Merge branch 'README'
diff --git a/pom.xml b/pom.xml
index a8a2f24..db6a7ef 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,63 +1,141 @@
<?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">
+<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-activities</artifactId>
- <version>1.3-SNAPSHOT</version>
+ <version>2.0-SNAPSHOT</version>
</parent>
<groupId>net.sf.taverna.t2.ui-activities</groupId>
<artifactId>localworker-activity-ui</artifactId>
+ <packaging>bundle</packaging>
<name>Taverna 2 Localworker Activity UI</name>
<dependencies>
<dependency>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>beanshell-activity-ui</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
<groupId>net.sf.taverna.t2.ui-api</groupId>
<artifactId>activity-icons-api</artifactId>
<version>${t2.ui.api.version}</version>
</dependency>
<dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>dependency-activity</artifactId>
- <version>${t2.activities.version}</version>
- </dependency>
- <dependency>
<groupId>net.sf.taverna.t2.ui-api</groupId>
<artifactId>activity-palette-api</artifactId>
<version>${t2.ui.api.version}</version>
</dependency>
<dependency>
- <groupId>net.sf.taverna.t2.ui-impl</groupId>
- <artifactId>file-impl</artifactId>
- <version>${t2.ui.impl.version}</version>
- <scope>test</scope>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>edits-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>file-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>menu-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-app-configuration-api</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-api</artifactId>
+ <version>${scufl2.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>2.2.2</version>
</dependency>
- <!-- testing dependencies -->
+ <!-- category:biojava -->
+ <!-- net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker -->
+ <!-- net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker -->
+ <!-- net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker -->
+ <!-- net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker -->
<dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <scope>test</scope>
+ <groupId>uk.org.mygrid.resources</groupId>
+ <artifactId>biojava</artifactId>
+ <version>1.4pre1</version>
</dependency>
+ <!-- category:xml -->
+ <!-- net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker -->
<dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>beanshell-activity</artifactId>
- <version>${t2.activities.version}</version>
+ <groupId>org.dom4j</groupId>
+ <artifactId>com.springsource.org.dom4j</artifactId>
+ <version>${dom4j.version}</version>
</dependency>
+ <!-- <dependency>
+ <groupId>dom4j</groupId>
+ <artifactId>dom4j</artifactId>
+ <version>1.6</version>
+ </dependency> -->
+ <!-- category:net -->
+ <!-- org.embl.ebi.escience.scuflworkers.java.SendEmail -->
<dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>localworker-activity</artifactId>
- <version>${t2.activities.version}</version>
+ <groupId>javax.mail</groupId>
+ <artifactId>com.springsource.javax.mail</artifactId>
+ <version>${mail.version}</version>
</dependency>
+ <!-- <dependency>
+ <groupId>javax.mail</groupId>
+ <artifactId>mail</artifactId>
+ <version>1.4</version>
+ </dependency> -->
<dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-impl</artifactId>
- <version>${t2.core.version}</version>
+ <groupId>javax.activation</groupId>
+ <artifactId>com.springsource.javax.activation</artifactId>
+ <version>1.1.1</version>
</dependency>
+ <!-- <dependency>
+ <groupId>javax.activation</groupId>
+ <artifactId>activation</artifactId>
+ <version>1.1</version>
+ </dependency> -->
+ <!-- category:base64 -->
+ <!-- org.embl.ebi.escience.scuflworkers.java.EncodeBase64 -->
+ <!-- org.embl.ebi.escience.scuflworkers.java.DecodeBase64 -->
<dependency>
- <groupId>net.sf.taverna.t2.ui-activities</groupId>
- <artifactId>beanshell-activity-ui</artifactId>
- <version>${project.version}</version>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>com.springsource.org.apache.commons.codec</artifactId>
+ <version>${commons.codec.version}</version>
</dependency>
+ <!-- <dependency>
+ <groupId>commons-codec</groupId>
+ <artifactId>commons-codec</artifactId>
+ <version>1.3</version>
+ </dependency> -->
</dependencies>
+ <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>
</project>
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/actions/LocalworkerActivityConfigurationAction.java b/src/main/java/net/sf/taverna/t2/activities/localworker/actions/LocalworkerActivityConfigurationAction.java
index 9d1d28b..2016ad0 100644
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/actions/LocalworkerActivityConfigurationAction.java
+++ b/src/main/java/net/sf/taverna/t2/activities/localworker/actions/LocalworkerActivityConfigurationAction.java
@@ -1,19 +1,19 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
+ * 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
@@ -22,74 +22,70 @@
import java.awt.Frame;
import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
import javax.swing.Action;
-import javax.swing.JDialog;
import javax.swing.JOptionPane;
-import org.apache.log4j.Logger;
-
-import net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean;
-import net.sf.taverna.t2.activities.localworker.LocalworkerActivity;
-import net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean;
import net.sf.taverna.t2.activities.localworker.views.LocalworkerActivityConfigView;
-import net.sf.taverna.t2.annotation.AnnotationAssertion;
-import net.sf.taverna.t2.annotation.AnnotationChain;
-import net.sf.taverna.t2.annotation.annotationbeans.HostInstitution;
-import net.sf.taverna.t2.lang.ui.ModelMap;
-import net.sf.taverna.t2.workbench.ModelMapConstants;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
-import net.sf.taverna.t2.workbench.helper.Helper;
+import net.sf.taverna.t2.workbench.file.FileManager;
import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.EditsRegistry;
+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 com.fasterxml.jackson.databind.JsonNode;
/**
- * The {@link LocalworkerActivity}s have pre-defined scripts, ports etc in a
- * serialised form on disk. So if the user wants to change them they have to do
- * so at own risk.
- *
+ * The {@link LocalworkerActivity}s have pre-defined scripts, ports etc in a serialised form on
+ * disk. So if the user wants to change them they have to do so at own risk.
+ *
* @author Ian Dunlop
- *
*/
@SuppressWarnings("serial")
-public class LocalworkerActivityConfigurationAction extends
- ActivityConfigurationAction<LocalworkerActivity, BeanshellActivityConfigurationBean> {
+public class LocalworkerActivityConfigurationAction extends ActivityConfigurationAction {
- private static Logger logger = Logger.getLogger(LocalworkerActivityConfigurationAction.class);
-
public static final String EDIT_LOCALWORKER_SCRIPT = "Edit beanshell script";
- private final Frame owner;
+ private final EditManager editManager;
- public LocalworkerActivityConfigurationAction(LocalworkerActivity activity,
- Frame owner) {
- super(activity);
+ private final FileManager fileManager;
+
+ private final ApplicationConfiguration applicationConfiguration;
+
+ private Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ public LocalworkerActivityConfigurationAction(Activity activity, Frame owner,
+ EditManager editManager, FileManager fileManager,
+ ActivityIconManager activityIconManager,
+ ServiceDescriptionRegistry serviceDescriptionRegistry,
+ ApplicationConfiguration applicationConfiguration) {
+ super(activity, activityIconManager, serviceDescriptionRegistry);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.applicationConfiguration = applicationConfiguration;
putValue(Action.NAME, EDIT_LOCALWORKER_SCRIPT);
- this.owner = owner;
}
/**
- * If the localworker has not been changed it pops up a {@link JOptionPane}
- * warning the user that they change things at their own risk. Otherwise
- * just show the config view
+ * If the localworker has not been changed it pops up a {@link JOptionPane} warning the user
+ * that they change things at their own risk. Otherwise just show the config view
*/
public void actionPerformed(ActionEvent e) {
Object[] options = { "Continue", "Cancel" };
- if (!activity.isAltered()) {
+ Configuration configuration = scufl2Tools.configurationFor(activity, activity.getParent());
+ JsonNode json = configuration.getJson();
+ if (!json.get("isAltered").booleanValue()) {
int n = JOptionPane
.showOptionDialog(
null,
"Changing the properties of a Local Worker may affect its behaviour. Do you want to continue?",
- "WARNING", JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE, null, // do not use a
+ "WARNING", JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE,
+ null, // do not use a
// custom Icon
options, options[0]);
@@ -100,23 +96,22 @@
// do nothing
}
} else {
- openDialog();
+ openDialog();
}
}
private void openDialog() {
- ActivityConfigurationDialog<LocalworkerActivity, LocalworkerActivityConfigurationBean> currentDialog = ActivityConfigurationAction.getDialog(getActivity());
+ ActivityConfigurationDialog currentDialog = ActivityConfigurationAction
+ .getDialog(getActivity());
if (currentDialog != null) {
currentDialog.toFront();
return;
}
- final LocalworkerActivity activity = (LocalworkerActivity) getActivity();
- final LocalworkerActivityConfigView localworkerConfigView =
- new LocalworkerActivityConfigView(activity);
- final ActivityConfigurationDialog dialog =
- new ActivityConfigurationDialog (getActivity(), localworkerConfigView);
- ActivityConfigurationAction.setDialog(getActivity(), dialog);
+ final LocalworkerActivityConfigView localworkerConfigView = new LocalworkerActivityConfigView(
+ getActivity(), applicationConfiguration);
+ final ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(getActivity(),
+ localworkerConfigView, editManager);
+ ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
-
}
}
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/menu/ConfigureLocalworkerMenuAction.java b/src/main/java/net/sf/taverna/t2/activities/localworker/menu/ConfigureLocalworkerMenuAction.java
index ba81789..3afed8d 100644
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/menu/ConfigureLocalworkerMenuAction.java
+++ b/src/main/java/net/sf/taverna/t2/activities/localworker/menu/ConfigureLocalworkerMenuAction.java
@@ -2,28 +2,61 @@
import javax.swing.Action;
-import net.sf.taverna.t2.activities.beanshell.actions.BeanshellActivityConfigurationAction;
-import net.sf.taverna.t2.activities.localworker.LocalworkerActivity;
-import net.sf.taverna.t2.activities.localworker.actions.LocalworkerActivityConfigurationAction;
-import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
-public class ConfigureLocalworkerMenuAction extends
- AbstractConfigureActivityMenuAction<LocalworkerActivity> {
+import net.sf.taverna.t2.activities.beanshell.actions.BeanshellActivityConfigurationAction;
+import net.sf.taverna.t2.activities.localworker.actions.LocalworkerActivityConfigurationAction;
+import net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceDescription;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.MenuComponent;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+
+public class ConfigureLocalworkerMenuAction extends AbstractConfigureActivityMenuAction implements
+ MenuComponent, ContextualMenuComponent {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ApplicationConfiguration applicationConfiguration;
public ConfigureLocalworkerMenuAction() {
- super(LocalworkerActivity.class);
+ super(LocalworkerServiceDescription.ACTIVITY_TYPE);
}
-
+
@Override
protected Action createAction() {
- LocalworkerActivity a = findActivity();
Action result = null;
- result = new LocalworkerActivityConfigurationAction(
- findActivity(), getParentFrame());
- result.putValue(Action.NAME, BeanshellActivityConfigurationAction.EDIT_BEANSHELL_SCRIPT);
- addMenuDots(result);
+ result = new LocalworkerActivityConfigurationAction(findActivity(), getParentFrame(),
+ editManager, fileManager, activityIconManager, serviceDescriptionRegistry,
+ applicationConfiguration);
+ result.putValue(Action.NAME, BeanshellActivityConfigurationAction.EDIT_BEANSHELL_SCRIPT);
+ addMenuDots(result);
return result;
}
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
+ this.applicationConfiguration = applicationConfiguration;
+ }
}
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java b/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java
index c7697ac..7d6bb5a 100644
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java
+++ b/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java
@@ -1,55 +1,52 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
+ * 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.activities.localworker.servicedescriptions;
+import java.net.URI;
+
import javax.swing.Icon;
import javax.swing.ImageIcon;
-import net.sf.taverna.t2.activities.localworker.LocalworkerActivity;
import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
/**
- *
- * @author Alex Nenadic
*
+ * @author Alex Nenadic
+ * @author David Withers
*/
-public class LocalworkerActivityIcon implements ActivityIconSPI{
-
+public class LocalworkerActivityIcon implements ActivityIconSPI {
+
private static Icon icon;
- public int canProvideIconScore(Activity<?> activity) {
- if (activity.getClass().getName().equals(LocalworkerActivity.class.getName())) {
- LocalworkerActivity localActivity = (LocalworkerActivity) activity;
- if (!localActivity.isAltered()) {
- return DEFAULT_ICON + 2;
- }
- }
- return NO_ICON;
+ public int canProvideIconScore(URI activityType) {
+ if (LocalworkerServiceDescription.ACTIVITY_TYPE.equals(activityType))
+ return DEFAULT_ICON + 1;
+ else
+ return NO_ICON;
}
- public Icon getIcon(Activity<?> activity) {
+ public Icon getIcon(URI activityType) {
return getLocalworkerIcon();
}
-
+
public static Icon getLocalworkerIcon() {
if (icon == null) {
icon = new ImageIcon(LocalworkerActivityIcon.class
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java b/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java
index 35e4e76..38718b8 100644
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java
+++ b/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java
@@ -1,50 +1,42 @@
package net.sf.taverna.t2.activities.localworker.servicedescriptions;
+import java.net.URI;
import java.util.Arrays;
-import java.util.LinkedHashSet;
import java.util.List;
import javax.swing.Icon;
-import net.sf.taverna.raven.repository.BasicArtifact;
-import net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean;
-import net.sf.taverna.t2.activities.localworker.LocalworkerActivity;
-import net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean;
-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.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean;
-import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean;
-public class LocalworkerServiceDescription extends ServiceDescription<BeanshellActivityConfigurationBean>{
-
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+public class LocalworkerServiceDescription extends ServiceDescription {
+
+ public static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/localworker");
+
private static final String LOCALWORKER = ServiceDescription.LOCAL_SERVICES;
- private String script;
- private List<ActivityOutputPortDefinitionBean> outputPorts;
- private List<ActivityInputPortDefinitionBean> inputPorts;
+ private JsonNode json;
private String operation;
private String category;
private String provider;
-
private String localworkerName;
- public String getLocalworkerName() {
- return localworkerName;
+
+ public JsonNode getJson() {
+ return json;
}
- public void setLocalworkerName(String localworkerName) {
- this.localworkerName = localworkerName;
+ public void setJson(JsonNode json) {
+ this.json = json;
}
- private List<String> dependencies; // from old code - this property is not in use any more
- private LinkedHashSet<BasicArtifact> artifactDependencies;
- // Note that localworkers have no local dependencies, only artifatct ones
-
- public String getProvider() {
- return provider;
+ public String getOperation() {
+ return operation;
}
- public void setProvider(String provider) {
- this.provider = provider;
+ public void setOperation(String operation) {
+ this.operation = operation;
}
public String getCategory() {
@@ -55,33 +47,37 @@
this.category = category;
}
+ public String getProvider() {
+ return provider;
+ }
+
+ public void setProvider(String provider) {
+ this.provider = provider;
+ }
+
+ public String getLocalworkerName() {
+ return localworkerName;
+ }
+
+ public void setLocalworkerName(String localworkerName) {
+ this.localworkerName = localworkerName;
+ }
+
public String getType() {
return "Localworker";
}
@Override
- public Class<? extends Activity<BeanshellActivityConfigurationBean>> getActivityClass() {
- return LocalworkerActivity.class;
+ public URI getActivityType() {
+ return ACTIVITY_TYPE;
}
@Override
- public BeanshellActivityConfigurationBean getActivityConfiguration() {
- // TODO Auto-generated method stub
- // different bean for each type of localworker, get xml version of bean
- // and create BeanshellConfig
- LocalworkerActivityConfigurationBean bean = new LocalworkerActivityConfigurationBean();
-
- bean.setScript(this.script);
- bean.setInputPortDefinitions(this.inputPorts);
- bean.setOutputPortDefinitions(this.outputPorts);
- bean.setDependencies(this.dependencies); // this field is deprecated (replaced by artifactDependencies), but for backward compatibility we leave it here
- // Local worker only has artifact dependencies
- bean.setArtifactDependencies(artifactDependencies);
- bean.setLocalworkerName(getLocalworkerName());
-
- // FIXME needs some mime types from the annotations (done as strings
- // inside the port at the moment)
- return bean;
+ public Configuration getActivityConfiguration() {
+ Configuration configuration = new Configuration();
+ configuration.setType(ACTIVITY_TYPE.resolve("#Config"));
+ configuration.setJson(getJson());
+ return configuration;
}
@Override
@@ -95,83 +91,15 @@
}
@Override
- public List<? extends Comparable> getPath() {
+ public List<? extends Comparable<?>> getPath() {
List<String> result =
Arrays.asList (LOCALWORKER, category);
return result;
}
-
- @PropertyAnnotation(hidden=true)
- public String getScript() {
- return script;
- }
-
- public void setScript(String script) {
- this.script = script;
- }
-
- public void setOutputPorts(
- List<ActivityOutputPortDefinitionBean> outputPortBeans) {
- this.outputPorts = outputPortBeans;
- }
-
- public List<ActivityOutputPortDefinitionBean> getOutputPorts() {
- return outputPorts;
- }
-
- public void setInputPorts(
- List<ActivityInputPortDefinitionBean> inputPortBeans) {
- this.inputPorts = inputPortBeans;
- }
-
- public List<ActivityInputPortDefinitionBean> getInputPorts() {
- return inputPorts;
- }
-
- public String getOperation() {
- return operation;
- }
-
- public void setOperation(String operation) {
- this.operation = operation;
- }
- ///////////// From old code //////////////////
- /**
- * Returns the dependencies.
- *
- * @return the dependencies
- */
- public List<String> getDependencies() {
- return dependencies;
- }
-
- /**
- * Sets the dependencies.
- *
- * @param dependencies the new dependencies
- */
- public void setDependencies(List<String> dependencies) {
- this.dependencies = dependencies;
- }
- ///////////// From old code /////////////////
- /**
- * @return the artifactDependencies
- */
- public LinkedHashSet<BasicArtifact> getArtifactDependencies() {
- return artifactDependencies;
- }
-
- /**
- * @param artifactDependencies the artifactDependencies to set
- */
- public void setArtifactDependencies(LinkedHashSet<BasicArtifact> artifactDependencies) {
- this.artifactDependencies = artifactDependencies;
- }
-
@Override
protected List<Object> getIdentifyingData() {
- return Arrays.<Object>asList(getScript());
+ return Arrays.<Object>asList(getJson());
}
}
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java b/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
index 0b5119d..42345db 100644
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
+++ b/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
@@ -7,238 +7,169 @@
import java.net.URI;
import java.util.ArrayList;
import java.util.HashMap;
-import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import javax.swing.Icon;
-import net.sf.taverna.raven.repository.BasicArtifact;
-import net.sf.taverna.t2.activities.beanshell.BeanshellActivity;
-import net.sf.taverna.t2.activities.localworker.LocalworkerActivity;
-import net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean;
import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider;
import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean;
-import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean;
-import net.sf.taverna.t2.workflowmodel.serialization.xml.ActivityXMLDeserializer;
import org.apache.log4j.Logger;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
public class LocalworkerServiceProvider implements ServiceDescriptionProvider {
private static final String LOCALWORKER_NAMES = "/localworker_names";
-
+
private static final String LOCALWORKER_SERVICE = "Local service";
private static Logger logger = Logger.getLogger(Logger.class);
private static final URI providerId = URI
- .create("http://taverna.sf.net/2010/service-provider/localworker");
-
+ .create("http://taverna.sf.net/2010/service-provider/localworker");
+
/** Used to deserialize the Activities stored on disk */
- private ActivityXMLDeserializer deserializer = ActivityXMLDeserializer.getInstance();;
+ private ObjectMapper objectMapper = new ObjectMapper();
private static Map<String, String> localWorkerToScript = new HashMap<String, String>();
static {
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.ByteArrayToString",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.ByteArrayToString",
"Byte Array To String");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.DecodeBase64",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.DecodeBase64",
"Decode Base 64 to byte Array");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.EchoList", "Echo List");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.EchoList", "Echo List");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings",
"Create Lots Of Strings");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.EncodeBase64",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.EncodeBase64",
"Encode Byte Array to Base 64");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks",
"Get image URLs from HTTP document");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.FilterStringList",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.FilterStringList",
"Filter List of Strings by regex");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.FlattenList",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.FlattenList",
"Flatten List");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.PadNumber",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.PadNumber",
"Pad numeral with leading 0s");
- localWorkerToScript
- .put(
- "org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList",
- "Filter list of strings extracting match to a regex");
localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.SendEmail",
+ "org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList",
+ "Filter list of strings extracting match to a regex");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.SendEmail",
"Send an Email");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.SliceList",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.SliceList",
"Extract Elements from a List");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.SplitByRegex",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.SplitByRegex",
"Split string into string list by regular expression");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.StringConcat",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringConcat",
"Concatenate two strings");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.StringListMerge",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringListMerge",
"Merge String List to a String");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.StringSetDifference",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringSetDifference",
"String List Difference");
- localWorkerToScript
- .put(
- "org.embl.ebi.escience.scuflworkers.java.StringSetIntersection",
- "String List Intersection");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.StringSetUnion",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringSetIntersection",
+ "String List Intersection");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringSetUnion",
"String List Union");
- localWorkerToScript
- .put(
- "org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates",
- "Remove String Duplicates");
- localWorkerToScript
- .put(
- "org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor",
- "Always Fails");
- localWorkerToScript
- .put(
- "org.embl.ebi.escience.scuflworkers.java.TestSometimesFails",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates",
+ "Remove String Duplicates");
+ localWorkerToScript.put(
+ "org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor",
+ "Always Fails");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.TestSometimesFails",
"Sometimes Fails");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.WebImageFetcher",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.WebImageFetcher",
"Get Image From URL");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.WebPageFetcher",
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.WebPageFetcher",
"Get Web Page from URL");
// xml:XPathText
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker",
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker",
"XPath From Text");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.xml.XSLTWorker",
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.xml.XSLTWorker",
"Transform XML");
+ localWorkerToScript.put(
+ "net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters",
+ "Transform XML with parameters");
// biojava
- localWorkerToScript
- .put(
- "net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker",
- "Read Gen Bank File");
- localWorkerToScript
- .put(
- "net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker",
- "Reverse Complement DNA");
- localWorkerToScript
- .put(
- "net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker",
- "Read Swiss Prot File");
- localWorkerToScript
- .put(
- "net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker",
- "Transcribe DNA");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker",
+ "Read Gen Bank File");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker",
+ "Reverse Complement DNA");
+ localWorkerToScript.put(
+ "net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker",
+ "Read Swiss Prot File");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker",
+ "Transcribe DNA");
// io
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.io.TextFileReader",
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.TextFileReader",
"Read Text File");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.io.TextFileWriter",
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.TextFileWriter",
"Write Text File");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.io.LocalCommand",
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.LocalCommand",
"Execute Command Line App");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.io.FileListByExtTask",
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.FileListByExtTask",
"List Files by Extension");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask",
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask",
"List Files By Regex");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.io.DataRangeTask",
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.DataRangeTask",
"Select Data Range From File");
- localWorkerToScript
- .put(
- "net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker",
- "Concatenate Files");
localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker",
+ "net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker",
+ "Concatenate Files");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker",
"Get Environment Variables as XML");
// ui
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ui.AskWorker",
- "Ask");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ui.SelectWorker",
- "Select");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ui.ChooseWorker",
- "Choose");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ui.TellWorker",
- "Tell");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ui.WarnWorker",
- "Warn");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker",
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.AskWorker", "Ask");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.SelectWorker", "Select");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.ChooseWorker", "Choose");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.TellWorker", "Tell");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.WarnWorker", "Warn");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker",
"Select File");
// ncbi
- localWorkerToScript
- .put(
- "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker",
- "Get Nucleotide FASTA");
- localWorkerToScript
- .put(
- "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker",
- "Get Nucleotide GBSeq XML");
- localWorkerToScript
- .put(
- "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker",
- "Get Nucleotide INSDSeq XML");
- localWorkerToScript
- .put(
- "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker",
- "Get Nucleotide TinySeq XML");
-
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker",
+ "Get Nucleotide FASTA");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker",
+ "Get Nucleotide GBSeq XML");
localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker",
+ "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker",
+ "Get Nucleotide INSDSeq XML");
+ localWorkerToScript.put(
+ "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker",
+ "Get Nucleotide TinySeq XML");
+
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker",
"Get Protein FASTA");
- localWorkerToScript
- .put(
- "net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker",
- "Get Protein INSDSeq XML");
localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker",
+ "net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker",
+ "Get Protein INSDSeq XML");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker",
"Get Protein GBSeq XML");
- localWorkerToScript
- .put(
- "net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker",
- "Get Protein TinySeq XML");
+ localWorkerToScript.put(
+ "net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker",
+ "Get Protein TinySeq XML");
- localWorkerToScript
- .put(
- "net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker",
- "Search PubMed XML");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker",
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker",
+ "Search PubMed XML");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker",
"Get PubMed XML By PMID");
-
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker",
+
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker",
"Execute SQL Query");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker",
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker",
"Execute SQL Update");
+
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.net.BrowseUrl",
+ "Open web browser at a URL");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.net.ExtractHeader",
+ "Extract HTTP Header");
}
public String getName() {
@@ -246,29 +177,26 @@
}
/**
- * Use the
- * {@link net.sf.taverna.t2.activities.localworker.translator.LocalworkerTranslator}
- * to get a {@link Map} of all the local workers. Use the keys in this map
+ * Use the {@link net.sf.taverna.t2.activities.localworker.translator.LocalworkerTranslator} to
+ * get a {@link Map} of all the local workers. Use the keys in this map
* to load all the serialized activities from disk by using
* <code> getClass().getResourceAsStream("/" + className) </code> to get
- * them and then the {@link ActivityXMLDeserializer} to get the actual
- * {@link Activity}. Create the {@link LocalworkerActivityItem} by
+ * them and then the {@link ActivityXMLDeserializer} to get the actual {@link Activity}. Create
+ * the {@link LocalworkerActivityItem} by
* populating them with the correct ports and depths. Sets the category to
* match the T1 version so that a query by category will split the local
* workers in to the correct place.
*/
public void findServiceDescriptionsAsync(FindServiceDescriptionsCallBack callBack) {
- List<ServiceDescription> items = new ArrayList <ServiceDescription>();
-
- InputStream inputStream = getClass().getResourceAsStream(
- LOCALWORKER_NAMES);
+ List<ServiceDescription> items = new ArrayList<ServiceDescription>();
+
+ InputStream inputStream = getClass().getResourceAsStream(LOCALWORKER_NAMES);
if (inputStream == null) {
logger.error("Could not find resource " + LOCALWORKER_NAMES);
return;
}
- BufferedReader inputReader = new BufferedReader(new InputStreamReader(
- inputStream));
+ BufferedReader inputReader = new BufferedReader(new InputStreamReader(inputStream));
String line = "";
String category = null;
try {
@@ -290,8 +218,7 @@
}
}
} catch (IOException e1) {
- logger.warn("Could not read local worker definitions from "
- + LOCALWORKER_NAMES);
+ logger.warn("Could not read local worker definitions from " + LOCALWORKER_NAMES);
}
callBack.partialResults(items);
callBack.finished();
@@ -299,7 +226,7 @@
}
@SuppressWarnings("serial")
- private class ItemCreationException extends Exception {
+ public class ItemCreationException extends Exception {
public ItemCreationException() {
super();
@@ -320,97 +247,32 @@
}
/**
- * Loads the deserialised local worker from disk and creates a
- * {@link LocalworkerActivityItem} with the correct ports and script from it
- *
+ * Loads the deserialised local worker from disk and creates a {@link LocalworkerActivityItem}
+ * with the correct ports and script from it
+ *
* @param line
* @return a LocalWorker with the appropriate Input/Output ports and script
* @throws ItemCreationException
*/
- private LocalworkerServiceDescription createItem(String line)
- throws ItemCreationException {
- //String[] split = line.split("[.]");
+ private LocalworkerServiceDescription createItem(String line) throws ItemCreationException {
// get the file from disk
- String resource = "/" + line;
+ String resource = "/" + line + ".json";
InputStream resourceAsStream = getClass().getResourceAsStream(resource);
if (resourceAsStream == null) {
- throw new ItemCreationException("Could not find resource "
- + resource);
+ throw new ItemCreationException("Could not find resource " + resource);
}
- SAXBuilder builder = new SAXBuilder();
- Element detachRootElement = null;
+ JsonNode json;
try {
- detachRootElement = builder.build(resourceAsStream)
- .detachRootElement();
- } catch (JDOMException e) {
- throw new ItemCreationException("Could not parse resource "
- + resource, e);
+ json = objectMapper.readTree(resourceAsStream);
} catch (IOException e) {
- throw new ItemCreationException("Could not read resource "
- + resource, e);
+ throw new ItemCreationException("Could not read resource " + resource, e);
}
- LocalworkerActivity activity = null;
- try {
- activity = (LocalworkerActivity) deserializer
- .deserializeActivity(detachRootElement,
- new HashMap<String, Element>(), getClass()
- .getClassLoader());
- } catch (Exception e) {
- logger.error("Could not create LocalWorkerServiceDescription", e);
- throw new ItemCreationException(e);
- }
- List<ActivityInputPortDefinitionBean> inputPortBeans = new ArrayList<ActivityInputPortDefinitionBean>();
- LocalworkerActivityConfigurationBean configuration = (LocalworkerActivityConfigurationBean) activity
- .getConfiguration();
-
- // Translate the old dependencies field into artifactDependencies field
- // The local worker definition xml files still have the old dependencies field
- LinkedHashSet<BasicArtifact> artifactDependencies = new LinkedHashSet<BasicArtifact>();
- for (String dep : configuration.getDependencies()){
- String[] artifactParts = dep.split(":");
- if (artifactParts.length == 3) {
- artifactDependencies.add(new BasicArtifact(artifactParts[0], artifactParts[1],
- artifactParts[2]));
- }
- }
- configuration.setArtifactDependencies(artifactDependencies);
-
- for (ActivityInputPortDefinitionBean bean : configuration
- .getInputPortDefinitions()) {
- bean.setDepth(bean.getDepth());
- bean.setName(bean.getName());
- bean.setHandledReferenceSchemes(bean.getHandledReferenceSchemes());
- bean.setTranslatedElementType(bean.getTranslatedElementType());
- // bean.setMimeTypes(bean.getMimeTypes());
- inputPortBeans.add(bean);
- }
- List<ActivityOutputPortDefinitionBean> outputPortBeans = new ArrayList<ActivityOutputPortDefinitionBean>();
- for (ActivityOutputPortDefinitionBean bean : configuration
- .getOutputPortDefinitions()) {
- bean.setDepth(bean.getDepth());
- bean.setGranularDepth(bean.getGranularDepth());
- bean.setName(bean.getName());
- bean.setMimeTypes(bean.getMimeTypes());
- outputPortBeans.add(bean);
- }
-
- String script = ((BeanshellActivity) activity).getConfiguration()
- .getScript();
LocalworkerServiceDescription item = new LocalworkerServiceDescription();
- item.setScript(script);
- item.setOutputPorts(outputPortBeans);
- item.setInputPorts(inputPortBeans);
+ item.setJson(json);
item.setLocalworkerName(line);
- // name is last part of the class name that was split
- //String operation = split[split.length - 1];
- String operationName = localWorkerToScript.get(line);
- item.setOperation(operationName);
- item.setDependencies(((BeanshellActivity) activity).getConfiguration()
- .getDependencies()); // this property is not in use any more
- item.setArtifactDependencies(configuration.getArtifactDependencies());
-// item.setOperation(operation);
+ item.setOperation(localWorkerToScript.get(line));
return item;
}
@@ -418,12 +280,12 @@
public Icon getIcon() {
return LocalworkerActivityIcon.getLocalworkerIcon();
}
-
+
@Override
public String toString() {
return "Local workers provider";
}
-
+
public static String getServiceNameFromClassname(String classname) {
return (localWorkerToScript.get(classname));
}
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityConfigView.java b/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityConfigView.java
index 025190f..155c631 100644
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityConfigView.java
+++ b/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityConfigView.java
@@ -1,84 +1,42 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
+ * 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.activities.localworker.views;
-import net.sf.taverna.t2.activities.beanshell.views.BeanshellConfigView;
-import net.sf.taverna.t2.activities.localworker.LocalworkerActivity;
-import net.sf.taverna.t2.annotation.annotationbeans.HostInstitution;
-import net.sf.taverna.t2.lang.ui.ModelMap;
-import net.sf.taverna.t2.workbench.ModelMapConstants;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.EditsRegistry;
-
-import org.apache.log4j.Logger;
-
+import net.sf.taverna.t2.activities.beanshell.views.BeanshellConfigurationPanel;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
@SuppressWarnings("serial")
-public class LocalworkerActivityConfigView extends BeanshellConfigView{
+public class LocalworkerActivityConfigView extends BeanshellConfigurationPanel {
- private static Logger logger = Logger.getLogger(LocalworkerActivityConfigView.class);
-
- public LocalworkerActivityConfigView(LocalworkerActivity activity) {
- super(activity);
- initLocalworker();
+ public LocalworkerActivityConfigView(Activity activity, ApplicationConfiguration applicationConfiguration) {
+ super(activity, applicationConfiguration);
}
- private void initLocalworker() {
- }
-
- public void noteConfiguration() {
- if (isConfigurationChanged()) {
- super.noteConfiguration();
- addAnnotation();
+ public boolean isConfigurationChanged() {
+ boolean configurationChanged = super.isConfigurationChanged();
+ if (configurationChanged) {
+ getJson().put("isAltered", true);
}
- }
-
- /**
- * Annotate the Activity with the name of the Institution or person who
- * created the activity. Useful for Localworkers that have been altered by a
- * user
- */
- private void addAnnotation() {
- // FIXME use a more useful name or a different type of annotation, this
- // is just here as a marker so that
- // the colour manager works
- HostInstitution hostInstitutionAnnotation = new HostInstitution();
- hostInstitutionAnnotation.setText("UserNameHere");
-
- try {
- // force the dataflow view to update with the annotation added,
- // therefore triggering the localworker to be coloured as a
- // beanshell
- EditManager.getInstance().doDataflowEdit(
- (Dataflow) ModelMap.getInstance().getModel(
- ModelMapConstants.CURRENT_DATAFLOW),
- EditsRegistry.getEdits().getAddAnnotationChainEdit(
- activity, hostInstitutionAnnotation));
- ActivityIconManager.getInstance().resetIcon(activity);
- } catch (EditException e) {
- logger.error(e);
- }
+ return configurationChanged;
}
}
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityContextualView.java b/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityContextualView.java
index db79cdd..fc09d57 100644
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityContextualView.java
+++ b/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityContextualView.java
@@ -1,19 +1,19 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
+ * 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
@@ -24,60 +24,75 @@
import javax.swing.Action;
-import net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean;
-import net.sf.taverna.t2.activities.localworker.LocalworkerActivity;
-import net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean;
import net.sf.taverna.t2.activities.localworker.actions.LocalworkerActivityConfigurationAction;
import net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceProvider;
-import net.sf.taverna.t2.annotation.AnnotationAssertion;
-import net.sf.taverna.t2.annotation.AnnotationChain;
-import net.sf.taverna.t2.annotation.annotationbeans.HostInstitution;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean;
-import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+import uk.org.taverna.scufl2.api.port.InputActivityPort;
+import uk.org.taverna.scufl2.api.port.OutputActivityPort;
+
+import com.fasterxml.jackson.databind.JsonNode;
@SuppressWarnings("serial")
-public class LocalworkerActivityContextualView extends
- HTMLBasedActivityContextualView<LocalworkerActivityConfigurationBean> {
+public class LocalworkerActivityContextualView extends HTMLBasedActivityContextualView {
- public LocalworkerActivityContextualView(Activity<?> activity) {
- super(activity);
+ private final EditManager editManager;
+ private final FileManager fileManager;
+ private final ActivityIconManager activityIconManager;
+ private final ServiceDescriptionRegistry serviceDescriptionRegistry;
+
+ private final ApplicationConfiguration applicationConfiguration;
+
+ public LocalworkerActivityContextualView(Activity activity, EditManager editManager,
+ FileManager fileManager, ColourManager colourManager,
+ ActivityIconManager activityIconManager,
+ ServiceDescriptionRegistry serviceDescriptionRegistry,
+ ApplicationConfiguration applicationConfiguration) {
+ super(activity, colourManager);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.activityIconManager = activityIconManager;
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ this.applicationConfiguration = applicationConfiguration;
}
@Override
protected String getRawTableRowsHtml() {
- String html = "<tr><th>Input Port Name</th><th>Depth</th></tr>";
- for (ActivityInputPortDefinitionBean bean : getConfigBean()
- .getInputPortDefinitions()) {
- html = html + "<tr><td>" + bean.getName() + "</td><td>"
- + bean.getDepth() + "</td></tr>";
+ StringBuilder html = new StringBuilder();
+ html.append("<tr><th>Input Port Name</th><th>Depth</th></tr>");
+ for (InputActivityPort inputActivityPort : getActivity().getInputPorts()) {
+ html.append("<tr><td>" + inputActivityPort.getName() + "</td><td>");
+ html.append(inputActivityPort.getDepth() + "</td></tr>");
}
- html = html
- + "<tr><th>Output Port Name</th><th>Depth</th></tr>";
- for (ActivityOutputPortDefinitionBean bean : getConfigBean()
- .getOutputPortDefinitions()) {
- html = html + "<tr></td>" + bean.getName() + "</td><td>"
- + bean.getDepth() + "</td>" //<td>" + bean.getGranularDepth()
- //+ "</td>"
- + "</tr>";
+ html.append("<tr><th>Output Port Name</th><th>Depth</th></tr>");
+ for (OutputActivityPort outputActivityPort : getActivity().getOutputPorts()) {
+ html.append("<tr><td>" + outputActivityPort.getName() + "</td><td>");
+ html.append(outputActivityPort.getDepth() + "</td></tr>");
}
- return html;
+ return html.toString();
}
@Override
public String getViewTitle() {
String result = "";
- LocalworkerActivity localActivity = (LocalworkerActivity) getActivity();
- if (localActivity.isAltered()) {
+ Configuration configuration = getConfigBean();
+ JsonNode json = configuration.getJson();
+ String workerName = LocalworkerServiceProvider.getServiceNameFromClassname(json.get(
+ "localworkerName").textValue());
+ if (json.get("isAltered").booleanValue()) {
result = "Altered local worker service";
- String workerName = LocalworkerServiceProvider.getServiceNameFromClassname(localActivity.getConfiguration().getLocalworkerName());
if ((workerName != null) && !workerName.equals("")) {
result += " - originally " + workerName;
}
} else {
result = "Local worker service";
- String workerName = LocalworkerServiceProvider.getServiceNameFromClassname(localActivity.getConfiguration().getLocalworkerName());
if ((workerName != null) && !workerName.equals("")) {
result += " - " + workerName;
}
@@ -85,22 +100,11 @@
return result;
}
- private boolean checkAnnotations() {
- for (AnnotationChain chain : getActivity().getAnnotations()) {
- for (AnnotationAssertion<?> assertion : chain.getAssertions()) {
- Object detail = assertion.getDetail();
- if (detail instanceof HostInstitution) {
- return true;
- }
- }
- }
- return false;
- }
-
@Override
public Action getConfigureAction(Frame owner) {
- return new LocalworkerActivityConfigurationAction(
- (LocalworkerActivity) getActivity(), owner);
+ return new LocalworkerActivityConfigurationAction(getActivity(), owner, editManager,
+ fileManager, activityIconManager, serviceDescriptionRegistry,
+ applicationConfiguration);
}
@Override
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityViewFactory.java b/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityViewFactory.java
index f173776..4fec0a2 100644
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityViewFactory.java
+++ b/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityViewFactory.java
@@ -1,19 +1,19 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
+ * 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
@@ -23,19 +23,60 @@
import java.util.Arrays;
import java.util.List;
-import net.sf.taverna.t2.activities.localworker.LocalworkerActivity;
+import net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceDescription;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+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;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
-public class LocalworkerActivityViewFactory implements
- ContextualViewFactory<LocalworkerActivity> {
+public class LocalworkerActivityViewFactory implements ContextualViewFactory<Activity> {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+ private ColourManager colourManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ApplicationConfiguration applicationConfiguration;
public boolean canHandle(Object object) {
- return object instanceof LocalworkerActivity;
+ return object instanceof Activity
+ && ((Activity) object).getType()
+ .equals(LocalworkerServiceDescription.ACTIVITY_TYPE);
}
- public List<ContextualView> getViews(LocalworkerActivity activity) {
- return Arrays.asList(new ContextualView[] {new LocalworkerActivityContextualView(activity)});
+ public List<ContextualView> getViews(Activity activity) {
+ return Arrays.asList(new ContextualView[] { new LocalworkerActivityContextualView(activity,
+ editManager, fileManager, colourManager, activityIconManager,
+ serviceDescriptionRegistry, applicationConfiguration) });
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setColourManager(ColourManager colourManager) {
+ this.colourManager = colourManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
+ this.applicationConfiguration = applicationConfiguration;
}
}
diff --git a/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml b/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml
new file mode 100644
index 0000000..dd4c7a8
--- /dev/null
+++ b/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml
@@ -0,0 +1,24 @@
+<?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="LocalworkerActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
+
+ <service ref="LocalworkerServiceProvider" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
+
+ <service ref="ConfigureLocalworkerMenuAction" auto-export="interfaces" />
+
+ <service ref="LocalworkerActivityViewFactory" 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="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
+ <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
+ <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" />
+ <reference id="applicationConfiguration" interface="uk.org.taverna.configuration.app.ApplicationConfiguration" />
+
+</beans:beans>
diff --git a/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml b/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml
new file mode 100644
index 0000000..edcd6be
--- /dev/null
+++ b/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml
@@ -0,0 +1,27 @@
+<?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="LocalworkerActivityIcon" class="net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerActivityIcon" />
+
+ <bean id="LocalworkerServiceProvider" class="net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceProvider" />
+
+ <bean id="ConfigureLocalworkerMenuAction" class="net.sf.taverna.t2.activities.localworker.menu.ConfigureLocalworkerMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="applicationConfiguration" ref="applicationConfiguration" />
+ </bean>
+
+ <bean id="LocalworkerActivityViewFactory" class="net.sf.taverna.t2.activities.localworker.views.LocalworkerActivityViewFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="colourManager" ref="colourManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="applicationConfiguration" ref="applicationConfiguration" />
+ </bean>
+
+</beans>
diff --git a/src/main/resources/localworker_names b/src/main/resources/localworker_names
index fd03268..3df452c 100644
--- a/src/main/resources/localworker_names
+++ b/src/main/resources/localworker_names
@@ -21,6 +21,7 @@
category:xml
net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
+net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters
category:list
org.embl.ebi.escience.scuflworkers.java.EchoList
org.embl.ebi.escience.scuflworkers.java.FlattenList
@@ -45,6 +46,8 @@
org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks
org.embl.ebi.escience.scuflworkers.java.SendEmail
+net.sourceforge.taverna.scuflworkers.net.BrowseUrl
+net.sourceforge.taverna.scuflworkers.net.ExtractHeader
category:base64
org.embl.ebi.escience.scuflworkers.java.EncodeBase64
org.embl.ebi.escience.scuflworkers.java.DecodeBase64
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker
index 978504b..d6c62b2 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker
@@ -19,7 +19,11 @@
}
return new BufferedReader(reader);
}
-
+
+if ((fileUrl == void) || (fileUrl == null)) {
+ throw new RuntimeException("The fileUrl must be specified");
+}
+
BufferedReader br = getReader(fileUrl);
// read the GenBank File
@@ -37,7 +41,9 @@
sb.append(os.toString());
}
-genbankdata = sb.toString()
+genbankdata = sb.toString();
+br.close();
+ps.close();
</script>
<dependencies class="java.util.Collections$SingletonList">
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker.json
new file mode 100644
index 0000000..452850f
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import org.biojava.bio.seq.Sequence;\nimport org.biojava.bio.seq.SequenceIterator;\nimport org.biojava.bio.seq.io.SeqIOTools;\nimport org.biojava.bio.seq.io.agave.AgaveWriter;\n\nBufferedReader getReader (String fileUrl) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\treader = new FileReader(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\treader = new InputStreamReader (url.openStream());\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\nif ((fileUrl == void) || (fileUrl == null)) {\n throw new RuntimeException(\"The fileUrl must be specified\");\n}\n\nBufferedReader br = getReader(fileUrl);\n\n// read the GenBank File\nSequenceIterator sequences = SeqIOTools.readGenbank(br);\n\n// iterate through the sequences\nByteArrayOutputStream os = new ByteArrayOutputStream();\nStringBuffer sb = new StringBuffer();\nAgaveWriter writer = new AgaveWriter();\nPrintStream ps = new PrintStream(os);\n\nwhile (sequences.hasNext()) {\n\tSequence seq = sequences.nextSequence();\n\twriter.writeSequence(seq, ps);\n\tsb.append(os.toString());\n}\n\ngenbankdata = sb.toString();\nbr.close();\nps.close();\n \n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker",
+ "inputPorts" : [ {
+ "name" : "fileUrl",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "genbankdata",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
index 11855e4..0044c82 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
@@ -2,6 +2,10 @@
<script>import org.biojava.bio.seq.DNATools;
import org.biojava.bio.symbol.SymbolList;
+if ((rawSeq == void) || (rawSeq == null)) {
+ throw new RuntimeException("The rawSeq must be specified");
+}
+
// make a DNA SymbolListbena
SymbolList symL = DNATools.createDNA(rawSeq);
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json
new file mode 100644
index 0000000..c214819
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import org.biojava.bio.seq.DNATools;\nimport org.biojava.bio.symbol.SymbolList;\n\nif ((rawSeq == void) || (rawSeq == null)) {\n throw new RuntimeException(\"The rawSeq must be specified\");\n}\n\n// make a DNA SymbolListbena\nSymbolList symL = DNATools.createDNA(rawSeq);\n\n// reverse complement it\nsymL = DNATools.reverseComplement(symL);\n\n// prove that it worked\nrevSeq = symL.seqString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker",
+ "inputPorts" : [ {
+ "name" : "rawSeq",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "revSeq",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker
index e886280..7f64778 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker
@@ -17,6 +17,10 @@
return new BufferedReader(reader);
}
+if ((fileUrl == void) || (fileUrl == null)) {
+ throw new RuntimeException("The fileUrl must be specified");
+}
+
BufferedReader br = getReader(fileUrl);
// read the EMBL File
@@ -35,6 +39,9 @@
sb.append(os.toString());
}
results = sb.toString();
+
+br.close();
+ps.close();
</script>
<dependencies class="java.util.Collections$SingletonList">
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json
new file mode 100644
index 0000000..929c316
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import org.biojava.bio.seq.Sequence;\nimport org.biojava.bio.seq.SequenceIterator;\nimport org.biojava.bio.seq.io.SeqIOTools;\nimport org.biojava.bio.seq.io.agave.AgaveWriter;\n\nBufferedReader getReader (String fileUrl) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\treader = new FileReader(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\treader = new InputStreamReader (url.openStream());\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\t\nif ((fileUrl == void) || (fileUrl == null)) {\n throw new RuntimeException(\"The fileUrl must be specified\");\n}\n\t\nBufferedReader br = getReader(fileUrl);\n\n// read the EMBL File\nSequenceIterator sequences = SeqIOTools.readSwissprot(br);\n\n// Prepare the writer\nAgaveWriter writer = new AgaveWriter();\nByteArrayOutputStream os = new ByteArrayOutputStream();\nStringBuffer sb = new StringBuffer();\nPrintStream ps = new PrintStream(os);\n\n// iterate through the sequences\nwhile (sequences.hasNext()) {\n\tSequence seq = sequences.nextSequence();\n\twriter.writeSequence(seq, ps);\n\tsb.append(os.toString());\n}\nresults = sb.toString();\n\nbr.close();\nps.close();\n \n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker",
+ "inputPorts" : [ {
+ "name" : "fileUrl",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "results",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker
index c6998af..e46e219 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker
@@ -3,6 +3,10 @@
import org.biojava.bio.seq.RNATools;
import org.biojava.bio.symbol.SymbolList;
+if ((dna_seq == void) || (dna_seq == null)) {
+ throw new RuntimeException("The dna_seq must be specified");
+}
+
// make a DNA SymbolList
SymbolList symL = DNATools.createDNA(dna_seq);
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker.json
new file mode 100644
index 0000000..767852c
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import org.biojava.bio.seq.DNATools;\nimport org.biojava.bio.seq.RNATools;\nimport org.biojava.bio.symbol.SymbolList;\n\nif ((dna_seq == void) || (dna_seq == null)) {\n\tthrow new RuntimeException(\"The dna_seq must be specified\");\n}\n\n// make a DNA SymbolList\nSymbolList symL = DNATools.createDNA(dna_seq);\n\n// transcribe it to RNA (after BioJava 1.4 this method is\n// deprecated)\nsymL = RNATools.transcribe(symL);\n\n// (after BioJava 1.4 use this method instead)\n// symL = DNATools.toRNA(symL);\n\n// just to prove it worked\nrna_seq = symL.seqString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker",
+ "inputPorts" : [ {
+ "name" : "dna_seq",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "rna_seq",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker.json
new file mode 100644
index 0000000..d91d466
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "BufferedReader getReader (String fileUrl) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\treader = new FileReader(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\treader = new InputStreamReader (url.openStream());\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\nString NEWLINE = System.getProperty(\"line.separator\");\n\nboolean displayResults = false;\nif (displayresults != void) {\n\tdisplayResults = Boolean.valueOf(displayresults).booleanValue();\n}\n\nStringBuffer sb = new StringBuffer(2000);\n\nif (outputfile == void) {\n\tthrow new RuntimeException(\"The 'outputfile' parameter cannot be null\");\n}\n\nif (filelist == null) {\n\tthrow new RuntimeException(\"The 'filelist' parameter cannot be null\");\n}\n\nString str = null;\n\nWriter writer = new FileWriter(outputfile);\nfor (int i = 0; i < filelist.size(); i++) {\n\tBufferedReader reader = getReader(filelist.get(i));\n\twhile ((str = reader.readLine()) != null) {\n\t\twriter.write(str);\n\t\twriter.write(NEWLINE);\n\n\t\tif (displayResults) {\n\t\t\tsb.append(str);\n\t\t\tsb.append(NEWLINE);\n\t\t}\n\t}\n\n\treader.close();\n\n}\nwriter.flush();\nwriter.close();\n\nif (displayResults) {\n\tresults= sb.toString();\n}\n\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker",
+ "inputPorts" : [ {
+ "name" : "filelist",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "outputfile",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "displayresults",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "results",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker.json
new file mode 100644
index 0000000..5dc2349
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker.json
@@ -0,0 +1,11 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.net.URLEncoder;\n\nProperties sysProps = System.getProperties();\nSet keys = sysProps.keySet();\nIterator it = keys.iterator();\nString currKey = null;\nStringBuffer sb = new StringBuffer();\nsb.append(\"<?xml version=\\\"1.0\\\"?>\\n\");\nsb.append(\"<property-list>\\n\");\nwhile (it.hasNext()) {\n\tcurrKey = (String) it.next();\n\tsb.append(\"<property \");\n\tsb.append(\" name=\\\"\" + URLEncoder.encode(currKey) + \"\\\"\");\n\tsb.append(\" value=\\\"\" + URLEncoder.encode(sysProps.getProperty(currKey)) + \"\\\"/>\\n\");\n}\nsb.append(\"</property-list>\");\n\nproperties = sb.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker",
+ "outputPorts" : [ {
+ "name" : "properties",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask.json
new file mode 100644
index 0000000..656453e
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "class FileExtFilter implements FileFilter {\n\n\tpublic FileExtFilter(String ext) {\n\t\tthis.ext = ext;\n\t}\n\n\tpublic boolean accept(File file) {\n\t\treturn file.getName().endsWith(ext);\n\t}\n\n\tString ext = null;\n}\n\nif (extension == void || extension.equals(\"\")) {\n\tthrow new RuntimeException(\n\t\t\t\"The 'extension' parameter cannot be null. Please enter a valid file extension.\");\n}\n\nif (directory == void || directory.equals(\"\")) {\n\tthrow new RuntimeException(\n\t\t\t\"The 'directory' parameter cannot be null. Please enter a valid file directory.\");\n}\n\nFile dirObj = new File(directory);\n\nif (!dirObj.exists()) {\n\tthrow new RuntimeException(\"The 'directory' parameter specified:\" + directory\n\t\t\t+ \"does not exist. Please enter a valid file directory.\");\n}\n\nFile[] fileObjList = dirObj.listFiles(new FileExtFilter(extension));\nList filelist = new ArrayList();\nfor (int i = 0; i < fileObjList.length; i++) {\n\tfilelist.add(fileObjList[i].getAbsolutePath());\n}\n\n\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.FileListByExtTask",
+ "inputPorts" : [ {
+ "name" : "directory",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "extension",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "filelist",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask.json
new file mode 100644
index 0000000..35cdb01
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "class FileRegexFilter implements FileFilter {\n\n\tpublic FileRegexFilter(String regex) {\n\t\tthis.regex = regex;\n\t}\n\n\tpublic boolean accept(File file) {\n\t\treturn file.getName().matches(regex);\n\t}\n\n\tString regex = null;\n}\n\nif (regex == void || regex.equals(\"\")) {\n\tthrow new RuntimeException(\n\t\t\t\"The 'regex' parameter cannot be null. Please enter a valid file extension.\");\n}\n\nif (directory == void || directory.equals(\"\")) {\n\tthrow new RuntimeException(\n\t\t\t\"The 'directory' parameter cannot be null. Please enter a valid file directory.\");\n}\n\nFile dirObj = new File(directory);\n\nif (!dirObj.exists()) {\n\tthrow new RuntimeException(\"The 'directory' parameter specified:\" + directory\n\t\t\t+ \"does not exist. Please enter a valid file directory.\");\n}\n\nFile[] fileObjList = dirObj.listFiles(new FileRegexFilter(regex));\nList filelist = new ArrayList();\nfor (int i = 0; i < fileObjList.length; i++) {\n\tfilelist.add(fileObjList[i].getAbsolutePath());\n}\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask",
+ "inputPorts" : [ {
+ "name" : "directory",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "regex",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "filelist",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand
index 5ca3f94..c0adc09 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand
@@ -7,10 +7,8 @@
String osName = System.getProperty("os.name");
String[] cmdArray = null;
-if (osName.equals("Windows NT") || osName.equals("Windows XP")) {
+if (osName.contains("Windows")) {
cmdArray = new String[] { "cmd.exe", "/c", command };
-} else if (osName.equals("Windows 95")) {
- cmdArray = new String[] { "command.exe", "/c", command };
} else {// TODO: investigate if this will work in Linux and OSX
cmdArray = new String[] { command };
}
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand.json
new file mode 100644
index 0000000..f6ddf4f
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if (command == void || command.equals(\"\")) {\n\tthrow new RuntimeException(\"The 'command' port cannot be null.\");\n}\nProcess proc = null;\nRuntime rt = Runtime.getRuntime();\n\nString osName = System.getProperty(\"os.name\");\nString[] cmdArray = null;\nif (osName.contains(\"Windows\")) {\n\tcmdArray = new String[] { \"cmd.exe\", \"/c\", command };\n} else {// TODO: investigate if this will work in Linux and OSX\n\tcmdArray = new String[] { command };\n}\n\n// concatenate the arrays\nif ((args == void) || (args == null)) {\n\targs = new ArrayList();\n}\n\nint argSize = cmdArray.length + args.size();\nArrayList appArray = new ArrayList(argSize);\nfor (int i = 0; i < cmdArray.length; i++) {\n\tappArray.add(cmdArray[i]);\n}\n\nfor (int i = 0; i < args.size(); i++) {\n\tappArray.add(args.get(i));\n}\n\nString[] applist = new String[argSize];\nappArray.toArray(applist);\nproc = rt.exec(applist);\n\n// Get the input stream and read from it\nInputStream in = proc.getInputStream();\n\nint c;\nStringBuffer sb = new StringBuffer();\nwhile ((c = in.read()) != -1) {\n\tsb.append((char) c);\n}\nin.close();\nresult = sb.toString();\n \n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.LocalCommand",
+ "inputPorts" : [ {
+ "name" : "command",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "args",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "result",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader
index 767fd3d..6e9adb4 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader
@@ -1,13 +1,21 @@
<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>BufferedReader getReader (String fileUrl) throws IOException {
+ <script>BufferedReader getReader (String fileUrl, String encoding) throws IOException {
InputStreamReader reader;
try {
- reader = new FileReader(fileUrl);
+ if (encoding == null) {
+ reader = new FileReader(fileUrl);
+ } else {
+ reader = new InputStreamReader(new FileInputStream(fileUrl),encoding);
+ }
}
catch (FileNotFoundException e) {
// try a real URL instead
URL url = new URL(fileUrl);
- reader = new InputStreamReader (url.openStream());
+ if (encoding == null) {
+ reader = new InputStreamReader (url.openStream());
+ } else {
+ reader = new InputStreamReader (url.openStream(), encoding);
+ }
}
return new BufferedReader(reader);
}
@@ -16,7 +24,11 @@
StringBuffer sb = new StringBuffer(4000);
-BufferedReader in = getReader(fileurl);
+if (encoding == void) {
+ encoding = null;
+}
+
+BufferedReader in = getReader(fileurl, encoding);
String str;
String lineEnding = System.getProperty("line.separator");
@@ -40,6 +52,16 @@
<string>'text/plain'</string>
</mimeTypes>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>encoding</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>
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader.json
new file mode 100644
index 0000000..1424433
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "BufferedReader getReader (String fileUrl, String encoding) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\tif (encoding == null) {\n\t\t\t\treader = new FileReader(fileUrl);\n\t\t\t} else {\n\t\t\t\treader = new InputStreamReader(new FileInputStream(fileUrl),encoding); \n\t\t\t}\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\tif (encoding == null) {\n\t\t\t\treader = new InputStreamReader (url.openStream());\n\t\t\t} else {\n\t\t\t\treader = new InputStreamReader (url.openStream(), encoding);\n\t\t\t}\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\n\n\nStringBuffer sb = new StringBuffer(4000);\n\nif (encoding == void) {\n\tencoding = null;\n}\n\nBufferedReader in = getReader(fileurl, encoding);\nString str;\nString lineEnding = System.getProperty(\"line.separator\");\n\nwhile ((str = in.readLine()) != null) {\n\tsb.append(str);\n\tsb.append(lineEnding);\n}\nin.close();\nfilecontents = sb.toString();\n \n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.TextFileReader",
+ "inputPorts" : [ {
+ "name" : "fileurl",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "encoding",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "filecontents",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter
index 6d46180..88ac962 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter
@@ -1,6 +1,14 @@
<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>BufferedWriter out = new BufferedWriter(new FileWriter(outputFile));
+ <script>
+ BufferedWriter out;
+ if (encoding == void) {
+ out = new BufferedWriter(new FileWriter(outputFile));
+ }
+ else {
+ out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(outputFile), encoding));
+ }
out.write(filecontents);
+out.flush();
out.close();
outputFile = filecontents;
</script>
@@ -26,7 +34,16 @@
<string>'text/plain'</string>
</mimeTypes>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>encoding</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>
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter.json
new file mode 100644
index 0000000..5a9f368
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "\n BufferedWriter out;\n if (encoding == void) {\n \tout = new BufferedWriter(new FileWriter(outputFile));\n }\n else {\n \tout = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(outputFile), encoding)); \n }\nout.write(filecontents);\nout.flush();\nout.close();\noutputFile = filecontents;\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.TextFileWriter",
+ "inputPorts" : [ {
+ "name" : "outputFile",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "filecontents",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "encoding",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputFile",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
index 1af0c9d..b6263cf 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
@@ -7,6 +7,7 @@
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.ResultSetMetaData;
+import java.sql.SQLException;
import javax.sql.rowset.WebRowSet;
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker.json
new file mode 100644
index 0000000..da1f005
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker.json
@@ -0,0 +1,44 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "\n import java.sql.Driver;\nimport java.sql.DriverManager;\nimport java.sql.Connection;\nimport java.sql.PreparedStatement;\nimport java.sql.ResultSet;\nimport java.sql.ResultSetMetaData;\nimport java.sql.SQLException;\n\nimport javax.sql.rowset.WebRowSet;\n\nimport com.sun.rowset.WebRowSetImpl;\n\n\n\nif ((driver == void) || (driver == null) || driver.equals(\"\")) {\n\tthrow new RuntimeException(\"The driver must be specified\");\n}\n\nif ((url == void) || (url == null) || url.equals(\"\")) {\n\tthrow new RuntimeException(\"The url must be specified\");\n}\n\nboolean provideXmlBoolean = ((provideXml != void) && (provideXml != null) && Boolean.valueOf(provideXml));\n\nif ((params == void) || (params == null)) {\n params = new ArrayList();\n}\n\nif ((sql == void) || (sql == null) || sql.equals(\"\")) {\n\tthrow new RuntimeException(\"The sql must be specified\");\n}\n\nClass c = Thread.currentThread().getContextClassLoader().loadClass(driver);\n\nif (c == null) {\n\tthrow new RuntimeException(\"Class \" + driver + \" not found\");\n}\n\nDriver d = c.newInstance();\nif (d == null) {\n\tthrow new RuntimeException(\"Could not create instance of driver\");\n}\n\nProperties p = new Properties();\n\nif ((userid == void) || (userid == null)) {\n\tuserid = \"\";\n}\n\np.setProperty(\"user\", userid);\n\nif ((password == void) || (password == null)) {\n\tpassword = \"\";\n}\n\np.setProperty(\"password\", password);\n\nConnection con = null;\nPreparedStatement ps = null;\nResultSet rs = null;\ntry {\n\n\tcon = d.connect(url, p);\n\tps = con.prepareStatement(sql);\n\n\tint paramSize = params.size();\n\tfor (int i = 0; i < paramSize; i++) {\n\t\tps.setObject(i + 1, params.get(i));\n\t}\n\n\trs = ps.executeQuery();\n\n\tif (provideXmlBoolean) {\n\t\tWebRowSet webrs = new WebRowSetImpl();\n\t\tStringWriter sw = new StringWriter();\n\t\twebrs.writeXml(rs, sw);\n\t\txmlresults = sw.toString();\n\t} else {\n\t\txmlresults = \"\";\n\t}\n\n\ttry {\n\t\trs.beforeFirst();\n\t} catch (SQLException e) {\n\t\t// redo the query\n\t\trs = ps.executeQuery();\n\t}\n\n\tResultSetMetaData rsmd = rs.getMetaData();\n\tint numCols = rsmd.getColumnCount();\n\tresultList = new ArrayList();\n\t\n\t// put the results into the results list.\n\twhile (rs.next()) {\n\t\tList row = new ArrayList(numCols);\n\t\tfor (int i = 0; i < numCols; i++) {\n\t\t\tString str = rs.getString(i + 1); \n\t\t\trow.add(str == null ? \"null\" : str); \n\t\t}\n\t\tresultList.add(row);\n\t}\n}\nfinally {\n\tif (rs != null) {\n\t\trs.close();\n\t}\n\tif (ps != null) {\n\t\tps.close();\n\t}\n\tif (con != null) {\n\t\tcon.close();\n\t}\n}\n \n\n ",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker",
+ "inputPorts" : [ {
+ "name" : "driver",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "password",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "userid",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "url",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "provideXml",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "sql",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "params",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "resultList",
+ "depth" : 2,
+ "granularDepth" : 2
+ }, {
+ "name" : "xmlresults",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker.json
new file mode 100644
index 0000000..3144afd
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker.json
@@ -0,0 +1,36 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.sql.Driver;\nimport java.sql.DriverManager;\nimport java.sql.Connection;\nimport java.sql.PreparedStatement;\n\nif ((driver == void) || (driver == null) || driver.equals(\"\")) {\n\tthrow new RuntimeException(\"The driver must be specified\");\n}\n\nif ((url == void) || (url == null) || url.equals(\"\")) {\n\tthrow new RuntimeException(\"The url must be specified\");\n}\n\nif ((params == void) || (params == null)) {\n params = new ArrayList();\n}\n\nif ((sql == void) || (sql == null) || sql.equals(\"\")) {\n\tthrow new RuntimeException(\"The sql must be specified\");\n}\n\nClass c = Thread.currentThread().getContextClassLoader().loadClass(driver);\n\nif (c == null) {\n\tthrow new RuntimeException(\"Class \" + driver + \" not found\");\n}\n\nDriver d = c.newInstance();\nif (d == null) {\n\tthrow new RuntimeException(\"Could not create instance of driver\");\n}\n\nProperties p = new Properties();\n\nif ((userid == void) || (userid == null)) {\n\tuserid = \"\";\n}\n\np.setProperty(\"user\", userid);\n\nif ((password == void) || (password == null)) {\n\tpassword = \"\";\n}\n\np.setProperty(\"password\", password);\n\nConnection con = null;\nPreparedStatement ps = null;\n\ntry {\n\tcon = d.connect(url, p);\n\tps = con.prepareStatement(sql);\n\n\tint paramsSize = params.size();\n\tfor (int i = 0; i < paramsSize; i++) {\n\t\tps.setObject(i + 1, params.get(i));\n\t}\n\n\tps.executeUpdate();\n\n\tresultList = \"update successful\";\n}\nfinally {\n\tif (ps != null) {\n\t\tps.close();\n\t}\n\tif (con != null) {\n\t\tcon.close();\n\t}\n}\n\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker",
+ "inputPorts" : [ {
+ "name" : "driver",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "password",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "userid",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "url",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "sql",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "params",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "resultList",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker
index 8ff169f..8b7a680 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker
@@ -16,6 +16,7 @@
}
writer.write(buffer, 0, r);
}
+reader.close();
outputText = writer.toString();
</script>
<dependencies />
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker.json
new file mode 100644
index 0000000..feb26cc
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=nucleotide&retmode=text&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
index 3d054b6..80f791a 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
@@ -16,6 +16,7 @@
}
writer.write(buffer, 0, r);
}
+reader.close();
outputText = writer.toString();
</script>
<dependencies />
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker.json
new file mode 100644
index 0000000..e616f51
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gb&db=nucleotide&retmode=xml&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker
index 900e346..2ce601b 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker
@@ -16,6 +16,7 @@
}
writer.write(buffer, 0, r);
}
+reader.close();
outputText = writer.toString();
</script>
<dependencies />
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker.json
new file mode 100644
index 0000000..8dfbdbe
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&db=nucleotide&retmode=xml&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker
index 7d0bce6..aad694a 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker
@@ -16,6 +16,7 @@
}
writer.write(buffer, 0, r);
}
+reader.close();
outputText = writer.toString();
</script>
<dependencies />
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker.json
new file mode 100644
index 0000000..3867455
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=nucleotide&retmode=xml&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
index 16236ff..c07b04e 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
@@ -16,6 +16,7 @@
}
writer.write(buffer, 0, r);
}
+reader.close();
outputText = writer.toString();
</script>
<dependencies />
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker.json
new file mode 100644
index 0000000..fc5b181
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=text&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker
index 901b26c..bf85c2b 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker
@@ -16,6 +16,7 @@
}
writer.write(buffer, 0, r);
}
+reader.close();
outputText = writer.toString();
</script>
<dependencies />
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker.json
new file mode 100644
index 0000000..160ce92
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gb&db=protein&retmode=xml&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
index 43f04fc..c82209f 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
@@ -16,6 +16,7 @@
}
writer.write(buffer, 0, r);
}
+reader.close();
outputText = writer.toString();
</script>
<dependencies />
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker.json
new file mode 100644
index 0000000..6e36120
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&db=protein&retmode=xml&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker
index 65b5aec..b6f9337 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker
@@ -16,6 +16,7 @@
}
writer.write(buffer, 0, r);
}
+reader.close();
outputText = writer.toString();
</script>
<dependencies />
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker.json
new file mode 100644
index 0000000..471e000
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=xml&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker
index 3ff4024..71fef3c 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker
@@ -19,6 +19,7 @@
}
writer.write(buffer, 0, r);
}
+reader.close();
outputText = writer.toString();
</script>
<dependencies />
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker.json
new file mode 100644
index 0000000..5e2a7df
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed\" +\n\"&rettype=\" + (((rettype == void ) || (rettype == null)) ? \"full\" : rettype) +\n\"&retmode=\" + (((retmode == void) || (retmode == null)) ? \"xml\" : retmode) +\n\"&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "rettype",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "retmode",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
index 4cf502c..37c440c 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
@@ -25,6 +25,7 @@
}
writer.write(buffer, 0, r);
}
+reader.close();
outputText = writer.toString();
</script>
<dependencies />
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker.json
new file mode 100644
index 0000000..bd29f82
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker.json
@@ -0,0 +1,44 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((term == void) || (term == null) || term.equals(\"\")) {\n\tthrow new RunTimeException(\"port term must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed\" +\n(field == void ? \"\" : (\"&field=\" + field)) +\n(retstart == void ? \"\" : (\"&retstart=\" + retstart)) +\n(retmax == void ? \"\" : (\"&retmax=\" + retmax)) +\n(mindate == void ? \"\" : (\"&mindate=\" + mindate)) +\n(maxdate == void ? \"\" : (\"&maxdate=\" + maxdate)) +\n\"&rettype=\" + (rettype == void ? \"full\" : rettype) +\n\"&retmode=\" + (retmode == void ? \"xml\" : retmode) +\n\"&tool=taverna\" +\n\"&term=\" + term);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker",
+ "inputPorts" : [ {
+ "name" : "term",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "db",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "field",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "retstart",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "retmax",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "mindate",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "maxdate",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "rettype",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl b/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl
new file mode 100644
index 0000000..a2317c5
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl
@@ -0,0 +1,31 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>url</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <script>import java.awt.Desktop;
+import java.net.URI;
+
+if ((url == void) || (url == null)) {
+ throw new RuntimeException("Url must be specified");
+}
+
+URI uri = null;
+
+uri = new URI(url);
+
+Desktop.getDesktop().browse(uri);</script>
+ <dependencies />
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity>
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl.json
new file mode 100644
index 0000000..1a2155e
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl.json
@@ -0,0 +1,11 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.awt.Desktop;\nimport java.net.URI;\n\nif ((url == void) || (url == null)) {\n\tthrow new RuntimeException(\"Url must be specified\");\n}\n\nURI uri = null;\n\nuri = new URI(url);\n\nDesktop.getDesktop().browse(uri);",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.net.BrowseUrl",
+ "inputPorts" : [ {
+ "name" : "url",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader b/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader
new file mode 100644
index 0000000..d3149d6
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader
@@ -0,0 +1,55 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>headers</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>header_key</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <name>header_value</name>
+ <depth>0</depth>
+ <mimeTypes />
+ <granularDepth>0</granularDepth>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <script>if ((headers == void) || (headers == null)) {
+ throw new RuntimeException("Headers must be specified");
+}
+
+if ((header_key == void) || (header_key == null)) {
+ throw new RuntimeException("Header_key must be specified");
+}
+
+String header_value = "";
+if (!header_key.endsWith(":")) {
+ header_key += ":";
+}
+for (String h : headers) {
+ if (h.startsWith(header_key)) {
+ header_value = h.substring(header_key.length());
+ header_value = header_value.trim();
+ break;
+ }
+}</script>
+ <dependencies />
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity>
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader.json
new file mode 100644
index 0000000..0e510fa
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((headers == void) || (headers == null)) {\n\tthrow new RuntimeException(\"Headers must be specified\");\n}\n\nif ((header_key == void) || (header_key == null)) {\n\tthrow new RuntimeException(\"Header_key must be specified\");\n}\n\nString header_value = \"\";\nif (!header_key.endsWith(\":\")) {\n\theader_key += \":\";\n}\nfor (String h : headers) {\n\tif (h.startsWith(header_key)) {\n\t\theader_value = h.substring(header_key.length());\n\t\theader_value = header_value.trim();\n\t\tbreak;\n\t}\n}",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.net.ExtractHeader",
+ "inputPorts" : [ {
+ "name" : "headers",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "header_key",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "header_value",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker.json
new file mode 100644
index 0000000..c2095cc
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import javax.swing.JOptionPane;\n\nanswer = JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE);\n\n\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.AskWorker",
+ "inputPorts" : [ {
+ "name" : "title",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "message",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "answer",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker
index b45960b..5244d77 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker
@@ -6,6 +6,10 @@
import javax.swing.JPanel;
import javax.swing.JRadioButton;
+if ((selectionValues == void) || (selectionValues == null) || (selectionValues.isEmpty())) {
+ throw new RuntimeException("selectionValues must be specified and non-empty");
+}
+
ButtonGroup group = new ButtonGroup();
JPanel messagePanel = new JPanel();
messagePanel.setLayout(new BoxLayout(messagePanel,BoxLayout.Y_AXIS));
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker.json
new file mode 100644
index 0000000..0410fc7
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import javax.swing.BoxLayout;\nimport javax.swing.ButtonGroup;\nimport javax.swing.JLabel;\nimport javax.swing.JOptionPane;\nimport javax.swing.JPanel;\nimport javax.swing.JRadioButton;\n\nif ((selectionValues == void) || (selectionValues == null) || (selectionValues.isEmpty())) {\n throw new RuntimeException(\"selectionValues must be specified and non-empty\");\n}\n\nButtonGroup group = new ButtonGroup();\nJPanel messagePanel = new JPanel();\nmessagePanel.setLayout(new BoxLayout(messagePanel,BoxLayout.Y_AXIS));\n\nmessagePanel.add(new JLabel((message == void ? null : message)));\n\t\t\nJRadioButton[] buttonArray = new JRadioButton[selectionValues.size()];\nfor (int i = 0; i < buttonArray.length; i++) {\t\t\t\n\tbuttonArray[i] = new JRadioButton(selectionValues.get(i));\n\tif (i==0) buttonArray[i].setSelected(true);\n\tgroup.add(buttonArray[i]);\n\tmessagePanel.add(buttonArray[i]);\n}\t\t\t\t\n\nJOptionPane.showOptionDialog(null, messagePanel, (title == void ? null : title),\n\t\tJOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, new Object[]{\"OK\"}, null);\n\t\t\nString answer=\"\";\nfor (JRadioButton button : buttonArray) {\n\tif (button.isSelected()) {\n\t\tanswer=button.getText();\n\t}\n}\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.ChooseWorker",
+ "inputPorts" : [ {
+ "name" : "title",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "message",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "selectionValues",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "answer",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker.json
new file mode 100644
index 0000000..1d71cef
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.awt.CardLayout;\nimport java.awt.Image;\nimport java.awt.Toolkit;\nimport java.io.File;\nimport java.util.HashMap;\nimport java.util.Map;\n\nimport javax.swing.ImageIcon;\nimport javax.swing.JEditorPane;\nimport javax.swing.JFileChooser;\nimport javax.swing.JLabel;\nimport javax.swing.JPanel;\nimport javax.swing.filechooser.FileFilter;\n\nclass FileExtFilter extends FileFilter {\n\n\tpublic FileExtFilter(String ext, String label, boolean includeDir) {\n\t\tthis.ext = ext;\n\t\tthis.label = label;\n\t\tthis.includeDir = includeDir;\n\t}\n\n\tpublic String getDescription() {\n\t\treturn this.label;\n\t}\n\n\tpublic boolean accept(File file) {\n\t\tif (file.isDirectory() && includeDir) {\n\t\t\treturn true;\n\t\t} else {\n\t\t\treturn file.getName().endsWith(this.ext);\n\t\t}\n\t}\n\n\tString ext, label;\n\n\tboolean includeDir;\n}\n\nif (title == void) {\n\ttitle = null;\n}\n\nif ((fileExtensions == void) || (fileExtensions == null)) {\n\tfileExtensions = \"\";\n}\n\nif ((fileExtLabels == void) || (fileExtLabels == null)) {\n\tfileExtLabels = \"\";\n}\n\nJFileChooser chooser = new JFileChooser();\nchooser.setDialogTitle(title);\n\nString[] fileTypeList = fileExtensions.split(\",\");\nString[] filterLabelList = fileExtLabels.split(\",\");\n\nif (fileTypeList != null && filterLabelList != null && fileTypeList.length != filterLabelList.length) {\n\tthrow new RuntimeException(\"The list of extensions and file filter labels must be the same length\");\n}\n\n// create the file filters\nfor (int i = 0; i < fileTypeList.length; i++) {\n\tFileExtFilter filter = new FileExtFilter(fileTypeList[i], filterLabelList[i], true);\n\tchooser.setFileFilter(filter);\n}\n\nchooser.showOpenDialog(null);\nFile file = chooser.getSelectedFile();\nselectedFile = file.getAbsolutePath();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker",
+ "inputPorts" : [ {
+ "name" : "title",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "fileExtensions",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "fileExtLabels",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "selectedFile",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker
index ed72043..1745844 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker
@@ -1,6 +1,10 @@
<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
<script>import javax.swing.JOptionPane;
+if ((valueList == void) || (valueList == null) || (valueList.isEmpty())) {
+ throw new RuntimeException("valueList must be specified and non-empty");
+}
+
answer = (String) JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE, null, valueList.toArray(), valueList.get(0));
</script>
<dependencies />
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker.json
new file mode 100644
index 0000000..6c287b6
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import javax.swing.JOptionPane;\n\nif ((valueList == void) || (valueList == null) || (valueList.isEmpty())) {\n throw new RuntimeException(\"valueList must be specified and non-empty\");\n}\n\nanswer = (String) JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE, null, valueList.toArray(), valueList.get(0));\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.SelectWorker",
+ "inputPorts" : [ {
+ "name" : "valueList",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "message",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "title",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "answer",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker.json
new file mode 100644
index 0000000..8037a42
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import javax.swing.JOptionPane;\n\nJOptionPane.showMessageDialog(null, (message == void ? null : message), (title == void ? null : title),\tJOptionPane.INFORMATION_MESSAGE);\n\nanswer = \"answer\";\n\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.TellWorker",
+ "inputPorts" : [ {
+ "name" : "title",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "message",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "answer",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker.json
new file mode 100644
index 0000000..eaa8c93
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import javax.swing.JOptionPane;\n\nJOptionPane.showMessageDialog(null, (message == void ? null : message), (title == void ? null : title),\tJOptionPane.WARNING_MESSAGE);\n\nanswer = \"answer\";\n \n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.WarnWorker",
+ "inputPorts" : [ {
+ "name" : "title",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "message",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "answer",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker.json
new file mode 100644
index 0000000..3fa2385
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import org.dom4j.Document;\nimport org.dom4j.Node;\nimport org.dom4j.io.SAXReader;\n\nSAXReader reader = new SAXReader(false);\nreader.setIncludeInternalDTDDeclarations(false);\nreader.setIncludeExternalDTDDeclarations(false);\n\nDocument document = reader.read(new StringReader(xmltext));\nList nodelist = document.selectNodes(xpath);\n\n// Process the elements in the nodelist\nArrayList outputList = new ArrayList();\nArrayList outputXmlList = new ArrayList();\n\nString val = null;\nString xmlVal = null;\nfor (Iterator iter = nodelist.iterator(); iter.hasNext();) {\n\tNode element = (Node) iter.next();\n\txmlVal = element.asXML();\n\tval = element.getStringValue();\n\tif (val != null && !val.equals(\"\")) {\n\t\toutputList.add(val);\n\t\toutputXmlList.add(xmlVal);\n\t}\n\n}\n\nList nodelist=outputList;\nList nodelistAsXML=outputXmlList;",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker",
+ "inputPorts" : [ {
+ "name" : "xpath",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "xml-text",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "nodelist",
+ "depth" : 1,
+ "granularDepth" : 1
+ }, {
+ "name" : "nodelistAsXML",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
index a405aef..1532b63 100644
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
@@ -76,7 +76,8 @@
Transformer xformer = template.newTransformer();
// Prepare the input and output files
-Source source = new StreamSource(getReader(inFileURL));
+Reader sourceReader = getReader(inFileURL);
+Source source = new StreamSource(sourceReader);
StringWriter resultStr = new StringWriter();
Result result = new StreamResult(resultStr);
@@ -92,7 +93,9 @@
out.write(outputStr);
out.close();
-}</script>
+}
+sourceReader.close();
+</script>
<dependencies />
<inputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker.json
new file mode 100644
index 0000000..09aff0d
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker.json
@@ -0,0 +1,28 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.io.BufferedReader;\nimport java.io.BufferedWriter;\nimport java.io.FileInputStream;\nimport java.io.FileNotFoundException;\nimport java.io.FileReader;\nimport java.io.FileWriter;\nimport java.io.IOException;\nimport java.io.InputStreamReader;\nimport java.io.OutputStreamWriter;\nimport java.io.StringWriter;\nimport java.io.Writer;\nimport java.net.URL;\nimport java.util.HashMap;\nimport java.util.Map;\n\nimport javax.xml.transform.Result;\nimport javax.xml.transform.Source;\nimport javax.xml.transform.SourceLocator;\nimport javax.xml.transform.Templates;\nimport javax.xml.transform.Transformer;\nimport javax.xml.transform.TransformerConfigurationException;\nimport javax.xml.transform.TransformerException;\nimport javax.xml.transform.TransformerFactory;\nimport javax.xml.transform.stream.StreamResult;\nimport javax.xml.transform.stream.StreamSource;\n\nBufferedReader getReader (String fileUrl) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\treader = new FileReader(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\treader = new InputStreamReader (url.openStream());\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\t\nBufferedWriter getWriter (String fileUrl) throws IOException {\n\t\tWriter writer;\n\t\ttry {\n\t\t\twriter = new FileWriter(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\twriter = new OutputStreamWriter (url.openConnection().getOutputStream());\n\t\t}\n\t\treturn new BufferedWriter(writer);\n\t}\n\t\nString xslFilename = xslFileURL;\nString outFilename;\nif (outFileURL != void) {\n outFilename = outFileURL;\n}\n\nString ext;\nif (outputExt != void) {\n ext = outputExt;\n}\n\nif (((outFilename == null) || outFilename.equals(\"\")) && (ext != null)) {\n\t\toutFilename = inFileURL.substring(0, inFileURL.indexOf(\".\")+1) + ext;\n}\n\n// Create transformer factory\nTransformerFactory factory = TransformerFactory.newInstance();\n\n// Use the factory to create a template containing the xsl file\nTemplates template = factory.newTemplates(new StreamSource(getReader(xslFilename)));\n\n// Use the template to create a transformer\nTransformer xformer = template.newTransformer();\n\n// Prepare the input and output files\nReader sourceReader = getReader(inFileURL);\nSource source = new StreamSource(sourceReader);\nStringWriter resultStr = new StringWriter();\nResult result = new StreamResult(resultStr);\n\n// Apply the xsl file to the source file and write the result to the\n// output file\nxformer.transform(source, result);\n\noutputStr = resultStr.toString();\n\nif ((outFilename != null) && !outFilename.equals(\"\")) {\n\n\tBufferedWriter out = getWriter(outFilename);\n\n\tout.write(outputStr);\n\tout.close();\n}\nsourceReader.close();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.xml.XSLTWorker",
+ "inputPorts" : [ {
+ "name" : "xslFileURL",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "outFileURL",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "inFileURL",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "outputExt",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputStr",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters
new file mode 100644
index 0000000..768c8f9
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters
@@ -0,0 +1,100 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow">
+ <class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class>
+ <inputMap>
+ <map from="xsltString" to="xsltString" />
+ <map from="paramList" to="paramList" />
+ <map from="sourceString" to="sourceString" />
+ </inputMap>
+ <outputMap>
+ <map from="outputString" to="outputString" />
+ </outputMap>
+ <configBean encoding="xstream">
+ <net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>sourceString</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>xsltString</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>paramList</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <name>outputString</name>
+ <depth>0</depth>
+ <mimeTypes />
+ <granularDepth>0</granularDepth>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <script>//From a proposal by Mikolaj Rybinski
+import javax.xml.transform.Source;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.transform.stream.StreamSource;
+
+param(paramstr) {
+ nameAndValue = paramstr.split("=");
+ if (nameAndValue.length != 2) {
+ throw new RuntimeException("Wrong parameter format: \"" + paramstr + "\".");
+ }
+ name = nameAndValue[0].trim();
+ value = nameAndValue[1].trim();
+ return this;
+}
+
+if ((sourceString == void) || (sourceString == null)) {
+ throw new RuntimeException("sourceString must be specified");
+}
+
+if ((xsltString == void) || (xsltString == null)) {
+ throw new RuntimeException("xsltString must be specified");
+}
+
+Source inSource = new StreamSource(new StringReader(sourceString));
+Source xslSource = new StreamSource(new StringReader(xsltString));
+
+// the factory pattern supports different XSLT processors
+// e.g. set the "javax.xml.transform.TransformerFactory" system property
+TransformerFactory tnfFact = TransformerFactory.newInstance();
+Transformer tnf = tnfFact.newTransformer(xslSource);
+
+if (paramList != void) {
+ for (String paramstr : paramList) {
+ p = param(paramstr);
+ tnf.setParameter(p.name, p.value);
+ }
+}
+
+Writer outputWriter = new StringWriter();
+tnf.transform(inSource, new StreamResult(outputWriter));
+outputString = outputWriter.toString();</script>
+ <dependencies />
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity>
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters.json
new file mode 100644
index 0000000..0800c76
--- /dev/null
+++ b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "//From a proposal by Mikolaj Rybinski\nimport javax.xml.transform.Source;\nimport javax.xml.transform.Transformer;\nimport javax.xml.transform.TransformerFactory;\nimport javax.xml.transform.stream.StreamResult;\nimport javax.xml.transform.stream.StreamSource;\n\nparam(paramstr) {\n nameAndValue = paramstr.split(\"=\");\n if (nameAndValue.length != 2) {\n throw new RuntimeException(\"Wrong parameter format: \\\"\" + paramstr + \"\\\".\");\n }\n name = nameAndValue[0].trim();\n value = nameAndValue[1].trim();\n return this;\n}\n\nif ((sourceString == void) || (sourceString == null)) {\n throw new RuntimeException(\"sourceString must be specified\");\n}\n\nif ((xsltString == void) || (xsltString == null)) {\n throw new RuntimeException(\"xsltString must be specified\");\n}\n\nSource inSource = new StreamSource(new StringReader(sourceString));\nSource xslSource = new StreamSource(new StringReader(xsltString));\n\n// the factory pattern supports different XSLT processors\n// e.g. set the \"javax.xml.transform.TransformerFactory\" system property\nTransformerFactory tnfFact = TransformerFactory.newInstance();\nTransformer tnf = tnfFact.newTransformer(xslSource);\n\nif (paramList != void) {\n for (String paramstr : paramList) {\n p = param(paramstr);\n tnf.setParameter(p.name, p.value);\n }\n}\n\nWriter outputWriter = new StringWriter();\ntnf.transform(inSource, new StreamResult(outputWriter));\noutputString = outputWriter.toString();",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters",
+ "inputPorts" : [ {
+ "name" : "sourceString",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "xsltString",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "paramList",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputString",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
index 61acb18..35b50d0 100644
--- a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
@@ -1,5 +1,12 @@
<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>string = new String(bytes);
+ <script>if ((bytes == void) || (bytes == null)) {
+ throw new RuntimeException("The 'bytes' parameter must be specified");
+}
+if (encoding == void) {
+ string = new String(bytes);
+} else {
+ string = new String(bytes, encoding);
+}
</script>
<dependencies />
<inputs>
@@ -13,6 +20,16 @@
<string>'application/octet-stream'</string>
</mimeTypes>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>encoding</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>
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString.json
new file mode 100644
index 0000000..ae7f934
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((bytes == void) || (bytes == null)) {\n\tthrow new RuntimeException(\"The 'bytes' parameter must be specified\");\n}\nif (encoding == void) {\n\tstring = new String(bytes);\n} else {\n\tstring = new String(bytes, encoding);\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.ByteArrayToString",
+ "inputPorts" : [ {
+ "name" : "bytes",
+ "depth" : 0,
+ "type" : "byte[]"
+ }, {
+ "name" : "encoding",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "string",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.DecodeBase64.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.DecodeBase64.json
new file mode 100644
index 0000000..1cb0f62
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.DecodeBase64.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import org.apache.commons.codec.binary.Base64;\n\nbytes = Base64.decodeBase64(base64.getBytes());\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.DecodeBase64",
+ "inputPorts" : [ {
+ "name" : "base64",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "bytes",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EchoList.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EchoList.json
new file mode 100644
index 0000000..aa0d198
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EchoList.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "outputlist = inputlist;",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.EchoList",
+ "inputPorts" : [ {
+ "name" : "inputlist",
+ "depth" : 1,
+ "type" : "byte[]"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputlist",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings.json
new file mode 100644
index 0000000..4afc1f8
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings.json
@@ -0,0 +1,11 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "List strings = new ArrayList();\nfor (int i = 0; i < 40; i++) {\n\tstrings.add(\"String\" + i);\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings",
+ "outputPorts" : [ {
+ "name" : "strings",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EncodeBase64.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EncodeBase64.json
new file mode 100644
index 0000000..5cbd786
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EncodeBase64.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import org.apache.commons.codec.binary.Base64;\n\nbase64 = new String(Base64.encodeBase64(bytes));",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.EncodeBase64",
+ "inputPorts" : [ {
+ "name" : "bytes",
+ "depth" : 0,
+ "type" : "byte[]"
+ } ],
+ "outputPorts" : [ {
+ "name" : "base64",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks.json
new file mode 100644
index 0000000..2a23a47
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "String lowerCaseContent = document.toLowerCase();\nint index = 0;\nList imagelinks = new ArrayList();\nwhile ((index = lowerCaseContent.indexOf(\"<img\", index)) != -1) {\n\tif ((index = lowerCaseContent.indexOf(\"src\", index)) == -1)\n\t\tbreak;\n\tif ((index = lowerCaseContent.indexOf(\"=\", index)) == -1)\n\t\tbreak;\n\tindex++;\n\tString remaining = document.substring(index);\n\tStringTokenizer st = new StringTokenizer(remaining, \"\\t\\n\\r\\\">#\");\n\tString strLink = st.nextToken();\n\timagelinks.add(strLink);\n}\n\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks",
+ "inputPorts" : [ {
+ "name" : "document",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "imagelinks",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FilterStringList.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FilterStringList.json
new file mode 100644
index 0000000..0f26e3e
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FilterStringList.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "filteredlist = new ArrayList();\nfor (Iterator i = stringlist.iterator(); i.hasNext();) {\n\tString item = (String) i.next();\n\tif (item.matches(regex)) {\n\t\tfilteredlist.add(item);\n\t}\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.FilterStringList",
+ "inputPorts" : [ {
+ "name" : "stringlist",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "regex",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "filteredlist",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FlattenList.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FlattenList.json
new file mode 100644
index 0000000..4992e0b
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FlattenList.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "flatten(inputs, outputs, depth) {\n\tfor (i = inputs.iterator(); i.hasNext();) {\n\t element = i.next();\n\t\tif (element instanceof Collection && depth > 0) {\n\t\t\tflatten(element, outputs, depth - 1);\n\t\t} else {\n\t\t\toutputs.add(element);\n\t\t}\n\t}\n}\n\noutputlist = new ArrayList();\n\nflatten(inputlist, outputlist, 1);",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.FlattenList",
+ "inputPorts" : [ {
+ "name" : "inputlist",
+ "depth" : 2,
+ "type" : "byte[]"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputlist",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.PadNumber.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.PadNumber.json
new file mode 100644
index 0000000..37828ea
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.PadNumber.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "int targetLengthInt = 7;\nif (targetlength != void) {\n\ttargetLengthInt = Integer.parseInt(targetlength);\n}\nint currentLength = input.length();\nwhile (input.length() < targetLengthInt) {\n\tinput = \"0\" + input;\n}\npadded = input;",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.PadNumber",
+ "inputPorts" : [ {
+ "name" : "input",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "targetlength",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "padded",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList.json
new file mode 100644
index 0000000..86378fb
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.util.regex.*;\n\nfilteredlist = new ArrayList();\nPattern thePat = Pattern.compile(regex);\nint theGroup = Integer.parseInt(group);\n\nfor (Iterator i = stringlist.iterator(); i.hasNext();) {\n\tString item = (String) i.next();\n\tMatcher matcher = thePat.matcher(item);\n\n\tif (matcher.find()) {\n\t\tfilteredlist.add(matcher.group(theGroup));\n\t}\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList",
+ "inputPorts" : [ {
+ "name" : "stringlist",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "regex",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "group",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "filteredlist",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SendEmail.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SendEmail.json
new file mode 100644
index 0000000..9a7365d
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SendEmail.json
@@ -0,0 +1,27 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import javax.mail.Message;\nimport javax.mail.Session;\nimport javax.mail.Transport;\nimport javax.mail.internet.MimeMessage;\nimport javax.mail.internet.InternetAddress;\n\nif (subject == void) {\n\tsubject = \"No subject\";\n}\nif (body == void) {\n\tthrow new Exception(\"No body specified for message\");\n}\n\nProperties mailProps = System.getProperties();\nif (smtpserver != void) {\n\tmailProps.put(\"mail.smtp.host\", smtpserver);\n}\n\nSession session = Session.getDefaultInstance(mailProps, null);\nMimeMessage message = new MimeMessage(session);\nmessage.setFrom(new InternetAddress(from));\nmessage.addRecipient(Message.RecipientType.TO, new InternetAddress(to));\nmessage.setSubject(subject);\nmessage.setText(body);\nTransport.send(message);\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.SendEmail",
+ "inputPorts" : [ {
+ "name" : "to",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "from",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "subject",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "body",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "smtpserver",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SplitByRegex.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SplitByRegex.json
new file mode 100644
index 0000000..afbdc78
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SplitByRegex.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "List split = new ArrayList();\nif (!string.equals(\"\")) {\n\tString regexString = \",\";\n\tif (regex != void) {\n\t\tregexString = regex;\n\t}\n\tString[] result = string.split(regexString);\n\tfor (int i = 0; i < result.length; i++) {\n\t\tsplit.add(result[i]);\n\t}\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.SplitByRegex",
+ "inputPorts" : [ {
+ "name" : "string",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "regex",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "split",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringConcat.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringConcat.json
new file mode 100644
index 0000000..24a3fa9
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringConcat.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "output = string1 + string2;",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.StringConcat",
+ "inputPorts" : [ {
+ "name" : "string1",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "string2",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "output",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringListMerge.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringListMerge.json
new file mode 100644
index 0000000..a0b860f
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringListMerge.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "String seperatorString = \"\\n\";\nif (seperator != void) {\n\tseperatorString = seperator;\n}\nStringBuffer sb = new StringBuffer();\nfor (Iterator i = stringlist.iterator(); i.hasNext();) {\n\tString item = (String) i.next();\n\tsb.append(item);\n\tif (i.hasNext()) {\n\t\tsb.append(seperatorString);\n\t}\n}\nconcatenated = sb.toString();\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.StringListMerge",
+ "inputPorts" : [ {
+ "name" : "stringlist",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "seperator",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "concatenated",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetDifference.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetDifference.json
new file mode 100644
index 0000000..c844322
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetDifference.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "List difference = new ArrayList();\nfor (Iterator i = list1.iterator(); i.hasNext();) {\n\tObject o = i.next();\n\tif (!list2.contains(o)) {\n\t\tdifference.add(o);\n\t}\n}\nfor (Iterator i = list2.iterator(); i.hasNext();) {\n\tObject o = i.next();\n\tif (!list1.contains(o)) {\n\t\tdifference.add(o);\n\t}\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.StringSetDifference",
+ "inputPorts" : [ {
+ "name" : "list1",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "list2",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "difference",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetIntersection.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetIntersection.json
new file mode 100644
index 0000000..0404922
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetIntersection.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "List intersection = new ArrayList();\nfor (Iterator i = list1.iterator(); i.hasNext();) {\n\tObject o = i.next();\n\tif (list2.contains(o)) {\n\t\tintersection.add(o);\n\t}\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.StringSetIntersection",
+ "inputPorts" : [ {
+ "name" : "list1",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "list2",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "intersection",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetUnion.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetUnion.json
new file mode 100644
index 0000000..25960be
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetUnion.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "Set results = new HashSet();\nresults.addAll(list1);\nresults.addAll(list2);\nList union = new ArrayList();\nunion.addAll(results);\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.StringSetUnion",
+ "inputPorts" : [ {
+ "name" : "list1",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "list2",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "union",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates.json
new file mode 100644
index 0000000..c5fecee
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "List strippedlist = new ArrayList();\nfor (Iterator i = stringlist.iterator(); i.hasNext();) {\n\tString item = (String) i.next();\n\tif (strippedlist.contains(item) == false) {\n\t\tstrippedlist.add(item);\n\t}\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates",
+ "inputPorts" : [ {
+ "name" : "stringlist",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "strippedlist",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor.json
new file mode 100644
index 0000000..4a5b7d8
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "throw new Exception(\"This script fails\");",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor",
+ "inputPorts" : [ {
+ "name" : "foo",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "bar",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "urgle",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestSometimesFails.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestSometimesFails.json
new file mode 100644
index 0000000..9ecf11d
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestSometimesFails.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.util.Random;\n\nRandom r = new Random();\n\nif ((r.nextInt() % 4) == 0) {\n\tthrow new RuntimeException(\"Fails every four runs!\");\n}\n\nout = in;",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.TestSometimesFails",
+ "inputPorts" : [ {
+ "name" : "in",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "out",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher
index ea26a07..db3a73a 100644
--- a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher
@@ -1,36 +1,32 @@
<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>URL inputURL = null;
+ <script>if ((url == void) || (url == null)) {
+ throw new RuntimeException("The url must be specified");
+}
+
+URL inputURL = null;
if (base != void) {
inputURL = new URL(new URL(base), url);
} else {
inputURL = new URL(url);
}
-byte[] contents;
-if (inputURL.openConnection().getContentLength() == -1) {
- // Content size unknown, must read first...
- byte[] buffer = new byte[1024];
- int bytesRead = 0;
- int totalBytesRead = 0;
- InputStream is = inputURL.openStream();
- while (bytesRead != -1) {
- totalBytesRead += bytesRead;
- bytesRead = is.read(buffer, 0, 1024);
- }
- contents = new byte[totalBytesRead];
-} else {
- contents = new byte[inputURL.openConnection().getContentLength()];
-}
int bytesRead = 0;
int totalBytesRead = 0;
InputStream is = inputURL.openStream();
-while (bytesRead != -1) {
- bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead);
- totalBytesRead += bytesRead;
- if (contents.length==totalBytesRead) break;
+ByteArrayOutputStream os = new ByteArrayOutputStream();
+byte[] buffer = new byte[2048];
+while (true) {
+ bytesRead = is.read(buffer);
+ if (bytesRead == -1) {
+ break;
+ }
+
+ os.write(buffer, 0, bytesRead);
}
-image = contents;
+image = os.toByteArray();
+is.close();
+os.close();
</script>
<dependencies />
<inputs>
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher.json
new file mode 100644
index 0000000..a65b448
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((url == void) || (url == null)) {\n\tthrow new RuntimeException(\"The url must be specified\");\n}\n\nURL inputURL = null;\nif (base != void) {\n\tinputURL = new URL(new URL(base), url);\n} else {\n\tinputURL = new URL(url);\n}\n\nint bytesRead = 0;\nint totalBytesRead = 0;\nInputStream is = inputURL.openStream();\nByteArrayOutputStream os = new ByteArrayOutputStream();\nbyte[] buffer = new byte[2048];\nwhile (true) {\n\tbytesRead = is.read(buffer);\n\tif (bytesRead == -1) {\n\t\tbreak;\t\n\t}\n\n\tos.write(buffer, 0, bytesRead);\n}\n\nimage = os.toByteArray();\nis.close();\nos.close();\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.WebImageFetcher",
+ "inputPorts" : [ {
+ "name" : "url",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "base",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "image",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
index 5752124..dcd76a6 100644
--- a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
@@ -1,5 +1,9 @@
<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>URL inputURL = null;
+ <script>if ((url == void) || (url == null)) {
+ throw new RuntimeException("The url must be specified");
+}
+
+URL inputURL = null;
if (base != void) {
inputURL = new URL(new URL(base), url);
}
@@ -9,35 +13,24 @@
URLConnection con = inputURL.openConnection();
InputStream in = con.getInputStream();
-InputStreamReader isr = new InputStreamReader(in);
-Reader inReader = new BufferedReader(isr);
+StringBuffer result = new StringBuffer();
+BufferedReader reader;
-StringBuffer buf = new StringBuffer();
-int ch;
-while ((ch = inReader.read()) > -1) {
- buf.append((char)ch);
+String encoding = con.getContentEncoding();
+if (encoding == null) {
+ reader = new BufferedReader(new InputStreamReader(in));
+} else {
+ reader = new BufferedReader(new InputStreamReader(in, encoding));
}
-inReader.close();
-contents = buf.toString();
+String line = null;
+String NEWLINE = System.getProperty("line.separator");
+while ((line = reader.readLine()) != null) {
+ result.append(line);
+ result.append(NEWLINE);
+}
-
-//String NEWLINE = System.getProperty("line.separator");
-//
-//URL inputURL = null;
-//if (base != void) {
-// inputURL = new URL(new URL(base), url);
-//} else {
-// inputURL = new URL(url);
-//}
-//StringBuffer result = new StringBuffer();
-//BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream()));
-//String line = null;
-//while ((line = reader.readLine()) != null) {
-// result.append(line);
-// result.append(NEWLINE);
-//}
-//
-//contents = result.toString();
+reader.close();
+contents = result.toString();
</script>
<dependencies />
<inputs>
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher.json
new file mode 100644
index 0000000..ad7a5b6
--- /dev/null
+++ b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((url == void) || (url == null)) {\n\tthrow new RuntimeException(\"The url must be specified\");\n}\n\nURL inputURL = null;\nif (base != void) {\n inputURL = new URL(new URL(base), url);\n}\nelse {\n inputURL = new URL(url);\n}\nURLConnection con = inputURL.openConnection();\nInputStream in = con.getInputStream();\n\nStringBuffer result = new StringBuffer();\nBufferedReader reader;\n\nString encoding = con.getContentEncoding();\nif (encoding == null) {\n reader = new BufferedReader(new InputStreamReader(in));\n} else {\n reader = new BufferedReader(new InputStreamReader(in, encoding));\n}\nString line = null;\nString NEWLINE = System.getProperty(\"line.separator\");\nwhile ((line = reader.readLine()) != null) {\n\tresult.append(line);\n\tresult.append(NEWLINE);\n}\n\nreader.close();\ncontents = result.toString();\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.WebPageFetcher",
+ "inputPorts" : [ {
+ "name" : "url",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "base",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "contents",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
diff --git a/src/test/java/net/sf/taverna/t2/activities/localworker/views/TestContextualViewFactory.java b/src/test/java/net/sf/taverna/t2/activities/localworker/views/TestContextualViewFactory.java
deleted file mode 100644
index 07182a5..0000000
--- a/src/test/java/net/sf/taverna/t2/activities/localworker/views/TestContextualViewFactory.java
+++ /dev/null
@@ -1,57 +0,0 @@
-/*******************************************************************************
- * 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.activities.localworker.views;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.List;
-
-import net.sf.taverna.t2.activities.beanshell.views.BeanshellActivityViewFactory;
-import net.sf.taverna.t2.activities.localworker.LocalworkerActivity;
-import net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean;
-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.workbench.ui.views.contextualviews.activity.ContextualViewFactoryRegistry;
-
-import org.junit.Test;
-
-public class TestContextualViewFactory {
-
- @SuppressWarnings("unchecked")
- @Test
- public void getLocalworkerFactoryAndConfigure() throws Exception {
- LocalworkerActivity localworkerActivity = new LocalworkerActivity();
- LocalworkerActivityConfigurationBean bean = new LocalworkerActivityConfigurationBean();
- localworkerActivity.configure(bean);
-
- List<ContextualViewFactory> viewFactoriesForBeanType = ContextualViewFactoryRegistry.getInstance().getViewFactoriesForObject(localworkerActivity);
- assertTrue("The localworker view factory should not be empty", !viewFactoriesForBeanType.isEmpty());
- LocalworkerActivityViewFactory factory = null;
- for (ContextualViewFactory cvf : viewFactoriesForBeanType) {
- if (cvf instanceof LocalworkerActivityViewFactory) {
- factory = (LocalworkerActivityViewFactory) cvf;
- }
- }
- assertTrue("No localworker view factory", factory != null);
- }
-
-}
