org.apache.taverna
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/7a011350 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/tree/7a011350 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/diff/7a011350 Branch: refs/heads/master Commit: 7a011350db60b49999dca5a9605e44ace1f11a21 Parents: b19294a Author: Stian Soiland-Reyes <[email protected]> Authored: Sun Oct 18 19:20:33 2015 +0100 Committer: Stian Soiland-Reyes <[email protected]> Committed: Sun Oct 18 19:20:33 2015 +0100 ---------------------------------------------------------------------- .../org/apache/taverna/platform/ActivityIT.java | 84 ++ .../org/apache/taverna/platform/PlatformIT.java | 151 +++ .../java/org/apache/taverna/platform/RunIT.java | 954 +++++++++++++++++++ .../uk/org/taverna/platform/ActivityIT.java | 84 -- .../uk/org/taverna/platform/PlatformIT.java | 151 --- .../java/uk/org/taverna/platform/RunIT.java | 954 ------------------- 6 files changed, 1189 insertions(+), 1189 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7a011350/taverna-integration-tests/src/test/java/org/apache/taverna/platform/ActivityIT.java ---------------------------------------------------------------------- diff --git a/taverna-integration-tests/src/test/java/org/apache/taverna/platform/ActivityIT.java b/taverna-integration-tests/src/test/java/org/apache/taverna/platform/ActivityIT.java new file mode 100644 index 0000000..152c81b --- /dev/null +++ b/taverna-integration-tests/src/test/java/org/apache/taverna/platform/ActivityIT.java @@ -0,0 +1,84 @@ +/******************************************************************************* + * 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 org.junit.AfterClass; +import org.junit.BeforeClass; +import org.junit.Ignore; +import org.junit.Test; +import org.osgi.framework.BundleContext; + +import org.apache.taverna.osgi.starter.TavernaStarter; +import org.apache.taverna.platform.execution.api.ExecutionEnvironment; +import org.apache.taverna.platform.run.api.RunService; + +public class ActivityIT extends PlatformIT { + + private static TavernaStarter tavernaStarter; + private static BundleContext bundleContext; + private static RunService runService; + + @BeforeClass + public static void setup() throws Exception { + tavernaStarter = new TavernaStarter(new File("/tmp")); + tavernaStarter.start(); + runService = tavernaStarter.getRunService(); + } + + @AfterClass + public static void shutdown() throws Exception { + tavernaStarter.stop(); + } + + @Test + public void testGetActivityURIs() { + System.out.println("================= Available Activities ==================="); + for (ExecutionEnvironment executionEnvironment : runService.getExecutionEnvironments()) { + for (URI uri : executionEnvironment.getActivityTypes()) { + System.out.println(uri); + } + } + System.out.println("=========================================================="); + System.out.println(""); + } + + public void testCreateActivity() throws Exception { +// for (URI uri : activityService.getActivityTypes()) { +// System.out.println("Creating activity " + uri); +// Activity<?> activity = activityService.createActivity(uri, null); +// } + } + + @Test + public void testGetActivityConfigurationDefinition() throws Exception { + System.out.println("============ Activity Configuration Definitions =========="); + for (ExecutionEnvironment executionEnvironment : runService.getExecutionEnvironments()) { + for (URI uri : executionEnvironment.getActivityTypes()) { + System.out.println(executionEnvironment.getActivityConfigurationSchema(uri)); + } + } + System.out.println("=========================================================="); + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7a011350/taverna-integration-tests/src/test/java/org/apache/taverna/platform/PlatformIT.java ---------------------------------------------------------------------- diff --git a/taverna-integration-tests/src/test/java/org/apache/taverna/platform/PlatformIT.java b/taverna-integration-tests/src/test/java/org/apache/taverna/platform/PlatformIT.java new file mode 100644 index 0000000..23ffe8f --- /dev/null +++ b/taverna-integration-tests/src/test/java/org/apache/taverna/platform/PlatformIT.java @@ -0,0 +1,151 @@ +/******************************************************************************* + * 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 static org.junit.Assert.assertNotNull; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.IOException; +import java.net.URI; +import java.net.URL; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.junit.Ignore; + +import org.apache.taverna.databundle.DataBundles; +import org.apache.taverna.databundle.ErrorDocument; +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.WorkflowBundleIO; + +@Ignore +public class PlatformIT { + + public WorkflowBundle loadWorkflow(String t2FlowFile, WorkflowBundleIO workflowBundleIO) + throws Exception { + URL wfResource = getClass().getResource(t2FlowFile); + assertNotNull(wfResource); + return workflowBundleIO.readBundle(wfResource.openStream(), null); + } + + public File loadFile(String fileName) throws IOException, FileNotFoundException { + File file = File.createTempFile("platform-test", null); + file.deleteOnExit(); + FileUtils.copyURLToFile(getClass().getResource(fileName), file); + return file; + } + + public void printErrors(Path error) { + try { + ErrorDocument errorDocument = DataBundles.getError(error); + String message = errorDocument.getMessage(); + if (message != null) { + System.out.println(message); + } + String trace = errorDocument.getTrace(); + if (trace != null) { + System.out.println(trace); + } + } catch (IOException e) { + e.printStackTrace(); + } + } + + public boolean checkResult(Path result, String expectedResult) { + if (DataBundles.isError(result)) { + printErrors(result); + return false; + } else { + String resultValue; + if (DataBundles.isValue(result)) { + try { + resultValue = DataBundles.getStringValue(result); + } catch (IOException e) { + e.printStackTrace(); + return false; + } + } else if (DataBundles.isReference(result)) { + try { + URI reference = DataBundles.getReference(result); + resultValue = IOUtils.toString(reference); + } catch (IOException e) { + e.printStackTrace(); + return false; + } + } else { + System.out.println("Expected a value or reference"); + return false; + } + 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); + } + if (printReport) { + System.out.println(report); + } + return report.getState().equals(state); + } + + public void waitForResults(Path outputs, WorkflowReport report, String... ports) + throws InterruptedException { + int wait = 0; + while (!resultsReady(outputs, ports) && wait++ < 20) { + System.out.println(report); + Thread.sleep(500); + } + } + + private boolean resultsReady(Path outputs, String... ports) { + for (String port : ports) { + try { + if (DataBundles.isMissing(DataBundles.getPort(outputs, port))) { + return false; + } + } catch (IOException e) { + return false; + } + } + return true; + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7a011350/taverna-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java ---------------------------------------------------------------------- diff --git a/taverna-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java b/taverna-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java new file mode 100644 index 0000000..b586d9e --- /dev/null +++ b/taverna-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java @@ -0,0 +1,954 @@ +/******************************************************************************* + * 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 static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertNotNull; +import static org.junit.Assert.assertTrue; +import static org.junit.Assume.assumeTrue; + +import java.io.File; +import java.net.URI; +import java.net.URL; +import java.nio.file.Path; +import java.security.cert.CertificateFactory; +import java.security.cert.X509Certificate; +import java.util.List; +import java.util.Set; + +import net.sf.taverna.t2.security.credentialmanager.CredentialManager; +import net.sf.taverna.t2.security.credentialmanager.MasterPasswordProvider; +import net.sf.taverna.t2.security.credentialmanager.UsernamePassword; + +import org.junit.AfterClass; +import org.junit.BeforeClass; +import org.junit.Ignore; +import org.junit.Test; +import org.osgi.framework.BundleContext; +import org.apache.taverna.robundle.Bundle; + +import org.apache.taverna.databundle.DataBundles; +import org.apache.taverna.osgi.starter.TavernaStarter; +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; +import org.apache.taverna.scufl2.api.io.WorkflowBundleIO; + +public class RunIT extends PlatformIT { + + private static TavernaStarter tavernaStarter; + private static BundleContext bundleContext; + private static WorkflowBundleIO workflowBundleIO; + private static CredentialManager credentialManager; + private static RunService runService; + + public WorkflowBundle loadWorkflow(String t2FlowFile) throws Exception { + return super.loadWorkflow(t2FlowFile, workflowBundleIO); + } + + @BeforeClass + public static void setup() throws Exception { + tavernaStarter = new TavernaStarter(new File("/tmp")); + tavernaStarter.start(); + bundleContext = tavernaStarter.getContext(); + runService = tavernaStarter.getRunService(); + credentialManager = tavernaStarter.getCredentialManager(); + workflowBundleIO = tavernaStarter.getWorkflowBundleIO(); + + bundleContext.registerService( + "net.sf.taverna.t2.security.credentialmanager.MasterPasswordProvider", + new MasterPasswordProvider() { + public String getMasterPassword(boolean firstTime) { + return "test"; + } + + public void setMasterPassword(String password) { + } + + public int getProviderPriority() { + return 0; + } + }, null); + + } + + @AfterClass + public static void shutdown() throws Exception { + tavernaStarter.stop(); + } + + @Test + public void testRun() throws Exception { + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/in-out.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Bundle inputBundle = DataBundles.createBundle(); + Path inputs = DataBundles.getInputs(inputBundle); + Path port = DataBundles.getPort(inputs, "in"); + DataBundles.setStringValue(port, "test-input"); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult(DataBundles.getPort(outputs, "out"), "test-input")); + } + } + + @Test + public void testRunApiConsumer() throws Exception { + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/apiconsumer.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Bundle inputBundle = DataBundles.createBundle(); + Path inputs = DataBundles.getInputs(inputBundle); + Path port = DataBundles.getPort(inputs, "in"); + DataBundles.setStringValue(port, "test-input"); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult(DataBundles.getPort(outputs, "out"), "TEST-INPUT")); + } + } + + @Test + public void testRunBeanshell() throws Exception { + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/beanshell.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Bundle inputBundle = DataBundles.createBundle(); + Path inputs = DataBundles.getInputs(inputBundle); + Path port = DataBundles.getPort(inputs, "in"); + DataBundles.setStringValue(port, "test-input"); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + Path outPort = DataBundles.getPort(outputs, "out"); + assertTrue(DataBundles.isList(outPort)); + List<Path> result = DataBundles.getList(outPort); + assertEquals(1000, result.size()); + assertEquals("test-input:0", DataBundles.getStringValue(result.get(0))); + } + } + + @Test + public void testRunBiomart() throws Exception { + 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, DataBundles.createBundle())); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + Path outPort = DataBundles.getPort(outputs, "out"); + assertTrue(DataBundles.isList(outPort)); + List<Path> result = DataBundles.getList(outPort); + assertEquals(6, result.size()); + assertEquals("ENSBTAG00000018278", DataBundles.getStringValue(result.get(0))); + } + } + + @Test + @Ignore + public void testRunBiomoby() throws Exception { + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/biomoby.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assumeTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + + String runId = runService + .createRun(new RunProfile(executionEnvironment, workflowBundle, DataBundles.createBundle())); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + Path outPort = DataBundles.getPort(outputs, "out"); + assertTrue(DataBundles.isList(outPort)); + List<Path> result = DataBundles.getList(outPort); + assertEquals(5, result.size()); + assertEquals("ENSBTAG00000018854", DataBundles.getStringValue(result.get(0))); + } + } + + @Test + public void testRunDataflow() throws Exception { + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/dataflow.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Bundle inputBundle = DataBundles.createBundle(); + Path inputs = DataBundles.getInputs(inputBundle); + Path port = DataBundles.getPort(inputs, "in"); + DataBundles.setStringValue(port, "test-input"); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult(DataBundles.getPort(outputs, "out"), "nested dataflow : test-input")); + } + } + + @Test + public void testRunLocalworker() throws Exception { + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/localworker.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Bundle inputBundle = DataBundles.createBundle(); + Path inputs = DataBundles.getInputs(inputBundle); + Path port = DataBundles.getPort(inputs, "in"); + DataBundles.setStringValue(port, "Tom"); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult(DataBundles.getPort(outputs, "out"), "Hello Tom")); + } + } + + @Test + public void testRunRest() throws Exception { + 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, DataBundles.createBundle())); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + String outString = DataBundles.getStringValue(DataBundles.getPort(outputs, "out")); + assertTrue(outString.contains("<name>AATM_RABIT</name>")); + } + } + + @Test + public void testRunRestSecureBasic() throws Exception { + 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, DataBundles.createBundle())); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult( + DataBundles.getPort(outputs, "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>")); + } + } + + @Test + public void testRunRestSecureBasicHttps() throws Exception { + 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, DataBundles.createBundle())); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult( + DataBundles.getPort(outputs, "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>")); + } + } + + @Test + public void testRunRestSecureDigest() throws Exception { + 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, DataBundles.createBundle())); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult( + DataBundles.getPort(outputs, "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>")); + } + } + + @Test + public void testRunRestSecureDigestHttps() throws Exception { + 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, DataBundles.createBundle())); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult( + DataBundles.getPort(outputs, "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>")); + } + } + + @Test + public void testRunSpreadsheetImport() throws Exception { + 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, DataBundles.createBundle())); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + Path outPort = DataBundles.getPort(outputs, "out"); + assertTrue(DataBundles.isList(outPort)); + List<Path> result = DataBundles.getList(outPort); + assertEquals(35, result.size()); + assertEquals("1971.0", DataBundles.getStringValue(result.get(1))); + assertEquals("2004.0", DataBundles.getStringValue(result.get(34))); + } + } + + @Test + public void testRunSoaplab() throws Exception { + // TODO find new soaplab service for testing + 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, DataBundles.createBundle())); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult(DataBundles.getPort(outputs, "sequence"), + "ID X52524; SV 1; linear; genomic DNA; STD; INV; 4507 BP.")); + } + } + + @Test + public void testRunStringConstant() throws Exception { + 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, DataBundles.createBundle())); + WorkflowReport report = runService.getWorkflowReport(runId); + assertEquals(State.CREATED, runService.getState(runId)); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult(DataBundles.getPort(outputs, "out"), "Test Value")); + } + } + + @Test + public void testRunTool() throws Exception { + 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, DataBundles.createBundle())); + WorkflowReport report = runService.getWorkflowReport(runId); + assertEquals(State.CREATED, runService.getState(runId)); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult(DataBundles.getPort(outputs, "out"), "HelloWorld")); + } + } + + @Test + public void testRunIteration() throws Exception { + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/iteration.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Bundle inputBundle = DataBundles.createBundle(); + Path inputs = DataBundles.getInputs(inputBundle); + Path port = DataBundles.getPort(inputs, "in"); + DataBundles.setStringValue(port, "test"); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + Path crossPort = DataBundles.getPort(outputs, "cross"); + assertTrue(DataBundles.isList(crossPort)); + List<Path> crossResult = DataBundles.getList(crossPort); + assertEquals(10, crossResult.size()); + assertEquals(10, DataBundles.getList(crossResult.get(0)).size()); + assertEquals(10, DataBundles.getList(crossResult.get(5)).size()); + assertEquals("test:0test:0", DataBundles.getStringValue(DataBundles.getListItem(DataBundles.getListItem(crossPort, 0), 0))); + assertEquals("test:0test:1", DataBundles.getStringValue(DataBundles.getListItem(DataBundles.getListItem(crossPort, 0), 1))); + assertEquals("test:4test:2", DataBundles.getStringValue(DataBundles.getListItem(DataBundles.getListItem(crossPort, 4), 2))); + assertEquals("test:7test:6", DataBundles.getStringValue(DataBundles.getListItem(DataBundles.getListItem(crossPort, 7), 6))); + + Path dotPort = DataBundles.getPort(outputs, "dot"); + assertTrue(DataBundles.isList(dotPort)); + List<Path> dotResult = DataBundles.getList(dotPort); + assertEquals(10, dotResult.size()); + assertEquals("test:0test:0", DataBundles.getStringValue(DataBundles.getListItem(dotPort, 0))); + assertEquals("test:5test:5", DataBundles.getStringValue(DataBundles.getListItem(dotPort, 5))); + + Path crossdotPort = DataBundles.getPort(outputs, "crossdot"); + assertTrue(DataBundles.isList(crossdotPort)); + List<Path> crossdotResult = DataBundles.getList(crossdotPort); + assertEquals(10, crossdotResult.size()); + assertEquals(10, DataBundles.getList(crossdotResult.get(0)).size()); + assertEquals(10, DataBundles.getList(crossdotResult.get(5)).size()); + assertEquals("test:0test:0test", DataBundles.getStringValue(DataBundles.getListItem(DataBundles.getListItem(crossdotPort, 0), 0))); + assertEquals("test:0test:1test", DataBundles.getStringValue(DataBundles.getListItem(DataBundles.getListItem(crossdotPort, 0), 1))); + assertEquals("test:4test:2test", DataBundles.getStringValue(DataBundles.getListItem(DataBundles.getListItem(crossdotPort, 4), 2))); + assertEquals("test:7test:6test", DataBundles.getStringValue(DataBundles.getListItem(DataBundles.getListItem(crossdotPort, 7), 6))); + + Path dotcrossPort = DataBundles.getPort(outputs, "dotcross"); + assertTrue(DataBundles.isList(dotcrossPort)); + List<Path> dotcrossResult = DataBundles.getList(crossdotPort); + assertEquals(10, dotcrossResult.size()); + assertEquals("test:0test:0test", DataBundles.getStringValue(DataBundles.getListItem(dotcrossPort, 0))); + assertEquals("test:5test:5test", DataBundles.getStringValue(DataBundles.getListItem(dotcrossPort, 5))); + + Path dotdotPort = DataBundles.getPort(outputs, "dotdot"); + assertTrue(DataBundles.isList(dotdotPort)); + List<Path> dotdotResult = DataBundles.getList(crossdotPort); + assertEquals(10, dotdotResult.size()); + assertEquals("test:0test:0test:0", DataBundles.getStringValue(DataBundles.getListItem(dotdotPort, 0))); + assertEquals("test:5test:5test:5", DataBundles.getStringValue(DataBundles.getListItem(dotdotPort, 5))); + } + } + + @Test + public void testRunWSDL() throws Exception { + 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, DataBundles.createBundle())); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + // assertTrue(checkResult(results.get("out"), + // "Apache Axis version: 1.4\nBuilt on Apr 22, 2006 (06:55:48 PDT)")); + assertTrue(checkResult(DataBundles.getPort(outputs, "out"), + "Apache Axis version: 1.2\nBuilt on May 03, 2005 (02:20:24 EDT)")); + } + } + + @Test + public void testRunWSDLSecure() throws Exception { + 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, DataBundles.createBundle())); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult(DataBundles.getPort(outputs, "out"), "Hello Alan!")); + } + } + + @Test + public void testRunWSDLSecureFull() throws Exception { + 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, DataBundles.createBundle())); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult(DataBundles.getPort(outputs, "out_plaintext"), "Hello Alan!")); + assertTrue(checkResult(DataBundles.getPort(outputs, "out_digest"), "Hello Stian!")); + assertTrue(checkResult(DataBundles.getPort(outputs, "out_digest_timestamp"), "Hello David!")); + assertTrue(checkResult(DataBundles.getPort(outputs, "out_plaintext_timestamp"), "Hello Alex!")); + } + } + + @Test + public void testRunWSDLSecureSsh() throws Exception { + 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, DataBundles.createBundle())); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult(DataBundles.getPort(outputs, "out_plaintext"), "Hello Alan!")); + assertTrue(checkResult(DataBundles.getPort(outputs, "out_digest"), "Hello Stian!")); + assertTrue(checkResult(DataBundles.getPort(outputs, "out_digest_timestamp"), "Hello David!")); + assertTrue(checkResult(DataBundles.getPort(outputs, "out_plaintext_timestamp"), "Hello Alex!")); + } + } + + @Test + public void testRunXMLSplitter() throws Exception { + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/xmlSplitter.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Bundle inputBundle = DataBundles.createBundle(); + Path inputs = DataBundles.getInputs(inputBundle); + DataBundles.setStringValue(DataBundles.getPort(inputs, "firstName"), "John"); + DataBundles.setStringValue(DataBundles.getPort(inputs, "lastName"), "Smith"); + DataBundles.setStringValue(DataBundles.getPort(inputs, "age"), "21"); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult(DataBundles.getPort(outputs, "out"), + "John Smith (21) of 40, Oxford Road. Manchester.")); + } + } + + @Test + public void testRunXPath() throws Exception { + 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, DataBundles.createBundle())); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult(DataBundles.getPort(outputs, "out"), "<test-element>test</test-element>")); + } + } + + @Test + public void testRunFromFile() throws Exception { + WorkflowBundle workflowBundle = loadWorkflow("/t2flow/in-out.t2flow"); + + Set<ExecutionEnvironment> executionEnvironments = runService + .getExecutionEnvironments(workflowBundle); + assertTrue(executionEnvironments.size() > 0); + for (ExecutionEnvironment executionEnvironment : executionEnvironments) { + Bundle inputBundle = DataBundles.createBundle(); + Path inputs = DataBundles.getInputs(inputBundle); + File file = loadFile("/t2flow/input.txt"); + DataBundles.setReference(DataBundles.getPort(inputs, "in"), file.toURI()); + assertTrue(DataBundles.isReference(DataBundles.getPort(inputs, "in"))); + assertFalse(DataBundles.isValue(DataBundles.getPort(inputs, "in"))); + + String runId = runService.createRun(new RunProfile(executionEnvironment, + workflowBundle, inputBundle)); + assertEquals(State.CREATED, runService.getState(runId)); + + WorkflowReport report = runService.getWorkflowReport(runId); + System.out.println(report); + + runService.start(runId); + assertTrue(waitForState(report, State.COMPLETED)); + + Bundle outputBundle = runService.getDataBundle(runId); + assertNotNull(outputBundle); + Path outputs = DataBundles.getOutputs(outputBundle); + + assertTrue(checkResult(DataBundles.getPort(outputs, "out"), "test input value")); + } + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7a011350/taverna-integration-tests/src/test/java/uk/org/taverna/platform/ActivityIT.java ---------------------------------------------------------------------- diff --git a/taverna-integration-tests/src/test/java/uk/org/taverna/platform/ActivityIT.java b/taverna-integration-tests/src/test/java/uk/org/taverna/platform/ActivityIT.java deleted file mode 100644 index 65f0986..0000000 --- a/taverna-integration-tests/src/test/java/uk/org/taverna/platform/ActivityIT.java +++ /dev/null @@ -1,84 +0,0 @@ -/******************************************************************************* - * 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 uk.org.taverna.platform; - -import java.io.File; -import java.net.URI; - -import org.junit.AfterClass; -import org.junit.BeforeClass; -import org.junit.Ignore; -import org.junit.Test; -import org.osgi.framework.BundleContext; - -import org.apache.taverna.osgi.starter.TavernaStarter; -import org.apache.taverna.platform.execution.api.ExecutionEnvironment; -import org.apache.taverna.platform.run.api.RunService; - -public class ActivityIT extends PlatformIT { - - private static TavernaStarter tavernaStarter; - private static BundleContext bundleContext; - private static RunService runService; - - @BeforeClass - public static void setup() throws Exception { - tavernaStarter = new TavernaStarter(new File("/tmp")); - tavernaStarter.start(); - runService = tavernaStarter.getRunService(); - } - - @AfterClass - public static void shutdown() throws Exception { - tavernaStarter.stop(); - } - - @Test - public void testGetActivityURIs() { - System.out.println("================= Available Activities ==================="); - for (ExecutionEnvironment executionEnvironment : runService.getExecutionEnvironments()) { - for (URI uri : executionEnvironment.getActivityTypes()) { - System.out.println(uri); - } - } - System.out.println("=========================================================="); - System.out.println(""); - } - - public void testCreateActivity() throws Exception { -// for (URI uri : activityService.getActivityTypes()) { -// System.out.println("Creating activity " + uri); -// Activity<?> activity = activityService.createActivity(uri, null); -// } - } - - @Test - public void testGetActivityConfigurationDefinition() throws Exception { - System.out.println("============ Activity Configuration Definitions =========="); - for (ExecutionEnvironment executionEnvironment : runService.getExecutionEnvironments()) { - for (URI uri : executionEnvironment.getActivityTypes()) { - System.out.println(executionEnvironment.getActivityConfigurationSchema(uri)); - } - } - System.out.println("=========================================================="); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7a011350/taverna-integration-tests/src/test/java/uk/org/taverna/platform/PlatformIT.java ---------------------------------------------------------------------- diff --git a/taverna-integration-tests/src/test/java/uk/org/taverna/platform/PlatformIT.java b/taverna-integration-tests/src/test/java/uk/org/taverna/platform/PlatformIT.java deleted file mode 100644 index 2a5b6a0..0000000 --- a/taverna-integration-tests/src/test/java/uk/org/taverna/platform/PlatformIT.java +++ /dev/null @@ -1,151 +0,0 @@ -/******************************************************************************* - * 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 uk.org.taverna.platform; - -import static org.junit.Assert.assertNotNull; - -import java.io.File; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.net.URI; -import java.net.URL; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.commons.io.IOUtils; -import org.junit.Ignore; - -import org.apache.taverna.databundle.DataBundles; -import org.apache.taverna.databundle.ErrorDocument; -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.WorkflowBundleIO; - -@Ignore -public class PlatformIT { - - public WorkflowBundle loadWorkflow(String t2FlowFile, WorkflowBundleIO workflowBundleIO) - throws Exception { - URL wfResource = getClass().getResource(t2FlowFile); - assertNotNull(wfResource); - return workflowBundleIO.readBundle(wfResource.openStream(), null); - } - - public File loadFile(String fileName) throws IOException, FileNotFoundException { - File file = File.createTempFile("platform-test", null); - file.deleteOnExit(); - FileUtils.copyURLToFile(getClass().getResource(fileName), file); - return file; - } - - public void printErrors(Path error) { - try { - ErrorDocument errorDocument = DataBundles.getError(error); - String message = errorDocument.getMessage(); - if (message != null) { - System.out.println(message); - } - String trace = errorDocument.getTrace(); - if (trace != null) { - System.out.println(trace); - } - } catch (IOException e) { - e.printStackTrace(); - } - } - - public boolean checkResult(Path result, String expectedResult) { - if (DataBundles.isError(result)) { - printErrors(result); - return false; - } else { - String resultValue; - if (DataBundles.isValue(result)) { - try { - resultValue = DataBundles.getStringValue(result); - } catch (IOException e) { - e.printStackTrace(); - return false; - } - } else if (DataBundles.isReference(result)) { - try { - URI reference = DataBundles.getReference(result); - resultValue = IOUtils.toString(reference); - } catch (IOException e) { - e.printStackTrace(); - return false; - } - } else { - System.out.println("Expected a value or reference"); - return false; - } - 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); - } - if (printReport) { - System.out.println(report); - } - return report.getState().equals(state); - } - - public void waitForResults(Path outputs, WorkflowReport report, String... ports) - throws InterruptedException { - int wait = 0; - while (!resultsReady(outputs, ports) && wait++ < 20) { - System.out.println(report); - Thread.sleep(500); - } - } - - private boolean resultsReady(Path outputs, String... ports) { - for (String port : ports) { - try { - if (DataBundles.isMissing(DataBundles.getPort(outputs, port))) { - return false; - } - } catch (IOException e) { - return false; - } - } - return true; - } - -}
