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Posted to commits@taverna.apache.org by st...@apache.org on 2016/04/28 00:56:02 UTC
[14/26] incubator-taverna-engine git commit: Moved
taverna-platform-integration-tests to branch
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/4f01028b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java
deleted file mode 100644
index d6741e3..0000000
--- a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java
+++ /dev/null
@@ -1,998 +0,0 @@
-/*
-* Licensed to the Apache Software Foundation (ASF) under one
-* or more contributor license agreements. See the NOTICE file
-* distributed with this work for additional information
-* regarding copyright ownership. The ASF licenses this file
-* to you under the Apache License, Version 2.0 (the
-* "License"); you may not use this file except in compliance
-* with the License. You may obtain a copy of the License at
-*
-* http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing,
-* software distributed under the License is distributed on an
-* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-* KIND, either express or implied. See the License for the
-* specific language governing permissions and limitations
-* under the License.
-*/
-package org.apache.taverna.platform;
-
-import java.io.File;
-import java.net.URI;
-import java.net.URL;
-import java.security.cert.CertificateFactory;
-import java.security.cert.X509Certificate;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.osgi.framework.ServiceReference;
-
-import org.apache.taverna.platform.execution.api.ExecutionEnvironment;
-import org.apache.taverna.platform.report.State;
-import org.apache.taverna.platform.report.WorkflowReport;
-import org.apache.taverna.platform.run.api.RunProfile;
-import org.apache.taverna.platform.run.api.RunService;
-import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-
-public class RunIT extends PlatformIT {
-
- private RunService runService;
-
- protected void setup() throws Exception {
- super.setup();
- if (runService == null) {
- ServiceReference runServiceReference = bundleContext
- .getServiceReference("org.apache.taverna.platform.run.api.RunService");
- runService = (RunService) bundleContext.getService(runServiceReference);
- }
- if (dataService == null) {
- ServiceReference dataServiceReference = bundleContext
- .getServiceReference("org.apache.taverna.platform.data.DataService");
- dataService = (DataService) bundleContext.getService(dataServiceReference);
- }
- databaseConfiguration.setProvenanceEnabled(false);
- }
-
- public void testRun() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/in-out.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- inputs.put("in", dataService.create("test-input"));
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- assertNotNull(results);
- waitForResults(results, runService.getWorkflowReport(runId), "out");
-
- assertTrue(checkResult(results.get("out"), "test-input"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunApiConsumer() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/apiconsumer.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- inputs.put("in", dataService.create("test-input"));
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- assertNotNull(results);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"), "TEST-INPUT"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunBeanshell() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/beanshell.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- inputs.put("in", dataService.create("test-input"));
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- assertNotNull(results);
- waitForResults(results, report, "out");
-
- List<Data> result = results.get("out").getElements();
- assertEquals(1000, result.size());
- assertEquals("test-input:0", result.get(0).getValue());
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunBiomart() throws Exception {
- setup();
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/biomart.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- assertNotNull(results);
- waitForResults(results, report, "out");
-
- List<Data> result = results.get("out").getElements();
- assertEquals(5, result.size());
- assertEquals("ENSBTAG00000018854", result.get(0).getValue());
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- // public void testRunBiomoby() throws Exception {
- // setup();
- // WorkflowBundle workflowBundle = loadWorkflow("/t2flow/biomoby.t2flow");
- //
- // Set<ExecutionEnvironment> executionEnvironments = runService
- // .getExecutionEnvironments(workflowBundle);
- // for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- //
- //
- // String runId = runService.createRun(new RunProfile(executionEnvironment, workflowBundle));
- // assertEquals(State.CREATED, runService.getState(runId));
- //
- // WorkflowReport report = runService.getWorkflowReport(runId);
- // System.out.println(report);
- //
- // runService.start(runId);
- // assertTrue(runService.getState(runId).equals(State.RUNNING)
- // || runService.getState(runId).equals(State.COMPLETED));
- // System.out.println(report);
- //
- // Map<String, Data> results = runService.getOutputs(runId);
- // assertNotNull(results);
- // waitForResults(results, report, "out");
- //
- // T2Reference resultReference = results.get("out");
- // if (resultReference.containsErrors()) {
- // printErrors(referenceService, resultReference);
- // }
- // assertFalse(resultReference.containsErrors());
- // @SuppressWarnings("unchecked")
- // List<String> result = (List<String>) referenceService.renderIdentifier(resultReference,
- // String.class, null);
- // assertEquals(5, result.size());
- // assertEquals("ENSBTAG00000018854", result.get(0));
- // assertEquals(State.COMPLETED, runService.getState(runId));
- // System.out.println(report);
- // }
- // }
-
- public void testRunDataflow() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/dataflow.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- inputs.put("in", dataService.create("test input"));
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertFalse(runService.getState(runId).equals(State.CREATED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"),
- "nested dataflow : test input"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunLocalworker() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/localworker.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- inputs.put("in", dataService.create("Tom"));
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- assertNotNull(results);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"), "Hello Tom"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunRest() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/rest.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- Object outResult = results.get("out").getValue();
- if (outResult instanceof byte[]) {
- outResult = new String((byte[]) outResult);
- }
- assertTrue(outResult instanceof String);
- String outString = (String) outResult;
- assertTrue(outString.contains("<name>AATM_RABIT</name>"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunRestSecureBasic() throws Exception {
- setup();
- credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser",
- "testpasswd"), URI
- .create("http://heater.cs.man.ac.uk:7070/#Example+HTTP+BASIC+Authentication"));
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-basic-authentication.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"),
- "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n"
- + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n"
- + "<META http-equiv=Content-Type content=\"text/html\">\n"
- + "</HEAD>\n"
- + "<BODY>\n"
- + "<P>\n"
- + "<H3>Secure Apache Tomcat Examples</H3>\n"
- + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Basic Authentication.</P>\n"
- + "</BODY></HTML>"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunRestSecureBasicHttps() throws Exception {
- setup();
- credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser",
- "testpasswd"), URI
- .create("https://heater.cs.man.ac.uk:7443/#Example+HTTP+BASIC+Authentication"));
-
- URL trustedCertficateFileURL = getClass().getResource(
- "/security/tomcat_heater_certificate.pem");
- CertificateFactory certFactory = CertificateFactory.getInstance("X.509");
- X509Certificate trustedCertficate = (X509Certificate) certFactory
- .generateCertificate(trustedCertficateFileURL.openStream());
- credentialManager.addTrustedCertificate(trustedCertficate);
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-basic-authentication-https.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"),
- "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n"
- + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n"
- + "<META http-equiv=Content-Type content=\"text/html\">\n"
- + "</HEAD>\n"
- + "<BODY>\n"
- + "<P>\n"
- + "<H3>Secure Apache Tomcat Examples</H3>\n"
- + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Basic Authentication.</P>\n"
- + "</BODY></HTML>"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunRestSecureDigest() throws Exception {
- setup();
- credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser",
- "testpasswd"), URI
- .create("http://heater.cs.man.ac.uk:7070/#Example+HTTP+BASIC+Authentication"));
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-digest-authentication.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"),
- "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n"
- + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n"
- + "<META http-equiv=Content-Type content=\"text/html\">\n"
- + "</HEAD>\n"
- + "<BODY>\n"
- + "<P>\n"
- + "<H3>Secure Apache Tomcat Examples</H3>\n"
- + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Digest Authentication.</P>\n"
- + "</BODY></HTML>"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunRestSecureDigestHttps() throws Exception {
- setup();
- credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser",
- "testpasswd"), URI
- .create("http://heater.cs.man.ac.uk:7443/#Example+HTTP+BASIC+Authentication"));
-
- URL trustedCertficateFileURL = getClass().getResource(
- "/security/tomcat_heater_certificate.pem");
- CertificateFactory certFactory = CertificateFactory.getInstance("X.509");
- X509Certificate trustedCertficate = (X509Certificate) certFactory
- .generateCertificate(trustedCertficateFileURL.openStream());
- credentialManager.addTrustedCertificate(trustedCertficate);
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-digest-authentication-https.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"),
- "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n"
- + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n"
- + "<META http-equiv=Content-Type content=\"text/html\">\n"
- + "</HEAD>\n"
- + "<BODY>\n"
- + "<P>\n"
- + "<H3>Secure Apache Tomcat Examples</H3>\n"
- + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Digest Authentication.</P>\n"
- + "</BODY></HTML>"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunSpreadsheetImport() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/spreadsheetimport.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- List<Data> result = results.get("out").getElements();
- assertEquals(35, result.size());
- assertEquals("1971.0", result.get(1).getValue());
- assertEquals("2004.0", result.get(34).getValue());
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunSoaplab() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/soaplab.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "sequence");
-
- assertTrue(checkResult(results.get("sequence"),
- "ID X52524; SV 1; linear; genomic DNA; STD; INV; 4507 BP."));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunStringConstant() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/stringconstant.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- WorkflowReport report = runService.getWorkflowReport(runId);
- assertEquals(State.CREATED, runService.getState(runId));
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"), "Test Value"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- }
- }
-
- public void testRunTool() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/tool.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- WorkflowReport report = runService.getWorkflowReport(runId);
- assertEquals(State.CREATED, runService.getState(runId));
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"), "HelloWorld"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- }
- }
-
- public void testRunIteration() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/iteration.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- inputs.put("in", dataService.create("test"));
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
-
- waitForResults(results, report, "cross");
- List<Data> crossResult = results.get("cross").getElements();
- assertEquals(10, crossResult.size());
- assertEquals(10, crossResult.get(0).getElements().size());
- assertEquals(10, crossResult.get(5).getElements().size());
- assertEquals("test:0test:0", crossResult.get(0).getElements().get(0).getValue());
- assertEquals("test:0test:1", crossResult.get(0).getElements().get(1).getValue());
- assertEquals("test:4test:2", crossResult.get(4).getElements().get(2).getValue());
- assertEquals("test:7test:6", crossResult.get(7).getElements().get(6).getValue());
-
- waitForResults(results, report, "dot");
-
- List<Data> dotResult = results.get("dot").getElements();
- assertEquals(10, dotResult.size());
- assertEquals("test:0test:0", dotResult.get(0).getValue());
- assertEquals("test:5test:5", dotResult.get(5).getValue());
-
- waitForResults(results, report, "crossdot");
-
- List<Data> crossdotResult = results.get("crossdot").getElements();
- assertEquals(10, crossdotResult.size());
- assertEquals(10, crossdotResult.get(0).getElements().size());
- assertEquals(10, crossdotResult.get(5).getElements().size());
- assertEquals("test:0test:0test", crossdotResult.get(0).getElements().get(0).getValue());
- assertEquals("test:0test:1test", crossdotResult.get(0).getElements().get(1).getValue());
- assertEquals("test:4test:2test", crossdotResult.get(4).getElements().get(2).getValue());
- assertEquals("test:7test:6test", crossdotResult.get(7).getElements().get(6).getValue());
-
- waitForResults(results, report, "dotcross");
-
- List<Data> dotcrossResult = results.get("dotcross").getElements();
- assertEquals(10, dotResult.size());
- assertEquals("test:0test:0test", dotcrossResult.get(0).getValue());
- assertEquals("test:5test:5test", dotcrossResult.get(5).getValue());
-
- waitForResults(results, report, "dotdot");
-
- List<Data> dotdotResult = results.get("dotdot").getElements();
- assertEquals(10, dotResult.size());
- assertEquals("test:0test:0test:0", dotdotResult.get(0).getValue());
- assertEquals("test:5test:5test:5", dotdotResult.get(5).getValue());
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunWSDL() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/wsdl.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- // assertTrue(checkResult(results.get("out"),
- // "Apache Axis version: 1.4\nBuilt on Apr 22, 2006 (06:55:48 PDT)"));
- assertTrue(checkResult(results.get("out"),
- "Apache Axis version: 1.2\nBuilt on May 03, 2005 (02:20:24 EDT)"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunWSDLSecure() throws Exception {
- setup();
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl"));
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/wsdl-secure.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"), "Hello Alan!"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunWSDLSecureFull() throws Exception {
- setup();
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl"));
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-DigestPassword?wsdl"));
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-DigestPassword-Timestamp?wsdl"));
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword-Timestamp?wsdl"));
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-ws.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out_plaintext", "out_digest", "out_digest_timestamp",
- "out_plaintext_timestamp");
-
- assertTrue(checkResult(results.get("out_plaintext"), "Hello Alan!"));
- assertTrue(checkResult(results.get("out_digest"), "Hello Stian!"));
- assertTrue(checkResult(results.get("out_digest_timestamp"),
- "Hello David!"));
- assertTrue(checkResult(results.get("out_plaintext_timestamp"),
- "Hello Alex!"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunWSDLSecureSsh() throws Exception {
- setup();
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword?wsdl"));
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-DigestPassword?wsdl"));
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-DigestPassword-Timestamp?wsdl"));
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword-Timestamp?wsdl"));
-
- URL trustedCertficateFileURL = getClass().getResource(
- "/security/tomcat_heater_certificate.pem");
- CertificateFactory certFactory = CertificateFactory.getInstance("X.509");
- X509Certificate trustedCertficate = (X509Certificate) certFactory
- .generateCertificate(trustedCertficateFileURL.openStream());
- credentialManager.addTrustedCertificate(trustedCertficate);
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-ws-https.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out_plaintext", "out_digest", "out_digest_timestamp",
- "out_plaintext_timestamp");
-
- assertTrue(checkResult(results.get("out_plaintext"), "Hello Alan!"));
- assertTrue(checkResult(results.get("out_digest"), "Hello Stian!"));
- assertTrue(checkResult(results.get("out_digest_timestamp"),
- "Hello David!"));
- assertTrue(checkResult(results.get("out_plaintext_timestamp"),
- "Hello Alex!"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunXMLSplitter() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/xmlSplitter.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- inputs.put("firstName", dataService.create("John"));
- inputs.put("lastName", dataService.create("Smith"));
- inputs.put("age", dataService.create("21"));
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"),
- "John Smith (21) of 40, Oxford Road. Manchester."));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunXPath() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/xpath.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"),
- "<test-element>test</test-element>"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunFromFile() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/in-out.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- File file = loadFile("/t2flow/input.txt");
- Data data = dataService.create(file.toURI());
- assertTrue(data.isReference());
- inputs.put("in", data);
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- assertNotNull(results);
- waitForResults(results, runService.getWorkflowReport(runId), "out");
-
- assertTrue(checkResult(results.get("out"), "test input value"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/4f01028b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunParallelIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunParallelIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunParallelIT.java
deleted file mode 100644
index 6d51d02..0000000
--- a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunParallelIT.java
+++ /dev/null
@@ -1,91 +0,0 @@
-/*
-* Licensed to the Apache Software Foundation (ASF) under one
-* or more contributor license agreements. See the NOTICE file
-* distributed with this work for additional information
-* regarding copyright ownership. The ASF licenses this file
-* to you under the Apache License, Version 2.0 (the
-* "License"); you may not use this file except in compliance
-* with the License. You may obtain a copy of the License at
-*
-* http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing,
-* software distributed under the License is distributed on an
-* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-* KIND, either express or implied. See the License for the
-* specific language governing permissions and limitations
-* under the License.
-*/
-package org.apache.taverna.platform;
-
-import java.net.URI;
-import java.util.HashSet;
-import java.util.Set;
-
-import org.osgi.framework.ServiceReference;
-
-import org.apache.taverna.platform.execution.api.ExecutionEnvironment;
-import org.apache.taverna.platform.report.State;
-import org.apache.taverna.platform.report.WorkflowReport;
-import org.apache.taverna.platform.run.api.RunProfile;
-import org.apache.taverna.platform.run.api.RunService;
-import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-
-public class RunParallelIT extends PlatformIT {
-
- private RunService runService;
-
- private ExecutionEnvironment executionEnvironment;
-
- protected void setup() throws Exception {
- super.setup();
- if (runService == null) {
- ServiceReference runServiceReference = bundleContext
- .getServiceReference("org.apache.taverna.platform.run.api.RunService");
- runService = (RunService) bundleContext.getService(runServiceReference);
- }
- if (executionEnvironment == null) {
- executionEnvironment = runService.getExecutionEnvironments().iterator().next();
- }
- credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser",
- "testpasswd"), URI
- .create("http://heater.cs.man.ac.uk:7070/#Example+HTTP+BASIC+Authentication"));
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl"));
- }
-
- public void testRun() throws Exception {
- setup();
-
- String[] workflows = { "biomart", "rest", "secure-basic-authentication",
- "spreadsheetimport", "stringconstant", "wsdl", "wsdl-secure", "xpath" };
- Set<String> runIDs= new HashSet<String>();
-
- for (int i = 0; i < workflows.length; i++) {
- int runs = Math.max(1, (int) Math.ceil(Math.random() * 10));
- System.out.println("Creating " + runs + " runs for workflow " + workflows[i]);
- for (int j = 0; j < runs; j++) {
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/" + workflows[i] + ".t2flow");
- String run = runService.createRun(new RunProfile(executionEnvironment, workflowBundle));
- runService.getWorkflowReport(run).getSubject().setName(workflows[i] + j);
- runIDs.add(run);
- }
- }
-
- for (String runId : runIDs) {
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println("Starting " + report.getSubject().getName());
- runService.start(runId);
- }
-
- for (String runId : runIDs) {
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println("Waiting for " + report.getSubject().getName() + " to complete");
- assertTrue(waitForState(report, State.COMPLETED, false));
- }
-
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/4f01028b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunWorkflowsIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunWorkflowsIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunWorkflowsIT.java
deleted file mode 100644
index 18d0ed7..0000000
--- a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunWorkflowsIT.java
+++ /dev/null
@@ -1,132 +0,0 @@
-/*
-* Licensed to the Apache Software Foundation (ASF) under one
-* or more contributor license agreements. See the NOTICE file
-* distributed with this work for additional information
-* regarding copyright ownership. The ASF licenses this file
-* to you under the Apache License, Version 2.0 (the
-* "License"); you may not use this file except in compliance
-* with the License. You may obtain a copy of the License at
-*
-* http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing,
-* software distributed under the License is distributed on an
-* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-* KIND, either express or implied. See the License for the
-* specific language governing permissions and limitations
-* under the License.
-*/
-package org.apache.taverna.platform;
-
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.osgi.framework.ServiceReference;
-
-import org.apache.taverna.platform.execution.api.ExecutionEnvironment;
-import org.apache.taverna.platform.report.State;
-import org.apache.taverna.platform.report.WorkflowReport;
-import org.apache.taverna.platform.run.api.RunProfile;
-import org.apache.taverna.platform.run.api.RunService;
-import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-
-public class RunWorkflowsIT extends PlatformIT {
-
- private RunService runService;
-
- protected void setup() throws Exception {
- super.setup();
- if (runService == null) {
- ServiceReference runServiceReference = bundleContext
- .getServiceReference("org.apache.taverna.platform.run.api.RunService");
- runService = (RunService) bundleContext.getService(runServiceReference);
- }
- }
-
- public void testRunFetchTodaysXkcdComic() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/FetchTodaysXkcdComic.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- assertNotNull(results);
- waitForResults(results, report, "todaysXkcd");
-
- List<Data> result = results.get("todaysXkcd").getElements();
- assertEquals(1, result.size());
- Object value = result.get(0).getValue();
- assert(value instanceof byte[]);
- byte[] binaryValue = (byte[]) value;
- assertEquals('P', (char) binaryValue[1]);
- assertEquals('N', (char) binaryValue[2]);
- assertEquals('G', (char) binaryValue[3]);
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunGBSeqTest() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/GBSeqTest.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- assertNotNull(results);
- waitForResults(results, runService.getWorkflowReport(runId), "nuc_tiny");
-
- assertTrue(checkResult(results.get("nuc_tiny"),
- "<?xml version=\"1.0\"?>\n"
- + " <!DOCTYPE TSeqSet PUBLIC \"-//NCBI//NCBI TSeq/EN\" \"http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd\">\n"
- + " <TSeqSet>\n"
- + "<TSeq>\n"
- + " <TSeq_seqtype value=\"nucleotide\"/>\n"
- + " <TSeq_gi>119395733</TSeq_gi>\n"
- + " <TSeq_accver>NM_000059.3</TSeq_accver>\n"
- + " <TSeq_taxid>9606</TSeq_taxid>\n"
- + " <TSeq_orgname>Homo sapiens</TSeq_orgname>\n"
- + " <TSeq_defline>Homo sapiens breast cancer 2, early onset (BRCA2), mRNA</TSeq_defline>\n"
- + " <TSeq_length>11386</TSeq_length>\n"
- + " <TSeq_sequence>GTGGCGCGAGCTTCTGAAACTAGGCGGCAGAGGCGGAGCCGCTGTGGCACTGCTGCGCCTCTGCTGCGCCTCGGGTGTCTTTTGCGGCGGTGGGTCGCCGCCGGGAGAAGCGTGAGGGGACAGATTTGTGACCGGCGCGGTTTTTGTCAGCTTACTCCGGCCAAAAAAGAACTGCACCTCTGGAGCGGACTTATTTACCAAGCATTGGAGGAATATCGTAGGTAAAAATGCCTATTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGATTTAGGACCAATAAGTCTTAATTGGTTTGAAGAACTTTCTTCAGAAGCTCCACCCTATAATTCTGAACCTGCAGAAGAATCTGAACATAAAAACAACAATTACGAACCAAACCTATTTAAAACTCCACAAAGGAAACCATCTTATAATCAGCTGGCTTCAACTCCAATAATATTCAAAGAGCAAGGGCTGACTCTGCCGCTGTACCAATCTCCTGTAAAAGAATTAGATAAATTCAAATTAGACTTAGGAAGGAATGTTCCCAATAGTAGACATAAAAGTCTTCGCACAGTGAAAACTAAAATGGATCAAGCAGATGATGTTTCCTGTCCACTTCTAAATTCTTGTCTTAGTGAAAGTCCTGTTGTTCTACAATGTACACATGTAACACCACAAAGAGATAAGTCAGTGGTATGTGGGAGTTTGTTTCATACACCAAAGTTTGTGAAGGGTCGTCAGACACCAAAACATATTTCTGAAAGTCTAGGAGCTGAGGTGGATCCTGATATGTCTTGGTCAAGTTCTTTAGCTACACCACCCACCCTTAGTTCTACTGTGCTCATAGTCAGAAATGAAGAAGCATCTGAAACTGTATTTCCTCATGATACTACTGCTAATGTGAAAAGCTATTTTTCCAATCATGATGAAAGTCTGAAGAAAAATGATAGATTTATCGC
TTCTGTGACAGACAGTGAAAACACAAATCAAAGAGAAGCTGCAAGTCATGGATTTGGAAAAACATCAGGGAATTCATTTAAAGTAAATAGCTGCAAAGACCACATTGGAAAGTCAATGCCAAATGTCCTAGAAGATGAAGTATATGAAACAGTTGTAGATACCTCTGAAGAAGATAGTTTTTCATTATGTTTTTCTAAATGTAGAACAAAAAATCTACAAAAAGTAAGAACTAGCAAGACTAGGAAAAAAATTTTCCATGAAGCAAACGCTGATGAATGTGAAAAATCTAAAAACCAAGTGAAAGAAAAATACTCATTTGTATCTGAAGTGGAACCAAATGATACTGATCCATTAGATTCAAATGTAGCAAATCAGAAGCCCTTTGAGAGTGGAAGTGACAAAATCTCCAAGGAAGTTGTACCGTCTTTGGCCTGTGAATGGTCTCAACTAACCCTTTCAGGTCTAAATGGAGCCCAGATGGAGAAAATACCCCTATTGCATATTTCTTCATGTGACCAAAATATTTCAGAAAAAGACCTATTAGACACAGAGAACAAAAGAAAGAAAGATTTTCTTACTTCAGAGAATTCTTTGCCACGTATTTCTAGCCTACCAAAATCAGAGAAGCCATTAAATGAGGAAACAGTGGTAAATAAGAGAGATGAAGAGCAGCATCTTGAATCTCATACAGACTGCATTCTTGCAGTAAAGCAGGCAATATCTGGAACTTCTCCAGTGGCTTCTTCATTTCAGGGTATCAAAAAGTCTATATTCAGAATAAGAGAATCACCTAAAGAGACTTTCAATGCAAGTTTTTCAGGTCATATGACTGATCCAAACTTTAAAAAAGAAACTGAAGCCTCTGAAAGTGGACTGGAAATACATACTGTTTGCTCACAGAAGGAGGACTCCTTATGTCCAAATTTAATTGATAATGGAAGCTGGCCAGCCACCACCACACAGAATTCTGTAGCTTTGAAGAATGCAGGTTTAATA
TCCACTTTGAAAAAGAAAACAAATAAGTTTATTTATGCTATACATGATGAAACATCTTATAAAGGAAAAAAAATACCGAAAGACCAAAAATCAGAACTAATTAACTGTTCAGCCCAGTTTGAAGCAAATGCTTTTGAAGCACCACTTACATTTGCAAATGCTGATTCAGGTTTATTGCATTCTTCTGTGAAAAGAAGCTGTTCACAGAATGATTCTGAAGAACCAACTTTGTCCTTAACTAGCTCTTTTGGGACAATTCTGAGGAAATGTTCTAGAAATGAAACATGTTCTAATAATACAGTAATCTCTCAGGATCTTGATTATAAAGAAGCAAAATGTAATAAGGAAAAACTACAGTTATTTATTACCCCAGAAGCTGATTCTCTGTCATGCCTGCAGGAAGGACAGTGTGAAAATGATCCAAAAAGCAAAAAAGTTTCAGATATAAAAGAAGAGGTCTTGGCTGCAGCATGTCACCCAGTACAACATTCAAAAGTGGAATACAGTGATACTGACTTTCAATCCCAGAAAAGTCTTTTATATGATCATGAAAATGCCAGCACTCTTATTTTAACTCCTACTTCCAAGGATGTTCTGTCAAACCTAGTCATGATTTCTAGAGGCAAAGAATCATACAAAATGTCAGACAAGCTCAAAGGTAACAATTATGAATCTGATGTTGAATTAACCAAAAATATTCCCATGGAAAAGAATCAAGATGTATGTGCTTTAAATGAAAATTATAAAAACGTTGAGCTGTTGCCACCTGAAAAATACATGAGAGTAGCATCACCTTCAAGAAAGGTACAATTCAACCAAAACACAAATCTAAGAGTAATCCAAAAAAATCAAGAAGAAACTACTTCAATTTCAAAAATAACTGTCAATCCAGACTCTGAAGAACTTTTCTCAGACAATGAGAATAATTTTGTCTTCCAAGTAGCTAATGAAAGGAATAATCTTGCTTTAGGAAATACTAAGGAACTTCATGAAACAG
ACTTGACTTGTGTAAACGAACCCATTTTCAAGAACTCTACCATGGTTTTATATGGAGACACAGGTGATAAACAAGCAACCCAAGTGTCAATTAAAAAAGATTTGGTTTATGTTCTTGCAGAGGAGAACAAAAATAGTGTAAAGCAGCATATAAAAATGACTCTAGGTCAAGATTTAAAATCGGACATCTCCTTGAATATAGATAAAATACCAGAAAAAAATAATGATTACATGAACAAATGGGCAGGACTCTTAGGTCCAATTTCAAATCACAGTTTTGGAGGTAGCTTCAGAACAGCTTCAAATAAGGAAATCAAGCTCTCTGAACATAACATTAAGAAGAGCAAAATGTTCTTCAAAGATATTGAAGAACAATATCCTACTAGTTTAGCTTGTGTTGAAATTGTAAATACCTTGGCATTAGATAATCAAAAGAAACTGAGCAAGCCTCAGTCAATTAATACTGTATCTGCACATTTACAGAGTAGTGTAGTTGTTTCTGATTGTAAAAATAGTCATATAACCCCTCAGATGTTATTTTCCAAGCAGGATTTTAATTCAAACCATAATTTAACACCTAGCCAAAAGGCAGAAATTACAGAACTTTCTACTATATTAGAAGAATCAGGAAGTCAGTTTGAATTTACTCAGTTTAGAAAACCAAGCTACATATTGCAGAAGAGTACATTTGAAGTGCCTGAAAACCAGATGACTATCTTAAAGACCACTTCTGAGGAATGCAGAGATGCTGATCTTCATGTCATAATGAATGCCCCATCGATTGGTCAGGTAGACAGCAGCAAGCAATTTGAAGGTACAGTTGAAATTAAACGGAAGTTTGCTGGCCTGTTGAAAAATGACTGTAACAAAAGTGCTTCTGGTTATTTAACAGATGAAAATGAAGTGGGGTTTAGGGGCTTTTATTCTGCTCATGGCACAAAACTGAATGTTTCTACTGAAGCTCTGCAAAAAGCTGTGAAACTGTTTAGTGATATTGA
GAATATTAGTGAGGAAACTTCTGCAGAGGTACATCCAATAAGTTTATCTTCAAGTAAATGTCATGATTCTGTTGTTTCAATGTTTAAGATAGAAAATCATAATGATAAAACTGTAAGTGAAAAAAATAATAAATGCCAACTGATATTACAAAATAATATTGAAATGACTACTGGCACTTTTGTTGAAGAAATTACTGAAAATTACAAGAGAAATACTGAAAATGAAGATAACAAATATACTGCTGCCAGTAGAAATTCTCATAACTTAGAATTTGATGGCAGTGATTCAAGTAAAAATGATACTGTTTGTATTCATAAAGATGAAACGGACTTGCTATTTACTGATCAGCACAACATATGTCTTAAATTATCTGGCCAGTTTATGAAGGAGGGAAACACTCAGATTAAAGAAGATTTGTCAGATTTAACTTTTTTGGAAGTTGCGAAAGCTCAAGAAGCATGTCATGGTAATACTTCAAATAAAGAACAGTTAACTGCTACTAAAACGGAGCAAAATATAAAAGATTTTGAGACTTCTGATACATTTTTTCAGACTGCAAGTGGGAAAAATATTAGTGTCGCCAAAGAGTCATTTAATAAAATTGTAAATTTCTTTGATCAGAAACCAGAAGAATTGCATAACTTTTCCTTAAATTCTGAATTACATTCTGACATAAGAAAGAACAAAATGGACATTCTAAGTTATGAGGAAACAGACATAGTTAAACACAAAATACTGAAAGAAAGTGTCCCAGTTGGTACTGGAAATCAACTAGTGACCTTCCAGGGACAACCCGAACGTGATGAAAAGATCAAAGAACCTACTCTATTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAATCTTTGGACAAAGTGAAAAACCTTTTTGATGAAAAAGAGCAAGGTACTAGTGAAATCACCAGTTTTAGCCATCAATGGGCAAAGACCCTAAAGTACAGAGAGGCCTGTAAAGACCTTGAA
TTAGCATGTGAGACCATTGAGATCACAGCTGCCCCAAAGTGTAAAGAAATGCAGAATTCTCTCAATAATGATAAAAACCTTGTTTCTATTGAGACTGTGGTGCCACCTAAGCTCTTAAGTGATAATTTATGTAGACAAACTGAAAATCTCAAAACATCAAAAAGTATCTTTTTGAAAGTTAAAGTACATGAAAATGTAGAAAAAGAAACAGCAAAAAGTCCTGCAACTTGTTACACAAATCAGTCCCCTTATTCAGTCATTGAAAATTCAGCCTTAGCTTTTTACACAAGTTGTAGTAGAAAAACTTCTGTGAGTCAGACTTCATTACTTGAAGCAAAAAAATGGCTTAGAGAAGGAATATTTGATGGTCAACCAGAAAGAATAAATACTGCAGATTATGTAGGAAATTATTTGTATGAAAATAATTCAAACAGTACTATAGCTGAAAATGACAAAAATCATCTCTCCGAAAAACAAGATACTTATTTAAGTAACAGTAGCATGTCTAACAGCTATTCCTACCATTCTGATGAGGTATATAATGATTCAGGATATCTCTCAAAAAATAAACTTGATTCTGGTATTGAGCCAGTATTGAAGAATGTTGAAGATCAAAAAAACACTAGTTTTTCCAAAGTAATATCCAATGTAAAAGATGCAAATGCATACCCACAAACTGTAAATGAAGATATTTGCGTTGAGGAACTTGTGACTAGCTCTTCACCCTGCAAAAATAAAAATGCAGCCATTAAATTGTCCATATCTAATAGTAATAATTTTGAGGTAGGGCCACCTGCATTTAGGATAGCCAGTGGTAAAATCGTTTGTGTTTCACATGAAACAATTAAAAAAGTGAAAGACATATTTACAGACAGTTTCAGTAAAGTAATTAAGGAAAACAACGAGAATAAATCAAAAATTTGCCAAACGAAAATTATGGCAGGTTGTTACGAGGCATTGGATGATTCAGAGGATATTCTTCATAACTCTCTAGATA
ATGATGAATGTAGCACGCATTCACATAAGGTTTTTGCTGACATTCAGAGTGAAGAAATTTTACAACATAACCAAAATATGTCTGGATTGGAGAAAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAAGCTTCATAAGTCAGTCTCATCTGCAAATACTTGTGGGATTTTTAGCACAGCAAGTGGAAAATCTGTCCAGGTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATATCCCAAAAAGGCTTTTCATATAATGTGGTAAATTCATCTGCTTTCTCTGGATTTAGTACAGCAAGTGGAAAGCAAGTTTCCATTTTAGAAAGTTCCTTACACAAAGTTAAGGGAGTGTTAGAGGAATTTGATTTAATCAGAACTGAGCATAGTCTTCACTATTCACCTACGTCTAGACAAAATGTATCAAAAATACTTCCTCGTGTTGATAAGAGAAACCCAGAGCACTGTGTAAACTCAGAAATGGAAAAAACCTGCAGTAAAGAATTTAAATTATCAAATAACTTAAATGTTGAAGGTGGTTCTTCAGAAAATAATCACTCTATTAAAGTTTCTCCATATCTCTCTCAATTTCAACAAGACAAACAACAGTTGGTATTAGGAACCAAAGTGTCACTTGTTGAGAACATTCATGTTTTGGGAAAAGAACAGGCTTCACCTAAAAACGTAAAAATGGAAATTGGTAAAACTGAAACTTTTTCTGATGTTCCTGTGAAAACAAATATAGAAGTTTGTTCTACTTACTCCAAAGATTCAGAAAACTACTTTGAAACAGAAGCAGTAGAAATTGCTAAAGCTTTTATGGAAGATGATGAACTGACAGA
TTCTAAACTGCCAAGTCATGCCACACATTCTCTTTTTACATGTCCCGAAAATGAGGAAATGGTTTTGTCAAATTCAAGAATTGGAAAAAGAAGAGGAGAGCCCCTTATCTTAGTGGGAGAACCCTCAATCAAAAGAAACTTATTAAATGAATTTGACAGGATAATAGAAAATCAAGAAAAATCCTTAAAGGCTTCAAAAAGCACTCCAGATGGCACAATAAAAGATCGAAGATTGTTTATGCATCATGTTTCTTTAGAGCCGATTACCTGTGTACCCTTTCGCACAACTAAGGAACGTCAAGAGATACAGAATCCAAATTTTACCGCACCTGGTCAAGAATTTCTGTCTAAATCTCATTTGTATGAACATCTGACTTTGGAAAAATCTTCAAGCAATTTAGCAGTTTCAGGACATCCATTTTATCAAGTTTCTGCTACAAGAAATGAAAAAATGAGACACTTGATTACTACAGGCAGACCAACCAAAGTCTTTGTTCCACCTTTTAAAACTAAATCACATTTTCACAGAGTTGAACAGTGTGTTAGGAATATTAACTTGGAGGAAAACAGACAAAAGCAAAACATTGATGGACATGGCTCTGATGATAGTAAAAATAAGATTAATGACAATGAGATTCATCAGTTTAACAAAAACAACTCCAATCAAGCAGCAGCTGTAACTTTCACAAAGTGTGAAGAAGAACCTTTAGATTTAATTACAAGTCTTCAGAATGCCAGAGATATACAGGATATGCGAATTAAGAAGAAACAAAGGCAACGCGTCTTTCCACAGCCAGGCAGTCTGTATCTTGCAAAAACATCCACTCTGCCTCGAATCTCTCTGAAAGCAGCAGTAGGAGGCCAAGTTCCCTCTGCGTGTTCTCATAAACAGCTGTATACGTATGGCGTTTCTAAACATTGCATAAAAATTAACAGCAAAAATGCAGAGTCTTTTCAGTTTCACACTGAAGATTATTTTGGTAAGGAAAGTTTATGG
ACTGGAAAAGGAATACAGTTGGCTGATGGTGGATGGCTCATACCCTCCAATGATGGAAAGGCTGGAAAAGAAGAATTTTATAGGGCTCTGTGTGACACTCCAGGTGTGGATCCAAAGCTTATTTCTAGAATTTGGGTTTATAATCACTATAGATGGATCATATGGAAACTGGCAGCTATGGAATGTGCCTTTCCTAAGGAATTTGCTAATAGATGCCTAAGCCCAGAAAGGGTGCTTCTTCAACTAAAATACAGATATGATACGGAAATTGATAGAAGCAGAAGATCGGCTATAAAAAAGATAATGGAAAGGGATGACACAGCTGCAAAAACACTTGTTCTCTGTGTTTCTGACATAATTTCATTGAGCGCAAATATATCTGAAACTTCTAGCAATAAAACTAGTAGTGCAGATACCCAAAAAGTGGCCATTATTGAACTTACAGATGGGTGGTATGCTGTTAAGGCCCAGTTAGATCCTCCCCTCTTAGCTGTCTTAAAGAATGGCAGACTGACAGTTGGTCAGAAGATTATTCTTCATGGAGCAGAACTGGTGGGCTCTCCTGATGCCTGTACACCTCTTGAAGCCCCAGAATCTCTTATGTTAAAGATTTCTGCTAACAGTACTCGGCCTGCTCGCTGGTATACCAAACTTGGATTCTTTCCTGACCCTAGACCTTTTCCTCTGCCCTTATCATCGCTTTTCAGTGATGGAGGAAATGTTGGTTGTGTTGATGTAATTATTCAAAGAGCATACCCTATACAGTGGATGGAGAAGACATCATCTGGATTATACATATTTCGCAATGAAAGAGAGGAAGAAAAGGAAGCAGCAAAATATGTGGAGGCCCAACAAAAGAGACTAGAAGCCTTATTCACTAAAATTCAGGAGGAATTTGAAGAACATGAAGAAAACACAACAAAACCATATTTACCATCACGTGCACTAACAAGACAGCAAGTTCGTGCTTTGCAAGATGGTGCAGAGCTTTATGAAG
CAGTGAAGAATGCAGCAGACCCAGCTTACCTTGAGGGTTATTTCAGTGAAGAGCAGTTAAGAGCCTTGAATAATCACAGGCAAATGTTGAATGATAAGAAACAAGCTCAGATCCAGTTGGAAATTAGGAAGGCCATGGAATCTGCTGAACAAAAGGAACAAGGTTTATCAAGGGATGTCACAACCGTGTGGAAGTTGCGTATTGTAAGCTATTCAAAAAAAGAAAAAGATTCAGTTATACTGAGTATTTGGCGTCCATCATCAGATTTATATTCTCTGTTAACAGAAGGAAAGAGATACAGAATTTATCATCTTGCAACTTCAAAATCTAAAAGTAAATCTGAAAGAGCTAACATACAGTTAGCAGCGACAAAAAAAACTCAGTATCAACAACTACCGGTTTCAGATGAAATTTTATTTCAGATTTACCAGCCACGGGAGCCCCTTCACTTCAGCAAATTTTTAGATCCAGACTTTCAGCCATCTTGTTCTGAGGTGGACCTAATAGGATTTGTCGTTTCTGTTGTGAAAAAAACAGGACTTGCCCCTTTCGTCTATTTGTCAGACGAATGTTACAATTTACTGGCAATAAAGTTTTGGATAGACCTTAATGAGGACATTATTAAGCCTCATATGTTAATTGCTGCAAGCAACCTCCAGTGGCGACCAGAATCCAAATCAGGCCTTCTTACTTTATTTGCTGGAGATTTTTCTGTGTTTTCTGCTAGTCCAAAAGAGGGCCACTTTCAAGAGACATTCAACAAAATGAAAAATACTGTTGAGAATATTGACATACTTTGCAATGAAGCAGAAAACAAGCTTATGCATATACTGCATGCAAATGATCCCAAGTGGTCCACCCCAACTAAAGACTGTACTTCAGGGCCGTACACTGCTCAAATCATTCCTGGTACAGGAAACAAGCTTCTGATGTCTTCTCCTAATTGTGAGATATATTATCAAAGTCCTTTATCACTTTGTATGGCCAAAAGGAAGTC
TGTTTCCACACCTGTCTCAGCCCAGATGACTTCAAAGTCTTGTAAAGGGGAGAAAGAGATTGATGACCAAAAGAACTGCAAAAAGAGAAGAGCCTTGGATTTCTTGAGTAGACTGCCTTTACCTCCACCTGTTAGTCCCATTTGTACATTTGTTTCTCCGGCTGCACAGAAGGCATTTCAGCCACCAAGGAGTTGTGGCACCAAATACGAAACACCCATAAAGAAAAAAGAACTGAATTCTCCTCAGATGACTCCATTTAAAAAATTCAATGAAATTTCTCTTTTGGAAAGTAATTCAATAGCTGACGAAGAACTTGCATTGATAAATACCCAAGCTCTTTTGTCTGGTTCAACAGGAGAAAAACAATTTATATCTGTCAGTGAATCCACTAGGACTGCTCCCACCAGTTCAGAAGATTATCTCAGACTGAAACGACGTTGTACTACATCTCTGATCAAAGAACAGGAGAGTTCCCAGGCCAGTACGGAAGAATGTGAGAAAAATAAGCAGGACACAATTACAACTAAAAAATATATCTAAGCATTTGCAAAGGCGACAATAAATTATTGACGCTTAACCTTTCCAGTTTATAAGACTGGAATATAATTTCAAACCACACATTAGTACTTATGTTGCACAATGAGAAAAGAAATTAGTTTCAAATTTACCTCAGCGTTTGTGTATCGGGCAAAAATCGTTTTGCCCGATTCCGTATTGGTATACTTTTGCTTCAGTTGCATATCTTAAAACTAAATGTAATTTATTAACTAATCAAGAAAAACATCTTTGGCTGAGCTCGGTGGCTCATGCCTGTAATCCCAACACTTTGAGAAGCTGAGGTGGGAGGAGTGCTTGAGGCCAGGAGTTCAAGACCAGCCTGGGCAACATAGGGAGACCCCCATCTTTACAAAGAAAAAAAAAAGGGGAAAAGAAAATCTTTTAAATCTTTGGATTTGATCACTACAAGTATTATTTTACAAGTGAAATAAACATACC
ATTTTCTTTTAGATTGTGTCATTAAATGGAATGAGGTCTCTTAGTACAGTTATTTTGATGCAGATAATTCCTTTTAGTTTAGCTACTATTTTAGGGGATTTTTTTTAGAGGTAACTCACTATGAAATAGTTCTCCTTAATGCAAATATGTTGGTTCTGCTATAGTTCCATCCTGTTCAAAAGTCAGGATGAATATGAAGAGTGGTGTTTCCTTTTGAGCAATTCTTCATCCTTAAGTCAGCATGATTATAAGAAAAATAGAACCCTCAGTGTAACTCTAATTCCTTTTTACTATTCCAGTGTGATCTCTGAAATTAAATTACTTCAACTAAAAATTCAAATACTTTAAATCAGAAGATTTCATAGTTAATTTATTTTTTTTTTCAACAAAATGGTCATCCAAACTCAAACTTGAGAAAATATCTTGCTTTCAAATTGGCACTGATT</TSeq_sequence>\n"
- + "</TSeq>\n" + "\n" + "</TSeqSet>"));
-
- waitForState(report, State.COMPLETED);
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/4f01028b/taverna-platform-integration-tests/src/test/resources/log4j.properties
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/resources/log4j.properties b/taverna-platform-integration-tests/src/test/resources/log4j.properties
deleted file mode 100644
index dcb75c9..0000000
--- a/taverna-platform-integration-tests/src/test/resources/log4j.properties
+++ /dev/null
@@ -1,11 +0,0 @@
-#log4j.rootLogger=DEBUG, CONSOLE
-log4j.rootLogger=WARN, CONSOLE
-#log4j.rootLogger=ERROR, CONSOLE
-
-log4j.logger.org.apache.taverna.platform.execution=DEBUG
-
-# Default output to console
-log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
-log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
-log4j.appender.CONSOLE.layout.ConversionPattern=%-5p %d{ISO8601} (%c:%L) - %m%n
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/4f01028b/taverna-platform-integration-tests/src/test/resources/security/tomcat_heater_certificate.pem
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/resources/security/tomcat_heater_certificate.pem b/taverna-platform-integration-tests/src/test/resources/security/tomcat_heater_certificate.pem
deleted file mode 100644
index c729258..0000000
--- a/taverna-platform-integration-tests/src/test/resources/security/tomcat_heater_certificate.pem
+++ /dev/null
@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDyDCCArCgAwIBAgIETlYTBzANBgkqhkiG9w0BAQUFADCBpTELMAkGA1UEBhMCVUsxGzAZBgNV
-BAgTEkdyZWF0ZXIgTWFuY2hlc3RlcjETMBEGA1UEBxMKTWFuY2hlc3RlcjEhMB8GA1UEChMYVW5p
-dmVyc2l0eSBvZiBNYW5jaGVzdGVyMSMwIQYDVQQLExpTY2hvb2wgb2YgQ29tcHV0ZXIgU2NpZW5j
-ZTEcMBoGA1UEAxMTaGVhdGVyLmNzLm1hbi5hYy51azAeFw0xMTA4MjUwOTE2NTVaFw0yMTA4MjIw
-OTE2NTVaMIGlMQswCQYDVQQGEwJVSzEbMBkGA1UECBMSR3JlYXRlciBNYW5jaGVzdGVyMRMwEQYD
-VQQHEwpNYW5jaGVzdGVyMSEwHwYDVQQKExhVbml2ZXJzaXR5IG9mIE1hbmNoZXN0ZXIxIzAhBgNV
-BAsTGlNjaG9vbCBvZiBDb21wdXRlciBTY2llbmNlMRwwGgYDVQQDExNoZWF0ZXIuY3MubWFuLmFj
-LnVrMIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA1/TuezSNYFpD2NTtw5UGECCPwClV
-Om08Nca1aanOVxv5rcn4eUVbu6Btm/dqgiCeV8nCyu7nEPvWP+Kvktseikx3LZ08qKdDRLpNa68/
-WrjcbS6ICs2hphhqftHSpl0OPnWkQicbI7Z4uUdqmF6DsLDOLpRfiYhh9lZ0FM7PD3yt42GR5E2B
-j465IJQweZxLCsRKwuZlvOsWJxnx1MHVj7ZFBYl7HSBfEpvThyqKL5R7FOZW0zpG3+Y+S9HmfQYk
-BipXrrNS1+lsIwPU8jD31PBzVPBNxIeKYHxXCKLf+EBah/tAKSxIzUihxhh1pdNEPvUyy2zY9vyv
-1PfXd8Uk0wIDAQABMA0GCSqGSIb3DQEBBQUAA4IBAQAtiPDBRlmjhFd9DP1NvbyfMApdjLufMLvr
-mzze3W6A4XUZj+kXR/Z3KYj84pWOnhe+Benvw5bIf2JM+sqIiSUA+TB8losx+SeY5hZ3lqEFY1wZ
-1qy47hH3rY98RdSAXlAhvGCEL/CktvIEHgaSlCmrOvK76ySwRCTYA9DJTWeB81R7bP7le2ewSg5c
-MY/Hy3VBkMGbVnZQoHhkUd7TIsPqD1SvYQDCug49JFsKsyrfep3nANAQO7uR8FYrCYtXj66z9ziO
-m0gZm+h/Rq8StgMrNwmi+3mGAgRJ6JKj4vAWJfyUSaOjLLf9u3BvrxVtQKCMSDGx25dBFlZXHIhE
-rONf
------END CERTIFICATE-----