git-svn-id: https://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.taverna-commandline/tags/taverna-commandline-1.2@11102 bf327186-88b3-11dd-a302-d386e5130c1c
diff --git a/taverna-commandline-1.2/pom.xml b/taverna-commandline-1.2/pom.xml
deleted file mode 100644
index f19408b..0000000
--- a/taverna-commandline-1.2/pom.xml
+++ /dev/null
@@ -1,117 +0,0 @@
-<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>
- <artifactId>parent</artifactId>
- <groupId>net.sf.taverna</groupId>
- <version>0.1.2009-02-12</version>
- </parent>
- <groupId>net.sf.taverna.t2.taverna-commandline</groupId>
- <artifactId>taverna-commandline</artifactId>
- <version>1.2</version>
- <packaging>pom</packaging>
-
- <properties>
- <t2.core.version>1.2</t2.core.version>
- <t2.reference-core-extensions.version>1.2</t2.reference-core-extensions.version>
- <t2.infrastructure.version>2.2</t2.infrastructure.version>
- <t2.core.provenanceconnector.version>1.2</t2.core.provenanceconnector.version>
- <taverna.version>1.7.2.2</taverna.version>
- <t2.ui-components.version>1.2</t2.ui-components.version>
- </properties>
-
- <name>Taverna Commandline</name>
- <scm>
- <connection>scm:svn:http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.taverna-commandline/tags/taverna-commandline-1.2/</connection>
- <developerConnection>scm:svn:https://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.taverna-commandline/tags/taverna-commandline-1.2/</developerConnection>
- <url>http://code.google.com/p/taverna/source/browse/#svn/taverna/engine/net.sf.taverna.t2.taverna-commandline/tags/taverna-commandline-1.2/</url>
- </scm>
- <build>
- <plugins>
- <plugin>
- <artifactId>maven-clover-plugin</artifactId>
- <executions>
- <execution>
- <phase>pre-site</phase>
- <goals>
- <goal>instrument</goal>
- <goal>aggregate</goal>
- </goals>
- </execution>
- </executions>
- <configuration>
- <jdk>1.5</jdk>
- <targetPercentage>50%</targetPercentage>
- <failOnViolation>false</failOnViolation>
- </configuration>
- </plugin>
- </plugins>
- </build>
-
- <modules>
- <module>taverna-commandline-common</module>
- </modules>
-
- <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>
- </repositories>
- <reporting>
- <plugins>
- <plugin>
- <artifactId>maven-checkstyle-plugin</artifactId>
- <configuration>
- <configLocation>
- ${basedir}/../checkstyle.xml
- </configLocation>
- </configuration>
- </plugin>
- <plugin>
- <artifactId>maven-clover-plugin</artifactId>
- <configuration>
- <generatePdf>true</generatePdf>
- <generateXml>true</generateXml>
- </configuration>
- </plugin>
- <plugin>
- <artifactId>maven-javadoc-plugin</artifactId>
- <configuration>
- <minmemory>128m</minmemory>
- <maxmemory>512</maxmemory>
- <aggregate>true</aggregate>
- <links>
- <link>
- http://www.mygrid.org.uk/taverna/api/
- </link>
- <link>
- http://java.sun.com/j2se/1.5.0/docs/api/
- </link>
- </links>
- </configuration>
- </plugin>
- <plugin>
- <artifactId>maven-surefire-plugin</artifactId>
- <configuration>
- <systemProperties>
- <property>
- <name>java.awt.headless</name>
- <value>true</value>
- </property>
- </systemProperties>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>jxr-maven-plugin</artifactId>
- </plugin>
- </plugins>
- </reporting>
-
-</project>
diff --git a/taverna-commandline-1.2/taverna-commandline-common/pom.xml b/taverna-commandline-1.2/taverna-commandline-common/pom.xml
deleted file mode 100644
index 8512535..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/pom.xml
+++ /dev/null
@@ -1,87 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>net.sf.taverna.t2.taverna-commandline</groupId>
- <artifactId>taverna-commandline</artifactId>
- <version>1.2</version>
- </parent>
- <groupId>net.sf.taverna.t2.taverna-commandline</groupId>
- <artifactId>taverna-commandline-common</artifactId>
- <packaging>jar</packaging>
-
-
- <name>Taverna Commandline Common</name>
- <dependencies>
-
- <dependency>
- <groupId>net.sf.taverna.t2.infrastructure</groupId>
- <artifactId>launcher-api</artifactId>
- <version>${t2.infrastructure.version}</version>
- </dependency>
-
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
-
- <dependency>
- <groupId>uk.org.mygrid.taverna.baclava</groupId>
- <artifactId>baclava-core</artifactId>
- <version>${taverna.version}</version>
- </dependency>
-
- <dependency>
- <groupId>net.sf.taverna.t2.ui-impl</groupId>
- <artifactId>data-management-config</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
-
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>reference-impl</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
-
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>provenanceconnector</artifactId>
- <version>${t2.core.provenanceconnector.version}</version>
- </dependency>
-
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>reference-core-extensions</artifactId>
- <version>${t2.reference-core-extensions.version}</version>
- </dependency>
-
- <dependency>
- <groupId>commons-cli</groupId>
- <artifactId>commons-cli</artifactId>
- <version>1.2</version>
- </dependency>
-
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <version>1.4</version>
- </dependency>
-
- <dependency>
- <groupId>uk.org.mygrid.resources.mimeutil</groupId>
- <artifactId>mime-util</artifactId>
- <version>2.1.2-3</version>
- </dependency>
-
- <!-- TEST -->
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>4.4</version>
- <scope>test</scope>
- </dependency>
-
- </dependencies>
-
-</project>
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineInvocationContext.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineInvocationContext.java
deleted file mode 100644
index 5c60ddf..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineInvocationContext.java
+++ /dev/null
@@ -1,78 +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.commandline;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.provenance.reporter.ProvenanceReporter;
-import net.sf.taverna.t2.reference.ReferenceService;
-/**
- * An InvocationContext used by the command line tool.
- *
- * @author Stuart Owen
- *
- */
-public class CommandLineInvocationContext implements InvocationContext {
-
- private final ReferenceService referenceService;
-
- private final ProvenanceReporter provenanceReporter;
-
- private List<Object> entities = Collections
- .synchronizedList(new ArrayList<Object>());
-
- public CommandLineInvocationContext(ReferenceService referenceService,
- ProvenanceReporter provenanceReporter) {
- this.referenceService = referenceService;
- this.provenanceReporter = provenanceReporter;
- }
-
- public void addEntity(Object entity) {
- entities.add(entity);
- }
-
- public <T extends Object> List<T> getEntities(Class<T> entityType) {
- List<T> entitiesOfType = new ArrayList<T>();
- synchronized (entities) {
- for (Object entity : entities) {
- if (entityType.isInstance(entity)) {
- entitiesOfType.add(entityType.cast(entity));
- }
- }
- }
- return entitiesOfType;
- }
-
- public ProvenanceReporter getProvenanceReporter() {
- return provenanceReporter;
- }
-
- public ReferenceService getReferenceService() {
- return referenceService;
- }
-
- public void removeEntity(Object entity) {
- entities.remove(entity);
- }
-}
\ No newline at end of file
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineLauncher.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineLauncher.java
deleted file mode 100644
index f3274b5..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineLauncher.java
+++ /dev/null
@@ -1,415 +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.commandline;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.MalformedURLException;
-import java.net.URISyntaxException;
-import java.net.URL;
-import java.sql.SQLException;
-import java.util.HashMap;
-import java.util.Map;
-
-import javax.naming.NamingException;
-
-import net.sf.taverna.platform.spring.RavenAwareClassPathXmlApplicationContext;
-import net.sf.taverna.raven.launcher.Launchable;
-import net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler;
-import net.sf.taverna.t2.commandline.data.InputsHandler;
-import net.sf.taverna.t2.commandline.data.SaveResultsHandler;
-import net.sf.taverna.t2.commandline.exceptions.DatabaseConfigurationException;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.exceptions.OpenDataflowException;
-import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-import net.sf.taverna.t2.facade.WorkflowInstanceFacade;
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.invocation.TokenOrderException;
-import net.sf.taverna.t2.invocation.WorkflowDataToken;
-import net.sf.taverna.t2.provenance.ProvenanceConnectorFactory;
-import net.sf.taverna.t2.provenance.ProvenanceConnectorFactoryRegistry;
-import net.sf.taverna.t2.provenance.connector.ProvenanceConnector;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.workbench.reference.config.DataManagementConfiguration;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.DataflowInputPort;
-import net.sf.taverna.t2.workflowmodel.DataflowOutputPort;
-import net.sf.taverna.t2.workflowmodel.DataflowValidationReport;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.EditsRegistry;
-import net.sf.taverna.t2.workflowmodel.InvalidDataflowException;
-import net.sf.taverna.t2.workflowmodel.serialization.DeserializationException;
-import net.sf.taverna.t2.workflowmodel.serialization.xml.XMLDeserializer;
-import net.sf.taverna.t2.workflowmodel.serialization.xml.XMLDeserializerRegistry;
-
-import org.apache.log4j.Level;
-import org.apache.log4j.LogManager;
-import org.apache.log4j.Logger;
-import org.apache.log4j.PatternLayout;
-import org.apache.log4j.PropertyConfigurator;
-import org.apache.log4j.RollingFileAppender;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
-import org.springframework.context.ApplicationContext;
-
-/**
- * A utility class that wraps the process of executing a workflow, allowing
- * workflows to be easily executed independently of the GUI.
- *
- * @author Stuart Owen
- */
-
-public class CommandLineLauncher implements Launchable {
-
- private static Logger logger = Logger.getLogger(CommandLineLauncher.class);
-
- /**
- * Main method, purely for development and debugging purposes. Full
- * execution of workflows will not work through this method.
- *
- * @param args
- * @throws Exception
- */
- public static void main(String[] args) {
- new CommandLineLauncher().launch(args);
- }
-
- public int launch(String[] args) {
-
- try {
- CommandLineOptions options = new CommandLineOptions(args);
- initialiseLogging(options);
- return setupAndExecute(args,options);
- } catch (EditException e) {
- error("There was an error opening the workflow: " + e.getMessage());
- } catch (DeserializationException e) {
- error("There was an error opening the workflow: " + e.getMessage());
- } catch (InvalidDataflowException e) {
- error("There was an error validating the workflow: "
- + e.getMessage());
- } catch (TokenOrderException e) {
- error("There was an error starting the workflow execution: "
- + e.getMessage());
- } catch (InvalidOptionException e) {
- error(e.getMessage());
- } catch (ReadInputException e) {
- error(e.getMessage());
- } catch (OpenDataflowException e) {
- error(e.getMessage());
- } catch (DatabaseConfigurationException e) {
- error(e.getMessage());
- }
- return 0;
- }
-
- private void initialiseLogging(CommandLineOptions options) {
- LogManager.resetConfiguration();
-
- if (System.getProperty("log4j.configuration") == null) {
- try {
- PropertyConfigurator.configure(CommandLineLauncher.class
- .getClassLoader().getResource("cl-log4j.properties")
- .toURI().toURL());
- } catch (MalformedURLException e) {
- logger
- .error(
- "There was a serious error reading the default logging configuration",
- e);
- } catch (URISyntaxException e) {
- logger
- .error(
- "There was a serious error reading the default logging configuration",
- e);
- }
-
- } else {
- PropertyConfigurator.configure(System
- .getProperty("log4j.configuration"));
- }
-
- if (options.hasLogFile()) {
- RollingFileAppender appender;
- try {
-
- PatternLayout layout = new PatternLayout(
- "%-5p %d{ISO8601} (%c:%L) - %m%n");
- appender = new RollingFileAppender(layout, options.getLogFile());
- appender.setMaxFileSize("1MB");
- appender.setEncoding("UTF-8");
- appender.setMaxBackupIndex(4);
- // Let root logger decide level
- appender.setThreshold(Level.ALL);
- LogManager.getRootLogger().addAppender(appender);
- } catch (IOException e) {
- System.err.println("Could not log to " + options.getLogFile());
- }
- }
- }
-
- public int setupAndExecute(String[] args,CommandLineOptions options) throws InvalidOptionException,
- EditException, DeserializationException, InvalidDataflowException,
- TokenOrderException, ReadInputException, OpenDataflowException,
- DatabaseConfigurationException {
-
-
- if (!options.askedForHelp()) {
- setupDatabase(options);
-
- if (options.getWorkflow() != null) {
- URL workflowURL = readWorkflowURL(options.getWorkflow());
-
- Dataflow dataflow = openDataflow(workflowURL);
- validateDataflow(dataflow);
-
- InvocationContext context = createInvocationContext();
-
- WorkflowInstanceFacade facade = compileFacade(dataflow, context);
- InputsHandler inputsHandler = new InputsHandler();
- Map<String, DataflowInputPort> portMap = new HashMap<String, DataflowInputPort>();
-
- for (DataflowInputPort port : dataflow.getInputPorts()) {
- portMap.put(port.getName(), port);
- }
- inputsHandler.checkProvidedInputs(portMap, options);
- Map<String, WorkflowDataToken> inputs = inputsHandler
- .registerInputs(portMap, options, context);
-
- CommandLineResultListener resultListener = addResultListener(
- facade, context, dataflow, options);
-
- executeWorkflow(facade, inputs, resultListener);
- }
- } else {
- options.displayHelp();
- }
-
- // wait until user hits CTRL-C before exiting
- if (options.getStartDatabaseOnly()) {
- // FIXME: need to do this more gracefully.
- while (true) {
- try {
- Thread.sleep(500);
- } catch (InterruptedException e) {
- return 0;
- }
- }
- }
-
- return 0;
- }
-
- protected void validateDataflow(Dataflow dataflow)
- throws InvalidDataflowException {
- // FIXME: this needs expanding upon to give more details info back to
- // the user
- // FIXME: added a getMessage to InvalidDataflowException may be good
- // place to do this.
- DataflowValidationReport report = dataflow.checkValidity();
- if (!report.isValid()) {
- throw new InvalidDataflowException(dataflow, report);
- }
- }
-
- protected void executeWorkflow(WorkflowInstanceFacade facade,
- Map<String, WorkflowDataToken> inputs,
- CommandLineResultListener resultListener)
- throws TokenOrderException {
- facade.fire();
- for (String inputName : inputs.keySet()) {
- WorkflowDataToken token = inputs.get(inputName);
- facade.pushData(token, inputName);
- }
-
- while (!resultListener.isComplete()) {
- try {
- Thread.sleep(100);
- } catch (InterruptedException e) {
- logger
- .warn(
- "Thread Interuption Exception whilst waiting for dataflow completion",
- e);
- }
- }
- }
-
- private void setupDatabase(CommandLineOptions options)
- throws DatabaseConfigurationException {
- DatabaseConfigurationHandler dbHandler = new DatabaseConfigurationHandler(
- options);
- dbHandler.configureDatabase();
- if (!options.isInMemory()) {
- try {
- dbHandler.testDatabaseConnection();
- } catch (NamingException e) {
- throw new DatabaseConfigurationException(
- "There was an error trying to setup the database datasource: "
- + e.getMessage(), e);
- } catch (SQLException e) {
- if (options.isClientServer()) {
- throw new DatabaseConfigurationException(
- "There was an error whilst making a test database connection. If running with -clientserver you should check that a server is running (check -startdb or -dbproperties)",
- e);
- }
- if (options.isEmbedded()) {
- throw new DatabaseConfigurationException(
- "There was an error whilst making a test database connection. If running with -embedded you should make sure that another process isn't using the database, or a server running through -startdb",
- e);
- }
- }
- }
-
- }
-
- private InvocationContext createInvocationContext() {
- ReferenceService referenceService = createReferenceServiceBean();
- ProvenanceConnector connector = null;
- DataManagementConfiguration dbConfig = DataManagementConfiguration
- .getInstance();
- if (dbConfig.isProvenanceEnabled()) {
- String connectorType = dbConfig.getConnectorType();
-
- for (ProvenanceConnectorFactory factory : ProvenanceConnectorFactoryRegistry
- .getInstance().getInstances()) {
- if (connectorType.equalsIgnoreCase(factory.getConnectorType())) {
- connector = factory.getProvenanceConnector();
- }
-
- }
- if (connector != null) {
- connector.init();
- } else {
- error("Unable to initialise the provenance - the ProvenanceConnector cannot be found.");
- }
- }
- InvocationContext context = new CommandLineInvocationContext(
- referenceService, connector);
- return context;
- }
-
- private File determineOutputDir(CommandLineOptions options,
- String dataflowName) {
- File result = null;
- if (options.getOutputDirectory() != null) {
- result = new File(options.getOutputDirectory());
- if (result.exists()) {
- error("The specified output directory '"
- + options.getOutputDirectory() + "' already exists");
- }
- } else if (options.getOutputDocument() == null) {
- result = new File(dataflowName + "_output");
- int x = 1;
- while (result.exists()) {
- result = new File(dataflowName + "_output_" + x);
- x++;
- }
- }
- if (result != null) {
- System.out.println("Outputs will be saved to the directory: "
- + result.getAbsolutePath());
- }
- return result;
- }
-
- protected void error(String msg) {
- System.err.println(msg);
- System.exit(-1);
- }
-
- private URL readWorkflowURL(String workflowOption)
- throws OpenDataflowException {
- URL url;
- try {
- url = new URL("file:");
- return new URL(url, workflowOption);
- } catch (MalformedURLException e) {
- throw new OpenDataflowException(
- "The was an error processing the URL to the workflow: "
- + e.getMessage(), e);
- }
- }
-
- private CommandLineResultListener addResultListener(
- WorkflowInstanceFacade facade, InvocationContext context,
- Dataflow dataflow, CommandLineOptions options) {
- File outputDir = null;
- File baclavaDoc = null;
-
- if (options.saveResultsToDirectory()) {
- outputDir = determineOutputDir(options, dataflow.getLocalName());
- }
- if (options.getOutputDocument() != null) {
- baclavaDoc = new File(options.getOutputDocument());
- }
-
- Map<String, Integer> outputPortNamesAndDepth = new HashMap<String, Integer>();
- for (DataflowOutputPort port : dataflow.getOutputPorts()) {
- outputPortNamesAndDepth.put(port.getName(), port.getDepth());
- }
- SaveResultsHandler resultsHandler = new SaveResultsHandler(
- outputPortNamesAndDepth, outputDir, baclavaDoc);
- CommandLineResultListener listener = new CommandLineResultListener(
- outputPortNamesAndDepth.size(), resultsHandler,
- outputDir != null, baclavaDoc != null);
- facade.addResultListener(listener);
- return listener;
-
- }
-
- protected ReferenceService createReferenceServiceBean() {
- ApplicationContext appContext = new RavenAwareClassPathXmlApplicationContext(
- DataManagementConfiguration.getInstance().getDatabaseContext());
- return (ReferenceService) appContext
- .getBean("t2reference.service.referenceService");
- }
-
- protected WorkflowInstanceFacade compileFacade(Dataflow dataflow,
- InvocationContext context) throws InvalidDataflowException {
- Edits edits = EditsRegistry.getEdits();
- return edits.createWorkflowInstanceFacade(dataflow, context, "");
- }
-
- protected Dataflow openDataflow(URL workflowURL)
- throws DeserializationException, EditException,
- OpenDataflowException {
- XMLDeserializer deserializer = XMLDeserializerRegistry.getInstance()
- .getDeserializer();
- SAXBuilder builder = new SAXBuilder();
- Element el;
- try {
- InputStream stream = workflowURL.openStream();
- el = builder.build(stream).detachRootElement();
- } catch (JDOMException e) {
- throw new OpenDataflowException(
- "There was a problem processing the workflow XML: "
- + e.getMessage(), e);
- } catch (IOException e) {
- throw new OpenDataflowException(
- "There was a problem reading the workflow file: "
- + e.getMessage(), e);
- }
- return deserializer.deserializeDataflow(el);
- }
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineResultListener.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineResultListener.java
deleted file mode 100644
index 3d72d0f..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineResultListener.java
+++ /dev/null
@@ -1,81 +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.commandline;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import net.sf.taverna.t2.commandline.data.SaveResultsHandler;
-import net.sf.taverna.t2.facade.ResultListener;
-import net.sf.taverna.t2.invocation.WorkflowDataToken;
-
-import org.apache.log4j.Logger;
-
-/**
- * A ResultListener that is using for collecting and storing results when running
- * workflows from the commandline.
- *
- * @author Stuart Owen
- */
-public class CommandLineResultListener implements ResultListener {
-
- private static final Logger logger = Logger.getLogger(CommandLineResultListener.class);
-
- private Map<String, WorkflowDataToken> outputMap = new HashMap<String, WorkflowDataToken>();
- private Map<String,WorkflowDataToken> finalTokens = new HashMap<String, WorkflowDataToken>();
- private final SaveResultsHandler saveResultsHandler;
- private final int numberOfOutputs;
- private final boolean saveIndividualResults;
- private final boolean saveOutputDocument;
-
- public CommandLineResultListener(int numberOfOutputs,SaveResultsHandler saveResultsHandler,boolean saveIndividualResults,boolean saveOutputDocument) {
- this.numberOfOutputs = numberOfOutputs;
- this.saveResultsHandler = saveResultsHandler;
- this.saveIndividualResults = saveIndividualResults;
- this.saveOutputDocument = saveOutputDocument;
- }
-
- public Map<String, WorkflowDataToken> getOutputMap() {
- return outputMap;
- }
-
- public boolean isComplete() {
- return finalTokens.size() == numberOfOutputs;
- }
-
- public void resultTokenProduced(WorkflowDataToken token, String portName) {
- if (saveIndividualResults) {
- saveResultsHandler.tokenReceived(token, portName);
- }
-
- if (token.isFinal()) {
- finalTokens.put(portName, token);
- if (isComplete() && saveOutputDocument) {
- try {
- saveResultsHandler.saveOutputDocument(finalTokens);
- } catch (Exception e) {
- logger.error("An error occurred saving the final results to -outputdoc",e);
- }
- }
- }
- }
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/BaclavaDocumentHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/BaclavaDocumentHandler.java
deleted file mode 100644
index e218bc6..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/BaclavaDocumentHandler.java
+++ /dev/null
@@ -1,246 +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.commandline.data;
-
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
-import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.invocation.WorkflowDataToken;
-import net.sf.taverna.t2.reference.DereferenceException;
-import net.sf.taverna.t2.reference.ErrorDocument;
-import net.sf.taverna.t2.reference.IdentifiedList;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.reference.T2ReferenceType;
-
-import org.apache.log4j.Logger;
-import org.embl.ebi.escience.baclava.DataThing;
-import org.embl.ebi.escience.baclava.factory.DataThingFactory;
-import org.embl.ebi.escience.baclava.factory.DataThingXMLFactory;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.Namespace;
-import org.jdom.input.SAXBuilder;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
-
-/**
- * Handles creating and reading of Baclava documents.
- * Baclava is a standard originating from Taverna 1.
- *
- * @author Stuart Owen
- *
- */
-public class BaclavaDocumentHandler {
-
- private static Namespace namespace = Namespace.getNamespace("b",
- "http://org.embl.ebi.escience/baclava/0.1alpha");
-
- private static final Logger logger = Logger
- .getLogger(BaclavaDocumentHandler.class);
-
- public Map<String, DataThing> readInputDocument(String inputDocPath)
- throws ReadInputException {
- URL url;
- try {
- url = new URL("file:");
- } catch (MalformedURLException e1) {
- // Should never happen, but just incase:
- throw new ReadInputException(
- "The was an internal error setting up the URL to open the inputs. You should contact Taverna support.",
- e1);
- }
- URL inputDocURL;
- try {
- inputDocURL = new URL(url, inputDocPath);
- } catch (MalformedURLException e1) {
- throw new ReadInputException(
- "The a error reading the input document from : "
- + inputDocPath + ", " + e1.getMessage(), e1);
- }
- SAXBuilder builder = new SAXBuilder();
- Document inputDoc;
- try {
- inputDoc = builder.build(inputDocURL.openStream());
- } catch (IOException e) {
- throw new ReadInputException(
- "There was an error reading the input document file: "
- + e.getMessage(), e);
- } catch (JDOMException e) {
- throw new ReadInputException(
- "There was a error processing the input document XML: "
- + e.getMessage(), e);
- }
- Map<String, DataThing> things = DataThingXMLFactory
- .parseDataDocument(inputDoc);
- return things;
- }
-
- public void storeDocument(Map<String, WorkflowDataToken> finalResults,
- File outputFile) throws DereferenceException, IOException {
-
- Map<String, DataThing> dataThings = backDataThingMapFromWorkflowDataTokens(finalResults);
-
- // Build the string containing the XML document from the result map
- Document doc = getDataDocument(dataThings);
- XMLOutputter xo = new XMLOutputter(Format.getPrettyFormat());
- String xmlString = xo.outputString(doc);
- PrintWriter out = new PrintWriter(new FileWriter(outputFile));
- out.print(xmlString);
- out.flush();
- out.close();
- }
-
- protected Object convertReferencesToObjects(T2Reference reference,
- InvocationContext context) {
-
- if (reference.getReferenceType() == T2ReferenceType.ReferenceSet) {
- // Dereference the object
- Object dataValue;
-
- dataValue = context.getReferenceService().renderIdentifier(
- reference, Object.class, context);
- return dataValue;
-
- } else if (reference.getReferenceType() == T2ReferenceType.ErrorDocument) {
- // Dereference the ErrorDocument and convert it to some string
- // representation
- ErrorDocument errorDocument = (ErrorDocument) context
- .getReferenceService().resolveIdentifier(reference, null,
- context);
- String errorString = ErrorDocumentHandler.buildErrorDocumentString(
- errorDocument, context);
- return errorString;
- } else { // it is an IdentifiedList<T2Reference> - go recursively
- IdentifiedList<T2Reference> identifiedList = context
- .getReferenceService().getListService().getList(reference);
- List<Object> list = new ArrayList<Object>();
-
- for (int j = 0; j < identifiedList.size(); j++) {
- T2Reference ref = identifiedList.get(j);
- list.add(convertReferencesToObjects(ref, context));
- }
- return list;
- }
- }
-
- /**
- * Returns a org.jdom.Document from a map of port named to DataThingS
- * containing the port's results.
- */
- public static Document getDataDocument(Map<String, DataThing> dataThings) {
- Element rootElement = new Element("dataThingMap", namespace);
- Document theDocument = new Document(rootElement);
- for (Iterator<String> i = dataThings.keySet().iterator(); i.hasNext();) {
- String key = (String) i.next();
- DataThing value = (DataThing) dataThings.get(key);
- Element dataThingElement = new Element("dataThing", namespace);
- dataThingElement.setAttribute("key", key);
- dataThingElement.addContent(value.getElement());
- rootElement.addContent(dataThingElement);
- }
- return theDocument;
- }
-
- /**
- * Returns a map of port names to DataThings from a map of port names to a
- * list of (lists of ...) result objects.
- */
- protected Map<String, DataThing> bakeDataThingMap(
- Map<String, Object> resultMap) {
-
- Map<String, DataThing> dataThingMap = new HashMap<String, DataThing>();
- for (Iterator<String> i = resultMap.keySet().iterator(); i.hasNext();) {
- String portName = (String) i.next();
- dataThingMap.put(portName, DataThingFactory.bake(resultMap
- .get(portName)));
- }
- return dataThingMap;
- }
-
- protected Map<String, DataThing> backDataThingMapFromWorkflowDataTokens(
- Map<String, WorkflowDataToken> tokenMap)
- throws DereferenceException, IOException {
- Map<String, DataThing> dataThingMap = new HashMap<String, DataThing>();
- for (Iterator<String> i = tokenMap.keySet().iterator(); i.hasNext();) {
- String portName = (String) i.next();
- WorkflowDataToken token = tokenMap.get(portName);
- InvocationContext context = token.getContext();
- List<String> mimeTypeList = new ArrayList<String>();
-
- if (token.getData().getReferenceType() == T2ReferenceType.ReferenceSet) {
-
- mimeTypeList
- .addAll(MimeTypeHandler.determineMimeTypes(token.getData(), context));
- DataThing thingy = DataThingFactory.bake(convertReferencesToObjects(token.getData(), context));
- thingy.getMetadata().setMIMETypes(mimeTypeList);
- dataThingMap.put(portName, thingy);
-
- } else if (token.getData().getReferenceType() == T2ReferenceType.ErrorDocument) {
-
- DataThing thingy = DataThingFactory.bake(convertReferencesToObjects(token.getData(), context));
- thingy.getMetadata().addMIMEType("text/plain");
- dataThingMap.put(portName, thingy);
-
- } else {
-
- IdentifiedList<T2Reference> identifiedList = context
- .getReferenceService().getListService().getList(
- token.getData());
- List<Object> list = new ArrayList<Object>();
-
- for (int j = 0; j < identifiedList.size(); j++) {
- T2Reference ref = identifiedList.get(j);
- list.add(convertReferencesToObjects(ref, context));
- }
-
- // ripple through to get the leaf, to find its mimetype. Seems a
- // limitation of Baclava
- // is that the mime-type is set on the entire list, and is not
- // possible for individual items
- T2Reference ref = token.getData();
- while (ref.getReferenceType() != T2ReferenceType.ReferenceSet
- && ref.getReferenceType() != T2ReferenceType.ErrorDocument) {
- identifiedList = context.getReferenceService()
- .getListService().getList(ref);
- ref = identifiedList.get(0);
- }
- mimeTypeList.addAll(MimeTypeHandler.determineMimeTypes(ref, context));
- DataThing thingy = DataThingFactory.bake(list);
- thingy.getMetadata().setMIMETypes(mimeTypeList);
- dataThingMap.put(portName, thingy);
-
- }
- }
- return dataThingMap;
- }
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java
deleted file mode 100644
index 174f7e2..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java
+++ /dev/null
@@ -1,152 +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.commandline.data;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.sql.Connection;
-import java.sql.SQLException;
-import java.util.Properties;
-
-import javax.naming.NamingException;
-
-import net.sf.taverna.t2.commandline.exceptions.DatabaseConfigurationException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-import net.sf.taverna.t2.workbench.reference.config.DataManagementConfiguration;
-import net.sf.taverna.t2.workbench.reference.config.DataManagementHelper;
-
-import org.apache.log4j.Logger;
-
-/**
- * Handles the initialisation and configuration of the data source according to
- * the command line arguments, or a properties file.
- * This also handles starting a network based instance of a Derby server, if requested.
- *
- * @author Stuart Owen
- *
- */
-public class DatabaseConfigurationHandler {
-
- private final CommandLineOptions options;
- private DataManagementConfiguration dbConfig;
- private static Logger logger = Logger.getLogger(DatabaseConfigurationHandler.class);
-
- public DatabaseConfigurationHandler(CommandLineOptions options) {
- this.options = options;
- dbConfig = DataManagementConfiguration.getInstance();
- dbConfig.disableAutoSave();
- }
-
- public void configureDatabase() throws DatabaseConfigurationException {
- overrideDefaults();
- useOptions();
- if (dbConfig.getStartInternalDerbyServer()) {
- DataManagementHelper.startDerbyNetworkServer();
- System.out.println("Started Derby Server on Port: "
- + dbConfig.getCurrentPort());
- }
- DataManagementHelper.setupDataSource();
- }
-
- public DataManagementConfiguration getDBConfig() {
- return dbConfig;
- }
-
- private void importConfigurationFromStream(InputStream inStr)
- throws IOException {
- Properties p = new Properties();
- p.load(inStr);
- for (Object key : p.keySet()) {
- dbConfig.setProperty((String)key, p.getProperty((String)key).trim());
- }
- }
-
- protected void overrideDefaults() throws DatabaseConfigurationException {
-
- InputStream inStr = DatabaseConfigurationHandler.class.getClassLoader().getResourceAsStream("database-defaults.properties");
- try {
- importConfigurationFromStream(inStr);
- } catch (IOException e) {
- throw new DatabaseConfigurationException("There was an error reading the default database configuration settings: "+e.getMessage(),e);
- }
- }
-
- protected void readConfigirationFromFile(String filename) throws IOException {
- FileInputStream fileInputStream = new FileInputStream(filename);
- importConfigurationFromStream(fileInputStream);
- fileInputStream.close();
- }
-
- public void testDatabaseConnection()
- throws DatabaseConfigurationException, NamingException, SQLException {
- //try and get a connection
- Connection con = null;
- try {
- con = DataManagementHelper.openConnection();
- } finally {
- if (con!=null)
- try {
- con.close();
- } catch (SQLException e) {
- logger.warn("There was an SQL error whilst closing the test connection: "+e.getMessage(),e);
- }
- }
- }
-
- public void useOptions() throws DatabaseConfigurationException {
-
- if (options.hasOption("port")) {
- dbConfig.setPort(options.getDatabasePort());
- }
-
- if (options.hasOption("startdb")) {
- dbConfig.setStartInternalDerbyServer(true);
- }
-
- if (options.hasOption("inmemory")) {
- dbConfig.setInMemory(true);
- }
-
- if (options.hasOption("embedded")) {
- dbConfig.setInMemory(false);
- dbConfig.setDriverClassName("org.apache.derby.jdbc.EmbeddedDriver");
- }
-
- if (options.hasOption("provenance")) {
- dbConfig.setProvenanceEnabled(true);
- }
-
- if (options.hasOption("clientserver")) {
- dbConfig.setInMemory(false);
- dbConfig.setDriverClassName("org.apache.derby.jdbc.ClientDriver");
- dbConfig.setJDBCUri("jdbc:derby://localhost:" + dbConfig.getPort() + "/t2-database;create=true;upgrade=true");
- }
-
- if (options.hasOption("dbproperties")) {
- try {
- readConfigirationFromFile(options.getDatabaseProperties());
- } catch (IOException e) {
- throw new DatabaseConfigurationException("There was an error reading the database configuration options at "+options.getDatabaseProperties()+" : "+e.getMessage(),e);
- }
- }
- }
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorDocumentHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorDocumentHandler.java
deleted file mode 100644
index 50b909c..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorDocumentHandler.java
+++ /dev/null
@@ -1,195 +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.commandline.data;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Set;
-
-import javax.swing.tree.DefaultMutableTreeNode;
-
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.reference.ErrorDocument;
-import net.sf.taverna.t2.reference.ErrorDocumentService;
-import net.sf.taverna.t2.reference.IdentifiedList;
-import net.sf.taverna.t2.reference.ListService;
-import net.sf.taverna.t2.reference.StackTraceElementBean;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.reference.T2ReferenceType;
-
-/**
- * Handles Error documents and transforming them into String representations
- * that can be stored as a file, or within a Baclava document.
- *
- * @author Stuart Owen
- *
- */
-public class ErrorDocumentHandler {
-
- /**
- * Creates a string representation of the ErrorDocument.
- */
- public static String buildErrorDocumentString(ErrorDocument errDocument,
- InvocationContext context) {
-
- String errDocumentString = "";
-
- String exceptionMessage = errDocument.getExceptionMessage();
- if (exceptionMessage != null && !exceptionMessage.equals("")) {
- DefaultMutableTreeNode exceptionMessageNode = new DefaultMutableTreeNode(
- exceptionMessage);
- errDocumentString += exceptionMessageNode + "\n";
- List<StackTraceElementBean> stackTrace = errDocument
- .getStackTraceStrings();
- if (stackTrace.size() > 0) {
- for (StackTraceElementBean stackTraceElement : stackTrace) {
- errDocumentString += getStackTraceElementString(stackTraceElement)
- + "\n";
- }
- }
- }
-
- Set<T2Reference> errorReferences = errDocument.getErrorReferences();
- if (!errorReferences.isEmpty()) {
- errDocumentString += "Set of ErrorDocumentS to follow." + "\n";
- }
- int errorCounter = 1;
- int listCounter = 0;
- for (T2Reference reference : errorReferences) {
- if (reference.getReferenceType().equals(
- T2ReferenceType.ErrorDocument)) {
- ErrorDocumentService errorDocumentService = context
- .getReferenceService().getErrorDocumentService();
- ErrorDocument causeErrorDocument = errorDocumentService
- .getError(reference);
- if (listCounter == 0) {
- errDocumentString += "ErrorDocument " + (errorCounter++)
- + "\n";
- } else {
- errDocumentString += "ErrorDocument " + listCounter + "."
- + (errorCounter++) + "\n";
- }
- errDocumentString += buildErrorDocumentString(
- causeErrorDocument, context)
- + "\n";
- } else if (reference.getReferenceType().equals(
- T2ReferenceType.IdentifiedList)) {
- List<ErrorDocument> errorDocuments = getErrorDocuments(
- reference, context);
- errDocumentString += "ErrorDocument list " + (++listCounter)
- + "\n";
- for (ErrorDocument causeErrorDocument : errorDocuments) {
- errDocumentString += buildErrorDocumentString(
- causeErrorDocument, context)
- + "\n";
- }
- }
- }
-
- return errDocumentString;
- }
-
- public static void buildErrorDocumentTree(DefaultMutableTreeNode node,
- ErrorDocument errorDocument, InvocationContext context) {
- DefaultMutableTreeNode child = new DefaultMutableTreeNode(errorDocument);
- String exceptionMessage = errorDocument.getExceptionMessage();
- if (exceptionMessage != null && !exceptionMessage.equals("")) {
- DefaultMutableTreeNode exceptionMessageNode = new DefaultMutableTreeNode(
- exceptionMessage);
- child.add(exceptionMessageNode);
- List<StackTraceElementBean> stackTrace = errorDocument
- .getStackTraceStrings();
- if (stackTrace.size() > 0) {
- for (StackTraceElementBean stackTraceElement : stackTrace) {
- exceptionMessageNode.add(new DefaultMutableTreeNode(
- getStackTraceElementString(stackTraceElement)));
- }
- }
-
- }
- node.add(child);
-
- Set<T2Reference> errorReferences = errorDocument.getErrorReferences();
- for (T2Reference reference : errorReferences) {
- if (reference.getReferenceType().equals(
- T2ReferenceType.ErrorDocument)) {
- ErrorDocumentService errorDocumentService = context
- .getReferenceService().getErrorDocumentService();
- ErrorDocument causeErrorDocument = errorDocumentService
- .getError(reference);
- if (errorReferences.size() == 1) {
- buildErrorDocumentTree(node, causeErrorDocument, context);
- } else {
- buildErrorDocumentTree(child, causeErrorDocument, context);
- }
- } else if (reference.getReferenceType().equals(
- T2ReferenceType.IdentifiedList)) {
- List<ErrorDocument> errorDocuments = getErrorDocuments(
- reference, context);
- if (errorDocuments.size() == 1) {
- buildErrorDocumentTree(node, errorDocuments.get(0), context);
- } else {
- for (ErrorDocument errorDocument2 : errorDocuments) {
- buildErrorDocumentTree(child, errorDocument2, context);
- }
- }
- }
- }
- }
-
- private static String getStackTraceElementString(
- StackTraceElementBean stackTraceElement) {
- StringBuilder sb = new StringBuilder();
- sb.append(stackTraceElement.getClassName());
- sb.append('.');
- sb.append(stackTraceElement.getMethodName());
- if (stackTraceElement.getFileName() == null) {
- sb.append("(unknown file)");
- } else {
- sb.append('(');
- sb.append(stackTraceElement.getFileName());
- sb.append(':');
- sb.append(stackTraceElement.getLineNumber());
- sb.append(')');
- }
- return sb.toString();
- }
-
- public static List<ErrorDocument> getErrorDocuments(T2Reference reference,
- InvocationContext context) {
- List<ErrorDocument> errorDocuments = new ArrayList<ErrorDocument>();
- if (reference.getReferenceType().equals(T2ReferenceType.ErrorDocument)) {
- ErrorDocumentService errorDocumentService = context
- .getReferenceService().getErrorDocumentService();
- errorDocuments.add(errorDocumentService.getError(reference));
- } else if (reference.getReferenceType().equals(
- T2ReferenceType.IdentifiedList)) {
- ListService listService = context.getReferenceService()
- .getListService();
- IdentifiedList<T2Reference> list = listService.getList(reference);
- for (T2Reference listReference : list) {
- errorDocuments
- .addAll(getErrorDocuments(listReference, context));
- }
- }
- return errorDocuments;
- }
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
deleted file mode 100644
index f688efb..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
+++ /dev/null
@@ -1,235 +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.commandline.data;
-
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import net.sf.taverna.t2.commandline.exceptions.InputMismatchException;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.invocation.WorkflowDataToken;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.workflowmodel.DataflowInputPort;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-import org.embl.ebi.escience.baclava.DataThing;
-
-/**
- *
- * Handles the reading, or processing, or input values according to arguments provided to the commandline.
- * The may be either as direct values, from a file, or from a Baclava document.
- *
- * Also handles registering the input values with the Reference Service, ready to initiate
- * the workflow run.
- *
- * @author Stuart Owen
- *
- */
-public class InputsHandler {
-
- private static Logger logger = Logger.getLogger(InputsHandler.class);
-
-
- public void checkProvidedInputs(Map<String, DataflowInputPort> portMap, CommandLineOptions options) throws InputMismatchException {
- //we dont check for the document
- if (options.getInputDocument()==null) {
- Set<String> providedInputNames = new HashSet<String>();
- for (int i=0;i<options.getInputFiles().length;i+=2) {
- providedInputNames.add(options.getInputFiles()[i]);
- }
-
- for (int i=0;i<options.getInputValues().length;i+=2) {
- providedInputNames.add(options.getInputValues()[i]);
- }
-
- if (portMap.size()*2 != (options.getInputFiles().length + options.getInputValues().length)) {
- throw new InputMismatchException("The number of inputs provided does not match the number of input ports.",portMap.keySet(),providedInputNames);
- }
-
- for (String portName : portMap.keySet()) {
- if (!providedInputNames.contains(portName)) {
- throw new InputMismatchException("The provided inputs does not contain an input for the port '"+portName+"'",portMap.keySet(),providedInputNames);
- }
- }
- }
- }
-
-
- public Map<String, WorkflowDataToken> registerInputs(Map<String, DataflowInputPort> portMap, CommandLineOptions options,
- InvocationContext context) throws InvalidOptionException, ReadInputException {
- Map<String,WorkflowDataToken> inputs = new HashMap<String, WorkflowDataToken>();
- URL url;
- try {
- url = new URL("file:");
- } catch (MalformedURLException e1) {
- //Should never happen, but just incase:
- throw new ReadInputException("The was an internal error setting up the URL to open the inputs. You should contact Taverna support.",e1);
- }
-
- if (options.hasInputFiles()) {
- String[] inputParams = options.getInputFiles();
- for (int i = 0; i < inputParams.length; i = i + 2) {
- String inputName = inputParams[i];
- try {
- URL inputURL = new URL(url, inputParams[i + 1]);
- DataflowInputPort port = portMap.get(inputName);
-
- if (port==null) {
- throw new InvalidOptionException("Cannot find an input port named '"+inputName+"'");
- }
-
- T2Reference entityId=null;
-
- if (options.hasDelimiterFor(inputName)) {
- String delimiter=options.inputDelimiter(inputName);
- Object value = IOUtils.toString(inputURL.openStream()).split(delimiter);
-
- value=checkForDepthMismatch(1, port.getDepth(), inputName, value);
- entityId=context.getReferenceService().register(value, port.getDepth(), true, context);
- }
- else
- {
- Object value = IOUtils.toByteArray(inputURL.openStream());
- value=checkForDepthMismatch(0, port.getDepth(), inputName, value);
- entityId=context.getReferenceService().register(value, port.getDepth(), true, context);
- }
-
- WorkflowDataToken token = new WorkflowDataToken("",new int[]{}, entityId, context);
- inputs.put(inputName, token);
-
- } catch (IndexOutOfBoundsException e) {
- throw new InvalidOptionException("Missing input filename for input "+ inputName);
- } catch (IOException e) {
- throw new InvalidOptionException("Could not read input " + inputName + ": " + e.getMessage());
- }
- }
- }
-
- if (options.hasInputValues()) {
- String[] inputParams = options.getInputValues();
- for (int i = 0; i < inputParams.length; i = i + 2) {
- String inputName = inputParams[i];
- try {
- String inputValue = inputParams[i + 1];
- DataflowInputPort port = portMap.get(inputName);
-
- if (port==null) {
- throw new InvalidOptionException("Cannot find an input port named '"+inputName+"'");
- }
-
- T2Reference entityId=null;
- if (options.hasDelimiterFor(inputName)) {
- String delimiter=options.inputDelimiter(inputName);
- Object value=checkForDepthMismatch(1, port.getDepth(), inputName, inputValue.split(delimiter));
- entityId=context.getReferenceService().register(value, port.getDepth(), true, context);
- }
- else
- {
- Object value=checkForDepthMismatch(0, port.getDepth(), inputName, inputValue);
- entityId=context.getReferenceService().register(value, port.getDepth(), true, context);
- }
-
- WorkflowDataToken token = new WorkflowDataToken("",new int[]{}, entityId, context);
- inputs.put(inputName, token);
-
- } catch (IndexOutOfBoundsException e) {
- throw new InvalidOptionException("Missing input value for input "+ inputName);
- }
- }
-
- }
-
- if (options.getInputDocument()!=null) {
- String inputDocPath = options.getInputDocument();
- Map<String, DataThing> things = new BaclavaDocumentHandler().readInputDocument(inputDocPath);
- for (String inputName : things.keySet()) {
- DataThing thing = things.get(inputName);
- Object object = thing.getDataObject();
- T2Reference entityId=context.getReferenceService().register(object,getObjectDepth(object), true, context);
- WorkflowDataToken token = new WorkflowDataToken("",new int[]{}, entityId, context);
- inputs.put(inputName, token);
- }
- }
-
- return inputs;
- }
-
- private Object checkForDepthMismatch(int inputDepth,int portDepth,String inputName,Object inputValue) throws InvalidOptionException {
- if (inputDepth!=portDepth) {
- if (inputDepth<portDepth) {
- logger.warn("Wrapping input for '" + inputName + "' from a depth of "+inputDepth+" to the required depth of "+portDepth);
- while (inputDepth<portDepth) {
- List<Object> l=new ArrayList<Object>();
- l.add(inputValue);
- inputValue=l;
- inputDepth++;
- }
- }
- else {
- String msg="There is a mismatch between depth of the list for the input port '"+inputName+"' and the data presented. The input port requires a "+depthToString(portDepth)+" and the data presented is a "+depthToString(inputDepth);
- throw new InvalidOptionException(msg);
- }
- }
-
- return inputValue;
- }
-
- private String depthToString(int depth) {
- switch (depth) {
- case 0:
- return "single item";
- case 1:
- return "list";
- case 2:
- return "list of lists";
- default:
- return "list of depth "+depth;
- }
- }
-
-
- @SuppressWarnings("unchecked")
- private int getObjectDepth(Object o) {
- int result = 0;
- if (o instanceof Iterable) {
- result++;
- Iterator i = ((Iterable) o).iterator();
-
- if (i.hasNext()) {
- Object child = i.next();
- result = result + getObjectDepth(child);
- }
- }
- return result;
- }
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/MimeTypeHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/MimeTypeHandler.java
deleted file mode 100644
index 2e026d6..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/MimeTypeHandler.java
+++ /dev/null
@@ -1,123 +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.commandline.data;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.ReferenceSet;
-import net.sf.taverna.t2.reference.ReferencedDataNature;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.reference.T2ReferenceType;
-
-import org.apache.log4j.Logger;
-
-import eu.medsea.mimeutil.MimeType;
-import eu.medsea.mimeutil.MimeUtil2;
-
-/**
- * Handles identifying mime-types for a given data stream, or T2Reference
- *
- * @author Stuart Owen
- */
-public class MimeTypeHandler {
-
- private static Logger logger = Logger.getLogger(MimeTypeHandler.class);
-
- @SuppressWarnings("unchecked")
- public static List<MimeType> getMimeTypes(InputStream inputStream,InvocationContext context) throws IOException {
- List<MimeType> mimeList = new ArrayList<MimeType>();
- MimeUtil2 mimeUtil = new MimeUtil2();
- mimeUtil
- .registerMimeDetector("eu.medsea.mimeutil.detector.ExtensionMimeDetector");
- mimeUtil
- .registerMimeDetector("eu.medsea.mimeutil.detector.MagicMimeMimeDetector");
- mimeUtil
- .registerMimeDetector("eu.medsea.mimeutil.detector.WindowsRegistryMimeDetector");
- mimeUtil
- .registerMimeDetector("eu.medsea.mimeutil.detector.ExtraMimeTypes");
-
- try {
- byte[] bytes = new byte[2048];
- inputStream.read(bytes);
- Collection mimeTypes2 = mimeUtil.getMimeTypes(bytes);
- mimeList.addAll(mimeTypes2);
- } finally {
- try {
- inputStream.close();
- } catch (IOException e) {
- logger.error(
- "Failed to close stream after determining mimetype", e);
- }
- }
- return mimeList;
- }
-
- public static List<String> determineMimeTypes(T2Reference reference,
- InvocationContext context) throws IOException {
- List<String> mimeTypeList = new ArrayList<String>();
-
- if (reference.getReferenceType() == T2ReferenceType.ErrorDocument) {
- mimeTypeList.add("text/plain");
- } else {
- ReferenceSet referenceSet = (ReferenceSet) context
- .getReferenceService().resolveIdentifier(reference,
- null, context);
- if (!referenceSet.getExternalReferences().isEmpty()) {
-
- ExternalReferenceSPI externalReference = referenceSet
- .getExternalReferences().iterator().next();
-
- List<MimeType> mimeTypes = getMimeTypes(
- externalReference.openStream(context), context);
-
- for (MimeType type : mimeTypes) {
- if (!type.toString().equals("text/plain")
- && !type.toString().equals(
- "application/octet-stream")) {
- mimeTypeList.add(type.toString());
- }
- }
- if (externalReference.getDataNature() == ReferencedDataNature.TEXT) {
- mimeTypeList.add("text/plain");
- } else {
- mimeTypeList.add("application/octet-stream");
- }
- }
-
- }
-
- return mimeTypeList;
- }
-
- public static List<MimeType> getMimeTypes(
- ExternalReferenceSPI externalReference, InvocationContext context) throws IOException {
-
- InputStream inputStream = externalReference.openStream(context);
- return getMimeTypes(inputStream, context);
- }
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java
deleted file mode 100644
index a5b20a1..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java
+++ /dev/null
@@ -1,241 +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.commandline.data;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.util.HashMap;
-import java.util.Map;
-
-import net.sf.taverna.t2.commandline.CommandLineResultListener;
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.invocation.WorkflowDataToken;
-import net.sf.taverna.t2.reference.ErrorDocument;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.Identified;
-import net.sf.taverna.t2.reference.IdentifiedList;
-import net.sf.taverna.t2.reference.ReferenceSet;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.reference.T2ReferenceType;
-
-import org.apache.log4j.Logger;
-
-/**
- * Handles all recording of results as they are received by the {@link CommandLineResultListener}
- * or when the workflow enactment has completed.
- * This includes saving as a Baclava Document, or storing individual results.
- *
- * @author Stuart Owen
- * @see BaclavaDocumentHandler
- * @see CommandLineResultListener
- *
- */
-public class SaveResultsHandler {
-
- private final Map<String, Integer> portsAndDepth;
- private HashMap<String, Integer> depthSeen;
- private final File rootDirectory;
- private static Logger logger = Logger
- .getLogger(CommandLineResultListener.class);
- private final File outputDocumentFile;
-
- public SaveResultsHandler(Map<String, Integer> portsAndDepth,
- File rootDirectory, File outputDocumentFile) {
-
- this.portsAndDepth = portsAndDepth;
- this.rootDirectory = rootDirectory;
- this.outputDocumentFile = outputDocumentFile;
-
- depthSeen = new HashMap<String, Integer>();
- for (String portName : portsAndDepth.keySet()) {
- depthSeen.put(portName, -1);
- }
- }
-
- public void tokenReceived(WorkflowDataToken token, String portName) {
- if (rootDirectory != null) { //only save individual results if a directory is specified
- if (portsAndDepth.containsKey(portName)) {
- int[] index = token.getIndex();
- if (depthSeen.get(portName) == -1)
- depthSeen.put(portName, index.length);
- if (index.length >= depthSeen.get(portName)) {
- storeToken(token, portName);
- }
- } else {
- logger
- .error("Result recieved for unexpected Port: "
- + portName);
- }
- }
- }
-
- public void saveOutputDocument(Map<String,WorkflowDataToken> allResults) throws Exception {
- if (outputDocumentFile!=null) {
- new BaclavaDocumentHandler().storeDocument(allResults, outputDocumentFile);
- }
- }
-
- protected void storeToken(WorkflowDataToken token, String portName) {
-
- if (token.getData().getReferenceType() == T2ReferenceType.IdentifiedList) {
- saveList(token, portName);
- } else {
- File dataDirectory = rootDirectory;
- File dataFile = null;
-
- if (token.getIndex().length > 0) {
- dataDirectory = new File(rootDirectory, portName);
- for (int i = 0; i < token.getIndex().length - 1; i++) {
- dataDirectory = new File(dataDirectory, String
- .valueOf(token.getIndex()[i] + 1));
- }
- dataFile = new File(dataDirectory, String.valueOf(token
- .getIndex()[token.getIndex().length - 1] + 1));
- } else {
- dataFile = new File(dataDirectory, portName);
- }
-
- if (!dataDirectory.exists()) {
- dataDirectory.mkdirs();
- }
-
- if (dataFile.exists()) {
- System.err.println("There is already data saved to: "
- + dataFile.getAbsolutePath());
- System.exit(-1);
- }
-
- saveIndividualDataFile(token.getData(), dataFile, token
- .getContext());
- }
- }
-
- private void saveList(WorkflowDataToken token, String portName) {
- File dataDirectory = null;
- int[] index = token.getIndex();
-
- if (index.length > 0) {
- dataDirectory = new File(rootDirectory, portName);
- for (int i = 0; i < index.length - 1; i++) {
- dataDirectory = new File(dataDirectory, String.valueOf(token
- .getIndex()[i] + 1));
- }
- dataDirectory = new File(dataDirectory, String.valueOf(token
- .getIndex()[index.length - 1]+ 1));
- } else {
- dataDirectory = new File(rootDirectory, portName);
- }
-
- T2Reference reference = token.getData();
- IdentifiedList<T2Reference> list = token.getContext()
- .getReferenceService().getListService().getList(reference);
- saveListItems(token.getContext(), dataDirectory, list);
- }
-
- private void saveListItems(InvocationContext context, File dataDirectory,IdentifiedList<T2Reference> list) {
- int c = 0;
- if (!dataDirectory.exists()) {
- dataDirectory.mkdirs();
- }
- for (T2Reference id : list) {
- File dataFile = new File(dataDirectory, String.valueOf(c+1));
- if (id.getReferenceType() == T2ReferenceType.IdentifiedList) {
- IdentifiedList<T2Reference> innerList = context
- .getReferenceService().getListService().getList(id);
- saveListItems(context, dataFile, innerList);
- }
- else {
- saveIndividualDataFile(id, dataFile, context);
- }
- c++;
- }
- }
-
- protected void saveIndividualDataFile(T2Reference reference, File dataFile,
- InvocationContext context) {
-
- if (dataFile.exists()) {
- System.err.println("There is already data saved to: "
- + dataFile.getAbsolutePath());
- System.exit(-1);
- }
-
- Object data = null;
- if (reference.containsErrors()) {
- ErrorDocument errorDoc = context.getReferenceService()
- .getErrorDocumentService().getError(reference);
- data = ErrorDocumentHandler.buildErrorDocumentString(errorDoc, context);
- dataFile = new File(dataFile.getAbsolutePath()+".error");
- } else {
- // FIXME: this really should be done using a stream rather
- // than an instance of the object in memory
-
- Identified identified = context.getReferenceService().resolveIdentifier(reference, null, context);
- ReferenceSet referenceSet = (ReferenceSet) identified;
-
- if (referenceSet.getExternalReferences().isEmpty()) {
- data = context.getReferenceService().renderIdentifier(reference,
- Object.class, context);
- }
- else {
- ExternalReferenceSPI externalReference = referenceSet.getExternalReferences().iterator().next();
- data = externalReference.openStream(context);
- }
- }
-
- FileOutputStream fos;
- try {
- fos = new FileOutputStream(dataFile);
- if (data instanceof InputStream) {
- InputStream inStream = (InputStream)data;
- int c;
- while ( ( c = inStream.read() ) != -1 ) {
- fos.write( (char) c);
- }
- fos.flush();
- fos.close();
- }
- if (data instanceof byte[]) {
- fos.write((byte[]) data);
- fos.flush();
- fos.close();
- } else {
- PrintWriter out = new PrintWriter(new OutputStreamWriter(fos));
- out.print(data.toString());
- out.flush();
- out.close();
- }
- } catch (FileNotFoundException e) {
- logger.error("Unable to find the file: '"
- + dataFile.getAbsolutePath() + "' for writing results", e);
- } catch (IOException e) {
- logger.error("IO Error writing resuts to: '"
- + dataFile.getAbsolutePath(), e);
- }
- }
-
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java
deleted file mode 100644
index 616fb70..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java
+++ /dev/null
@@ -1,43 +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.commandline.exceptions;
-
-public class DatabaseConfigurationException extends Exception {
-
- private static final long serialVersionUID = -4128248547532355697L;
-
- public DatabaseConfigurationException() {
-
- }
-
- public DatabaseConfigurationException(String message) {
- super(message);
- }
-
- public DatabaseConfigurationException(Throwable cause) {
- super(cause);
- }
-
- public DatabaseConfigurationException(String message, Throwable cause) {
- super(message, cause);
- }
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java
deleted file mode 100644
index eb4a289..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java
+++ /dev/null
@@ -1,54 +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.commandline.exceptions;
-
-import java.util.Set;
-
-public class InputMismatchException extends InvalidOptionException {
-
- private static final long serialVersionUID = -5368068332397293706L;
- private final Set<String> expectedInputNames;
- private final Set<String> providedInputNames;
-
- public InputMismatchException(String msg, Set<String> expectedInputNames, Set<String> providedInputNames) {
- super(msg);
- this.expectedInputNames = expectedInputNames;
- this.providedInputNames = providedInputNames;
- }
-
- public String getMessage() {
- String result = super.getMessage();
- result += "\n" + expectedInputNames.size() + " inputs were expected";
- if (expectedInputNames.size()>0) result += " which are:\n";
- for (String name : expectedInputNames) {
- result += "'"+name+"' ";
- }
-
- result += "\n" + providedInputNames.size() + " inputs were provided";
- if (providedInputNames.size()>0) result += " which are:\n";
- for (String name : providedInputNames) {
- result += "'"+name+"' ";
- }
- return result;
- }
-
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java
deleted file mode 100644
index c07a19f..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java
+++ /dev/null
@@ -1,30 +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.commandline.exceptions;
-
-public class InvalidOptionException extends Exception {
-
- private static final long serialVersionUID = 2467409785164223258L;
-
- public InvalidOptionException(String message) {
- super(message);
- }
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java
deleted file mode 100644
index 664ab71..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java
+++ /dev/null
@@ -1,44 +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.commandline.exceptions;
-
-public class OpenDataflowException extends Exception {
-
-
- private static final long serialVersionUID = 4778578311101082197L;
-
- public OpenDataflowException() {
-
- }
-
- public OpenDataflowException(String message) {
- super(message);
- }
-
- public OpenDataflowException(Throwable cause) {
- super(cause);
- }
-
- public OpenDataflowException(String message, Throwable cause) {
- super(message, cause);
- }
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java
deleted file mode 100644
index 226d6ea..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java
+++ /dev/null
@@ -1,35 +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.commandline.exceptions;
-
-public class ReadInputException extends Exception {
-
- private static final long serialVersionUID = -3494432791254643055L;
-
- public ReadInputException(String msg) {
- super(msg);
- }
-
- public ReadInputException(String msg, Throwable e) {
- super(msg,e);
- }
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
deleted file mode 100644
index 07a6cce..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
+++ /dev/null
@@ -1,399 +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.commandline.options;
-
-import java.io.IOException;
-import java.io.InputStream;
-
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.GnuParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.OptionBuilder;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-
-/**
- * Handles the processing of command line arguments for enacting a workflow.
- * This class encapsulates all command line options, and exposes them through higher-level
- * accessors. Upon creation it checks the validity of the command line options and raises an
- * {@link InvalidOptionException} if they are invalid.
- *
- * @author Stuart Owen
- *
- */
-public class CommandLineOptions {
-
- private static final Logger logger = Logger
- .getLogger(CommandLineOptions.class);
- private Options options;
- private CommandLine commandLine;
-
- public CommandLineOptions(String[] args) throws InvalidOptionException {
- this.options = intitialiseOptions();
- this.commandLine = processArgs(args);
- checkForInvalid();
- }
-
- public boolean askedForHelp() {
- return hasOption("help") || (getArgs().length==0 && getOptions().length==0);
- }
-
- protected void checkForInvalid() throws InvalidOptionException {
- if (askedForHelp()) return;
- if (hasOption("provenance")
- && !(hasOption("embedded") || hasOption("clientserver") || hasOption("dbproperties")))
- throw new InvalidOptionException(
- "You should be running with a database to use provenance");
- if (hasOption("provenance") && hasOption("inmemory"))
- throw new InvalidOptionException(
- "You should be running with a database to use provenance");
- if ((hasOption("inputfile") || hasOption("inputvalue"))
- && hasOption("inputdoc"))
- throw new InvalidOptionException(
- "You can't provide both -input and -inputdoc arguments");
-
- if (hasOption("inputdelimiter") && hasOption("inputdoc"))
- throw new InvalidOptionException("You cannot combine the -inputdelimiter and -inputdoc arguments");
-
- if (getArgs().length == 0
- && !(hasOption("help") || hasOption("startdb")))
- throw new InvalidOptionException("You must specify a workflow");
-
- if (hasOption("inmemory") && hasOption("embedded"))
- throw new InvalidOptionException(
- "The options -embedded, -clientserver and -inmemory cannot be used together");
- if (hasOption("inmemory") && hasOption("clientserver"))
- throw new InvalidOptionException(
- "The options -embedded, -clientserver and -inmemory cannot be used together");
- if (hasOption("embedded") && hasOption("clientserver"))
- throw new InvalidOptionException(
- "The options -embedded, -clientserver and -inmemory cannot be used together");
- }
-
- public void displayHelp() {
- boolean full = false;
- if (hasOption("help")) full=true;
- displayHelp(full);
- }
-
- public void displayHelp(boolean showFullText) {
-
- HelpFormatter formatter = new HelpFormatter();
- try {
- formatter
- .printHelp("executeworkflow [options] [workflow]", options);
- if (showFullText) {
- InputStream helpStream = CommandLineOptions.class
- .getClassLoader().getResourceAsStream("help.txt");
- String helpText = IOUtils.toString(helpStream);
- System.out.println(helpText);
- }
-
- } catch (IOException e) {
- logger.error("Error reading the help document", e);
- System.exit(-1);
- }
- }
-
- public String[] getArgs() {
- return commandLine.getArgs();
- }
-
- /**
- *
- * @return the port that the database should run on
- */
- public String getDatabasePort() {
- return getOptionValue("port");
- }
-
- /**
- *
- * @return a path to a properties file that contains database configuration
- * settings
- */
- public String getDatabaseProperties() {
- return getOptionValue("dbproperties");
- }
-
- /**
- *
- * @return the path to the input document
- */
- public String getInputDocument() {
- return getOptionValue("inputdoc");
- }
-
- /**
- * Returns an array that alternates between a portname and path to a file
- * containing the input values. Therefore the array will always contain an
- * even number of elements
- *
- * @return an array of portname and path to files containing individual
- * inputs.
- */
- public String[] getInputFiles() {
- if (hasInputFiles()) {
- return getOptionValues("inputfile");
- } else {
- return new String[] {};
- }
- }
-
- public String[] getInputValues() {
- if (hasInputValues()) {
- return getOptionValues("inputvalue");
- } else {
- return new String[] {};
- }
- }
-
- public String getLogFile() {
- return getOptionValue("logfile");
- }
-
- public Option [] getOptions() {
- return commandLine.getOptions();
- }
-
- private String getOptionValue(String opt) {
- return commandLine.getOptionValue(opt);
- }
-
- private String[] getOptionValues(String arg0) {
- return commandLine.getOptionValues(arg0);
- }
-
- /**
- *
- * @return the directory to write the results to
- */
- public String getOutputDirectory() {
- return getOptionValue("outputdir");
- }
-
- /**
- *
- * @return the path to the output document
- */
- public String getOutputDocument() {
- return getOptionValue("outputdoc");
- }
-
- public boolean getStartDatabase() {
- return hasOption("startdb");
- }
-
- public boolean getStartDatabaseOnly() throws InvalidOptionException {
- return (getStartDatabase() && (getWorkflow() == null));
- }
-
- public String getWorkflow() throws InvalidOptionException {
- if (getArgs().length == 0) {
- return null;
- } else if (getArgs().length != 1) {
- throw new InvalidOptionException(
- "You should only specify one workflow file");
- } else {
- return getArgs()[0];
- }
- }
-
- public boolean hasDelimiterFor(String inputName) {
- boolean result = false;
- if (hasOption("inputdelimiter")) {
- String [] values = getOptionValues("inputdelimiter");
- for (int i=0;i<values.length;i+=2) {
- if (values[i].equals(inputName))
- {
- result=true;
- break;
- }
- }
- }
- return result;
- }
-
- public boolean hasInputFiles() {
- return hasOption("inputfile");
- }
-
- public boolean hasInputValues() {
- return hasOption("inputvalue");
- }
-
- public boolean hasLogFile() {
- return hasOption("logfile");
- }
-
- public boolean hasOption(String option) {
- return commandLine.hasOption(option);
- }
-
- public String inputDelimiter(String inputName) {
- String result = null;
- if (hasOption("inputdelimiter")) {
- String [] values = getOptionValues("inputdelimiter");
- for (int i=0;i<values.length;i+=2) {
- if (values[i].equals(inputName))
- {
- result=values[i+1];
- break;
- }
- }
- }
- return result;
- }
-
- @SuppressWarnings("static-access")
- private Options intitialiseOptions() {
- Option helpOption = new Option("help", "displays comprehensive help information");
-
- Option outputOption = OptionBuilder
- .withArgName("directory")
- .hasArg()
- .withDescription(
- "save outputs as files in directory, default "
- + "is to make a new directory workflowName_output")
- .create("outputdir");
-
- Option outputdocOption = OptionBuilder.withArgName("document").hasArg()
- .withDescription("save outputs to a new Baclava document")
- .create("outputdoc");
-
- Option logFileOption = OptionBuilder
- .withArgName("filename")
- .hasArg()
- .withDescription(
- "the logfile to which more verbose logging will be written to")
- .create("logfile");
-
- Option inputdocOption = OptionBuilder.withArgName("document").hasArg()
- .withDescription("load inputs from a Baclava document").create(
- "inputdoc");
-
- Option inputFileOption = OptionBuilder
- .withArgName("inputname filename").hasArgs(2)
- .withValueSeparator(' ').withDescription(
- "load the named input from file or URL").create(
- "inputfile");
-
- Option inputValueOption = OptionBuilder.withArgName("inputname value")
- .hasArgs(2).withValueSeparator(' ').withDescription(
- "directly use the value for the named input").create(
- "inputvalue");
-
- Option inputDelimiterOption = OptionBuilder
- .withArgName("inputname delimiter")
- .hasArgs(2)
- .withValueSeparator(' ')
- .withDescription(
- "causes an inputvalue or inputfile to be split into a list according to the delimiter. The associated workflow input must be expected to receive a list")
- .create("inputdelimiter");
-
- Option dbProperties = OptionBuilder.withArgName("filename").hasArg()
- .withDescription(
- "loads a properties file to configure the database")
- .create("dbproperties");
-
- Option port = OptionBuilder
- .withArgName("portnumber")
- .hasArg()
- .withDescription(
- "the port that the database is running on. If set requested to start its own internal server, this is the start port that will be used.")
- .create("port");
-
- Option embedded = new Option("embedded",
- "connects to an embedded Derby database. This can prevent mulitple invocations");
- Option clientserver = new Option("clientserver",
- "connects as a client to a derby server instance.");
- Option inMemOption = new Option(
- "inmemory",
- "runs the workflow with data stored in-memory rather than in a database. This can give performance inprovements, at the cost of overall memory usage");
- Option startDB = new Option("startdb",
- "automatically starts an internal Derby database server.");
- Option provenance = new Option("provenance",
- "generates provenance information and stores it in the database.");
-
- Options options = new Options();
- options.addOption(helpOption);
- options.addOption(inputFileOption);
- options.addOption(inputValueOption);
- options.addOption(inputDelimiterOption);
- options.addOption(inputdocOption);
- options.addOption(outputOption);
- options.addOption(outputdocOption);
- options.addOption(inMemOption);
- options.addOption(embedded);
- options.addOption(clientserver);
- options.addOption(dbProperties);
- options.addOption(port);
- options.addOption(startDB);
- options.addOption(provenance);
- options.addOption(logFileOption);
-
- return options;
-
- }
-
- public boolean isClientServer() {
- return hasOption("clientserver");
- }
-
- public boolean isEmbedded() {
- return hasOption("embedded");
- }
-
- public boolean isInMemory() {
- return hasOption("inmemory");
- }
-
- private CommandLine processArgs(String[] args) {
- CommandLineParser parser = new GnuParser();
- CommandLine line = null;
- try {
- // parse the command line arguments
- line = parser.parse(options, args);
- } catch (ParseException exp) {
- // oops, something went wrong
- System.err.println("Parsing failed. Reason: " + exp.getMessage());
- System.exit(1);
- }
- return line;
- }
-
- /**
- * Save the results to a directory if -output has been explicitly defined,
- * and/or if -outputdoc hasn't been defined
- *
- * @return boolean
- */
- public boolean saveResultsToDirectory() {
- return (options.hasOption("outputdir") || !options
- .hasOption("outputdoc"));
- }
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/META-INF/services/net.sf.taverna.raven.launcher.Launchable b/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/META-INF/services/net.sf.taverna.raven.launcher.Launchable
deleted file mode 100644
index 1314920..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/META-INF/services/net.sf.taverna.raven.launcher.Launchable
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.commandline.CommandLineLauncher
\ No newline at end of file
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/cl-log4j.properties b/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/cl-log4j.properties
deleted file mode 100644
index 8c17461..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/cl-log4j.properties
+++ /dev/null
@@ -1,27 +0,0 @@
-# By default, WARN (our external libraries)
-log4j.rootLogger=INFO, CONSOLE
-
-# Log INFO from anything Taverna
-log4j.logger.net.sf.taverna.t2=INFO
-
-
-
-# Restrict logging from classes that like to complain a lot
-log4j.logger.net.sf.taverna.raven=WARN
-log4j.logger.net.sf.taverna.t2.workbench.configuration.ConfigurationManager=WARN
-log4j.logger.net.sf.taverna.t2.workbench.views.graph.GraphViewComponent=WARN
-log4j.logger.net.sf.taverna.t2.workbench.ui.impl.WorkbenchPerspectives=WARN
-log4j.logger.net.sf.taverna.t2.workbench.ui.impl.DataflowEditsListener=WARN
-log4j.logger.net.sf.taverna.t2.workbench.ui.views.contextualviews.annotated.AnnotatedContextualView=WARN
-log4j.logger.net.sf.taverna.t2.workbench.ui.workflowview.WorkflowView=WARN
-log4j.logger.net.sf.taverna.t2.ui.menu.impl.MenuManagerImpl=ERROR
-
-log4j.logger.org.apache.commons.httpclient=ERROR
-
-
-# Default output to console is restrictive
-log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
-log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
-log4j.appender.CONSOLE.layout.ConversionPattern=%-5p %d{ISO8601} (%c:%L) - %m%n
-# Output WARN and above to console -
-log4j.appender.CONSOLE.Threshold=ERROR
\ No newline at end of file
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/database-defaults.properties b/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/database-defaults.properties
deleted file mode 100644
index 1080856..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/database-defaults.properties
+++ /dev/null
@@ -1,11 +0,0 @@
-in_memory = true
-provenance = false
-connector = derby
-port = 1527
-dialect = org.hibernate.dialect.DerbyDialect
-start_derby = false
-pool_max_active = 50
-pool_min_idle = 50
-pool_max_idle = 10
-driver = org.apache.derby.jdbc.EmbeddedDriver
-jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
\ No newline at end of file
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/help.txt b/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/help.txt
deleted file mode 100644
index 580ee42..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/help.txt
+++ /dev/null
@@ -1,73 +0,0 @@
-By default, the workflow is executed using the -inmemory option, and the
-results are written out to a directory named after the workflow name.
-
-If this directory already exists then an new directory is created, and
-appended with _<n>, where n is incremented to the next available index.
-
-Results are written out to files named after the output port for that result.
-If a result is composed of lists, then a directory is created for the output
-port and individual list items are named after the list element index (with 1
-being the first index). The the output is the result of an error, the filename
-is appended with '.error'.
-
-You can provide your own output directory with the -outputdir option. There
-will be an error if the directory already exists.
-
-You can also record your results to a Baclava document using -outputdoc
-option. The document will be overwritten if it already exists.
-
-Inputs can be provided in three ways. Both -inputfile and -inputvalue options
-can be used together; -inputdoc option must be used on its own. -inputfile and
--inputvalue options both take two additional arguments, the name of the port
-for the input, and either a file containing the input data, or the input value
-itself respectively.
-
-If one of more of you workflow inputs is described as a list, you can create a
-list by using the -inputdelimiter option, which may be used with either
--inputfile or -inputvalue. This option takes two parameters - an input name
-and the delimiter by which to split the input into a list.
-
-The delimiter may be a simple character, such as a comma or a new-line
-character, or a regular expression. The input string, or file, will then be
-converted into a list being split by the delimiter specified. Make sure to
-put the delimiter character in quotes as it may be interpreted by the shell
-as a special character, e.g. ;.
-
-If a list of greater depth (i.e. a list or lists or deeper) is required then
-you will need to use the -inputdoc option. However, if you provide an input
-of lower depth to that required, then it will automatically be wrapped in one
-or more lists up to the required depth. Providing an input of greater depth
-than that required will result in an error.
-
-If a workflow has a high memory requirement, then it may be better to run it
-using a database to store data rather than storing it in memory, which is the
-default option. There are three options for using a database:
-
--embedded option, runs with an embedded database. This is slightly faster than
-the -clientserver option (below), but has the limitation that only one
-executeworkflow script may be executed simultaneously.
-
--clientserver option allows the workflow to be executed backed by the database
-running as a server. By default a database is not started for you, but may be
-started using -startdb option.
-
--startdb option starts a database. It may be used without providing a workflow
-to allow a database to be started separately, allowing multiple simultaneous
-executeworkflow script runs.
-
-More advanced database configurations can be specified using -dbproperties
-option, allowing you to take full control over the database used. This takes a
-second argument, the filename of the propeties file, for which the following
-example contains the default settings used:
-
-in_memory = true
-provenance = false
-connector = derby
-port = 1527
-dialect = org.hibernate.dialect.DerbyDialect
-start_derby = false
-driver = org.apache.derby.jdbc.EmbeddedDriver
-jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
-
-Note that when using -dbproperties together with other options, the other
-options take precedence.
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestCommandLineOptionsHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestCommandLineOptionsHandler.java
deleted file mode 100644
index dddeba6..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestCommandLineOptionsHandler.java
+++ /dev/null
@@ -1,266 +0,0 @@
-package net.sf.taverna.t2.commandline;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-
-import org.junit.Test;
-
-public class TestCommandLineOptionsHandler {
-
- @Test
- public void testWorkflowName() throws Exception {
- CommandLineOptions handler = new CommandLineOptions(
- new String[] { "myworkflow.t2flow" });
- assertEquals("myworkflow.t2flow", handler.getWorkflow());
- }
-
- @Test
- public void shouldShowHelp() throws Exception {
- CommandLineOptions options = new CommandLineOptions(
- new String[] { "-help" });
- assertTrue(options.askedForHelp());
- options = new CommandLineOptions(
- new String[] {});
- assertTrue(options.askedForHelp());
- options = new CommandLineOptions(new String[] { "myworkflow.t2flow" });
- assertFalse(options.askedForHelp());
- }
-
- @Test
- public void getWorkflow() throws Exception {
- CommandLineOptions options = new CommandLineOptions(
- new String[] { "-help" });
- assertNull(options.getWorkflow());
- options = new CommandLineOptions(new String[] { "myworkflow.t2flow" });
- assertEquals("myworkflow.t2flow", options.getWorkflow());
- }
-
- @Test(expected = InvalidOptionException.class)
- public void cannotProvideInputFileAndInputDoc() throws Exception {
- new CommandLineOptions(new String[] { "-inputfile", "fred", "fred.txt",
- "-inputdoc", "myworkflow.t2flow" });
- }
-
- @Test(expected = InvalidOptionException.class)
- public void cannotProvideInputValueAndInputDoc() throws Exception {
- new CommandLineOptions(new String[] { "-inputvalue", "fred", "fred.txt",
- "-inputdoc", "myworkflow.t2flow" });
- }
-
- @Test
- public void canProvideInputValueAndFileTogether() throws Exception {
- //should not be an error
- new CommandLineOptions(new String[] { "-inputvalue", "fred", "abc",
- "-inputfile","fred2","fred2.txt","myworkflow.t2flow" });
- }
-
- @Test
- public void getInputs() throws Exception {
- CommandLineOptions options = new CommandLineOptions(new String[] {
- "-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
- assertEquals(2, options.getInputFiles().length);
- assertEquals("fred", options.getInputFiles()[0]);
- assertEquals("fred.txt", options.getInputFiles()[1]);
-
- options = new CommandLineOptions(new String[] { "-inputfile", "fred",
- "fred.txt", "-inputfile", "fred2", "fred2.txt",
- "myworkflow.t2flow" });
- assertEquals(4, options.getInputFiles().length);
- assertEquals("fred", options.getInputFiles()[0]);
- assertEquals("fred.txt", options.getInputFiles()[1]);
- assertEquals("fred2", options.getInputFiles()[2]);
- assertEquals("fred2.txt", options.getInputFiles()[3]);
-
- options = new CommandLineOptions(new String[] { "myworkflow.t2flow" });
- assertNotNull(options.getInputFiles());
- assertEquals(0, options.getInputFiles().length);
-
- }
-
- @Test
- public void hasInputValue() throws Exception {
- CommandLineOptions options = new CommandLineOptions(new String[] {
- "-inputvalue", "fred", "abc", "myworkflow.t2flow" });
- assertTrue(options.hasInputValues());
-
- options = new CommandLineOptions(new String[] { "myworkflow.t2flow" });
- assertFalse(options.hasInputValues());
- }
-
- @Test
- public void getInputValues() throws Exception {
- CommandLineOptions options = new CommandLineOptions(new String[] {
- "-inputvalue", "fred", "abc", "myworkflow.t2flow" });
- assertEquals(2, options.getInputValues().length);
-
- options = new CommandLineOptions(new String[] { "myworkflow.t2flow" });
- assertNotNull(options.getInputValues());
- assertEquals(0,options.getInputValues().length);
- }
-
- @Test
- public void hasInputs() throws Exception {
- CommandLineOptions options = new CommandLineOptions(new String[] {
- "-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
- assertTrue(options.hasInputFiles());
-
- options = new CommandLineOptions(new String[] { "myworkflow.t2flow" });
- assertFalse(options.hasInputFiles());
- }
-
- @Test
- public void noWorkflowNameButStartDB() throws Exception {
- // should not throw an error
- CommandLineOptions options = new CommandLineOptions(
- new String[] { "-startdb" });
- assertTrue(options.getStartDatabase());
- assertTrue(options.getStartDatabaseOnly());
- }
-
- @Test
- public void workflowNameAndStartDB() throws Exception {
- // should not throw an error
- CommandLineOptions options = new CommandLineOptions(new String[] {
- "-startdb", "myworkflow.t2flow" });
- assertTrue(options.getStartDatabase());
- assertFalse(options.getStartDatabaseOnly());
- }
-
- @Test(expected = InvalidOptionException.class)
- public void provenanceButNoDatabase() throws Exception {
- new CommandLineOptions(new String[] { "-provenance",
- "myworkflow.t2flow" });
- }
-
- @Test(expected = InvalidOptionException.class)
- public void provenanceButNoDatabase2() throws Exception {
- new CommandLineOptions(new String[] { "-provenance", "-inmemory",
- "myworkflow.t2flow" });
- }
-
- @Test
- public void provenanceDatabase() throws Exception {
- // should be no errors
- new CommandLineOptions(new String[] { "-provenance", "-embedded",
- "myworkflow.t2flow" });
- new CommandLineOptions(new String[] { "-provenance", "-clientserver",
- "myworkflow.t2flow" });
- new CommandLineOptions(new String[] { "-provenance", "-dbproperties",
- "dbproperties.properties", "myworkflow.t2flow" });
- }
-
- @Test
- public void testHasInputDelimiter() throws Exception {
- CommandLineOptions options = new CommandLineOptions(new String[] {
- "-inputvalue","in1","1,2,3","-inputdelimiter","in1",",","-inputdelimiter","in2",",","myworkflow.t2flow" });
- assertTrue(options.hasDelimiterFor("in1"));
- assertTrue(options.hasDelimiterFor("in2"));
- assertFalse(options.hasDelimiterFor("in3"));
- }
-
- @Test(expected = InvalidOptionException.class)
- public void testInputDelimiterInvalidWithInputDoc() throws Exception {
- new CommandLineOptions(new String[] {
- "-inputdoc","doc.xml","-inputdelimiter","in1",",","myworkflow.t2flow" });
- }
-
-
- @Test
- public void testInputDelimiter() throws Exception {
- CommandLineOptions options = new CommandLineOptions(new String[] {
- "-inputvalue","in1","1,2,3","-inputdelimiter","in1",",","-inputdelimiter","in2","!","myworkflow.t2flow" });
- assertEquals(",",options.inputDelimiter("in1"));
- assertEquals("!",options.inputDelimiter("in2"));
- assertNull(options.inputDelimiter("in3"));
- }
-
- @Test
- public void testInMemory() throws Exception {
- CommandLineOptions handler = new CommandLineOptions(new String[] {
- "-inmemory", "myworkflow.t2flow" });
- assertTrue(handler.hasOption("inmemory"));
- }
-
- @Test
- public void testEmbedded() throws Exception {
- CommandLineOptions handler = new CommandLineOptions(new String[] {
- "-embedded", "myworkflow.t2flow" });
- assertTrue(handler.hasOption("embedded"));
- }
-
- @Test
- public void testClientServer() throws Exception {
- CommandLineOptions handler = new CommandLineOptions(new String[] {
- "-clientserver", "myworkflow.t2flow" });
- assertTrue(handler.hasOption("clientserver"));
- }
-
- @Test(expected = InvalidOptionException.class)
- public void testInvalidEmbeddedAndClientServer() throws Exception {
- new CommandLineOptions(new String[] { "-clientserver", "-embedded",
- "myworkflow.t2flow" });
- }
-
- @Test(expected = InvalidOptionException.class)
- public void testInvalidEmbeddedAndMemory() throws Exception {
- new CommandLineOptions(new String[] { "-embedded", "-inmemory",
- "myworkflow.t2flow" });
- }
-
- @Test(expected = InvalidOptionException.class)
- public void testInvalidClientServerAndInMemory() throws Exception {
- new CommandLineOptions(new String[] { "-clientserver", "-inmemory",
- "myworkflow.t2flow" });
- }
-
- @Test
- public void isInMemory() throws Exception {
- CommandLineOptions options = new CommandLineOptions(new String[] {
- "-inmemory", "myworkflow.t2flow" });
-
- assertTrue(options.isInMemory());
- assertFalse(options.isClientServer());
- assertFalse(options.isEmbedded());
- }
-
- @Test
- public void isClientServer() throws Exception {
- CommandLineOptions options = new CommandLineOptions(new String[] {
- "-clientserver", "myworkflow.t2flow" });
-
- assertTrue(options.isClientServer());
- assertFalse(options.isInMemory());
- assertFalse(options.isEmbedded());
- }
-
- @Test
- public void hasLogFile() throws Exception {
- CommandLineOptions options = new CommandLineOptions(new String[] {
- "-logfile","/tmp/logging", "myworkflow.t2flow" });
-
- assertTrue(options.hasLogFile());
- assertEquals("/tmp/logging", options.getLogFile());
- }
-
- @Test(expected = InvalidOptionException.class)
- public void hasLogFileNotValidWithoutWorkflow() throws Exception{
- CommandLineOptions options = new CommandLineOptions(new String[] {
- "-logfile","/tmp/logging"});
- }
-
- @Test
- public void isEmbedded() throws Exception {
- CommandLineOptions options = new CommandLineOptions(new String[] {
- "-embedded", "myworkflow.t2flow" });
-
- assertTrue(options.isEmbedded());
- assertFalse(options.isInMemory());
- assertFalse(options.isClientServer());
- }
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestDatabaseConfigurationHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestDatabaseConfigurationHandler.java
deleted file mode 100644
index 555a1a6..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestDatabaseConfigurationHandler.java
+++ /dev/null
@@ -1,20 +0,0 @@
-package net.sf.taverna.t2.commandline;
-
-import static org.junit.Assert.assertEquals;
-import net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-import net.sf.taverna.t2.workbench.reference.config.DataManagementConfiguration;
-
-import org.junit.Test;
-
-public class TestDatabaseConfigurationHandler {
-
- @Test
- public void testDefaults() throws Exception {
- CommandLineOptions opts = new CommandLineOptions(new String[]{"myworkflow.t2flow"});
- DatabaseConfigurationHandler handler = new DatabaseConfigurationHandler(opts);
- handler.configureDatabase();
- assertEquals("org.apache.derby.jdbc.EmbeddedDriver", DataManagementConfiguration.getInstance().getDriverClassName());
- assertEquals(false, DataManagementConfiguration.getInstance().getStartInternalDerbyServer());
- }
-}
