http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7a011350/taverna-integration-tests/src/test/java/uk/org/taverna/platform/RunIT.java
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diff --git
a/taverna-integration-tests/src/test/java/uk/org/taverna/platform/RunIT.java
b/taverna-integration-tests/src/test/java/uk/org/taverna/platform/RunIT.java
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--- a/taverna-integration-tests/src/test/java/uk/org/taverna/platform/RunIT.java
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@@ -1,954 +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.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"));
- }
- }
-
-}
