Attempt to update package to org.apache.taverna .. but won't really combine because of error in spring dependency?
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/commit/50373179 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/tree/50373179 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/diff/50373179 Branch: refs/heads/master Commit: 50373179a0ab245d08d94b3dc9e6b0c2ad738315 Parents: 9012593 Author: Stian Soiland-Reyes <[email protected]> Authored: Sun Oct 18 19:12:38 2015 +0100 Committer: Stian Soiland-Reyes <[email protected]> Committed: Sun Oct 18 19:12:38 2015 +0100 ---------------------------------------------------------------------- .../org/apache/taverna/platform/ActivityIT.java | 68 ++ .../taverna/platform/CommandLineToolIT.java | 88 ++ .../apache/taverna/platform/ExecutionIT.java | 128 +++ .../taverna/platform/LocalExecutionIT.java | 117 ++ .../taverna/platform/OSGIFrameworkIT.java | 92 ++ .../org/apache/taverna/platform/PlatformIT.java | 375 +++++++ .../java/org/apache/taverna/platform/RunIT.java | 1000 +++++++++++++++++ .../apache/taverna/platform/RunParallelIT.java | 93 ++ .../apache/taverna/platform/RunWorkflowsIT.java | 134 +++ .../uk/org/taverna/platform/ActivityIT.java | 72 -- .../org/taverna/platform/CommandLineToolIT.java | 91 -- .../uk/org/taverna/platform/ExecutionIT.java | 134 --- .../org/taverna/platform/LocalExecutionIT.java | 120 --- .../org/taverna/platform/OSGIFrameworkIT.java | 93 -- .../uk/org/taverna/platform/PlatformIT.java | 378 ------- .../java/uk/org/taverna/platform/RunIT.java | 1005 ------------------ .../uk/org/taverna/platform/RunParallelIT.java | 95 -- .../uk/org/taverna/platform/RunWorkflowsIT.java | 135 --- 18 files changed, 2095 insertions(+), 2123 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ActivityIT.java ---------------------------------------------------------------------- diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ActivityIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ActivityIT.java new file mode 100644 index 0000000..ec5e483 --- /dev/null +++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ActivityIT.java @@ -0,0 +1,68 @@ +/******************************************************************************* + * Copyright (C) 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 org.apache.taverna.platform; + +import java.net.URI; +import java.util.List; + +import org.apache.taverna.platform.capability.api.ActivityConfigurationException; +import org.apache.taverna.platform.capability.api.ActivityNotFoundException; +import org.osgi.framework.ServiceReference; + + +public class ActivityIT extends PlatformIT { + + public void testGetActivityURIs() { + ServiceReference activityServiceReference = bundleContext.getServiceReference("org.apache.taverna.platform.capability.api.ActivityService"); + ActivityService activityService = (ActivityService) bundleContext.getService(activityServiceReference); + List<URI> activityURIs = activityService.getActivityURIs(); + System.out.println("================= Available Activities ==================="); + for (URI uri : activityURIs) { + System.out.println(uri); + } + System.out.println("=========================================================="); + System.out.println(""); + } + + public void testCreateActivity() throws ActivityNotFoundException, ActivityConfigurationException { + ServiceReference activityServiceReference = bundleContext.getServiceReference("org.apache.taverna.platform.capability.api.ActivityService"); + ActivityService activityService = (ActivityService) bundleContext.getService(activityServiceReference); + List<URI> activityURIs = activityService.getActivityURIs(); + for (URI uri : activityURIs) { + System.out.println("Creating activity " + uri); + Activity<?> activity = activityService.createActivity(uri, null); + } + } + + public void testGetActivityConfigurationDefinition() throws Exception { + ServiceReference activityServiceReference = bundleContext.getServiceReference("org.apache.taverna.platform.capability.api.ActivityService"); + ActivityService activityService = (ActivityService) bundleContext.getService(activityServiceReference); + + List<URI> activityURIs = activityService.getActivityURIs(); + System.out.println("============ Activity Configuration Definitions =========="); + for (URI uri : activityURIs) { + ConfigurationDefinition configurationDefinition = activityService.getActivityConfigurationDefinition(uri); + System.out.println(configurationDefinition); + } + System.out.println("=========================================================="); + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/CommandLineToolIT.java ---------------------------------------------------------------------- diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/CommandLineToolIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/CommandLineToolIT.java new file mode 100644 index 0000000..f42cb77 --- /dev/null +++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/CommandLineToolIT.java @@ -0,0 +1,88 @@ +/******************************************************************************* + * Copyright (C) 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 org.apache.taverna.platform; + +import org.osgi.framework.ServiceReference; + +import org.apache.taverna.platform.run.api.RunService; +import org.apache.taverna.scufl2.api.io.WorkflowBundleIO; +import org.apache.taverna.scufl2.api.io.WorkflowBundleReader; + +public class CommandLineToolIT extends PlatformIT { + + private RunService runService; + private WorkflowBundleIO workflowBundleIO; + private WorkflowBundleReader workflowReader; + + protected void setup() throws Exception { + super.setup(); + if (runService == null) { + ServiceReference runServiceReference = bundleContext + .getServiceReference("org.apache.taverna.platform.run.api.RunService"); + runService = (RunService) bundleContext.getService(runServiceReference); + } + + if (workflowReader == null) { + ServiceReference workflowBundleReaderServiceReference = bundleContext + .getServiceReferences("org.apache.taverna.scufl2.api.io.WorkflowBundleReader", + "(mediaType=application/vnd.taverna.t2flow+xml)")[0]; + workflowBundleReader = (WorkflowBundleReader) bundleContext + .getService(workflowBundleReaderServiceReference); + } + + if (workflowBundleIO == null) { + ServiceReference workflowBundleIOServiceReference = bundleContext + .getServiceReference("org.apache.taverna.scufl2.api.io.WorkflowBundleIO"); + workflowBundleIO = (WorkflowBundleIO) bundleContext + .getService(workflowBundleIOServiceReference); + } + } + + public void testCommandLineTool() throws Exception { + + setup(); + + CommandLineTool cmdTool = new CommandLineTool(); + cmdTool.setRunService(runService); + cmdTool.setCredentialManager(credentialManager); + cmdTool.setWorkflowBundleIO(workflowBundleIO); + cmdTool.setCommandLineArgumentsService(new CommandLineArguments() { + public String[] getCommandLineArguments() { + return new String[] { "-outputdoc", "/tmp/taverna3/baclava-output1.xml", + "/Users/alex/Desktop/t2flows/simple-wf-no-inputs-one-output.t2flow" }; + } + + }); + cmdTool.run(); + + cmdTool.setCommandLineArgumentsService(new CommandLineArguments() { + public String[] getCommandLineArguments() { + return new String[] { "-inputvalue", "in", "Taverna 3 Platform rules", + "-outputdoc", "/tmp/taverna3/baclava-output2.xml", + "/Users/alex/Desktop/t2flows/simple-wf-one-input-one-output.t2flow" }; + } + + }); + cmdTool.run(); + + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ExecutionIT.java ---------------------------------------------------------------------- diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ExecutionIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ExecutionIT.java new file mode 100644 index 0000000..d28ac5d --- /dev/null +++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ExecutionIT.java @@ -0,0 +1,128 @@ +/******************************************************************************* + * Copyright (C) 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 org.apache.taverna.platform; + +import java.net.URI; +import java.util.Collections; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import org.osgi.framework.ServiceReference; + +import org.apache.taverna.platform.execution.api.AbstractExecutionEnvironment; +import org.apache.taverna.platform.execution.api.AbstractExecutionService; +import org.apache.taverna.platform.execution.api.Execution; +import org.apache.taverna.platform.execution.api.ExecutionEnvironment; +import org.apache.taverna.platform.execution.api.ExecutionEnvironmentService; +import org.apache.taverna.platform.execution.api.InvalidWorkflowException; +import org.apache.taverna.scufl2.api.container.WorkflowBundle; +import org.apache.taverna.scufl2.api.core.Workflow; +import org.apache.taverna.scufl2.api.profiles.Profile; + +public class ExecutionIT extends PlatformIT { + + private ExecutionEnvironmentService executionEnvironmentService; + + protected void setup() throws Exception { + super.setup(); + ServiceReference[] executionServiceReferences = bundleContext.getServiceReferences( + "org.apache.taverna.platform.execution.api.ExecutionEnvironmentService", null); + assertEquals(1, executionServiceReferences.length); + executionEnvironmentService = (ExecutionEnvironmentService) bundleContext + .getService(executionServiceReferences[0]); + + } + + public void testGetExecutionEnvironments() throws Exception { + setup(); + + Set<ExecutionEnvironment> executionEnvironments = executionEnvironmentService + .getExecutionEnvironments(); + int size = executionEnvironments.size(); + + bundleContext.registerService("org.apache.taverna.platform.execution.api.ExecutionService", + new AbstractExecutionService("test id", "test name", "test description") { + public Set<ExecutionEnvironment> getExecutionEnvivonments() { + return Collections + .<ExecutionEnvironment> singleton(new AbstractExecutionEnvironment( + "test id", "test name", "test description", this) { + public List<URI> getDispatchLayerURIs() { + return Collections.singletonList(URI + .create("http://ns.taverna.org.uk/2010/dispatchlayer/testDispatchLayer";)); + } + + public List<URI> getActivityURIs() { + return Collections.singletonList(URI + .create("http://ns.taverna.org.uk/2010/activity/testActivity";)); + } + + public boolean dispatchLayerExists(URI uri) { + return false; + } + + public boolean activityExists(URI uri) { + return false; + } + + public ConfigurationDefinition getActivityConfigurationDefinition( + URI uri) throws ActivityNotFoundException, + ActivityConfigurationException { + return null; + } + + public ConfigurationDefinition getDispatchLayerConfigurationDefinition( + URI uri) throws DispatchLayerNotFoundException, + DispatchLayerConfigurationException { + return null; + } + }); + } + + protected Execution createExecutionImpl(WorkflowBundle workflowBundle, + Workflow workflow, Profile profile, Map<String, Data> inputs) throws InvalidWorkflowException { + return null; + } + }, null); + + + executionEnvironments = executionEnvironmentService + .getExecutionEnvironments(); + assertEquals(size + 1, executionEnvironments.size()); + + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + System.out.println(executionEnvironment); + } + } + + public void testGetExecutionEnvironmentsProfile() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/beanshell.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = executionEnvironmentService + .getExecutionEnvironments(workflowBundle.getMainProfile()); + assertTrue(executionEnvironments.size() > 0); + + System.out.println(executionEnvironments.iterator().next()); + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/LocalExecutionIT.java ---------------------------------------------------------------------- diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/LocalExecutionIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/LocalExecutionIT.java new file mode 100644 index 0000000..431aa88 --- /dev/null +++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/LocalExecutionIT.java @@ -0,0 +1,117 @@ +/******************************************************************************* + * Copyright (C) 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 org.apache.taverna.platform; + +import java.util.Collections; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import org.osgi.framework.ServiceReference; + +import org.apache.taverna.platform.execution.api.ExecutionEnvironment; +import org.apache.taverna.platform.execution.api.ExecutionService; +import org.apache.taverna.platform.report.State; +import org.apache.taverna.platform.report.WorkflowReport; +import org.apache.taverna.scufl2.api.container.WorkflowBundle; +import org.apache.taverna.scufl2.api.core.Workflow; +import org.apache.taverna.scufl2.api.profiles.Profile; + +public class LocalExecutionIT extends PlatformIT { + + private ExecutionService executionService; + private Set<ExecutionEnvironment> executionEnvironments; + + protected void setup() throws Exception { + super.setup(); + if (executionService == null) { + ServiceReference[] executionServiceReferences = bundleContext.getServiceReferences( + "org.apache.taverna.platform.execution.api.ExecutionService", + "(org.springframework.osgi.bean.name=localExecution)"); + assertEquals(1, executionServiceReferences.length); + executionService = (ExecutionService) bundleContext + .getService(executionServiceReferences[0]); + executionEnvironments = executionService.getExecutionEnvivonments(); + assertEquals(1, executionEnvironments.size()); + } + if (dataService == null) { + ServiceReference dataServiceReference = bundleContext + .getServiceReference("org.apache.taverna.platform.data.DataService"); + dataService = (DataService) bundleContext.getService(dataServiceReference); + } + } + + public void testLocalExecution() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/in-out.t2flow"); + Workflow workflow = workflowBundle.getMainWorkflow(); + Profile profile = workflowBundle.getMainProfile(); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Map<String, Data> inputs = Collections.singletonMap("in", dataService.create("test-input")); + + String executionId = executionService.createExecution(executionEnvironment, + workflowBundle, workflow, profile, inputs); + WorkflowReport report = executionService.getWorkflowReport(executionId); + assertEquals(State.CREATED, report.getState()); + executionService.start(executionId); + + Map<String, Data> results = report.getOutputs(); + assertNotNull(results); + waitForResults(results, report, "out"); + + Object result = results.get("out").getValue(); + assertEquals("test-input", result); + assertEquals(State.COMPLETED, report.getState()); + System.out.println(report); + } + } + + public void testLocalExecution2() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/beanshell.t2flow"); + Workflow workflow = workflowBundle.getMainWorkflow(); + Profile profile = workflowBundle.getMainProfile(); + + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Map<String, Data> inputs = Collections.singletonMap("in", dataService.create("test-input")); + + String executionId = executionService.createExecution(executionEnvironment, + workflowBundle, workflow, profile, inputs); + WorkflowReport report = executionService.getWorkflowReport(executionId); + System.out.println(report); + assertEquals(State.CREATED, report.getState()); + executionService.start(executionId); + System.out.println(report); + + Map<String, Data> results = report.getOutputs(); + waitForResults(results, report, "out"); + + List<Data> result = results.get("out").getElements(); + assertEquals(1000, result.size()); + assertEquals("test-input:0", result.get(0).getValue()); + assertEquals(State.COMPLETED, report.getState()); + System.out.println(report); + } + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/OSGIFrameworkIT.java ---------------------------------------------------------------------- diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/OSGIFrameworkIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/OSGIFrameworkIT.java new file mode 100644 index 0000000..b73b1ed --- /dev/null +++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/OSGIFrameworkIT.java @@ -0,0 +1,92 @@ +/******************************************************************************* + * Copyright (C) 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 org.apache.taverna.platform; + +import java.io.IOException; + +import org.osgi.framework.Bundle; +import org.springframework.osgi.util.OsgiStringUtils; + +public class OSGIFrameworkIT extends PlatformIT { + + public void testOsgiEnvironment() throws Exception { + Bundle[] bundles = bundleContext.getBundles(); + for (int i = 0; i < bundles.length; i++) { + System.out.println(OsgiStringUtils.nullSafeName(bundles[i])); + } + System.out.println(); + } + + protected String[] getTestFrameworkBundlesNames() { + String[] frameworkBundles = super.getTestFrameworkBundlesNames(); + System.out.println("Test Framework bundles:"); + for (String bundle : frameworkBundles) { + System.out.println(" " + bundle); + } + return frameworkBundles; + } + + protected String[] getTestBundlesNames() { + String[] frameworkBundles = super.getTestBundlesNames(); + System.out.println("Framework bundles:"); + for (String bundle : frameworkBundles) { + System.out.println(" " + bundle); + } + return frameworkBundles; + } + + public void testPrintConfig() throws IOException { + Resource[] bundles = getTestBundles(); + Resource[] testBundles = getTestFrameworkBundles(); + StringBuilder sb = new StringBuilder(); + StringBuilder sb2 = new StringBuilder(); + System.out.println("mkdir platform"); + System.out.println("mkdir platform/configuration"); + sb2.append("cp "); + sb.append("osgi.bundles="); + boolean printComma = false; + for (Resource resource : bundles) { + if (printComma) { + sb.append(", "); + sb2.append(" "); + } + sb.append(resource.getFilename() + "@start"); + sb2.append(resource.getFile()); + printComma = true; + } + for (Resource resource : testBundles) { + if (!resource.getFilename().contains("test")) { + if (printComma) { + sb.append(", "); + sb2.append(" "); + } + sb.append(resource.getFilename() + "@start"); + sb2.append(resource.getFile()); + printComma = true; + } + } + sb2.append(" platform"); + System.out.println("echo \"" + sb.toString() + "\" > platform/configuration/config.ini"); + System.out.println(sb2.toString()); + System.out.println("zip platform.zip platform/*"); + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/PlatformIT.java ---------------------------------------------------------------------- diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/PlatformIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/PlatformIT.java new file mode 100644 index 0000000..822f5f2 --- /dev/null +++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/PlatformIT.java @@ -0,0 +1,375 @@ +/******************************************************************************* + * Copyright (C) 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 org.apache.taverna.platform; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; +import java.net.URL; +import java.util.Map; +import java.util.Properties; + + +import org.eclipse.osgi.framework.internal.core.Constants; +import org.osgi.framework.ServiceReference; +import org.osgi.service.jndi.JNDIContextManager; +import org.springframework.osgi.test.AbstractConfigurableBundleCreatorTests; +import org.springframework.osgi.test.platform.OsgiPlatform; +import org.springframework.osgi.test.platform.Platforms; + +import org.apache.taverna.configuration.app.ApplicationConfiguration; +import org.apache.taverna.configuration.database.DatabaseConfiguration; +import org.apache.taverna.platform.report.State; +import org.apache.taverna.platform.report.WorkflowReport; +import org.apache.taverna.scufl2.api.container.WorkflowBundle; +import org.apache.taverna.scufl2.api.io.WorkflowBundleReader; +import org.apache.taverna.scufl2.translator.t2flow.T2FlowReader; +import org.apache.taverna.security.credentialmanager.CredentialManager; +import org.apache.taverna.security.credentialmanager.MasterPasswordProvider; + +public class PlatformIT extends AbstractConfigurableBundleCreatorTests { + + protected WorkflowBundleReader workflowBundleReader; + protected CredentialManager credentialManager; + protected MasterPasswordProvider masterPasswordProvider; + protected DatabaseConfiguration databaseConfiguration; + protected JNDIContextManager jndiContextManager; + protected ApplicationConfiguration applicationConfiguration; + + protected String getPlatformName() { + // return Platforms.FELIX; + return Platforms.EQUINOX; + } + + @Override + protected OsgiPlatform createPlatform() { + OsgiPlatform platform = super.createPlatform(); + Properties config = platform.getConfigurationProperties(); + config.setProperty("org.osgi.framework.system.packages.extra", + "com.sun.org.apache.xml.internal.utils"); + return platform; + } + + @Override + protected String[] getTestBundlesNames() { + return new String[] { + "com.jcraft.jsch, com.springsource.com.jcraft.jsch, 0.1.41", + "com.sun.xml, com.springsource.com.sun.xml.bind, 2.2.0", + "com.sun.xml, com.springsource.com.sun.xml.fastinfoset, 1.2.2", + "com.thoughtworks.xstream, com.springsource.com.thoughtworks.xstream, 1.2.2", + "commons-dbcp, commons-dbcp, 1.4", + "commons-pool, commons-pool, 1.5.6", + "javax.activation, com.springsource.javax.activation, 1.1.1", + "javax.jms, com.springsource.javax.jms, 1.1.0", + "javax.mail, com.springsource.javax.mail, 1.4.0", + "javax.servlet, com.springsource.javax.servlet, 2.5.0", + "javax.transaction, com.springsource.javax.transaction, 1.1.0",// for derby client + "javax.wsdl, com.springsource.javax.wsdl, 1.6.1", + "javax.xml.bind, com.springsource.javax.xml.bind, 2.2.0", + "javax.xml.rpc, com.springsource.javax.xml.rpc, 1.1.0", + "javax.xml.soap, com.springsource.javax.xml.soap, 1.3.0", + "javax.xml.stream, com.springsource.javax.xml.stream, 1.0.1", + "org.antlr, com.springsource.antlr, 2.7.6", + "org.apache.aries, org.apache.aries.util, 0.3", + "org.apache.aries.proxy, org.apache.aries.proxy.api, 0.3", + "org.apache.aries.jndi, org.apache.aries.jndi, 0.3", + "org.apache.axis, com.springsource.org.apache.axis, 1.4.0", + "org.apache.commons, com.springsource.org.apache.commons.cli, 1.2.0", + "org.apache.commons, com.springsource.org.apache.commons.codec, 1.4.0", + "org.apache.commons, com.springsource.org.apache.commons.csv, 1.0.0.BUILD-20080106", + "org.apache.commons, com.springsource.org.apache.commons.collections, 3.2.0", + "org.apache.commons, com.springsource.org.apache.commons.discovery, 0.4.0", + "org.apache.commons, com.springsource.org.apache.commons.httpclient, 3.1.0", + "org.apache.commons, com.springsource.org.apache.commons.io, 1.4.0", + "org.apache.commons, com.springsource.org.apache.commons.lang, 2.5.0", + "org.apache.commons, com.springsource.org.apache.commons.logging, 1.1.1", + "org.apache.commons, com.springsource.org.apache.commons.net, 1.4.1", + // "org.apache.derby, derby, 10.5.3.0_1", + "org.apache.derby, com.springsource.org.apache.derby, 10.5.1000001.764942", + "org.apache.derby, com.springsource.org.apache.derby.client, 10.5.1000001.764942", + "org.apache.derby, com.springsource.org.apache.derby.drda, 10.5.1000001.764942", + "org.apache.httpcomponents, com.springsource.org.apache.httpcomponents.httpclient, 4.1.1", + "org.apache.httpcore, com.springsource.org.apache.httpcomponents.httpcore, 4.1", + "org.apache.log4j, com.springsource.org.apache.log4j, 1.2.16", + "org.apache.ws, com.springsource.org.apache.ws.security, 1.5.8", + // "org.apache.ws.security, wss4j, 1.5.12", + "org.apache.xml, com.springsource.org.apache.xml.resolver, 1.2.0", + "org.apache.xmlbeans, com.springsource.org.apache.xmlbeans, 2.4.0", + "org.apache.xmlcommons, com.springsource.org.apache.xmlcommons, 1.3.4", + "org.apache.xalan, com.springsource.org.apache.xalan, 2.7.1", + "org.apache.xalan, com.springsource.org.apache.xml.serializer, 2.7.1", + "org.apache.xerces, com.springsource.org.apache.xerces, 2.9.1", + "org.apache.xml, com.springsource.org.apache.xml.security, 1.4.2", + "org.aspectj, com.springsource.org.aspectj.runtime, 1.6.0", + "org.aspectj, com.springsource.org.aspectj.weaver, 1.6.0", + "org.beanshell, com.springsource.bsh, 2.0.0.b4", + "org.biomart, martservice, 2.0-SNAPSHOT", + "org.bouncycastle, bcprov-jdk16, 1.46", + "org.dom4j, com.springsource.org.dom4j, 1.6.1", + "org.hibernate, com.springsource.org.hibernate, 3.2.6.ga", + "org.jaxen, com.springsource.org.jaxen, 1.1.1", + "org.jboss.javassist, com.springsource.javassist, 3.3.0.ga", + "org.jdom, com.springsource.org.jdom, 1.1.0", + "org.jvnet.staxex, com.springsource.org.jvnet.staxex, 1.0.0", + "org.objectweb.asm, com.springsource.org.objectweb.asm, 1.5.3", + "org.objectweb.asm, com.springsource.org.objectweb.asm.attrs, 1.5.3", + "org.opensaml, com.springsource.org.opensaml, 1.1.0", + "org.springframework, org.springframework.jdbc, 3.0.0.RC1", + "org.springframework, org.springframework.orm, 3.0.0.RC1", + "org.springframework, org.springframework.transaction, 3.0.0.RC1", + // "org.springframework, org.springframework.beans, 3.0.5.RELEASE", + // "org.springframework, org.springframework.core, 3.0.5.RELEASE", + // "org.springframework, org.springframework.context, 3.0.5.RELEASE", + // "org.springframework, org.springframework.transaction, 3.0.5.RELEASE", + "org.xmlpull, com.springsource.org.xmlpull, 1.1.3.4-O", + "net.sf.taverna, wsdl-generic, 1.10-SNAPSHOT", + "net.sf.taverna.jedit, jedit-syntax, 2.2.4-SNAPSHOT", + "net.sf.taverna.t2.activities, apiconsumer-activity, 2.0-SNAPSHOT", + "net.sf.taverna.t2.activities, beanshell-activity, 2.0-SNAPSHOT", + "net.sf.taverna.t2.activities, biomart-activity, 2.0-SNAPSHOT", + // "net.sf.taverna.t2.activities, biomoby-activity, 2.0-SNAPSHOT", + "net.sf.taverna.t2.activities, dataflow-activity, 2.0-SNAPSHOT", + "net.sf.taverna.t2.activities, dependency-activity, 2.0-SNAPSHOT", + "net.sf.taverna.t2.activities, external-tool-activity, 2.0-SNAPSHOT", + "net.sf.taverna.t2.activities, localworker-activity, 2.0-SNAPSHOT", + "net.sf.taverna.t2.activities, rest-activity, 2.0-SNAPSHOT", + "net.sf.taverna.t2.activities, rshell-activity, 2.0-SNAPSHOT", + "net.sf.taverna.t2.activities, soaplab-activity, 2.0-SNAPSHOT", + "net.sf.taverna.t2.activities, spreadsheet-import-activity, 2.0-SNAPSHOT", + "net.sf.taverna.t2.activities, stringconstant-activity, 2.0-SNAPSHOT", + "net.sf.taverna.t2.activities, wsdl-activity, 2.0-SNAPSHOT", + "net.sf.taverna.t2.activities, xpath-activity, 2.0-SNAPSHOT", + "net.sf.taverna.t2.core, provenance-derby, 2.0-SNAPSHOT", + "net.sf.taverna.t2.core, provenance-mysql, 2.0-SNAPSHOT", + "net.sf.taverna.t2.core, provenanceconnector, 2.0-SNAPSHOT", + "net.sf.taverna.t2.core, reference-api, 2.0-SNAPSHOT", + "net.sf.taverna.t2.core, reference-core-extensions, 2.0-SNAPSHOT", + "net.sf.taverna.t2.core, reference-impl, 2.0-SNAPSHOT", + "net.sf.taverna.t2.core, workflowmodel-api, 2.0-SNAPSHOT", + "net.sf.taverna.t2.core, workflowmodel-core-extensions, 2.0-SNAPSHOT", + "net.sf.taverna.t2.core, workflowmodel-impl, 2.0-SNAPSHOT", + // "net.sf.taverna.t2.infrastructure, appconfig, 3.0-SNAPSHOT", + "net.sf.taverna.t2.lang, ui, 2.0-SNAPSHOT", + "net.sf.taverna.t2.lang, observer, 2.0-SNAPSHOT", + "net.sf.taverna.t2.security, credential-manager, 2.0-SNAPSHOT", + "net.sf.taverna.t2.security, credential-manager-impl, 2.0-SNAPSHOT", + "net.sourceforge.cglib, com.springsource.net.sf.cglib, 2.1.3", + "uk.org.taverna.configuration, taverna-app-configuration-api, 0.1.0-SNAPSHOT", + "uk.org.taverna.configuration, taverna-app-configuration-impl, 0.1.0-SNAPSHOT", + "uk.org.taverna.configuration, taverna-configuration-api, 0.1.0-SNAPSHOT", + "uk.org.taverna.configuration, taverna-configuration-impl, 0.1.0-SNAPSHOT", + "uk.org.taverna.configuration, taverna-database-configuration-api, 0.1.0-SNAPSHOT", + "uk.org.taverna.configuration, taverna-database-configuration-impl, 0.1.0-SNAPSHOT", + "org.apache.taverna.platform, report, 0.1.2-SNAPSHOT", + "org.apache.taverna.platform, data, 0.1.2-SNAPSHOT", + "org.apache.taverna.platform, execution-local, 0.1.2-SNAPSHOT", + "org.apache.taverna.platform, execution-remote, 0.1.2-SNAPSHOT", + "org.apache.taverna.platform, taverna-capability-api, 0.1.2-SNAPSHOT", + "org.apache.taverna.platform, taverna-capability-impl, 0.1.2-SNAPSHOT", + "org.apache.taverna.platform, taverna-execution-api, 0.1.2-SNAPSHOT", + "org.apache.taverna.platform, taverna-execution-impl, 0.1.2-SNAPSHOT", + "org.apache.taverna.platform, taverna-run-api, 0.1.2-SNAPSHOT", + "org.apache.taverna.platform, taverna-run-impl, 0.1.2-SNAPSHOT", + "uk.org.taverna.osgi.services, xml-parser-service, 0.0.1-SNAPSHOT", + "uk.org.taverna.osgi.services, xml-transformer-service, 0.0.1-SNAPSHOT", + // FIXME: Add the other scufl2 modules + "org.apache.taverna.scufl2, scufl2-api, 0.9.2", + "org.apache.taverna.scufl2, scufl2-rdfxml, 0.9.2", + "org.apache.taverna.scufl2, scufl2-ucfpackage, 0.9.2", + "org.apache.taverna.scufl2, scufl2-t2flow, 0.9.2", + "org.apache.taverna.scufl2, scufl2-validation, 0.9.2", + "org.apache.taverna.scufl2, scufl2-validation-correctness, 0.9.2", + "org.apache.taverna.scufl2, scufl2-validation-structural, 0.9.2", + "net.sf.taverna.t2, results, 2.0-SNAPSHOT", + "net.sf.taverna.t2, baclava, 0.1-SNAPSHOT", + // "net.sf.taverna.t2.taverna-commandline, taverna-commandline-common, 2.0-SNAPSHOT" + }; + } + + protected void setup() throws Exception { + + if (masterPasswordProvider == null) { + masterPasswordProvider = new MasterPasswordProvider() { + public String getMasterPassword(boolean firstTime) { + return "test"; + } + + public void setMasterPassword(String password) { + } + + public int getProviderPriority() { + return 0; + } + }; + bundleContext.registerService( + "net.sf.taverna.t2.security.credentialmanager.MasterPasswordProvider", + masterPasswordProvider, null); + } + + if (credentialManager == null) { + ServiceReference credentialManagerReference = bundleContext + .getServiceReference("net.sf.taverna.t2.security.credentialmanager.CredentialManager"); + credentialManager = (CredentialManager) bundleContext + .getService(credentialManagerReference); + } + + if (workflowBundleReader == null) { + ServiceReference[] workflowBundleReaderReferences = bundleContext.getServiceReferences( + "org.apache.taverna.scufl2.api.io.WorkflowBundleReader", null); + for (ServiceReference serviceReference : workflowBundleReaderReferences) { + workflowBundleReader = (WorkflowBundleReader) bundleContext + .getService(serviceReference); + if (workflowBundleReader.getMediaTypes().contains( + T2FlowReader.APPLICATION_VND_TAVERNA_T2FLOW_XML)) { + break; + } + } + } + + if (databaseConfiguration == null) { + ServiceReference databaseConfigurationReference = bundleContext + .getServiceReference("uk.org.taverna.configuration.database.DatabaseConfiguration"); + databaseConfiguration = (DatabaseConfiguration) bundleContext + .getService(databaseConfigurationReference); + ServiceReference jndiContextManagerReference = bundleContext + .getServiceReference("org.osgi.service.jndi.JNDIContextManager"); + jndiContextManager = (JNDIContextManager) bundleContext + .getService(jndiContextManagerReference); + ServiceReference applicationConfigurationReference = bundleContext + .getServiceReference("uk.org.taverna.configuration.app.ApplicationConfiguration"); + applicationConfiguration = (ApplicationConfiguration) bundleContext + .getService(applicationConfigurationReference); + } + + } + + public void testOsgiPlatformStarts() throws Exception { + System.out.println(Constants.FRAMEWORK_VENDOR + " = " + + bundleContext.getProperty(Constants.FRAMEWORK_VENDOR)); + System.out.println(Constants.FRAMEWORK_VERSION + " = " + + bundleContext.getProperty(Constants.FRAMEWORK_VERSION)); + System.out.println(Constants.FRAMEWORK_EXECUTIONENVIRONMENT + " = " + + bundleContext.getProperty(Constants.FRAMEWORK_EXECUTIONENVIRONMENT)); + System.out.println(Constants.OSGI_IMPL_VERSION_KEY + " = " + + bundleContext.getProperty(Constants.OSGI_IMPL_VERSION_KEY)); + } + + public WorkflowBundle loadWorkflow(String t2FlowFile) throws Exception { + URL wfResource = getClass().getResource(t2FlowFile); + assertNotNull(wfResource); + return workflowBundleReader.readBundle(wfResource.openStream(), + T2FlowReader.APPLICATION_VND_TAVERNA_T2FLOW_XML); + } + + public File loadFile(String fileName) throws IOException, FileNotFoundException { + File file = File.createTempFile("platform-test", null); + InputStream inputStream = getClass().getResource(fileName).openStream(); + OutputStream outputStream = new FileOutputStream(file); + byte[] buffer = new byte[64]; + int length = -1; + while ((length = inputStream.read(buffer)) >= 0) { + outputStream.write(buffer, 0, length); + } + outputStream.flush(); + outputStream.close(); + return file; + } + +// public void printErrors(Data data) { +// ErrorDocument error = (ErrorDocument) data.getValue(); +// String message = error.getMessage(); +// if (message != null) { +// System.out.println(message); +// } +// String exceptionMessage = error.getExceptionMessage(); +// if (exceptionMessage != null) { +// System.out.println(exceptionMessage); +// } +// for (StackTraceElementBean stackTraceElementBean : error.getStackTraceStrings()) { +// System.out.println(stackTraceElementBean.getClassName()); +// System.out.println(stackTraceElementBean.getMethodName()); +// System.out.println(stackTraceElementBean.getLineNumber()); +// } +//// Set<T2Reference> errorReferences = error.getErrorReferences(); +//// for (T2Reference t2Reference : errorReferences) { +//// printErrors(referenceService, t2Reference); +//// } +// } +// +// public boolean checkResult(Data result, String expectedResult) { +// if (result.isError()) { +// printErrors(result); +// return false; +// } else { +// Object resultObject = result.getValue(); +// String resultValue = null; +// if (resultObject instanceof byte[]) { +// resultValue = new String((byte[]) resultObject); +// } else { +// resultValue = (String) resultObject; +// } +// +// if (resultValue.startsWith(expectedResult)) { +// return true; +// } else { +// System.out.println("Expected: " + expectedResult + ", Actual: " + resultValue); +// return false; +// } +// } +// } + + public boolean waitForState(WorkflowReport report, State state) throws InterruptedException { + return waitForState(report, state, true); + } + + public boolean waitForState(WorkflowReport report, State state, boolean printReport) + throws InterruptedException { + int wait = 0; + while (!report.getState().equals(state) && wait++ < 30) { + if (printReport) + System.out.println(report); + Thread.sleep(500); + } + return report.getState().equals(state); + } + +// public void waitForResults(Map<String, Data> results, WorkflowReport report, String... ports) +// throws InterruptedException { +// int wait = 0; +// while (!resultsReady(results, ports) && wait++ < 20) { +// System.out.println(report); +// Thread.sleep(500); +// } +// } +// +// private boolean resultsReady(Map<String, Data> results, String... ports) { +// for (String port : ports) { +// if (!results.containsKey(port)) { +// return false; +// } +// } +// return true; +// } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java ---------------------------------------------------------------------- diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java new file mode 100644 index 0000000..5387afd --- /dev/null +++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java @@ -0,0 +1,1000 @@ +/******************************************************************************* + * Copyright (C) 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 org.apache.taverna.platform; + +import java.io.File; +import java.net.URI; +import java.net.URL; +import java.security.cert.CertificateFactory; +import java.security.cert.X509Certificate; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import org.osgi.framework.ServiceReference; + +import org.apache.taverna.platform.execution.api.ExecutionEnvironment; +import org.apache.taverna.platform.report.State; +import org.apache.taverna.platform.report.WorkflowReport; +import org.apache.taverna.platform.run.api.RunProfile; +import org.apache.taverna.platform.run.api.RunService; +import org.apache.taverna.scufl2.api.container.WorkflowBundle; + +public class RunIT extends PlatformIT { + + private RunService runService; + + protected void setup() throws Exception { + super.setup(); + if (runService == null) { + ServiceReference runServiceReference = bundleContext + .getServiceReference("org.apache.taverna.platform.run.api.RunService"); + runService = (RunService) bundleContext.getService(runServiceReference); + } + if (dataService == null) { + ServiceReference dataServiceReference = bundleContext + .getServiceReference("org.apache.taverna.platform.data.DataService"); + dataService = (DataService) bundleContext.getService(dataServiceReference); + } + databaseConfiguration.setProvenanceEnabled(false); + } + + public void testRun() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/in-out.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Map<String, Data> inputs = new HashMap<String, Data>(); + inputs.put("in", dataService.create("test-input")); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputs)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(runService.getState(runId).equals(State.RUNNING) + || runService.getState(runId).equals(State.COMPLETED)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + assertNotNull(results); + waitForResults(results, runService.getWorkflowReport(runId), "out"); + + assertTrue(checkResult(results.get("out"), "test-input")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunApiConsumer() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/apiconsumer.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Map<String, Data> inputs = new HashMap<String, Data>(); + inputs.put("in", dataService.create("test-input")); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputs)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(runService.getState(runId).equals(State.RUNNING) + || runService.getState(runId).equals(State.COMPLETED)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + assertNotNull(results); + waitForResults(results, report, "out"); + + assertTrue(checkResult(results.get("out"), "TEST-INPUT")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunBeanshell() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/beanshell.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Map<String, Data> inputs = new HashMap<String, Data>(); + inputs.put("in", dataService.create("test-input")); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputs)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(runService.getState(runId).equals(State.RUNNING) + || runService.getState(runId).equals(State.COMPLETED)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + assertNotNull(results); + waitForResults(results, report, "out"); + + List<Data> result = results.get("out").getElements(); + assertEquals(1000, result.size()); + assertEquals("test-input:0", result.get(0).getValue()); + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunBiomart() throws Exception { + setup(); + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/biomart.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(runService.getState(runId).equals(State.RUNNING) + || runService.getState(runId).equals(State.COMPLETED)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + assertNotNull(results); + waitForResults(results, report, "out"); + + List<Data> result = results.get("out").getElements(); + assertEquals(5, result.size()); + assertEquals("ENSBTAG00000018854", result.get(0).getValue()); + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + // public void testRunBiomoby() throws Exception { + // setup(); + // WorkflowBundle workflowBundle = loadWorkflow("/t2flow/biomoby.t2flow"); + // + // Set<ExecutionEnvironment> executionEnvironments = runService + // .getExecutionEnvironments(workflowBundle); + // for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + // + // + // String runId = runService.createRun(new RunProfile(executionEnvironment, workflowBundle)); + // assertEquals(State.CREATED, runService.getState(runId)); + // + // WorkflowReport report = runService.getWorkflowReport(runId); + // System.out.println(report); + // + // runService.start(runId); + // assertTrue(runService.getState(runId).equals(State.RUNNING) + // || runService.getState(runId).equals(State.COMPLETED)); + // System.out.println(report); + // + // Map<String, Data> results = runService.getOutputs(runId); + // assertNotNull(results); + // waitForResults(results, report, "out"); + // + // T2Reference resultReference = results.get("out"); + // if (resultReference.containsErrors()) { + // printErrors(referenceService, resultReference); + // } + // assertFalse(resultReference.containsErrors()); + // @SuppressWarnings("unchecked") + // List<String> result = (List<String>) referenceService.renderIdentifier(resultReference, + // String.class, null); + // assertEquals(5, result.size()); + // assertEquals("ENSBTAG00000018854", result.get(0)); + // assertEquals(State.COMPLETED, runService.getState(runId)); + // System.out.println(report); + // } + // } + + public void testRunDataflow() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/dataflow.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Map<String, Data> inputs = new HashMap<String, Data>(); + inputs.put("in", dataService.create("test input")); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputs)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertFalse(runService.getState(runId).equals(State.CREATED)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out"); + + assertTrue(checkResult(results.get("out"), + "nested dataflow : test input")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunLocalworker() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/localworker.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Map<String, Data> inputs = new HashMap<String, Data>(); + inputs.put("in", dataService.create("Tom")); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputs)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(runService.getState(runId).equals(State.RUNNING) + || runService.getState(runId).equals(State.COMPLETED)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + assertNotNull(results); + waitForResults(results, report, "out"); + + assertTrue(checkResult(results.get("out"), "Hello Tom")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunRest() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/rest.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertEquals(State.RUNNING, runService.getState(runId)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out"); + + Object outResult = results.get("out").getValue(); + if (outResult instanceof byte[]) { + outResult = new String((byte[]) outResult); + } + assertTrue(outResult instanceof String); + String outString = (String) outResult; + assertTrue(outString.contains("<name>AATM_RABIT</name>")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunRestSecureBasic() throws Exception { + setup(); + credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser", + "testpasswd"), URI + .create("http://heater.cs.man.ac.uk:7070/#Example+HTTP+BASIC+Authentication";)); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-basic-authentication.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertEquals(State.RUNNING, runService.getState(runId)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out"); + + assertTrue(checkResult(results.get("out"), + "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n" + + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n" + + "<META http-equiv=Content-Type content=\"text/html\">\n" + + "</HEAD>\n" + + "<BODY>\n" + + "<P>\n" + + "<H3>Secure Apache Tomcat Examples</H3>\n" + + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Basic Authentication.</P>\n" + + "</BODY></HTML>")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunRestSecureBasicHttps() throws Exception { + setup(); + credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser", + "testpasswd"), URI + .create("https://heater.cs.man.ac.uk:7443/#Example+HTTP+BASIC+Authentication";)); + + URL trustedCertficateFileURL = getClass().getResource( + "/security/tomcat_heater_certificate.pem"); + CertificateFactory certFactory = CertificateFactory.getInstance("X.509"); + X509Certificate trustedCertficate = (X509Certificate) certFactory + .generateCertificate(trustedCertficateFileURL.openStream()); + credentialManager.addTrustedCertificate(trustedCertficate); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-basic-authentication-https.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertEquals(State.RUNNING, runService.getState(runId)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out"); + + assertTrue(checkResult(results.get("out"), + "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n" + + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n" + + "<META http-equiv=Content-Type content=\"text/html\">\n" + + "</HEAD>\n" + + "<BODY>\n" + + "<P>\n" + + "<H3>Secure Apache Tomcat Examples</H3>\n" + + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Basic Authentication.</P>\n" + + "</BODY></HTML>")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunRestSecureDigest() throws Exception { + setup(); + credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser", + "testpasswd"), URI + .create("http://heater.cs.man.ac.uk:7070/#Example+HTTP+BASIC+Authentication";)); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-digest-authentication.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertEquals(State.RUNNING, runService.getState(runId)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out"); + + assertTrue(checkResult(results.get("out"), + "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n" + + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n" + + "<META http-equiv=Content-Type content=\"text/html\">\n" + + "</HEAD>\n" + + "<BODY>\n" + + "<P>\n" + + "<H3>Secure Apache Tomcat Examples</H3>\n" + + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Digest Authentication.</P>\n" + + "</BODY></HTML>")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunRestSecureDigestHttps() throws Exception { + setup(); + credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser", + "testpasswd"), URI + .create("http://heater.cs.man.ac.uk:7443/#Example+HTTP+BASIC+Authentication";)); + + URL trustedCertficateFileURL = getClass().getResource( + "/security/tomcat_heater_certificate.pem"); + CertificateFactory certFactory = CertificateFactory.getInstance("X.509"); + X509Certificate trustedCertficate = (X509Certificate) certFactory + .generateCertificate(trustedCertficateFileURL.openStream()); + credentialManager.addTrustedCertificate(trustedCertficate); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-digest-authentication-https.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertEquals(State.RUNNING, runService.getState(runId)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out"); + + assertTrue(checkResult(results.get("out"), + "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n" + + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n" + + "<META http-equiv=Content-Type content=\"text/html\">\n" + + "</HEAD>\n" + + "<BODY>\n" + + "<P>\n" + + "<H3>Secure Apache Tomcat Examples</H3>\n" + + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Digest Authentication.</P>\n" + + "</BODY></HTML>")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunSpreadsheetImport() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/spreadsheetimport.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertEquals(State.RUNNING, runService.getState(runId)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out"); + + List<Data> result = results.get("out").getElements(); + assertEquals(35, result.size()); + assertEquals("1971.0", result.get(1).getValue()); + assertEquals("2004.0", result.get(34).getValue()); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunSoaplab() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/soaplab.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertEquals(State.RUNNING, runService.getState(runId)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "sequence"); + + assertTrue(checkResult(results.get("sequence"), + "ID X52524; SV 1; linear; genomic DNA; STD; INV; 4507 BP.")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunStringConstant() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/stringconstant.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + WorkflowReport report = runService.getWorkflowReport(runId); + assertEquals(State.CREATED, runService.getState(runId)); + + runService.start(runId); + assertTrue(runService.getState(runId).equals(State.RUNNING) + || runService.getState(runId).equals(State.COMPLETED)); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out"); + + assertTrue(checkResult(results.get("out"), "Test Value")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + } + } + + public void testRunTool() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/tool.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + WorkflowReport report = runService.getWorkflowReport(runId); + assertEquals(State.CREATED, runService.getState(runId)); + + runService.start(runId); + assertTrue(runService.getState(runId).equals(State.RUNNING) + || runService.getState(runId).equals(State.COMPLETED)); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out"); + + assertTrue(checkResult(results.get("out"), "HelloWorld")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + } + } + + public void testRunIteration() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/iteration.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Map<String, Data> inputs = new HashMap<String, Data>(); + inputs.put("in", dataService.create("test")); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputs)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertEquals(State.RUNNING, runService.getState(runId)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + + waitForResults(results, report, "cross"); + List<Data> crossResult = results.get("cross").getElements(); + assertEquals(10, crossResult.size()); + assertEquals(10, crossResult.get(0).getElements().size()); + assertEquals(10, crossResult.get(5).getElements().size()); + assertEquals("test:0test:0", crossResult.get(0).getElements().get(0).getValue()); + assertEquals("test:0test:1", crossResult.get(0).getElements().get(1).getValue()); + assertEquals("test:4test:2", crossResult.get(4).getElements().get(2).getValue()); + assertEquals("test:7test:6", crossResult.get(7).getElements().get(6).getValue()); + + waitForResults(results, report, "dot"); + + List<Data> dotResult = results.get("dot").getElements(); + assertEquals(10, dotResult.size()); + assertEquals("test:0test:0", dotResult.get(0).getValue()); + assertEquals("test:5test:5", dotResult.get(5).getValue()); + + waitForResults(results, report, "crossdot"); + + List<Data> crossdotResult = results.get("crossdot").getElements(); + assertEquals(10, crossdotResult.size()); + assertEquals(10, crossdotResult.get(0).getElements().size()); + assertEquals(10, crossdotResult.get(5).getElements().size()); + assertEquals("test:0test:0test", crossdotResult.get(0).getElements().get(0).getValue()); + assertEquals("test:0test:1test", crossdotResult.get(0).getElements().get(1).getValue()); + assertEquals("test:4test:2test", crossdotResult.get(4).getElements().get(2).getValue()); + assertEquals("test:7test:6test", crossdotResult.get(7).getElements().get(6).getValue()); + + waitForResults(results, report, "dotcross"); + + List<Data> dotcrossResult = results.get("dotcross").getElements(); + assertEquals(10, dotResult.size()); + assertEquals("test:0test:0test", dotcrossResult.get(0).getValue()); + assertEquals("test:5test:5test", dotcrossResult.get(5).getValue()); + + waitForResults(results, report, "dotdot"); + + List<Data> dotdotResult = results.get("dotdot").getElements(); + assertEquals(10, dotResult.size()); + assertEquals("test:0test:0test:0", dotdotResult.get(0).getValue()); + assertEquals("test:5test:5test:5", dotdotResult.get(5).getValue()); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunWSDL() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/wsdl.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertEquals(State.RUNNING, runService.getState(runId)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out"); + + // assertTrue(checkResult(results.get("out"), + // "Apache Axis version: 1.4\nBuilt on Apr 22, 2006 (06:55:48 PDT)")); + assertTrue(checkResult(results.get("out"), + "Apache Axis version: 1.2\nBuilt on May 03, 2005 (02:20:24 EDT)")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunWSDLSecure() throws Exception { + setup(); + credentialManager + .addUsernameAndPasswordForService( + new UsernamePassword("testuser", "testpasswd"), + URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl";)); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/wsdl-secure.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertEquals(State.RUNNING, runService.getState(runId)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out"); + + assertTrue(checkResult(results.get("out"), "Hello Alan!")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunWSDLSecureFull() throws Exception { + setup(); + credentialManager + .addUsernameAndPasswordForService( + new UsernamePassword("testuser", "testpasswd"), + URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl";)); + credentialManager + .addUsernameAndPasswordForService( + new UsernamePassword("testuser", "testpasswd"), + URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-DigestPassword?wsdl";)); + credentialManager + .addUsernameAndPasswordForService( + new UsernamePassword("testuser", "testpasswd"), + URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-DigestPassword-Timestamp?wsdl";)); + credentialManager + .addUsernameAndPasswordForService( + new UsernamePassword("testuser", "testpasswd"), + URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword-Timestamp?wsdl";)); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-ws.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertEquals(State.RUNNING, runService.getState(runId)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out_plaintext", "out_digest", "out_digest_timestamp", + "out_plaintext_timestamp"); + + assertTrue(checkResult(results.get("out_plaintext"), "Hello Alan!")); + assertTrue(checkResult(results.get("out_digest"), "Hello Stian!")); + assertTrue(checkResult(results.get("out_digest_timestamp"), + "Hello David!")); + assertTrue(checkResult(results.get("out_plaintext_timestamp"), + "Hello Alex!")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunWSDLSecureSsh() throws Exception { + setup(); + credentialManager + .addUsernameAndPasswordForService( + new UsernamePassword("testuser", "testpasswd"), + URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword?wsdl";)); + credentialManager + .addUsernameAndPasswordForService( + new UsernamePassword("testuser", "testpasswd"), + URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-DigestPassword?wsdl";)); + credentialManager + .addUsernameAndPasswordForService( + new UsernamePassword("testuser", "testpasswd"), + URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-DigestPassword-Timestamp?wsdl";)); + credentialManager + .addUsernameAndPasswordForService( + new UsernamePassword("testuser", "testpasswd"), + URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword-Timestamp?wsdl";)); + + URL trustedCertficateFileURL = getClass().getResource( + "/security/tomcat_heater_certificate.pem"); + CertificateFactory certFactory = CertificateFactory.getInstance("X.509"); + X509Certificate trustedCertficate = (X509Certificate) certFactory + .generateCertificate(trustedCertficateFileURL.openStream()); + credentialManager.addTrustedCertificate(trustedCertficate); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-ws-https.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertEquals(State.RUNNING, runService.getState(runId)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out_plaintext", "out_digest", "out_digest_timestamp", + "out_plaintext_timestamp"); + + assertTrue(checkResult(results.get("out_plaintext"), "Hello Alan!")); + assertTrue(checkResult(results.get("out_digest"), "Hello Stian!")); + assertTrue(checkResult(results.get("out_digest_timestamp"), + "Hello David!")); + assertTrue(checkResult(results.get("out_plaintext_timestamp"), + "Hello Alex!")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunXMLSplitter() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/xmlSplitter.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Map<String, Data> inputs = new HashMap<String, Data>(); + inputs.put("firstName", dataService.create("John")); + inputs.put("lastName", dataService.create("Smith")); + inputs.put("age", dataService.create("21")); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputs)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(runService.getState(runId).equals(State.RUNNING) + || runService.getState(runId).equals(State.COMPLETED)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out"); + + assertTrue(checkResult(results.get("out"), + "John Smith (21) of 40, Oxford Road. Manchester.")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunXPath() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/xpath.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(runService.getState(runId).equals(State.RUNNING) + || runService.getState(runId).equals(State.COMPLETED)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + waitForResults(results, report, "out"); + + assertTrue(checkResult(results.get("out"), + "<test-element>test</test-element>")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + + public void testRunFromFile() throws Exception { + setup(); + + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/in-out.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Map<String, Data> inputs = new HashMap<String, Data>(); + File file = loadFile("/t2flow/input.txt"); + Data data = dataService.create(file.toURI()); + assertTrue(data.isReference()); + inputs.put("in", data); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputs)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(runService.getState(runId).equals(State.RUNNING) + || runService.getState(runId).equals(State.COMPLETED)); + System.out.println(report); + + Map<String, Data> results = runService.getOutputs(runId); + assertNotNull(results); + waitForResults(results, runService.getWorkflowReport(runId), "out"); + + assertTrue(checkResult(results.get("out"), "test input value")); + + assertEquals(State.COMPLETED, runService.getState(runId)); + System.out.println(report); + } + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunParallelIT.java ---------------------------------------------------------------------- diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunParallelIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunParallelIT.java new file mode 100644 index 0000000..d9398ab --- /dev/null +++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunParallelIT.java @@ -0,0 +1,93 @@ +/******************************************************************************* + * Copyright (C) 2011 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 org.apache.taverna.platform; + +import java.net.URI; +import java.util.HashSet; +import java.util.Set; + +import org.osgi.framework.ServiceReference; + +import org.apache.taverna.platform.execution.api.ExecutionEnvironment; +import org.apache.taverna.platform.report.State; +import org.apache.taverna.platform.report.WorkflowReport; +import org.apache.taverna.platform.run.api.RunProfile; +import org.apache.taverna.platform.run.api.RunService; +import org.apache.taverna.scufl2.api.container.WorkflowBundle; + +public class RunParallelIT extends PlatformIT { + + private RunService runService; + + private ExecutionEnvironment executionEnvironment; + + protected void setup() throws Exception { + super.setup(); + if (runService == null) { + ServiceReference runServiceReference = bundleContext + .getServiceReference("org.apache.taverna.platform.run.api.RunService"); + runService = (RunService) bundleContext.getService(runServiceReference); + } + if (executionEnvironment == null) { + executionEnvironment = runService.getExecutionEnvironments().iterator().next(); + } + credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser", + "testpasswd"), URI + .create("http://heater.cs.man.ac.uk:7070/#Example+HTTP+BASIC+Authentication";)); + credentialManager + .addUsernameAndPasswordForService( + new UsernamePassword("testuser", "testpasswd"), + URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl";)); + } + + public void testRun() throws Exception { + setup(); + + String[] workflows = { "biomart", "rest", "secure-basic-authentication", + "spreadsheetimport", "stringconstant", "wsdl", "wsdl-secure", "xpath" }; + Set<String> runIDs= new HashSet<String>(); + + for (int i = 0; i < workflows.length; i++) { + int runs = Math.max(1, (int) Math.ceil(Math.random() * 10)); + System.out.println("Creating " + runs + " runs for workflow " + workflows[i]); + for (int j = 0; j < runs; j++) { + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/" + workflows[i] + ".t2flow"); + String run = runService.createRun(new RunProfile(executionEnvironment, workflowBundle)); + runService.getWorkflowReport(run).getSubject().setName(workflows[i] + j); + runIDs.add(run); + } + } + + for (String runId : runIDs) { + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println("Starting " + report.getSubject().getName()); + runService.start(runId); + } + + for (String runId : runIDs) { + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println("Waiting for " + report.getSubject().getName() + " to complete"); + assertTrue(waitForState(report, State.COMPLETED, false)); + } + + } + +}
