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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/23 11:18:58 UTC
[6/8] incubator-taverna-commandline git commit: Revert "temporarily
empty repository"
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java
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diff --git a/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java
new file mode 100644
index 0000000..07df1c3
--- /dev/null
+++ b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java
@@ -0,0 +1,485 @@
+/*******************************************************************************
+ * Copyright (C) 2012 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package uk.org.taverna.commandline;
+
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.junit.Assume.assumeTrue;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.net.URI;
+import java.net.URL;
+import java.text.MessageFormat;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.comparator.NameFileComparator;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+
+import uk.org.taverna.commandline.WorkflowTestSuite.Workflows;
+import uk.org.taverna.scufl2.api.container.WorkflowBundle;
+import uk.org.taverna.scufl2.api.io.WorkflowBundleIO;
+import uk.org.taverna.scufl2.rdfxml.RDFXMLReader;
+
+/**
+ * Regression tests for Taverna Command Line Tool.
+ *
+ * @author David Withers
+ */
+@RunWith(WorkflowTestSuite.class)
+public class TavernaCommandLineTest {
+
+ private static String baseVersion = "2.4.0";
+ private static boolean baseVersionReleased = true;
+
+ private static String testVersion = "3.0.1-SNAPSHOT";
+ private static boolean testVersionReleased = false;
+ private static boolean testVersionSupportsScufl2 = true;
+
+ private static String script = "executeworkflow.sh";
+ private static String baseName = "taverna-commandline-" + baseVersion;
+ private static String testName = "taverna-command-line-" + testVersion;
+ private static String releasedLocation = "https://launchpad.net/taverna/t2/";
+ private static String unreleasedLocation = "http://build.mygrid.org.uk/ci/job/t3-taverna-commandline-product/lastSuccessfulBuild/net.sf.taverna.t2$taverna-commandline/artifact/net.sf.taverna.t2/taverna-commandline/";
+
+ private static String baseVersionLocation = (baseVersionReleased ? releasedLocation
+ : unreleasedLocation) + baseVersion + "/+download/" + baseName + ".zip";
+ private static String testVersionLocation = (testVersionReleased ? releasedLocation
+ : unreleasedLocation)
+ + testVersion
+ + "/"
+ + testName
+ + (testVersionReleased ? ".zip" : "-bin.zip");
+
+ private static String baseCommand;
+ private static String testCommand;
+
+ private static File buildDirectory;
+
+ private File workflowDirectory;
+ private File baseOutput;
+ private File testOutput;
+ private boolean secure;
+ private List<File> inputs;
+ private String ignorePort;
+ private String message;
+
+ public TavernaCommandLineTest(File workflowDirectory) throws Exception {
+ this.workflowDirectory = workflowDirectory;
+ if (buildDirectory == null) {
+ String buildDirectoryLocation = System.getProperty("buildDirectory");
+ if (buildDirectoryLocation == null) {
+ buildDirectoryLocation = System.getProperty("user.dir")
+ + System.getProperty("file.separator") + "target";
+ }
+ buildDirectory = new File(buildDirectoryLocation);
+ buildDirectory.mkdirs();
+ }
+ if (baseCommand == null) {
+ File commandDirectory = new File(buildDirectory, baseName);
+ if (!commandDirectory.exists()) {
+ System.out.println("Fetching " + baseName);
+ fetchTaverna(baseVersionLocation, baseName);
+ }
+ baseCommand = new File(baseName, script).getPath();
+ }
+ if (testCommand == null) {
+ File commandDirectory = new File(buildDirectory, testName);
+ if (!commandDirectory.exists()) {
+ System.out.println("Fetching " + testName);
+ fetchTaverna(testVersionLocation, testName);
+ }
+ testCommand = new File(testName, script).getPath();
+ }
+ File outputsDirectory = new File(buildDirectory, "test-outputs");
+ baseOutput = new File(outputsDirectory, workflowDirectory.getName() + "-" + baseVersion);
+ testOutput = new File(outputsDirectory, workflowDirectory.getName() + "-" + testVersion);
+ secure = workflowDirectory.getName().startsWith("secure");
+ inputs = getInputs();
+ ignorePort = getIgnorePort();
+ message = "Running {0} with version {1}";
+ }
+
+ @Workflows
+ public static List<File> workflows() {
+ List<File> workflows = new ArrayList<File>();
+ for (File workflowDirectory : getResources("workflows")) {
+ workflows.add(workflowDirectory);
+ }
+ for (File workflowDirectory : getResources("myexperiment")) {
+ workflows.add(workflowDirectory);
+ }
+ return workflows;
+ }
+
+ @Before
+ public void setup() throws Exception {
+ if (!baseOutput.exists()) {
+ if (baseVersion.equals("2.3.0") && workflowDirectory.getName().equals("tool"))
+ return;// version 2.3.0 is missing tool plugin
+ String workflow = getWorkflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, baseVersion)
+ + (inputs.size() > 0 ? " using input values" : ""));
+ runWorkflow(baseCommand, workflow, baseOutput, true, secure, false);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ baseOutput.exists());
+ }
+ }
+
+ public boolean testExcluded() {
+ // version 3.0.0 is missing biomoby activity
+ if (testVersion.startsWith("3.") && workflowDirectory.getName().contains("biomoby"))
+ return true;
+ // version 3.0.0 is missing tool activity
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("unix_external_tools_with_zip_and_unzip"))
+ return true;
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("unix_numerically_adding_two_values"))
+ return true;
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("unix_tool_service_using_string_replacement"))
+ return true;
+ // version 3.0.0 is missing looping configuration
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("ebi_interproscan_newservices"))
+ return true;
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("biomartandembossanalysis"))
+ return true;
+ return false;
+ }
+
+ @Test
+ public void testWorkflowWithoutInputs() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(inputs.isEmpty());
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getWorkflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, testVersion));
+ runWorkflow(testCommand, workflow, testOutput, true, secure, false);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ @Test
+ public void testWorkflowWithInputValues() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(inputs.size() > 0);
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getWorkflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, testVersion)
+ + " using input values");
+ runWorkflow(testCommand, workflow, testOutput, true, secure, false);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ @Test
+ public void testWorkflowWithInputFiles() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(inputs.size() > 0);
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getWorkflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, testVersion)
+ + " using input files");
+ runWorkflow(testCommand, workflow, testOutput, false, secure, false);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ @Test
+ @Ignore
+ public void testWorkflowWithDatabase() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(inputs.size() > 0);
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getWorkflow().toASCIIString();
+ System.out
+ .println(MessageFormat.format(message, workflow, testVersion) + " using database");
+ runWorkflow(testCommand, workflow, testOutput, true, secure, true);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ @Test
+ public void testScufl2Workflow() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(testVersionSupportsScufl2);
+
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getScufl2Workflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, testVersion)
+ + (inputs.size() > 0 ? " using input values" : ""));
+ runWorkflow(testCommand, workflow, testOutput, true, secure, true);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ private synchronized void runWorkflow(String command, String workflow, File outputsDirectory,
+ boolean inputValues, boolean secure, boolean database) throws Exception {
+ ProcessBuilder processBuilder = new ProcessBuilder("sh", command);
+ processBuilder.redirectErrorStream(true);
+ processBuilder.directory(buildDirectory);
+ List<String> args = processBuilder.command();
+ for (File input : inputs) {
+ if (inputValues) {
+ args.add("-inputvalue");
+ args.add(input.getName());
+ args.add(IOUtils.toString(new FileReader(input)));
+ } else {
+ args.add("-inputfile");
+ args.add(input.getName());
+ args.add(input.getAbsolutePath());
+ }
+ }
+ args.add("-outputdir");
+ args.add(outputsDirectory.getPath());
+ if (secure) {
+ args.add("-cmdir");
+ args.add(getClass().getResource("/security").getFile());
+ args.add("-cmpassword");
+ }
+ if (database) {
+ args.add("-embedded");
+ }
+ args.add(workflow);
+ Process process = processBuilder.start();
+ if (secure) {
+ PrintStream outputStream = new PrintStream(process.getOutputStream());
+ outputStream.println("test");
+ outputStream.flush();
+ }
+ waitFor(process);
+ }
+
+ private URI getWorkflow() throws Exception {
+ File workflow = new File(workflowDirectory, workflowDirectory.getName() + ".t2flow");
+ if (!workflow.exists()) {
+ workflow = new File(workflowDirectory, workflowDirectory.getName() + ".url");
+ return new URI(IOUtils.toString(new FileReader(workflow)));
+ }
+ return workflow.toURI();
+ }
+
+ private URI getScufl2Workflow() throws Exception {
+ File workflow = new File(buildDirectory, workflowDirectory.getName() + ".wfbundle");
+ // if (!workflow.exists()) {
+ WorkflowBundleIO workflowBundleIO = new WorkflowBundleIO();
+ WorkflowBundle bundle = workflowBundleIO.readBundle(getWorkflow().toURL(), null);
+ workflowBundleIO.writeBundle(bundle, workflow,
+ RDFXMLReader.APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE);
+ // }
+ return workflow.toURI();
+ }
+
+ private synchronized int waitFor(Process process) throws IOException {
+ while (true) {
+ try {
+ wait(500);
+ } catch (InterruptedException e) {
+ }
+ IOUtils.copy(process.getInputStream(), System.out);
+ try {
+ return process.exitValue();
+ } catch (IllegalThreadStateException e) {
+ }
+ }
+ }
+
+ private void assertOutputsEquals(File directory1, File directory2) {
+ File[] directory1Files = directory1.listFiles();
+ File[] directory2Files = directory2.listFiles();
+ // assert directories contain same number of files
+ assertEquals(String.format("%s has %s files but %s has %s files", directory1.getName(),
+ directory1Files.length, directory2.getName(), directory2Files.length),
+ directory1Files.length, directory2Files.length);
+ // sort files in directory
+ Arrays.sort(directory1Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
+ Arrays.sort(directory2Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
+ for (int i = 0; i < directory1Files.length; i++) {
+ assertFilesEqual(directory1Files[i], directory2Files[i], !directory1Files[i].getName()
+ .equals(ignorePort));
+ }
+ }
+
+ private void assertDirectoriesEquals(File directory1, File directory2, boolean checkFileContents) {
+ if (directory1.exists()) {
+ assertTrue(String.format("%s exists but %s does not", directory1, directory2),
+ directory2.exists());
+ } else {
+ assertFalse(String.format("%s does not exists but %s does", directory1, directory2),
+ directory2.exists());
+ }
+ File[] directory1Files = directory1.listFiles();
+ File[] directory2Files = directory2.listFiles();
+ // assert directories contain same number of files
+ assertEquals(String.format("%s has %s files but %s has %s files", directory1.getName(),
+ directory1Files.length, directory2.getName(), directory2Files.length),
+ directory1Files.length, directory2Files.length);
+ // sort files in directory
+ Arrays.sort(directory1Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
+ Arrays.sort(directory2Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
+ for (int i = 0; i < directory1Files.length; i++) {
+ assertFilesEqual(directory1Files[i], directory2Files[i], checkFileContents);
+ }
+ }
+
+ private void assertFilesEqual(File file1, File file2, boolean checkFileContents) {
+ if (file1.isHidden()) {
+ assertTrue(String.format("%s is hidden but %s is not", file1, file2), file2.isHidden());
+ } else {
+ assertFalse(String.format("%s is not hidden but %s is", file1, file2), file2.isHidden());
+ assertEquals(file1.getName(), file2.getName());
+ if (file1.isDirectory()) {
+ assertTrue(String.format("%s is a directory but %s is not", file1, file2),
+ file2.isDirectory());
+ assertDirectoriesEquals(file1, file2, checkFileContents);
+ } else {
+ assertFalse(String.format("%s is not a directory but %s is", file1, file2),
+ file2.isDirectory());
+ if (isZipFile(file1)) {
+ assertZipFilesEqual(file1, file2);
+ } else if (checkFileContents) {
+ assertEquals(String.format("%s is a different length to %s", file1, file2),
+ file1.length(), file2.length());
+ try {
+ byte[] byteArray1 = IOUtils.toByteArray(new FileReader(file1));
+ byte[] byteArray2 = IOUtils.toByteArray(new FileReader(file2));
+ assertArrayEquals(String.format("%s != %s", file1, file2), byteArray1,
+ byteArray2);
+ } catch (FileNotFoundException e) {
+ fail(e.getMessage());
+ } catch (IOException e) {
+ fail(e.getMessage());
+ }
+ }
+ }
+ }
+ }
+
+ private void assertZipFilesEqual(File file1, File file2) {
+ ZipFile zipFile1 = null;
+ ZipFile zipFile2 = null;
+ try {
+ zipFile1 = new ZipFile(file1);
+ zipFile2 = new ZipFile(file2);
+ } catch (Exception e) {
+ assertTrue(String.format("%s and %s are not both zip files"), zipFile1 == null);
+ }
+ if (zipFile1 != null && zipFile2 != null) {
+ Enumeration<? extends ZipEntry> entries1 = zipFile1.entries();
+ Enumeration<? extends ZipEntry> entries2 = zipFile2.entries();
+ while (entries1.hasMoreElements()) {
+ assertTrue(entries2.hasMoreElements());
+ ZipEntry zipEntry1 = entries1.nextElement();
+ ZipEntry zipEntry2 = entries2.nextElement();
+ assertEquals(
+ String.format("%s and %s are not both directories", zipEntry1, zipEntry2),
+ zipEntry1.isDirectory(), zipEntry2.isDirectory());
+ assertEquals(String.format("%s and %s have different names", zipEntry1, zipEntry2),
+ zipEntry1.getName(), zipEntry2.getName());
+ assertEquals(String.format("%s and %s have different sizes", zipEntry1, zipEntry2),
+ zipEntry1.getSize(), zipEntry2.getSize());
+ try {
+ byte[] byteArray1 = IOUtils.toByteArray(zipFile1.getInputStream(zipEntry1));
+ byte[] byteArray2 = IOUtils.toByteArray(zipFile2.getInputStream(zipEntry2));
+ assertArrayEquals(String.format("%s != %s", zipEntry1, zipEntry2), byteArray1,
+ byteArray2);
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ assertFalse(entries2.hasMoreElements());
+ }
+ }
+
+ private boolean isZipFile(File file) {
+ try {
+ new ZipFile(file);
+ return true;
+ } catch (Exception e) {
+ return false;
+ }
+ }
+
+ private static File[] getResources(String directory) {
+ return new File(TavernaCommandLineTest.class.getResource("/" + directory).getFile())
+ .listFiles();
+ }
+
+ private List<File> getInputs() {
+ File inputsDirectory = new File(workflowDirectory, "inputs");
+ if (inputsDirectory.exists() && inputsDirectory.isDirectory()) {
+ return Arrays.asList(inputsDirectory.listFiles());
+ }
+ return Collections.emptyList();
+ }
+
+ private String getIgnorePort() throws Exception {
+ File ignorePort = new File(workflowDirectory, "ignorePort");
+ if (ignorePort.exists()) {
+ return IOUtils.toString(new FileReader(ignorePort));
+ }
+ return "";
+ }
+
+ private void fetchTaverna(String location, String name) throws Exception {
+ File zipFile = new File(buildDirectory, name + ".zip");
+ IOUtils.copy(new URL(location).openStream(), new FileOutputStream(zipFile));
+ ProcessBuilder processBuilder = new ProcessBuilder("unzip", "-q", name);
+ processBuilder.redirectErrorStream(true);
+ processBuilder.directory(buildDirectory);
+ System.out.println(processBuilder.command());
+ Process process = processBuilder.start();
+ waitFor(process);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java
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diff --git a/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java
new file mode 100644
index 0000000..56ed82d
--- /dev/null
+++ b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java
@@ -0,0 +1,70 @@
+/*******************************************************************************
+ * Copyright (C) 2012 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package uk.org.taverna.commandline;
+
+import java.io.File;
+import java.util.List;
+
+import org.junit.runner.notification.RunNotifier;
+import org.junit.runners.BlockJUnit4ClassRunner;
+import org.junit.runners.model.FrameworkMethod;
+import org.junit.runners.model.InitializationError;
+import org.junit.runners.model.Statement;
+
+/**
+ * Test runner for running workflows.
+ *
+ * @author David Withers
+ */
+public class WorkflowTestRunner extends BlockJUnit4ClassRunner {
+ private File workflow;
+
+ public WorkflowTestRunner(Class<?> type, File workflow) throws InitializationError {
+ super(type);
+ this.workflow = workflow;
+ }
+
+ @Override
+ public Object createTest() throws Exception {
+ return getTestClass().getOnlyConstructor().newInstance(workflow);
+ }
+
+ @Override
+ protected String getName() {
+ return String.format("[%s]", workflow.getName());
+ }
+
+ @Override
+ protected String testName(final FrameworkMethod method) {
+ return String.format("%s[%s]", method.getName(), workflow.getName());
+ }
+
+ @Override
+ protected void validateConstructor(List<Throwable> errors) {
+ validateOnlyOneConstructor(errors);
+ }
+
+ @Override
+ protected Statement classBlock(RunNotifier notifier) {
+ return childrenInvoker(notifier);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java
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diff --git a/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java
new file mode 100644
index 0000000..140dec6
--- /dev/null
+++ b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java
@@ -0,0 +1,79 @@
+/*******************************************************************************
+ * Copyright (C) 2012 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package uk.org.taverna.commandline;
+
+import java.io.File;
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+import java.lang.reflect.Modifier;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.junit.runner.Runner;
+import org.junit.runners.Suite;
+import org.junit.runners.model.FrameworkMethod;
+import org.junit.runners.model.TestClass;
+
+/**
+ * Test suite for running workflows specified by a method annotated by @Workflows.
+ *
+ * @author David Withers
+ */
+public class WorkflowTestSuite extends Suite {
+
+ @Retention(RetentionPolicy.RUNTIME)
+ @Target(ElementType.METHOD)
+ public static @interface Workflows {}
+
+ private ArrayList<Runner> runners = new ArrayList<Runner>();
+
+ public WorkflowTestSuite(Class<?> klass) throws Throwable {
+ super(klass, Collections.<Runner>emptyList());
+ for (File workflow : getWorkflows(getTestClass())) {
+ runners.add(new WorkflowTestRunner(getTestClass().getJavaClass(), workflow));
+ }
+ }
+
+ @Override
+ protected List<Runner> getChildren() {
+ return runners;
+ }
+
+ @SuppressWarnings("unchecked")
+ private List<File> getWorkflows(TestClass klass) throws Throwable {
+ return (List<File>) getWorkflowsMethod(klass).invokeExplosively(null);
+ }
+
+ public FrameworkMethod getWorkflowsMethod(TestClass testClass) throws Exception {
+ List<FrameworkMethod> methods = testClass.getAnnotatedMethods(Workflows.class);
+ for (FrameworkMethod method : methods) {
+ int modifiers = method.getMethod().getModifiers();
+ if (Modifier.isStatic(modifiers) && Modifier.isPublic(modifiers)) {
+ return method;
+ }
+ }
+ throw new Exception("No public static Workflows annotated method on class " + testClass.getName());
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url
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diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url b/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url
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+http://www.myexperiment.org/workflows/1794/download/biomartandembossanalysis_457009.t2flow?version=4
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/ignorePort
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+outputPlot
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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
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+++ b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/biomoby_tutorial_workflow.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1366/download/biomoby_tutorial_workflow_877727.t2flow?version=1
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+restrict_out
\ No newline at end of file
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+656461
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/namespace
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+NCBI_gi
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-tests/src/test/resources/myexperiment/demonstration_of_configurable_iteration/demonstration_of_configurable_iteration.url
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+http://www.myexperiment.org/workflows/1367/download/demonstration_of_configurable_iteration_114130.t2flow?version=1
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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
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--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/ebi_interproscan_newservices.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1767/download/ebi_interproscan_newservices_421482.t2flow?version=2
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@@ -0,0 +1 @@
+Graphical_output
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/email
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+++ b/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/email
@@ -0,0 +1 @@
+test@mygrid.org.uk
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/sequence
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--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/sequence
@@ -0,0 +1,8 @@
+>sp|Q9BTV4|TMM43_HUMAN Transmembrane protein 43 OS=Homo sapiens GN=TMEM43 PE=1 SV=1
+MAANYSSTSTRREHVKVKTSSQPGFLERLSETSGGMFVGLMAFLLSFYLIFTNEGRALKT
+ATSLAEGLSLVVSPDSIHSVAPENEGRLVHIIGALRTSKLLSDPNYGVHLPAVKLRRHVE
+MYQWVETEESREYTEDGQVKKETRYSYNTEWRSEIINSKNFDREIGHKNPSAMAVESFMA
+TAPFVQIGRFFLSSGLIDKVDNFKSLSLSKLEDPHVDIIRRGDFFYHSENPKYPEVGDLR
+VSFSYAGLSGDDPDLGPAHVVTVIARQRGDQLVPFSTKSGDTLLLLHHGDFSAEEVFHRE
+LRSNSMKTWGLRAAGWMAMFMGLNLMTRILYTLVDWFPVFRDLVNIGLKAFAFCVATSLT
+LLTVAAGWLFYRPLWALLIAGLALVPILVARTRVPAKKLE
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-tests/src/test/resources/myexperiment/example_of_conditional_invocation/example_of_conditional_invocation.url
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+http://www.myexperiment.org/workflows/2561/download/example_of_conditional_invocation_369634.t2flow?version=1
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+true
\ No newline at end of file
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+http://www.myexperiment.org/workflows/2562/download/example_of_explicit_looping_785852.t2flow?version=1
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+14
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+-3
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+3
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+http://www.myexperiment.org/workflows/1510/download/example_workflow_for_rest_and_xpath_activities_650957.t2flow?version=1
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+London
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+http://www.myexperiment.org/workflows/1005/download/fetch_dragon_images_from_biomoby_830269.t2flow?version=2
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+http://www.myexperiment.org/workflows/1369/download/fetch_pdb_flatfile_from_rcsb_server_969361.t2flow?version=1
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+http://www.myexperiment.org/workflows/1370/download/fetch_today_s_xkcd_comic_568671.t2flow?version=1
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+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><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
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/inputs/in
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/inputs/in b/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/inputs/in
new file mode 100644
index 0000000..fede229
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/inputs/in
@@ -0,0 +1 @@
+test-input
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-tests/src/test/resources/workflows/beanshell/beanshell.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/beanshell/beanshell.t2flow b/taverna-commandline-tests/src/test/resources/workflows/beanshell/beanshell.t2flow
new file mode 100644
index 0000000..8c5968c
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/beanshell/beanshell.t2flow
@@ -0,0 +1,137 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="78cb1427-d57f-42c2-a385-1d20c1580f3b" role="top"><name>Workflow13</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Echo</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfi
gurationBean 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
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-tests/src/test/resources/workflows/beanshell/inputs/in
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diff --git a/taverna-commandline-tests/src/test/resources/workflows/beanshell/inputs/in b/taverna-commandline-tests/src/test/resources/workflows/beanshell/inputs/in
new file mode 100644
index 0000000..fede229
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+++ b/taverna-commandline-tests/src/test/resources/workflows/beanshell/inputs/in
@@ -0,0 +1 @@
+test-input
\ No newline at end of file