Revert "temporarily empty repository"
This reverts commit d57ed128cd36e12f5cc1e3304f67bd5c10f0735c.
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..ebe0e5b
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,24 @@
+# ignore project files #
+.classpath
+.project
+.settings/
+catalog-v001.xml
+
+# ignore target files #
+target/
+bin/
+build/
+dist/
+apidoc/
+*.swp
+
+# ignore svn files if there
+.svn
+
+# ignore log files #
+*.log
+/logs/*
+*/logs/*
+
+
+
diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..dff5f3a
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1 @@
+language: java
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..bcd653c
--- /dev/null
+++ b/README.md
@@ -0,0 +1,6 @@
+# Apache Taverna Commandline
+
+[](https://travis-ci.org/taverna-incubator/incubator-taverna-commandline)
+
+After building, see taverna-commandline-product/target/apache-taverna-commandline-3.1.0-incubating-SNAPSHOT-dev/apache-taverna-commandline-3.1.0-incubating-SNAPSHOT/ or equivalent
+
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..0355623
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,40 @@
+<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/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>1-incubating-SNAPSHOT</version>
+ </parent>
+ <groupId>org.apache.taverna.commandline</groupId>
+ <artifactId>taverna-commandline</artifactId>
+ <version>3.1.0.incubating-SNAPSHOT</version>
+ <packaging>pom</packaging>
+ <name>Apache Taverna Command Line</name>
+ <properties>
+ <taverna.language.version>0.15.0-incubating-SNAPSHOT</taverna.language.version>
+ <taverna.osgi.version>0.2.0-incubating-SNAPSHOT</taverna.osgi.version>
+ <taverna.engine.version>3.1.0-incubating-SNAPSHOT</taverna.engine.version>
+ <taverna.commonactivities.version>2.1.0-incubating-SNAPSHOT</taverna.commonactivities.version>
+ </properties>
+ <modules>
+ <module>taverna-commandline-api</module>
+ <module>taverna-commandline-common</module>
+ <module>taverna-commandline-launcher</module>
+ <module>taverna-commandline-product</module>
+ <!--
+ <module>taverna-commandline-tests</module>
+ -->
+ </modules>
+ <repositories>
+ <repository>
+ <id>taverna-incubating</id>
+ <name>Apache Taverna incubating Repository</name>
+ <url>http://repository.mygrid.org.uk/artifactory/incubator-snapshot-local/</url>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ </repository>
+ </repositories>
+</project>
diff --git a/taverna-commandline-api/pom.xml b/taverna-commandline-api/pom.xml
new file mode 100644
index 0000000..98ae247
--- /dev/null
+++ b/taverna-commandline-api/pom.xml
@@ -0,0 +1,12 @@
+<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/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.taverna.commandline</groupId>
+ <artifactId>taverna-commandline</artifactId>
+ <version>3.1.0.incubating-SNAPSHOT</version>
+ </parent>
+ <packaging>bundle</packaging>
+ <artifactId>taverna-commandline-api</artifactId>
+ <name>Apache Taverna Commandline API</name>
+</project>
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ArgumentsParsingException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ArgumentsParsingException.java
new file mode 100644
index 0000000..eb21cd7
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ArgumentsParsingException.java
@@ -0,0 +1,34 @@
+/*******************************************************************************
+ * 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;
+
+@SuppressWarnings("serial")
+public class ArgumentsParsingException extends Exception {
+
+ public ArgumentsParsingException(String message) {
+ super(message);
+ }
+
+ public ArgumentsParsingException(String message, Throwable cause) {
+ super(message, cause);
+ }
+}
+
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/CommandLineMasterPasswordException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/CommandLineMasterPasswordException.java
new file mode 100644
index 0000000..0714275
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/CommandLineMasterPasswordException.java
@@ -0,0 +1,34 @@
+/*******************************************************************************
+ * 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;
+
+@SuppressWarnings("serial")
+public class CommandLineMasterPasswordException extends Exception {
+
+ public CommandLineMasterPasswordException(String message) {
+ super(message);
+ }
+
+ public CommandLineMasterPasswordException(String message, Throwable cause) {
+ super(message, cause);
+ }
+}
+
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java
new file mode 100644
index 0000000..616fb70
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java
@@ -0,0 +1,43 @@
+/*******************************************************************************
+ * 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-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java
new file mode 100644
index 0000000..da03891
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java
@@ -0,0 +1,61 @@
+/*******************************************************************************
+ * 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();
+
+ if (expectedInputNames != null){
+ result += "\n" + expectedInputNames.size() + " inputs were expected";
+ if (expectedInputNames.size()>0) result += " which are:\n";
+ for (String name : expectedInputNames) {
+ result += "'"+name+"' ";
+ }
+ }
+
+ if (providedInputNames != null){
+ 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-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java
new file mode 100644
index 0000000..c07a19f
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java
@@ -0,0 +1,30 @@
+/*******************************************************************************
+ * 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-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java
new file mode 100644
index 0000000..664ab71
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java
@@ -0,0 +1,44 @@
+/*******************************************************************************
+ * 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-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java
new file mode 100644
index 0000000..226d6ea
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java
@@ -0,0 +1,35 @@
+/*******************************************************************************
+ * 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-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/SaveResultsException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/SaveResultsException.java
new file mode 100644
index 0000000..7ad460d
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/SaveResultsException.java
@@ -0,0 +1,34 @@
+/*******************************************************************************
+ * 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;
+
+@SuppressWarnings("serial")
+public class SaveResultsException extends Exception {
+
+ public SaveResultsException(String message) {
+ super(message);
+ }
+
+ public SaveResultsException(String message, Throwable cause) {
+ super(message, cause);
+ }
+}
+
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
new file mode 100644
index 0000000..dd8e20f
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
@@ -0,0 +1,119 @@
+/*******************************************************************************
+ * Copyright (C) 2013 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 net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
+
+/**
+ *
+ *
+ * @author David Withers
+ */
+public interface CommandLineOptions {
+
+ public static final String CREDENTIAL_MANAGER_DIR_OPTION = "cmdir";
+ public static final String CREDENTIAL_MANAGER_PASSWORD_OPTION = "cmpassword";
+
+ public boolean askedForHelp();
+
+ public boolean isProvenanceEnabled();
+
+ public void displayHelp();
+
+ public void displayHelp(boolean showFullText);
+
+ public String[] getArgs();
+
+ /**
+ *
+ * @return the port that the database should run on
+ */
+ public String getDatabasePort();
+
+ /**
+ *
+ * @return a path to a properties file that contains database configuration
+ * settings
+ */
+ public String getDatabaseProperties();
+
+ /**
+ * 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();
+
+ public String[] getInputValues();
+
+ public String getLogFile();
+
+ /**
+ *
+ * @return the directory to write the results to
+ */
+ public String getOutputDirectory();
+
+ public boolean getStartDatabase();
+
+ /**
+ * @return the directory with Credential Manager's files
+ */
+ public String getCredentialManagerDir();
+
+ public boolean getStartDatabaseOnly() throws InvalidOptionException;
+
+ public String getWorkflow() throws InvalidOptionException;
+
+ public boolean hasDelimiterFor(String inputName);
+
+ public boolean hasInputFiles();
+
+ public boolean hasInputValues();
+
+ public boolean hasLogFile();
+
+ public boolean hasOption(String option);
+
+ public boolean hasSaveResultsToBundle() ;
+
+ public String inputDelimiter(String inputName);
+
+ public boolean isClientServer();
+
+ public boolean isEmbedded();
+
+ public boolean isInMemory();
+
+ /**
+ * Save the results to a directory if -outputdir has been explicitly defined,
+ * or if -outputdoc has not been defined.
+ *
+ * @return boolean
+ */
+ public boolean saveResultsToDirectory();
+
+ public String saveResultsToBundle();
+
+}
\ No newline at end of file
diff --git a/taverna-commandline-common/pom.xml b/taverna-commandline-common/pom.xml
new file mode 100644
index 0000000..17c6a42
--- /dev/null
+++ b/taverna-commandline-common/pom.xml
@@ -0,0 +1,88 @@
+<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>org.apache.taverna.commandline</groupId>
+ <artifactId>taverna-commandline</artifactId>
+ <version>3.1.0.incubating-SNAPSHOT</version>
+ </parent>
+ <artifactId>taverna-commandline-common</artifactId>
+ <packaging>bundle</packaging>
+ <name>Apache Taverna Commandline Common</name>
+ <dependencies>
+ <dependency>
+ <groupId>${project.parent.groupId}</groupId>
+ <artifactId>taverna-commandline-api</artifactId>
+ <version>${project.parent.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-run-api</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-database-configuration-api</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-api</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-validation</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-validation-structural</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-validation-correctness</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-databundle</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+
+<!--
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>provenanceconnector</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ -->
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-credential-manager</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>${commons.io.version}</version>
+ </dependency>
+
+ <!-- <dependency> <groupId>uk.org.mygrid.resources.mimeutil</groupId> <artifactId>mime-util</artifactId>
+ <version>2.1.2-2</version> </dependency> -->
+
+ <!-- TEST -->
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+ </dependencies>
+
+</project>
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineMasterPasswordProvider.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineMasterPasswordProvider.java
new file mode 100644
index 0000000..048e582
--- /dev/null
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineMasterPasswordProvider.java
@@ -0,0 +1,184 @@
+/*******************************************************************************
+ * Copyright (C) 2008-2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline;
+
+import java.io.BufferedReader;
+import java.io.Console;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+
+import net.sf.taverna.t2.commandline.exceptions.CommandLineMasterPasswordException;
+import net.sf.taverna.t2.commandline.options.CommandLineOptions;
+import net.sf.taverna.t2.security.credentialmanager.MasterPasswordProvider;
+
+import org.apache.log4j.Logger;
+
+/**
+ * An implementation of {@link MasterPasswordProvider} that reads Credential Manager's
+ * master password from stdin (pipe or terminal) is -cmpassword option is present in command
+ * line arguments. Otherwise it tries to read it from a special file password.txt in a special
+ * directory specified by -cmdir option, if present.
+ *
+ * @author Alex Nenadic
+ */
+public class CommandLineMasterPasswordProvider implements MasterPasswordProvider {
+
+ private static final String CREDENTIAL_MANAGER_MASTER_PASSWORD_OPTION = "cmpassword";
+ private static final String CREDENTIAL_MANAGER_DIRECTORY_OPTION = "cmdir";
+
+ private static Logger logger = Logger.getLogger(CommandLineMasterPasswordProvider.class);
+
+ private String masterPassword = null;
+ private int priority = 200;
+
+ private boolean finishedReadingPassword = false;
+ private final CommandLineOptions commandLineOptions;
+
+ public CommandLineMasterPasswordProvider(CommandLineOptions commandLineOptions) {
+ this.commandLineOptions = commandLineOptions;
+ }
+
+ @Override
+ public String getMasterPassword(boolean firstTime) {
+ if (!finishedReadingPassword) {
+ // -cmpassword option was present in the command line arguments
+ if (commandLineOptions.hasOption(CREDENTIAL_MANAGER_MASTER_PASSWORD_OPTION)) {
+ // Try to read the password from stdin (terminal or pipe)
+ try {
+ masterPassword = getCredentialManagerPasswordFromStdin();
+ } catch (CommandLineMasterPasswordException e) {
+ masterPassword = null;
+ }
+ }
+ // -cmpassword option was not present in the command line arguments
+ // and -cmdir option was there - try to get the master password from
+ // the "special" password file password.txt inside the Cred. Manager directory.
+ else {
+ if (commandLineOptions.hasOption(CREDENTIAL_MANAGER_DIRECTORY_OPTION)) {
+ // Try to read the password from a special file located in
+ // Credential Manager directory (if the dir was not null)
+ try {
+ masterPassword = getCredentialManagerPasswordFromFile();
+ } catch (CommandLineMasterPasswordException ex) {
+ masterPassword = null;
+ }
+ }
+ }
+ finishedReadingPassword = true; // we do not want to attempt to read from stdin several
+ // times
+ }
+ return masterPassword;
+ }
+
+ public void setMasterPassword(String masterPassword) {
+ this.masterPassword = masterPassword;
+ finishedReadingPassword = true;
+ }
+
+ @Override
+ public int getProviderPriority() {
+ return priority;
+ }
+
+ private String getCredentialManagerPasswordFromStdin()
+ throws CommandLineMasterPasswordException {
+
+ String password = null;
+
+ Console console = System.console();
+
+ if (console == null) { // password is being piped in, not entered in the terminal by user
+ BufferedReader buffReader = null;
+ try {
+ buffReader = new BufferedReader(new InputStreamReader(System.in));
+ password = buffReader.readLine();
+ } catch (IOException ex) {
+ // For some reason the error of the exception thrown
+ // does not get printed from the Launcher so print it here as
+ // well as it gives more clue as to what is going wrong.
+ logger.error(
+ "An error occured while trying to read Credential Manager's password that was piped in: "
+ + ex.getMessage(), ex);
+ throw new CommandLineMasterPasswordException(
+ "An error occured while trying to read Credential Manager's password that was piped in: "
+ + ex.getMessage(), ex);
+ } finally {
+ try {
+ buffReader.close();
+ } catch (Exception ioe1) {
+ // Ignore
+ }
+ }
+ } else { // read the password from the terminal as entered by the user
+ try {
+ // Block until user enters password
+ char passwordArray[] = console.readPassword("Password for Credential Manager: ");
+ if (passwordArray != null) { // user did not abort input
+ password = new String(passwordArray);
+ } // else password will be null
+
+ } catch (Exception ex) {
+ // For some reason the error of the exception thrown
+ // does not get printed from the Launcher so print it here as
+ // well as it gives more clue as to what is going wrong.
+ logger.error(
+ "An error occured while trying to read Credential Manager's password from the terminal: "
+ + ex.getMessage(), ex);
+ throw new CommandLineMasterPasswordException(
+ "An error occured while trying to read Credential Manager's password from the terminal: "
+ + ex.getMessage(), ex);
+ }
+ }
+ return password;
+ }
+
+ private String getCredentialManagerPasswordFromFile() throws CommandLineMasterPasswordException {
+ String password = null;
+ if (commandLineOptions.hasOption(CREDENTIAL_MANAGER_DIRECTORY_OPTION)) {
+ String cmDir = commandLineOptions.getCredentialManagerDir();
+
+ File passwordFile = new File(cmDir, "password.txt");
+ BufferedReader buffReader = null;
+ try {
+ buffReader = new BufferedReader(new FileReader(passwordFile));
+ password = buffReader.readLine();
+ } catch (IOException ioe) {
+ // For some reason the error of the exception thrown
+ // does not get printed from the Launcher so print it here as
+ // well as it gives more clue as to what is going wrong.
+ logger.error("There was an error reading the Credential Manager password from "
+ + passwordFile.toString() + ": " + ioe.getMessage(), ioe);
+ throw new CommandLineMasterPasswordException(
+ "There was an error reading the Credential Manager password from "
+ + passwordFile.toString() + ": " + ioe.getMessage(), ioe);
+ } finally {
+ try {
+ buffReader.close();
+ } catch (Exception ioe1) {
+ // Ignore
+ }
+ }
+ }
+ return password;
+ }
+}
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
new file mode 100644
index 0000000..368527d
--- /dev/null
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
@@ -0,0 +1,437 @@
+/*******************************************************************************
+ * 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.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.sql.SQLException;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
+import javax.naming.NamingException;
+
+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.InputMismatchException;
+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.security.credentialmanager.CMException;
+import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
+
+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.purl.wf4ever.robundle.Bundle;
+
+import uk.org.taverna.configuration.database.DatabaseConfiguration;
+import uk.org.taverna.configuration.database.DatabaseManager;
+import uk.org.taverna.databundle.DataBundles;
+import uk.org.taverna.platform.execution.api.ExecutionEnvironment;
+import uk.org.taverna.platform.execution.api.InvalidExecutionIdException;
+import uk.org.taverna.platform.execution.api.InvalidWorkflowException;
+import uk.org.taverna.platform.report.State;
+import uk.org.taverna.platform.report.WorkflowReport;
+import uk.org.taverna.platform.run.api.InvalidRunIdException;
+import uk.org.taverna.platform.run.api.RunProfile;
+import uk.org.taverna.platform.run.api.RunProfileException;
+import uk.org.taverna.platform.run.api.RunService;
+import uk.org.taverna.platform.run.api.RunStateException;
+import uk.org.taverna.scufl2.api.common.NamedSet;
+import uk.org.taverna.scufl2.api.container.WorkflowBundle;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.io.ReaderException;
+import uk.org.taverna.scufl2.api.io.WorkflowBundleIO;
+import uk.org.taverna.scufl2.api.port.InputWorkflowPort;
+import uk.org.taverna.scufl2.api.port.OutputWorkflowPort;
+import uk.org.taverna.scufl2.validation.ValidationException;
+import uk.org.taverna.scufl2.validation.correctness.CorrectnessValidator;
+import uk.org.taverna.scufl2.validation.correctness.ReportCorrectnessValidationListener;
+import uk.org.taverna.scufl2.validation.structural.ReportStructuralValidationListener;
+import uk.org.taverna.scufl2.validation.structural.StructuralValidator;
+
+/**
+ * A utility class that wraps the process of executing a workflow, allowing workflows to be easily
+ * executed independently of the GUI.
+ *
+ * @author Stuart Owen
+ * @author Alex Nenadic
+ */
+public class CommandLineTool {
+ private static boolean BOOTSTRAP_LOGGING = false;
+ private static Logger logger = Logger.getLogger(CommandLineTool.class);
+
+ private RunService runService;
+ private CredentialManager credentialManager;
+ private CommandLineOptions commandLineOptions;
+ private WorkflowBundle workflowBundle;
+ private WorkflowBundleIO workflowBundleIO;
+ private DatabaseConfiguration databaseConfiguration;
+ private DatabaseManager databaseManager;
+
+ public void run() {
+ try {
+ if (BOOTSTRAP_LOGGING)
+ initialiseLogging();
+ int result = setupAndExecute();
+ System.exit(result);
+ } catch (InvalidOptionException | IOException | ReadInputException
+ | InvalidRunIdException | RunStateException
+ | InvalidExecutionIdException | OpenDataflowException
+ | RunProfileException e) {
+ error(e.getMessage());
+ } catch (CMException e) {
+ error("There was an error initializing Taverna's SSLSocketFactory from Credential Manager. "
+ + e.getMessage());
+ } catch (ReaderException e) {
+ error("There was an error reading the workflow: " + e.getMessage());
+ } catch (ValidationException e) {
+ error("There was an error validating the workflow: " + e.getMessage());
+ } catch (InvalidWorkflowException e) {
+ error("There was an error validating the workflow: " + e.getMessage());
+ } catch (DatabaseConfigurationException e) {
+ error("There was an error configuring the database: " + e.getMessage());
+ }
+ System.exit(1);
+ }
+
+ private void initialiseLogging() {
+ LogManager.resetConfiguration();
+
+ if (System.getProperty("log4j.configuration") == null) {
+ try {
+ PropertyConfigurator.configure(CommandLineTool.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 (commandLineOptions.hasLogFile()) {
+ RollingFileAppender appender;
+ try {
+
+ PatternLayout layout = new PatternLayout("%-5p %d{ISO8601} (%c:%L) - %m%n");
+ appender = new RollingFileAppender(layout, commandLineOptions.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 " + commandLineOptions.getLogFile());
+ }
+ }
+ }
+
+ public int setupAndExecute() throws InputMismatchException, InvalidOptionException,
+ CMException, OpenDataflowException, ReaderException, IOException, ValidationException,
+ ReadInputException, InvalidWorkflowException, RunProfileException,
+ InvalidRunIdException, RunStateException, InvalidExecutionIdException, DatabaseConfigurationException {
+
+ if (!commandLineOptions.askedForHelp()) {
+ setupDatabase(commandLineOptions);
+
+ if (commandLineOptions.getWorkflow() != null) {
+
+ /* Set context class loader to us,
+ * so that things such as JSON-LD caching of
+ * robundle works.
+ */
+
+ Thread.currentThread().setContextClassLoader(getClass().getClassLoader());
+
+
+ /*
+ * Initialise Credential Manager and SSL stuff quite early as
+ * parsing and validating the workflow may require it
+ */
+ String credentialManagerDirPath = commandLineOptions.getCredentialManagerDir();
+
+ /*
+ * If credentialManagerDirPath is null, the Credential Manager
+ * will be initialized from the default location in
+ * <TAVERNA_HOME>/security somewhere inside user's home
+ * directory. This should not be used when running command line
+ * tool on a server and the Credential Manager dir path should
+ * always be passed in as we do not want to store the security
+ * files in user's home directory on the server (we do not even
+ * know which user the command line tool will be running as).
+ */
+ if (credentialManagerDirPath != null) {
+ credentialManager.setConfigurationDirectoryPath(new File(
+ credentialManagerDirPath));
+ }
+
+ // Initialise the SSL stuff - set the SSLSocketFactory
+ // to use Taverna's Keystore and Truststore.
+ credentialManager.initializeSSL();
+
+ URL workflowURL = readWorkflowURL(commandLineOptions.getWorkflow());
+
+ workflowBundle = workflowBundleIO.readBundle(workflowURL, null);
+
+ logger.debug("Read the wf bundle");
+
+ validateWorkflowBundle(workflowBundle);
+ logger.debug("Validated the wf bundle");
+
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments();
+
+ ExecutionEnvironment executionEnvironment = null;
+
+ /*
+ * Find the right execution environment, e.g. local execution
+ * with the correct reference service based on command line
+ * options
+ */
+ while (executionEnvironments.iterator().hasNext()) {
+ // TODO Choose the right one
+ // take the fist one for now
+ executionEnvironment = executionEnvironments.iterator().next();
+ break;
+ }
+
+ logger.debug("Got the execution environment");
+
+ InputsHandler inputsHandler = new InputsHandler();
+ Map<String, InputWorkflowPort> portMap = new HashMap<String, InputWorkflowPort>();
+
+ Workflow workflow = workflowBundle.getMainWorkflow();
+
+ for (InputWorkflowPort port : workflow.getInputPorts()) {
+ portMap.put(port.getName(), port);
+ }
+ inputsHandler.checkProvidedInputs(portMap, commandLineOptions);
+ logger.debug("Checked inputs");
+
+ Bundle inputs = inputsHandler.registerInputs(portMap, commandLineOptions, null);
+ logger.debug("Registered inputs");
+
+ RunProfile runProfile = new RunProfile(executionEnvironment, workflowBundle, inputs);
+
+ String runId = runService.createRun(runProfile);
+
+ runService.start(runId);
+ logger.debug("Started wf run");
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+
+ while (!workflowFinished(report)) {
+ try {
+ Thread.sleep(500);
+ } catch (InterruptedException e) {
+ System.err.println("Interrupted while waiting for workflow to finish");
+ return 1;
+ }
+ }
+
+ NamedSet<OutputWorkflowPort> workflowOutputPorts = workflow.getOutputPorts();
+ if (!workflowOutputPorts.isEmpty()) {
+ File outputDir = null;
+
+ if (commandLineOptions.saveResultsToDirectory()) {
+ outputDir = determineOutputDir(commandLineOptions, workflowBundle.getName());
+ outputDir.mkdirs();
+ }
+
+ Path outputs = DataBundles.getOutputs(runService.getDataBundle(runId));
+
+ if (outputDir != null) {
+ SaveResultsHandler saveResultsHandler = new SaveResultsHandler(outputDir);
+
+ for (OutputWorkflowPort outputWorkflowPort : workflowOutputPorts) {
+ String workflowOutputPortName = outputWorkflowPort.getName();
+ Path output = DataBundles.getPort(outputs, workflowOutputPortName);
+ if (!DataBundles.isMissing(output)) {
+ saveResultsHandler.saveResultsForPort(workflowOutputPortName, output);
+ }
+ }
+ }
+ }
+ if (commandLineOptions.saveResultsToBundle() != null) {
+ Path bundlePath = Paths.get(commandLineOptions.saveResultsToBundle());
+ DataBundles.closeAndSaveBundle(runService.getDataBundle(runId), bundlePath);
+ System.out.println("Workflow Run Bundle saved to: " + bundlePath.toAbsolutePath());
+ } else {
+ System.out.println("Workflow Run Bundle: " + runService.getDataBundle(runId).getSource());
+ // For debugging we'll leave it in /tmp for now
+ runService.getDataBundle(runId).setDeleteOnClose(false);
+ DataBundles.closeBundle(runService.getDataBundle(runId));
+ }
+
+ if (report.getState().equals(State.FAILED)) {
+ System.out.println("Workflow failed - see report below.");
+ System.out.println(report);
+ } else if (report.getState().equals(State.COMPLETED)) {
+ System.out.println("Workflow completed.");
+ }
+
+ }
+ } else {
+ commandLineOptions.displayHelp();
+ }
+
+ // wait until user hits CTRL-C before exiting
+ if (commandLineOptions.getStartDatabaseOnly()) {
+ // FIXME: need to do this more gracefully.
+ while (true) {
+ try {
+ Thread.sleep(500);
+ } catch (InterruptedException e) {
+ return 0;
+ }
+ }
+ }
+
+ return 0;
+ }
+
+ private boolean workflowFinished(WorkflowReport report) {
+ State state = report.getState();
+ if (state == State.CANCELLED || state == State.COMPLETED || state == State.FAILED) {
+ return true;
+ }
+ return false;
+ }
+
+ protected void validateWorkflowBundle(WorkflowBundle workflowBundle) throws ValidationException {
+ CorrectnessValidator cv = new CorrectnessValidator();
+ ReportCorrectnessValidationListener rcvl = new ReportCorrectnessValidationListener();
+ cv.checkCorrectness(workflowBundle, true, rcvl);
+ if (rcvl.detectedProblems()) {
+ throw rcvl.getException();
+ }
+
+ StructuralValidator sv = new StructuralValidator();
+ ReportStructuralValidationListener rsvl = new ReportStructuralValidationListener();
+ sv.checkStructure(workflowBundle, rsvl);
+ if (rsvl.detectedProblems()) {
+ throw rcvl.getException();
+ }
+ }
+
+ private void setupDatabase(CommandLineOptions options)
+ throws DatabaseConfigurationException {
+ DatabaseConfigurationHandler dbHandler = new DatabaseConfigurationHandler(
+ options, databaseConfiguration, databaseManager);
+ dbHandler.configureDatabase();
+ try {
+ if (!options.isInMemory())
+ 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 File determineOutputDir(CommandLineOptions options, String dataflowName) {
+ File result = new File(dataflowName + "_output");
+ int x = 1;
+ while (result.exists()) {
+ result = new File(dataflowName + "_output_" + x);
+ x++;
+ }
+ System.out.println("Outputs will be saved to the directory: "
+ + result.getAbsolutePath());
+ return result;
+ }
+
+ protected void error(String msg) {
+ System.err.println(msg);
+ }
+
+ private URL readWorkflowURL(String workflowOption) throws OpenDataflowException {
+ try {
+ return new URL(new URL("file:"), workflowOption);
+ } catch (MalformedURLException e) {
+ throw new OpenDataflowException("The was an error processing the URL to the workflow: "
+ + e.getMessage(), e);
+ }
+ }
+
+ public void setCommandLineOptions(CommandLineOptions commandLineOptions){
+ this.commandLineOptions = commandLineOptions;
+ }
+
+ public void setRunService(RunService runService) {
+ this.runService = runService;
+ }
+
+ public void setCredentialManager(CredentialManager credentialManager) {
+ this.credentialManager = credentialManager;
+ }
+
+ public void setWorkflowBundleIO(WorkflowBundleIO workflowBundleIO) {
+ this.workflowBundleIO = workflowBundleIO;
+ }
+
+ /**
+ * Sets the databaseConfiguration.
+ *
+ * @param databaseConfiguration the new value of databaseConfiguration
+ */
+ public void setDatabaseConfiguration(DatabaseConfiguration databaseConfiguration) {
+ this.databaseConfiguration = databaseConfiguration;
+ }
+
+ /**
+ * Sets the databaseManager.
+ *
+ * @param databaseManager the new value of databaseManager
+ */
+ public void setDatabaseManager(DatabaseManager databaseManager) {
+ this.databaseManager = databaseManager;
+ }
+
+}
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java
new file mode 100644
index 0000000..46b6c92
--- /dev/null
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java
@@ -0,0 +1,154 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.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 org.apache.log4j.Logger;
+
+import uk.org.taverna.configuration.database.DatabaseConfiguration;
+import uk.org.taverna.configuration.database.DatabaseManager;
+
+/**
+ * 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 static Logger logger = Logger.getLogger(DatabaseConfigurationHandler.class);
+ private final CommandLineOptions options;
+ private final DatabaseConfiguration dbConfig;
+ private final DatabaseManager databaseManager;
+
+ public DatabaseConfigurationHandler(CommandLineOptions options, DatabaseConfiguration databaseConfiguration, DatabaseManager databaseManager) {
+ this.options = options;
+ this.dbConfig = databaseConfiguration;
+ this.databaseManager = databaseManager;
+ databaseConfiguration.disableAutoSave();
+ }
+
+ public void configureDatabase() throws DatabaseConfigurationException {
+ overrideDefaults();
+ useOptions();
+ if (dbConfig.getStartInternalDerbyServer()) {
+ databaseManager.startDerbyNetworkServer();
+ System.out.println("Started Derby Server on Port: "
+ + dbConfig.getCurrentPort());
+ }
+ }
+
+ public DatabaseConfiguration 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 = databaseManager.getConnection();
+ } 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.isProvenanceEnabled()) {
+ 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-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorValueHandler.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorValueHandler.java
new file mode 100644
index 0000000..44faea5
--- /dev/null
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorValueHandler.java
@@ -0,0 +1,72 @@
+/*******************************************************************************
+ * 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.nio.file.Path;
+import java.util.List;
+
+import javax.swing.tree.DefaultMutableTreeNode;
+
+import uk.org.taverna.databundle.DataBundles;
+import uk.org.taverna.databundle.ErrorDocument;
+
+/**
+ * Handles ErrorValues and transforming them into String representations
+ * that can be stored as a file, or within a Baclava document.
+ *
+ * @author Stuart Owen
+ * @author David Withers
+ */
+public class ErrorValueHandler {
+
+ /**
+ * Creates a string representation of the ErrorValue.
+ * @throws IOException
+ */
+ public static String buildErrorValueString(ErrorDocument errorValue) throws IOException {
+
+ String errDocumentString = errorValue.getMessage() + "\n";
+
+ String exceptionMessage = errorValue.getMessage();
+ if (exceptionMessage != null && !exceptionMessage.equals("")) {
+ DefaultMutableTreeNode exceptionMessageNode = new DefaultMutableTreeNode(
+ exceptionMessage);
+ errDocumentString += exceptionMessageNode + "\n";
+ errDocumentString += errorValue.getTrace();
+ }
+
+ List<Path> errorReferences = errorValue.getCausedBy();
+ if (!errorReferences.isEmpty()) {
+ errDocumentString += "Set of cause errors to follow." + "\n";
+ }
+ int errorCounter = 1;
+ for (Path cause : errorReferences) {
+ if (DataBundles.isError(cause)) {
+ errDocumentString += "ErrorValue " + (errorCounter++) + "\n";
+ errDocumentString += buildErrorValueString(DataBundles.getError(cause)) + "\n";
+ }
+ }
+
+ return errDocumentString;
+ }
+
+}
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
new file mode 100644
index 0000000..bcaa7fb
--- /dev/null
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
@@ -0,0 +1,280 @@
+/*******************************************************************************
+ * 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.IOException;
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.StandardOpenOption;
+import java.util.ArrayList;
+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 org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+import org.jdom.JDOMException;
+import org.purl.wf4ever.robundle.Bundle;
+
+import uk.org.taverna.databundle.DataBundles;
+import uk.org.taverna.scufl2.api.port.InputWorkflowPort;
+
+/**
+ * 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 Data 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, InputWorkflowPort> portMap,
+ CommandLineOptions options) throws InputMismatchException {
+ // we dont check for the document
+ Set<String> providedInputNames = new HashSet<String>();
+ for (int i = 0; i < options.getInputFiles().length; i += 2) {
+ // If it already contains a value for the input port, e.g
+ // two inputs are provided for the same port
+ if (providedInputNames.contains(options.getInputFiles()[i])) {
+ throw new InputMismatchException(
+ "Two input values were provided for the same input port "
+ + options.getInputFiles()[i] + ".", null, null);
+ }
+ providedInputNames.add(options.getInputFiles()[i]);
+ }
+
+ for (int i = 0; i < options.getInputValues().length; i += 2) {
+ // If it already contains a value for the input port, e.g
+ // two inputs are provided for the same port
+ if (providedInputNames.contains(options.getInputValues()[i])) {
+ throw new InputMismatchException(
+ "Two input values were provided for the same input port "
+ + options.getInputValues()[i] + ".", null, null);
+ }
+ 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 Bundle registerInputs(Map<String, InputWorkflowPort> portMap,
+ CommandLineOptions options, InvocationContext context) throws InvalidOptionException,
+ ReadInputException, IOException {
+ Bundle inputDataBundle;
+ inputDataBundle = DataBundles.createBundle();
+ inputDataBundle.setDeleteOnClose(false);
+ System.out.println("Bundle: " + inputDataBundle.getSource());
+
+ Path inputs = DataBundles.getInputs(inputDataBundle);
+
+ URL url;
+ try {
+ url = new URL("file:");
+ } catch (MalformedURLException e1) {
+ // Should never happen, but just in case:
+ 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()) {
+ regesterInputsFromFiles(portMap, options, inputs, url);
+ }
+
+ if (options.hasInputValues()) {
+ registerInputsFromValues(portMap, options, inputs);
+
+ }
+
+ return inputDataBundle;
+ }
+
+ private void registerInputsFromValues(Map<String, InputWorkflowPort> portMap,
+ CommandLineOptions options, Path inputs) throws InvalidOptionException {
+ String[] inputParams = options.getInputValues();
+ for (int i = 0; i < inputParams.length; i = i + 2) {
+ String inputName = inputParams[i];
+ try {
+ String inputValue = inputParams[i + 1];
+ InputWorkflowPort port = portMap.get(inputName);
+
+ if (port == null) {
+ throw new InvalidOptionException("Cannot find an input port named '"
+ + inputName + "'");
+ }
+
+ Path portPath = DataBundles.getPort(inputs, inputName);
+ if (options.hasDelimiterFor(inputName)) {
+ String delimiter = options.inputDelimiter(inputName);
+ Object value = checkForDepthMismatch(1, port.getDepth(), inputName,
+ inputValue.split(delimiter));
+ setValue(portPath, value);
+ } else {
+ Object value = checkForDepthMismatch(0, port.getDepth(), inputName, inputValue);
+ setValue(portPath, value);
+ }
+
+ } catch (IndexOutOfBoundsException e) {
+ throw new InvalidOptionException("Missing input value for input " + inputName);
+ } catch (IOException e) {
+ throw new InvalidOptionException("Error creating value for input " + inputName);
+ }
+ }
+ }
+
+ private void regesterInputsFromFiles(Map<String, InputWorkflowPort> portMap,
+ CommandLineOptions options, Path inputs, URL url) throws InvalidOptionException {
+ 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]);
+ InputWorkflowPort port = portMap.get(inputName);
+
+ if (port == null) {
+ throw new InvalidOptionException("Cannot find an input port named '"
+ + inputName + "'");
+ }
+
+ Path portPath = DataBundles.getPort(inputs, inputName);
+ if (options.hasDelimiterFor(inputName)) {
+ String delimiter = options.inputDelimiter(inputName);
+ Object value = IOUtils.toString(inputURL.openStream()).split(delimiter);
+ value = checkForDepthMismatch(1, port.getDepth(), inputName, value);
+ setValue(portPath, value);
+ } else {
+ Object value = IOUtils.toByteArray(inputURL.openStream());
+ value = checkForDepthMismatch(0, port.getDepth(), inputName, value);
+ setValue(portPath, value);
+ }
+ } 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());
+ }
+ }
+ }
+
+ private void setValue(Path port, Object userInput) throws IOException {
+ if (userInput instanceof File) {
+ DataBundles.setReference(port, ((File) userInput).toURI());
+ } else if (userInput instanceof URL) {
+ try {
+ DataBundles.setReference(port, ((URL) userInput).toURI());
+ } catch (URISyntaxException e) {
+ logger.warn(String.format("Error converting %1$s to URI", userInput), e);
+ }
+ } else if (userInput instanceof String) {
+ DataBundles.setStringValue(port, (String) userInput);
+ } else if (userInput instanceof byte[]) {
+ Files.write(port, (byte[]) userInput, StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.CREATE);
+ } else if (userInput instanceof List<?>) {
+ DataBundles.createList(port);
+ List<?> list = (List<?>) userInput;
+ for (Object object : list) {
+ setValue(DataBundles.newListItem(port), object);
+ }
+ } else {
+ logger.warn("Unknown input type : " + userInput.getClass().getName());
+ }
+ }
+
+ 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;
+ }
+ }
+
+ 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-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java
new file mode 100644
index 0000000..1df05c2
--- /dev/null
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java
@@ -0,0 +1,87 @@
+/*******************************************************************************
+ * 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.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+import java.util.Map;
+
+import uk.org.taverna.databundle.DataBundles;
+
+/**
+ * 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 BaclavaHandler
+ * @see CommandLineResultListener
+ */
+public class SaveResultsHandler {
+
+ private final File outputDirectory;
+
+ public SaveResultsHandler(File rootOutputDir) {
+ this.outputDirectory = rootOutputDir;
+ }
+
+ /**
+ * Given the Data on an output port, saves the data on a disk in the
+ * output directory.
+ *
+ * @param portName
+ * @param data
+ * @throws IOException
+ */
+ public void saveResultsForPort(String portName, Path data) throws IOException {
+ if (DataBundles.isList(data)) {
+ Path outputPath = outputDirectory.toPath().resolve(portName);
+ Files.createDirectories(outputPath);
+ saveList(DataBundles.getList(data), outputPath);
+ } else if (DataBundles.isError(data)) {
+ Files.copy(data, outputDirectory.toPath().resolve(portName + ".error"));
+ } else {
+ Files.copy(data, outputDirectory.toPath().resolve(portName));
+ }
+ }
+
+ private void saveList(List<Path> list, Path destination) throws IOException {
+ int index = 1;
+ for (Path data : list) {
+ if (data != null) {
+ if (DataBundles.isList(data)) {
+ Path outputPath = destination.resolve(String.valueOf(index));
+ Files.createDirectories(outputPath);
+ saveList(DataBundles.getList(data), outputPath);
+ } else if (DataBundles.isError(data)) {
+ Files.copy(data, destination.resolve(String.valueOf(index) + ".error"));
+ } else {
+ Files.copy(data, destination.resolve(String.valueOf(index)));
+ }
+ }
+ index++;
+ }
+ }
+
+}
diff --git a/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context-osgi.xml b/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context-osgi.xml
new file mode 100644
index 0000000..e7ae701
--- /dev/null
+++ b/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context-osgi.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+
+ <service ref="commandLineMasterPasswordProvider" interface="net.sf.taverna.t2.security.credentialmanager.MasterPasswordProvider" />
+
+ <reference id="commandLineOptions" interface="net.sf.taverna.t2.commandline.options.CommandLineOptions"/>
+ <reference id="runService" interface="uk.org.taverna.platform.run.api.RunService"/>
+ <reference id="credentialManager" interface="net.sf.taverna.t2.security.credentialmanager.CredentialManager" />
+ <reference id="databaseConfiguration" interface="uk.org.taverna.configuration.database.DatabaseConfiguration" />
+ <reference id="databaseManager" interface="uk.org.taverna.configuration.database.DatabaseManager" />
+
+ <reference id="workflowBundleIO" interface="uk.org.taverna.scufl2.api.io.WorkflowBundleIO" />
+ <reference id="t2flowWorkflowBundleReader" interface="uk.org.taverna.scufl2.api.io.WorkflowBundleReader" filter="(mediaType=application/vnd.taverna.t2flow+xml)"/>
+ <reference id="rdfXMLWorkflowBundleReader" interface="uk.org.taverna.scufl2.api.io.WorkflowBundleReader" filter="(org.springframework.osgi.bean.name=rdfXMLReader)"/>
+
+</beans:beans>
diff --git a/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context.xml b/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context.xml
new file mode 100644
index 0000000..52c0f29
--- /dev/null
+++ b/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="commandLineTool" class="net.sf.taverna.t2.commandline.CommandLineTool" init-method="run">
+ <property name="commandLineOptions" ref="commandLineOptions" />
+ <property name="runService" ref="runService" />
+ <property name="credentialManager" ref="credentialManager" />
+ <property name="workflowBundleIO" ref="workflowBundleIO" />
+ <property name="databaseConfiguration" ref="databaseConfiguration" />
+ <property name="databaseManager" ref="databaseManager" />
+ </bean>
+
+ <bean id="commandLineMasterPasswordProvider"
+ class="net.sf.taverna.t2.commandline.CommandLineMasterPasswordProvider">
+ <constructor-arg name="commandLineOptions"
+ ref="commandLineOptions" />
+ </bean>
+</beans>
diff --git a/taverna-commandline-common/src/main/resources/database-defaults.properties b/taverna-commandline-common/src/main/resources/database-defaults.properties
new file mode 100644
index 0000000..1080856
--- /dev/null
+++ b/taverna-commandline-common/src/main/resources/database-defaults.properties
@@ -0,0 +1,11 @@
+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-common/src/main/resources/help.txt b/taverna-commandline-common/src/main/resources/help.txt
new file mode 100644
index 0000000..fb082cc
--- /dev/null
+++ b/taverna-commandline-common/src/main/resources/help.txt
@@ -0,0 +1,87 @@
+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 a 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 your workflow inputs is a list, you can create a list
+input 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 properties file, for which the following
+example contains the default settings:
+
+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.
+
+-cmdir option lets you specify an absolute path to a directory where
+Credential Manager's files (keystore and truststore - containing user's
+credentials and trusted certificates for accessing secure services) are stored.
+If not specified and the workflow requires access to these files, Taverna will
+try to find them in the default location in <TAVERNA_HOME>/security somewhere
+inside user's home directory (depending on the platform).
+
+-cmpassword option can be used to tell Taverna to expect the password for the
+Credential Manager on standard input. If the password is not piped in, Taverna
+will prompt you for it in the terminal and block until it is entered. Do not
+enter your password in the command line! If -cmpassword option is not specified
+and -cmdir option is used, Taverna will try to find the password in a special
+file password.txt in the directory specified with -cmdir option.
diff --git a/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestDatabaseConfigurationHandler.java b/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestDatabaseConfigurationHandler.java
new file mode 100644
index 0000000..4c00e3a
--- /dev/null
+++ b/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestDatabaseConfigurationHandler.java
@@ -0,0 +1,21 @@
+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.Ignore;
+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());
+// }
+}
diff --git a/taverna-commandline-launcher/pom.xml b/taverna-commandline-launcher/pom.xml
new file mode 100644
index 0000000..42208e3
--- /dev/null
+++ b/taverna-commandline-launcher/pom.xml
@@ -0,0 +1,83 @@
+<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/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.taverna.commandline</groupId>
+ <artifactId>taverna-commandline</artifactId>
+ <version>3.1.0.incubating-SNAPSHOT</version>
+ </parent>
+ <artifactId>taverna-commandline-launcher</artifactId>
+ <name>Apache Taverna Commandline Launcher</name>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-jar-plugin</artifactId>
+ <version>2.4</version>
+ <configuration>
+ <archive>
+ <manifest>
+ <addClasspath>true</addClasspath>
+ <mainClass>uk.org.taverna.commandline.TavernaCommandLine</mainClass>
+ <classpathLayoutType>custom</classpathLayoutType>
+ <customClasspathLayout>../${artifact.groupId}/${artifact.artifactId}-${artifact.baseVersion}${dashClassifier?}.${artifact.extension}</customClasspathLayout>
+ </manifest>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+ <dependencies>
+ <dependency>
+ <groupId>${project.parent.groupId}</groupId>
+ <artifactId>taverna-commandline-api</artifactId>
+ <version>${project.parent.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.osgi</groupId>
+ <artifactId>osgi-launcher</artifactId>
+ <version>${taverna.osgi.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.osgi</groupId>
+ <artifactId>taverna-app-configuration-impl</artifactId>
+ <version>${taverna.osgi.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>com.springsource.org.apache.commons.cli</artifactId>
+ <version>${commons.cli.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>${commons.io.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ <version>${log4j.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.eclipse</groupId>
+ <artifactId>org.eclipse.osgi</artifactId>
+ <version>${osgi.equinox.version}</version>
+ </dependency>
+ <!-- TODO: replace equinox with:
+ <dependency>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>org.apache.felix.main</artifactId>
+ <version>4.4.1</version>
+ </dependency>
+ -->
+
+
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+</project>
diff --git a/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
new file mode 100644
index 0000000..b702e03
--- /dev/null
+++ b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
@@ -0,0 +1,445 @@
+/*******************************************************************************
+ * 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 uk.org.taverna.commandline;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+import net.sf.taverna.t2.commandline.exceptions.ArgumentsParsingException;
+import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
+import net.sf.taverna.t2.commandline.options.CommandLineOptions;
+
+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
+ * @author David Withers
+ */
+public class CommandLineOptionsImpl implements CommandLineOptions {
+
+ private static final String OUTPUTDIR = "outputdir";
+ private static final String BUNDLE = "bundle";
+ private static final Logger logger = Logger.getLogger(CommandLineOptionsImpl.class);
+ private Options options;
+ private CommandLine commandLine;
+
+ public CommandLineOptionsImpl(String[] args) throws ArgumentsParsingException, InvalidOptionException {
+ this.options = intitialiseOptions();
+ this.commandLine = processArgs(args);
+ checkForInvalid();
+ }
+
+ @Override
+ public boolean askedForHelp() {
+ return hasOption("help") || (getArgs().length==0 && getOptions().length==0);
+ }
+
+ @Override
+ public boolean isProvenanceEnabled() {
+ return hasOption("provenance");
+ }
+
+ protected void checkForInvalid() throws InvalidOptionException {
+ if (askedForHelp()) return;
+ if (isProvenanceEnabled()
+ && !(hasOption("embedded") || hasOption("clientserver") || hasOption("dbproperties")))
+ throw new InvalidOptionException(
+ "You should be running with a database to use provenance");
+ if (isProvenanceEnabled() && 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");
+ }
+
+ @Override
+ public void displayHelp() {
+ boolean full = false;
+ if (hasOption("help")) full=true;
+ displayHelp(full);
+ }
+
+ @Override
+ public void displayHelp(boolean showFullText) {
+
+ HelpFormatter formatter = new HelpFormatter();
+ try {
+ formatter
+ .printHelp("executeworkflow [options] [workflow]", options);
+ if (showFullText) {
+ InputStream helpStream = CommandLineOptionsImpl.class
+ .getClassLoader().getResourceAsStream("help.txt");
+ String helpText = IOUtils.toString(helpStream);
+ System.out.println(helpText);
+ }
+
+ } catch (IOException e) {
+ logger.error("Failed to load the help document", e);
+ System.out.println("Failed to load the help document");
+ //System.exit(-1);
+ }
+ }
+
+ @Override
+ public String[] getArgs() {
+ return commandLine.getArgs();
+ }
+
+ /**
+ *
+ * @return the port that the database should run on
+ */
+ @Override
+ public String getDatabasePort() {
+ return getOptionValue("port");
+ }
+
+ /**
+ *
+ * @return a path to a properties file that contains database configuration
+ * settings
+ */
+ @Override
+ public String getDatabaseProperties() {
+ return getOptionValue("dbproperties");
+ }
+
+ /**
+ * 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.
+ */
+ @Override
+ public String[] getInputFiles() {
+ if (hasInputFiles()) {
+ return getOptionValues("inputfile");
+ } else {
+ return new String[] {};
+ }
+ }
+
+ @Override
+ public String[] getInputValues() {
+ if (hasInputValues()) {
+ return getOptionValues("inputvalue");
+ } else {
+ return new String[] {};
+ }
+ }
+
+ @Override
+ 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
+ */
+ @Override
+ public String getOutputDirectory() {
+ return getOptionValue(OUTPUTDIR);
+ }
+
+ @Override
+ public boolean getStartDatabase() {
+ return hasOption("startdb");
+ }
+
+ /**
+ * @return the directory with Credential Manager's files
+ */
+ @Override
+ public String getCredentialManagerDir() {
+ return getOptionValue(CREDENTIAL_MANAGER_DIR_OPTION);
+ }
+
+ @Override
+ public boolean getStartDatabaseOnly() throws InvalidOptionException {
+ return (getStartDatabase() && (getWorkflow() == null));
+ }
+
+ @Override
+ 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];
+ }
+ }
+
+ @Override
+ 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;
+ }
+
+ @Override
+ public boolean hasInputFiles() {
+ return hasOption("inputfile");
+ }
+
+ @Override
+ public boolean hasInputValues() {
+ return hasOption("inputvalue");
+ }
+
+ @Override
+ public boolean hasLogFile() {
+ return hasOption("logfile");
+ }
+
+ @Override
+ public boolean hasOption(String option) {
+ return commandLine.hasOption(option);
+ }
+
+ @Override
+ 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", "Display 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 bundleOption = OptionBuilder.withArgName(BUNDLE).hasArg()
+ .withDescription("Save outputs to a new Workflow Run Bundle (zip).")
+ .create(BUNDLE);
+
+ 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(
+ "Cause 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(
+ "Load 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",
+ "Connect to an embedded Derby database. This can prevent mulitple invocations.");
+ Option clientserver = new Option("clientserver",
+ "Connect as a client to a derby server instance.");
+ Option inMemOption = new Option(
+ "inmemory",
+ "Run the workflow with data stored in-memory rather than in a database (this is the default option). This can give performance inprovements, at the cost of overall memory usage.");
+ Option startDB = new Option("startdb",
+ "Automatically start an internal Derby database server.");
+ Option provenance = new Option("provenance",
+ "Generate provenance information and store it in the database.");
+
+
+ Option credentialManagerDirectory = OptionBuilder.withArgName("directory path").
+ hasArg().withDescription(
+ "Absolute path to a directory where Credential Manager's files (keystore and truststore) are located.")
+ .create(CREDENTIAL_MANAGER_DIR_OPTION);
+ Option credentialManagerPassword = new Option(CREDENTIAL_MANAGER_PASSWORD_OPTION, "Indicate that the master password for Credential Manager will be provided on standard input."); // optional password option, to be read from standard input
+
+ Options options = new Options();
+ options.addOption(helpOption);
+ options.addOption(inputFileOption);
+ options.addOption(inputValueOption);
+ options.addOption(inputDelimiterOption);
+ options.addOption(inputdocOption);
+ options.addOption(outputOption);
+ options.addOption(bundleOption);
+ options.addOption(inMemOption);
+ options.addOption(embedded);
+ options.addOption(clientserver);
+ options.addOption(dbProperties);
+ options.addOption(port);
+ options.addOption(startDB);
+ options.addOption(provenance);
+ options.addOption(logFileOption);
+ options.addOption(credentialManagerDirectory);
+ options.addOption(credentialManagerPassword);
+
+ return options;
+ }
+
+ @Override
+ public boolean isClientServer() {
+ return hasOption("clientserver");
+ }
+
+ @Override
+ public boolean isEmbedded() {
+ return hasOption("embedded");
+ }
+
+ @Override
+ public boolean isInMemory() {
+ return hasOption("inmemory");
+ }
+
+ private CommandLine processArgs(String[] args) throws ArgumentsParsingException {
+ 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("Taverna command line arguments' parsing failed. Reason: " + exp.getMessage());
+// System.exit(1);
+ throw new ArgumentsParsingException("Taverna command line arguments' parsing failed. Reason: " + exp.getMessage(), exp);
+ }
+ return line;
+ }
+
+ /**
+ * Save the results to a directory if -outputdir has been explicitly defined,
+ * or if -outputdoc has not been defined.
+ *
+ * @return boolean
+ */
+ @Override
+ public boolean saveResultsToDirectory() {
+ return (options.hasOption(OUTPUTDIR) || !hasSaveResultsToBundle());
+ }
+
+ @Override
+ public String saveResultsToBundle() {
+ if (! hasSaveResultsToBundle()) {
+ return null;
+ }
+ return getOptionValue(BUNDLE);
+ }
+
+ @Override
+ public boolean hasSaveResultsToBundle() {
+ return hasOption(BUNDLE);
+ }
+
+}
diff --git a/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
new file mode 100644
index 0000000..426ab98
--- /dev/null
+++ b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
@@ -0,0 +1,143 @@
+/*******************************************************************************
+ * Copyright (C) 2012 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 uk.org.taverna.commandline;
+
+import java.io.File;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import net.sf.taverna.t2.commandline.exceptions.ArgumentsParsingException;
+import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
+import net.sf.taverna.t2.commandline.options.CommandLineOptions;
+
+import org.osgi.framework.BundleContext;
+import org.osgi.framework.BundleException;
+
+import uk.org.taverna.commons.profile.xml.jaxb.ApplicationProfile;
+import uk.org.taverna.commons.profile.xml.jaxb.BundleInfo;
+import uk.org.taverna.commons.profile.xml.jaxb.FrameworkConfiguration;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.configuration.app.impl.ApplicationConfigurationImpl;
+import uk.org.taverna.configuration.app.impl.Log4JConfiguration;
+import uk.org.taverna.osgi.OsgiLauncher;
+
+/**
+ * Main entry point for starting the Taverna Command Line Tool.
+ *
+ * @author David Withers
+ */
+public class TavernaCommandLine {
+
+ private static final String COMMANDLINE_BUNDLE_NAME = "org.apache.taverna.commandline.taverna-commandline-common";
+
+ private static File commandlineBundle = null;
+
+ private static ApplicationConfiguration applicationConfiguration = new ApplicationConfigurationImpl();
+
+ private static Log4JConfiguration log4jConfiguration = new Log4JConfiguration();
+
+ /**
+ * Starts the Taverna Command Line Tool.
+ *
+ * @param args
+ * Taverna Command Line arguments
+ */
+ public static void main(final String[] args) {
+ try {
+ CommandLineOptions commandLineOptions = new CommandLineOptionsImpl(args);
+ if (commandLineOptions.askedForHelp()) {
+ commandLineOptions.displayHelp();
+ } else {
+ log4jConfiguration.setApplicationConfiguration(applicationConfiguration);
+ log4jConfiguration.prepareLog4J();
+ setDerbyPaths();
+ OsgiLauncher osgilauncher = new OsgiLauncher(getAppDirectory(), getBundleURIs());
+ setFrameworkConfiguration(osgilauncher);
+ osgilauncher.start();
+ BundleContext context = osgilauncher.getContext();
+ context.registerService("net.sf.taverna.t2.commandline.options.CommandLineOptions",
+ commandLineOptions, null);
+ osgilauncher.startServices(true);
+ if (commandlineBundle == null) {
+ System.err.println("Can't locate command line bundle " + COMMANDLINE_BUNDLE_NAME);
+ System.exit(1);
+ }
+ osgilauncher.startBundle(osgilauncher.installBundle(commandlineBundle.toURI()));
+ }
+ } catch (ArgumentsParsingException e) {
+ System.out.println(e.getMessage());
+ } catch (InvalidOptionException e) {
+ System.out.println(e.getMessage());
+ } catch (BundleException e) {
+ System.out.println(e.getMessage());
+ }
+ }
+
+ /**
+ * Sets the OSGi Framework configuration.
+ *
+ * @param osgilauncher
+ */
+ private static void setFrameworkConfiguration(OsgiLauncher osgilauncher) {
+ ApplicationProfile applicationProfile = applicationConfiguration.getApplicationProfile();
+ List<FrameworkConfiguration> frameworkConfigurations = applicationProfile
+ .getFrameworkConfiguration();
+ if (!frameworkConfigurations.isEmpty()) {
+ Map<String, String> configurationMap = new HashMap<String, String>();
+ for (FrameworkConfiguration frameworkConfiguration : frameworkConfigurations) {
+ configurationMap.put(frameworkConfiguration.getName(),
+ frameworkConfiguration.getValue());
+ }
+ osgilauncher.setFrameworkConfiguration(configurationMap);
+ }
+ }
+
+ private static List<URI> getBundleURIs() {
+ List<URI> bundleURIs = new ArrayList<URI>();
+ ApplicationProfile applicationProfile = applicationConfiguration.getApplicationProfile();
+ File libDir = new File(applicationConfiguration.getStartupDir(), "lib");
+ if (applicationProfile != null) {
+ for (BundleInfo bundle : applicationProfile.getBundle()) {
+ File bundleFile = new File(libDir, bundle.getFileName());
+ if (bundle.getSymbolicName().equals(COMMANDLINE_BUNDLE_NAME)) {
+ commandlineBundle = bundleFile;
+ } else {
+ bundleURIs.add(bundleFile.toURI());
+ }
+ }
+ }
+ return bundleURIs;
+ }
+
+ private static File getAppDirectory() {
+ return new File(applicationConfiguration.getApplicationHomeDir().getAbsolutePath());
+ }
+
+ private static void setDerbyPaths() {
+ System.setProperty("derby.system.home", getAppDirectory().getAbsolutePath());
+ File logFile = new File(applicationConfiguration.getLogDir(), "derby.log");
+ System.setProperty("derby.stream.error.file", logFile.getAbsolutePath());
+ }
+
+}
diff --git a/taverna-commandline-launcher/src/main/resources/help.txt b/taverna-commandline-launcher/src/main/resources/help.txt
new file mode 100644
index 0000000..fb082cc
--- /dev/null
+++ b/taverna-commandline-launcher/src/main/resources/help.txt
@@ -0,0 +1,87 @@
+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 a 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 your workflow inputs is a list, you can create a list
+input 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 properties file, for which the following
+example contains the default settings:
+
+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.
+
+-cmdir option lets you specify an absolute path to a directory where
+Credential Manager's files (keystore and truststore - containing user's
+credentials and trusted certificates for accessing secure services) are stored.
+If not specified and the workflow requires access to these files, Taverna will
+try to find them in the default location in <TAVERNA_HOME>/security somewhere
+inside user's home directory (depending on the platform).
+
+-cmpassword option can be used to tell Taverna to expect the password for the
+Credential Manager on standard input. If the password is not piped in, Taverna
+will prompt you for it in the terminal and block until it is entered. Do not
+enter your password in the command line! If -cmpassword option is not specified
+and -cmdir option is used, Taverna will try to find the password in a special
+file password.txt in the directory specified with -cmdir option.
diff --git a/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java b/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
new file mode 100644
index 0000000..3e1d0f4
--- /dev/null
+++ b/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
@@ -0,0 +1,267 @@
+package uk.org.taverna.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 CommandLineOptionsImpl(
+ new String[] { "myworkflow.t2flow" });
+ assertEquals("myworkflow.t2flow", handler.getWorkflow());
+ }
+
+ @Test
+ public void shouldShowHelp() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(
+ new String[] { "-help" });
+ assertTrue(options.askedForHelp());
+ options = new CommandLineOptionsImpl(
+ new String[] {});
+ assertTrue(options.askedForHelp());
+ options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+ assertFalse(options.askedForHelp());
+ }
+
+ @Test
+ public void getWorkflow() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(
+ new String[] { "-help" });
+ assertNull(options.getWorkflow());
+ options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+ assertEquals("myworkflow.t2flow", options.getWorkflow());
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void cannotProvideInputFileAndInputDoc() throws Exception {
+ new CommandLineOptionsImpl(new String[] { "-inputfile", "fred", "fred.txt",
+ "-inputdoc", "myworkflow.t2flow" });
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void cannotProvideInputValueAndInputDoc() throws Exception {
+ new CommandLineOptionsImpl(new String[] { "-inputvalue", "fred", "fred.txt",
+ "-inputdoc", "myworkflow.t2flow" });
+ }
+
+ @Test
+ public void canProvideInputValueAndFileTogether() throws Exception {
+ //should not be an error
+ new CommandLineOptionsImpl(new String[] { "-inputvalue", "fred", "abc",
+ "-inputfile","fred2","fred2.txt","myworkflow.t2flow" });
+ }
+
+ @Test
+ public void getInputs() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(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 CommandLineOptionsImpl(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 CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+ assertNotNull(options.getInputFiles());
+ assertEquals(0, options.getInputFiles().length);
+
+ }
+
+ @Test
+ public void hasInputValue() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-inputvalue", "fred", "abc", "myworkflow.t2flow" });
+ assertTrue(options.hasInputValues());
+
+ options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+ assertFalse(options.hasInputValues());
+ }
+
+ @Test
+ public void getInputValues() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-inputvalue", "fred", "abc", "myworkflow.t2flow" });
+ assertEquals(2, options.getInputValues().length);
+
+ options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+ assertNotNull(options.getInputValues());
+ assertEquals(0,options.getInputValues().length);
+ }
+
+ @Test
+ public void hasInputs() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
+ assertTrue(options.hasInputFiles());
+
+ options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+ assertFalse(options.hasInputFiles());
+ }
+
+ @Test
+ public void noWorkflowNameButStartDB() throws Exception {
+ // should not throw an error
+ CommandLineOptions options = new CommandLineOptionsImpl(
+ new String[] { "-startdb" });
+ assertTrue(options.getStartDatabase());
+ assertTrue(options.getStartDatabaseOnly());
+ }
+
+ @Test
+ public void workflowNameAndStartDB() throws Exception {
+ // should not throw an error
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-startdb", "myworkflow.t2flow" });
+ assertTrue(options.getStartDatabase());
+ assertFalse(options.getStartDatabaseOnly());
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void provenanceButNoDatabase() throws Exception {
+ new CommandLineOptionsImpl(new String[] { "-provenance",
+ "myworkflow.t2flow" });
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void provenanceButNoDatabase2() throws Exception {
+ new CommandLineOptionsImpl(new String[] { "-provenance", "-inmemory",
+ "myworkflow.t2flow" });
+ }
+
+ @Test
+ public void provenanceDatabase() throws Exception {
+ // should be no errors
+ new CommandLineOptionsImpl(new String[] { "-provenance", "-embedded",
+ "myworkflow.t2flow" });
+ new CommandLineOptionsImpl(new String[] { "-provenance", "-clientserver",
+ "myworkflow.t2flow" });
+ new CommandLineOptionsImpl(new String[] { "-provenance", "-dbproperties",
+ "dbproperties.properties", "myworkflow.t2flow" });
+ }
+
+ @Test
+ public void testHasInputDelimiter() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(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 CommandLineOptionsImpl(new String[] {
+ "-inputdoc","doc.xml","-inputdelimiter","in1",",","myworkflow.t2flow" });
+ }
+
+
+ @Test
+ public void testInputDelimiter() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(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 CommandLineOptionsImpl(new String[] {
+ "-inmemory", "myworkflow.t2flow" });
+ assertTrue(handler.hasOption("inmemory"));
+ }
+
+ @Test
+ public void testEmbedded() throws Exception {
+ CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
+ "-embedded", "myworkflow.t2flow" });
+ assertTrue(handler.hasOption("embedded"));
+ }
+
+ @Test
+ public void testClientServer() throws Exception {
+ CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
+ "-clientserver", "myworkflow.t2flow" });
+ assertTrue(handler.hasOption("clientserver"));
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void testInvalidEmbeddedAndClientServer() throws Exception {
+ new CommandLineOptionsImpl(new String[] { "-clientserver", "-embedded",
+ "myworkflow.t2flow" });
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void testInvalidEmbeddedAndMemory() throws Exception {
+ new CommandLineOptionsImpl(new String[] { "-embedded", "-inmemory",
+ "myworkflow.t2flow" });
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void testInvalidClientServerAndInMemory() throws Exception {
+ new CommandLineOptionsImpl(new String[] { "-clientserver", "-inmemory",
+ "myworkflow.t2flow" });
+ }
+
+ @Test
+ public void isInMemory() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-inmemory", "myworkflow.t2flow" });
+
+ assertTrue(options.isInMemory());
+ assertFalse(options.isClientServer());
+ assertFalse(options.isEmbedded());
+ }
+
+ @Test
+ public void isClientServer() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-clientserver", "myworkflow.t2flow" });
+
+ assertTrue(options.isClientServer());
+ assertFalse(options.isInMemory());
+ assertFalse(options.isEmbedded());
+ }
+
+ @Test
+ public void hasLogFile() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-logfile","/tmp/logging", "myworkflow.t2flow" });
+
+ assertTrue(options.hasLogFile());
+ assertEquals("/tmp/logging", options.getLogFile());
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ @SuppressWarnings("unused")
+ public void hasLogFileNotValidWithoutWorkflow() throws Exception{
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-logfile","/tmp/logging"});
+ }
+
+ @Test
+ public void isEmbedded() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-embedded", "myworkflow.t2flow" });
+
+ assertTrue(options.isEmbedded());
+ assertFalse(options.isInMemory());
+ assertFalse(options.isClientServer());
+ }
+
+}
diff --git a/taverna-commandline-product/pom.xml b/taverna-commandline-product/pom.xml
new file mode 100644
index 0000000..38bcb42
--- /dev/null
+++ b/taverna-commandline-product/pom.xml
@@ -0,0 +1,529 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.taverna.commandline</groupId>
+ <artifactId>taverna-commandline</artifactId>
+ <version>3.1.0.incubating-SNAPSHOT</version>
+ </parent>
+ <artifactId>taverna-command-line-product</artifactId>
+ <name>Apache Taverna Commandline Product</name>
+ <packaging>taverna-application</packaging>
+ <profiles>
+ <profile>
+ <id>developer</id>
+ <activation>
+ <activeByDefault>true</activeByDefault>
+ </activation>
+ <properties>
+ <assembly.descriptor>src/main/assembly/developer-assembly.xml</assembly.descriptor>
+ <!-- See http://updates.taverna.org.uk/ -->
+ <profile.updateSite>https://taverna.incubator.apache.org/updates/commandline/</profile.updateSite>
+ <profile.pluginSite>https://taverna.incubator.apache.org/plugins/commandline/</profile.pluginSite>
+ </properties>
+ </profile>
+ <profile>
+ <id>nightly</id>
+ <properties>
+ <assembly.descriptor>src/main/assembly/nightly-assembly.xml</assembly.descriptor>
+ <profile.updateSite>https://taverna.incubator.apache.org/updates/commandline/</profile.updateSite>
+ <profile.pluginSite>https://taverna.incubator.apache.org/plugins/commandline/</profile.pluginSite>
+ </properties>
+ </profile>
+ <profile>
+ <id>release</id>
+ <properties>
+ <assembly.descriptor>src/main/assembly/release-assembly.xml</assembly.descriptor>
+ <profile.updateSite>https://taverna.incubator.apache.org/updates/commandline/</profile.updateSite>
+ <profile.pluginSite>https://taverna.incubator.apache.org/plugins/commandline/</profile.pluginSite>
+ </properties>
+ </profile>
+ </profiles>
+ <build>
+ <finalName>apache-taverna-commandline-${project.version}</finalName>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <version>2.4</version>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <descriptors>
+ <descriptor>${assembly.descriptor}</descriptor>
+ </descriptors>
+ <archiverConfig>
+ <directoryMode>493</directoryMode> <!-- 493(dec) = 755(oct) -->
+ <defaultDirectoryMode>493</defaultDirectoryMode>
+ </archiverConfig>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>buildnumber-maven-plugin</artifactId>
+ <version>1.0-beta-3</version>
+ <executions>
+ <execution>
+ <id>buildnumber-validate</id>
+ <phase>validate</phase>
+ <goals>
+ <goal>create</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <format>{0,date,yyyyMMdd}T{0,date,HHmm}</format>
+ <items>
+ <item>timestamp</item>
+ </items>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.taverna.osgi</groupId>
+ <artifactId>taverna-maven-plugin</artifactId>
+ <version>${taverna.osgi.version}</version>
+ <extensions>true</extensions>
+ <configuration>
+ <buildNumber>${buildNumber}</buildNumber>
+ <updateSite>${profile.updateSite}</updateSite>
+ <pluginSite>${profile.pluginSite}</pluginSite>
+ <frameworkConfigurations>
+ <frameworkConfiguration>
+ <name>org.osgi.framework.bootdelegation</name>
+ <value>sun.*,com.sun.*,java.*,javax.*,org.xml.*,org.w3c.*,apple.*,com.apple.*,org.omg.*,org.ietf.jgss.*,org.jcp.xml.dsig.internal.*</value>
+ </frameworkConfiguration>
+ <frameworkConfiguration>
+ <name>org.osgi.framework.system.packages.extra</name>
+ <value>com.sun.org.apache.xml.internal.utils,com.sun.source.util,com.sun.source.tree,org.apache.log4j;version=${log4j.version},net.sf.taverna.t2.commandline.options;version=${project.parent.version}</value>
+ </frameworkConfiguration>
+ <frameworkConfiguration>
+ <name>org.osgi.framework.storage.clean</name>
+ <value>onFirstInit</value>
+ </frameworkConfiguration>
+ </frameworkConfigurations>
+ </configuration>
+ </plugin>
+ </plugins>
+ <pluginManagement>
+ <plugins>
+ <!--This plugin's configuration is used to store Eclipse m2e settings
+ only. It has no influence on the Maven build itself. -->
+ <plugin>
+ <groupId>org.eclipse.m2e</groupId>
+ <artifactId>lifecycle-mapping</artifactId>
+ <version>1.0.0</version>
+ <configuration>
+ <lifecycleMappingMetadata>
+ <pluginExecutions>
+ <pluginExecution>
+ <pluginExecutionFilter>
+ <groupId>org.apache.taverna.osgi</groupId>
+ <artifactId>taverna-maven-plugin</artifactId>
+ <versionRange>[0.3.1-SNAPSHOT,)</versionRange>
+ <goals>
+ <goal>profile-generate</goal>
+ </goals>
+ </pluginExecutionFilter>
+ <action>
+ <execute>
+ <runOnIncremental>false</runOnIncremental>
+ </execute>
+ </action>
+ </pluginExecution>
+ </pluginExecutions>
+ </lifecycleMappingMetadata>
+ </configuration>
+ </plugin>
+ </plugins>
+ </pluginManagement>
+ </build>
+
+ <dependencies>
+
+ <!-- Explicit org.osgi.* with <scope>provided as these are also provided
+ by the felix osgi package. Avoids: Caused by: java.lang.SecurityException:
+ class "org.osgi.framework.hooks.bundle.CollisionHook"'s signer information
+ does not match signer information of other classes in the same package -->
+
+ <dependency>
+ <groupId>org.osgi</groupId>
+ <artifactId>org.osgi.core</artifactId>
+ <version>${osgi.core.version}</version>
+ <scope>provided</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.osgi</groupId>
+ <artifactId>org.osgi.compendium</artifactId>
+ <version>${osgi.core.version}</version>
+ <scope>provided</scope>
+ </dependency>
+
+ <!-- Invalid manifest header Import-Package: "com.sun.jdmk.comm;resolution:="optional"" : Cannot import a package more than once "com.sun.jdmk.comm"-->
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ <version>${log4j.version}</version>
+ <scope>provided</scope>
+ </dependency>
+
+ <!-- Spring DM -->
+ <dependency>
+ <groupId>net.sourceforge.cglib</groupId>
+ <artifactId>com.springsource.net.sf.cglib</artifactId>
+ <version>${cglib.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.springframework.osgi</groupId>
+ <artifactId>spring-osgi-annotation</artifactId>
+ <version>${spring.dm.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.springframework.osgi</groupId>
+ <artifactId>spring-osgi-extender</artifactId>
+ <version>${spring.dm.version}</version>
+ </dependency>
+ <!-- Spring -->
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>org.springframework.context</artifactId>
+ <version>${spring.version}</version>
+ </dependency>
+
+ <!-- Java Extension Implementations -->
+ <!-- Appears unrequired dependency>
+ <groupId>javax.xml.bind</groupId>
+ <artifactId>com.springsource.javax.xml.bind</artifactId>
+ <version>2.2.0</version>
+ </dependency-->
+ <dependency>
+ <groupId>javax.activation</groupId>
+ <artifactId>com.springsource.javax.activation</artifactId>
+ <version>${activation.version}</version>
+ </dependency>
+ <!-- The bundle "com.springsource.bsh_2.0.0.b4 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.servlet; version="[2.5.0,3.0.0)" -->
+ <dependency>
+ <groupId>javax.servlet</groupId>
+ <artifactId>com.springsource.javax.servlet</artifactId>
+ <version>2.5.0</version>
+ </dependency>
+ <!-- The bundle "com.springsource.org.apache.axis_1.4.0 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.jms; version="[1.1.0,2.0.0)" -->
+ <dependency>
+ <groupId>javax.jms</groupId>
+ <artifactId>com.springsource.javax.jms</artifactId>
+ <version>1.1.0</version>
+ </dependency>
+ <!-- The bundle "com.springsource.javax.xml.rpc_1.1.0 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.xml.soap; version="[1.3.0,2.0.0)" -->
+ <dependency>
+ <groupId>javax.xml.soap</groupId>
+ <artifactId>com.springsource.javax.xml.soap</artifactId>
+ <version>1.3.0</version>
+ </dependency>
+ <!-- The bundle "com.springsource.com.thoughtworks.xstream_1.4.1" could not be resolved. Reason: Missing Constraint: Import-Package: javax.xml.stream; version="[1.0.1,2.0.0)" -->
+ <dependency>
+ <groupId>javax.xml.stream</groupId>
+ <artifactId>com.springsource.javax.xml.stream</artifactId>
+ <version>1.0.1</version>
+ </dependency>
+ <dependency>
+ <groupId>javax.mail</groupId>
+ <artifactId>com.springsource.javax.mail</artifactId>
+ <version>${mail.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-codec</groupId>
+ <artifactId>commons-codec</artifactId>
+ <version>${commons.codec.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-configuration</groupId>
+ <artifactId>commons-configuration</artifactId>
+ <version>1.10</version>
+ </dependency>
+ <dependency>
+ <groupId>com.sun.xml.bind</groupId>
+ <artifactId>jaxb-impl</artifactId>
+ <version>2.2.11</version>
+ </dependency>
+
+
+ <!-- OSGi Enterprise Services -->
+ <dependency>
+ <groupId>org.apache.taverna.osgi</groupId>
+ <artifactId>xml-parser-service</artifactId>
+ <version>${taverna.osgi.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.osgi</groupId>
+ <artifactId>xml-transformer-service</artifactId>
+ <version>${taverna.osgi.version}</version>
+ </dependency>
+ <!-- The bundle "uk.org.taverna.commons.taverna-plugin-impl_0.1.0.SNAPSHOT" could not be resolved. Reason: Missing Constraint: Import-Package: org.osgi.service.event; version="[1.3.0,2.0.0)" -->
+ <dependency>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>org.apache.felix.eventadmin</artifactId>
+ <version>1.3.2</version>
+ </dependency>
+ <!-- Appears unrequired dependency>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>org.apache.felix.configadmin</artifactId>
+ <version>1.6.0</version>
+ </dependency-->
+
+ <!-- Taverna Activities -->
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-dataflow-activity</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-stringconstant-activity</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+
+ <!-- Taverna Common Activities -->
+ <dependency>
+ <groupId>org.apache.taverna.commonactivities</groupId>
+ <artifactId>taverna-beanshell-activity</artifactId>
+ <version>${taverna.commonactivities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.commonactivities</groupId>
+ <artifactId>taverna-external-tool-activity</artifactId>
+ <version>${taverna.commonactivities.version}</version>
+ </dependency>
+ <!-- VERY broken :(
+ <dependency>
+ <groupId>org.apache.taverna.commonactivities</groupId>
+ <artifactId>taverna-interaction-activity</artifactId>
+ <version>${taverna.commonactivities.version}</version>
+ </dependency>
+ -->
+ <dependency>
+ <groupId>org.apache.taverna.commonactivities</groupId>
+ <artifactId>taverna-rest-activity</artifactId>
+ <version>${taverna.commonactivities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.commonactivities</groupId>
+ <artifactId>taverna-spreadsheet-import-activity</artifactId>
+ <version>${taverna.commonactivities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.commonactivities</groupId>
+ <artifactId>taverna-wsdl-activity</artifactId>
+ <version>${taverna.commonactivities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.commonactivities</groupId>
+ <artifactId>taverna-xpath-activity</artifactId>
+ <version>${taverna.commonactivities.version}</version>
+ </dependency>
+
+
+ <!-- Taverna Commandline -->
+ <dependency>
+ <groupId>${project.parent.groupId}</groupId>
+ <artifactId>taverna-commandline-common</artifactId>
+ <version>${project.parent.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>${project.parent.groupId}</groupId>
+ <artifactId>taverna-commandline-launcher</artifactId>
+ <version>${project.parent.version}</version>
+ </dependency>
+
+ <!-- Taverna Platform -->
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-capability-impl</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-run-impl</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-execution-impl</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-execution-local</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-database-configuration-impl</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-services-impl</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+
+ <!-- Taverna OSGi -->
+ <dependency>
+ <groupId>org.apache.taverna.osgi</groupId>
+ <artifactId>taverna-configuration-impl</artifactId>
+ <version>${taverna.osgi.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.osgi</groupId>
+ <artifactId>taverna-app-configuration-impl</artifactId>
+ <version>${taverna.osgi.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.osgi</groupId>
+ <artifactId>taverna-download-impl</artifactId>
+ <version>${taverna.osgi.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.osgi</groupId>
+ <artifactId>taverna-plugin-impl</artifactId>
+ <version>${taverna.osgi.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.osgi</groupId>
+ <artifactId>taverna-update-impl</artifactId>
+ <version>${taverna.osgi.version}</version>
+ </dependency>
+
+ <!-- Scufl2 -->
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-rdfxml</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-t2flow</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-validation-structural</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-validation-correctness</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+
+ <!-- Data bundle -->
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-databundle</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+ <!-- HTTP client needed by Data Bundle -->
+ <!-- Appears unrequired dependency>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpclient-osgi</artifactId>
+ <version>4.2.5</version>
+ </dependency-->
+ <!-- Appears unrequired dependency>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpcore-osgi</artifactId>
+ <version>4.2.5</version>
+ </dependency-->
+ <!-- Jena bundle needed by jsonld-java-jena -->
+ <!-- See https://github.com/stain/jena/tree/jena-bundle/jena-bundle -->
+ <dependency>
+ <groupId>org.apache.jena</groupId>
+ <artifactId>jena-osgi</artifactId>
+ <version>2.12.2-SNAPSHOT</version>
+ </dependency>
+ <!-- slf4j implementation -->
+ <!-- The bundle "org.purl.wf4ever.robundle_0.3.1 " could not be resolved. Reason: Missing Constraint: Import-Package: org.slf4j; version="[1.7.0,2.0.0)"-->
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-api</artifactId>
+ <version>${slf4j.version}</version>
+ </dependency>
+
+ <!-- Appears unrequired: -->
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-log4j12</artifactId>
+ <version>${slf4j.version}</version>
+ </dependency>
+
+ <!-- Taverna Security -->
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-credential-manager-impl</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+
+ <!-- Taverna Workflow Engine -->
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-workflowmodel-impl</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-workflowmodel-core-extensions</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-reference-impl</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-reference-types</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+
+ <!-- Taverna Provenance -->
+ <!--dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>provenance-derby</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>provenance-mysql</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency-->
+ <!-- The bundle "org.purl.wf4ever.robundle_0.3.1 " could not be resolved. Reason: Missing Constraint: Import-Package: com.fasterxml.jackson.annotation; version="[2.3.0,3.0.0)"-->
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-core</artifactId>
+ <version>2.3.0</version>
+ </dependency>
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-annotations</artifactId>
+ <version>2.3.0</version>
+ </dependency>
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>2.3.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>nu.validator.htmlparser</groupId>
+ <artifactId>htmlparser</artifactId>
+ <version>${htmlparser.version}</version>
+ </dependency>
+
+
+
+ </dependencies>
+
+</project>
diff --git a/taverna-commandline-product/src/main/assembly/dependencies-component.xml b/taverna-commandline-product/src/main/assembly/dependencies-component.xml
new file mode 100644
index 0000000..0e8640e
--- /dev/null
+++ b/taverna-commandline-product/src/main/assembly/dependencies-component.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<component
+ xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/component/1.1.2"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/component/1.1.2 http://maven.apache.org/xsd/component-1.1.2.xsd">
+
+ <fileSets>
+ <fileSet>
+ <directory>src/main/etc</directory>
+ <fileMode>0755</fileMode>
+ <outputDirectory></outputDirectory>
+ <filtered>true</filtered>
+ </fileSet>
+ <fileSet>
+ <directory>${project.build.directory}/taverna-tmp</directory>
+ <fileMode>0755</fileMode>
+ <outputDirectory></outputDirectory>
+ </fileSet>
+ </fileSets>
+
+</component>
\ No newline at end of file
diff --git a/taverna-commandline-product/src/main/assembly/developer-assembly.xml b/taverna-commandline-product/src/main/assembly/developer-assembly.xml
new file mode 100644
index 0000000..ae2a7c3
--- /dev/null
+++ b/taverna-commandline-product/src/main/assembly/developer-assembly.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<assembly
+ xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+ <id>dev</id>
+ <formats>
+ <format>dir</format>
+ </formats>
+ <componentDescriptors>
+ <componentDescriptor>dependencies-component.xml</componentDescriptor>
+ </componentDescriptors>
+</assembly>
diff --git a/taverna-commandline-product/src/main/assembly/nightly-assembly.xml b/taverna-commandline-product/src/main/assembly/nightly-assembly.xml
new file mode 100644
index 0000000..f82e793
--- /dev/null
+++ b/taverna-commandline-product/src/main/assembly/nightly-assembly.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<assembly
+ xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+ <id>nightly</id>
+ <baseDirectory>taverna-command-line-${project.version}-${buildNumber}-nightly</baseDirectory>
+ <formats>
+ <!-- <format>dir</format> -->
+ <format>zip</format>
+ </formats>
+ <componentDescriptors>
+ <componentDescriptor>dependencies-component.xml</componentDescriptor>
+ </componentDescriptors>
+</assembly>
diff --git a/taverna-commandline-product/src/main/assembly/release-assembly.xml b/taverna-commandline-product/src/main/assembly/release-assembly.xml
new file mode 100644
index 0000000..61da752
--- /dev/null
+++ b/taverna-commandline-product/src/main/assembly/release-assembly.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<assembly
+ xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+ <id>release</id>
+ <baseDirectory>taverna-command-line-${project.version}</baseDirectory>
+ <formats>
+ <!-- <format>dir</format> -->
+ <format>zip</format>
+ </formats>
+ <componentDescriptors>
+ <componentDescriptor>dependencies-component.xml</componentDescriptor>
+ </componentDescriptors>
+</assembly>
diff --git a/taverna-commandline-product/src/main/etc/conf/log4j.properties b/taverna-commandline-product/src/main/etc/conf/log4j.properties
new file mode 100644
index 0000000..5014f2b
--- /dev/null
+++ b/taverna-commandline-product/src/main/etc/conf/log4j.properties
@@ -0,0 +1,14 @@
+# By default, WARN (our external libraries)
+log4j.rootLogger=INFO, CONSOLE
+
+# Get rid of some xml sec warnings
+log4j.logger.org.apache.ws.security=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-product/src/main/etc/conf/logging.properties b/taverna-commandline-product/src/main/etc/conf/logging.properties
new file mode 100644
index 0000000..b03a43f
--- /dev/null
+++ b/taverna-commandline-product/src/main/etc/conf/logging.properties
@@ -0,0 +1,10 @@
+handlers = java.util.logging.ConsoleHandler, java.util.logging.FileHandler
+
+.level = ALL
+
+java.util.logging.ConsoleHandler.level = WARNING
+java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
+
+java.util.logging.FileHandler.level = ALL
+java.util.logging.FileHandler.count = 5
+java.util.logging.FileHandler.limit = 1048576
diff --git a/taverna-commandline-product/src/main/etc/conf/taverna.app.properties b/taverna-commandline-product/src/main/etc/conf/taverna.app.properties
new file mode 100644
index 0000000..91522d4
--- /dev/null
+++ b/taverna-commandline-product/src/main/etc/conf/taverna.app.properties
@@ -0,0 +1,2 @@
+taverna.app.name=taverna-cl-3.0.0
+taverna.app.title=Taverna Command Line 3.0.0
diff --git a/taverna-commandline-product/src/main/etc/executeworkflow.bat b/taverna-commandline-product/src/main/etc/executeworkflow.bat
new file mode 100644
index 0000000..2e18831
--- /dev/null
+++ b/taverna-commandline-product/src/main/etc/executeworkflow.bat
@@ -0,0 +1,17 @@
+@ECHO OFF
+
+REM Taverna startup script
+
+REM distribution directory
+set TAVERNA_HOME=%~dp0
+
+
+REM 1 GB memory, 400 MB for classes
+set ARGS=-Xmx1g -XX:MaxPermSize=400m
+
+REM Taverna system properties
+set ARGS=%ARGS% "-Dlog4j.configuration=file:///%TAVERNA_HOME%conf/log4j.properties"
+set ARGS=%ARGS% "-Djava.util.logging.config.file=%TAVERNA_HOME%conf/logging.properties"
+set ARGS=%ARGS% "-Dtaverna.app.startup=%TAVERNA_HOME%."
+
+java %ARGS% -jar "%TAVERNA_HOME%lib\/lib/org.apache.taverna.commandline/taverna-commandline-launcher-3.1.0.incubating-SNAPSHOT.jar" %*
diff --git a/taverna-commandline-product/src/main/etc/executeworkflow.sh b/taverna-commandline-product/src/main/etc/executeworkflow.sh
new file mode 100644
index 0000000..5ef0916
--- /dev/null
+++ b/taverna-commandline-product/src/main/etc/executeworkflow.sh
@@ -0,0 +1,25 @@
+#!/bin/sh
+
+set -e
+
+## resolve links - $0 may be a symlink
+prog="$0"
+
+real_path() {
+ readlink -m "$1" 2>/dev/null || python -c 'import os,sys;print os.path.realpath(sys.argv[1])' "$1"
+}
+
+realprog=`real_path "$prog"`
+taverna_home=`dirname "$realprog"`
+javabin=java
+if test -x "$JAVA_HOME/bin/java"; then
+ javabin="$JAVA_HOME/bin/java"
+fi
+
+# 1 GB memory, 400 MB for classes
+exec "$javabin" -Xmx1g -XX:MaxPermSize=400m \
+ "-Dlog4j.configuration=file://$taverna_home/conf/log4j.properties " \
+ "-Djava.util.logging.config.file=$taverna_home/conf/logging.properties " \
+ "-Dtaverna.app.startup=$taverna_home" \
+ -jar "$taverna_home/lib/org.apache.taverna.commandline/taverna-commandline-launcher-3.1.0.incubating-SNAPSHOT.jar" \
+ ${1+"$@"}
diff --git a/taverna-commandline-tests/pom.xml b/taverna-commandline-tests/pom.xml
new file mode 100644
index 0000000..e28c4a0
--- /dev/null
+++ b/taverna-commandline-tests/pom.xml
@@ -0,0 +1,71 @@
+<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/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.taverna.commandline</groupId>
+ <artifactId>taverna-commandline</artifactId>
+ <version>3.1.0-incubating-SNAPSHOT</version>
+ </parent>
+ <artifactId>taverna-command-line-tests</artifactId>
+ <name>Apache Taverna Commandline Tests</name>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>2.12</version>
+ <configuration>
+ <systemPropertyVariables>
+ <buildDirectory>${project.build.directory}</buildDirectory>
+ </systemPropertyVariables>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-t2flow</artifactId>
+ <version>${taverna.language.version}</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-rdfxml</artifactId>
+ <version>${taverna.language.version}</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.8.1</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>2.2</version>
+ <scope>test</scope>
+ </dependency>
+ <!-- Optional for scufl2-xdfxml -->
+ <dependency>
+ <groupId>com.sun.xml.bind</groupId>
+ <artifactId>jaxb-impl</artifactId>
+ <version>2.2.4-1</version>
+ <scope>test</scope>
+ </dependency>
+ <!-- Required by scufl2-xdfxml, see SCUFL2-122 -->
+ <dependency>
+ <groupId>org.jdom</groupId>
+ <artifactId>com.springsource.org.jdom</artifactId>
+ <version>1.1.0</version>
+ <scope>test</scope>
+ </dependency>
+ <!-- <dependency>
+ <groupId>org.jdom</groupId>
+ <artifactId>jdom</artifactId>
+ <version>1.1.2</version>
+ <scope>test</scope>
+ </dependency> -->
+ </dependencies>
+</project>
diff --git a/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java
new file mode 100644
index 0000000..07df1c3
--- /dev/null
+++ b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java
@@ -0,0 +1,485 @@
+/*******************************************************************************
+ * Copyright (C) 2012 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 uk.org.taverna.commandline;
+
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.junit.Assume.assumeTrue;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.net.URI;
+import java.net.URL;
+import java.text.MessageFormat;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.comparator.NameFileComparator;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+
+import uk.org.taverna.commandline.WorkflowTestSuite.Workflows;
+import uk.org.taverna.scufl2.api.container.WorkflowBundle;
+import uk.org.taverna.scufl2.api.io.WorkflowBundleIO;
+import uk.org.taverna.scufl2.rdfxml.RDFXMLReader;
+
+/**
+ * Regression tests for Taverna Command Line Tool.
+ *
+ * @author David Withers
+ */
+@RunWith(WorkflowTestSuite.class)
+public class TavernaCommandLineTest {
+
+ private static String baseVersion = "2.4.0";
+ private static boolean baseVersionReleased = true;
+
+ private static String testVersion = "3.0.1-SNAPSHOT";
+ private static boolean testVersionReleased = false;
+ private static boolean testVersionSupportsScufl2 = true;
+
+ private static String script = "executeworkflow.sh";
+ private static String baseName = "taverna-commandline-" + baseVersion;
+ private static String testName = "taverna-command-line-" + testVersion;
+ private static String releasedLocation = "https://launchpad.net/taverna/t2/";
+ private static String unreleasedLocation = "http://build.mygrid.org.uk/ci/job/t3-taverna-commandline-product/lastSuccessfulBuild/net.sf.taverna.t2$taverna-commandline/artifact/net.sf.taverna.t2/taverna-commandline/";
+
+ private static String baseVersionLocation = (baseVersionReleased ? releasedLocation
+ : unreleasedLocation) + baseVersion + "/+download/" + baseName + ".zip";
+ private static String testVersionLocation = (testVersionReleased ? releasedLocation
+ : unreleasedLocation)
+ + testVersion
+ + "/"
+ + testName
+ + (testVersionReleased ? ".zip" : "-bin.zip");
+
+ private static String baseCommand;
+ private static String testCommand;
+
+ private static File buildDirectory;
+
+ private File workflowDirectory;
+ private File baseOutput;
+ private File testOutput;
+ private boolean secure;
+ private List<File> inputs;
+ private String ignorePort;
+ private String message;
+
+ public TavernaCommandLineTest(File workflowDirectory) throws Exception {
+ this.workflowDirectory = workflowDirectory;
+ if (buildDirectory == null) {
+ String buildDirectoryLocation = System.getProperty("buildDirectory");
+ if (buildDirectoryLocation == null) {
+ buildDirectoryLocation = System.getProperty("user.dir")
+ + System.getProperty("file.separator") + "target";
+ }
+ buildDirectory = new File(buildDirectoryLocation);
+ buildDirectory.mkdirs();
+ }
+ if (baseCommand == null) {
+ File commandDirectory = new File(buildDirectory, baseName);
+ if (!commandDirectory.exists()) {
+ System.out.println("Fetching " + baseName);
+ fetchTaverna(baseVersionLocation, baseName);
+ }
+ baseCommand = new File(baseName, script).getPath();
+ }
+ if (testCommand == null) {
+ File commandDirectory = new File(buildDirectory, testName);
+ if (!commandDirectory.exists()) {
+ System.out.println("Fetching " + testName);
+ fetchTaverna(testVersionLocation, testName);
+ }
+ testCommand = new File(testName, script).getPath();
+ }
+ File outputsDirectory = new File(buildDirectory, "test-outputs");
+ baseOutput = new File(outputsDirectory, workflowDirectory.getName() + "-" + baseVersion);
+ testOutput = new File(outputsDirectory, workflowDirectory.getName() + "-" + testVersion);
+ secure = workflowDirectory.getName().startsWith("secure");
+ inputs = getInputs();
+ ignorePort = getIgnorePort();
+ message = "Running {0} with version {1}";
+ }
+
+ @Workflows
+ public static List<File> workflows() {
+ List<File> workflows = new ArrayList<File>();
+ for (File workflowDirectory : getResources("workflows")) {
+ workflows.add(workflowDirectory);
+ }
+ for (File workflowDirectory : getResources("myexperiment")) {
+ workflows.add(workflowDirectory);
+ }
+ return workflows;
+ }
+
+ @Before
+ public void setup() throws Exception {
+ if (!baseOutput.exists()) {
+ if (baseVersion.equals("2.3.0") && workflowDirectory.getName().equals("tool"))
+ return;// version 2.3.0 is missing tool plugin
+ String workflow = getWorkflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, baseVersion)
+ + (inputs.size() > 0 ? " using input values" : ""));
+ runWorkflow(baseCommand, workflow, baseOutput, true, secure, false);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ baseOutput.exists());
+ }
+ }
+
+ public boolean testExcluded() {
+ // version 3.0.0 is missing biomoby activity
+ if (testVersion.startsWith("3.") && workflowDirectory.getName().contains("biomoby"))
+ return true;
+ // version 3.0.0 is missing tool activity
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("unix_external_tools_with_zip_and_unzip"))
+ return true;
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("unix_numerically_adding_two_values"))
+ return true;
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("unix_tool_service_using_string_replacement"))
+ return true;
+ // version 3.0.0 is missing looping configuration
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("ebi_interproscan_newservices"))
+ return true;
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("biomartandembossanalysis"))
+ return true;
+ return false;
+ }
+
+ @Test
+ public void testWorkflowWithoutInputs() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(inputs.isEmpty());
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getWorkflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, testVersion));
+ runWorkflow(testCommand, workflow, testOutput, true, secure, false);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ @Test
+ public void testWorkflowWithInputValues() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(inputs.size() > 0);
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getWorkflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, testVersion)
+ + " using input values");
+ runWorkflow(testCommand, workflow, testOutput, true, secure, false);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ @Test
+ public void testWorkflowWithInputFiles() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(inputs.size() > 0);
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getWorkflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, testVersion)
+ + " using input files");
+ runWorkflow(testCommand, workflow, testOutput, false, secure, false);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ @Test
+ @Ignore
+ public void testWorkflowWithDatabase() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(inputs.size() > 0);
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getWorkflow().toASCIIString();
+ System.out
+ .println(MessageFormat.format(message, workflow, testVersion) + " using database");
+ runWorkflow(testCommand, workflow, testOutput, true, secure, true);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ @Test
+ public void testScufl2Workflow() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(testVersionSupportsScufl2);
+
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getScufl2Workflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, testVersion)
+ + (inputs.size() > 0 ? " using input values" : ""));
+ runWorkflow(testCommand, workflow, testOutput, true, secure, true);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ private synchronized void runWorkflow(String command, String workflow, File outputsDirectory,
+ boolean inputValues, boolean secure, boolean database) throws Exception {
+ ProcessBuilder processBuilder = new ProcessBuilder("sh", command);
+ processBuilder.redirectErrorStream(true);
+ processBuilder.directory(buildDirectory);
+ List<String> args = processBuilder.command();
+ for (File input : inputs) {
+ if (inputValues) {
+ args.add("-inputvalue");
+ args.add(input.getName());
+ args.add(IOUtils.toString(new FileReader(input)));
+ } else {
+ args.add("-inputfile");
+ args.add(input.getName());
+ args.add(input.getAbsolutePath());
+ }
+ }
+ args.add("-outputdir");
+ args.add(outputsDirectory.getPath());
+ if (secure) {
+ args.add("-cmdir");
+ args.add(getClass().getResource("/security").getFile());
+ args.add("-cmpassword");
+ }
+ if (database) {
+ args.add("-embedded");
+ }
+ args.add(workflow);
+ Process process = processBuilder.start();
+ if (secure) {
+ PrintStream outputStream = new PrintStream(process.getOutputStream());
+ outputStream.println("test");
+ outputStream.flush();
+ }
+ waitFor(process);
+ }
+
+ private URI getWorkflow() throws Exception {
+ File workflow = new File(workflowDirectory, workflowDirectory.getName() + ".t2flow");
+ if (!workflow.exists()) {
+ workflow = new File(workflowDirectory, workflowDirectory.getName() + ".url");
+ return new URI(IOUtils.toString(new FileReader(workflow)));
+ }
+ return workflow.toURI();
+ }
+
+ private URI getScufl2Workflow() throws Exception {
+ File workflow = new File(buildDirectory, workflowDirectory.getName() + ".wfbundle");
+ // if (!workflow.exists()) {
+ WorkflowBundleIO workflowBundleIO = new WorkflowBundleIO();
+ WorkflowBundle bundle = workflowBundleIO.readBundle(getWorkflow().toURL(), null);
+ workflowBundleIO.writeBundle(bundle, workflow,
+ RDFXMLReader.APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE);
+ // }
+ return workflow.toURI();
+ }
+
+ private synchronized int waitFor(Process process) throws IOException {
+ while (true) {
+ try {
+ wait(500);
+ } catch (InterruptedException e) {
+ }
+ IOUtils.copy(process.getInputStream(), System.out);
+ try {
+ return process.exitValue();
+ } catch (IllegalThreadStateException e) {
+ }
+ }
+ }
+
+ private void assertOutputsEquals(File directory1, File directory2) {
+ File[] directory1Files = directory1.listFiles();
+ File[] directory2Files = directory2.listFiles();
+ // assert directories contain same number of files
+ assertEquals(String.format("%s has %s files but %s has %s files", directory1.getName(),
+ directory1Files.length, directory2.getName(), directory2Files.length),
+ directory1Files.length, directory2Files.length);
+ // sort files in directory
+ Arrays.sort(directory1Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
+ Arrays.sort(directory2Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
+ for (int i = 0; i < directory1Files.length; i++) {
+ assertFilesEqual(directory1Files[i], directory2Files[i], !directory1Files[i].getName()
+ .equals(ignorePort));
+ }
+ }
+
+ private void assertDirectoriesEquals(File directory1, File directory2, boolean checkFileContents) {
+ if (directory1.exists()) {
+ assertTrue(String.format("%s exists but %s does not", directory1, directory2),
+ directory2.exists());
+ } else {
+ assertFalse(String.format("%s does not exists but %s does", directory1, directory2),
+ directory2.exists());
+ }
+ File[] directory1Files = directory1.listFiles();
+ File[] directory2Files = directory2.listFiles();
+ // assert directories contain same number of files
+ assertEquals(String.format("%s has %s files but %s has %s files", directory1.getName(),
+ directory1Files.length, directory2.getName(), directory2Files.length),
+ directory1Files.length, directory2Files.length);
+ // sort files in directory
+ Arrays.sort(directory1Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
+ Arrays.sort(directory2Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
+ for (int i = 0; i < directory1Files.length; i++) {
+ assertFilesEqual(directory1Files[i], directory2Files[i], checkFileContents);
+ }
+ }
+
+ private void assertFilesEqual(File file1, File file2, boolean checkFileContents) {
+ if (file1.isHidden()) {
+ assertTrue(String.format("%s is hidden but %s is not", file1, file2), file2.isHidden());
+ } else {
+ assertFalse(String.format("%s is not hidden but %s is", file1, file2), file2.isHidden());
+ assertEquals(file1.getName(), file2.getName());
+ if (file1.isDirectory()) {
+ assertTrue(String.format("%s is a directory but %s is not", file1, file2),
+ file2.isDirectory());
+ assertDirectoriesEquals(file1, file2, checkFileContents);
+ } else {
+ assertFalse(String.format("%s is not a directory but %s is", file1, file2),
+ file2.isDirectory());
+ if (isZipFile(file1)) {
+ assertZipFilesEqual(file1, file2);
+ } else if (checkFileContents) {
+ assertEquals(String.format("%s is a different length to %s", file1, file2),
+ file1.length(), file2.length());
+ try {
+ byte[] byteArray1 = IOUtils.toByteArray(new FileReader(file1));
+ byte[] byteArray2 = IOUtils.toByteArray(new FileReader(file2));
+ assertArrayEquals(String.format("%s != %s", file1, file2), byteArray1,
+ byteArray2);
+ } catch (FileNotFoundException e) {
+ fail(e.getMessage());
+ } catch (IOException e) {
+ fail(e.getMessage());
+ }
+ }
+ }
+ }
+ }
+
+ private void assertZipFilesEqual(File file1, File file2) {
+ ZipFile zipFile1 = null;
+ ZipFile zipFile2 = null;
+ try {
+ zipFile1 = new ZipFile(file1);
+ zipFile2 = new ZipFile(file2);
+ } catch (Exception e) {
+ assertTrue(String.format("%s and %s are not both zip files"), zipFile1 == null);
+ }
+ if (zipFile1 != null && zipFile2 != null) {
+ Enumeration<? extends ZipEntry> entries1 = zipFile1.entries();
+ Enumeration<? extends ZipEntry> entries2 = zipFile2.entries();
+ while (entries1.hasMoreElements()) {
+ assertTrue(entries2.hasMoreElements());
+ ZipEntry zipEntry1 = entries1.nextElement();
+ ZipEntry zipEntry2 = entries2.nextElement();
+ assertEquals(
+ String.format("%s and %s are not both directories", zipEntry1, zipEntry2),
+ zipEntry1.isDirectory(), zipEntry2.isDirectory());
+ assertEquals(String.format("%s and %s have different names", zipEntry1, zipEntry2),
+ zipEntry1.getName(), zipEntry2.getName());
+ assertEquals(String.format("%s and %s have different sizes", zipEntry1, zipEntry2),
+ zipEntry1.getSize(), zipEntry2.getSize());
+ try {
+ byte[] byteArray1 = IOUtils.toByteArray(zipFile1.getInputStream(zipEntry1));
+ byte[] byteArray2 = IOUtils.toByteArray(zipFile2.getInputStream(zipEntry2));
+ assertArrayEquals(String.format("%s != %s", zipEntry1, zipEntry2), byteArray1,
+ byteArray2);
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ assertFalse(entries2.hasMoreElements());
+ }
+ }
+
+ private boolean isZipFile(File file) {
+ try {
+ new ZipFile(file);
+ return true;
+ } catch (Exception e) {
+ return false;
+ }
+ }
+
+ private static File[] getResources(String directory) {
+ return new File(TavernaCommandLineTest.class.getResource("/" + directory).getFile())
+ .listFiles();
+ }
+
+ private List<File> getInputs() {
+ File inputsDirectory = new File(workflowDirectory, "inputs");
+ if (inputsDirectory.exists() && inputsDirectory.isDirectory()) {
+ return Arrays.asList(inputsDirectory.listFiles());
+ }
+ return Collections.emptyList();
+ }
+
+ private String getIgnorePort() throws Exception {
+ File ignorePort = new File(workflowDirectory, "ignorePort");
+ if (ignorePort.exists()) {
+ return IOUtils.toString(new FileReader(ignorePort));
+ }
+ return "";
+ }
+
+ private void fetchTaverna(String location, String name) throws Exception {
+ File zipFile = new File(buildDirectory, name + ".zip");
+ IOUtils.copy(new URL(location).openStream(), new FileOutputStream(zipFile));
+ ProcessBuilder processBuilder = new ProcessBuilder("unzip", "-q", name);
+ processBuilder.redirectErrorStream(true);
+ processBuilder.directory(buildDirectory);
+ System.out.println(processBuilder.command());
+ Process process = processBuilder.start();
+ waitFor(process);
+ }
+
+}
diff --git a/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java
new file mode 100644
index 0000000..56ed82d
--- /dev/null
+++ b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java
@@ -0,0 +1,70 @@
+/*******************************************************************************
+ * Copyright (C) 2012 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 uk.org.taverna.commandline;
+
+import java.io.File;
+import java.util.List;
+
+import org.junit.runner.notification.RunNotifier;
+import org.junit.runners.BlockJUnit4ClassRunner;
+import org.junit.runners.model.FrameworkMethod;
+import org.junit.runners.model.InitializationError;
+import org.junit.runners.model.Statement;
+
+/**
+ * Test runner for running workflows.
+ *
+ * @author David Withers
+ */
+public class WorkflowTestRunner extends BlockJUnit4ClassRunner {
+ private File workflow;
+
+ public WorkflowTestRunner(Class<?> type, File workflow) throws InitializationError {
+ super(type);
+ this.workflow = workflow;
+ }
+
+ @Override
+ public Object createTest() throws Exception {
+ return getTestClass().getOnlyConstructor().newInstance(workflow);
+ }
+
+ @Override
+ protected String getName() {
+ return String.format("[%s]", workflow.getName());
+ }
+
+ @Override
+ protected String testName(final FrameworkMethod method) {
+ return String.format("%s[%s]", method.getName(), workflow.getName());
+ }
+
+ @Override
+ protected void validateConstructor(List<Throwable> errors) {
+ validateOnlyOneConstructor(errors);
+ }
+
+ @Override
+ protected Statement classBlock(RunNotifier notifier) {
+ return childrenInvoker(notifier);
+ }
+
+}
diff --git a/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java
new file mode 100644
index 0000000..140dec6
--- /dev/null
+++ b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java
@@ -0,0 +1,79 @@
+/*******************************************************************************
+ * Copyright (C) 2012 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 uk.org.taverna.commandline;
+
+import java.io.File;
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+import java.lang.reflect.Modifier;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.junit.runner.Runner;
+import org.junit.runners.Suite;
+import org.junit.runners.model.FrameworkMethod;
+import org.junit.runners.model.TestClass;
+
+/**
+ * Test suite for running workflows specified by a method annotated by @Workflows.
+ *
+ * @author David Withers
+ */
+public class WorkflowTestSuite extends Suite {
+
+ @Retention(RetentionPolicy.RUNTIME)
+ @Target(ElementType.METHOD)
+ public static @interface Workflows {}
+
+ private ArrayList<Runner> runners = new ArrayList<Runner>();
+
+ public WorkflowTestSuite(Class<?> klass) throws Throwable {
+ super(klass, Collections.<Runner>emptyList());
+ for (File workflow : getWorkflows(getTestClass())) {
+ runners.add(new WorkflowTestRunner(getTestClass().getJavaClass(), workflow));
+ }
+ }
+
+ @Override
+ protected List<Runner> getChildren() {
+ return runners;
+ }
+
+ @SuppressWarnings("unchecked")
+ private List<File> getWorkflows(TestClass klass) throws Throwable {
+ return (List<File>) getWorkflowsMethod(klass).invokeExplosively(null);
+ }
+
+ public FrameworkMethod getWorkflowsMethod(TestClass testClass) throws Exception {
+ List<FrameworkMethod> methods = testClass.getAnnotatedMethods(Workflows.class);
+ for (FrameworkMethod method : methods) {
+ int modifiers = method.getMethod().getModifiers();
+ if (Modifier.isStatic(modifiers) && Modifier.isPublic(modifiers)) {
+ return method;
+ }
+ }
+ throw new Exception("No public static Workflows annotated method on class " + testClass.getName());
+ }
+
+}
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url b/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url
new file mode 100644
index 0000000..5846961
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1794/download/biomartandembossanalysis_457009.t2flow?version=4
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/ignorePort b/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/ignorePort
new file mode 100644
index 0000000..e0cb526
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/ignorePort
@@ -0,0 +1 @@
+outputPlot
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/biomoby_tutorial_workflow.url b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/biomoby_tutorial_workflow.url
new file mode 100644
index 0000000..a73b8c4
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/biomoby_tutorial_workflow.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1366/download/biomoby_tutorial_workflow_877727.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/ignorePort b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/ignorePort
new file mode 100644
index 0000000..f8e22dd
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/ignorePort
@@ -0,0 +1 @@
+restrict_out
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/id b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/id
new file mode 100644
index 0000000..1dfd176
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/id
@@ -0,0 +1 @@
+656461
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/namespace b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/namespace
new file mode 100644
index 0000000..c188363
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/namespace
@@ -0,0 +1 @@
+NCBI_gi
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/demonstration_of_configurable_iteration/demonstration_of_configurable_iteration.url b/taverna-commandline-tests/src/test/resources/myexperiment/demonstration_of_configurable_iteration/demonstration_of_configurable_iteration.url
new file mode 100644
index 0000000..38abe3a
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/demonstration_of_configurable_iteration/demonstration_of_configurable_iteration.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1367/download/demonstration_of_configurable_iteration_114130.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/ebi_interproscan_newservices.url b/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/ebi_interproscan_newservices.url
new file mode 100644
index 0000000..a329afc
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/ebi_interproscan_newservices.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1767/download/ebi_interproscan_newservices_421482.t2flow?version=2
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/ignorePort b/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/ignorePort
new file mode 100644
index 0000000..1ec3d86
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/ignorePort
@@ -0,0 +1 @@
+Graphical_output
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/email b/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/email
new file mode 100644
index 0000000..38133d0
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/email
@@ -0,0 +1 @@
+test@mygrid.org.uk
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/sequence b/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/sequence
new file mode 100644
index 0000000..19a43dd
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/sequence
@@ -0,0 +1,8 @@
+>sp|Q9BTV4|TMM43_HUMAN Transmembrane protein 43 OS=Homo sapiens GN=TMEM43 PE=1 SV=1
+MAANYSSTSTRREHVKVKTSSQPGFLERLSETSGGMFVGLMAFLLSFYLIFTNEGRALKT
+ATSLAEGLSLVVSPDSIHSVAPENEGRLVHIIGALRTSKLLSDPNYGVHLPAVKLRRHVE
+MYQWVETEESREYTEDGQVKKETRYSYNTEWRSEIINSKNFDREIGHKNPSAMAVESFMA
+TAPFVQIGRFFLSSGLIDKVDNFKSLSLSKLEDPHVDIIRRGDFFYHSENPKYPEVGDLR
+VSFSYAGLSGDDPDLGPAHVVTVIARQRGDQLVPFSTKSGDTLLLLHHGDFSAEEVFHRE
+LRSNSMKTWGLRAAGWMAMFMGLNLMTRILYTLVDWFPVFRDLVNIGLKAFAFCVATSLT
+LLTVAAGWLFYRPLWALLIAGLALVPILVARTRVPAKKLE
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/example_of_conditional_invocation/example_of_conditional_invocation.url b/taverna-commandline-tests/src/test/resources/myexperiment/example_of_conditional_invocation/example_of_conditional_invocation.url
new file mode 100644
index 0000000..350a27f
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/example_of_conditional_invocation/example_of_conditional_invocation.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/2561/download/example_of_conditional_invocation_369634.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/example_of_conditional_invocation/inputs/condition b/taverna-commandline-tests/src/test/resources/myexperiment/example_of_conditional_invocation/inputs/condition
new file mode 100644
index 0000000..f32a580
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/example_of_conditional_invocation/inputs/condition
@@ -0,0 +1 @@
+true
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/example_of_explicit_looping.url b/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/example_of_explicit_looping.url
new file mode 100644
index 0000000..a8773c4
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/example_of_explicit_looping.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/2562/download/example_of_explicit_looping_785852.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/inputs/end b/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/inputs/end
new file mode 100644
index 0000000..da2d398
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/inputs/end
@@ -0,0 +1 @@
+14
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/inputs/start b/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/inputs/start
new file mode 100644
index 0000000..7d105a7
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/inputs/start
@@ -0,0 +1 @@
+-3
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/inputs/step b/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/inputs/step
new file mode 100644
index 0000000..e440e5c
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/inputs/step
@@ -0,0 +1 @@
+3
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/example_workflow_for_rest_and_xpath_activities.url b/taverna-commandline-tests/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/example_workflow_for_rest_and_xpath_activities.url
new file mode 100644
index 0000000..bd3ff3d
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/example_workflow_for_rest_and_xpath_activities.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1510/download/example_workflow_for_rest_and_xpath_activities_650957.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/inputs/Name_Of_Location_for_Weather_Forecast b/taverna-commandline-tests/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/inputs/Name_Of_Location_for_Weather_Forecast
new file mode 100644
index 0000000..bbab6f1
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/inputs/Name_Of_Location_for_Weather_Forecast
@@ -0,0 +1 @@
+London
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/fetch_dragon_images_from_biomoby/fetch_dragon_images_from_biomoby.url b/taverna-commandline-tests/src/test/resources/myexperiment/fetch_dragon_images_from_biomoby/fetch_dragon_images_from_biomoby.url
new file mode 100644
index 0000000..1aeab4b
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/fetch_dragon_images_from_biomoby/fetch_dragon_images_from_biomoby.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1005/download/fetch_dragon_images_from_biomoby_830269.t2flow?version=2
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/fetch_pdb_flatfile_from_rcsb_server/fetch_pdb_flatfile_from_rcsb_server.url b/taverna-commandline-tests/src/test/resources/myexperiment/fetch_pdb_flatfile_from_rcsb_server/fetch_pdb_flatfile_from_rcsb_server.url
new file mode 100644
index 0000000..5d10074
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/fetch_pdb_flatfile_from_rcsb_server/fetch_pdb_flatfile_from_rcsb_server.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1369/download/fetch_pdb_flatfile_from_rcsb_server_969361.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/fetch_pdb_flatfile_from_rcsb_server/inputs/pdbID b/taverna-commandline-tests/src/test/resources/myexperiment/fetch_pdb_flatfile_from_rcsb_server/inputs/pdbID
new file mode 100644
index 0000000..7f3db81
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/fetch_pdb_flatfile_from_rcsb_server/inputs/pdbID
@@ -0,0 +1 @@
+1crn
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/fetch_today_s_xkcd_comic/fetch_today_s_xkcd_comic.url b/taverna-commandline-tests/src/test/resources/myexperiment/fetch_today_s_xkcd_comic/fetch_today_s_xkcd_comic.url
new file mode 100644
index 0000000..48f849f
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/fetch_today_s_xkcd_comic/fetch_today_s_xkcd_comic.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1370/download/fetch_today_s_xkcd_comic_568671.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/gbseq_test/gbseq_test.url b/taverna-commandline-tests/src/test/resources/myexperiment/gbseq_test/gbseq_test.url
new file mode 100644
index 0000000..c0f40c5
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/gbseq_test/gbseq_test.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1371/download/gbseq_test_457824.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/hello_anyone/hello_anyone.url b/taverna-commandline-tests/src/test/resources/myexperiment/hello_anyone/hello_anyone.url
new file mode 100644
index 0000000..f4181b8
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/hello_anyone/hello_anyone.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/2649/download/hello_anyone_895936.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/hello_anyone/inputs/name b/taverna-commandline-tests/src/test/resources/myexperiment/hello_anyone/inputs/name
new file mode 100644
index 0000000..d565a0b
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/hello_anyone/inputs/name
@@ -0,0 +1 @@
+Fred
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/hello_world/hello_world.url b/taverna-commandline-tests/src/test/resources/myexperiment/hello_world/hello_world.url
new file mode 100644
index 0000000..c596de4
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/hello_world/hello_world.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/2648/download/hello_world_190236.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/pipelined_list_iteration/inputs/input b/taverna-commandline-tests/src/test/resources/myexperiment/pipelined_list_iteration/inputs/input
new file mode 100644
index 0000000..4701cc7
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/pipelined_list_iteration/inputs/input
@@ -0,0 +1 @@
+150
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/pipelined_list_iteration/pipelined_list_iteration.url b/taverna-commandline-tests/src/test/resources/myexperiment/pipelined_list_iteration/pipelined_list_iteration.url
new file mode 100644
index 0000000..dd3c98c
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/pipelined_list_iteration/pipelined_list_iteration.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1372/download/pipelined_list_iteration_902021.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/retrieve_sequence_in_embl_format/retrieve_sequence_in_embl_format.url b/taverna-commandline-tests/src/test/resources/myexperiment/retrieve_sequence_in_embl_format/retrieve_sequence_in_embl_format.url
new file mode 100644
index 0000000..2b4ab46
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/retrieve_sequence_in_embl_format/retrieve_sequence_in_embl_format.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1373/download/retrieve_sequence_in_embl_format_32794.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/secure_rest_service_call_example/secure_rest_service_call_example.url b/taverna-commandline-tests/src/test/resources/myexperiment/secure_rest_service_call_example/secure_rest_service_call_example.url
new file mode 100644
index 0000000..03cf409
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/secure_rest_service_call_example/secure_rest_service_call_example.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/2253/download/secure_rest_service_call_example_19600.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/secure_web_service_call_example/secure_web_service_call_example.url b/taverna-commandline-tests/src/test/resources/myexperiment/secure_web_service_call_example/secure_web_service_call_example.url
new file mode 100644
index 0000000..c2a4ad4
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/secure_web_service_call_example/secure_web_service_call_example.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/2254/download/secure_web_service_call_example_565494.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/spreadsheed_data_import_example/spreadsheed_data_import_example.url b/taverna-commandline-tests/src/test/resources/myexperiment/spreadsheed_data_import_example/spreadsheed_data_import_example.url
new file mode 100644
index 0000000..98d8ed4
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/spreadsheed_data_import_example/spreadsheed_data_import_example.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1417/download/spreadsheed_data_import_example_492836.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/unix_external_tools_with_zip_and_unzip/unix_external_tools_with_zip_and_unzip.url b/taverna-commandline-tests/src/test/resources/myexperiment/unix_external_tools_with_zip_and_unzip/unix_external_tools_with_zip_and_unzip.url
new file mode 100644
index 0000000..958de61
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/unix_external_tools_with_zip_and_unzip/unix_external_tools_with_zip_and_unzip.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/2230/download/example_for_external_tools_with_zip_and_unzip_57117.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/inputs/a b/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/inputs/a
new file mode 100644
index 0000000..56a6051
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/inputs/a
@@ -0,0 +1 @@
+1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/inputs/b b/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/inputs/b
new file mode 100644
index 0000000..d8263ee
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/inputs/b
@@ -0,0 +1 @@
+2
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/unix_numerically_adding_two_values.url b/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/unix_numerically_adding_two_values.url
new file mode 100644
index 0000000..72ef715
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/unix_numerically_adding_two_values.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/2231/download/numerically_adding_two_values._763485.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/unix_tool_service_using_string_replacement/unix_tool_service_using_string_replacement.url b/taverna-commandline-tests/src/test/resources/myexperiment/unix_tool_service_using_string_replacement/unix_tool_service_using_string_replacement.url
new file mode 100644
index 0000000..155d7e4
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/unix_tool_service_using_string_replacement/unix_tool_service_using_string_replacement.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/2229/download/unix_tool_service_using_string_replacement_219870.t2flow?version=1
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/security/t2keystore.ubr b/taverna-commandline-tests/src/test/resources/security/t2keystore.ubr
new file mode 100644
index 0000000..c79eddf
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/security/t2keystore.ubr
Binary files differ
diff --git a/taverna-commandline-tests/src/test/resources/security/t2truststore.ubr b/taverna-commandline-tests/src/test/resources/security/t2truststore.ubr
new file mode 100644
index 0000000..ec1717d
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/security/t2truststore.ubr
Binary files differ
diff --git a/taverna-commandline-tests/src/test/resources/security/taverna-keystore.ubr b/taverna-commandline-tests/src/test/resources/security/taverna-keystore.ubr
new file mode 100644
index 0000000..c79eddf
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/security/taverna-keystore.ubr
Binary files differ
diff --git a/taverna-commandline-tests/src/test/resources/security/taverna-truststore.ubr b/taverna-commandline-tests/src/test/resources/security/taverna-truststore.ubr
new file mode 100644
index 0000000..ec1717d
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/security/taverna-truststore.ubr
Binary files differ
diff --git a/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/apiconsumer.t2flow b/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/apiconsumer.t2flow
new file mode 100644
index 0000000..66ef4ac
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/apiconsumer.t2flow
@@ -0,0 +1,178 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="8bf2b5e5-a3e0-4fbd-bfd2-aefc7b2a6b8a" role="top"><name>Workflow4</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>String</name><inputPorts><port><name>string</name><depth>0</depth></port></inputPorts><outputPorts><port><name>object</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>apiconsumer-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity</class><inputMap><map from="string" to="string" /></inputMap><outputMap><map from="object" to="object" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean xmlns="">
+ <inputs />
+ <outputs />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <apiConsumerName>No name</apiConsumerName>
+ <apiConsumerDescription>No description</apiConsumerDescription>
+ <description />
+ <className>java.lang.String</className>
+ <methodName>String</methodName>
+ <parameterNames>
+ <string>string</string>
+ </parameterNames>
+ <parameterDimensions>
+ <int>0</int>
+ </parameterDimensions>
+ <parameterTypes>
+ <string>java.lang.String</string>
+ </parameterTypes>
+ <returnType>java.lang.String</returnType>
+ <returnDimension>0</returnDimension>
+ <isMethodStatic>false</isMethodStatic>
+ <isMethodConstructor>true</isMethodConstructor>
+</net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="string" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>toUpperCase</name><inputPorts><port><name>object</name><depth>0</depth></port></inputPorts><outputPorts><port><name>result</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>apiconsumer-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity</class><inputMap><map from="object" to="object" /></inputMap><outputMap><map from="result" to="result" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean xmlns="">
+ <inputs />
+ <outputs />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <apiConsumerName>No name</apiConsumerName>
+ <apiConsumerDescription>No description</apiConsumerDescription>
+ <description />
+ <className>java.lang.String</className>
+ <methodName>toUpperCase</methodName>
+ <parameterNames />
+ <parameterDimensions />
+ <parameterTypes />
+ <returnType>java.lang.String</returnType>
+ <returnDimension>0</returnDimension>
+ <isMethodStatic>false</isMethodStatic>
+ <isMethodConstructor>false</isMethodConstructor>
+</net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="object" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>String</processor><port>string</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>toUpperCase</processor><port>object</port></sink><source type="processor"><processor>String</processor><port>object</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>toUpperCase</processor><port>result</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>483d65c6-98c1-4b94-b628-d5bcbf351e97</identification>
+ </annotationBean>
+ <date>2011-05-16 13:07:03.385 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>d460e60a-43bb-47fc-a9f4-89e15274b100</identification>
+ </annotationBean>
+ <date>2011-11-02 12:43:09.911 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>0d977496-aa5d-4274-9827-85400d5f13a2</identification>
+ </annotationBean>
+ <date>2011-05-16 13:06:33.69 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>8bf2b5e5-a3e0-4fbd-bfd2-aefc7b2a6b8a</identification>
+ </annotationBean>
+ <date>2011-11-02 12:46:41.313 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>58f30a52-57df-46ce-b1bb-b9533984f8dd</identification>
+ </annotationBean>
+ <date>2011-11-02 12:29:15.575 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>c2693c41-1373-48cf-afbe-d8bbe0ea9e35</identification>
+ </annotationBean>
+ <date>2011-11-02 12:31:01.678 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>1ce7f3a0-71f4-4794-8bbd-dbb6de42442d</identification>
+ </annotationBean>
+ <date>2011-05-16 12:57:01.975 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>4c2b6995-eecb-47a7-b72c-63cfb96b6852</identification>
+ </annotationBean>
+ <date>2011-11-02 12:43:51.355 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>225db881-4e07-4cdb-920c-343dc1536edc</identification>
+ </annotationBean>
+ <date>2011-05-16 13:10:54.588 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>404e203c-ce51-4a9f-907c-1dab7f2eaaa2</identification>
+ </annotationBean>
+ <date>2011-05-16 12:44:02.533 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>0b6881f1-aa8d-483e-a7bb-7ad38b1da778</identification>
+ </annotationBean>
+ <date>2011-05-16 12:26:38.721 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/inputs/in b/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/inputs/in
new file mode 100644
index 0000000..fede229
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/inputs/in
@@ -0,0 +1 @@
+test-input
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/beanshell/beanshell.t2flow b/taverna-commandline-tests/src/test/resources/workflows/beanshell/beanshell.t2flow
new file mode 100644
index 0000000..8c5968c
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/beanshell/beanshell.t2flow
@@ -0,0 +1,137 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="78cb1427-d57f-42c2-a385-1d20c1580f3b" role="top"><name>Workflow13</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Echo</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out=in;</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>ListGenerator</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out = new ArrayList();
+
+for (int i = 0; i < 1000; i++) {
+ out.add(in + ":" + i);
+}</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>out</name>
+ <depth>1</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Echo</processor><port>in</port></sink><source type="processor"><processor>ListGenerator</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>ListGenerator</processor><port>in</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Echo</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>13c70169-dfaa-4ea6-b6ab-3551dae7fa84</identification>
+ </annotationBean>
+ <date>2010-08-19 12:28:57.881 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>7ef10e93-7376-41a9-9255-552149094142</identification>
+ </annotationBean>
+ <date>2010-08-31 13:06:57.536 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>3b7c0b9c-572d-466b-af6d-0fb40699e8a5</identification>
+ </annotationBean>
+ <date>2010-08-31 12:50:40.306 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eb6a550d-f34e-4de9-b0fc-1b3df8ab36c4</identification>
+ </annotationBean>
+ <date>2010-08-31 14:32:44.634 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>78cb1427-d57f-42c2-a385-1d20c1580f3b</identification>
+ </annotationBean>
+ <date>2010-08-31 14:36:00.297 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ad638364-a6e0-4852-abca-9f609c9553d2</identification>
+ </annotationBean>
+ <date>2010-08-19 13:43:43.797 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/beanshell/inputs/in b/taverna-commandline-tests/src/test/resources/workflows/beanshell/inputs/in
new file mode 100644
index 0000000..fede229
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/beanshell/inputs/in
@@ -0,0 +1 @@
+test-input
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/biomart/biomart.t2flow b/taverna-commandline-tests/src/test/resources/workflows/biomart/biomart.t2flow
new file mode 100644
index 0000000..f82f340
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/biomart/biomart.t2flow
@@ -0,0 +1,30 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="4a959e22-8166-4e8b-ae94-6e85c8807e35" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>btaurus_gene_ensembl</name><inputPorts /><outputPorts><port><name>btaurus_gene_ensembl.ensembl_gene_id</name><depth>1</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomart-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.biomart.BiomartActivity</class><inputMap /><outputMap><map from="btaurus_gene_ensembl.ensembl_gene_id" to="btaurus_gene_ensembl.ensembl_gene_id" /></outputMap><configBean encoding="jdomxml"><MartQuery xmlns=""><MartService location="http://www.biomart.org/biomart/martservice" /><MartDataset displayName="Bos taurus genes (UMD3.1)" name="btaurus_gene_ensembl" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2011-09-07 22:16:01"><MartURLLocation database="ensembl_mart_64" default="1" displayName="ENSEMBL GENES 64 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice" port="80" serverVirtualSchema="default" virtualSchema="default" visible="1" redirect="0" /></MartDataset><Query virtualSchemaName="default" count="0" uniqueRows="1" softwareVersion="0.6" requestId="taverna"><Dataset name="btaurus_gene_ensembl"><Attribute name="ensembl_gene_id" /><Filter name="chromosome_name" value="1" /><Filter name="with_affy_bovine" excluded="0" /><Filter name="go_evidence_code" value="IDA" /></Dataset></Query></MartQuery></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>btaurus_gene_ensembl</processor><port>btaurus_gene_ensembl.ensembl_gene_id</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>4a959e22-8166-4e8b-ae94-6e85c8807e35</identification>
+ </annotationBean>
+ <date>2011-10-27 14:33:16.228 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>5859741c-a0ba-4dae-8b81-1dd7c928562f</identification>
+ </annotationBean>
+ <date>2011-10-27 14:32:47.106 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/dataflow/dataflow.t2flow b/taverna-commandline-tests/src/test/resources/workflows/dataflow/dataflow.t2flow
new file mode 100644
index 0000000..c9366c2
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/dataflow/dataflow.t2flow
@@ -0,0 +1,217 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="ac4ce40a-57b9-486c-bb4c-eb8609c6cc48" role="top"><name>Workflow1</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Nested_workflow</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="dataflow"><dataflow ref="c6b258ac-3588-4828-b71c-207bad8b63c4" /></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>echo</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ <granularDepth>0</granularDepth>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <script>out = in;</script>
+ <dependencies />
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>echo_2</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ <granularDepth>0</granularDepth>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <script>out = in;</script>
+ <dependencies />
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Nested_workflow</processor><port>in</port></sink><source type="processor"><processor>echo</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>echo</processor><port>in</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>echo_2</processor><port>in</port></sink><source type="processor"><processor>Nested_workflow</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>echo_2</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>437a237a-03a0-489f-97c6-fd5acc5db18e</identification>
+ </annotationBean>
+ <date>2011-11-09 10:59:10.221 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ae7626c8-13a4-4560-9496-59a8cc0693be</identification>
+ </annotationBean>
+ <date>2011-02-16 11:57:10.514 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>96d450ff-aaf8-473b-91a1-4acce7371c3b</identification>
+ </annotationBean>
+ <date>2011-02-16 11:55:55.618 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ac4ce40a-57b9-486c-bb4c-eb8609c6cc48</identification>
+ </annotationBean>
+ <date>2011-11-09 11:02:29.60 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>9f957cde-a7ad-4453-a09f-7231c8c8c4f3</identification>
+ </annotationBean>
+ <date>2011-02-16 11:52:40.88 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>f847ed6f-2834-4861-a8af-73ab737c6a91</identification>
+ </annotationBean>
+ <date>2011-11-09 11:00:41.783 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="c6b258ac-3588-4828-b71c-207bad8b63c4" role="nested"><name>Workflow4</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>echo</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ <granularDepth>0</granularDepth>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <script>out = "nested dataflow : " + in;</script>
+ <dependencies />
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>echo</processor><port>in</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>echo</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>f8dd3fb7-7051-4242-a3af-d82056934cf6</identification>
+ </annotationBean>
+ <date>2011-02-16 11:55:01.559 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>0a0b6f17-8ebf-4017-ad4c-0719a9d44806</identification>
+ </annotationBean>
+ <date>2011-11-09 11:00:37.241 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>c6b258ac-3588-4828-b71c-207bad8b63c4</identification>
+ </annotationBean>
+ <date>2011-11-09 11:02:26.99 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eaa8b2a0-e71b-4d6a-b8ad-c299a8ad6e18</identification>
+ </annotationBean>
+ <date>2011-02-16 11:53:12.59 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/dataflow/inputs/in b/taverna-commandline-tests/src/test/resources/workflows/dataflow/inputs/in
new file mode 100644
index 0000000..fede229
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/dataflow/inputs/in
@@ -0,0 +1 @@
+test-input
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/in-out/in-out.t2flow b/taverna-commandline-tests/src/test/resources/workflows/in-out/in-out.t2flow
new file mode 100644
index 0000000..ecfb4e8
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/in-out/in-out.t2flow
@@ -0,0 +1,12 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="4d8a491e-fa11-4918-98ce-7df19051d5c5" role="top"><name>Workflow6</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors /><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="dataflow"><port>in</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>4d8a491e-fa11-4918-98ce-7df19051d5c5</identification>
+ </annotationBean>
+ <date>2012-04-03 15:34:41.4 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/in-out/inputs/in b/taverna-commandline-tests/src/test/resources/workflows/in-out/inputs/in
new file mode 100644
index 0000000..fede229
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/in-out/inputs/in
@@ -0,0 +1 @@
+test-input
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/iteration/inputs/in b/taverna-commandline-tests/src/test/resources/workflows/iteration/inputs/in
new file mode 100644
index 0000000..30d74d2
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/iteration/inputs/in
@@ -0,0 +1 @@
+test
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/iteration/iteration.t2flow b/taverna-commandline-tests/src/test/resources/workflows/iteration/iteration.t2flow
new file mode 100644
index 0000000..bec4c2d
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/iteration/iteration.t2flow
@@ -0,0 +1,474 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="80c80b32-1faa-4c8e-9294-eb85d6aaa764" role="top"><name>Workflow13</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>cross</name><annotations /></port><port><name>dot</name><annotations /></port><port><name>crossdot</name><annotations /></port><port><name>dotdot</name><annotations /></port><port><name>dotcross</name><annotations /></port></outputPorts><processors><processor><name>cross</name><inputPorts><port><name>in1</name><depth>0</depth></port><port><name>in2</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out=in1 + in2;</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in1</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in2</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in1" depth="0" /><port name="in2" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>ListGenerator1</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out = new ArrayList();
+
+for (int i = 0; i < 10; i++) {
+ out.add(in + ":" + i);
+}</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>out</name>
+ <depth>1</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>ListGenerator2</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out = new ArrayList();
+
+for (int i = 0; i < 10; i++) {
+ out.add(in + ":" + i);
+}</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>out</name>
+ <depth>1</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>dot</name><inputPorts><port><name>in2</name><depth>0</depth></port><port><name>in1</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out=in1 + in2;</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in1</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in2</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><dot><port name="in2" depth="0" /><port name="in1" depth="0" /></dot></strategy></iteration></iterationStrategyStack></processor><processor><name>crossdot</name><inputPorts><port><name>in1</name><depth>0</depth></port><port><name>in2</name><depth>0</depth></port><port><name>in3</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /><map from="in3" to="in3" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out = in1 + in2 + in3;</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in1</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in2</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in3</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in1" depth="0" /><port name="in2" depth="0" /><dot><port name="in3" depth="0" /></dot></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>dotcross</name><inputPorts><port><name>in1</name><depth>0</depth></port><port><name>in2</name><depth>0</depth></port><port><name>in3</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /><map from="in3" to="in3" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out = in1 + in2 + in3;</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in1</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in2</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in3</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in3" depth="0" /><dot><port name="in2" depth="0" /><port name="in1" depth="0" /></dot></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>dotdot</name><inputPorts><port><name>in1</name><depth>0</depth></port><port><name>in2</name><depth>0</depth></port><port><name>in3</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /><map from="in3" to="in3" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out = in1 + in2 + in3;</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in1</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in2</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in3</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><dot><port name="in1" depth="0" /><port name="in2" depth="0" /><dot><port name="in3" depth="0" /></dot></dot></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>cross</processor><port>in1</port></sink><source type="processor"><processor>ListGenerator1</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>cross</processor><port>in2</port></sink><source type="processor"><processor>ListGenerator2</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>ListGenerator1</processor><port>in</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>ListGenerator2</processor><port>in</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>dot</processor><port>in2</port></sink><source type="processor"><processor>ListGenerator2</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>dot</processor><port>in1</port></sink><source type="processor"><processor>ListGenerator1</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>crossdot</processor><port>in1</port></sink><source type="processor"><processor>ListGenerator1</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>crossdot</processor><port>in2</port></sink><source type="processor"><processor>ListGenerator2</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>crossdot</processor><port>in3</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>dotcross</processor><port>in1</port></sink><source type="processor"><processor>ListGenerator1</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>dotcross</processor><port>in2</port></sink><source type="processor"><processor>ListGenerator2</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>dotcross</processor><port>in3</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>dotdot</processor><port>in1</port></sink><source type="processor"><processor>ListGenerator1</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>dotdot</processor><port>in2</port></sink><source type="processor"><processor>ListGenerator2</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>dotdot</processor><port>in3</port></sink><source type="processor"><processor>ListGenerator2</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>cross</port></sink><source type="processor"><processor>cross</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>dot</port></sink><source type="processor"><processor>dot</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>crossdot</port></sink><source type="processor"><processor>crossdot</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>dotdot</port></sink><source type="processor"><processor>dotdot</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>dotcross</port></sink><source type="processor"><processor>dotcross</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ad638364-a6e0-4852-abca-9f609c9553d2</identification>
+ </annotationBean>
+ <date>2010-08-19 13:43:43.797 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>3fb7f0a7-26f8-43e1-a122-87a25889f57d</identification>
+ </annotationBean>
+ <date>2011-02-22 08:25:53.793 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>13c70169-dfaa-4ea6-b6ab-3551dae7fa84</identification>
+ </annotationBean>
+ <date>2010-08-19 12:28:57.881 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>af1f698b-820d-4b35-a92e-9091c90b493e</identification>
+ </annotationBean>
+ <date>2011-02-22 09:30:17.881 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>be50375c-4f68-44aa-8604-9a80d8d97570</identification>
+ </annotationBean>
+ <date>2011-02-22 09:03:28.97 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eb6a550d-f34e-4de9-b0fc-1b3df8ab36c4</identification>
+ </annotationBean>
+ <date>2010-08-31 14:32:44.634 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ac70d4c0-5db9-48b1-ba32-8e11fff8ae59</identification>
+ </annotationBean>
+ <date>2011-02-22 08:31:32.90 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>78cb1427-d57f-42c2-a385-1d20c1580f3b</identification>
+ </annotationBean>
+ <date>2010-08-31 14:36:00.297 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>3b7c0b9c-572d-466b-af6d-0fb40699e8a5</identification>
+ </annotationBean>
+ <date>2010-08-31 12:50:40.306 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>7a22acbb-2f0f-41dd-a526-d2a9b4e267c5</identification>
+ </annotationBean>
+ <date>2011-02-22 08:59:59.964 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>80c80b32-1faa-4c8e-9294-eb85d6aaa764</identification>
+ </annotationBean>
+ <date>2011-02-22 09:40:37.744 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>bc9c64da-9143-4811-a22e-657c92fcfe94</identification>
+ </annotationBean>
+ <date>2011-02-22 09:23:49.109 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>c072030e-b367-4885-a770-7d892672d979</identification>
+ </annotationBean>
+ <date>2011-02-22 09:31:03.727 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>7ef10e93-7376-41a9-9255-552149094142</identification>
+ </annotationBean>
+ <date>2010-08-31 13:06:57.536 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/localworker/inputs/in b/taverna-commandline-tests/src/test/resources/workflows/localworker/inputs/in
new file mode 100644
index 0000000..cadf8b6
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/localworker/inputs/in
@@ -0,0 +1 @@
+Tom
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/localworker/localworker.t2flow b/taverna-commandline-tests/src/test/resources/workflows/localworker/localworker.t2flow
new file mode 100644
index 0000000..b3b2053
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/localworker/localworker.t2flow
@@ -0,0 +1,67 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="5eebce20-72f5-4ac7-a4bf-8086d59d0c9e" role="top"><name>Workflow5</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Concatenate_two_strings</name><inputPorts><port><name>string2</name><depth>0</depth></port><port><name>string1</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="string2" to="string2" /><map from="string1" to="string1" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
+ <script>output = string1 + string2;</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>string1</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>string2</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>output</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="string2" depth="0" /><port name="string1" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>string1_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Hello </value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string2</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string1</port></sink><source type="processor"><processor>string1_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Concatenate_two_strings</processor><port>output</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>5eebce20-72f5-4ac7-a4bf-8086d59d0c9e</identification>
+ </annotationBean>
+ <date>2011-02-21 13:44:43.621 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/rest/rest.t2flow b/taverna-commandline-tests/src/test/resources/workflows/rest/rest.t2flow
new file mode 100644
index 0000000..f3f90b8
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/rest/rest.t2flow
@@ -0,0 +1,154 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="8e36176a-2975-498b-93f7-f2beba774532" role="top"><name>Workflow11</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>REST_Service</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
+ <httpMethod>GET</httpMethod>
+ <urlSignature>http://www.uniprot.org/uniprot/{id}.xml</urlSignature>
+ <acceptsHeaderValue>text/plain</acceptsHeaderValue>
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>
+ <outgoingDataFormat>String</outgoingDataFormat>
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>
+ <escapeParameters>true</escapeParameters>
+ <otherHTTPHeaders />
+ <activityInputs>
+ <entry>
+ <string>id</string>
+ <java-class>java.lang.String</java-class>
+ </entry>
+ </activityInputs>
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>id_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>P12345</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>REST_Service</processor><port>id</port></sink><source type="processor"><processor>id_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>REST_Service</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>30c58a3d-4037-4b92-b7d6-3aea761bdada</identification>
+ </annotationBean>
+ <date>2011-11-02 08:52:32.796 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>d090ff3c-c84d-461f-9027-ccd07fe0a352</identification>
+ </annotationBean>
+ <date>2011-11-02 10:09:35.558 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>1e2069a6-54c3-4e09-b639-c9bb27356eb9</identification>
+ </annotationBean>
+ <date>2011-11-02 09:59:38.235 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>f88604da-4047-4ab9-bd19-23cbbb8be88b</identification>
+ </annotationBean>
+ <date>2011-11-02 10:12:00.757 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>8e36176a-2975-498b-93f7-f2beba774532</identification>
+ </annotationBean>
+ <date>2012-02-10 15:56:15.960 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b3887d66-e945-444d-820a-ddb5c1d6cecb</identification>
+ </annotationBean>
+ <date>2011-11-02 10:00:26.717 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>bbf68124-dbeb-482b-80c6-e461d264a98b</identification>
+ </annotationBean>
+ <date>2011-11-02 10:12:59.372 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>c2802c60-cc0e-4bc0-b401-473476811e46</identification>
+ </annotationBean>
+ <date>2011-11-02 10:02:16.255 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>d73137e0-8cfb-4536-849e-6d30b1b1f4dc</identification>
+ </annotationBean>
+ <date>2011-11-02 08:49:30.655 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>3f67a647-2d0e-4d7e-9937-5bde3d562fde</identification>
+ </annotationBean>
+ <date>2011-11-02 10:10:29.316 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>f76689f8-2629-4168-b0a6-e70c88acaca9</identification>
+ </annotationBean>
+ <date>2012-02-10 15:49:11.156 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication-https/secure-basic-authentication-https.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication-https/secure-basic-authentication-https.t2flow
new file mode 100644
index 0000000..0cbff10
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication-https/secure-basic-authentication-https.t2flow
@@ -0,0 +1,74 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="12203b36-f878-45f7-a16e-863e1bbc81b8" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Basic_AuthN_and_HTTPS</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
+ <httpMethod>GET</httpMethod>
+ <urlSignature>https://heater.cs.man.ac.uk:7443/examples-basic-authentication/taverna-test-page.html</urlSignature>
+ <acceptsHeaderValue>text/plain</acceptsHeaderValue>
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>
+ <outgoingDataFormat>String</outgoingDataFormat>
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>
+ <escapeParameters>true</escapeParameters>
+ <otherHTTPHeaders />
+ <activityInputs />
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Basic_AuthN_and_HTTPS</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>adb25995-c890-40c7-b091-2c2512024864</identification>
+ </annotationBean>
+ <date>2010-11-29 10:35:54.270 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>12203b36-f878-45f7-a16e-863e1bbc81b8</identification>
+ </annotationBean>
+ <date>2010-11-29 15:35:51.711 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
+ </annotationBean>
+ <date>2010-11-22 14:15:20.380 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:43.484 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>388333c0-fd34-4571-ab0c-f67c10c2ed64</identification>
+ </annotationBean>
+ <date>2010-11-22 14:21:12.760 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication/secure-basic-authentication.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication/secure-basic-authentication.t2flow
new file mode 100644
index 0000000..998b69a
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication/secure-basic-authentication.t2flow
@@ -0,0 +1,74 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="6eca35ba-d7d4-43d9-8593-93eba828cc46" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Basic_AuthN</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
+ <httpMethod>GET</httpMethod>
+ <urlSignature>http://heater.cs.man.ac.uk:7070/examples-basic-authentication/taverna-test-page.html</urlSignature>
+ <acceptsHeaderValue>text/plain</acceptsHeaderValue>
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>
+ <outgoingDataFormat>String</outgoingDataFormat>
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>
+ <escapeParameters>true</escapeParameters>
+ <otherHTTPHeaders />
+ <activityInputs />
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Basic_AuthN</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
+ </annotationBean>
+ <date>2010-11-22 14:15:20.380 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>6eca35ba-d7d4-43d9-8593-93eba828cc46</identification>
+ </annotationBean>
+ <date>2010-11-29 10:41:02.602 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>adb25995-c890-40c7-b091-2c2512024864</identification>
+ </annotationBean>
+ <date>2010-11-29 10:35:54.270 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:43.484 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>388333c0-fd34-4571-ab0c-f67c10c2ed64</identification>
+ </annotationBean>
+ <date>2010-11-22 14:21:12.760 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-client-cert-authentication-https/secure-client-cert-authentication-https.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-client-cert-authentication-https/secure-client-cert-authentication-https.t2flow
new file mode 100644
index 0000000..1c5d317
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-client-cert-authentication-https/secure-client-cert-authentication-https.t2flow
@@ -0,0 +1,162 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="b982dcd5-dc2a-4fc5-b6dd-8d0b90a2f58e" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Client_Cert_AuthN_and_HTTPS</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
+ <httpMethod>GET</httpMethod>
+ <urlSignature>https://heater.cs.man.ac.uk:7444/examples-client-cert-authentication/taverna-test-page.html</urlSignature>
+ <acceptsHeaderValue>text/plain</acceptsHeaderValue>
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>
+ <outgoingDataFormat>String</outgoingDataFormat>
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>
+ <escapeParameters>true</escapeParameters>
+ <otherHTTPHeaders />
+ <activityInputs />
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Client_Cert_AuthN_and_HTTPS</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b982dcd5-dc2a-4fc5-b6dd-8d0b90a2f58e</identification>
+ </annotationBean>
+ <date>2011-06-23 11:14:45.626 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>23616693-e035-42e5-a52e-e1ddb0269d9c</identification>
+ </annotationBean>
+ <date>2011-06-21 15:49:05.979 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>47ad844e-df8e-4c65-803a-8a20c8197e8e</identification>
+ </annotationBean>
+ <date>2010-11-29 15:36:29.390 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>1f90ea89-a32f-41c1-b30c-2a5afd622984</identification>
+ </annotationBean>
+ <date>2010-11-22 14:20:41.517 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>e7fb38b1-b3ec-4c47-a584-36c68eeda25e</identification>
+ </annotationBean>
+ <date>2010-11-22 14:19:49.664 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
+ </annotationBean>
+ <date>2010-11-22 14:15:20.380 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eaff435f-9025-429b-9a12-97fc94d90e73</identification>
+ </annotationBean>
+ <date>2010-11-22 14:18:46.551 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:43.484 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>5b302294-d370-4639-acb1-2a8452cc6d92</identification>
+ </annotationBean>
+ <date>2010-11-29 10:34:55.185 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>d9be6132-9d40-43f6-bd0b-8d29dca1163b</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:58.860 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>18b60848-4715-4532-b50c-45539ca00b44</identification>
+ </annotationBean>
+ <date>2011-06-21 16:24:23.704 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b982dcd5-dc2a-4fc5-b6dd-8d0b90a2f58e</identification>
+ </annotationBean>
+ <date>2011-06-21 16:36:50.208 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>06a9fa6d-ba8d-4045-945b-a4a259a275e4</identification>
+ </annotationBean>
+ <date>2011-06-23 11:13:58.558 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication-https/secure-digest-authentication-https.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication-https/secure-digest-authentication-https.t2flow
new file mode 100644
index 0000000..5d2f893
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication-https/secure-digest-authentication-https.t2flow
@@ -0,0 +1,107 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="47ad844e-df8e-4c65-803a-8a20c8197e8e" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Digest_AuthN_and_HTTPS</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
+ <httpMethod>GET</httpMethod>
+ <urlSignature>https://heater.cs.man.ac.uk:7443/examples-digest-authentication/taverna-test-page.html</urlSignature>
+ <acceptsHeaderValue>text/plain</acceptsHeaderValue>
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>
+ <outgoingDataFormat>String</outgoingDataFormat>
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>
+ <escapeParameters>true</escapeParameters>
+ <otherHTTPHeaders />
+ <activityInputs />
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Digest_AuthN_and_HTTPS</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:43.484 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eaff435f-9025-429b-9a12-97fc94d90e73</identification>
+ </annotationBean>
+ <date>2010-11-22 14:18:46.551 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>d9be6132-9d40-43f6-bd0b-8d29dca1163b</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:58.860 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>1f90ea89-a32f-41c1-b30c-2a5afd622984</identification>
+ </annotationBean>
+ <date>2010-11-22 14:20:41.517 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>e7fb38b1-b3ec-4c47-a584-36c68eeda25e</identification>
+ </annotationBean>
+ <date>2010-11-22 14:19:49.664 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>5b302294-d370-4639-acb1-2a8452cc6d92</identification>
+ </annotationBean>
+ <date>2010-11-29 10:34:55.185 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
+ </annotationBean>
+ <date>2010-11-22 14:15:20.380 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>47ad844e-df8e-4c65-803a-8a20c8197e8e</identification>
+ </annotationBean>
+ <date>2010-11-29 15:36:29.390 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication/secure-digest-authentication.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication/secure-digest-authentication.t2flow
new file mode 100644
index 0000000..449e9db
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication/secure-digest-authentication.t2flow
@@ -0,0 +1,129 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="a218f0b5-b675-4eed-b7a8-a5c63181ff3e" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Digest_AuthN</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
+ <httpMethod>GET</httpMethod>
+ <urlSignature>http://heater.cs.man.ac.uk:7070/examples-digest-authentication/taverna-test-page.html</urlSignature>
+ <acceptsHeaderValue>text/plain</acceptsHeaderValue>
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>
+ <outgoingDataFormat>String</outgoingDataFormat>
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>
+ <escapeParameters>true</escapeParameters>
+ <otherHTTPHeaders />
+ <activityInputs />
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Digest_AuthN</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:43.484 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>d9be6132-9d40-43f6-bd0b-8d29dca1163b</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:58.860 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
+ </annotationBean>
+ <date>2010-11-22 14:15:20.380 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>1f90ea89-a32f-41c1-b30c-2a5afd622984</identification>
+ </annotationBean>
+ <date>2010-11-22 14:20:41.517 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>e7fb38b1-b3ec-4c47-a584-36c68eeda25e</identification>
+ </annotationBean>
+ <date>2010-11-22 14:19:49.664 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eaff435f-9025-429b-9a12-97fc94d90e73</identification>
+ </annotationBean>
+ <date>2010-11-22 14:18:46.551 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>5b302294-d370-4639-acb1-2a8452cc6d92</identification>
+ </annotationBean>
+ <date>2010-11-29 10:34:55.185 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>fd59d61c-50f8-457b-a183-c162453b026b</identification>
+ </annotationBean>
+ <date>2010-11-29 15:29:08.570 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>435023d5-0063-4914-ae4c-28a7a031ec0d</identification>
+ </annotationBean>
+ <date>2010-11-29 10:40:30.468 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>a218f0b5-b675-4eed-b7a8-a5c63181ff3e</identification>
+ </annotationBean>
+ <date>2010-11-29 15:39:35.589 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-ws-https/secure-ws-https.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-ws-https/secure-ws-https.t2flow
new file mode 100644
index 0000000..13637c4
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-ws-https/secure-ws-https.t2flow
@@ -0,0 +1,180 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="c71621ca-196c-46cd-9073-48af82b4bd4f" role="top"><name>Workflow13</name><inputPorts /><outputPorts><port><name>out_plaintext</name><annotations /></port><port><name>out_plaintext_timestamp</name><annotations /></port><port><name>out_digest</name><annotations /></port><port><name>out_digest_timestamp</name><annotations /></port></outputPorts><processors><processor><name>hello_plaintext_password</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityUsernameTokenPlainTextPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Alan</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>hello_plaintext_password_timestamp</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword-Timestamp?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityTimestampUsernameTokenPlainTextPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_1</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Alex</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>hello_digest_password</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>https://heater.cs.man.ac.uk:7443/axis/services/HelloService-DigestPassword?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityUsernameTokenDigestPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_2</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Stian</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>hello_digest_password_timestamp</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>https://heater.cs.man.ac.uk:7443/axis/services/HelloService-DigestPassword-Timestamp?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityTimestampUsernameTokenDigestPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_3</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>David</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions><condition control="hello_plaintext_password" target="hello_digest_password" /><condition control="hello_digest_password_timestamp" target="hello_plaintext_password_timestamp" /><condition control="hello_digest_password" target="hello_digest_password_timestamp" /></conditions><datalinks><datalink><sink type="processor"><processor>hello_plaintext_password</processor><port>in0</port></sink><source type="processor"><processor>in0_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>hello_plaintext_password_timestamp</processor><port>in0</port></sink><source type="processor"><processor>in0_value_1</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>hello_digest_password</processor><port>in0</port></sink><source type="processor"><processor>in0_value_2</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>hello_digest_password_timestamp</processor><port>in0</port></sink><source type="processor"><processor>in0_value_3</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out_plaintext</port></sink><source type="processor"><processor>hello_plaintext_password</processor><port>helloReturn</port></source></datalink><datalink><sink type="dataflow"><port>out_plaintext_timestamp</port></sink><source type="processor"><processor>hello_plaintext_password_timestamp</processor><port>helloReturn</port></source></datalink><datalink><sink type="dataflow"><port>out_digest</port></sink><source type="processor"><processor>hello_digest_password</processor><port>helloReturn</port></source></datalink><datalink><sink type="dataflow"><port>out_digest_timestamp</port></sink><source type="processor"><processor>hello_digest_password_timestamp</processor><port>helloReturn</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>c71621ca-196c-46cd-9073-48af82b4bd4f</identification>
+ </annotationBean>
+ <date>2011-06-21 12:11:30.87 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>56cadac0-c944-4b9e-83c3-078f57738405</identification>
+ </annotationBean>
+ <date>2011-01-21 16:02:09.633 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>3d76be4c-83c4-413b-91f2-b0ce69dcbd97</identification>
+ </annotationBean>
+ <date>2010-11-22 13:29:43.282 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ca8fb5c5-0e8c-4e68-84f0-bdc85a77e2b3</identification>
+ </annotationBean>
+ <date>2010-11-22 13:29:26.400 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>e61023d9-d603-4df6-87e5-175603f106a5</identification>
+ </annotationBean>
+ <date>2010-11-22 13:28:31.68 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>394aced4-ee5d-4355-8ebe-9fc8bcfe5303</identification>
+ </annotationBean>
+ <date>2011-06-21 12:07:46.327 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>8175c97b-6385-460a-98ab-5cf974010d51</identification>
+ </annotationBean>
+ <date>2010-11-22 12:11:59.610 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>a388d568-ca08-43b4-abaf-3744a6801d45</identification>
+ </annotationBean>
+ <date>2010-11-22 13:30:28.898 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>7153a2dd-18bd-4f25-80ab-1efa8afc567d</identification>
+ </annotationBean>
+ <date>2011-01-21 16:02:39.43 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-ws/secure-ws.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-ws/secure-ws.t2flow
new file mode 100644
index 0000000..764b810
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-ws/secure-ws.t2flow
@@ -0,0 +1,180 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="c71621ca-196c-46cd-9073-48af82b4bd4f" role="top"><name>Workflow13</name><inputPorts /><outputPorts><port><name>out_plaintext</name><annotations /></port><port><name>out_plaintext_timestamp</name><annotations /></port><port><name>out_digest</name><annotations /></port><port><name>out_digest_timestamp</name><annotations /></port></outputPorts><processors><processor><name>hello_plaintext_password</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityUsernameTokenPlainTextPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Alan</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>hello_plaintext_password_timestamp</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword-Timestamp?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityTimestampUsernameTokenPlainTextPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_1</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Alex</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>hello_digest_password</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>http://heater.cs.man.ac.uk:7070/axis/services/HelloService-DigestPassword?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityUsernameTokenDigestPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_2</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Stian</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>hello_digest_password_timestamp</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>http://heater.cs.man.ac.uk:7070/axis/services/HelloService-DigestPassword-Timestamp?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityTimestampUsernameTokenDigestPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_3</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>David</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions><condition control="hello_plaintext_password" target="hello_digest_password" /><condition control="hello_digest_password_timestamp" target="hello_plaintext_password_timestamp" /><condition control="hello_digest_password" target="hello_digest_password_timestamp" /></conditions><datalinks><datalink><sink type="processor"><processor>hello_plaintext_password</processor><port>in0</port></sink><source type="processor"><processor>in0_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>hello_plaintext_password_timestamp</processor><port>in0</port></sink><source type="processor"><processor>in0_value_1</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>hello_digest_password</processor><port>in0</port></sink><source type="processor"><processor>in0_value_2</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>hello_digest_password_timestamp</processor><port>in0</port></sink><source type="processor"><processor>in0_value_3</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out_plaintext</port></sink><source type="processor"><processor>hello_plaintext_password</processor><port>helloReturn</port></source></datalink><datalink><sink type="dataflow"><port>out_plaintext_timestamp</port></sink><source type="processor"><processor>hello_plaintext_password_timestamp</processor><port>helloReturn</port></source></datalink><datalink><sink type="dataflow"><port>out_digest</port></sink><source type="processor"><processor>hello_digest_password</processor><port>helloReturn</port></source></datalink><datalink><sink type="dataflow"><port>out_digest_timestamp</port></sink><source type="processor"><processor>hello_digest_password_timestamp</processor><port>helloReturn</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>c71621ca-196c-46cd-9073-48af82b4bd4f</identification>
+ </annotationBean>
+ <date>2011-06-21 12:11:30.87 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>56cadac0-c944-4b9e-83c3-078f57738405</identification>
+ </annotationBean>
+ <date>2011-01-21 16:02:09.633 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>3d76be4c-83c4-413b-91f2-b0ce69dcbd97</identification>
+ </annotationBean>
+ <date>2010-11-22 13:29:43.282 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ca8fb5c5-0e8c-4e68-84f0-bdc85a77e2b3</identification>
+ </annotationBean>
+ <date>2010-11-22 13:29:26.400 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>e61023d9-d603-4df6-87e5-175603f106a5</identification>
+ </annotationBean>
+ <date>2010-11-22 13:28:31.68 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>394aced4-ee5d-4355-8ebe-9fc8bcfe5303</identification>
+ </annotationBean>
+ <date>2011-06-21 12:07:46.327 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>8175c97b-6385-460a-98ab-5cf974010d51</identification>
+ </annotationBean>
+ <date>2010-11-22 12:11:59.610 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>a388d568-ca08-43b4-abaf-3744a6801d45</identification>
+ </annotationBean>
+ <date>2010-11-22 13:30:28.898 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>7153a2dd-18bd-4f25-80ab-1efa8afc567d</identification>
+ </annotationBean>
+ <date>2011-01-21 16:02:39.43 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-wsdl/secure-wsdl.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-wsdl/secure-wsdl.t2flow
new file mode 100644
index 0000000..4db4ad5
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-wsdl/secure-wsdl.t2flow
@@ -0,0 +1,131 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="b23a2149-976e-4e98-b120-e5b8580839ef" role="top"><name>Workflow13</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>hello_plaintext_password</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityUsernameTokenPlainTextPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Alan</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>hello_plaintext_password</processor><port>in0</port></sink><source type="processor"><processor>in0_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>hello_plaintext_password</processor><port>helloReturn</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ca8fb5c5-0e8c-4e68-84f0-bdc85a77e2b3</identification>
+ </annotationBean>
+ <date>2010-11-22 13:29:26.400 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>7153a2dd-18bd-4f25-80ab-1efa8afc567d</identification>
+ </annotationBean>
+ <date>2011-01-21 16:02:39.43 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>394aced4-ee5d-4355-8ebe-9fc8bcfe5303</identification>
+ </annotationBean>
+ <date>2011-06-21 12:07:46.327 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>c71621ca-196c-46cd-9073-48af82b4bd4f</identification>
+ </annotationBean>
+ <date>2011-06-21 12:11:30.87 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>8175c97b-6385-460a-98ab-5cf974010d51</identification>
+ </annotationBean>
+ <date>2010-11-22 12:11:59.610 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>56cadac0-c944-4b9e-83c3-078f57738405</identification>
+ </annotationBean>
+ <date>2011-01-21 16:02:09.633 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>a388d568-ca08-43b4-abaf-3744a6801d45</identification>
+ </annotationBean>
+ <date>2010-11-22 13:30:28.898 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b23a2149-976e-4e98-b120-e5b8580839ef</identification>
+ </annotationBean>
+ <date>2011-08-23 13:40:15.238 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>3d76be4c-83c4-413b-91f2-b0ce69dcbd97</identification>
+ </annotationBean>
+ <date>2010-11-22 13:29:43.282 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>e61023d9-d603-4df6-87e5-175603f106a5</identification>
+ </annotationBean>
+ <date>2010-11-22 13:28:31.68 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/soaplab/soaplab.t2flow b/taverna-commandline-tests/src/test/resources/workflows/soaplab/soaplab.t2flow
new file mode 100644
index 0000000..f1ef82b
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/soaplab/soaplab.t2flow
@@ -0,0 +1,84 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="db8053e3-1837-42cc-ba27-5fd0a83f119e" role="top"><name>Retrieve_sequence_in_EMBL_format</name><inputPorts /><outputPorts><port><name>sequence</name><annotations /></port></outputPorts><processors><processor><name>sequence_feature</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>true</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>sequence_id</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>embl:x52524</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>sequence_format</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>embl</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>seqret</name><inputPorts><port><name>sequence_usa</name><depth>0</depth></port><port><name>feature</name><depth>0</depth></port><port><name>osformat_outseq</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outseq</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="osformat_outseq" to="osformat_outseq" /><map from="feature" to="feature" /><map from="sequence_usa" to="sequence_usa" /></inputMap><outputMap><map from="outseq" to="outseq" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
+ <endpoint>http://www.ebi.ac.uk/soaplab/services/edit.seqret</endpoint>
+ <pollingInterval>0</pollingInterval>
+ <pollingBackoff>1.0</pollingBackoff>
+ <pollingIntervalMax>0</pollingIntervalMax>
+</net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="sequence_usa" depth="0" /><port name="feature" depth="0" /><port name="osformat_outseq" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>seqret</processor><port>sequence_usa</port></sink><source type="processor"><processor>sequence_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>seqret</processor><port>feature</port></sink><source type="processor"><processor>sequence_feature</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>seqret</processor><port>osformat_outseq</port></sink><source type="processor"><processor>sequence_format</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>sequence</port></sink><source type="processor"><processor>seqret</processor><port>outseq</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
+ <text>Retrieve sequence in EMBL format</text>
+ </annotationBean>
+ <date>2009-12-15 20:21:29.202 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
+ <text>Franck Tanoh</text>
+ </annotationBean>
+ <date>2009-12-15 20:21:20.965 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>db8053e3-1837-42cc-ba27-5fd0a83f119e</identification>
+ </annotationBean>
+ <date>2010-07-04 17:49:51.364 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
+ <text>This workflow retrieves a sequence associated with its features in embl format</text>
+ </annotationBean>
+ <date>2009-12-15 20:21:39.30 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/spreadsheetimport/spreadsheetimport.t2flow b/taverna-commandline-tests/src/test/resources/workflows/spreadsheetimport/spreadsheetimport.t2flow
new file mode 100644
index 0000000..7360186
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/spreadsheetimport/spreadsheetimport.t2flow
@@ -0,0 +1,646 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="fa4ef38e-fa3f-4662-97e5-59c3b51aa322" role="top"><name>Spreadsheet_Import_Example</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>SpreadsheetImport</name><inputPorts><port><name>fileurl</name><depth>0</depth></port></inputPorts><outputPorts><port><name>other</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>other_industry</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>year</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>spreadsheet-import-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportActivity</class><inputMap><map from="fileurl" to="fileurl" /></inputMap><outputMap><map from="other" to="other" /><map from="year" to="year" /><map from="other_industry" to="other_industry" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration xmlns="">
+ <columnRange>
+ <start>1</start>
+ <end>6</end>
+ <excludes />
+ </columnRange>
+ <rowRange>
+ <start>7</start>
+ <end>41</end>
+ <excludes />
+ </rowRange>
+ <emptyCellValue />
+ <columnNames>
+ <entry>
+ <string>D</string>
+ <string>other</string>
+ </entry>
+ <entry>
+ <string>E</string>
+ <string>fish_farming</string>
+ </entry>
+ <entry>
+ <string>F</string>
+ <string>other_industry</string>
+ </entry>
+ <entry>
+ <string>G</string>
+ <string>public_water_supply</string>
+ </entry>
+ <entry>
+ <string>A</string>
+ <string>over</string>
+ </entry>
+ <entry>
+ <string>B</string>
+ <string>year</string>
+ </entry>
+ <entry>
+ <string>C</string>
+ <string>electricity</string>
+ </entry>
+ <entry>
+ <string>L</string>
+ <string>2001</string>
+ </entry>
+ <entry>
+ <string>N</string>
+ <string>2002</string>
+ </entry>
+ <entry>
+ <string>H</string>
+ <string>1999</string>
+ </entry>
+ <entry>
+ <string>J</string>
+ <string>2000</string>
+ </entry>
+ <entry>
+ <string>T</string>
+ <string>2005</string>
+ </entry>
+ <entry>
+ <string>V</string>
+ <string>2006</string>
+ </entry>
+ <entry>
+ <string>P</string>
+ <string>2003</string>
+ </entry>
+ <entry>
+ <string>R</string>
+ <string>2004</string>
+ </entry>
+ <entry>
+ <string>X</string>
+ <string>2007</string>
+ </entry>
+ <entry>
+ <string>Z</string>
+ <string>2008</string>
+ </entry>
+ </columnNames>
+ <allRows>false</allRows>
+ <excludeFirstRow>false</excludeFirstRow>
+ <ignoreBlankRows>false</ignoreBlankRows>
+ <emptyCellPolicy>EMPTY_STRING</emptyCellPolicy>
+ <outputFormat>PORT_PER_COLUMN</outputFormat>
+ <csvDelimiter>,</csvDelimiter>
+</net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="fileurl" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>url_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>http://www.myexperiment.org/files/410/download/WaterUse.xlsx</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>SpreadsheetImport</processor><port>fileurl</port></sink><source type="processor"><processor>url_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>SpreadsheetImport</processor><port>year</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>41265789-c464-4ee2-b145-95ece9388305</identification>
+ </annotationBean>
+ <date>2010-07-07 22:34:29.364 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b4363407-ef56-4cf3-998f-8e780a8dc816</identification>
+ </annotationBean>
+ <date>2010-07-07 16:41:31.230 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>486a5356-0f3e-424d-b14e-249295875f2d</identification>
+ </annotationBean>
+ <date>2010-07-13 12:31:34.664 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
+ <text>David Withers</text>
+ </annotationBean>
+ <date>2010-07-13 11:09:24.988 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>cf60043b-e08a-49d7-a150-711f413d3d18</identification>
+ </annotationBean>
+ <date>2010-07-07 22:52:10.583 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>812e7abc-4866-43dc-b9d4-44370a399e4e</identification>
+ </annotationBean>
+ <date>2010-07-07 17:23:44.739 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>cca71cbe-6d97-4896-90c2-d91016f12882</identification>
+ </annotationBean>
+ <date>2010-07-07 22:45:31.148 BST</date>
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+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>70c23010-0b47-424e-a1ce-73c040c3d3c6</identification>
+ </annotationBean>
+ <date>2010-07-07 16:43:47.690 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
+ <text>Example using the SpreadsheetImport service to import data from an Excel spreadsheet.
+The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date.
+The source data is from http://data.gov.uk/</text>
+ </annotationBean>
+ <date>2010-07-13 11:16:31.908 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>27965b7c-1a89-46ac-8c9b-a4c6bf9144f0</identification>
+ </annotationBean>
+ <date>2010-07-13 11:22:36.27 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>6c2a0ecf-5d91-4722-adf6-607c912ed54c</identification>
+ </annotationBean>
+ <date>2010-07-07 16:54:20.460 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>808e3725-2a08-4907-9706-fb7f0f08f62f</identification>
+ </annotationBean>
+ <date>2010-07-13 11:20:05.749 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>6e069c36-8d88-4017-96cf-c1fa87007777</identification>
+ </annotationBean>
+ <date>2010-07-07 16:20:48.694 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>73ce4e99-6b83-45d0-8605-896d6d48b7f0</identification>
+ </annotationBean>
+ <date>2010-07-07 17:01:14.713 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/stringconstant/stringconstant.t2flow b/taverna-commandline-tests/src/test/resources/workflows/stringconstant/stringconstant.t2flow
new file mode 100644
index 0000000..41266d0
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/stringconstant/stringconstant.t2flow
@@ -0,0 +1,32 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="48c5c70e-ffde-4ff0-8508-015577ab263c" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>String_constant</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Test Value</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>String_constant</processor><port>value</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>48c5c70e-ffde-4ff0-8508-015577ab263c</identification>
+ </annotationBean>
+ <date>2010-12-14 11:57:31.126 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>186f09f7-d9a7-4ae2-bf84-8ee83f41f4e3</identification>
+ </annotationBean>
+ <date>2010-12-14 11:56:50.253 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/tool/tool.t2flow b/taverna-commandline-tests/src/test/resources/workflows/tool/tool.t2flow
new file mode 100644
index 0000000..d77a851
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/tool/tool.t2flow
@@ -0,0 +1,158 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="82a5216a-8b82-41db-a114-ece396f9b85c" role="top"><name>Workflow4</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Tool</name><inputPorts><port><name>in1</name><depth>0</depth></port><port><name>in2</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean xmlns="">
+ <mechanismType>789663B8-DA91-428A-9F7D-B3F3DA185FD4</mechanismType>
+ <mechanismName>default local</mechanismName>
+ <mechanismXML><?xml version="1.0" encoding="UTF-8"?>
+<localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation>
+</mechanismXML>
+ <externaltoolid>607ceaee-59ba-4cbb-a650-84e51d8498e3</externaltoolid>
+ <useCaseDescription>
+ <usecaseid />
+ <description />
+ <command>cat in1 > out; echo %%in2%% >> out
+ </command>
+ <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
+ <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
+ <tags>
+ <string>in2</string>
+ </tags>
+ <REs />
+ <queue__preferred />
+ <queue__deny />
+ <static__inputs>
+ <de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
+ <tag>hi</tag>
+ <file>true</file>
+ <tempFile>false</tempFile>
+ <binary>false</binary>
+ <charsetName>MacRoman</charsetName>
+ <forceCopy>false</forceCopy>
+ <content class="string">hi</content>
+ </de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
+ <de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
+ <tag>google</tag>
+ <file>true</file>
+ <tempFile>false</tempFile>
+ <binary>false</binary>
+ <charsetName>MacRoman</charsetName>
+ <forceCopy>false</forceCopy>
+ <url>http://www.google.com/</url>
+ </de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
+ </static__inputs>
+ <inputs>
+ <entry>
+ <string>in2</string>
+ <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
+ <tag>in2</tag>
+ <file>false</file>
+ <tempFile>false</tempFile>
+ <binary>false</binary>
+ <charsetName>MacRoman</charsetName>
+ <forceCopy>false</forceCopy>
+ <list>false</list>
+ <concatenate>false</concatenate>
+ <mime />
+ </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
+ </entry>
+ <entry>
+ <string>in1</string>
+ <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
+ <tag>in1</tag>
+ <file>true</file>
+ <tempFile>false</tempFile>
+ <binary>false</binary>
+ <charsetName>MacRoman</charsetName>
+ <forceCopy>false</forceCopy>
+ <list>false</list>
+ <concatenate>false</concatenate>
+ <mime />
+ </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
+ </entry>
+ </inputs>
+ <outputs>
+ <entry>
+ <string>out</string>
+ <de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
+ <path>out</path>
+ <binary>false</binary>
+ <mime />
+ </de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
+ </entry>
+ </outputs>
+ <includeStdIn>false</includeStdIn>
+ <includeStdOut>true</includeStdOut>
+ <includeStdErr>true</includeStdErr>
+ <validReturnCodes>
+ <int>0</int>
+ </validReturnCodes>
+ </useCaseDescription>
+ <edited>false</edited>
+</net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in1" depth="0" /><port name="in2" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Hello</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>in2_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>World</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Tool</processor><port>in1</port></sink><source type="processor"><processor>in_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Tool</processor><port>in2</port></sink><source type="processor"><processor>in2_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Tool</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>6090defe-8eba-4775-8dd6-ab48813d23ab</identification>
+ </annotationBean>
+ <date>2011-10-27 18:50:36.777 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>8312a5c9-b291-4a20-a468-0cdd8888115b</identification>
+ </annotationBean>
+ <date>2011-10-27 18:46:58.794 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>82a5216a-8b82-41db-a114-ece396f9b85c</identification>
+ </annotationBean>
+ <date>2011-11-10 17:19:20.269 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>436555c3-0df8-4e5c-93f3-313124bf045c</identification>
+ </annotationBean>
+ <date>2011-10-27 18:52:22.981 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/wsdl/wsdl.t2flow b/taverna-commandline-tests/src/test/resources/workflows/wsdl/wsdl.t2flow
new file mode 100644
index 0000000..4dea6bb
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/wsdl/wsdl.t2flow
@@ -0,0 +1,22 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="eed49d32-8563-45ff-8716-347b20800129" role="top"><name>Workflow5</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>getVersion</name><inputPorts /><outputPorts><port><name>getVersionReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap /><outputMap><map from="getVersionReturn" to="getVersionReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>http://www.mygrid.org.uk/axis/services/Version?wsdl</wsdl>
+ <operation>getVersion</operation>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>getVersion</processor><port>getVersionReturn</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eed49d32-8563-45ff-8716-347b20800129</identification>
+ </annotationBean>
+ <date>2011-01-25 16:37:45.583 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/age b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/age
new file mode 100644
index 0000000..b5045cc
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/age
@@ -0,0 +1 @@
+21
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/firstName b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/firstName
new file mode 100644
index 0000000..08df4e7
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/firstName
@@ -0,0 +1 @@
+John
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/lastName b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/lastName
new file mode 100644
index 0000000..b77017e
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/lastName
@@ -0,0 +1 @@
+Smith
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/xmlSplitter.t2flow b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/xmlSplitter.t2flow
new file mode 100644
index 0000000..bd0875d
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/xmlSplitter.t2flow
@@ -0,0 +1,339 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="52ddd8d4-d1fc-4b62-932a-288df52b77cf" role="top"><name>Workflow1</name><inputPorts><port><name>lastName</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
+ <text>Smith</text>
+ </annotationBean>
+ <date>2011-02-17 10:48:23.657 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>firstName</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
+ <text>John</text>
+ </annotationBean>
+ <date>2011-02-17 10:48:16.703 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>age</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
+ <text>John</text>
+ </annotationBean>
+ <date>2011-02-17 10:47:56.513 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
+ <text>21</text>
+ </annotationBean>
+ <date>2011-02-17 10:48:30.905 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>personToString</name><inputPorts><port><name>parameters</name><depth>0</depth></port></inputPorts><outputPorts><port><name>parameters</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="parameters" to="parameters" /></inputMap><outputMap><map from="parameters" to="parameters" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>http://www.mygrid.org.uk/menagerie/xfire/Complex-dlw?wsdl</wsdl>
+ <operation>personToString</operation>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="parameters" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>personToString_output</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
+ <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="personToStringResponse" name="parameters" qname="{http://xfire.codehaus.org/BookService}personToStringResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="out" qname="{http://xfire.codehaus.org/BookService}&gt;personToStringResponse&gt;out" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>input</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/xml'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/plain'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>personToString_input</name><inputPorts><port><name>person</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="person" to="person" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
+ <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="personToString" name="parameters" qname="{http://xfire.codehaus.org/BookService}personToString"><s:elements><s:complextype optional="false" unbounded="false" typename="Person" name="person" qname="{http://xfire.codehaus.org/BookService}&gt;personToString&gt;person"><s:elements><s:complextype optional="true" unbounded="false" typename="Address" name="address" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;address"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="city" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;city" /><s:basetype optional="true" unbounded="false" typename="string" name="road" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;road" /><s:basetype optional="true" unbounded="false" typename="int" name="roadNumber" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;roadNumber" /></s:elements></s:complextype><s:basetype optional="true" unbounded="false" typename="int" name="age" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;age" /><s:basetype optional="true" unbounded="false" typename="string" name="firstName" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;firstName" /><s:basetype optional="true" unbounded="false" typename="string" name="lastName" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;lastName" /></s:elements></s:complextype></s:elements></s:complextype></s:extensions></wrappedTypeXML>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>person</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/xml'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>output</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/xml'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="person" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>personToString_person</name><inputPorts><port><name>lastName</name><depth>0</depth></port><port><name>firstName</name><depth>0</depth></port><port><name>age</name><depth>0</depth></port><port><name>address</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="lastName" to="lastName" /><map from="address" to="address" /><map from="age" to="age" /><map from="firstName" to="firstName" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
+ <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="Person" name="person" qname="{http://xfire.codehaus.org/BookService}&gt;personToString&gt;person"><s:elements><s:complextype optional="true" unbounded="false" typename="Address" name="address" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;address"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="city" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;city" /><s:basetype optional="true" unbounded="false" typename="string" name="road" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;road" /><s:basetype optional="true" unbounded="false" typename="int" name="roadNumber" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;roadNumber" /></s:elements></s:complextype><s:basetype optional="true" unbounded="false" typename="int" name="age" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;age" /><s:basetype optional="true" unbounded="false" typename="string" name="firstName" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;firstName" /><s:basetype optional="true" unbounded="false" typename="string" name="lastName" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;lastName" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>address</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/xml'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>age</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/plain'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>firstName</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/plain'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>lastName</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/plain'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>output</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/xml'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="lastName" depth="0" /><port name="firstName" depth="0" /><port name="age" depth="0" /><port name="address" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>person_address</name><inputPorts><port><name>city</name><depth>0</depth></port><port><name>road</name><depth>0</depth></port><port><name>roadNumber</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="road" to="road" /><map from="roadNumber" to="roadNumber" /><map from="city" to="city" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
+ <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="Address" name="address" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;address"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="city" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;city" /><s:basetype optional="true" unbounded="false" typename="string" name="road" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;road" /><s:basetype optional="true" unbounded="false" typename="int" name="roadNumber" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;roadNumber" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>city</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/plain'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>road</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/plain'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>roadNumber</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/plain'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>output</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/xml'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="city" depth="0" /><port name="road" depth="0" /><port name="roadNumber" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>city_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Manchester</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>road_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Oxford Road</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>roadNumber_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>40</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>personToString</processor><port>parameters</port></sink><source type="processor"><processor>personToString_input</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>personToString_output</processor><port>input</port></sink><source type="processor"><processor>personToString</processor><port>parameters</port></source></datalink><datalink><sink type="processor"><processor>personToString_input</processor><port>person</port></sink><source type="processor"><processor>personToString_person</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>personToString_person</processor><port>lastName</port></sink><source type="dataflow"><port>lastName</port></source></datalink><datalink><sink type="processor"><processor>personToString_person</processor><port>firstName</port></sink><source type="dataflow"><port>firstName</port></source></datalink><datalink><sink type="processor"><processor>personToString_person</processor><port>age</port></sink><source type="dataflow"><port>age</port></source></datalink><datalink><sink type="processor"><processor>personToString_person</processor><port>address</port></sink><source type="processor"><processor>person_address</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>person_address</processor><port>city</port></sink><source type="processor"><processor>city_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>person_address</processor><port>road</port></sink><source type="processor"><processor>road_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>person_address</processor><port>roadNumber</port></sink><source type="processor"><processor>roadNumber_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>personToString_output</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>d79eeb60-919e-4076-af14-70ac4d605bec</identification>
+ </annotationBean>
+ <date>2011-02-17 10:49:46.785 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>52ddd8d4-d1fc-4b62-932a-288df52b77cf</identification>
+ </annotationBean>
+ <date>2011-02-17 10:53:16.981 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>8815f1ea-2659-4b7e-a90e-787c6a3c4ad6</identification>
+ </annotationBean>
+ <date>2011-02-17 10:29:40.492 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eee0128a-4afe-4566-851a-fe50dcb36340</identification>
+ </annotationBean>
+ <date>2011-02-17 10:48:35.150 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>e64ae430-dd6e-468d-b3dd-de1fea9c717b</identification>
+ </annotationBean>
+ <date>2011-02-17 10:20:55.279 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>2aa76794-f001-42f9-b945-797badfeebb1</identification>
+ </annotationBean>
+ <date>2011-02-17 10:17:24.893 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>2ece2565-7498-4154-9d61-996d8a1db5f3</identification>
+ </annotationBean>
+ <date>2011-02-17 10:24:47.509 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>97fbd479-a423-4e8c-9033-bfc28f1a7885</identification>
+ </annotationBean>
+ <date>2011-02-17 10:42:59.63 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>24e8b191-9f48-4864-82be-d9578f1b8450</identification>
+ </annotationBean>
+ <date>2011-02-17 10:25:38.788 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
diff --git a/taverna-commandline-tests/src/test/resources/workflows/xpath/xpath.t2flow b/taverna-commandline-tests/src/test/resources/workflows/xpath/xpath.t2flow
new file mode 100644
index 0000000..0691ccc
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/xpath/xpath.t2flow
@@ -0,0 +1,127 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="9fb6e3ea-f314-4f9f-8eb3-ba3dbf2b494f" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>XPath_Service</name><inputPorts><port><name>xml_text</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodelistAsXML</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>xpath-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.xpath.XPathActivity</class><inputMap><map from="xml_text" to="xml_text" /></inputMap><outputMap><map from="nodelistAsXML" to="nodelistAsXML" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean xmlns="">
+ <xmlDocument><?xml version="1.0" encoding="UTF-8"?>
+<test name="test-name">
+<test-element>test</test-element>
+</test></xmlDocument>
+ <xpathExpression>/test/test-element</xpathExpression>
+ <xpathNamespaceMap />
+</net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="xml_text" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>xml_text_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value><?xml version="1.0" encoding="UTF-8"?> <test name="test-name"> <test-element>test</test-element> </test></value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>Merge_String_List_to_a_String</name><inputPorts><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>concatenated</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="stringlist" to="stringlist" /></inputMap><outputMap><map from="concatenated" to="concatenated" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>stringlist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>seperator</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <name>concatenated</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ <granularDepth>0</granularDepth>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <script>String seperatorString = "\n";
+if (seperator != void) {
+ seperatorString = seperator;
+}
+StringBuffer sb = new StringBuffer();
+for (Iterator i = stringlist.iterator(); i.hasNext();) {
+ String item = (String) i.next();
+ sb.append(item);
+ if (i.hasNext()) {
+ sb.append(seperatorString);
+ }
+}
+concatenated = sb.toString();
+</script>
+ <dependencies />
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringListMerge</localworkerName>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>XPath_Service</processor><port>xml_text</port></sink><source type="processor"><processor>xml_text_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>stringlist</port></sink><source type="processor"><processor>XPath_Service</processor><port>nodelistAsXML</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Merge_String_List_to_a_String</processor><port>concatenated</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>9fb6e3ea-f314-4f9f-8eb3-ba3dbf2b494f</identification>
+ </annotationBean>
+ <date>2011-11-03 14:17:32.152 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>bed5342f-45e0-4fc9-a85d-bcd1ea01e33d</identification>
+ </annotationBean>
+ <date>2011-11-03 12:55:28.941 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>9f0cedc9-4a53-4564-aeb5-d0b7f7b2b4e1</identification>
+ </annotationBean>
+ <date>2011-11-03 12:56:36.620 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>94104add-ec12-4c5a-a4f6-b5c1b6d0a700</identification>
+ </annotationBean>
+ <date>2011-11-03 12:56:00.6 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
