpleViewer.allocateSimpleViewer(this, adapter);
+ }
+
+ public JmolSimpleViewer getViewer() {
+ return viewer;
+ }
+
+ final Dimension currentSize = new Dimension();
+ final Rectangle rectClip = new Rectangle();
+
+ @Override
+ public void paint(Graphics g) {
+ getSize(currentSize);
+ g.getClipBounds(rectClip);
+ viewer.renderScreenImage(g, currentSize, rectClip);
+ }
+ }
+
+ /**
+ * Work out size of file in megabytes to 1 decimal place
+ *
+ * @param bytes
+ * @return
+ */
+ private int bytesToMeg(long bytes) {
+ float f = bytes / MEGABYTE;
+ return Math.round(f);
+ }
+}
diff --git a/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/PDFRenderer.java b/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/PDFRenderer.java
new file mode 100644
index 0000000..cb86daa
--- /dev/null
+++ b/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/PDFRenderer.java
@@ -0,0 +1,124 @@
+package net.sf.taverna.t2.renderers;
+
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+
+import java.io.InputStream;
+import java.nio.file.Path;
+import java.util.regex.Pattern;
+
+import javax.swing.JComponent;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
+
+import org.apache.log4j.Logger;
+import org.icepdf.ri.common.SwingController;
+import org.icepdf.ri.common.SwingViewBuilder;
+
+/**
+ * PDF renderer for MIME type application/pdf using the ICE PDF Java viewer.
+ *
+ * @author Peter Li
+ */
+public class PDFRenderer implements Renderer {
+ private Logger logger = Logger.getLogger(PDFRenderer.class);
+
+ private Pattern pattern;
+
+ private float MEGABYTE = 1024 * 1024;
+ private int meg = 1048576;
+
+ public PDFRenderer() {
+ pattern = Pattern.compile(".*application/pdf.*");
+ }
+
+ @Override
+ public boolean canHandle(String mimeType) {
+ return pattern.matcher(mimeType).matches();
+ }
+
+ public boolean isTerminal() {
+ return true;
+ }
+
+ @Override
+ public String getType() {
+ return "PDF";
+ }
+
+ @Override
+ public JComponent getComponent(Path path) throws RendererException {
+ long approximateSizeInBytes = 0;
+ try {
+ approximateSizeInBytes = RendererUtils.getSizeInBytes(path);
+ } catch (Exception ex) {
+ logger.error("Failed to get the size of the data", ex);
+ return new JTextArea(
+ "Failed to get the size of the data (see error log for more details): \n"
+ + ex.getMessage());
+ }
+
+ if (approximateSizeInBytes > meg) {
+ int response = JOptionPane
+ .showConfirmDialog(
+ null,
+ "Result is approximately "
+ + bytesToMeg(approximateSizeInBytes)
+ + " Mb in size, there could be issues with rendering this inside Taverna\nDo you want to continue?",
+ "Render this as text/html?", JOptionPane.YES_NO_OPTION);
+
+ if (response == JOptionPane.NO_OPTION) {
+ return new JTextArea(
+ "Rendering cancelled due to size of file. Try saving and viewing in an external application");
+ }
+ }
+
+ try (InputStream inputStream = RendererUtils.getInputStream(path)) {
+ // Build a controller
+ SwingController controller = new SwingController();
+ // Build a SwingViewFactory configured with the controller
+ SwingViewBuilder factory = new SwingViewBuilder(controller);
+ // Use the factory to build a JPanel that is pre-configured
+ // with a complete, active Viewer UI.
+ JPanel viewerComponentPanel = factory.buildViewerPanel();
+ // Open a PDF document to view
+ controller.openDocument(inputStream, "PDF Viewer", null);
+ return viewerComponentPanel;
+ } catch (Exception e) {
+ logger.error("Failed to create PDF renderer", e);
+ return new JTextArea(
+ "Failed to create PDF renderer (see error log for more details): \n" + e.getMessage());
+ }
+ }
+
+ /**
+ * Work out size of file in megabytes to 1 decimal place
+ *
+ * @param bytes
+ * @return
+ */
+ private int bytesToMeg(long bytes) {
+ float f = bytes / MEGABYTE;
+ Math.round(f);
+ return Math.round(f);
+ }
+}
diff --git a/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/SVGRenderer.java b/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/SVGRenderer.java
new file mode 100644
index 0000000..e8edd91
--- /dev/null
+++ b/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/SVGRenderer.java
@@ -0,0 +1,154 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.renderers;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Path;
+import java.util.regex.Pattern;
+
+import javax.swing.JComponent;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
+
+import org.apache.batik.swing.JSVGCanvas;
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.databundle.DataBundles;
+
+/**
+ * This class renders SVG Documents.
+ * Last edited by $Author: sowen70 $
+ *
+ * @author Mark
+ * @author Ian Dunlop
+ * @author Alex Nenadic
+ */
+public class SVGRenderer implements Renderer {
+
+ private int MEGABYTE = 1024 * 1024;
+
+ private static Logger logger = Logger.getLogger(SVGRenderer.class);
+
+ private Pattern pattern;
+
+ public SVGRenderer() {
+ pattern = Pattern.compile(".*image/svg[+]xml.*");
+ }
+
+ @Override
+ public boolean canHandle(String mimeType) {
+ return pattern.matcher(mimeType).matches();
+ }
+
+ @Override
+ public String getType() {
+ return "SVG";
+ }
+
+ @SuppressWarnings("serial")
+ public JComponent getComponent(Path path) throws RendererException {
+ if (DataBundles.isValue(path) || DataBundles.isReference(path)) {
+ long approximateSizeInBytes = 0;
+ try {
+ approximateSizeInBytes = RendererUtils.getSizeInBytes(path);
+ } catch (Exception ex) {
+ logger.error("Failed to get the size of the data", ex);
+ return new JTextArea(
+ "Failed to get the size of the data (see error log for more details): \n"
+ + ex.getMessage());
+ }
+
+ if (approximateSizeInBytes > MEGABYTE) {
+ int response = JOptionPane
+ .showConfirmDialog(
+ null,
+ "Result is approximately "
+ + bytesToMeg(approximateSizeInBytes)
+ + " MB in size, there could be issues with rendering this inside Taverna\nDo you want to continue?",
+ "Render as SVG?", JOptionPane.YES_NO_OPTION);
+
+ if (response != JOptionPane.YES_OPTION) {
+ return new JTextArea(
+ "Rendering cancelled due to size of data. Try saving and viewing in an external application.");
+ }
+ }
+
+ String resolve = null;
+ try {
+ // Resolve it as a string
+ resolve = RendererUtils.getString(path);
+ } catch (Exception e) {
+ logger.error("Reference Service failed to render data as string", e);
+ return new JTextArea(
+ "Reference Service failed to render data as string (see error log for more details): \n"
+ + e.getMessage());
+ }
+
+ final JSVGCanvas svgCanvas = new JSVGCanvas();
+ File tmpFile = null;
+ try {
+ tmpFile = File.createTempFile("taverna", "svg");
+ tmpFile.deleteOnExit();
+ FileUtils.writeStringToFile(tmpFile, resolve, "utf8");
+ } catch (IOException e) {
+ logger.error("SVG Renderer: Failed to write the data to temporary file", e);
+ return new JTextArea(
+ "Failed to write the data to temporary file (see error log for more details): \n"
+ + e.getMessage());
+ }
+ try {
+ svgCanvas.setURI(tmpFile.toURI().toASCIIString());
+ } catch (Exception e) {
+ logger.error("Failed to create SVG renderer", e);
+ return new JTextArea(
+ "Failed to create SVG renderer (see error log for more details): \n"
+ + e.getMessage());
+ }
+ JPanel jp = new JPanel() {
+ @Override
+ protected void finalize() throws Throwable {
+ svgCanvas.stopProcessing();
+ super.finalize();
+ }
+ };
+ jp.add(svgCanvas);
+ return jp;
+ } else {
+ logger.error("Failed to obtain the data to render: data is not a value or reference");
+ return new JTextArea(
+ "Failed to obtain the data to render: data is not a value or reference");
+ }
+ }
+
+ /**
+ * Work out size of file in megabytes to 1 decimal place
+ *
+ * @param bytes
+ * @return
+ */
+ private int bytesToMeg(long bytes) {
+ float f = bytes / MEGABYTE;
+ return Math.round(f);
+ }
+}
diff --git a/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/SeqVistaRenderer.java b/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/SeqVistaRenderer.java
new file mode 100644
index 0000000..d4aaf5a
--- /dev/null
+++ b/taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/SeqVistaRenderer.java
@@ -0,0 +1,167 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.renderers;
+
+import java.nio.file.Path;
+
+import javax.swing.JComponent;
+import javax.swing.JOptionPane;
+import javax.swing.JTextArea;
+import javax.swing.LookAndFeel;
+import javax.swing.UIManager;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.databundle.DataBundles;
+import cht.svista.SeqVISTA;
+
+/**
+ * Uses the SeqVista renderer to draw an EMBL or SwissProt sequence
+ *
+ * @author Ian Dunlop
+ * @author anonymous from T1
+ * @author Alex Nenadic
+ */
+public class SeqVistaRenderer implements Renderer {
+
+ private Logger logger = Logger.getLogger(SeqVistaRenderer.class);
+
+ private int MEGABYTE = 1024 * 1024;
+
+ private String seqType = "fasta";
+ // 0 = auto, 1 = nucleotide, 2 = protein
+ private int np = 0;
+
+ @Override
+ public boolean canHandle(String mimeType) {
+ if (mimeType.matches(".*chemical/x-swissprot.*")) {
+ seqType = "embl";
+ np = 2;
+ return true;
+ } else if (mimeType.matches(".*chemical/x-embl-dl-nucleotide.*")) {
+ seqType = "embl";
+ np = 1;
+ return true;
+ } else if (mimeType.matches(".*chemical/x-fasta.*")) {
+ seqType = "fasta";
+ np = 0;
+ return true;
+ } else if (mimeType.matches(".*chemical/x-ppd.*")) {
+ seqType = "ppd";
+ return true;
+ } else if (mimeType.matches(".*chemical/seq-na-genbank.*")) {
+ seqType = "auto";
+ np = 1;
+ return true;
+ } else if (mimeType.matches(".*chemical/seq-aa-genpept.*")) {
+ seqType = "auto";
+ np = 2;
+ return true;
+ }
+ return false;
+ }
+
+ @Override
+ public String getType() {
+ return "Seq Vista";
+ }
+
+ @SuppressWarnings("serial")
+ public JComponent getComponent(Path path) throws RendererException {
+ if (DataBundles.isValue(path) || DataBundles.isReference(path)) {
+ long approximateSizeInBytes = 0;
+ try {
+ approximateSizeInBytes = RendererUtils.getSizeInBytes(path);
+ } catch (Exception ex) {
+ logger.error("Failed to get the size of the data", ex);
+ return new JTextArea(
+ "Failed to get the size of the data (see error log for more details): \n"
+ + ex.getMessage());
+ }
+
+ if (approximateSizeInBytes > MEGABYTE) {
+ int response = JOptionPane
+ .showConfirmDialog(
+ null,
+ "Result is approximately "
+ + bytesToMeg(approximateSizeInBytes)
+ + " MB in size, there could be issues with rendering this inside Taverna\nDo you want to continue?",
+ "Render as sequence?", JOptionPane.YES_NO_OPTION);
+
+ if (response != JOptionPane.YES_OPTION) {
+ return new JTextArea(
+ "Rendering cancelled due to size of data. Try saving and viewing in an external application.");
+ }
+ }
+
+ String resolve = null;
+ try {
+ // Resolve it as a string
+ resolve = RendererUtils.getString(path);
+ } catch (Exception e) {
+ logger.error("Reference Service failed to render data as string", e);
+ return new JTextArea(
+ "Reference Service failed to render data as string (see error log for more details): \n"
+ + e.getMessage());
+ }
+ // Save LAF as SeqVista is messing with it
+ LookAndFeel currentLookAndFeel = UIManager.getLookAndFeel();
+ SeqVISTA vista = new SeqVISTA() {
+ @Override
+ public java.awt.Dimension getPreferredSize() {
+ return new java.awt.Dimension(100, 100);
+ }
+ };
+ // Reset LAF messed up by SeqVista
+ try {
+ UIManager.setLookAndFeel(currentLookAndFeel);
+ } catch (Exception e) {
+ logger.info("Can't reset look and feel to " + currentLookAndFeel
+ + " after SeqVista renderer messed it up", e);
+ }
+
+ try {
+ vista.loadFromText(resolve, false, seqType, np);
+ } catch (Exception e) {
+ logger.error("Failed to create Sequence Vista renderer", e);
+ return new JTextArea(
+ "Failed to create Sequence Vista renderer (see error log for more details): \n"
+ + e.getMessage());
+ }
+ return vista;
+ } else {
+ logger.error("Failed to obtain the data to render: data is not a value or reference");
+ return new JTextArea(
+ "Failed to obtain the data to render: data is not a value or reference");
+ }
+ }
+
+ /**
+ * Work out size of file in megabytes to 1 decimal place
+ *
+ * @param bytes
+ * @return
+ */
+ private int bytesToMeg(long bytes) {
+ float f = bytes / MEGABYTE;
+ return Math.round(f);
+ }
+}
diff --git a/taverna-workbench-renderers-exts/src/main/resources/META-INF/services/net.sf.taverna.t2.renderers.Renderer b/taverna-workbench-renderers-exts/src/main/resources/META-INF/services/net.sf.taverna.t2.renderers.Renderer
new file mode 100644
index 0000000..ca01b3b
--- /dev/null
+++ b/taverna-workbench-renderers-exts/src/main/resources/META-INF/services/net.sf.taverna.t2.renderers.Renderer
@@ -0,0 +1,5 @@
+net.sf.taverna.t2.renderers.JMolRenderer
+net.sf.taverna.t2.renderers.SeqVistaRenderer
+net.sf.taverna.t2.renderers.SVGRenderer
+net.sf.taverna.t2.renderers.PDFRenderer
+net.sf.taverna.t2.renderers.HTMLBrowserRenderer
\ No newline at end of file
diff --git a/taverna-workbench-renderers-exts/src/main/resources/META-INF/spring/renderers-exts-context-osgi.xml b/taverna-workbench-renderers-exts/src/main/resources/META-INF/spring/renderers-exts-context-osgi.xml
new file mode 100644
index 0000000..0383fd6
--- /dev/null
+++ b/taverna-workbench-renderers-exts/src/main/resources/META-INF/spring/renderers-exts-context-osgi.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="JMolRenderer" interface="net.sf.taverna.t2.renderers.Renderer" />
+ <service ref="SeqVistaRenderer" interface="net.sf.taverna.t2.renderers.Renderer" />
+ <service ref="SVGRenderer" interface="net.sf.taverna.t2.renderers.Renderer" />
+ <service ref="PDFRenderer" interface="net.sf.taverna.t2.renderers.Renderer" />
+ <service ref="HTMLBrowserRenderer" interface="net.sf.taverna.t2.renderers.Renderer" />
+
+</beans:beans>
diff --git a/taverna-workbench-renderers-exts/src/main/resources/META-INF/spring/renderers-exts-context.xml b/taverna-workbench-renderers-exts/src/main/resources/META-INF/spring/renderers-exts-context.xml
new file mode 100644
index 0000000..690aa3f
--- /dev/null
+++ b/taverna-workbench-renderers-exts/src/main/resources/META-INF/spring/renderers-exts-context.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="JMolRenderer" class="net.sf.taverna.t2.renderers.JMolRenderer" />
+ <bean id="SeqVistaRenderer" class="net.sf.taverna.t2.renderers.SeqVistaRenderer" />
+ <bean id="SVGRenderer" class="net.sf.taverna.t2.renderers.SVGRenderer" />
+ <bean id="PDFRenderer" class="net.sf.taverna.t2.renderers.PDFRenderer" />
+ <bean id="HTMLBrowserRenderer" class="net.sf.taverna.t2.renderers.HTMLBrowserRenderer" />
+
+</beans>
diff --git a/taverna-workbench-renderers-exts/src/test/java/net/sf/taverna/t2/renderers/TestRendererSPI.java b/taverna-workbench-renderers-exts/src/test/java/net/sf/taverna/t2/renderers/TestRendererSPI.java
new file mode 100644
index 0000000..c113c7b
--- /dev/null
+++ b/taverna-workbench-renderers-exts/src/test/java/net/sf/taverna/t2/renderers/TestRendererSPI.java
@@ -0,0 +1,153 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.renderers;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.util.HashSet;
+import java.util.List;
+
+import org.junit.Before;
+import org.junit.Test;
+
+
+public class TestRendererSPI {
+
+ private static final String TEST_NS = "testNS";
+
+ @Test
+ public void doNothing() {
+ //do nothing for the moment
+ }
+
+// @Test
+// public void getAllRenderers() {
+// RendererRegistry rendererRegistry = new RendererRegistry();
+// assertEquals(rendererRegistry.getInstances().size(), 10);
+// }
+//
+// @Test
+// public void checkTextHtmlMimeType() throws EmptyListException, MalformedListException, UnsupportedObjectTypeException {
+// String mimeType = "text/html";
+// String html = "<HTML><HEAD></HEAD><BODY>hello</BODY></HTML>";
+// EntityIdentifier entityIdentifier = facade.register(html, "utf-8");
+// RendererRegistry rendererRegistry = new RendererRegistry();
+// List<Renderer> renderersForMimeType = rendererRegistry.getRenderersForMimeType(facade, entityIdentifier, mimeType);
+// assertEquals(renderersForMimeType.size(),2);
+// assertEquals(renderersForMimeType.get(0).getClass().getSimpleName(), "TextRenderer");
+// assertEquals(renderersForMimeType.get(1).getClass().getSimpleName(), "TextHtmlRenderer");
+// assertTrue(renderersForMimeType.get(0).canHandle("text/html"));
+// }
+//
+// @Test
+// public void checkURLMimeType() throws EmptyListException, MalformedListException, UnsupportedObjectTypeException {
+// String mimeType = "text/x-taverna-web-url.text";
+// String url = "http://google.com";
+// EntityIdentifier entityIdentifier = facade.register(url);
+// RendererRegistry rendererRegistry = new RendererRegistry();
+// List<Renderer> renderersForMimeType = rendererRegistry.getRenderersForMimeType(facade, entityIdentifier, mimeType);
+// assertEquals(renderersForMimeType.size(),2);
+// assertEquals(renderersForMimeType.get(0).getClass().getSimpleName(), "TextRenderer");
+// assertEquals(renderersForMimeType.get(1).getClass().getSimpleName(), "TextTavernaWebUrlRenderer");
+// assertTrue(renderersForMimeType.get(1).canHandle("text/x-taverna-web-url.text"));
+// }
+//
+// @Test
+// public void checkJMolMimeType() throws EmptyListException, MalformedListException, UnsupportedObjectTypeException {
+// String mimeType ="chemical/x-pdb";
+// String jmol = "jmol";
+// EntityIdentifier entityIdentifier = facade.register(jmol);
+// RendererRegistry rendererRegistry = new RendererRegistry();
+// List<Renderer> renderersForMimeType = rendererRegistry.getRenderersForMimeType(facade, entityIdentifier, mimeType);
+// assertEquals(renderersForMimeType.size(), 1);
+// assertEquals(renderersForMimeType.get(0).getClass().getSimpleName(), "JMolRenderer");
+// assertTrue(renderersForMimeType.get(0).canHandle("chemical/x-mdl-molfile"));
+// assertTrue(renderersForMimeType.get(0).canHandle("chemical/x-cml"));
+// }
+//
+// @Test
+// public void checkSeqVistaMimeType() throws EmptyListException, MalformedListException, UnsupportedObjectTypeException {
+// String mimeType ="chemical/x-swissprot";
+// String type = "seqvista";
+// EntityIdentifier entityIdentifier = facade.register(type);
+// RendererRegistry rendererRegistry = new RendererRegistry();
+// List<Renderer> renderersForMimeType = rendererRegistry.getRenderersForMimeType(facade, entityIdentifier, mimeType);
+// assertEquals(renderersForMimeType.size(), 1);
+// assertEquals(renderersForMimeType.get(0).getClass().getSimpleName(), "SeqVistaRenderer");
+// assertTrue(renderersForMimeType.get(0).canHandle("chemical/x-embl-dl-nucleotide"));
+// assertTrue(renderersForMimeType.get(0).canHandle("chemical/x-fasta"));
+// }
+//
+// @Test
+// public void checkSVGMimeType() throws EmptyListException, MalformedListException, UnsupportedObjectTypeException {
+// String mimeType ="image/svg+xml";
+// String type = "SVG";
+// EntityIdentifier entityIdentifier = facade.register(type);
+// RendererRegistry rendererRegistry = new RendererRegistry();
+// List<Renderer> renderersForMimeType = rendererRegistry.getRenderersForMimeType(facade, entityIdentifier, mimeType);
+// assertEquals(renderersForMimeType.size(), 2);
+// assertEquals(renderersForMimeType.get(1).getClass().getSimpleName(), "SVGRenderer");
+// }
+//
+// @Test
+// public void checkTextMimeType() throws EmptyListException, MalformedListException, UnsupportedObjectTypeException {
+// String mimeType ="text/text";
+// String type = "text";
+// EntityIdentifier entityIdentifier = facade.register(type);
+// RendererRegistry rendererRegistry = new RendererRegistry();
+// List<Renderer> renderersForMimeType = rendererRegistry.getRenderersForMimeType(facade, entityIdentifier, mimeType);
+// assertEquals(renderersForMimeType.size(), 1);
+// assertEquals(renderersForMimeType.get(0).getClass().getSimpleName(), "TextRenderer");
+// }
+//
+// @Test
+// public void checkTextRtfMimeType() throws EmptyListException, MalformedListException, UnsupportedObjectTypeException {
+// String mimeType ="text/rtf";
+// String type = "textRTF";
+// EntityIdentifier entityIdentifier = facade.register(type);
+// RendererRegistry rendererRegistry = new RendererRegistry();
+// List<Renderer> renderersForMimeType = rendererRegistry.getRenderersForMimeType(facade, entityIdentifier, mimeType);
+// assertEquals(renderersForMimeType.size(), 2);
+// assertEquals(renderersForMimeType.get(1).getClass().getSimpleName(), "TextRtfRenderer");
+// }
+//
+// @Test
+// public void checkTextXMLMimeType() throws EmptyListException, MalformedListException, UnsupportedObjectTypeException {
+// String mimeType ="text/xml";
+// String type = "textXML";
+// EntityIdentifier entityIdentifier = facade.register(type);
+// RendererRegistry rendererRegistry = new RendererRegistry();
+// List<Renderer> renderersForMimeType = rendererRegistry.getRenderersForMimeType(facade, entityIdentifier, mimeType);
+// assertEquals(renderersForMimeType.size(), 2);
+// assertEquals(renderersForMimeType.get(1).getClass().getSimpleName(), "TextXMLRenderer");
+// }
+//
+// @Before
+// public void setDataManager() {
+// // dManager = new FileDataManager("testNS",
+// // new HashSet<LocationalContext>(), new File("/tmp/fish"));
+// dManager = new InMemoryDataManager(TEST_NS,
+// new HashSet<LocationalContext>());
+// facade = new DataFacade(dManager);
+// }
+
+}
diff --git a/taverna-workbench-report-explainer/pom.xml b/taverna-workbench-report-explainer/pom.xml
new file mode 100644
index 0000000..4be9bd9
--- /dev/null
+++ b/taverna-workbench-report-explainer/pom.xml
@@ -0,0 +1,102 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna.t2</groupId>
+ <artifactId>ui-exts</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>report-explainer</artifactId>
+ <packaging>bundle</packaging>
+ <name>Report explainer</name>
+ <description>
+ Explanations of reports
+ </description>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>report-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>retry-ui</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>dataflow-activity-ui</artifactId>
+ <version>${t2.ui.activities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>disabled-activity-ui</artifactId>
+ <version>${t2.ui.activities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>wsdl-activity</artifactId>
+ <version>${t2.activities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>dataflow-activity</artifactId>
+ <version>${t2.activities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>workflowmodel-api</artifactId>
+ <version>${t2.core.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>edits-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>file-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>configuration-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>report-view</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>design-ui</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>workflowmodel-impl</artifactId>
+ <version>${t2.core.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.lang</groupId>
+ <artifactId>ui</artifactId>
+ <version>${t2.lang.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.log4j</groupId>
+ <artifactId>com.springsource.org.apache.log4j</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>BrowserLauncher2</groupId>
+ <artifactId>BrowserLauncher2</artifactId>
+ <version>1.3</version>
+ </dependency>
+ </dependencies>
+</project>
diff --git a/taverna-workbench-report-explainer/src/main/java/net/sf/taverna/t2/workbench/report/explainer/BasicExplainer.java b/taverna-workbench-report-explainer/src/main/java/net/sf/taverna/t2/workbench/report/explainer/BasicExplainer.java
new file mode 100644
index 0000000..cba6a98
--- /dev/null
+++ b/taverna-workbench-report-explainer/src/main/java/net/sf/taverna/t2/workbench/report/explainer/BasicExplainer.java
@@ -0,0 +1,1294 @@
+/*******************************************************************************
+ * Copyright (C) 2008-2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.report.explainer;
+
+import java.awt.Desktop;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.SystemColor;
+import java.awt.event.ActionEvent;
+import java.io.File;
+import java.io.IOException;
+import java.net.URI;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+
+import javax.net.ssl.SSLException;
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+
+import net.sf.taverna.t2.activities.dataflow.DataflowActivity;
+import net.sf.taverna.t2.activities.dataflow.actions.EditNestedDataflowAction;
+import net.sf.taverna.t2.activities.disabled.actions.DisabledActivityConfigurationAction;
+import net.sf.taverna.t2.activities.wsdl.InputPortTypeDescriptorActivity;
+import net.sf.taverna.t2.activities.wsdl.xmlsplitter.AddXMLSplitterEdit;
+import net.sf.taverna.t2.lang.ui.ReadOnlyTextArea;
+import net.sf.taverna.t2.visit.DataflowCollation;
+import net.sf.taverna.t2.visit.VisitKind;
+import net.sf.taverna.t2.visit.VisitReport;
+import net.sf.taverna.t2.visit.fragility.FragilityCheck;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.design.actions.AddDataflowOutputAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.report.FailedEntityKind;
+import net.sf.taverna.t2.workbench.report.IncompleteDataflowKind;
+import net.sf.taverna.t2.workbench.report.InvalidDataflowKind;
+import net.sf.taverna.t2.workbench.report.ReportManager;
+import net.sf.taverna.t2.workbench.report.UnresolvedOutputKind;
+import net.sf.taverna.t2.workbench.report.UnsatisfiedEntityKind;
+import net.sf.taverna.t2.workbench.report.view.ReportViewConfigureAction;
+import net.sf.taverna.t2.workbench.retry.RetryConfigureAction;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.impl.configuration.ui.T2ConfigurationFrame;
+import net.sf.taverna.t2.workflowmodel.CompoundEdit;
+import net.sf.taverna.t2.workflowmodel.Dataflow;
+import net.sf.taverna.t2.workflowmodel.DataflowOutputPort;
+import net.sf.taverna.t2.workflowmodel.Datalink;
+import net.sf.taverna.t2.workflowmodel.Edit;
+import net.sf.taverna.t2.workflowmodel.EditException;
+import net.sf.taverna.t2.workflowmodel.Merge;
+import net.sf.taverna.t2.workflowmodel.Processor;
+import net.sf.taverna.t2.workflowmodel.ProcessorInputPort;
+import net.sf.taverna.t2.workflowmodel.ProcessorOutputPort;
+import net.sf.taverna.t2.workflowmodel.TokenProcessingEntity;
+import net.sf.taverna.t2.workflowmodel.health.HealthCheck;
+import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
+import net.sf.taverna.t2.workflowmodel.processor.activity.DisabledActivity;
+import net.sf.taverna.t2.workflowmodel.processor.dispatch.DispatchLayer;
+import net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry;
+import net.sf.taverna.t2.workflowmodel.utils.Tools;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.configuration.ConfigurationUIFactory;
+
+/**
+ * @author alanrw
+ *
+ */
+public class BasicExplainer implements VisitExplainer {
+
+ private static Logger logger = Logger.getLogger(BasicExplainer.class);
+
+ private static String PLEASE_CONTACT = "Please contact the service provider or workflow creator.";
+
+ private EditManager editManager;
+
+ private FileManager fileManager;
+
+ private ReportManager reportManager;
+
+ private SelectionManager selectionManager;
+
+ private List<ConfigurationUIFactory> configurationUIFactories;
+
+ private ActivityIconManager activityIconManager;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * net.sf.taverna.t2.workbench.report.explainer.VisitExplainer#canExplain
+ * (net.sf.taverna.t2.visit.VisitKind, int)
+ */
+ public boolean canExplain(VisitKind vk, int resultId) {
+ if (vk instanceof DataflowCollation) {
+ return true;
+ }
+ if (vk instanceof FailedEntityKind) {
+ return true;
+ }
+ if (vk instanceof IncompleteDataflowKind) {
+ return true;
+ }
+ if (vk instanceof InvalidDataflowKind) {
+ return true;
+ }
+ if (vk instanceof UnresolvedOutputKind) {
+ return true;
+ }
+ if (vk instanceof UnsatisfiedEntityKind) {
+ return true;
+ }
+ if (vk instanceof FragilityCheck) {
+ return true;
+ }
+ if ((vk instanceof HealthCheck)
+ && ((resultId == HealthCheck.INVALID_SCRIPT)
+ || (resultId == HealthCheck.CONNECTION_PROBLEM)
+ || (resultId == HealthCheck.INVALID_URL)
+ || (resultId == HealthCheck.IO_PROBLEM)
+ || (resultId == HealthCheck.TIME_OUT)
+ || (resultId == HealthCheck.MISSING_DEPENDENCY)
+ || (resultId == HealthCheck.DEFAULT_VALUE)
+ || (resultId == HealthCheck.BAD_WSDL)
+ || (resultId == HealthCheck.NOT_HTTP)
+ || (resultId == HealthCheck.UNSUPPORTED_STYLE)
+ || (resultId == HealthCheck.UNKNOWN_OPERATION)
+ || (resultId == HealthCheck.NO_ENDPOINTS)
+ || (resultId == HealthCheck.INVALID_CONFIGURATION)
+ || (resultId == HealthCheck.NULL_DATATYPE)
+ || (resultId == HealthCheck.DISABLED)
+ || (resultId == HealthCheck.DATATYPE_SOURCE)
+ || (resultId == HealthCheck.UNRECOGNIZED)
+ || (resultId == HealthCheck.LOOP_CONNECTION)
+ || (resultId == HealthCheck.UNMANAGED_LOCATION) || (resultId == HealthCheck.INCOMPATIBLE_MIMETYPES))) {
+ return true;
+ }
+ return false;
+ }
+
+ public JComponent getExplanation(VisitReport vr) {
+ VisitKind vk = vr.getKind();
+ int resultId = vr.getResultId();
+ if (vk instanceof DataflowCollation) {
+ return explanationDataflowCollation(vr);
+ }
+ if (vk instanceof FailedEntityKind) {
+ return explanationFailedEntity(vr);
+ }
+ if ((vk instanceof IncompleteDataflowKind)
+ && (resultId == IncompleteDataflowKind.INCOMPLETE_DATAFLOW)) {
+ return explanationDataflowIncomplete(vr);
+ }
+ if (vk instanceof InvalidDataflowKind) {
+ return explanationInvalidDataflow(vr);
+ }
+ if (vk instanceof UnresolvedOutputKind) {
+ return explanationUnresolvedOutput(vr);
+ }
+ if (vk instanceof UnsatisfiedEntityKind) {
+ return explanationUnsatisfiedEntity(vr);
+ }
+
+ if ((vk instanceof FragilityCheck)
+ && (resultId == FragilityCheck.SOURCE_FRAGILE)) {
+ return explanationSourceFragile(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.INVALID_SCRIPT)) {
+ return explanationBeanshellInvalidScript(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.CONNECTION_PROBLEM)) {
+ return explanationConnectionProblem(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.INVALID_URL)) {
+ return explanationInvalidUrl(vr);
+ }
+ if ((vk instanceof HealthCheck) && (resultId == HealthCheck.TIME_OUT)) {
+ return explanationTimeOut(vr);
+ }
+ if ((vk instanceof HealthCheck) && (resultId == HealthCheck.IO_PROBLEM)) {
+ return explanationIoProblem(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.MISSING_DEPENDENCY)) {
+ return explanationMissingDependency(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.DEFAULT_VALUE)) {
+ return explanationDefaultValue(vr);
+ }
+ if ((vk instanceof HealthCheck) && (resultId == HealthCheck.BAD_WSDL)) {
+ return explanationBadWSDL(vr);
+ }
+ if ((vk instanceof HealthCheck) && (resultId == HealthCheck.NOT_HTTP)) {
+ return explanationNotHTTP(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.UNSUPPORTED_STYLE)) {
+ return explanationUnsupportedStyle(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.UNKNOWN_OPERATION)) {
+ return explanationUnknownOperation(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.NO_ENDPOINTS)) {
+ return explanationNoEndpoints(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.INVALID_CONFIGURATION)) {
+ return explanationInvalidConfiguration(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.NULL_DATATYPE)) {
+ return explanationNullDatatype(vr);
+ }
+ if ((vk instanceof HealthCheck) && (resultId == HealthCheck.DISABLED)) {
+ return explanationDisabled(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.DATATYPE_SOURCE)) {
+ return explanationDatatypeSource(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.UNRECOGNIZED)) {
+ return explanationUnrecognized(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.LOOP_CONNECTION)) {
+ return explanationLoopConnection(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.UNMANAGED_LOCATION)) {
+ return explanationUnmanagedLocation(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.INCOMPATIBLE_MIMETYPES)) {
+ return explanationIncompatibleMimetypes(vr);
+ }
+ return null;
+ }
+
+ public JComponent getSolution(VisitReport vr) {
+ VisitKind vk = vr.getKind();
+ int resultId = vr.getResultId();
+ if (vk instanceof DataflowCollation) {
+ return solutionDataflowCollation(vr);
+ }
+ if (vk instanceof FailedEntityKind) {
+ return solutionFailedEntity(vr);
+ }
+ if ((vk instanceof IncompleteDataflowKind)
+ && (resultId == IncompleteDataflowKind.INCOMPLETE_DATAFLOW)) {
+ return solutionDataflowIncomplete(vr);
+ }
+ if (vk instanceof InvalidDataflowKind) {
+ return solutionInvalidDataflow(vr);
+ }
+ if (vk instanceof UnresolvedOutputKind) {
+ return solutionUnresolvedOutput(vr);
+ }
+ if (vk instanceof UnsatisfiedEntityKind) {
+ return solutionUnsatisfiedEntity(vr);
+ }
+
+ if ((vk instanceof FragilityCheck)
+ && (resultId == FragilityCheck.SOURCE_FRAGILE)) {
+ return solutionSourceFragile(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.INVALID_SCRIPT)) {
+ return solutionBeanshellInvalidScript(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.CONNECTION_PROBLEM)) {
+ return solutionConnectionProblem(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.INVALID_URL)) {
+ return solutionInvalidUrl(vr);
+ }
+ if ((vk instanceof HealthCheck) && (resultId == HealthCheck.TIME_OUT)) {
+ return solutionTimeOut(vr);
+ }
+ if ((vk instanceof HealthCheck) && (resultId == HealthCheck.IO_PROBLEM)) {
+ return solutionIoProblem(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.MISSING_DEPENDENCY)) {
+ return solutionMissingDependency(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.DEFAULT_VALUE)) {
+ return solutionDefaultValue(vr);
+ }
+ if ((vk instanceof HealthCheck) && (resultId == HealthCheck.BAD_WSDL)) {
+ return solutionBadWSDL(vr);
+ }
+ if ((vk instanceof HealthCheck) && (resultId == HealthCheck.NOT_HTTP)) {
+ return solutionNotHTTP(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.UNSUPPORTED_STYLE)) {
+ return solutionUnsupportedStyle(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.UNKNOWN_OPERATION)) {
+ return solutionUnknownOperation(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.NO_ENDPOINTS)) {
+ return solutionNoEndpoints(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.INVALID_CONFIGURATION)) {
+ return solutionInvalidConfiguration(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.NULL_DATATYPE)) {
+ return solutionNullDatatype(vr);
+ }
+ if ((vk instanceof HealthCheck) && (resultId == HealthCheck.DISABLED)) {
+ return solutionDisabled(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.DATATYPE_SOURCE)) {
+ return solutionDatatypeSource(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.UNRECOGNIZED)) {
+ return solutionUnrecognized(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.LOOP_CONNECTION)) {
+ return solutionLoopConnection(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.UNMANAGED_LOCATION)) {
+ return solutionUnmanagedLocation(vr);
+ }
+ if ((vk instanceof HealthCheck)
+ && (resultId == HealthCheck.INCOMPATIBLE_MIMETYPES)) {
+ return solutionIncompatibleMimetypes(vr);
+ }
+ return null;
+ }
+
+ private static JComponent explanationFailedEntity(VisitReport vr) {
+ if (vr.getSubject() instanceof Processor) {
+ Processor p = (Processor) (vr.getSubject());
+ DataflowActivity da = null;
+ for (Activity a : p.getActivityList()) {
+ if (a instanceof DataflowActivity) {
+ da = (DataflowActivity) a;
+ break;
+ }
+ }
+ String message = "There is possibly a problem with the service's list handling";
+ if (da != null) {
+ message += ", or a problem with the nested workflow";
+ }
+ return createPanel(new Object[] { message + "." });
+ } else if (vr.getSubject() instanceof Merge) {
+ return createPanel(new Object[] { "The merge is combining data of different depths." });
+ }
+ return null;
+ }
+
+ private static JComponent explanationInvalidDataflow(VisitReport vr) {
+ return createPanel(new Object[] { "The workflow contains errors - see other reports." });
+ }
+
+ private static JComponent explanationUnresolvedOutput(VisitReport vr) {
+ DataflowOutputPort dop = (DataflowOutputPort) vr.getSubject();
+ Datalink incomingLink = dop.getInternalInputPort().getIncomingLink();
+ String message;
+ if (incomingLink == null) {
+ message = "The workflow output port is not connected.";
+ } else {
+ message = "The workflow output port is connected to a service or port that has errors.";
+ }
+ return createPanel(new Object[] { message });
+ }
+
+ private static JComponent explanationUnsatisfiedEntity(VisitReport vr) {
+ return createPanel(new Object[] { "The service could not be properly checked." });
+ }
+
+ private static JComponent explanationDataflowCollation(VisitReport vr) {
+ if (vr.getStatus().equals(VisitReport.Status.SEVERE)) {
+ return createPanel(new Object[] { "There are errors in the nested workflow." });
+ } else {
+ return createPanel(new Object[] { "There are warnings in the nested workflow." });
+ }
+ }
+
+ private static JComponent explanationDataflowIncomplete(VisitReport vr) {
+ return createPanel(new Object[] { "A workflow must contain at least one service or at least one output port." });
+ }
+
+ private static JComponent explanationSourceFragile(VisitReport vr) {
+ ProcessorInputPort pip = (ProcessorInputPort) vr
+ .getProperty("sinkPort");
+ Processor sourceProcessor = (Processor) vr
+ .getProperty("sourceProcessor");
+ String message = "A single error input into ";
+ if (pip == null) {
+ message += "an input port ";
+ } else {
+ message += "\"" + pip.getName() + "\" ";
+ }
+ if (sourceProcessor != null) {
+ message += "from \"" + sourceProcessor.getLocalName() + "\"";
+ }
+ message += " will cause this service to fail. ";
+ message += "If "
+ + (sourceProcessor == null ? "the source" : sourceProcessor
+ .getLocalName())
+ + " is unlikely to fail (for example if it is a StringConstant) then this warning can be ignored.";
+ return createPanel(new Object[] { message });
+ }
+
+ private static JComponent explanationConnectionProblem(VisitReport vr) {
+ String endpoint = (String) (vr.getProperty("endpoint"));
+ if (endpoint == null) {
+ endpoint = "the endpoint";
+ }
+ String responseCode = (String) (vr.getProperty("responseCode"));
+ if (responseCode == null) {
+ responseCode = "an unexpected response code";
+ } else {
+ responseCode = "response code: " + responseCode;
+ }
+ return createPanel(new Object[] { "Taverna connected to \"" + endpoint
+ + "\" but received " + responseCode
+ + ". The service may still work." });
+ }
+
+ private static JComponent explanationIoProblem(VisitReport vr) {
+ String message = "Reading from ";
+ String endpoint = (String) (vr.getProperty("endpoint"));
+ if (endpoint == null) {
+ message += "the endpoint";
+ } else {
+ message += "\"" + endpoint + "\"";
+ }
+ message += " caused ";
+ Exception e = (Exception) (vr.getProperty("exception"));
+ if (e == null) {
+ message += "an error";
+ } else {
+ message += e.getClass().getCanonicalName() + ": \""
+ + e.getMessage() + "\"";
+ }
+ return createPanel(new Object[] { message + "." });
+ }
+
+ private static JComponent explanationInvalidUrl(VisitReport vr) {
+ String endpoint = (String) (vr.getProperty("endpoint"));
+ if (endpoint == null) {
+ endpoint = "the endpoint";
+ }
+ return createPanel(new Object[] { "Taverna was unable to connect to \""
+ + endpoint + "\" because it is not a valid URL." });
+ }
+
+ private static JComponent explanationTimeOut(VisitReport vr) {
+ String endpoint = (String) (vr.getProperty("endpoint"));
+ if (endpoint == null) {
+ endpoint = "the endpoint";
+ }
+ String timeOutString = (String) (vr.getProperty("timeOut"));
+ if (timeOutString == null) {
+ timeOutString = " the timeout limit";
+ } else {
+ try {
+ Integer timeOut = Integer.parseInt(timeOutString);
+ if (timeOut > 1000) {
+ timeOutString = Float.toString(timeOut / 1000) + "s";
+ } else {
+ timeOutString += "ms";
+ }
+ } catch (NumberFormatException ex) {
+ timeOutString = " the timeout limit";
+ }
+ }
+ return createPanel(new Object[] { "Taverna was unable to connect to \""
+ + endpoint + "\" within " + timeOutString + "." });
+ }
+
+ private static JComponent explanationMissingDependency(VisitReport vr) {
+ Set<String> dependencies = (Set<String>) (vr
+ .getProperty("dependencies"));
+ String message = "Taverna could not find ";
+ if (dependencies == null) {
+ message += "some dependencies";
+ } else {
+ for (Iterator i = dependencies.iterator(); i.hasNext();) {
+ String s = (String) i.next();
+ message += s;
+ if (i.hasNext()) {
+ message += " and ";
+ }
+ }
+ }
+ File directory = (File) vr.getProperty("directory");
+ if (directory != null) {
+ try {
+ message += " in directory " + directory.getCanonicalPath();
+ } catch (IOException e) {
+ logger.error("Could not get path", e);
+ }
+ }
+ return createPanel(new Object[] { message + "." });
+ }
+
+ private static JComponent explanationDefaultValue(VisitReport vr) {
+ String value = (String) (vr.getProperty("value"));
+ if (value == null) {
+ value = "the default value";
+ }
+ return createPanel(new Object[] { "The service still has its value set to \""
+ + value + "\"" });
+ }
+
+ private static JComponent explanationBadWSDL(VisitReport vr) {
+ Exception e = (Exception) (vr.getProperty("exception"));
+ String message = "Parsing the WSDL caused ";
+ if (e == null) {
+ message += " an exception";
+ } else {
+ message += "\"" + e.getMessage() + "\"";
+ }
+ return createPanel(new Object[] { message + "." });
+ }
+
+ private static JComponent explanationNotHTTP(VisitReport vr) {
+ String endpoint = (String) (vr.getProperty("endpoint"));
+ if (endpoint == null) {
+ endpoint = "The endpoint";
+ } else {
+ endpoint = "\"" + endpoint + "\"";
+ }
+ return createPanel(new Object[] { endpoint
+ + " might not be accessible if you run the workflow on a different machine." });
+ }
+
+ private static JComponent explanationUnsupportedStyle(VisitReport vr) {
+ String message = "Taverna does not support ";
+ String style = (String) (vr.getProperty("style"));
+ String use = (String) (vr.getProperty("use"));
+ String kind = null;
+ if ((style != null) && (use != null)) {
+ kind = style + "/" + use;
+ }
+ if (kind == null) {
+ message += " the kind of message the service uses.";
+ } else {
+ message += " the \"" + kind + "\" messages that the service uses.";
+ }
+ return createPanel(new Object[] { message });
+ }
+
+ private static JComponent explanationUnknownOperation(VisitReport vr) {
+ String message = "Taverna could not find the operation ";
+ String operationName = (String) vr.getProperty("operationName");
+ if (operationName == null) {
+ operationName = "called by the service";
+ } else {
+ operationName = "\"" + operationName + "\"";
+ }
+ return createPanel(new Object[] { message + operationName + "." });
+ }
+
+ private static JComponent explanationNoEndpoints(VisitReport vr) {
+ String message = "Taverna found the operation ";
+ String operationName = (String) vr.getProperty("operationName");
+ if (operationName == null) {
+ operationName = "called by the service";
+ } else {
+ operationName = "\"" + operationName + "\"";
+ }
+ message += operationName;
+ message += " but is unable to call it due to lack of location information.";
+ return createPanel(new Object[] { message + operationName });
+ }
+
+ private static JComponent explanationInvalidConfiguration(VisitReport vr) {
+ Exception e = (Exception) (vr.getProperty("exception"));
+ String message = "Trying to understand the XML splitter caused ";
+ if (e == null) {
+ message += " an exception";
+ } else {
+ message += "\"" + e.getMessage() + "\"";
+ }
+ return createPanel(new Object[] { message });
+ }
+
+ private static JComponent explanationNullDatatype(VisitReport vr) {
+ String message = "The XML splitter appears to have a NULL datatype.";
+ return createPanel(new Object[] { message });
+ }
+
+ private static JComponent explanationDisabled(VisitReport vr) {
+ String message = "Taverna could not contact the service when the workflow was opened.";
+ return createPanel(new Object[] { message });
+ }
+
+ private static JComponent explanationDatatypeSource(VisitReport vr) {
+ String message = "The data going into ";
+ String sinkPortName = (String) vr.getProperty("sinkPortName");
+ if (sinkPortName == null) {
+ sinkPortName = "a port";
+ } else {
+ sinkPortName = "port \"" + sinkPortName + "\"";
+ }
+ message += sinkPortName;
+ String sourceName = (String) vr.getProperty("sourceName");
+ String isProcessorSource = (String) vr.getProperty("isProcessorSource");
+ if (sourceName != null) {
+ message += " from ";
+ if (isProcessorSource != null) {
+ if (isProcessorSource.equals("true")) {
+ message += "service ";
+ } else {
+ message += "port ";
+ }
+ }
+ message += "\"" + sourceName + "\"";
+ }
+ message += " may not be XML. The service requires XML as input.";
+ return createPanel(new Object[] { message });
+ }
+
+ private static JComponent explanationBeanshellInvalidScript(VisitReport vr) {
+ Exception e = (Exception) vr.getProperty("exception");
+ String exceptionMessage = null;
+ if (e != null) {
+ exceptionMessage = e.getMessage();
+ }
+ return createPanel(new Object[] {
+ "There are errors in the script of the service.\nWhen the workflow runs, any calls of the service will fail with error: ",
+ exceptionMessage + "." });
+ }
+
+ private static JComponent explanationUnrecognized(VisitReport vr) {
+ String message = "Taverna could not recognize the service when the workflow was opened.";
+ return createPanel(new Object[] { message });
+ }
+
+ private static JComponent explanationLoopConnection(VisitReport vr) {
+ return createPanel(new Object[] { "Port \""
+ + vr.getProperty("portname") + "\" must be connected" });
+ }
+
+ private static JComponent explanationUnmanagedLocation(VisitReport vr) {
+ return createPanel(new Object[] { "The external tool service is configured to run on a location that is not currently known to the Location Manager. It is a good idea to change it to a known location" });
+ }
+
+ private static JComponent explanationIncompatibleMimetypes(VisitReport vr) {
+ ProcessorInputPort pip = (ProcessorInputPort) vr
+ .getProperty("sinkPort");
+ ProcessorOutputPort pop = (ProcessorOutputPort) vr
+ .getProperty("sourcePort");
+ Processor sourceProcessor = (Processor) vr
+ .getProperty("sourceProcessor");
+ String message = "The data";
+ if (pop != null) {
+ message += " from port \"" + pop.getName() + "\"";
+ if (sourceProcessor != null) {
+ message += " of service \"" + sourceProcessor.getLocalName()
+ + "\"";
+ }
+ }
+ if (pip != null) {
+ message += " into port \"" + pip.getName() + "\"";
+ }
+ message += " does not have a compatible mime type";
+ return createPanel(new Object[] { message });
+ }
+
+ private JComponent solutionFailedEntity(VisitReport vr) {
+ if (vr.getSubject() instanceof Processor) {
+ Processor p = (Processor) (vr.getSubject());
+ DataflowActivity da = null;
+ for (Activity a : p.getActivityList()) {
+ if (a instanceof DataflowActivity) {
+ da = (DataflowActivity) a;
+ break;
+ }
+ }
+ String message = "Check the list handling of the service, including the predicted behavior of the service's inputs and outputs";
+ JButton button = null;
+ if (da != null) {
+ message += ", or edit the nested workflow";
+ button = new JButton();
+ button.setAction(new EditNestedDataflowAction(da, fileManager));
+ button.setText("Edit \"" + p.getLocalName() + "\"");
+ }
+ return createPanel(new Object[] { message + ".", button });
+ } else if (vr.getSubject() instanceof Merge) {
+ return createPanel(new Object[] { "Check the predicted behaviour of the data being merged." });
+ }
+ return null;
+ }
+
+ private static JComponent solutionInvalidDataflow(VisitReport vr) {
+ String message = "Fix the errors within the workflow.";
+ return createPanel(new Object[] { message });
+ }
+
+ private JComponent solutionUnresolvedOutput(VisitReport vr) {
+ JButton deleteButton = null;
+
+ DataflowOutputPort port = (DataflowOutputPort) vr.getSubject();
+ DataflowOutputPort dop = (DataflowOutputPort) vr.getSubject();
+ Datalink incomingLink = dop.getInternalInputPort().getIncomingLink();
+ String message;
+ if (incomingLink == null) {
+ message = "Connect the workflow output port to a service or a workflow input port. Alternatively,";
+ final Dataflow d = fileManager.getCurrentDataflow();
+ final DataflowOutputPort p = port;
+ deleteButton = new JButton(new AbstractAction("Remove port") {
+ public void actionPerformed(ActionEvent e) {
+ Edit removeEdit = editManager.getEdits()
+ .getRemoveDataflowOutputPortEdit(d, p);
+ try {
+ editManager.doDataflowEdit(d, removeEdit);
+ } catch (EditException ex) {
+ logger.error("Could not perform edit", ex);
+ }
+ }
+ });
+ } else {
+ message = "Fix the errors of the service that the output port is connected to.";
+ }
+ return createPanel(new Object[] { message, deleteButton });
+ }
+
+ private JComponent solutionUnsatisfiedEntity(VisitReport vr) {
+ String message = "";
+ Dataflow currentDataflow = fileManager.getCurrentDataflow();
+ Tools.ProcessorSplit ps = Tools.splitProcessors(
+ currentDataflow.getProcessors(),
+ (TokenProcessingEntity) (vr.getSubject()));
+ Set<Processor> upStream = ps.getUpStream();
+ boolean plural = false;
+ for (Processor p : upStream) {
+ Set<VisitReport> reports = reportManager.getReports(currentDataflow, p);
+ for (VisitReport report : reports) {
+ if (report.getKind() instanceof FailedEntityKind) {
+ if (!message.equals("")) {
+ message += " and";
+ plural = true;
+ }
+ message += " " + p.getLocalName();
+ }
+ }
+ }
+ if (message.equals("")) {
+ return null;
+ }
+ if (!plural) {
+ message = "The underlying error is caused by" + message;
+ } else {
+ message = "The underlying errors are caused by" + message;
+ }
+ return createPanel(new Object[] { message + "." });
+ }
+
+ private JComponent solutionDataflowCollation(VisitReport vr) {
+ String message = "Edit the nested workflow to fix its problems.";
+ JButton button = null;
+ Processor p = (Processor) (vr.getSubject());
+ DataflowActivity da = null;
+ for (Activity a : p.getActivityList()) {
+ if (a instanceof DataflowActivity) {
+ da = (DataflowActivity) a;
+ break;
+ }
+ }
+ if (da != null) {
+ button = new JButton();
+ button.setAction(new EditNestedDataflowAction(da, fileManager));
+ button.setText("Edit \"" + p.getLocalName() + "\"");
+ }
+ String reminder = "Remember to save the nested workflow.";
+ return createPanel(new Object[] { message, button, reminder });
+ }
+
+ private JComponent solutionDataflowIncomplete(VisitReport vr) {
+ String message = "Add a service from the service panel to the workflow, or";
+ JButton button = new JButton();
+ button.setAction(new AddDataflowOutputAction(
+ (Dataflow) vr.getSubject(), null, editManager, selectionManager));
+ button.setText("Add an output port");
+ return createPanel(new Object[] { message, button });
+ }
+
+ private JComponent solutionSourceFragile(VisitReport vr) {
+ Processor sourceProcessor = (Processor) vr
+ .getProperty("sourceProcessor");
+ String labelText = "Make ";
+ if (sourceProcessor == null) {
+ labelText += "the source service ";
+ } else {
+ labelText += "\"" + sourceProcessor.getLocalName() + "\" ";
+ }
+ labelText += "more robust to failure by adding service retries.";
+ JButton button = null;
+ if (sourceProcessor != null) {
+ Retry retryLayer = null;
+ for (DispatchLayer dl : sourceProcessor.getDispatchStack()
+ .getLayers()) {
+ if (dl instanceof Retry) {
+ retryLayer = (Retry) dl;
+ break;
+ }
+ }
+ if (retryLayer != null) {
+ button = new JButton();
+ button.setAction(new RetryConfigureAction(null, null,
+ retryLayer, editManager, fileManager));
+ button.setText("Set retry");
+ }
+ }
+ return createPanel(new Object[] { labelText, button });
+ }
+
+ private static JComponent solutionBeanshellInvalidScript(VisitReport vr) {
+ JButton button = new JButton();
+ Processor p = (Processor) (vr.getSubject());
+ button.setAction(new ReportViewConfigureAction(p));
+ button.setText("Configure " + p.getLocalName());
+ return createPanel(new Object[] {
+ "Edit the service script, checking that the script is valid before saving it.",
+ button });
+ }
+
+ private JComponent solutionConnectionProblem(VisitReport vr) {
+ String endpoint = (String) (vr.getProperty("endpoint"));
+ String connectMessage = "";
+ JButton connectButton = null;
+ if (endpoint == null) {
+ endpoint = "the endpoint";
+ connectMessage = "Try to connect to the endpoint.";
+ } else {
+ connectMessage = "Try to connect to " + endpoint + " in a browser.";
+ final String end = endpoint;
+ connectButton = new JButton(new AbstractAction("Open in browser") {
+ public void actionPerformed(ActionEvent e) {
+ try {
+ Desktop.getDesktop().browse(new URI(end));
+ } catch (Exception ex) {
+ logger.error("Failed to open endpoint", ex);
+ }
+ }
+ });
+ }
+ String workedMessage = "If the connection did not work, please contact the service provider or workflow creator. Alternatively, check if you are using an HTTP Proxy, and edit Taverna's proxy settings.";
+ JButton preferencesButton = null;
+ if (endpoint != null) {
+ preferencesButton = new JButton(new AbstractAction(
+ "Change HTTP proxy") {
+ public void actionPerformed(ActionEvent e) {
+ T2ConfigurationFrame.showConfiguration("HTTP proxy", configurationUIFactories);
+ }
+ });
+ }
+ String editMessage = null;
+ JButton editButton = null;
+ DisabledActivity da = null;
+ for (Activity a : ((Processor) vr.getSubject()).getActivityList()) {
+ if (a instanceof DisabledActivity) {
+ da = (DisabledActivity) a;
+ break;
+ }
+ }
+ if (da != null) {
+ editMessage = "If the service has moved, change the service's properties to its new location.";
+ editButton = new JButton(new DisabledActivityConfigurationAction(
+ da, null, editManager, fileManager, reportManager, activityIconManager));
+ }
+ return createPanel(new Object[] { connectMessage, connectButton,
+ workedMessage, preferencesButton, editMessage, editButton });
+
+ }
+
+ private JComponent solutionInvalidUrl(VisitReport vr) {
+ String message = "Contact the service provider or workflow creator.";
+ String editMessage = "If the service has moved, change the service's properties to its new location.";
+ JButton editButton = null;
+ DisabledActivity da = null;
+ for (Activity a : ((Processor) vr.getSubject()).getActivityList()) {
+ if (a instanceof DisabledActivity) {
+ da = (DisabledActivity) a;
+ break;
+ }
+ }
+ if (da != null) {
+ editButton = new JButton(new DisabledActivityConfigurationAction(
+ da, null, editManager, fileManager, reportManager, activityIconManager));
+ }
+ return createPanel(new Object[] { message, editMessage, editButton });
+ }
+
+ private JComponent solutionTimeOut(VisitReport vr) {
+ String message = "Try to open ";
+ String endpoint = (String) (vr.getProperty("endpoint"));
+ JButton connectButton = null;
+ if (endpoint == null) {
+ message += "the endpoint ";
+ } else {
+ message += "\"" + endpoint + "\" ";
+ final String end = endpoint;
+ connectButton = new JButton(new AbstractAction("Open in browser") {
+ public void actionPerformed(ActionEvent e) {
+ try {
+ Desktop.getDesktop().browse(new URI(end));
+ } catch (Exception ex) {
+ logger.error("Failed to open endpoint", ex);
+ }
+ }
+ });
+ }
+ message += "in a file, or web, browser.";
+ String workedMessage = "If the browser opened the address, then alter the validation timeout in the preferences";
+ JButton preferencesButton = new JButton(new AbstractAction(
+ "Change timeout") {
+ public void actionPerformed(ActionEvent e) {
+ T2ConfigurationFrame.showConfiguration("Validation report", configurationUIFactories);
+ }
+ });
+ String didNotWorkMessage = "Alternatively, if the browser did not open the address, try later as the service may be temporarily offline. If the service remains offline, please contact the service provider or workflow creator.";
+ String editMessage = null;
+ JButton editButton = null;
+ DisabledActivity da = null;
+ for (Activity a : ((Processor) vr.getSubject()).getActivityList()) {
+ if (a instanceof DisabledActivity) {
+ da = (DisabledActivity) a;
+ break;
+ }
+ }
+ if (da != null) {
+ editMessage = "If the service has moved, change the service's properties to its new location.";
+ editButton = new JButton(new DisabledActivityConfigurationAction(
+ da, null, editManager, fileManager, reportManager, activityIconManager));
+ }
+ return createPanel(new Object[] { message, connectButton,
+ workedMessage, preferencesButton, didNotWorkMessage,
+ editMessage, editButton });
+ }
+
+ private JComponent solutionIoProblem(VisitReport vr) {
+ String message = "";
+ Exception e = (Exception) (vr.getProperty("exception"));
+ if (e != null && e instanceof SSLException) {
+ message += "There was a problem with establishing a HTTPS connection to the service. ";
+ if (e.getMessage().toLowerCase()
+ .contains("no trusted certificate found")) {
+ message += "Looks like the authenticity of the service could not be confirmed. Check that you have imported the service's certificate under 'Trusted Certificates' in Credential Manager. "
+ + "If this is a WSDL service, try restarting Taverna to refresh certificates used in HTTPS connections.\n\n";
+ } else if (e.getMessage().toLowerCase()
+ .contains("received fatal alert: bad_certificate")) {
+ message += "Looks like you could not be authenticated to the service. Check that you have imported your certificate under 'Your certificates' in Credential Manager. "
+ + "If this is a WSDL service, try restarting Taverna to refresh certificates used in HTTPS connections.\n\n";
+ } else {
+ message += "Check that you have imported the service's certificate under 'Trusted Certificates' in Credential Manager. "
+ + "If user authentication is required, also check that you have imported your certificate under 'Your certificates' in Credential Manager. "
+ + "If this is a WSDL service, try restarting Taverna to refresh certificates used in HTTPS connections.\n\n";
+ }
+ }
+ message += "Try to open ";
+ String endpoint = (String) (vr.getProperty("endpoint"));
+ JButton connectButton = null;
+ if (endpoint == null) {
+ message += "the endpoint ";
+ } else {
+ message += "\"" + endpoint + "\" ";
+ final String end = endpoint;
+ connectButton = new JButton(new AbstractAction("Open in browser") {
+ public void actionPerformed(ActionEvent e) {
+ try {
+ Desktop.getDesktop().browse(new URI(end));
+ } catch (Exception ex) {
+ logger.error("Failed to open endpoint", ex);
+ }
+ }
+ });
+ }
+ message += "in a file, or web, browser.";
+ String elseMessage = message.startsWith("Try to open") ? "If that does not work, please contact the service provider or workflow creator."
+ : null;
+ String editMessage = message.startsWith("Try to open") ? "If the service has moved, change the service's properties to its new location."
+ : null;
+ JButton editButton = null;
+ DisabledActivity da = null;
+ for (Activity a : ((Processor) vr.getSubject()).getActivityList()) {
+ if (a instanceof DisabledActivity) {
+ da = (DisabledActivity) a;
+ break;
+ }
+ }
+ if (da != null) {
+ editButton = new JButton(new DisabledActivityConfigurationAction(
+ da, null, editManager, fileManager, reportManager, activityIconManager));
+ }
+ return createPanel(new Object[] { message, connectButton, elseMessage,
+ editMessage, editButton });
+ }
+
+ private static JComponent solutionMissingDependency(VisitReport vr) {
+ String message = "Put ";
+ Set<String> dependencies = (Set<String>) (vr
+ .getProperty("dependencies"));
+ if (dependencies == null) {
+ message += "the dependencies";
+ } else {
+ for (Iterator i = dependencies.iterator(); i.hasNext();) {
+ String s = (String) i.next();
+ message += s;
+ if (i.hasNext()) {
+ message += " and ";
+ }
+ }
+ }
+ File directory = (File) vr.getProperty("directory");
+ if (directory != null) {
+ try {
+ message += " in directory " + directory.getCanonicalPath();
+ } catch (IOException e) {
+ logger.error("Could not get path", e);
+ }
+ } else {
+ message += " in the application directory.";
+ }
+ String elseMessage = "If you do not have the files, please contact the workflow creator.";
+ return createPanel(new Object[] { message, elseMessage });
+ }
+
+ private static JComponent solutionDefaultValue(VisitReport vr) {
+ String message = "Change the value of the service by clicking the \"Set value\" button";
+ JButton button = new JButton();
+ Processor p = (Processor) (vr.getSubject());
+ button.setAction(new ReportViewConfigureAction(p));
+ button.setText("Set value");
+ return createPanel(new Object[] { message, button });
+ }
+
+ private static JComponent solutionBadWSDL(VisitReport vr) {
+ return createPanel(new Object[] { PLEASE_CONTACT });
+ }
+
+ private static JComponent solutionNotHTTP(VisitReport vr) {
+ String endpoint = (String) (vr.getProperty("endpoint"));
+ if (endpoint == null) {
+ endpoint = "the endpoint";
+ } else {
+ endpoint = "\"" + endpoint + "\"";
+ }
+ String message = "Move the file at " + endpoint + " to a web server.";
+ return createPanel(new Object[] { message });
+ }
+
+ private static JComponent solutionUnsupportedStyle(VisitReport vr) {
+ String message = "Contact the service provider to see if there is an alternative style of service available.";
+ return createPanel(new Object[] { message });
+ }
+
+ private JComponent solutionUnknownOperation(VisitReport vr) {
+ String message = "Contact the service provider to see if the operation has been renamed.";
+ String editMessage = "If you know its new name, then please edit the service's properties.";
+ JButton editButton = null;
+ DisabledActivity da = null;
+ for (Activity a : ((Processor) vr.getSubject()).getActivityList()) {
+ if (a instanceof DisabledActivity) {
+ da = (DisabledActivity) a;
+ break;
+ }
+ }
+ if (da != null) {
+ editButton = new JButton(new DisabledActivityConfigurationAction(
+ da, null, editManager, fileManager, reportManager, activityIconManager));
+ }
+ return createPanel(new Object[] { message, editMessage, editButton });
+ }
+
+ private static JComponent solutionNoEndpoints(VisitReport vr) {
+ return createPanel(new Object[] { PLEASE_CONTACT });
+ }
+
+ private static JComponent solutionInvalidConfiguration(VisitReport vr) {
+ return createPanel(new Object[] { PLEASE_CONTACT });
+ }
+
+ private static JComponent solutionNullDatatype(VisitReport vr) {
+ return createPanel(new Object[] { PLEASE_CONTACT });
+ }
+
+ private static JComponent solutionDisabled(VisitReport vr) {
+ String message = "Validate the workflow and fix any errors on the service.";
+ return createPanel(new Object[] { message });
+ }
+
+ private JComponent solutionDatatypeSource(VisitReport vr) {
+ String sinkPortName = (String) vr.getProperty("sinkPortName");
+ if (sinkPortName == null) {
+ return null;
+ }
+ String removeMessage = "1. Remove the link to " + "port \""
+ + sinkPortName + "\"";
+ ProcessorInputPort pip = (ProcessorInputPort) vr
+ .getProperty("sinkPort");
+ final InputPortTypeDescriptorActivity a = (InputPortTypeDescriptorActivity) vr
+ .getProperty("activity");
+ String addSplitterMessage = "2. Add an XML splitter for " + "port \""
+ + sinkPortName + "\"";
+ JButton button = null;
+ if (pip != null) {
+ Datalink incomingLink = pip.getIncomingLink();
+ if (incomingLink != null) {
+ button = new JButton();
+ final Dataflow d = fileManager.getCurrentDataflow();
+ final String portName = sinkPortName;
+ final Datalink link = incomingLink;
+ button.setAction(new AbstractAction(
+ "Remove link and add XML splitter") {
+ public void actionPerformed(ActionEvent e) {
+ Edit removeLinkEdit = Tools
+ .getDisconnectDatalinkAndRemovePortsEdit(link, editManager.getEdits());
+ Edit addXMLEdit = new AddXMLSplitterEdit(d,
+ (Activity<?>) a, portName, true, editManager.getEdits());
+ List<Edit<?>> editList = Arrays.asList(new Edit<?>[] {
+ removeLinkEdit, addXMLEdit });
+ CompoundEdit ce = new CompoundEdit(editList);
+ try {
+ editManager.doDataflowEdit(d, ce);
+ } catch (EditException ex) {
+ logger.error("Could not perform edit", ex);
+ }
+ }
+ });
+ }
+ }
+ String addConnectionMessage = "3. Make a connection to the relevant port of the new XML splitter.";
+ return createPanel(new Object[] { removeMessage, addSplitterMessage,
+ button, addConnectionMessage });
+ }
+
+ private static JComponent solutionUnrecognized(VisitReport vr) {
+ String message = "Please contact the workflow creator to find out what additional plugins, if any, need to be installed in Taverna.";
+ return createPanel(new Object[] { message });
+ }
+
+ private static JComponent solutionLoopConnection(VisitReport vr) {
+ return createPanel(new Object[] { "Connect port \""
+ + vr.getProperty("portname") + "\"" });
+ }
+
+ private static JComponent solutionUnmanagedLocation(VisitReport vr) {
+ JButton button = new JButton();
+ Processor p = (Processor) (vr.getSubject());
+ button.setAction(new ReportViewConfigureAction(p));
+ button.setText("Configure " + p.getLocalName());
+ return createPanel(new Object[] {
+ "Change the run locaton of the service", button });
+ }
+
+ private JComponent solutionIncompatibleMimetypes(VisitReport vr) {
+ JButton sinkButton = new JButton();
+ Processor sinkProcessor = (Processor) (vr.getProperty("sinkProcessor"));
+ Processor sourceProcessor = (Processor) vr
+ .getProperty("sourceProcessor");
+ sinkButton.setAction(new ReportViewConfigureAction(sinkProcessor));
+ sinkButton.setText("Configure " + sinkProcessor.getLocalName());
+ JButton sourceButton = new JButton();
+ sourceButton.setAction(new ReportViewConfigureAction(sourceProcessor));
+ sourceButton.setText("Configure " + sourceProcessor.getLocalName());
+
+ JButton deleteLinkButton = new JButton();
+ final Datalink link = (Datalink) vr.getProperty("link");
+ final Dataflow d = fileManager.getCurrentDataflow();
+ deleteLinkButton.setAction(new AbstractAction("Remove link") {
+ public void actionPerformed(ActionEvent e) {
+ Edit removeLinkEdit = Tools
+ .getDisconnectDatalinkAndRemovePortsEdit(link, editManager.getEdits());
+ try {
+ editManager.doDataflowEdit(d, removeLinkEdit);
+ } catch (EditException ex) {
+ logger.error("Could not perform edit", ex);
+ }
+ }
+ });
+
+ return createPanel(new Object[] {
+ "Change the source or destination mimetype or remove the link",
+ sourceButton, sinkButton, deleteLinkButton });
+ }
+
+ private static JPanel createPanel(Object[] components) {
+ JPanel result = new JPanel(new GridBagLayout());
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.anchor = GridBagConstraints.NORTHWEST;
+ gbc.gridwidth = 1;
+ gbc.weightx = 0.9;
+ for (Object o : components) {
+ if (o == null) {
+ continue;
+ }
+ JComponent component = null;
+ if (o instanceof String) {
+ component = new ReadOnlyTextArea((String) o);
+ } else if (o instanceof JComponent) {
+ component = (JComponent) o;
+ } else {
+ logger.error("Unrecognized component " + o.getClass());
+ continue;
+ }
+ gbc.gridy++;
+ if (component instanceof JButton) {
+ gbc.weightx = 0;
+ gbc.gridwidth = 1;
+ gbc.fill = GridBagConstraints.NONE;
+ } else {
+ gbc.weightx = 0.9;
+ gbc.gridwidth = 2;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ }
+ result.add(component, gbc);
+ }
+ // gbc.weightx = 0.9;
+ // gbc.weighty = 0.9;
+ // gbc.gridx = 0;
+ // gbc.gridy++;
+ // gbc.gridwidth = 2;
+ // gbc.fill = GridBagConstraints.BOTH;
+ // result.add(new JPanel(), gbc);
+ result.setBackground(SystemColor.text);
+ return result;
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setReportManager(ReportManager reportManager) {
+ this.reportManager = reportManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setConfigurationUIFactories(List<ConfigurationUIFactory> configurationUIFactories) {
+ this.configurationUIFactories = configurationUIFactories;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+}
diff --git a/taverna-workbench-report-explainer/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.report.explainer.VisitExplainer b/taverna-workbench-report-explainer/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.report.explainer.VisitExplainer
new file mode 100644
index 0000000..109e3d1
--- /dev/null
+++ b/taverna-workbench-report-explainer/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.report.explainer.VisitExplainer
@@ -0,0 +1 @@
+net.sf.taverna.t2.workbench.report.explainer.BasicExplainer
diff --git a/taverna-workbench-report-explainer/src/main/resources/META-INF/spring/report-explainer-context-osgi.xml b/taverna-workbench-report-explainer/src/main/resources/META-INF/spring/report-explainer-context-osgi.xml
new file mode 100644
index 0000000..610d13c
--- /dev/null
+++ b/taverna-workbench-report-explainer/src/main/resources/META-INF/spring/report-explainer-context-osgi.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="BasicExplainer" interface="net.sf.taverna.t2.workbench.report.explainer.VisitExplainer" />
+
+ <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
+ <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
+ <reference id="reportManager" interface="net.sf.taverna.t2.workbench.report.ReportManager" />
+ <reference id="selectionManager" interface="net.sf.taverna.t2.workbench.selection.SelectionManager" />
+ <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
+
+ <list id="configurationUIFactories" interface="uk.org.taverna.configuration.ConfigurationUIFactory" cardinality="0..N" />
+
+</beans:beans>
diff --git a/taverna-workbench-report-explainer/src/main/resources/META-INF/spring/report-explainer-context.xml b/taverna-workbench-report-explainer/src/main/resources/META-INF/spring/report-explainer-context.xml
new file mode 100644
index 0000000..9bb083e
--- /dev/null
+++ b/taverna-workbench-report-explainer/src/main/resources/META-INF/spring/report-explainer-context.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="BasicExplainer" class="net.sf.taverna.t2.workbench.report.explainer.BasicExplainer">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="reportManager" ref="reportManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="configurationUIFactories" ref="configurationUIFactories" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ </bean>
+
+</beans>
diff --git a/taverna-workbench-retry-ui/pom.xml b/taverna-workbench-retry-ui/pom.xml
new file mode 100644
index 0000000..7c22ea6
--- /dev/null
+++ b/taverna-workbench-retry-ui/pom.xml
@@ -0,0 +1,42 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna.t2</groupId>
+ <artifactId>ui-exts</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>retry-ui</artifactId>
+ <packaging>bundle</packaging>
+ <name>Retry layer contextual view</name>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>contextual-views-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>menu-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>edits-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>selection-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>${jackson-databind.version}</version>
+ </dependency>
+ </dependencies>
+</project>
diff --git a/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryConfigurationPanel.java b/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryConfigurationPanel.java
new file mode 100644
index 0000000..280414a
--- /dev/null
+++ b/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryConfigurationPanel.java
@@ -0,0 +1,172 @@
+package net.sf.taverna.t2.workbench.retry;
+
+import java.awt.GridLayout;
+
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.border.EmptyBorder;
+
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+@SuppressWarnings("serial")
+public class RetryConfigurationPanel extends JPanel {
+
+ public static final double DEFAULT_BACKOFF = 1.0;
+ public static final int DEFAULT_INITIAL_DELAY = 1000;
+ public static final int DEFAULT_MAX_DELAY = 5000;
+ public static final int DEFAULT_RETRIES = 0;
+
+ private static final double MIN_BACKOFF = 1.0;
+ private static final int MIN_DELAY = 1;
+ private static final int MIN_RETRIES = 0;
+
+ private final ObjectNode json;
+
+ private JTextField maxRetriesField = new JTextField();
+ private JTextField initialDelayField = new JTextField();
+ private JTextField maximumDelayField = new JTextField();
+ private JTextField backoffFactorField = new JTextField();
+
+ public RetryConfigurationPanel(Configuration configuration) {
+ if (configuration.getJson().has("retry")) {
+ json = (ObjectNode) configuration.getJson().get("retry").deepCopy();
+ } else {
+ json = configuration.getJsonAsObjectNode().objectNode();
+ }
+ this.setLayout(new GridLayout(4,2));
+ this.setBorder(new EmptyBorder(10,10,10,10));
+ populate();
+ }
+
+ public void populate() {
+ readConfiguration();
+ this.removeAll();
+
+ JLabel maxRetriesLabel = new JLabel("Maximum number of retries");
+ maxRetriesLabel.setBorder(new EmptyBorder(0,0,0,10)); // give some right border to this label
+ this.add(maxRetriesLabel);
+ this.add(maxRetriesField);
+
+ this.add(new JLabel("Initial delay in ms"));
+ this.add(initialDelayField);
+
+ this.add(new JLabel("Maximum delay in ms"));
+ this.add(maximumDelayField);
+
+ this.add(new JLabel("Delay increase factor"));
+ this.add(backoffFactorField);
+ }
+
+ private void readConfiguration() {
+ int maxRetries = DEFAULT_RETRIES;
+ int initialDelay = DEFAULT_INITIAL_DELAY;
+ int maxDelay = DEFAULT_MAX_DELAY;
+ double backoffFactor = DEFAULT_BACKOFF;
+
+ if (json.has("maxRetries")) {
+ maxRetries = json.get("maxRetries").asInt();
+ }
+ if (json.has("initialDelay")) {
+ initialDelay = json.get("initialDelay").asInt();
+ }
+ if (json.has("maxDelay")) {
+ maxDelay = json.get("maxDelay").asInt();
+ }
+ if (json.has("backoffFactor")) {
+ backoffFactor = json.get("backoffFactor").asDouble();;
+ }
+
+ if (maxRetries < MIN_RETRIES) {
+ maxRetries = DEFAULT_RETRIES;
+ }
+ if (initialDelay < MIN_DELAY) {
+ initialDelay = DEFAULT_INITIAL_DELAY;
+ }
+ if (maxDelay < MIN_DELAY) {
+ maxDelay = DEFAULT_MAX_DELAY;
+ }
+ if (maxDelay < initialDelay) {
+ maxDelay = initialDelay;
+ }
+ if (backoffFactor < MIN_BACKOFF) {
+ backoffFactor = DEFAULT_BACKOFF;
+ }
+
+ maxRetriesField.setText(Integer.toString(maxRetries));
+ initialDelayField.setText(Integer.toString(initialDelay));
+ maximumDelayField.setText(Integer.toString(maxDelay));
+ backoffFactorField.setText(Double.toString(backoffFactor));
+ }
+
+ public boolean validateConfig() {
+ String errorText = "";
+ int maxRetries = -1;
+ int initialDelay = -1;
+ int maxDelay = -1;
+ float backoffFactor = -1;
+
+ try {
+ maxRetries = Integer.parseInt(maxRetriesField.getText());
+ if (maxRetries < MIN_RETRIES) {
+ errorText += "The number of retries must be non-negative.\n";
+ }
+ }
+ catch (NumberFormatException e) {
+ errorText += "The maximum number of retries must be an integer.\n";
+ }
+
+ try {
+ initialDelay = Integer.parseInt(initialDelayField.getText());
+ if (initialDelay < MIN_DELAY) {
+ errorText += "The initial delay must be a positive integer.\n";
+ }
+ }
+ catch (NumberFormatException e) {
+ errorText += "The initial delay must be an integer.\n";
+ }
+
+ try {
+ maxDelay = Integer.parseInt(maximumDelayField.getText());
+ if (maxDelay < MIN_DELAY) {
+ errorText += "The maximum delay must be a positive integer.\n";
+ }
+ else if (maxDelay < initialDelay) {
+ errorText += "The maximum delay must be greater than the initial delay.\n";
+ maxDelay = Math.max(MIN_DELAY, initialDelay);
+ maximumDelayField.setText(Integer.toString(maxDelay));
+ }
+ }
+ catch (NumberFormatException e) {
+ errorText += "The maximum delay must be an integer.\n";
+ }
+
+ try {
+ backoffFactor = Float.parseFloat(backoffFactorField.getText());
+ if (backoffFactor < MIN_BACKOFF) {
+ errorText += "The backoff factor must be greater than one.\n";
+ }
+ }
+ catch (NumberFormatException e) {
+ errorText += "The backoff factor must be a number.\n";
+ }
+ if (errorText.length() > 0) {
+ JOptionPane.showMessageDialog(this, errorText, "", JOptionPane.ERROR_MESSAGE);
+ return false;
+ }
+ return true;
+ }
+
+ public JsonNode getJson() {
+ json.put("backoffFactor", backoffFactorField.getText());
+ json.put("initialDelay", initialDelayField.getText());
+ json.put("maxDelay", maximumDelayField.getText());
+ json.put("maxRetries", maxRetriesField.getText());
+ return json;
+ }
+
+}
diff --git a/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryConfigureAction.java b/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryConfigureAction.java
new file mode 100644
index 0000000..f5f7c7f
--- /dev/null
+++ b/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryConfigureAction.java
@@ -0,0 +1,183 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.workbench.retry;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.util.Iterator;
+import java.util.Map.Entry;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+
+import net.sf.taverna.t2.workbench.edits.Edit;
+import net.sf.taverna.t2.workbench.edits.EditException;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workflow.edits.AddChildEdit;
+import net.sf.taverna.t2.workflow.edits.ChangeJsonEdit;
+
+import org.apache.log4j.Logger;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+import uk.org.taverna.scufl2.api.core.Processor;
+import uk.org.taverna.scufl2.api.profiles.Profile;
+
+/**
+ * @author alanrw
+ *
+ */
+@SuppressWarnings("serial")
+public class RetryConfigureAction extends AbstractAction {
+
+ private static Logger logger = Logger.getLogger(RetryConfigureAction.class);
+
+ private final Frame owner;
+ private final Processor processor;
+ private final RetryContextualView retryContextualView;
+
+ private final EditManager editManager;
+ private final SelectionManager selectionManager;
+
+ private final Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ private Configuration configuration;
+
+ public RetryConfigureAction(Frame owner, RetryContextualView retryContextualView,
+ Processor processor, EditManager editManager, SelectionManager selectionManager) {
+ super("Configure");
+ this.owner = owner;
+ this.retryContextualView = retryContextualView;
+ this.processor = processor;
+ this.editManager = editManager;
+ this.selectionManager = selectionManager;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ String title = "Retries for service " + processor.getName();
+ final JDialog dialog = new HelpEnabledDialog(owner, title, true);
+ Configuration configuration;
+ try {
+ configuration = scufl2Tools.configurationFor(processor, selectionManager.getSelectedProfile());
+ } catch (IndexOutOfBoundsException ex) {
+ configuration = new Configuration();
+ }
+ RetryConfigurationPanel retryConfigurationPanel = new RetryConfigurationPanel(configuration);
+ dialog.add(retryConfigurationPanel, BorderLayout.CENTER);
+
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout(new FlowLayout());
+
+ JButton okButton = new JButton(new OKAction(dialog, retryConfigurationPanel));
+ buttonPanel.add(okButton);
+
+ JButton resetButton = new JButton(new ResetAction(retryConfigurationPanel));
+ buttonPanel.add(resetButton);
+
+ JButton cancelButton = new JButton(new CancelAction(dialog));
+ buttonPanel.add(cancelButton);
+
+ dialog.add(buttonPanel, BorderLayout.SOUTH);
+ dialog.pack();
+ dialog.setLocationRelativeTo(null);
+ dialog.setVisible(true);
+ }
+
+ public class ResetAction extends AbstractAction {
+
+ private final RetryConfigurationPanel retryConfigurationPanel;
+
+ public ResetAction(RetryConfigurationPanel retryConfigurationPanel) {
+ super("Reset");
+ this.retryConfigurationPanel = retryConfigurationPanel;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ retryConfigurationPanel.populate();
+ }
+
+ }
+
+ public class OKAction extends AbstractAction {
+
+ private final RetryConfigurationPanel retryConfigurationPanel;
+ private final JDialog dialog;
+
+ public OKAction(JDialog dialog, RetryConfigurationPanel retryConfigurationPanel) {
+ super("OK");
+ this.dialog = dialog;
+ this.retryConfigurationPanel = retryConfigurationPanel;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (retryConfigurationPanel.validateConfig()) {
+ try {
+ try {
+ Configuration configuration = scufl2Tools.configurationFor(processor, selectionManager.getSelectedProfile());
+ ObjectNode json = configuration.getJsonAsObjectNode().deepCopy();
+ ObjectNode parallelizeNode = null;
+ if (json.has("retry")) {
+ parallelizeNode = (ObjectNode) json.get("retry");
+ } else {
+ parallelizeNode = json.objectNode();
+ json.put("retry", parallelizeNode);
+ }
+ JsonNode newParallelizeNode = retryConfigurationPanel.getJson();
+ Iterator<Entry<String, JsonNode>> fields = newParallelizeNode.fields();
+ while (fields.hasNext()) {
+ Entry<String, JsonNode> entry = fields.next();
+ parallelizeNode.set(entry.getKey(), entry.getValue());
+ }
+ Edit<Configuration> edit = new ChangeJsonEdit(configuration, json);
+ editManager.doDataflowEdit(selectionManager.getSelectedWorkflowBundle(), edit);
+ } catch (IndexOutOfBoundsException ex) {
+ Configuration configuration = new Configuration();
+ configuration.setConfigures(processor);
+ ObjectNode json = configuration.getJsonAsObjectNode();
+ json.put("retry", retryConfigurationPanel.getJson());
+ Edit<Profile> edit = new AddChildEdit<Profile>(selectionManager.getSelectedProfile(), configuration);
+ editManager.doDataflowEdit(selectionManager.getSelectedWorkflowBundle(), edit);
+ }
+ dialog.setVisible(false);
+ if (retryContextualView != null) {
+ retryContextualView.refreshView();
+ }
+ } catch (EditException e1) {
+ logger.warn("Could not configure retries", e1);
+ JOptionPane.showMessageDialog(owner, "Could not configure retries",
+ "An error occured when configuring retries: " + e1.getMessage(),
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ }
+
+ }
+
+ public class CancelAction extends AbstractAction {
+
+ private final JDialog dialog;
+
+ public CancelAction(JDialog dialog) {
+ super("Cancel");
+ this.dialog = dialog;
+
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ dialog.setVisible(false);
+ }
+
+ }
+
+}
diff --git a/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryConfigureMenuAction.java b/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryConfigureMenuAction.java
new file mode 100644
index 0000000..c88fd1e
--- /dev/null
+++ b/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryConfigureMenuAction.java
@@ -0,0 +1,77 @@
+/**********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.workbench.retry;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import uk.org.taverna.scufl2.api.core.Processor;
+
+public class RetryConfigureMenuAction extends AbstractContextualMenuAction {
+
+ public static final URI configureRunningSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/configureRunning");
+
+ private static final URI RETRY_CONFIGURE_URI = URI
+ .create("http://taverna.sf.net/2008/t2workbench/retryConfigure");
+
+ public static URI TYPE = URI.create("http://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Retry");
+
+ private EditManager editManager;
+
+ private SelectionManager selectionManager;
+
+ public RetryConfigureMenuAction() {
+ super(configureRunningSection, 30, RETRY_CONFIGURE_URI);
+ }
+
+ @SuppressWarnings("serial")
+ @Override
+ protected Action createAction() {
+ return new AbstractAction("Retries...") {
+ public void actionPerformed(ActionEvent e) {
+ Processor processor = (Processor) getContextualSelection().getSelection();
+ RetryConfigureAction retryConfigureAction = new RetryConfigureAction(null,
+ null, processor, editManager, selectionManager);
+ retryConfigureAction.actionPerformed(e);
+ }
+ };
+ }
+
+ public boolean isEnabled() {
+ return super.isEnabled() && (getContextualSelection().getSelection() instanceof Processor);
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
diff --git a/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryContextualView.java b/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryContextualView.java
new file mode 100644
index 0000000..9fef2e7
--- /dev/null
+++ b/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryContextualView.java
@@ -0,0 +1,165 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.retry;
+
+import java.awt.BorderLayout;
+import java.awt.Frame;
+
+import javax.swing.Action;
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+import net.sf.taverna.t2.lang.ui.ReadOnlyTextArea;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+import uk.org.taverna.scufl2.api.core.Processor;
+
+/**
+ * View of a processor, including it's iteration stack, activities, etc.
+ *
+ * @author Alan R Williams
+ *
+ */
+@SuppressWarnings("serial")
+public class RetryContextualView extends ContextualView {
+
+ private final Processor processor;
+
+ private final EditManager editManager;
+
+ private final SelectionManager selectionManager;
+
+ private final Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ private JPanel panel;
+
+ public RetryContextualView(Processor processor, EditManager editManager, SelectionManager selectionManager) {
+ super();
+ this.processor = processor;
+ this.editManager = editManager;
+ this.selectionManager = selectionManager;
+ initialise();
+ initView();
+ }
+
+ /*
+ * @Override public Action getConfigureAction(Frame owner) { return new
+ * ConfigureAction(owner); }
+ */
+ @Override
+ public void refreshView() {
+ initialise();
+ }
+
+ private void initialise() {
+ if (panel == null) {
+ panel = createPanel();
+ } else {
+ panel.removeAll();
+ }
+
+ JTextArea textArea = new ReadOnlyTextArea();
+ textArea.setEditable(false);
+ String text = "";
+ int maxRetries = RetryConfigurationPanel.DEFAULT_RETRIES;
+ int initialDelay = RetryConfigurationPanel.DEFAULT_INITIAL_DELAY;
+ int maxDelay = RetryConfigurationPanel.DEFAULT_MAX_DELAY;
+ double backoffFactor = RetryConfigurationPanel.DEFAULT_BACKOFF;
+
+ for (Configuration configuration : scufl2Tools.configurationsFor(processor, selectionManager.getSelectedProfile())) {
+ JsonNode processorConfig = configuration.getJson();
+ if (processorConfig.has("retry")) {
+ JsonNode retryConfig = processorConfig.get("retry");
+ if (retryConfig.has("maxRetries")) {
+ maxRetries = retryConfig.get("maxRetries").asInt();
+ }
+ if (retryConfig.has("initialDelay")) {
+ initialDelay = retryConfig.get("initialDelay").asInt();
+ }
+ if (retryConfig.has("maxDelay")) {
+ maxDelay = retryConfig.get("maxDelay").asInt();
+ }
+ if (retryConfig.has("backoffFactor")) {
+ backoffFactor = retryConfig.get("backoffFactor").asDouble();;
+ }
+ }
+ }
+
+ if (maxRetries < 1) {
+ text += "The service is not re-tried";
+ } else if (maxRetries == 1) {
+ text += "The service is re-tried once";
+ text += " after " + initialDelay + "ms";
+ } else {
+ text += "The service is re-tried " + maxRetries + " times. ";
+ if (backoffFactor == 1.0) {
+ text += "Each time after a delay of " + initialDelay + "ms.";
+ } else {
+ text += "The first delay is " + initialDelay + "ms";
+ int noMaxDelay = (int) (initialDelay * Math.pow(backoffFactor, maxRetries - 1));
+ if (noMaxDelay < maxDelay) {
+ maxDelay = noMaxDelay;
+ }
+ text += " with a maximum delay of " + maxDelay + "ms.";
+ text += " Each delay is increased by a factor of " + backoffFactor;
+ }
+ }
+ textArea.setText(text);
+ textArea.setBackground(panel.getBackground());
+ panel.add(textArea, BorderLayout.CENTER);
+ revalidate();
+ }
+
+ @Override
+ public JComponent getMainFrame() {
+ return panel;
+ }
+
+ @Override
+ public String getViewTitle() {
+ return "Retries";
+ }
+
+ protected JPanel createPanel() {
+ JPanel result = new JPanel();
+ result.setLayout(new BorderLayout());
+ result.setOpaque(false);
+
+ return result;
+ }
+
+ @Override
+ public int getPreferredPosition() {
+ return 400;
+ }
+
+ @Override
+ public Action getConfigureAction(Frame owner) {
+ return new RetryConfigureAction(owner, this, processor, editManager, selectionManager);
+ }
+
+}
diff --git a/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryContextualViewFactory.java b/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryContextualViewFactory.java
new file mode 100644
index 0000000..ab34f78
--- /dev/null
+++ b/taverna-workbench-retry-ui/src/main/java/net/sf/taverna/t2/workbench/retry/RetryContextualViewFactory.java
@@ -0,0 +1,58 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.workbench.retry;
+
+import java.net.URI;
+import java.util.Arrays;
+import java.util.List;
+
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+import uk.org.taverna.scufl2.api.core.Processor;
+
+public class RetryContextualViewFactory implements ContextualViewFactory<Processor> {
+
+ public static URI TYPE = URI.create("http://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Retry");
+
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+
+ public boolean canHandle(Object selection) {
+ return selection instanceof Processor;
+ }
+
+ public List<ContextualView> getViews(Processor selection) {
+ return Arrays.asList(new ContextualView[] { new RetryContextualView(selection, editManager,
+ selectionManager) });
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+
+}
diff --git a/taverna-workbench-retry-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-workbench-retry-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
new file mode 100644
index 0000000..6a3f2a0
--- /dev/null
+++ b/taverna-workbench-retry-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
@@ -0,0 +1 @@
+net.sf.taverna.t2.workbench.retry.RetryConfigureMenuAction
diff --git a/taverna-workbench-retry-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-workbench-retry-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
new file mode 100644
index 0000000..a4e53bf
--- /dev/null
+++ b/taverna-workbench-retry-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
@@ -0,0 +1 @@
+net.sf.taverna.t2.workbench.retry.RetryContextualViewFactory
diff --git a/taverna-workbench-retry-ui/src/main/resources/META-INF/spring/retry-ui-context-osgi.xml b/taverna-workbench-retry-ui/src/main/resources/META-INF/spring/retry-ui-context-osgi.xml
new file mode 100644
index 0000000..891a096
--- /dev/null
+++ b/taverna-workbench-retry-ui/src/main/resources/META-INF/spring/retry-ui-context-osgi.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="RetryConfigureMenuAction" auto-export="interfaces" />
+
+ <service ref="RetryContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+
+ <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
+ <reference id="selectionManager" interface="net.sf.taverna.t2.workbench.selection.SelectionManager" />
+
+</beans:beans>
diff --git a/taverna-workbench-retry-ui/src/main/resources/META-INF/spring/retry-ui-context.xml b/taverna-workbench-retry-ui/src/main/resources/META-INF/spring/retry-ui-context.xml
new file mode 100644
index 0000000..1b57ef4
--- /dev/null
+++ b/taverna-workbench-retry-ui/src/main/resources/META-INF/spring/retry-ui-context.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="RetryConfigureMenuAction" class="net.sf.taverna.t2.workbench.retry.RetryConfigureMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+
+ <bean id="RetryContextualViewFactory" class="net.sf.taverna.t2.workbench.retry.RetryContextualViewFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+
+</beans>
