temporarily empty repository
.. as Software Grant is not yet formally on file
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index ebe0e5b..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,24 +0,0 @@
-# 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
deleted file mode 100644
index dff5f3a..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1 +0,0 @@
-language: java
diff --git a/README.md b/README.md
deleted file mode 100644
index bcd653c..0000000
--- a/README.md
+++ /dev/null
@@ -1,6 +0,0 @@
-# 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
deleted file mode 100644
index 0355623..0000000
--- a/pom.xml
+++ /dev/null
@@ -1,40 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/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
deleted file mode 100644
index 98ae247..0000000
--- a/taverna-commandline-api/pom.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/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
deleted file mode 100644
index eb21cd7..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ArgumentsParsingException.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-@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
deleted file mode 100644
index 0714275..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/CommandLineMasterPasswordException.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-@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
deleted file mode 100644
index 616fb70..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-public class DatabaseConfigurationException extends Exception {
-
- private static final long serialVersionUID = -4128248547532355697L;
-
- public DatabaseConfigurationException() {
-
- }
-
- public DatabaseConfigurationException(String message) {
- super(message);
- }
-
- public DatabaseConfigurationException(Throwable cause) {
- super(cause);
- }
-
- public DatabaseConfigurationException(String message, Throwable cause) {
- super(message, cause);
- }
-
-}
diff --git a/taverna-commandline-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
deleted file mode 100644
index da03891..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-import java.util.Set;
-
-public class InputMismatchException extends InvalidOptionException {
-
- private static final long serialVersionUID = -5368068332397293706L;
- private final Set<String> expectedInputNames;
- private final Set<String> providedInputNames;
-
- public InputMismatchException(String msg, Set<String> expectedInputNames, Set<String> providedInputNames) {
- super(msg);
- this.expectedInputNames = expectedInputNames;
- this.providedInputNames = providedInputNames;
- }
-
- public String getMessage() {
- String result = super.getMessage();
-
- 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
deleted file mode 100644
index c07a19f..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-public class InvalidOptionException extends Exception {
-
- private static final long serialVersionUID = 2467409785164223258L;
-
- public InvalidOptionException(String message) {
- super(message);
- }
-}
diff --git a/taverna-commandline-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
deleted file mode 100644
index 664ab71..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-public class OpenDataflowException extends Exception {
-
-
- private static final long serialVersionUID = 4778578311101082197L;
-
- public OpenDataflowException() {
-
- }
-
- public OpenDataflowException(String message) {
- super(message);
- }
-
- public OpenDataflowException(Throwable cause) {
- super(cause);
- }
-
- public OpenDataflowException(String message, Throwable cause) {
- super(message, cause);
- }
-
-}
diff --git a/taverna-commandline-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
deleted file mode 100644
index 226d6ea..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-public class ReadInputException extends Exception {
-
- private static final long serialVersionUID = -3494432791254643055L;
-
- public ReadInputException(String msg) {
- super(msg);
- }
-
- public ReadInputException(String msg, Throwable e) {
- super(msg,e);
- }
-
-}
diff --git a/taverna-commandline-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
deleted file mode 100644
index 7ad460d..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/SaveResultsException.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-@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
deleted file mode 100644
index dd8e20f..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
+++ /dev/null
@@ -1,119 +0,0 @@
-/*******************************************************************************
- * 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
deleted file mode 100644
index 17c6a42..0000000
--- a/taverna-commandline-common/pom.xml
+++ /dev/null
@@ -1,88 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>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
deleted file mode 100644
index 048e582..0000000
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineMasterPasswordProvider.java
+++ /dev/null
@@ -1,184 +0,0 @@
-/*******************************************************************************
- * 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
deleted file mode 100644
index 368527d..0000000
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
+++ /dev/null
@@ -1,437 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline;
-
-import java.io.File;
-import java.io.IOException;
-import java.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
deleted file mode 100644
index 46b6c92..0000000
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java
+++ /dev/null
@@ -1,154 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.data;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.sql.Connection;
-import java.sql.SQLException;
-import java.util.Properties;
-
-import javax.naming.NamingException;
-
-import net.sf.taverna.t2.commandline.exceptions.DatabaseConfigurationException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-
-import 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
deleted file mode 100644
index 44faea5..0000000
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorValueHandler.java
+++ /dev/null
@@ -1,72 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.data;
-
-import java.io.IOException;
-import java.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
deleted file mode 100644
index bcaa7fb..0000000
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
+++ /dev/null
@@ -1,280 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.data;
-
-import java.io.File;
-import java.io.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
deleted file mode 100644
index 1df05c2..0000000
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java
+++ /dev/null
@@ -1,87 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.data;
-
-import java.io.File;
-import java.io.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
deleted file mode 100644
index e7ae701..0000000
--- a/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context-osgi.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?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
deleted file mode 100644
index 52c0f29..0000000
--- a/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?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
deleted file mode 100644
index 1080856..0000000
--- a/taverna-commandline-common/src/main/resources/database-defaults.properties
+++ /dev/null
@@ -1,11 +0,0 @@
-in_memory = true
-provenance = false
-connector = derby
-port = 1527
-dialect = org.hibernate.dialect.DerbyDialect
-start_derby = false
-pool_max_active = 50
-pool_min_idle = 50
-pool_max_idle = 10
-driver = org.apache.derby.jdbc.EmbeddedDriver
-jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
\ No newline at end of file
diff --git a/taverna-commandline-common/src/main/resources/help.txt b/taverna-commandline-common/src/main/resources/help.txt
deleted file mode 100644
index fb082cc..0000000
--- a/taverna-commandline-common/src/main/resources/help.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-By default, the workflow is executed using the -inmemory option, and the
-results are written out to a directory named after the workflow name.
-
-If this directory already exists then 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
deleted file mode 100644
index 4c00e3a..0000000
--- a/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestDatabaseConfigurationHandler.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package net.sf.taverna.t2.commandline;
-
-import static org.junit.Assert.assertEquals;
-import net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-//import net.sf.taverna.t2.workbench.reference.config.DataManagementConfiguration;
-
-import org.junit.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
deleted file mode 100644
index 42208e3..0000000
--- a/taverna-commandline-launcher/pom.xml
+++ /dev/null
@@ -1,83 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/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
deleted file mode 100644
index b702e03..0000000
--- a/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
+++ /dev/null
@@ -1,445 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package 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
deleted file mode 100644
index 426ab98..0000000
--- a/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
+++ /dev/null
@@ -1,143 +0,0 @@
-/*******************************************************************************
- * 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
deleted file mode 100644
index fb082cc..0000000
--- a/taverna-commandline-launcher/src/main/resources/help.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-By default, the workflow is executed using the -inmemory option, and the
-results are written out to a directory named after the workflow name.
-
-If this directory already exists then 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
deleted file mode 100644
index 3e1d0f4..0000000
--- a/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
+++ /dev/null
@@ -1,267 +0,0 @@
-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
deleted file mode 100644
index 38bcb42..0000000
--- a/taverna-commandline-product/pom.xml
+++ /dev/null
@@ -1,529 +0,0 @@
-<?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>${htmlparser.version}</version>
- </dependency>
-
-
-
- </dependencies>
-
-</project>
diff --git a/taverna-commandline-product/src/main/assembly/dependencies-component.xml b/taverna-commandline-product/src/main/assembly/dependencies-component.xml
deleted file mode 100644
index 0e8640e..0000000
--- a/taverna-commandline-product/src/main/assembly/dependencies-component.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<component
- xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/component/1.1.2"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/component/1.1.2 http://maven.apache.org/xsd/component-1.1.2.xsd">
-
- <fileSets>
- <fileSet>
- <directory>src/main/etc</directory>
- <fileMode>0755</fileMode>
- <outputDirectory></outputDirectory>
- <filtered>true</filtered>
- </fileSet>
- <fileSet>
- <directory>${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
deleted file mode 100644
index ae2a7c3..0000000
--- a/taverna-commandline-product/src/main/assembly/developer-assembly.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?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
deleted file mode 100644
index f82e793..0000000
--- a/taverna-commandline-product/src/main/assembly/nightly-assembly.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?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
deleted file mode 100644
index 61da752..0000000
--- a/taverna-commandline-product/src/main/assembly/release-assembly.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?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
deleted file mode 100644
index 5014f2b..0000000
--- a/taverna-commandline-product/src/main/etc/conf/log4j.properties
+++ /dev/null
@@ -1,14 +0,0 @@
-# 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
deleted file mode 100644
index b03a43f..0000000
--- a/taverna-commandline-product/src/main/etc/conf/logging.properties
+++ /dev/null
@@ -1,10 +0,0 @@
-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
deleted file mode 100644
index 91522d4..0000000
--- a/taverna-commandline-product/src/main/etc/conf/taverna.app.properties
+++ /dev/null
@@ -1,2 +0,0 @@
-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
deleted file mode 100644
index 2e18831..0000000
--- a/taverna-commandline-product/src/main/etc/executeworkflow.bat
+++ /dev/null
@@ -1,17 +0,0 @@
-@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
deleted file mode 100644
index 5ef0916..0000000
--- a/taverna-commandline-product/src/main/etc/executeworkflow.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/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
deleted file mode 100644
index e28c4a0..0000000
--- a/taverna-commandline-tests/pom.xml
+++ /dev/null
@@ -1,71 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/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
deleted file mode 100644
index 07df1c3..0000000
--- a/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java
+++ /dev/null
@@ -1,485 +0,0 @@
-/*******************************************************************************
- * 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
deleted file mode 100644
index 56ed82d..0000000
--- a/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/*******************************************************************************
- * 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
deleted file mode 100644
index 140dec6..0000000
--- a/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java
+++ /dev/null
@@ -1,79 +0,0 @@
-/*******************************************************************************
- * 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
deleted file mode 100644
index 5846961..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index e0cb526..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/ignorePort
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index a73b8c4..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/biomoby_tutorial_workflow.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index f8e22dd..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/ignorePort
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 1dfd176..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/id
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index c188363..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/namespace
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 38abe3a..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/demonstration_of_configurable_iteration/demonstration_of_configurable_iteration.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index a329afc..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/ebi_interproscan_newservices.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 1ec3d86..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/ignorePort
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 38133d0..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/email
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 19a43dd..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/sequence
+++ /dev/null
@@ -1,8 +0,0 @@
->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
deleted file mode 100644
index 350a27f..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/example_of_conditional_invocation/example_of_conditional_invocation.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index f32a580..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/example_of_conditional_invocation/inputs/condition
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index a8773c4..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/example_of_explicit_looping.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index da2d398..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/inputs/end
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 7d105a7..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/inputs/start
+++ /dev/null
@@ -1 +0,0 @@
--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
deleted file mode 100644
index e440e5c..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/example_of_explicit_looping/inputs/step
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index bd3ff3d..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/example_workflow_for_rest_and_xpath_activities.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index bbab6f1..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/inputs/Name_Of_Location_for_Weather_Forecast
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 1aeab4b..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/fetch_dragon_images_from_biomoby/fetch_dragon_images_from_biomoby.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 5d10074..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/fetch_pdb_flatfile_from_rcsb_server/fetch_pdb_flatfile_from_rcsb_server.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 7f3db81..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/fetch_pdb_flatfile_from_rcsb_server/inputs/pdbID
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 48f849f..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/fetch_today_s_xkcd_comic/fetch_today_s_xkcd_comic.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index c0f40c5..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/gbseq_test/gbseq_test.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index f4181b8..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/hello_anyone/hello_anyone.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index d565a0b..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/hello_anyone/inputs/name
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index c596de4..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/hello_world/hello_world.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 4701cc7..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/pipelined_list_iteration/inputs/input
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index dd3c98c..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/pipelined_list_iteration/pipelined_list_iteration.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 2b4ab46..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/retrieve_sequence_in_embl_format/retrieve_sequence_in_embl_format.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 03cf409..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/secure_rest_service_call_example/secure_rest_service_call_example.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index c2a4ad4..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/secure_web_service_call_example/secure_web_service_call_example.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 98d8ed4..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/spreadsheed_data_import_example/spreadsheed_data_import_example.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 958de61..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/unix_external_tools_with_zip_and_unzip/unix_external_tools_with_zip_and_unzip.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 56a6051..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/inputs/a
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index d8263ee..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/inputs/b
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 72ef715..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/unix_numerically_adding_two_values.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 155d7e4..0000000
--- a/taverna-commandline-tests/src/test/resources/myexperiment/unix_tool_service_using_string_replacement/unix_tool_service_using_string_replacement.url
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index c79eddf..0000000
--- a/taverna-commandline-tests/src/test/resources/security/t2keystore.ubr
+++ /dev/null
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
deleted file mode 100644
index ec1717d..0000000
--- a/taverna-commandline-tests/src/test/resources/security/t2truststore.ubr
+++ /dev/null
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
deleted file mode 100644
index c79eddf..0000000
--- a/taverna-commandline-tests/src/test/resources/security/taverna-keystore.ubr
+++ /dev/null
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
deleted file mode 100644
index ec1717d..0000000
--- a/taverna-commandline-tests/src/test/resources/security/taverna-truststore.ubr
+++ /dev/null
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
deleted file mode 100644
index 66ef4ac..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/apiconsumer.t2flow
+++ /dev/null
@@ -1,178 +0,0 @@
-<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
deleted file mode 100644
index fede229..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/inputs/in
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 8c5968c..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/beanshell/beanshell.t2flow
+++ /dev/null
@@ -1,137 +0,0 @@
-<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
deleted file mode 100644
index fede229..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/beanshell/inputs/in
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index f82f340..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/biomart/biomart.t2flow
+++ /dev/null
@@ -1,30 +0,0 @@
-<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
deleted file mode 100644
index c9366c2..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/dataflow/dataflow.t2flow
+++ /dev/null
@@ -1,217 +0,0 @@
-<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
deleted file mode 100644
index fede229..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/dataflow/inputs/in
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index ecfb4e8..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/in-out/in-out.t2flow
+++ /dev/null
@@ -1,12 +0,0 @@
-<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
deleted file mode 100644
index fede229..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/in-out/inputs/in
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 30d74d2..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/iteration/inputs/in
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index bec4c2d..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/iteration/iteration.t2flow
+++ /dev/null
@@ -1,474 +0,0 @@
-<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>
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- <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
deleted file mode 100644
index cadf8b6..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/localworker/inputs/in
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index b3b2053..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/localworker/localworker.t2flow
+++ /dev/null
@@ -1,67 +0,0 @@
-<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
deleted file mode 100644
index f3f90b8..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/rest/rest.t2flow
+++ /dev/null
@@ -1,154 +0,0 @@
-<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
deleted file mode 100644
index 0cbff10..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication-https/secure-basic-authentication-https.t2flow
+++ /dev/null
@@ -1,74 +0,0 @@
-<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
deleted file mode 100644
index 998b69a..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication/secure-basic-authentication.t2flow
+++ /dev/null
@@ -1,74 +0,0 @@
-<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
deleted file mode 100644
index 1c5d317..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/secure-client-cert-authentication-https/secure-client-cert-authentication-https.t2flow
+++ /dev/null
@@ -1,162 +0,0 @@
-<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
deleted file mode 100644
index 5d2f893..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication-https/secure-digest-authentication-https.t2flow
+++ /dev/null
@@ -1,107 +0,0 @@
-<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
deleted file mode 100644
index 449e9db..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication/secure-digest-authentication.t2flow
+++ /dev/null
@@ -1,129 +0,0 @@
-<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
deleted file mode 100644
index 13637c4..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/secure-ws-https/secure-ws-https.t2flow
+++ /dev/null
@@ -1,180 +0,0 @@
-<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
deleted file mode 100644
index 764b810..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/secure-ws/secure-ws.t2flow
+++ /dev/null
@@ -1,180 +0,0 @@
-<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>
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- <maxJobs>1</maxJobs>
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- <identification>c71621ca-196c-46cd-9073-48af82b4bd4f</identification>
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- <date>2011-06-21 12:11:30.87 BST</date>
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- <date>2011-01-21 16:02:09.633 GMT</date>
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- <date>2010-11-22 13:29:43.282 GMT</date>
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- <identification>ca8fb5c5-0e8c-4e68-84f0-bdc85a77e2b3</identification>
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- <date>2010-11-22 13:29:26.400 GMT</date>
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- <date>2010-11-22 13:28:31.68 GMT</date>
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- </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
deleted file mode 100644
index 4db4ad5..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/secure-wsdl/secure-wsdl.t2flow
+++ /dev/null
@@ -1,131 +0,0 @@
-<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
deleted file mode 100644
index f1ef82b..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/soaplab/soaplab.t2flow
+++ /dev/null
@@ -1,84 +0,0 @@
-<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
deleted file mode 100644
index 7360186..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/spreadsheetimport/spreadsheetimport.t2flow
+++ /dev/null
@@ -1,646 +0,0 @@
-<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>
- <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>e28f14b3-e4ae-4d0b-893d-3a8400625069</identification>
- </annotationBean>
- <date>2010-07-07 16:10:13.994 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>e263e793-b394-4a57-855e-13e69b8780c2</identification>
- </annotationBean>
- <date>2010-07-07 17:00:11.782 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>14724df6-fee6-4b24-8fbc-eeeeb3dc4e61</identification>
- </annotationBean>
- <date>2010-07-07 16:38:21.137 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>6622310c-9440-45a1-a051-729487b00b46</identification>
- </annotationBean>
- <date>2010-07-13 12:32:33.863 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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-The source data is from http://data.gov.uk/</text>
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- <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
deleted file mode 100644
index 41266d0..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/stringconstant/stringconstant.t2flow
+++ /dev/null
@@ -1,32 +0,0 @@
-<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
deleted file mode 100644
index d77a851..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/tool/tool.t2flow
+++ /dev/null
@@ -1,158 +0,0 @@
-<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
deleted file mode 100644
index 4dea6bb..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/wsdl/wsdl.t2flow
+++ /dev/null
@@ -1,22 +0,0 @@
-<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
deleted file mode 100644
index b5045cc..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/age
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 08df4e7..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/firstName
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index b77017e..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/lastName
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index bd0875d..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/xmlSplitter.t2flow
+++ /dev/null
@@ -1,339 +0,0 @@
-<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
deleted file mode 100644
index 0691ccc..0000000
--- a/taverna-commandline-tests/src/test/resources/workflows/xpath/xpath.t2flow
+++ /dev/null
@@ -1,127 +0,0 @@
-<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
