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Posted to commits@taverna.apache.org by st...@apache.org on 2015/10/18 20:13:54 UTC
[1/4] incubator-taverna-engine git commit: OSGi/Spring config:
uk.org.taverna.* -> org.apache.taverna
Repository: incubator-taverna-engine
Updated Branches:
refs/heads/master 634203a57 -> 50373179a
OSGi/Spring config: uk.org.taverna.* -> org.apache.taverna
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/commit/90125930
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/tree/90125930
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/diff/90125930
Branch: refs/heads/master
Commit: 90125930354ba5473864bc1cb9cadacffc60f3b7
Parents: 634203a
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Oct 18 18:57:03 2015 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Oct 18 18:57:03 2015 +0100
----------------------------------------------------------------------
.../src/main/resources/META-INF/spring/context-osgi.xml | 2 +-
taverna-capability-impl/pom.xml | 2 +-
.../resources/META-INF/spring/taverna-capability-context.xml | 4 ++--
.../META-INF/spring/credential-manager-impl-context-osgi.xml | 2 +-
taverna-database-configuration-impl/pom.xml | 2 +-
.../src/main/resources/META-INF/spring/database-context-osgi.xml | 4 ++--
.../src/main/resources/META-INF/spring/database-context.xml | 4 ++--
taverna-execution-impl/pom.xml | 2 +-
taverna-execution-local/pom.xml | 2 +-
.../resources/META-INF/spring/execution-local-context-osgi.xml | 4 ++--
taverna-execution-remote/pom.xml | 2 +-
taverna-run-impl/pom.xml | 2 +-
taverna-services-impl/pom.xml | 2 +-
.../resources/META-INF/spring/taverna-services-context-osgi.xml | 2 +-
14 files changed, 18 insertions(+), 18 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/90125930/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml b/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml
index 2485411..41a9297 100644
--- a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml
+++ b/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml
@@ -21,6 +21,6 @@
<reference id="activityIconManager" interface="org.apache.taverna.workbench.activityicons.ActivityIconManager" />
<reference id="colourManager" interface="org.apache.taverna.workbench.configuration.colour.ColourManager" />
<reference id="serviceDescriptionRegistry" interface="org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry" />
- <reference id="serviceRegistry" interface="org.apache.taverna.commons.services.ServiceRegistry" />
+ <reference id="serviceRegistry" interface="org.apache.taverna.services.ServiceRegistry" />
</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/90125930/taverna-capability-impl/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-capability-impl/pom.xml b/taverna-capability-impl/pom.xml
index c4fa489..0beabc3 100644
--- a/taverna-capability-impl/pom.xml
+++ b/taverna-capability-impl/pom.xml
@@ -15,7 +15,7 @@
<artifactId>maven-bundle-plugin</artifactId>
<configuration>
<instructions>
- <Import-Package>uk.org.taverna.platform.capability.api;provide:=true,*</Import-Package>
+ <Import-Package>org.apache.taverna.platform.capability.api;provide:=true,*</Import-Package>
</instructions>
</configuration>
</plugin>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/90125930/taverna-capability-impl/src/main/resources/META-INF/spring/taverna-capability-context.xml
----------------------------------------------------------------------
diff --git a/taverna-capability-impl/src/main/resources/META-INF/spring/taverna-capability-context.xml b/taverna-capability-impl/src/main/resources/META-INF/spring/taverna-capability-context.xml
index fad027e..3a752d4 100644
--- a/taverna-capability-impl/src/main/resources/META-INF/spring/taverna-capability-context.xml
+++ b/taverna-capability-impl/src/main/resources/META-INF/spring/taverna-capability-context.xml
@@ -3,11 +3,11 @@
xsi:schemaLocation="http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans.xsd">
- <bean id="activityService" class="uk.org.taverna.platform.capability.activity.impl.ActivityServiceImpl">
+ <bean id="activityService" class="org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl">
<property name="activityFactories" ref="activityFactories" />
</bean>
- <bean id="dispatchLayerService" class="uk.org.taverna.platform.capability.dispatch.impl.DispatchLayerServiceImpl">
+ <bean id="dispatchLayerService" class="org.apache.taverna.platform.capability.dispatch.impl.DispatchLayerServiceImpl">
<property name="dispatchLayerFactories" ref="dispatchLayerFactories" />
</bean>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/90125930/taverna-credential-manager-impl/src/main/resources/META-INF/spring/credential-manager-impl-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-credential-manager-impl/src/main/resources/META-INF/spring/credential-manager-impl-context-osgi.xml b/taverna-credential-manager-impl/src/main/resources/META-INF/spring/credential-manager-impl-context-osgi.xml
index 813cc31..f4c8bed 100644
--- a/taverna-credential-manager-impl/src/main/resources/META-INF/spring/credential-manager-impl-context-osgi.xml
+++ b/taverna-credential-manager-impl/src/main/resources/META-INF/spring/credential-manager-impl-context-osgi.xml
@@ -14,7 +14,7 @@
interface="org.apache.taverna.security.credentialmanager.DistinguishedNameParser" />
<reference id="applicationConfiguration"
- interface="uk.org.taverna.configuration.app.ApplicationConfiguration" />
+ interface="org.apache.taverna.configuration.app.ApplicationConfiguration" />
<list id="masterPasswordProviders"
interface="org.apache.taverna.security.credentialmanager.MasterPasswordProvider"
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/90125930/taverna-database-configuration-impl/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-database-configuration-impl/pom.xml b/taverna-database-configuration-impl/pom.xml
index 39034f4..db6b33a 100644
--- a/taverna-database-configuration-impl/pom.xml
+++ b/taverna-database-configuration-impl/pom.xml
@@ -17,7 +17,7 @@
<configuration>
<instructions>
<Import-Package>
- uk.org.taverna.configuration.database;provide:=true,
+ org.apache.taverna.configuration.database;provide:=true,
org.apache.derby.jdbc, *
</Import-Package>
</instructions>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/90125930/taverna-database-configuration-impl/src/main/resources/META-INF/spring/database-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-database-configuration-impl/src/main/resources/META-INF/spring/database-context-osgi.xml b/taverna-database-configuration-impl/src/main/resources/META-INF/spring/database-context-osgi.xml
index 9bc5909..1cc64fb 100644
--- a/taverna-database-configuration-impl/src/main/resources/META-INF/spring/database-context-osgi.xml
+++ b/taverna-database-configuration-impl/src/main/resources/META-INF/spring/database-context-osgi.xml
@@ -9,8 +9,8 @@
<service ref="databaseConfiguration" interface="org.apache.taverna.configuration.database.DatabaseConfiguration" />
<service ref="databaseManager" interface="org.apache.taverna.configuration.database.DatabaseManager" />
- <reference id="configurationManager" interface="uk.org.taverna.configuration.ConfigurationManager" />
- <reference id="applicationConfiguration" interface="uk.org.taverna.configuration.app.ApplicationConfiguration" />
+ <reference id="configurationManager" interface="org.apache.taverna.configuration.ConfigurationManager" />
+ <reference id="applicationConfiguration" interface="org.apache.taverna.configuration.app.ApplicationConfiguration" />
<!-- <reference id="dataSourceFactory" interface="org.osgi.service.jdbc.DataSourceFactory"
filter="(osgi.jdbc.driver.class=org.apache.derby.jdbc.EmbeddedDriver)" /> -->
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/90125930/taverna-database-configuration-impl/src/main/resources/META-INF/spring/database-context.xml
----------------------------------------------------------------------
diff --git a/taverna-database-configuration-impl/src/main/resources/META-INF/spring/database-context.xml b/taverna-database-configuration-impl/src/main/resources/META-INF/spring/database-context.xml
index f397933..6d6bad0 100644
--- a/taverna-database-configuration-impl/src/main/resources/META-INF/spring/database-context.xml
+++ b/taverna-database-configuration-impl/src/main/resources/META-INF/spring/database-context.xml
@@ -5,12 +5,12 @@
http://www.springframework.org/schema/beans/spring-beans.xsd">
<bean id="databaseConfiguration"
- class="uk.org.taverna.configuration.database.impl.DatabaseConfigurationImpl">
+ class="org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl">
<constructor-arg name="configurationManager" ref="configurationManager" />
</bean>
<bean id="databaseManager"
- class="uk.org.taverna.configuration.database.impl.DatabaseManagerImpl">
+ class="org.apache.taverna.configuration.database.impl.DatabaseManagerImpl">
<constructor-arg name="applicationConfiguration" ref="applicationConfiguration" />
<constructor-arg name="databaseConfiguration">
<ref local="databaseConfiguration" />
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/90125930/taverna-execution-impl/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-execution-impl/pom.xml b/taverna-execution-impl/pom.xml
index 3c1f0e8..6041af6 100644
--- a/taverna-execution-impl/pom.xml
+++ b/taverna-execution-impl/pom.xml
@@ -16,7 +16,7 @@
<artifactId>maven-bundle-plugin</artifactId>
<configuration>
<instructions>
- <Import-Package>uk.org.taverna.platform.execution.api;provide:=true,*</Import-Package>
+ <Import-Package>org.apache.taverna.platform.execution.api;provide:=true,*</Import-Package>
</instructions>
</configuration>
</plugin>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/90125930/taverna-execution-local/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-execution-local/pom.xml b/taverna-execution-local/pom.xml
index 83eea60..66de313 100644
--- a/taverna-execution-local/pom.xml
+++ b/taverna-execution-local/pom.xml
@@ -16,7 +16,7 @@
<artifactId>maven-bundle-plugin</artifactId>
<configuration>
<instructions>
- <Import-Package>uk.org.taverna.platform.execution.api;provide:=true,*</Import-Package>
+ <Import-Package>org.apache.taverna.platform.execution.api;provide:=true,*</Import-Package>
</instructions>
</configuration>
</plugin>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/90125930/taverna-execution-local/src/main/resources/META-INF/spring/execution-local-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-execution-local/src/main/resources/META-INF/spring/execution-local-context-osgi.xml b/taverna-execution-local/src/main/resources/META-INF/spring/execution-local-context-osgi.xml
index 9ed6854..b1e5ea8 100644
--- a/taverna-execution-local/src/main/resources/META-INF/spring/execution-local-context-osgi.xml
+++ b/taverna-execution-local/src/main/resources/META-INF/spring/execution-local-context-osgi.xml
@@ -8,8 +8,8 @@
<service ref="localExecution">
<interfaces>
- <beans:value>uk.org.taverna.platform.execution.api.ExecutionService</beans:value>
- <beans:value>uk.org.taverna.platform.execution.api.WorkflowCompiler</beans:value>
+ <beans:value>org.apache.taverna.platform.execution.api.ExecutionService</beans:value>
+ <beans:value>org.apache.taverna.platform.execution.api.WorkflowCompiler</beans:value>
</interfaces>
<service-properties>
<beans:entry key="executor" value="TavernaEngine" />
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/90125930/taverna-execution-remote/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-execution-remote/pom.xml b/taverna-execution-remote/pom.xml
index 81e039e..e5fca8a 100644
--- a/taverna-execution-remote/pom.xml
+++ b/taverna-execution-remote/pom.xml
@@ -17,7 +17,7 @@
<artifactId>maven-bundle-plugin</artifactId>
<configuration>
<instructions>
- <Import-Package>uk.org.taverna.platform.execution.api;provide:=true,*</Import-Package>
+ <Import-Package>org.apache.taverna.platform.execution.api;provide:=true,*</Import-Package>
</instructions>
</configuration>
</plugin>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/90125930/taverna-run-impl/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-run-impl/pom.xml b/taverna-run-impl/pom.xml
index 80429a1..6620081 100644
--- a/taverna-run-impl/pom.xml
+++ b/taverna-run-impl/pom.xml
@@ -15,7 +15,7 @@
<artifactId>maven-bundle-plugin</artifactId>
<configuration>
<instructions>
- <Import-Package>uk.org.taverna.platform.run.api;provide:=true,*</Import-Package>
+ <Import-Package>org.apache.taverna.platform.run.api;provide:=true,*</Import-Package>
</instructions>
</configuration>
</plugin>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/90125930/taverna-services-impl/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-services-impl/pom.xml b/taverna-services-impl/pom.xml
index a588e4d..2086a63 100644
--- a/taverna-services-impl/pom.xml
+++ b/taverna-services-impl/pom.xml
@@ -15,7 +15,7 @@
<artifactId>maven-bundle-plugin</artifactId>
<configuration>
<instructions>
- <Import-Package>uk.org.taverna.commons.services;provide:=true,*</Import-Package>
+ <Import-Package>org.apache.taverna.services;provide:=true,*</Import-Package>
</instructions>
</configuration>
</plugin>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/90125930/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context-osgi.xml b/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context-osgi.xml
index 9bd2f75..8528a69 100644
--- a/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context-osgi.xml
+++ b/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context-osgi.xml
@@ -8,6 +8,6 @@
<service ref="serviceRegistry" interface="org.apache.taverna.services.ServiceRegistry" />
- <reference id="activityService" interface="uk.org.taverna.platform.capability.api.ActivityService" />
+ <reference id="activityService" interface="org.apache.taverna.platform.capability.api.ActivityService" />
</beans:beans>
[2/4] incubator-taverna-engine git commit: Attempt to update package
to org.apache.taverna
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/RunIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/RunIT.java b/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/RunIT.java
deleted file mode 100644
index e1f2edd..0000000
--- a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/RunIT.java
+++ /dev/null
@@ -1,1005 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform;
-
-import java.io.File;
-import java.net.URI;
-import 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 net.sf.taverna.t2.security.credentialmanager.UsernamePassword;
-
-import org.osgi.framework.ServiceReference;
-
-import org.apache.taverna.platform.data.api.Data;
-import org.apache.taverna.platform.data.api.DataService;
-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;
- private DataService dataService;
-
- protected void setup() throws Exception {
- super.setup();
- if (runService == null) {
- ServiceReference runServiceReference = bundleContext
- .getServiceReference("uk.org.taverna.platform.run.api.RunService");
- runService = (RunService) bundleContext.getService(runServiceReference);
- }
- if (dataService == null) {
- ServiceReference dataServiceReference = bundleContext
- .getServiceReference("uk.org.taverna.platform.data.DataService");
- dataService = (DataService) bundleContext.getService(dataServiceReference);
- }
- databaseConfiguration.setProvenanceEnabled(false);
- }
-
- public void testRun() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/in-out.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- inputs.put("in", dataService.create("test-input"));
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- assertNotNull(results);
- waitForResults(results, runService.getWorkflowReport(runId), "out");
-
- assertTrue(checkResult(results.get("out"), "test-input"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunApiConsumer() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/apiconsumer.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- inputs.put("in", dataService.create("test-input"));
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- assertNotNull(results);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"), "TEST-INPUT"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunBeanshell() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/beanshell.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- inputs.put("in", dataService.create("test-input"));
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- assertNotNull(results);
- waitForResults(results, report, "out");
-
- List<Data> result = results.get("out").getElements();
- assertEquals(1000, result.size());
- assertEquals("test-input:0", result.get(0).getValue());
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunBiomart() throws Exception {
- setup();
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/biomart.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- assertNotNull(results);
- waitForResults(results, report, "out");
-
- List<Data> result = results.get("out").getElements();
- assertEquals(5, result.size());
- assertEquals("ENSBTAG00000018854", result.get(0).getValue());
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- // public void testRunBiomoby() throws Exception {
- // setup();
- // WorkflowBundle workflowBundle = loadWorkflow("/t2flow/biomoby.t2flow");
- //
- // Set<ExecutionEnvironment> executionEnvironments = runService
- // .getExecutionEnvironments(workflowBundle);
- // for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- //
- //
- // String runId = runService.createRun(new RunProfile(executionEnvironment, workflowBundle));
- // assertEquals(State.CREATED, runService.getState(runId));
- //
- // WorkflowReport report = runService.getWorkflowReport(runId);
- // System.out.println(report);
- //
- // runService.start(runId);
- // assertTrue(runService.getState(runId).equals(State.RUNNING)
- // || runService.getState(runId).equals(State.COMPLETED));
- // System.out.println(report);
- //
- // Map<String, Data> results = runService.getOutputs(runId);
- // assertNotNull(results);
- // waitForResults(results, report, "out");
- //
- // T2Reference resultReference = results.get("out");
- // if (resultReference.containsErrors()) {
- // printErrors(referenceService, resultReference);
- // }
- // assertFalse(resultReference.containsErrors());
- // @SuppressWarnings("unchecked")
- // List<String> result = (List<String>) referenceService.renderIdentifier(resultReference,
- // String.class, null);
- // assertEquals(5, result.size());
- // assertEquals("ENSBTAG00000018854", result.get(0));
- // assertEquals(State.COMPLETED, runService.getState(runId));
- // System.out.println(report);
- // }
- // }
-
- public void testRunDataflow() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/dataflow.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- inputs.put("in", dataService.create("test input"));
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertFalse(runService.getState(runId).equals(State.CREATED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"),
- "nested dataflow : test input"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunLocalworker() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/localworker.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- inputs.put("in", dataService.create("Tom"));
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- assertNotNull(results);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"), "Hello Tom"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunRest() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/rest.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- Object outResult = results.get("out").getValue();
- if (outResult instanceof byte[]) {
- outResult = new String((byte[]) outResult);
- }
- assertTrue(outResult instanceof String);
- String outString = (String) outResult;
- assertTrue(outString.contains("<name>AATM_RABIT</name>"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunRestSecureBasic() throws Exception {
- setup();
- credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser",
- "testpasswd"), URI
- .create("http://heater.cs.man.ac.uk:7070/#Example+HTTP+BASIC+Authentication"));
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-basic-authentication.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"),
- "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n"
- + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n"
- + "<META http-equiv=Content-Type content=\"text/html\">\n"
- + "</HEAD>\n"
- + "<BODY>\n"
- + "<P>\n"
- + "<H3>Secure Apache Tomcat Examples</H3>\n"
- + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Basic Authentication.</P>\n"
- + "</BODY></HTML>"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunRestSecureBasicHttps() throws Exception {
- setup();
- credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser",
- "testpasswd"), URI
- .create("https://heater.cs.man.ac.uk:7443/#Example+HTTP+BASIC+Authentication"));
-
- URL trustedCertficateFileURL = getClass().getResource(
- "/security/tomcat_heater_certificate.pem");
- CertificateFactory certFactory = CertificateFactory.getInstance("X.509");
- X509Certificate trustedCertficate = (X509Certificate) certFactory
- .generateCertificate(trustedCertficateFileURL.openStream());
- credentialManager.addTrustedCertificate(trustedCertficate);
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-basic-authentication-https.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"),
- "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n"
- + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n"
- + "<META http-equiv=Content-Type content=\"text/html\">\n"
- + "</HEAD>\n"
- + "<BODY>\n"
- + "<P>\n"
- + "<H3>Secure Apache Tomcat Examples</H3>\n"
- + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Basic Authentication.</P>\n"
- + "</BODY></HTML>"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunRestSecureDigest() throws Exception {
- setup();
- credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser",
- "testpasswd"), URI
- .create("http://heater.cs.man.ac.uk:7070/#Example+HTTP+BASIC+Authentication"));
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-digest-authentication.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"),
- "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n"
- + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n"
- + "<META http-equiv=Content-Type content=\"text/html\">\n"
- + "</HEAD>\n"
- + "<BODY>\n"
- + "<P>\n"
- + "<H3>Secure Apache Tomcat Examples</H3>\n"
- + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Digest Authentication.</P>\n"
- + "</BODY></HTML>"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunRestSecureDigestHttps() throws Exception {
- setup();
- credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser",
- "testpasswd"), URI
- .create("http://heater.cs.man.ac.uk:7443/#Example+HTTP+BASIC+Authentication"));
-
- URL trustedCertficateFileURL = getClass().getResource(
- "/security/tomcat_heater_certificate.pem");
- CertificateFactory certFactory = CertificateFactory.getInstance("X.509");
- X509Certificate trustedCertficate = (X509Certificate) certFactory
- .generateCertificate(trustedCertficateFileURL.openStream());
- credentialManager.addTrustedCertificate(trustedCertficate);
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-digest-authentication-https.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"),
- "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n"
- + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n"
- + "<META http-equiv=Content-Type content=\"text/html\">\n"
- + "</HEAD>\n"
- + "<BODY>\n"
- + "<P>\n"
- + "<H3>Secure Apache Tomcat Examples</H3>\n"
- + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Digest Authentication.</P>\n"
- + "</BODY></HTML>"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunSpreadsheetImport() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/spreadsheetimport.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- List<Data> result = results.get("out").getElements();
- assertEquals(35, result.size());
- assertEquals("1971.0", result.get(1).getValue());
- assertEquals("2004.0", result.get(34).getValue());
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunSoaplab() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/soaplab.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "sequence");
-
- assertTrue(checkResult(results.get("sequence"),
- "ID X52524; SV 1; linear; genomic DNA; STD; INV; 4507 BP."));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunStringConstant() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/stringconstant.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- WorkflowReport report = runService.getWorkflowReport(runId);
- assertEquals(State.CREATED, runService.getState(runId));
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"), "Test Value"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- }
- }
-
- public void testRunTool() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/tool.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- WorkflowReport report = runService.getWorkflowReport(runId);
- assertEquals(State.CREATED, runService.getState(runId));
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"), "HelloWorld"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- }
- }
-
- public void testRunIteration() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/iteration.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- inputs.put("in", dataService.create("test"));
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
-
- waitForResults(results, report, "cross");
- List<Data> crossResult = results.get("cross").getElements();
- assertEquals(10, crossResult.size());
- assertEquals(10, crossResult.get(0).getElements().size());
- assertEquals(10, crossResult.get(5).getElements().size());
- assertEquals("test:0test:0", crossResult.get(0).getElements().get(0).getValue());
- assertEquals("test:0test:1", crossResult.get(0).getElements().get(1).getValue());
- assertEquals("test:4test:2", crossResult.get(4).getElements().get(2).getValue());
- assertEquals("test:7test:6", crossResult.get(7).getElements().get(6).getValue());
-
- waitForResults(results, report, "dot");
-
- List<Data> dotResult = results.get("dot").getElements();
- assertEquals(10, dotResult.size());
- assertEquals("test:0test:0", dotResult.get(0).getValue());
- assertEquals("test:5test:5", dotResult.get(5).getValue());
-
- waitForResults(results, report, "crossdot");
-
- List<Data> crossdotResult = results.get("crossdot").getElements();
- assertEquals(10, crossdotResult.size());
- assertEquals(10, crossdotResult.get(0).getElements().size());
- assertEquals(10, crossdotResult.get(5).getElements().size());
- assertEquals("test:0test:0test", crossdotResult.get(0).getElements().get(0).getValue());
- assertEquals("test:0test:1test", crossdotResult.get(0).getElements().get(1).getValue());
- assertEquals("test:4test:2test", crossdotResult.get(4).getElements().get(2).getValue());
- assertEquals("test:7test:6test", crossdotResult.get(7).getElements().get(6).getValue());
-
- waitForResults(results, report, "dotcross");
-
- List<Data> dotcrossResult = results.get("dotcross").getElements();
- assertEquals(10, dotResult.size());
- assertEquals("test:0test:0test", dotcrossResult.get(0).getValue());
- assertEquals("test:5test:5test", dotcrossResult.get(5).getValue());
-
- waitForResults(results, report, "dotdot");
-
- List<Data> dotdotResult = results.get("dotdot").getElements();
- assertEquals(10, dotResult.size());
- assertEquals("test:0test:0test:0", dotdotResult.get(0).getValue());
- assertEquals("test:5test:5test:5", dotdotResult.get(5).getValue());
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunWSDL() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/wsdl.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- // assertTrue(checkResult(results.get("out"),
- // "Apache Axis version: 1.4\nBuilt on Apr 22, 2006 (06:55:48 PDT)"));
- assertTrue(checkResult(results.get("out"),
- "Apache Axis version: 1.2\nBuilt on May 03, 2005 (02:20:24 EDT)"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunWSDLSecure() throws Exception {
- setup();
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl"));
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/wsdl-secure.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"), "Hello Alan!"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunWSDLSecureFull() throws Exception {
- setup();
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl"));
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-DigestPassword?wsdl"));
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-DigestPassword-Timestamp?wsdl"));
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword-Timestamp?wsdl"));
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-ws.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out_plaintext", "out_digest", "out_digest_timestamp",
- "out_plaintext_timestamp");
-
- assertTrue(checkResult(results.get("out_plaintext"), "Hello Alan!"));
- assertTrue(checkResult(results.get("out_digest"), "Hello Stian!"));
- assertTrue(checkResult(results.get("out_digest_timestamp"),
- "Hello David!"));
- assertTrue(checkResult(results.get("out_plaintext_timestamp"),
- "Hello Alex!"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunWSDLSecureSsh() throws Exception {
- setup();
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword?wsdl"));
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-DigestPassword?wsdl"));
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-DigestPassword-Timestamp?wsdl"));
- credentialManager
- .addUsernameAndPasswordForService(
- new UsernamePassword("testuser", "testpasswd"),
- URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword-Timestamp?wsdl"));
-
- URL trustedCertficateFileURL = getClass().getResource(
- "/security/tomcat_heater_certificate.pem");
- CertificateFactory certFactory = CertificateFactory.getInstance("X.509");
- X509Certificate trustedCertficate = (X509Certificate) certFactory
- .generateCertificate(trustedCertficateFileURL.openStream());
- credentialManager.addTrustedCertificate(trustedCertficate);
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-ws-https.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertEquals(State.RUNNING, runService.getState(runId));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out_plaintext", "out_digest", "out_digest_timestamp",
- "out_plaintext_timestamp");
-
- assertTrue(checkResult(results.get("out_plaintext"), "Hello Alan!"));
- assertTrue(checkResult(results.get("out_digest"), "Hello Stian!"));
- assertTrue(checkResult(results.get("out_digest_timestamp"),
- "Hello David!"));
- assertTrue(checkResult(results.get("out_plaintext_timestamp"),
- "Hello Alex!"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunXMLSplitter() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/xmlSplitter.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- inputs.put("firstName", dataService.create("John"));
- inputs.put("lastName", dataService.create("Smith"));
- inputs.put("age", dataService.create("21"));
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"),
- "John Smith (21) of 40, Oxford Road. Manchester."));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunXPath() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/xpath.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- String runId = runService
- .createRun(new RunProfile(executionEnvironment, workflowBundle));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- waitForResults(results, report, "out");
-
- assertTrue(checkResult(results.get("out"),
- "<test-element>test</test-element>"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
- public void testRunFromFile() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/in-out.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = runService
- .getExecutionEnvironments(workflowBundle);
- assertTrue(executionEnvironments.size() > 0);
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = new HashMap<String, Data>();
- File file = loadFile("/t2flow/input.txt");
- Data data = dataService.create(file.toURI());
- assertTrue(data.isReference());
- inputs.put("in", data);
-
- String runId = runService.createRun(new RunProfile(executionEnvironment,
- workflowBundle, inputs));
- assertEquals(State.CREATED, runService.getState(runId));
-
- WorkflowReport report = runService.getWorkflowReport(runId);
- System.out.println(report);
-
- runService.start(runId);
- assertTrue(runService.getState(runId).equals(State.RUNNING)
- || runService.getState(runId).equals(State.COMPLETED));
- System.out.println(report);
-
- Map<String, Data> results = runService.getOutputs(runId);
- assertNotNull(results);
- waitForResults(results, runService.getWorkflowReport(runId), "out");
-
- assertTrue(checkResult(results.get("out"), "test input value"));
-
- assertEquals(State.COMPLETED, runService.getState(runId));
- System.out.println(report);
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/RunParallelIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/RunParallelIT.java b/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/RunParallelIT.java
deleted file mode 100644
index f38ad26..0000000
--- a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/RunParallelIT.java
+++ /dev/null
@@ -1,95 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform;
-
-import java.net.URI;
-import java.util.HashSet;
-import java.util.Set;
-
-import net.sf.taverna.t2.security.credentialmanager.UsernamePassword;
-
-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("uk.org.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/50373179/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/RunWorkflowsIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/RunWorkflowsIT.java b/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/RunWorkflowsIT.java
deleted file mode 100644
index 7eef935..0000000
--- a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/RunWorkflowsIT.java
+++ /dev/null
@@ -1,135 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform;
-
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.osgi.framework.ServiceReference;
-
-import org.apache.taverna.platform.data.api.Data;
-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("uk.org.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);
- }
- }
-
-}
[4/4] incubator-taverna-engine git commit: Attempt to update package
to org.apache.taverna
Posted by st...@apache.org.
Attempt to update package to org.apache.taverna
.. but won't really combine because of error in spring dependency?
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/commit/50373179
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/tree/50373179
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/diff/50373179
Branch: refs/heads/master
Commit: 50373179a0ab245d08d94b3dc9e6b0c2ad738315
Parents: 9012593
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Oct 18 19:12:38 2015 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Oct 18 19:12:38 2015 +0100
----------------------------------------------------------------------
.../org/apache/taverna/platform/ActivityIT.java | 68 ++
.../taverna/platform/CommandLineToolIT.java | 88 ++
.../apache/taverna/platform/ExecutionIT.java | 128 +++
.../taverna/platform/LocalExecutionIT.java | 117 ++
.../taverna/platform/OSGIFrameworkIT.java | 92 ++
.../org/apache/taverna/platform/PlatformIT.java | 375 +++++++
.../java/org/apache/taverna/platform/RunIT.java | 1000 +++++++++++++++++
.../apache/taverna/platform/RunParallelIT.java | 93 ++
.../apache/taverna/platform/RunWorkflowsIT.java | 134 +++
.../uk/org/taverna/platform/ActivityIT.java | 72 --
.../org/taverna/platform/CommandLineToolIT.java | 91 --
.../uk/org/taverna/platform/ExecutionIT.java | 134 ---
.../org/taverna/platform/LocalExecutionIT.java | 120 ---
.../org/taverna/platform/OSGIFrameworkIT.java | 93 --
.../uk/org/taverna/platform/PlatformIT.java | 378 -------
.../java/uk/org/taverna/platform/RunIT.java | 1005 ------------------
.../uk/org/taverna/platform/RunParallelIT.java | 95 --
.../uk/org/taverna/platform/RunWorkflowsIT.java | 135 ---
18 files changed, 2095 insertions(+), 2123 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ActivityIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ActivityIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ActivityIT.java
new file mode 100644
index 0000000..ec5e483
--- /dev/null
+++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ActivityIT.java
@@ -0,0 +1,68 @@
+/*******************************************************************************
+ * Copyright (C) 2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package org.apache.taverna.platform;
+
+import java.net.URI;
+import java.util.List;
+
+import org.apache.taverna.platform.capability.api.ActivityConfigurationException;
+import org.apache.taverna.platform.capability.api.ActivityNotFoundException;
+import org.osgi.framework.ServiceReference;
+
+
+public class ActivityIT extends PlatformIT {
+
+ public void testGetActivityURIs() {
+ ServiceReference activityServiceReference = bundleContext.getServiceReference("org.apache.taverna.platform.capability.api.ActivityService");
+ ActivityService activityService = (ActivityService) bundleContext.getService(activityServiceReference);
+ List<URI> activityURIs = activityService.getActivityURIs();
+ System.out.println("================= Available Activities ===================");
+ for (URI uri : activityURIs) {
+ System.out.println(uri);
+ }
+ System.out.println("==========================================================");
+ System.out.println("");
+ }
+
+ public void testCreateActivity() throws ActivityNotFoundException, ActivityConfigurationException {
+ ServiceReference activityServiceReference = bundleContext.getServiceReference("org.apache.taverna.platform.capability.api.ActivityService");
+ ActivityService activityService = (ActivityService) bundleContext.getService(activityServiceReference);
+ List<URI> activityURIs = activityService.getActivityURIs();
+ for (URI uri : activityURIs) {
+ System.out.println("Creating activity " + uri);
+ Activity<?> activity = activityService.createActivity(uri, null);
+ }
+ }
+
+ public void testGetActivityConfigurationDefinition() throws Exception {
+ ServiceReference activityServiceReference = bundleContext.getServiceReference("org.apache.taverna.platform.capability.api.ActivityService");
+ ActivityService activityService = (ActivityService) bundleContext.getService(activityServiceReference);
+
+ List<URI> activityURIs = activityService.getActivityURIs();
+ System.out.println("============ Activity Configuration Definitions ==========");
+ for (URI uri : activityURIs) {
+ ConfigurationDefinition configurationDefinition = activityService.getActivityConfigurationDefinition(uri);
+ System.out.println(configurationDefinition);
+ }
+ System.out.println("==========================================================");
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/CommandLineToolIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/CommandLineToolIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/CommandLineToolIT.java
new file mode 100644
index 0000000..f42cb77
--- /dev/null
+++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/CommandLineToolIT.java
@@ -0,0 +1,88 @@
+/*******************************************************************************
+ * Copyright (C) 2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package org.apache.taverna.platform;
+
+import org.osgi.framework.ServiceReference;
+
+import org.apache.taverna.platform.run.api.RunService;
+import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
+import org.apache.taverna.scufl2.api.io.WorkflowBundleReader;
+
+public class CommandLineToolIT extends PlatformIT {
+
+ private RunService runService;
+ private WorkflowBundleIO workflowBundleIO;
+ private WorkflowBundleReader workflowReader;
+
+ protected void setup() throws Exception {
+ super.setup();
+ if (runService == null) {
+ ServiceReference runServiceReference = bundleContext
+ .getServiceReference("org.apache.taverna.platform.run.api.RunService");
+ runService = (RunService) bundleContext.getService(runServiceReference);
+ }
+
+ if (workflowReader == null) {
+ ServiceReference workflowBundleReaderServiceReference = bundleContext
+ .getServiceReferences("org.apache.taverna.scufl2.api.io.WorkflowBundleReader",
+ "(mediaType=application/vnd.taverna.t2flow+xml)")[0];
+ workflowBundleReader = (WorkflowBundleReader) bundleContext
+ .getService(workflowBundleReaderServiceReference);
+ }
+
+ if (workflowBundleIO == null) {
+ ServiceReference workflowBundleIOServiceReference = bundleContext
+ .getServiceReference("org.apache.taverna.scufl2.api.io.WorkflowBundleIO");
+ workflowBundleIO = (WorkflowBundleIO) bundleContext
+ .getService(workflowBundleIOServiceReference);
+ }
+ }
+
+ public void testCommandLineTool() throws Exception {
+
+ setup();
+
+ CommandLineTool cmdTool = new CommandLineTool();
+ cmdTool.setRunService(runService);
+ cmdTool.setCredentialManager(credentialManager);
+ cmdTool.setWorkflowBundleIO(workflowBundleIO);
+ cmdTool.setCommandLineArgumentsService(new CommandLineArguments() {
+ public String[] getCommandLineArguments() {
+ return new String[] { "-outputdoc", "/tmp/taverna3/baclava-output1.xml",
+ "/Users/alex/Desktop/t2flows/simple-wf-no-inputs-one-output.t2flow" };
+ }
+
+ });
+ cmdTool.run();
+
+ cmdTool.setCommandLineArgumentsService(new CommandLineArguments() {
+ public String[] getCommandLineArguments() {
+ return new String[] { "-inputvalue", "in", "Taverna 3 Platform rules",
+ "-outputdoc", "/tmp/taverna3/baclava-output2.xml",
+ "/Users/alex/Desktop/t2flows/simple-wf-one-input-one-output.t2flow" };
+ }
+
+ });
+ cmdTool.run();
+
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ExecutionIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ExecutionIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ExecutionIT.java
new file mode 100644
index 0000000..d28ac5d
--- /dev/null
+++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/ExecutionIT.java
@@ -0,0 +1,128 @@
+/*******************************************************************************
+ * Copyright (C) 2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package org.apache.taverna.platform;
+
+import java.net.URI;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.osgi.framework.ServiceReference;
+
+import org.apache.taverna.platform.execution.api.AbstractExecutionEnvironment;
+import org.apache.taverna.platform.execution.api.AbstractExecutionService;
+import org.apache.taverna.platform.execution.api.Execution;
+import org.apache.taverna.platform.execution.api.ExecutionEnvironment;
+import org.apache.taverna.platform.execution.api.ExecutionEnvironmentService;
+import org.apache.taverna.platform.execution.api.InvalidWorkflowException;
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+import org.apache.taverna.scufl2.api.core.Workflow;
+import org.apache.taverna.scufl2.api.profiles.Profile;
+
+public class ExecutionIT extends PlatformIT {
+
+ private ExecutionEnvironmentService executionEnvironmentService;
+
+ protected void setup() throws Exception {
+ super.setup();
+ ServiceReference[] executionServiceReferences = bundleContext.getServiceReferences(
+ "org.apache.taverna.platform.execution.api.ExecutionEnvironmentService", null);
+ assertEquals(1, executionServiceReferences.length);
+ executionEnvironmentService = (ExecutionEnvironmentService) bundleContext
+ .getService(executionServiceReferences[0]);
+
+ }
+
+ public void testGetExecutionEnvironments() throws Exception {
+ setup();
+
+ Set<ExecutionEnvironment> executionEnvironments = executionEnvironmentService
+ .getExecutionEnvironments();
+ int size = executionEnvironments.size();
+
+ bundleContext.registerService("org.apache.taverna.platform.execution.api.ExecutionService",
+ new AbstractExecutionService("test id", "test name", "test description") {
+ public Set<ExecutionEnvironment> getExecutionEnvivonments() {
+ return Collections
+ .<ExecutionEnvironment> singleton(new AbstractExecutionEnvironment(
+ "test id", "test name", "test description", this) {
+ public List<URI> getDispatchLayerURIs() {
+ return Collections.singletonList(URI
+ .create("http://ns.taverna.org.uk/2010/dispatchlayer/testDispatchLayer"));
+ }
+
+ public List<URI> getActivityURIs() {
+ return Collections.singletonList(URI
+ .create("http://ns.taverna.org.uk/2010/activity/testActivity"));
+ }
+
+ public boolean dispatchLayerExists(URI uri) {
+ return false;
+ }
+
+ public boolean activityExists(URI uri) {
+ return false;
+ }
+
+ public ConfigurationDefinition getActivityConfigurationDefinition(
+ URI uri) throws ActivityNotFoundException,
+ ActivityConfigurationException {
+ return null;
+ }
+
+ public ConfigurationDefinition getDispatchLayerConfigurationDefinition(
+ URI uri) throws DispatchLayerNotFoundException,
+ DispatchLayerConfigurationException {
+ return null;
+ }
+ });
+ }
+
+ protected Execution createExecutionImpl(WorkflowBundle workflowBundle,
+ Workflow workflow, Profile profile, Map<String, Data> inputs) throws InvalidWorkflowException {
+ return null;
+ }
+ }, null);
+
+
+ executionEnvironments = executionEnvironmentService
+ .getExecutionEnvironments();
+ assertEquals(size + 1, executionEnvironments.size());
+
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ System.out.println(executionEnvironment);
+ }
+ }
+
+ public void testGetExecutionEnvironmentsProfile() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/beanshell.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = executionEnvironmentService
+ .getExecutionEnvironments(workflowBundle.getMainProfile());
+ assertTrue(executionEnvironments.size() > 0);
+
+ System.out.println(executionEnvironments.iterator().next());
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/LocalExecutionIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/LocalExecutionIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/LocalExecutionIT.java
new file mode 100644
index 0000000..431aa88
--- /dev/null
+++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/LocalExecutionIT.java
@@ -0,0 +1,117 @@
+/*******************************************************************************
+ * Copyright (C) 2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package org.apache.taverna.platform;
+
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.osgi.framework.ServiceReference;
+
+import org.apache.taverna.platform.execution.api.ExecutionEnvironment;
+import org.apache.taverna.platform.execution.api.ExecutionService;
+import org.apache.taverna.platform.report.State;
+import org.apache.taverna.platform.report.WorkflowReport;
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+import org.apache.taverna.scufl2.api.core.Workflow;
+import org.apache.taverna.scufl2.api.profiles.Profile;
+
+public class LocalExecutionIT extends PlatformIT {
+
+ private ExecutionService executionService;
+ private Set<ExecutionEnvironment> executionEnvironments;
+
+ protected void setup() throws Exception {
+ super.setup();
+ if (executionService == null) {
+ ServiceReference[] executionServiceReferences = bundleContext.getServiceReferences(
+ "org.apache.taverna.platform.execution.api.ExecutionService",
+ "(org.springframework.osgi.bean.name=localExecution)");
+ assertEquals(1, executionServiceReferences.length);
+ executionService = (ExecutionService) bundleContext
+ .getService(executionServiceReferences[0]);
+ executionEnvironments = executionService.getExecutionEnvivonments();
+ assertEquals(1, executionEnvironments.size());
+ }
+ if (dataService == null) {
+ ServiceReference dataServiceReference = bundleContext
+ .getServiceReference("org.apache.taverna.platform.data.DataService");
+ dataService = (DataService) bundleContext.getService(dataServiceReference);
+ }
+ }
+
+ public void testLocalExecution() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/in-out.t2flow");
+ Workflow workflow = workflowBundle.getMainWorkflow();
+ Profile profile = workflowBundle.getMainProfile();
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ Map<String, Data> inputs = Collections.singletonMap("in", dataService.create("test-input"));
+
+ String executionId = executionService.createExecution(executionEnvironment,
+ workflowBundle, workflow, profile, inputs);
+ WorkflowReport report = executionService.getWorkflowReport(executionId);
+ assertEquals(State.CREATED, report.getState());
+ executionService.start(executionId);
+
+ Map<String, Data> results = report.getOutputs();
+ assertNotNull(results);
+ waitForResults(results, report, "out");
+
+ Object result = results.get("out").getValue();
+ assertEquals("test-input", result);
+ assertEquals(State.COMPLETED, report.getState());
+ System.out.println(report);
+ }
+ }
+
+ public void testLocalExecution2() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/beanshell.t2flow");
+ Workflow workflow = workflowBundle.getMainWorkflow();
+ Profile profile = workflowBundle.getMainProfile();
+
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ Map<String, Data> inputs = Collections.singletonMap("in", dataService.create("test-input"));
+
+ String executionId = executionService.createExecution(executionEnvironment,
+ workflowBundle, workflow, profile, inputs);
+ WorkflowReport report = executionService.getWorkflowReport(executionId);
+ System.out.println(report);
+ assertEquals(State.CREATED, report.getState());
+ executionService.start(executionId);
+ System.out.println(report);
+
+ Map<String, Data> results = report.getOutputs();
+ waitForResults(results, report, "out");
+
+ List<Data> result = results.get("out").getElements();
+ assertEquals(1000, result.size());
+ assertEquals("test-input:0", result.get(0).getValue());
+ assertEquals(State.COMPLETED, report.getState());
+ System.out.println(report);
+ }
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/OSGIFrameworkIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/OSGIFrameworkIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/OSGIFrameworkIT.java
new file mode 100644
index 0000000..b73b1ed
--- /dev/null
+++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/OSGIFrameworkIT.java
@@ -0,0 +1,92 @@
+/*******************************************************************************
+ * Copyright (C) 2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package org.apache.taverna.platform;
+
+import java.io.IOException;
+
+import org.osgi.framework.Bundle;
+import org.springframework.osgi.util.OsgiStringUtils;
+
+public class OSGIFrameworkIT extends PlatformIT {
+
+ public void testOsgiEnvironment() throws Exception {
+ Bundle[] bundles = bundleContext.getBundles();
+ for (int i = 0; i < bundles.length; i++) {
+ System.out.println(OsgiStringUtils.nullSafeName(bundles[i]));
+ }
+ System.out.println();
+ }
+
+ protected String[] getTestFrameworkBundlesNames() {
+ String[] frameworkBundles = super.getTestFrameworkBundlesNames();
+ System.out.println("Test Framework bundles:");
+ for (String bundle : frameworkBundles) {
+ System.out.println(" " + bundle);
+ }
+ return frameworkBundles;
+ }
+
+ protected String[] getTestBundlesNames() {
+ String[] frameworkBundles = super.getTestBundlesNames();
+ System.out.println("Framework bundles:");
+ for (String bundle : frameworkBundles) {
+ System.out.println(" " + bundle);
+ }
+ return frameworkBundles;
+ }
+
+ public void testPrintConfig() throws IOException {
+ Resource[] bundles = getTestBundles();
+ Resource[] testBundles = getTestFrameworkBundles();
+ StringBuilder sb = new StringBuilder();
+ StringBuilder sb2 = new StringBuilder();
+ System.out.println("mkdir platform");
+ System.out.println("mkdir platform/configuration");
+ sb2.append("cp ");
+ sb.append("osgi.bundles=");
+ boolean printComma = false;
+ for (Resource resource : bundles) {
+ if (printComma) {
+ sb.append(", ");
+ sb2.append(" ");
+ }
+ sb.append(resource.getFilename() + "@start");
+ sb2.append(resource.getFile());
+ printComma = true;
+ }
+ for (Resource resource : testBundles) {
+ if (!resource.getFilename().contains("test")) {
+ if (printComma) {
+ sb.append(", ");
+ sb2.append(" ");
+ }
+ sb.append(resource.getFilename() + "@start");
+ sb2.append(resource.getFile());
+ printComma = true;
+ }
+ }
+ sb2.append(" platform");
+ System.out.println("echo \"" + sb.toString() + "\" > platform/configuration/config.ini");
+ System.out.println(sb2.toString());
+ System.out.println("zip platform.zip platform/*");
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/PlatformIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/PlatformIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/PlatformIT.java
new file mode 100644
index 0000000..822f5f2
--- /dev/null
+++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/PlatformIT.java
@@ -0,0 +1,375 @@
+/*******************************************************************************
+ * Copyright (C) 2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package org.apache.taverna.platform;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.net.URL;
+import java.util.Map;
+import java.util.Properties;
+
+
+import org.eclipse.osgi.framework.internal.core.Constants;
+import org.osgi.framework.ServiceReference;
+import org.osgi.service.jndi.JNDIContextManager;
+import org.springframework.osgi.test.AbstractConfigurableBundleCreatorTests;
+import org.springframework.osgi.test.platform.OsgiPlatform;
+import org.springframework.osgi.test.platform.Platforms;
+
+import org.apache.taverna.configuration.app.ApplicationConfiguration;
+import org.apache.taverna.configuration.database.DatabaseConfiguration;
+import org.apache.taverna.platform.report.State;
+import org.apache.taverna.platform.report.WorkflowReport;
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+import org.apache.taverna.scufl2.api.io.WorkflowBundleReader;
+import org.apache.taverna.scufl2.translator.t2flow.T2FlowReader;
+import org.apache.taverna.security.credentialmanager.CredentialManager;
+import org.apache.taverna.security.credentialmanager.MasterPasswordProvider;
+
+public class PlatformIT extends AbstractConfigurableBundleCreatorTests {
+
+ protected WorkflowBundleReader workflowBundleReader;
+ protected CredentialManager credentialManager;
+ protected MasterPasswordProvider masterPasswordProvider;
+ protected DatabaseConfiguration databaseConfiguration;
+ protected JNDIContextManager jndiContextManager;
+ protected ApplicationConfiguration applicationConfiguration;
+
+ protected String getPlatformName() {
+ // return Platforms.FELIX;
+ return Platforms.EQUINOX;
+ }
+
+ @Override
+ protected OsgiPlatform createPlatform() {
+ OsgiPlatform platform = super.createPlatform();
+ Properties config = platform.getConfigurationProperties();
+ config.setProperty("org.osgi.framework.system.packages.extra",
+ "com.sun.org.apache.xml.internal.utils");
+ return platform;
+ }
+
+ @Override
+ protected String[] getTestBundlesNames() {
+ return new String[] {
+ "com.jcraft.jsch, com.springsource.com.jcraft.jsch, 0.1.41",
+ "com.sun.xml, com.springsource.com.sun.xml.bind, 2.2.0",
+ "com.sun.xml, com.springsource.com.sun.xml.fastinfoset, 1.2.2",
+ "com.thoughtworks.xstream, com.springsource.com.thoughtworks.xstream, 1.2.2",
+ "commons-dbcp, commons-dbcp, 1.4",
+ "commons-pool, commons-pool, 1.5.6",
+ "javax.activation, com.springsource.javax.activation, 1.1.1",
+ "javax.jms, com.springsource.javax.jms, 1.1.0",
+ "javax.mail, com.springsource.javax.mail, 1.4.0",
+ "javax.servlet, com.springsource.javax.servlet, 2.5.0",
+ "javax.transaction, com.springsource.javax.transaction, 1.1.0",// for derby client
+ "javax.wsdl, com.springsource.javax.wsdl, 1.6.1",
+ "javax.xml.bind, com.springsource.javax.xml.bind, 2.2.0",
+ "javax.xml.rpc, com.springsource.javax.xml.rpc, 1.1.0",
+ "javax.xml.soap, com.springsource.javax.xml.soap, 1.3.0",
+ "javax.xml.stream, com.springsource.javax.xml.stream, 1.0.1",
+ "org.antlr, com.springsource.antlr, 2.7.6",
+ "org.apache.aries, org.apache.aries.util, 0.3",
+ "org.apache.aries.proxy, org.apache.aries.proxy.api, 0.3",
+ "org.apache.aries.jndi, org.apache.aries.jndi, 0.3",
+ "org.apache.axis, com.springsource.org.apache.axis, 1.4.0",
+ "org.apache.commons, com.springsource.org.apache.commons.cli, 1.2.0",
+ "org.apache.commons, com.springsource.org.apache.commons.codec, 1.4.0",
+ "org.apache.commons, com.springsource.org.apache.commons.csv, 1.0.0.BUILD-20080106",
+ "org.apache.commons, com.springsource.org.apache.commons.collections, 3.2.0",
+ "org.apache.commons, com.springsource.org.apache.commons.discovery, 0.4.0",
+ "org.apache.commons, com.springsource.org.apache.commons.httpclient, 3.1.0",
+ "org.apache.commons, com.springsource.org.apache.commons.io, 1.4.0",
+ "org.apache.commons, com.springsource.org.apache.commons.lang, 2.5.0",
+ "org.apache.commons, com.springsource.org.apache.commons.logging, 1.1.1",
+ "org.apache.commons, com.springsource.org.apache.commons.net, 1.4.1",
+ // "org.apache.derby, derby, 10.5.3.0_1",
+ "org.apache.derby, com.springsource.org.apache.derby, 10.5.1000001.764942",
+ "org.apache.derby, com.springsource.org.apache.derby.client, 10.5.1000001.764942",
+ "org.apache.derby, com.springsource.org.apache.derby.drda, 10.5.1000001.764942",
+ "org.apache.httpcomponents, com.springsource.org.apache.httpcomponents.httpclient, 4.1.1",
+ "org.apache.httpcore, com.springsource.org.apache.httpcomponents.httpcore, 4.1",
+ "org.apache.log4j, com.springsource.org.apache.log4j, 1.2.16",
+ "org.apache.ws, com.springsource.org.apache.ws.security, 1.5.8",
+ // "org.apache.ws.security, wss4j, 1.5.12",
+ "org.apache.xml, com.springsource.org.apache.xml.resolver, 1.2.0",
+ "org.apache.xmlbeans, com.springsource.org.apache.xmlbeans, 2.4.0",
+ "org.apache.xmlcommons, com.springsource.org.apache.xmlcommons, 1.3.4",
+ "org.apache.xalan, com.springsource.org.apache.xalan, 2.7.1",
+ "org.apache.xalan, com.springsource.org.apache.xml.serializer, 2.7.1",
+ "org.apache.xerces, com.springsource.org.apache.xerces, 2.9.1",
+ "org.apache.xml, com.springsource.org.apache.xml.security, 1.4.2",
+ "org.aspectj, com.springsource.org.aspectj.runtime, 1.6.0",
+ "org.aspectj, com.springsource.org.aspectj.weaver, 1.6.0",
+ "org.beanshell, com.springsource.bsh, 2.0.0.b4",
+ "org.biomart, martservice, 2.0-SNAPSHOT",
+ "org.bouncycastle, bcprov-jdk16, 1.46",
+ "org.dom4j, com.springsource.org.dom4j, 1.6.1",
+ "org.hibernate, com.springsource.org.hibernate, 3.2.6.ga",
+ "org.jaxen, com.springsource.org.jaxen, 1.1.1",
+ "org.jboss.javassist, com.springsource.javassist, 3.3.0.ga",
+ "org.jdom, com.springsource.org.jdom, 1.1.0",
+ "org.jvnet.staxex, com.springsource.org.jvnet.staxex, 1.0.0",
+ "org.objectweb.asm, com.springsource.org.objectweb.asm, 1.5.3",
+ "org.objectweb.asm, com.springsource.org.objectweb.asm.attrs, 1.5.3",
+ "org.opensaml, com.springsource.org.opensaml, 1.1.0",
+ "org.springframework, org.springframework.jdbc, 3.0.0.RC1",
+ "org.springframework, org.springframework.orm, 3.0.0.RC1",
+ "org.springframework, org.springframework.transaction, 3.0.0.RC1",
+ // "org.springframework, org.springframework.beans, 3.0.5.RELEASE",
+ // "org.springframework, org.springframework.core, 3.0.5.RELEASE",
+ // "org.springframework, org.springframework.context, 3.0.5.RELEASE",
+ // "org.springframework, org.springframework.transaction, 3.0.5.RELEASE",
+ "org.xmlpull, com.springsource.org.xmlpull, 1.1.3.4-O",
+ "net.sf.taverna, wsdl-generic, 1.10-SNAPSHOT",
+ "net.sf.taverna.jedit, jedit-syntax, 2.2.4-SNAPSHOT",
+ "net.sf.taverna.t2.activities, apiconsumer-activity, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.activities, beanshell-activity, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.activities, biomart-activity, 2.0-SNAPSHOT",
+ // "net.sf.taverna.t2.activities, biomoby-activity, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.activities, dataflow-activity, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.activities, dependency-activity, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.activities, external-tool-activity, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.activities, localworker-activity, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.activities, rest-activity, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.activities, rshell-activity, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.activities, soaplab-activity, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.activities, spreadsheet-import-activity, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.activities, stringconstant-activity, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.activities, wsdl-activity, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.activities, xpath-activity, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.core, provenance-derby, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.core, provenance-mysql, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.core, provenanceconnector, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.core, reference-api, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.core, reference-core-extensions, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.core, reference-impl, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.core, workflowmodel-api, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.core, workflowmodel-core-extensions, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.core, workflowmodel-impl, 2.0-SNAPSHOT",
+ // "net.sf.taverna.t2.infrastructure, appconfig, 3.0-SNAPSHOT",
+ "net.sf.taverna.t2.lang, ui, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.lang, observer, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.security, credential-manager, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2.security, credential-manager-impl, 2.0-SNAPSHOT",
+ "net.sourceforge.cglib, com.springsource.net.sf.cglib, 2.1.3",
+ "uk.org.taverna.configuration, taverna-app-configuration-api, 0.1.0-SNAPSHOT",
+ "uk.org.taverna.configuration, taverna-app-configuration-impl, 0.1.0-SNAPSHOT",
+ "uk.org.taverna.configuration, taverna-configuration-api, 0.1.0-SNAPSHOT",
+ "uk.org.taverna.configuration, taverna-configuration-impl, 0.1.0-SNAPSHOT",
+ "uk.org.taverna.configuration, taverna-database-configuration-api, 0.1.0-SNAPSHOT",
+ "uk.org.taverna.configuration, taverna-database-configuration-impl, 0.1.0-SNAPSHOT",
+ "org.apache.taverna.platform, report, 0.1.2-SNAPSHOT",
+ "org.apache.taverna.platform, data, 0.1.2-SNAPSHOT",
+ "org.apache.taverna.platform, execution-local, 0.1.2-SNAPSHOT",
+ "org.apache.taverna.platform, execution-remote, 0.1.2-SNAPSHOT",
+ "org.apache.taverna.platform, taverna-capability-api, 0.1.2-SNAPSHOT",
+ "org.apache.taverna.platform, taverna-capability-impl, 0.1.2-SNAPSHOT",
+ "org.apache.taverna.platform, taverna-execution-api, 0.1.2-SNAPSHOT",
+ "org.apache.taverna.platform, taverna-execution-impl, 0.1.2-SNAPSHOT",
+ "org.apache.taverna.platform, taverna-run-api, 0.1.2-SNAPSHOT",
+ "org.apache.taverna.platform, taverna-run-impl, 0.1.2-SNAPSHOT",
+ "uk.org.taverna.osgi.services, xml-parser-service, 0.0.1-SNAPSHOT",
+ "uk.org.taverna.osgi.services, xml-transformer-service, 0.0.1-SNAPSHOT",
+ // FIXME: Add the other scufl2 modules
+ "org.apache.taverna.scufl2, scufl2-api, 0.9.2",
+ "org.apache.taverna.scufl2, scufl2-rdfxml, 0.9.2",
+ "org.apache.taverna.scufl2, scufl2-ucfpackage, 0.9.2",
+ "org.apache.taverna.scufl2, scufl2-t2flow, 0.9.2",
+ "org.apache.taverna.scufl2, scufl2-validation, 0.9.2",
+ "org.apache.taverna.scufl2, scufl2-validation-correctness, 0.9.2",
+ "org.apache.taverna.scufl2, scufl2-validation-structural, 0.9.2",
+ "net.sf.taverna.t2, results, 2.0-SNAPSHOT",
+ "net.sf.taverna.t2, baclava, 0.1-SNAPSHOT",
+ // "net.sf.taverna.t2.taverna-commandline, taverna-commandline-common, 2.0-SNAPSHOT"
+ };
+ }
+
+ protected void setup() throws Exception {
+
+ if (masterPasswordProvider == null) {
+ masterPasswordProvider = new MasterPasswordProvider() {
+ public String getMasterPassword(boolean firstTime) {
+ return "test";
+ }
+
+ public void setMasterPassword(String password) {
+ }
+
+ public int getProviderPriority() {
+ return 0;
+ }
+ };
+ bundleContext.registerService(
+ "net.sf.taverna.t2.security.credentialmanager.MasterPasswordProvider",
+ masterPasswordProvider, null);
+ }
+
+ if (credentialManager == null) {
+ ServiceReference credentialManagerReference = bundleContext
+ .getServiceReference("net.sf.taverna.t2.security.credentialmanager.CredentialManager");
+ credentialManager = (CredentialManager) bundleContext
+ .getService(credentialManagerReference);
+ }
+
+ if (workflowBundleReader == null) {
+ ServiceReference[] workflowBundleReaderReferences = bundleContext.getServiceReferences(
+ "org.apache.taverna.scufl2.api.io.WorkflowBundleReader", null);
+ for (ServiceReference serviceReference : workflowBundleReaderReferences) {
+ workflowBundleReader = (WorkflowBundleReader) bundleContext
+ .getService(serviceReference);
+ if (workflowBundleReader.getMediaTypes().contains(
+ T2FlowReader.APPLICATION_VND_TAVERNA_T2FLOW_XML)) {
+ break;
+ }
+ }
+ }
+
+ if (databaseConfiguration == null) {
+ ServiceReference databaseConfigurationReference = bundleContext
+ .getServiceReference("uk.org.taverna.configuration.database.DatabaseConfiguration");
+ databaseConfiguration = (DatabaseConfiguration) bundleContext
+ .getService(databaseConfigurationReference);
+ ServiceReference jndiContextManagerReference = bundleContext
+ .getServiceReference("org.osgi.service.jndi.JNDIContextManager");
+ jndiContextManager = (JNDIContextManager) bundleContext
+ .getService(jndiContextManagerReference);
+ ServiceReference applicationConfigurationReference = bundleContext
+ .getServiceReference("uk.org.taverna.configuration.app.ApplicationConfiguration");
+ applicationConfiguration = (ApplicationConfiguration) bundleContext
+ .getService(applicationConfigurationReference);
+ }
+
+ }
+
+ public void testOsgiPlatformStarts() throws Exception {
+ System.out.println(Constants.FRAMEWORK_VENDOR + " = "
+ + bundleContext.getProperty(Constants.FRAMEWORK_VENDOR));
+ System.out.println(Constants.FRAMEWORK_VERSION + " = "
+ + bundleContext.getProperty(Constants.FRAMEWORK_VERSION));
+ System.out.println(Constants.FRAMEWORK_EXECUTIONENVIRONMENT + " = "
+ + bundleContext.getProperty(Constants.FRAMEWORK_EXECUTIONENVIRONMENT));
+ System.out.println(Constants.OSGI_IMPL_VERSION_KEY + " = "
+ + bundleContext.getProperty(Constants.OSGI_IMPL_VERSION_KEY));
+ }
+
+ public WorkflowBundle loadWorkflow(String t2FlowFile) throws Exception {
+ URL wfResource = getClass().getResource(t2FlowFile);
+ assertNotNull(wfResource);
+ return workflowBundleReader.readBundle(wfResource.openStream(),
+ T2FlowReader.APPLICATION_VND_TAVERNA_T2FLOW_XML);
+ }
+
+ public File loadFile(String fileName) throws IOException, FileNotFoundException {
+ File file = File.createTempFile("platform-test", null);
+ InputStream inputStream = getClass().getResource(fileName).openStream();
+ OutputStream outputStream = new FileOutputStream(file);
+ byte[] buffer = new byte[64];
+ int length = -1;
+ while ((length = inputStream.read(buffer)) >= 0) {
+ outputStream.write(buffer, 0, length);
+ }
+ outputStream.flush();
+ outputStream.close();
+ return file;
+ }
+
+// public void printErrors(Data data) {
+// ErrorDocument error = (ErrorDocument) data.getValue();
+// String message = error.getMessage();
+// if (message != null) {
+// System.out.println(message);
+// }
+// String exceptionMessage = error.getExceptionMessage();
+// if (exceptionMessage != null) {
+// System.out.println(exceptionMessage);
+// }
+// for (StackTraceElementBean stackTraceElementBean : error.getStackTraceStrings()) {
+// System.out.println(stackTraceElementBean.getClassName());
+// System.out.println(stackTraceElementBean.getMethodName());
+// System.out.println(stackTraceElementBean.getLineNumber());
+// }
+//// Set<T2Reference> errorReferences = error.getErrorReferences();
+//// for (T2Reference t2Reference : errorReferences) {
+//// printErrors(referenceService, t2Reference);
+//// }
+// }
+//
+// public boolean checkResult(Data result, String expectedResult) {
+// if (result.isError()) {
+// printErrors(result);
+// return false;
+// } else {
+// Object resultObject = result.getValue();
+// String resultValue = null;
+// if (resultObject instanceof byte[]) {
+// resultValue = new String((byte[]) resultObject);
+// } else {
+// resultValue = (String) resultObject;
+// }
+//
+// if (resultValue.startsWith(expectedResult)) {
+// return true;
+// } else {
+// System.out.println("Expected: " + expectedResult + ", Actual: " + resultValue);
+// return false;
+// }
+// }
+// }
+
+ public boolean waitForState(WorkflowReport report, State state) throws InterruptedException {
+ return waitForState(report, state, true);
+ }
+
+ public boolean waitForState(WorkflowReport report, State state, boolean printReport)
+ throws InterruptedException {
+ int wait = 0;
+ while (!report.getState().equals(state) && wait++ < 30) {
+ if (printReport)
+ System.out.println(report);
+ Thread.sleep(500);
+ }
+ return report.getState().equals(state);
+ }
+
+// public void waitForResults(Map<String, Data> results, WorkflowReport report, String... ports)
+// throws InterruptedException {
+// int wait = 0;
+// while (!resultsReady(results, ports) && wait++ < 20) {
+// System.out.println(report);
+// Thread.sleep(500);
+// }
+// }
+//
+// private boolean resultsReady(Map<String, Data> results, String... ports) {
+// for (String port : ports) {
+// if (!results.containsKey(port)) {
+// return false;
+// }
+// }
+// return true;
+// }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java
new file mode 100644
index 0000000..5387afd
--- /dev/null
+++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunIT.java
@@ -0,0 +1,1000 @@
+/*******************************************************************************
+ * Copyright (C) 2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package org.apache.taverna.platform;
+
+import java.io.File;
+import java.net.URI;
+import java.net.URL;
+import java.security.cert.CertificateFactory;
+import java.security.cert.X509Certificate;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.osgi.framework.ServiceReference;
+
+import org.apache.taverna.platform.execution.api.ExecutionEnvironment;
+import org.apache.taverna.platform.report.State;
+import org.apache.taverna.platform.report.WorkflowReport;
+import org.apache.taverna.platform.run.api.RunProfile;
+import org.apache.taverna.platform.run.api.RunService;
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+
+public class RunIT extends PlatformIT {
+
+ private RunService runService;
+
+ protected void setup() throws Exception {
+ super.setup();
+ if (runService == null) {
+ ServiceReference runServiceReference = bundleContext
+ .getServiceReference("org.apache.taverna.platform.run.api.RunService");
+ runService = (RunService) bundleContext.getService(runServiceReference);
+ }
+ if (dataService == null) {
+ ServiceReference dataServiceReference = bundleContext
+ .getServiceReference("org.apache.taverna.platform.data.DataService");
+ dataService = (DataService) bundleContext.getService(dataServiceReference);
+ }
+ databaseConfiguration.setProvenanceEnabled(false);
+ }
+
+ public void testRun() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/in-out.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ Map<String, Data> inputs = new HashMap<String, Data>();
+ inputs.put("in", dataService.create("test-input"));
+
+ String runId = runService.createRun(new RunProfile(executionEnvironment,
+ workflowBundle, inputs));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertTrue(runService.getState(runId).equals(State.RUNNING)
+ || runService.getState(runId).equals(State.COMPLETED));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ assertNotNull(results);
+ waitForResults(results, runService.getWorkflowReport(runId), "out");
+
+ assertTrue(checkResult(results.get("out"), "test-input"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunApiConsumer() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/apiconsumer.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ Map<String, Data> inputs = new HashMap<String, Data>();
+ inputs.put("in", dataService.create("test-input"));
+
+ String runId = runService.createRun(new RunProfile(executionEnvironment,
+ workflowBundle, inputs));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertTrue(runService.getState(runId).equals(State.RUNNING)
+ || runService.getState(runId).equals(State.COMPLETED));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ assertNotNull(results);
+ waitForResults(results, report, "out");
+
+ assertTrue(checkResult(results.get("out"), "TEST-INPUT"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunBeanshell() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/beanshell.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ Map<String, Data> inputs = new HashMap<String, Data>();
+ inputs.put("in", dataService.create("test-input"));
+
+ String runId = runService.createRun(new RunProfile(executionEnvironment,
+ workflowBundle, inputs));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertTrue(runService.getState(runId).equals(State.RUNNING)
+ || runService.getState(runId).equals(State.COMPLETED));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ assertNotNull(results);
+ waitForResults(results, report, "out");
+
+ List<Data> result = results.get("out").getElements();
+ assertEquals(1000, result.size());
+ assertEquals("test-input:0", result.get(0).getValue());
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunBiomart() throws Exception {
+ setup();
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/biomart.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertTrue(runService.getState(runId).equals(State.RUNNING)
+ || runService.getState(runId).equals(State.COMPLETED));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ assertNotNull(results);
+ waitForResults(results, report, "out");
+
+ List<Data> result = results.get("out").getElements();
+ assertEquals(5, result.size());
+ assertEquals("ENSBTAG00000018854", result.get(0).getValue());
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ // public void testRunBiomoby() throws Exception {
+ // setup();
+ // WorkflowBundle workflowBundle = loadWorkflow("/t2flow/biomoby.t2flow");
+ //
+ // Set<ExecutionEnvironment> executionEnvironments = runService
+ // .getExecutionEnvironments(workflowBundle);
+ // for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ //
+ //
+ // String runId = runService.createRun(new RunProfile(executionEnvironment, workflowBundle));
+ // assertEquals(State.CREATED, runService.getState(runId));
+ //
+ // WorkflowReport report = runService.getWorkflowReport(runId);
+ // System.out.println(report);
+ //
+ // runService.start(runId);
+ // assertTrue(runService.getState(runId).equals(State.RUNNING)
+ // || runService.getState(runId).equals(State.COMPLETED));
+ // System.out.println(report);
+ //
+ // Map<String, Data> results = runService.getOutputs(runId);
+ // assertNotNull(results);
+ // waitForResults(results, report, "out");
+ //
+ // T2Reference resultReference = results.get("out");
+ // if (resultReference.containsErrors()) {
+ // printErrors(referenceService, resultReference);
+ // }
+ // assertFalse(resultReference.containsErrors());
+ // @SuppressWarnings("unchecked")
+ // List<String> result = (List<String>) referenceService.renderIdentifier(resultReference,
+ // String.class, null);
+ // assertEquals(5, result.size());
+ // assertEquals("ENSBTAG00000018854", result.get(0));
+ // assertEquals(State.COMPLETED, runService.getState(runId));
+ // System.out.println(report);
+ // }
+ // }
+
+ public void testRunDataflow() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/dataflow.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ Map<String, Data> inputs = new HashMap<String, Data>();
+ inputs.put("in", dataService.create("test input"));
+
+ String runId = runService.createRun(new RunProfile(executionEnvironment,
+ workflowBundle, inputs));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertFalse(runService.getState(runId).equals(State.CREATED));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out");
+
+ assertTrue(checkResult(results.get("out"),
+ "nested dataflow : test input"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunLocalworker() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/localworker.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ Map<String, Data> inputs = new HashMap<String, Data>();
+ inputs.put("in", dataService.create("Tom"));
+
+ String runId = runService.createRun(new RunProfile(executionEnvironment,
+ workflowBundle, inputs));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertTrue(runService.getState(runId).equals(State.RUNNING)
+ || runService.getState(runId).equals(State.COMPLETED));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ assertNotNull(results);
+ waitForResults(results, report, "out");
+
+ assertTrue(checkResult(results.get("out"), "Hello Tom"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunRest() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/rest.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertEquals(State.RUNNING, runService.getState(runId));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out");
+
+ Object outResult = results.get("out").getValue();
+ if (outResult instanceof byte[]) {
+ outResult = new String((byte[]) outResult);
+ }
+ assertTrue(outResult instanceof String);
+ String outString = (String) outResult;
+ assertTrue(outString.contains("<name>AATM_RABIT</name>"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunRestSecureBasic() throws Exception {
+ setup();
+ credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser",
+ "testpasswd"), URI
+ .create("http://heater.cs.man.ac.uk:7070/#Example+HTTP+BASIC+Authentication"));
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-basic-authentication.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertEquals(State.RUNNING, runService.getState(runId));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out");
+
+ assertTrue(checkResult(results.get("out"),
+ "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n"
+ + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n"
+ + "<META http-equiv=Content-Type content=\"text/html\">\n"
+ + "</HEAD>\n"
+ + "<BODY>\n"
+ + "<P>\n"
+ + "<H3>Secure Apache Tomcat Examples</H3>\n"
+ + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Basic Authentication.</P>\n"
+ + "</BODY></HTML>"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunRestSecureBasicHttps() throws Exception {
+ setup();
+ credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser",
+ "testpasswd"), URI
+ .create("https://heater.cs.man.ac.uk:7443/#Example+HTTP+BASIC+Authentication"));
+
+ URL trustedCertficateFileURL = getClass().getResource(
+ "/security/tomcat_heater_certificate.pem");
+ CertificateFactory certFactory = CertificateFactory.getInstance("X.509");
+ X509Certificate trustedCertficate = (X509Certificate) certFactory
+ .generateCertificate(trustedCertficateFileURL.openStream());
+ credentialManager.addTrustedCertificate(trustedCertficate);
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-basic-authentication-https.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertEquals(State.RUNNING, runService.getState(runId));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out");
+
+ assertTrue(checkResult(results.get("out"),
+ "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n"
+ + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n"
+ + "<META http-equiv=Content-Type content=\"text/html\">\n"
+ + "</HEAD>\n"
+ + "<BODY>\n"
+ + "<P>\n"
+ + "<H3>Secure Apache Tomcat Examples</H3>\n"
+ + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Basic Authentication.</P>\n"
+ + "</BODY></HTML>"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunRestSecureDigest() throws Exception {
+ setup();
+ credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser",
+ "testpasswd"), URI
+ .create("http://heater.cs.man.ac.uk:7070/#Example+HTTP+BASIC+Authentication"));
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-digest-authentication.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertEquals(State.RUNNING, runService.getState(runId));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out");
+
+ assertTrue(checkResult(results.get("out"),
+ "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n"
+ + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n"
+ + "<META http-equiv=Content-Type content=\"text/html\">\n"
+ + "</HEAD>\n"
+ + "<BODY>\n"
+ + "<P>\n"
+ + "<H3>Secure Apache Tomcat Examples</H3>\n"
+ + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Digest Authentication.</P>\n"
+ + "</BODY></HTML>"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunRestSecureDigestHttps() throws Exception {
+ setup();
+ credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser",
+ "testpasswd"), URI
+ .create("http://heater.cs.man.ac.uk:7443/#Example+HTTP+BASIC+Authentication"));
+
+ URL trustedCertficateFileURL = getClass().getResource(
+ "/security/tomcat_heater_certificate.pem");
+ CertificateFactory certFactory = CertificateFactory.getInstance("X.509");
+ X509Certificate trustedCertficate = (X509Certificate) certFactory
+ .generateCertificate(trustedCertficateFileURL.openStream());
+ credentialManager.addTrustedCertificate(trustedCertficate);
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-digest-authentication-https.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertEquals(State.RUNNING, runService.getState(runId));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out");
+
+ assertTrue(checkResult(results.get("out"),
+ "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">\n"
+ + "<HTML><HEAD><TITLE>Apache Tomcat Examples</TITLE>\n"
+ + "<META http-equiv=Content-Type content=\"text/html\">\n"
+ + "</HEAD>\n"
+ + "<BODY>\n"
+ + "<P>\n"
+ + "<H3>Secure Apache Tomcat Examples</H3>\n"
+ + "<P>Congratulations! If you see this page that means that you have authenticated yourself successfully using HTTP Digest Authentication.</P>\n"
+ + "</BODY></HTML>"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunSpreadsheetImport() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/spreadsheetimport.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertEquals(State.RUNNING, runService.getState(runId));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out");
+
+ List<Data> result = results.get("out").getElements();
+ assertEquals(35, result.size());
+ assertEquals("1971.0", result.get(1).getValue());
+ assertEquals("2004.0", result.get(34).getValue());
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunSoaplab() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/soaplab.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertEquals(State.RUNNING, runService.getState(runId));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "sequence");
+
+ assertTrue(checkResult(results.get("sequence"),
+ "ID X52524; SV 1; linear; genomic DNA; STD; INV; 4507 BP."));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunStringConstant() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/stringconstant.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ runService.start(runId);
+ assertTrue(runService.getState(runId).equals(State.RUNNING)
+ || runService.getState(runId).equals(State.COMPLETED));
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out");
+
+ assertTrue(checkResult(results.get("out"), "Test Value"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ }
+ }
+
+ public void testRunTool() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/tool.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ runService.start(runId);
+ assertTrue(runService.getState(runId).equals(State.RUNNING)
+ || runService.getState(runId).equals(State.COMPLETED));
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out");
+
+ assertTrue(checkResult(results.get("out"), "HelloWorld"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ }
+ }
+
+ public void testRunIteration() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/iteration.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ Map<String, Data> inputs = new HashMap<String, Data>();
+ inputs.put("in", dataService.create("test"));
+
+ String runId = runService.createRun(new RunProfile(executionEnvironment,
+ workflowBundle, inputs));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertEquals(State.RUNNING, runService.getState(runId));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+
+ waitForResults(results, report, "cross");
+ List<Data> crossResult = results.get("cross").getElements();
+ assertEquals(10, crossResult.size());
+ assertEquals(10, crossResult.get(0).getElements().size());
+ assertEquals(10, crossResult.get(5).getElements().size());
+ assertEquals("test:0test:0", crossResult.get(0).getElements().get(0).getValue());
+ assertEquals("test:0test:1", crossResult.get(0).getElements().get(1).getValue());
+ assertEquals("test:4test:2", crossResult.get(4).getElements().get(2).getValue());
+ assertEquals("test:7test:6", crossResult.get(7).getElements().get(6).getValue());
+
+ waitForResults(results, report, "dot");
+
+ List<Data> dotResult = results.get("dot").getElements();
+ assertEquals(10, dotResult.size());
+ assertEquals("test:0test:0", dotResult.get(0).getValue());
+ assertEquals("test:5test:5", dotResult.get(5).getValue());
+
+ waitForResults(results, report, "crossdot");
+
+ List<Data> crossdotResult = results.get("crossdot").getElements();
+ assertEquals(10, crossdotResult.size());
+ assertEquals(10, crossdotResult.get(0).getElements().size());
+ assertEquals(10, crossdotResult.get(5).getElements().size());
+ assertEquals("test:0test:0test", crossdotResult.get(0).getElements().get(0).getValue());
+ assertEquals("test:0test:1test", crossdotResult.get(0).getElements().get(1).getValue());
+ assertEquals("test:4test:2test", crossdotResult.get(4).getElements().get(2).getValue());
+ assertEquals("test:7test:6test", crossdotResult.get(7).getElements().get(6).getValue());
+
+ waitForResults(results, report, "dotcross");
+
+ List<Data> dotcrossResult = results.get("dotcross").getElements();
+ assertEquals(10, dotResult.size());
+ assertEquals("test:0test:0test", dotcrossResult.get(0).getValue());
+ assertEquals("test:5test:5test", dotcrossResult.get(5).getValue());
+
+ waitForResults(results, report, "dotdot");
+
+ List<Data> dotdotResult = results.get("dotdot").getElements();
+ assertEquals(10, dotResult.size());
+ assertEquals("test:0test:0test:0", dotdotResult.get(0).getValue());
+ assertEquals("test:5test:5test:5", dotdotResult.get(5).getValue());
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunWSDL() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/wsdl.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertEquals(State.RUNNING, runService.getState(runId));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out");
+
+ // assertTrue(checkResult(results.get("out"),
+ // "Apache Axis version: 1.4\nBuilt on Apr 22, 2006 (06:55:48 PDT)"));
+ assertTrue(checkResult(results.get("out"),
+ "Apache Axis version: 1.2\nBuilt on May 03, 2005 (02:20:24 EDT)"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunWSDLSecure() throws Exception {
+ setup();
+ credentialManager
+ .addUsernameAndPasswordForService(
+ new UsernamePassword("testuser", "testpasswd"),
+ URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl"));
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/wsdl-secure.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertEquals(State.RUNNING, runService.getState(runId));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out");
+
+ assertTrue(checkResult(results.get("out"), "Hello Alan!"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunWSDLSecureFull() throws Exception {
+ setup();
+ credentialManager
+ .addUsernameAndPasswordForService(
+ new UsernamePassword("testuser", "testpasswd"),
+ URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl"));
+ credentialManager
+ .addUsernameAndPasswordForService(
+ new UsernamePassword("testuser", "testpasswd"),
+ URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-DigestPassword?wsdl"));
+ credentialManager
+ .addUsernameAndPasswordForService(
+ new UsernamePassword("testuser", "testpasswd"),
+ URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-DigestPassword-Timestamp?wsdl"));
+ credentialManager
+ .addUsernameAndPasswordForService(
+ new UsernamePassword("testuser", "testpasswd"),
+ URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword-Timestamp?wsdl"));
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-ws.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertEquals(State.RUNNING, runService.getState(runId));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out_plaintext", "out_digest", "out_digest_timestamp",
+ "out_plaintext_timestamp");
+
+ assertTrue(checkResult(results.get("out_plaintext"), "Hello Alan!"));
+ assertTrue(checkResult(results.get("out_digest"), "Hello Stian!"));
+ assertTrue(checkResult(results.get("out_digest_timestamp"),
+ "Hello David!"));
+ assertTrue(checkResult(results.get("out_plaintext_timestamp"),
+ "Hello Alex!"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunWSDLSecureSsh() throws Exception {
+ setup();
+ credentialManager
+ .addUsernameAndPasswordForService(
+ new UsernamePassword("testuser", "testpasswd"),
+ URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword?wsdl"));
+ credentialManager
+ .addUsernameAndPasswordForService(
+ new UsernamePassword("testuser", "testpasswd"),
+ URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-DigestPassword?wsdl"));
+ credentialManager
+ .addUsernameAndPasswordForService(
+ new UsernamePassword("testuser", "testpasswd"),
+ URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-DigestPassword-Timestamp?wsdl"));
+ credentialManager
+ .addUsernameAndPasswordForService(
+ new UsernamePassword("testuser", "testpasswd"),
+ URI.create("https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword-Timestamp?wsdl"));
+
+ URL trustedCertficateFileURL = getClass().getResource(
+ "/security/tomcat_heater_certificate.pem");
+ CertificateFactory certFactory = CertificateFactory.getInstance("X.509");
+ X509Certificate trustedCertficate = (X509Certificate) certFactory
+ .generateCertificate(trustedCertficateFileURL.openStream());
+ credentialManager.addTrustedCertificate(trustedCertficate);
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/secure-ws-https.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertEquals(State.RUNNING, runService.getState(runId));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out_plaintext", "out_digest", "out_digest_timestamp",
+ "out_plaintext_timestamp");
+
+ assertTrue(checkResult(results.get("out_plaintext"), "Hello Alan!"));
+ assertTrue(checkResult(results.get("out_digest"), "Hello Stian!"));
+ assertTrue(checkResult(results.get("out_digest_timestamp"),
+ "Hello David!"));
+ assertTrue(checkResult(results.get("out_plaintext_timestamp"),
+ "Hello Alex!"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunXMLSplitter() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/xmlSplitter.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ Map<String, Data> inputs = new HashMap<String, Data>();
+ inputs.put("firstName", dataService.create("John"));
+ inputs.put("lastName", dataService.create("Smith"));
+ inputs.put("age", dataService.create("21"));
+
+ String runId = runService.createRun(new RunProfile(executionEnvironment,
+ workflowBundle, inputs));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertTrue(runService.getState(runId).equals(State.RUNNING)
+ || runService.getState(runId).equals(State.COMPLETED));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out");
+
+ assertTrue(checkResult(results.get("out"),
+ "John Smith (21) of 40, Oxford Road. Manchester."));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunXPath() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/xpath.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ String runId = runService
+ .createRun(new RunProfile(executionEnvironment, workflowBundle));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertTrue(runService.getState(runId).equals(State.RUNNING)
+ || runService.getState(runId).equals(State.COMPLETED));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ waitForResults(results, report, "out");
+
+ assertTrue(checkResult(results.get("out"),
+ "<test-element>test</test-element>"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+ public void testRunFromFile() throws Exception {
+ setup();
+
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/in-out.t2flow");
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments(workflowBundle);
+ assertTrue(executionEnvironments.size() > 0);
+ for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
+ Map<String, Data> inputs = new HashMap<String, Data>();
+ File file = loadFile("/t2flow/input.txt");
+ Data data = dataService.create(file.toURI());
+ assertTrue(data.isReference());
+ inputs.put("in", data);
+
+ String runId = runService.createRun(new RunProfile(executionEnvironment,
+ workflowBundle, inputs));
+ assertEquals(State.CREATED, runService.getState(runId));
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println(report);
+
+ runService.start(runId);
+ assertTrue(runService.getState(runId).equals(State.RUNNING)
+ || runService.getState(runId).equals(State.COMPLETED));
+ System.out.println(report);
+
+ Map<String, Data> results = runService.getOutputs(runId);
+ assertNotNull(results);
+ waitForResults(results, runService.getWorkflowReport(runId), "out");
+
+ assertTrue(checkResult(results.get("out"), "test input value"));
+
+ assertEquals(State.COMPLETED, runService.getState(runId));
+ System.out.println(report);
+ }
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunParallelIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunParallelIT.java b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunParallelIT.java
new file mode 100644
index 0000000..d9398ab
--- /dev/null
+++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunParallelIT.java
@@ -0,0 +1,93 @@
+/*******************************************************************************
+ * Copyright (C) 2011 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package org.apache.taverna.platform;
+
+import java.net.URI;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.osgi.framework.ServiceReference;
+
+import org.apache.taverna.platform.execution.api.ExecutionEnvironment;
+import org.apache.taverna.platform.report.State;
+import org.apache.taverna.platform.report.WorkflowReport;
+import org.apache.taverna.platform.run.api.RunProfile;
+import org.apache.taverna.platform.run.api.RunService;
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+
+public class RunParallelIT extends PlatformIT {
+
+ private RunService runService;
+
+ private ExecutionEnvironment executionEnvironment;
+
+ protected void setup() throws Exception {
+ super.setup();
+ if (runService == null) {
+ ServiceReference runServiceReference = bundleContext
+ .getServiceReference("org.apache.taverna.platform.run.api.RunService");
+ runService = (RunService) bundleContext.getService(runServiceReference);
+ }
+ if (executionEnvironment == null) {
+ executionEnvironment = runService.getExecutionEnvironments().iterator().next();
+ }
+ credentialManager.addUsernameAndPasswordForService(new UsernamePassword("testuser",
+ "testpasswd"), URI
+ .create("http://heater.cs.man.ac.uk:7070/#Example+HTTP+BASIC+Authentication"));
+ credentialManager
+ .addUsernameAndPasswordForService(
+ new UsernamePassword("testuser", "testpasswd"),
+ URI.create("http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl"));
+ }
+
+ public void testRun() throws Exception {
+ setup();
+
+ String[] workflows = { "biomart", "rest", "secure-basic-authentication",
+ "spreadsheetimport", "stringconstant", "wsdl", "wsdl-secure", "xpath" };
+ Set<String> runIDs= new HashSet<String>();
+
+ for (int i = 0; i < workflows.length; i++) {
+ int runs = Math.max(1, (int) Math.ceil(Math.random() * 10));
+ System.out.println("Creating " + runs + " runs for workflow " + workflows[i]);
+ for (int j = 0; j < runs; j++) {
+ WorkflowBundle workflowBundle = loadWorkflow("/t2flow/" + workflows[i] + ".t2flow");
+ String run = runService.createRun(new RunProfile(executionEnvironment, workflowBundle));
+ runService.getWorkflowReport(run).getSubject().setName(workflows[i] + j);
+ runIDs.add(run);
+ }
+ }
+
+ for (String runId : runIDs) {
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println("Starting " + report.getSubject().getName());
+ runService.start(runId);
+ }
+
+ for (String runId : runIDs) {
+ WorkflowReport report = runService.getWorkflowReport(runId);
+ System.out.println("Waiting for " + report.getSubject().getName() + " to complete");
+ assertTrue(waitForState(report, State.COMPLETED, false));
+ }
+
+ }
+
+}
[3/4] incubator-taverna-engine git commit: Attempt to update package
to org.apache.taverna
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/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
new file mode 100644
index 0000000..758e872
--- /dev/null
+++ b/taverna-platform-integration-tests/src/test/java/org/apache/taverna/platform/RunWorkflowsIT.java
@@ -0,0 +1,134 @@
+/*******************************************************************************
+ * Copyright (C) 2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package org.apache.taverna.platform;
+
+import java.util.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/50373179/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/ActivityIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/ActivityIT.java b/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/ActivityIT.java
deleted file mode 100644
index 895633b..0000000
--- a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/ActivityIT.java
+++ /dev/null
@@ -1,72 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform;
-
-import java.net.URI;
-import java.util.List;
-
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-import org.osgi.framework.ServiceReference;
-
-import org.apache.taverna.platform.capability.activity.ActivityConfigurationException;
-import org.apache.taverna.platform.capability.activity.ActivityNotFoundException;
-import org.apache.taverna.platform.capability.activity.ActivityService;
-import org.apache.taverna.scufl2.api.configurations.ConfigurationDefinition;
-
-public class ActivityIT extends PlatformIT {
-
- public void testGetActivityURIs() {
- ServiceReference activityServiceReference = bundleContext.getServiceReference("uk.org.taverna.platform.activity.ActivityService");
- ActivityService activityService = (ActivityService) bundleContext.getService(activityServiceReference);
- List<URI> activityURIs = activityService.getActivityURIs();
- System.out.println("================= Available Activities ===================");
- for (URI uri : activityURIs) {
- System.out.println(uri);
- }
- System.out.println("==========================================================");
- System.out.println("");
- }
-
- public void testCreateActivity() throws ActivityNotFoundException, ActivityConfigurationException {
- ServiceReference activityServiceReference = bundleContext.getServiceReference("uk.org.taverna.platform.activity.ActivityService");
- ActivityService activityService = (ActivityService) bundleContext.getService(activityServiceReference);
- List<URI> activityURIs = activityService.getActivityURIs();
- for (URI uri : activityURIs) {
- System.out.println("Creating activity " + uri);
- Activity<?> activity = activityService.createActivity(uri, null);
- }
- }
-
- public void testGetActivityConfigurationDefinition() throws Exception {
- ServiceReference activityServiceReference = bundleContext.getServiceReference("uk.org.taverna.platform.activity.ActivityService");
- ActivityService activityService = (ActivityService) bundleContext.getService(activityServiceReference);
-
- List<URI> activityURIs = activityService.getActivityURIs();
- System.out.println("============ Activity Configuration Definitions ==========");
- for (URI uri : activityURIs) {
- ConfigurationDefinition configurationDefinition = activityService.getActivityConfigurationDefinition(uri);
- System.out.println(configurationDefinition);
- }
- System.out.println("==========================================================");
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/CommandLineToolIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/CommandLineToolIT.java b/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/CommandLineToolIT.java
deleted file mode 100644
index d0d79d3..0000000
--- a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/CommandLineToolIT.java
+++ /dev/null
@@ -1,91 +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 net.sf.taverna.t2.commandline.CommandLineTool;
-
-import org.osgi.framework.ServiceReference;
-
-import org.apache.taverna.commandline.args.CommandLineArguments;
-import org.apache.taverna.platform.run.api.RunService;
-import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
-import org.apache.taverna.scufl2.api.io.WorkflowBundleReader;
-
-public class CommandLineToolIT extends PlatformIT {
-
- private RunService runService;
- private WorkflowBundleIO workflowBundleIO;
- private WorkflowBundleReader workflowReader;
-
- protected void setup() throws Exception {
- super.setup();
- if (runService == null) {
- ServiceReference runServiceReference = bundleContext
- .getServiceReference("uk.org.taverna.platform.run.api.RunService");
- runService = (RunService) bundleContext.getService(runServiceReference);
- }
-
- if (workflowReader == null) {
- ServiceReference workflowBundleReaderServiceReference = bundleContext
- .getServiceReferences("org.apache.taverna.scufl2.api.io.WorkflowBundleReader",
- "(mediaType=application/vnd.taverna.t2flow+xml)")[0];
- workflowBundleReader = (WorkflowBundleReader) bundleContext
- .getService(workflowBundleReaderServiceReference);
- }
-
- if (workflowBundleIO == null) {
- ServiceReference workflowBundleIOServiceReference = bundleContext
- .getServiceReference("org.apache.taverna.scufl2.api.io.WorkflowBundleIO");
- workflowBundleIO = (WorkflowBundleIO) bundleContext
- .getService(workflowBundleIOServiceReference);
- }
- }
-
- public void testCommandLineTool() throws Exception {
-
- setup();
-
- CommandLineTool cmdTool = new CommandLineTool();
- cmdTool.setRunService(runService);
- cmdTool.setCredentialManager(credentialManager);
- cmdTool.setWorkflowBundleIO(workflowBundleIO);
- cmdTool.setCommandLineArgumentsService(new CommandLineArguments() {
- public String[] getCommandLineArguments() {
- return new String[] { "-outputdoc", "/tmp/taverna3/baclava-output1.xml",
- "/Users/alex/Desktop/t2flows/simple-wf-no-inputs-one-output.t2flow" };
- }
-
- });
- cmdTool.run();
-
- cmdTool.setCommandLineArgumentsService(new CommandLineArguments() {
- public String[] getCommandLineArguments() {
- return new String[] { "-inputvalue", "in", "Taverna 3 Platform rules",
- "-outputdoc", "/tmp/taverna3/baclava-output2.xml",
- "/Users/alex/Desktop/t2flows/simple-wf-one-input-one-output.t2flow" };
- }
-
- });
- cmdTool.run();
-
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/ExecutionIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/ExecutionIT.java b/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/ExecutionIT.java
deleted file mode 100644
index 3736c5e..0000000
--- a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/ExecutionIT.java
+++ /dev/null
@@ -1,134 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform;
-
-import java.net.URI;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.osgi.framework.ServiceReference;
-
-import org.apache.taverna.platform.capability.activity.ActivityConfigurationException;
-import org.apache.taverna.platform.capability.activity.ActivityNotFoundException;
-import org.apache.taverna.platform.data.api.Data;
-import org.apache.taverna.platform.capability.dispatch.DispatchLayerConfigurationException;
-import org.apache.taverna.platform.capability.dispatch.DispatchLayerNotFoundException;
-import org.apache.taverna.platform.execution.api.AbstractExecutionEnvironment;
-import org.apache.taverna.platform.execution.api.AbstractExecutionService;
-import org.apache.taverna.platform.execution.api.Execution;
-import org.apache.taverna.platform.execution.api.ExecutionEnvironment;
-import org.apache.taverna.platform.execution.api.ExecutionEnvironmentService;
-import org.apache.taverna.platform.execution.api.InvalidWorkflowException;
-import org.apache.taverna.scufl2.api.configurations.ConfigurationDefinition;
-import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-import org.apache.taverna.scufl2.api.core.Workflow;
-import org.apache.taverna.scufl2.api.profiles.Profile;
-
-public class ExecutionIT extends PlatformIT {
-
- private ExecutionEnvironmentService executionEnvironmentService;
-
- protected void setup() throws Exception {
- super.setup();
- ServiceReference[] executionServiceReferences = bundleContext.getServiceReferences(
- "uk.org.taverna.platform.execution.api.ExecutionEnvironmentService", null);
- assertEquals(1, executionServiceReferences.length);
- executionEnvironmentService = (ExecutionEnvironmentService) bundleContext
- .getService(executionServiceReferences[0]);
-
- }
-
- public void testGetExecutionEnvironments() throws Exception {
- setup();
-
- Set<ExecutionEnvironment> executionEnvironments = executionEnvironmentService
- .getExecutionEnvironments();
- int size = executionEnvironments.size();
-
- bundleContext.registerService("uk.org.taverna.platform.execution.api.ExecutionService",
- new AbstractExecutionService("test id", "test name", "test description") {
- public Set<ExecutionEnvironment> getExecutionEnvivonments() {
- return Collections
- .<ExecutionEnvironment> singleton(new AbstractExecutionEnvironment(
- "test id", "test name", "test description", this) {
- public List<URI> getDispatchLayerURIs() {
- return Collections.singletonList(URI
- .create("http://ns.taverna.org.uk/2010/dispatchlayer/testDispatchLayer"));
- }
-
- public List<URI> getActivityURIs() {
- return Collections.singletonList(URI
- .create("http://ns.taverna.org.uk/2010/activity/testActivity"));
- }
-
- public boolean dispatchLayerExists(URI uri) {
- return false;
- }
-
- public boolean activityExists(URI uri) {
- return false;
- }
-
- public ConfigurationDefinition getActivityConfigurationDefinition(
- URI uri) throws ActivityNotFoundException,
- ActivityConfigurationException {
- return null;
- }
-
- public ConfigurationDefinition getDispatchLayerConfigurationDefinition(
- URI uri) throws DispatchLayerNotFoundException,
- DispatchLayerConfigurationException {
- return null;
- }
- });
- }
-
- protected Execution createExecutionImpl(WorkflowBundle workflowBundle,
- Workflow workflow, Profile profile, Map<String, Data> inputs) throws InvalidWorkflowException {
- return null;
- }
- }, null);
-
-
- executionEnvironments = executionEnvironmentService
- .getExecutionEnvironments();
- assertEquals(size + 1, executionEnvironments.size());
-
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- System.out.println(executionEnvironment);
- }
- }
-
- public void testGetExecutionEnvironmentsProfile() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/beanshell.t2flow");
-
- Set<ExecutionEnvironment> executionEnvironments = executionEnvironmentService
- .getExecutionEnvironments(workflowBundle.getMainProfile());
- assertTrue(executionEnvironments.size() > 0);
-
- System.out.println(executionEnvironments.iterator().next());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/LocalExecutionIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/LocalExecutionIT.java b/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/LocalExecutionIT.java
deleted file mode 100644
index fefa498..0000000
--- a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/LocalExecutionIT.java
+++ /dev/null
@@ -1,120 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform;
-
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.osgi.framework.ServiceReference;
-
-import org.apache.taverna.platform.data.api.Data;
-import org.apache.taverna.platform.data.api.DataService;
-import org.apache.taverna.platform.execution.api.ExecutionEnvironment;
-import org.apache.taverna.platform.execution.api.ExecutionService;
-import org.apache.taverna.platform.report.State;
-import org.apache.taverna.platform.report.WorkflowReport;
-import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-import org.apache.taverna.scufl2.api.core.Workflow;
-import org.apache.taverna.scufl2.api.profiles.Profile;
-
-public class LocalExecutionIT extends PlatformIT {
-
- private ExecutionService executionService;
- private DataService dataService;
- private Set<ExecutionEnvironment> executionEnvironments;
-
- protected void setup() throws Exception {
- super.setup();
- if (executionService == null) {
- ServiceReference[] executionServiceReferences = bundleContext.getServiceReferences(
- "uk.org.taverna.platform.execution.api.ExecutionService",
- "(org.springframework.osgi.bean.name=localExecution)");
- assertEquals(1, executionServiceReferences.length);
- executionService = (ExecutionService) bundleContext
- .getService(executionServiceReferences[0]);
- executionEnvironments = executionService.getExecutionEnvivonments();
- assertEquals(1, executionEnvironments.size());
- }
- if (dataService == null) {
- ServiceReference dataServiceReference = bundleContext
- .getServiceReference("uk.org.taverna.platform.data.DataService");
- dataService = (DataService) bundleContext.getService(dataServiceReference);
- }
- }
-
- public void testLocalExecution() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/in-out.t2flow");
- Workflow workflow = workflowBundle.getMainWorkflow();
- Profile profile = workflowBundle.getMainProfile();
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = Collections.singletonMap("in", dataService.create("test-input"));
-
- String executionId = executionService.createExecution(executionEnvironment,
- workflowBundle, workflow, profile, inputs);
- WorkflowReport report = executionService.getWorkflowReport(executionId);
- assertEquals(State.CREATED, report.getState());
- executionService.start(executionId);
-
- Map<String, Data> results = report.getOutputs();
- assertNotNull(results);
- waitForResults(results, report, "out");
-
- Object result = results.get("out").getValue();
- assertEquals("test-input", result);
- assertEquals(State.COMPLETED, report.getState());
- System.out.println(report);
- }
- }
-
- public void testLocalExecution2() throws Exception {
- setup();
-
- WorkflowBundle workflowBundle = loadWorkflow("/t2flow/beanshell.t2flow");
- Workflow workflow = workflowBundle.getMainWorkflow();
- Profile profile = workflowBundle.getMainProfile();
-
- for (ExecutionEnvironment executionEnvironment : executionEnvironments) {
- Map<String, Data> inputs = Collections.singletonMap("in", dataService.create("test-input"));
-
- String executionId = executionService.createExecution(executionEnvironment,
- workflowBundle, workflow, profile, inputs);
- WorkflowReport report = executionService.getWorkflowReport(executionId);
- System.out.println(report);
- assertEquals(State.CREATED, report.getState());
- executionService.start(executionId);
- System.out.println(report);
-
- Map<String, Data> results = report.getOutputs();
- waitForResults(results, report, "out");
-
- List<Data> result = results.get("out").getElements();
- assertEquals(1000, result.size());
- assertEquals("test-input:0", result.get(0).getValue());
- assertEquals(State.COMPLETED, report.getState());
- System.out.println(report);
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/OSGIFrameworkIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/OSGIFrameworkIT.java b/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/OSGIFrameworkIT.java
deleted file mode 100644
index 38f46c7..0000000
--- a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/OSGIFrameworkIT.java
+++ /dev/null
@@ -1,93 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform;
-
-import java.io.IOException;
-
-import org.osgi.framework.Bundle;
-import org.springframework.core.io.Resource;
-import org.springframework.osgi.util.OsgiStringUtils;
-
-public class OSGIFrameworkIT extends PlatformIT {
-
- public void testOsgiEnvironment() throws Exception {
- Bundle[] bundles = bundleContext.getBundles();
- for (int i = 0; i < bundles.length; i++) {
- System.out.println(OsgiStringUtils.nullSafeName(bundles[i]));
- }
- System.out.println();
- }
-
- protected String[] getTestFrameworkBundlesNames() {
- String[] frameworkBundles = super.getTestFrameworkBundlesNames();
- System.out.println("Test Framework bundles:");
- for (String bundle : frameworkBundles) {
- System.out.println(" " + bundle);
- }
- return frameworkBundles;
- }
-
- protected String[] getTestBundlesNames() {
- String[] frameworkBundles = super.getTestBundlesNames();
- System.out.println("Framework bundles:");
- for (String bundle : frameworkBundles) {
- System.out.println(" " + bundle);
- }
- return frameworkBundles;
- }
-
- public void testPrintConfig() throws IOException {
- Resource[] bundles = getTestBundles();
- Resource[] testBundles = getTestFrameworkBundles();
- StringBuilder sb = new StringBuilder();
- StringBuilder sb2 = new StringBuilder();
- System.out.println("mkdir platform");
- System.out.println("mkdir platform/configuration");
- sb2.append("cp ");
- sb.append("osgi.bundles=");
- boolean printComma = false;
- for (Resource resource : bundles) {
- if (printComma) {
- sb.append(", ");
- sb2.append(" ");
- }
- sb.append(resource.getFilename() + "@start");
- sb2.append(resource.getFile());
- printComma = true;
- }
- for (Resource resource : testBundles) {
- if (!resource.getFilename().contains("test")) {
- if (printComma) {
- sb.append(", ");
- sb2.append(" ");
- }
- sb.append(resource.getFilename() + "@start");
- sb2.append(resource.getFile());
- printComma = true;
- }
- }
- sb2.append(" platform");
- System.out.println("echo \"" + sb.toString() + "\" > platform/configuration/config.ini");
- System.out.println(sb2.toString());
- System.out.println("zip platform.zip platform/*");
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/50373179/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/PlatformIT.java
----------------------------------------------------------------------
diff --git a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/PlatformIT.java b/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/PlatformIT.java
deleted file mode 100644
index 5191f33..0000000
--- a/taverna-platform-integration-tests/src/test/java/uk/org/taverna/platform/PlatformIT.java
+++ /dev/null
@@ -1,378 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.net.URL;
-import java.util.Map;
-import java.util.Properties;
-
-import net.sf.taverna.t2.reference.ErrorDocument;
-import net.sf.taverna.t2.reference.StackTraceElementBean;
-import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
-import net.sf.taverna.t2.security.credentialmanager.MasterPasswordProvider;
-
-import org.eclipse.osgi.framework.internal.core.Constants;
-import org.osgi.framework.ServiceReference;
-import org.osgi.service.jndi.JNDIContextManager;
-import org.springframework.osgi.test.AbstractConfigurableBundleCreatorTests;
-import org.springframework.osgi.test.platform.OsgiPlatform;
-import org.springframework.osgi.test.platform.Platforms;
-
-import org.apache.taverna.configuration.app.ApplicationConfiguration;
-import org.apache.taverna.configuration.database.DatabaseConfiguration;
-import org.apache.taverna.platform.data.api.Data;
-import org.apache.taverna.platform.report.State;
-import org.apache.taverna.platform.report.WorkflowReport;
-import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-import org.apache.taverna.scufl2.api.io.WorkflowBundleReader;
-import org.apache.taverna.scufl2.translator.t2flow.T2FlowReader;
-
-public class PlatformIT extends AbstractConfigurableBundleCreatorTests {
-
- protected WorkflowBundleReader workflowBundleReader;
- protected CredentialManager credentialManager;
- protected MasterPasswordProvider masterPasswordProvider;
- protected DatabaseConfiguration databaseConfiguration;
- protected JNDIContextManager jndiContextManager;
- protected ApplicationConfiguration applicationConfiguration;
-
- protected String getPlatformName() {
- // return Platforms.FELIX;
- return Platforms.EQUINOX;
- }
-
- @Override
- protected OsgiPlatform createPlatform() {
- OsgiPlatform platform = super.createPlatform();
- Properties config = platform.getConfigurationProperties();
- config.setProperty("org.osgi.framework.system.packages.extra",
- "com.sun.org.apache.xml.internal.utils");
- return platform;
- }
-
- @Override
- protected String[] getTestBundlesNames() {
- return new String[] {
- "com.jcraft.jsch, com.springsource.com.jcraft.jsch, 0.1.41",
- "com.sun.xml, com.springsource.com.sun.xml.bind, 2.2.0",
- "com.sun.xml, com.springsource.com.sun.xml.fastinfoset, 1.2.2",
- "com.thoughtworks.xstream, com.springsource.com.thoughtworks.xstream, 1.2.2",
- "commons-dbcp, commons-dbcp, 1.4",
- "commons-pool, commons-pool, 1.5.6",
- "javax.activation, com.springsource.javax.activation, 1.1.1",
- "javax.jms, com.springsource.javax.jms, 1.1.0",
- "javax.mail, com.springsource.javax.mail, 1.4.0",
- "javax.servlet, com.springsource.javax.servlet, 2.5.0",
- "javax.transaction, com.springsource.javax.transaction, 1.1.0",// for derby client
- "javax.wsdl, com.springsource.javax.wsdl, 1.6.1",
- "javax.xml.bind, com.springsource.javax.xml.bind, 2.2.0",
- "javax.xml.rpc, com.springsource.javax.xml.rpc, 1.1.0",
- "javax.xml.soap, com.springsource.javax.xml.soap, 1.3.0",
- "javax.xml.stream, com.springsource.javax.xml.stream, 1.0.1",
- "org.antlr, com.springsource.antlr, 2.7.6",
- "org.apache.aries, org.apache.aries.util, 0.3",
- "org.apache.aries.proxy, org.apache.aries.proxy.api, 0.3",
- "org.apache.aries.jndi, org.apache.aries.jndi, 0.3",
- "org.apache.axis, com.springsource.org.apache.axis, 1.4.0",
- "org.apache.commons, com.springsource.org.apache.commons.cli, 1.2.0",
- "org.apache.commons, com.springsource.org.apache.commons.codec, 1.4.0",
- "org.apache.commons, com.springsource.org.apache.commons.csv, 1.0.0.BUILD-20080106",
- "org.apache.commons, com.springsource.org.apache.commons.collections, 3.2.0",
- "org.apache.commons, com.springsource.org.apache.commons.discovery, 0.4.0",
- "org.apache.commons, com.springsource.org.apache.commons.httpclient, 3.1.0",
- "org.apache.commons, com.springsource.org.apache.commons.io, 1.4.0",
- "org.apache.commons, com.springsource.org.apache.commons.lang, 2.5.0",
- "org.apache.commons, com.springsource.org.apache.commons.logging, 1.1.1",
- "org.apache.commons, com.springsource.org.apache.commons.net, 1.4.1",
- // "org.apache.derby, derby, 10.5.3.0_1",
- "org.apache.derby, com.springsource.org.apache.derby, 10.5.1000001.764942",
- "org.apache.derby, com.springsource.org.apache.derby.client, 10.5.1000001.764942",
- "org.apache.derby, com.springsource.org.apache.derby.drda, 10.5.1000001.764942",
- "org.apache.httpcomponents, com.springsource.org.apache.httpcomponents.httpclient, 4.1.1",
- "org.apache.httpcore, com.springsource.org.apache.httpcomponents.httpcore, 4.1",
- "org.apache.log4j, com.springsource.org.apache.log4j, 1.2.16",
- "org.apache.ws, com.springsource.org.apache.ws.security, 1.5.8",
- // "org.apache.ws.security, wss4j, 1.5.12",
- "org.apache.xml, com.springsource.org.apache.xml.resolver, 1.2.0",
- "org.apache.xmlbeans, com.springsource.org.apache.xmlbeans, 2.4.0",
- "org.apache.xmlcommons, com.springsource.org.apache.xmlcommons, 1.3.4",
- "org.apache.xalan, com.springsource.org.apache.xalan, 2.7.1",
- "org.apache.xalan, com.springsource.org.apache.xml.serializer, 2.7.1",
- "org.apache.xerces, com.springsource.org.apache.xerces, 2.9.1",
- "org.apache.xml, com.springsource.org.apache.xml.security, 1.4.2",
- "org.aspectj, com.springsource.org.aspectj.runtime, 1.6.0",
- "org.aspectj, com.springsource.org.aspectj.weaver, 1.6.0",
- "org.beanshell, com.springsource.bsh, 2.0.0.b4",
- "org.biomart, martservice, 2.0-SNAPSHOT",
- "org.bouncycastle, bcprov-jdk16, 1.46",
- "org.dom4j, com.springsource.org.dom4j, 1.6.1",
- "org.hibernate, com.springsource.org.hibernate, 3.2.6.ga",
- "org.jaxen, com.springsource.org.jaxen, 1.1.1",
- "org.jboss.javassist, com.springsource.javassist, 3.3.0.ga",
- "org.jdom, com.springsource.org.jdom, 1.1.0",
- "org.jvnet.staxex, com.springsource.org.jvnet.staxex, 1.0.0",
- "org.objectweb.asm, com.springsource.org.objectweb.asm, 1.5.3",
- "org.objectweb.asm, com.springsource.org.objectweb.asm.attrs, 1.5.3",
- "org.opensaml, com.springsource.org.opensaml, 1.1.0",
- "org.springframework, org.springframework.jdbc, 3.0.0.RC1",
- "org.springframework, org.springframework.orm, 3.0.0.RC1",
- "org.springframework, org.springframework.transaction, 3.0.0.RC1",
- // "org.springframework, org.springframework.beans, 3.0.5.RELEASE",
- // "org.springframework, org.springframework.core, 3.0.5.RELEASE",
- // "org.springframework, org.springframework.context, 3.0.5.RELEASE",
- // "org.springframework, org.springframework.transaction, 3.0.5.RELEASE",
- "org.xmlpull, com.springsource.org.xmlpull, 1.1.3.4-O",
- "net.sf.taverna, wsdl-generic, 1.10-SNAPSHOT",
- "net.sf.taverna.jedit, jedit-syntax, 2.2.4-SNAPSHOT",
- "net.sf.taverna.t2.activities, apiconsumer-activity, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.activities, beanshell-activity, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.activities, biomart-activity, 2.0-SNAPSHOT",
- // "net.sf.taverna.t2.activities, biomoby-activity, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.activities, dataflow-activity, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.activities, dependency-activity, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.activities, external-tool-activity, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.activities, localworker-activity, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.activities, rest-activity, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.activities, rshell-activity, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.activities, soaplab-activity, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.activities, spreadsheet-import-activity, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.activities, stringconstant-activity, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.activities, wsdl-activity, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.activities, xpath-activity, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.core, provenance-derby, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.core, provenance-mysql, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.core, provenanceconnector, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.core, reference-api, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.core, reference-core-extensions, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.core, reference-impl, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.core, workflowmodel-api, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.core, workflowmodel-core-extensions, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.core, workflowmodel-impl, 2.0-SNAPSHOT",
- // "net.sf.taverna.t2.infrastructure, appconfig, 3.0-SNAPSHOT",
- "net.sf.taverna.t2.lang, ui, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.lang, observer, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.security, credential-manager, 2.0-SNAPSHOT",
- "net.sf.taverna.t2.security, credential-manager-impl, 2.0-SNAPSHOT",
- "net.sourceforge.cglib, com.springsource.net.sf.cglib, 2.1.3",
- "uk.org.taverna.configuration, taverna-app-configuration-api, 0.1.0-SNAPSHOT",
- "uk.org.taverna.configuration, taverna-app-configuration-impl, 0.1.0-SNAPSHOT",
- "uk.org.taverna.configuration, taverna-configuration-api, 0.1.0-SNAPSHOT",
- "uk.org.taverna.configuration, taverna-configuration-impl, 0.1.0-SNAPSHOT",
- "uk.org.taverna.configuration, taverna-database-configuration-api, 0.1.0-SNAPSHOT",
- "uk.org.taverna.configuration, taverna-database-configuration-impl, 0.1.0-SNAPSHOT",
- "uk.org.taverna.platform, report, 0.1.2-SNAPSHOT",
- "uk.org.taverna.platform, data, 0.1.2-SNAPSHOT",
- "uk.org.taverna.platform, execution-local, 0.1.2-SNAPSHOT",
- "uk.org.taverna.platform, execution-remote, 0.1.2-SNAPSHOT",
- "uk.org.taverna.platform, taverna-capability-api, 0.1.2-SNAPSHOT",
- "uk.org.taverna.platform, taverna-capability-impl, 0.1.2-SNAPSHOT",
- "uk.org.taverna.platform, taverna-execution-api, 0.1.2-SNAPSHOT",
- "uk.org.taverna.platform, taverna-execution-impl, 0.1.2-SNAPSHOT",
- "uk.org.taverna.platform, taverna-run-api, 0.1.2-SNAPSHOT",
- "uk.org.taverna.platform, taverna-run-impl, 0.1.2-SNAPSHOT",
- "uk.org.taverna.osgi.services, xml-parser-service, 0.0.1-SNAPSHOT",
- "uk.org.taverna.osgi.services, xml-transformer-service, 0.0.1-SNAPSHOT",
- // FIXME: Add the other scufl2 modules
- "org.apache.taverna.scufl2, scufl2-api, 0.9.2",
- "org.apache.taverna.scufl2, scufl2-rdfxml, 0.9.2",
- "org.apache.taverna.scufl2, scufl2-ucfpackage, 0.9.2",
- "org.apache.taverna.scufl2, scufl2-t2flow, 0.9.2",
- "org.apache.taverna.scufl2, scufl2-validation, 0.9.2",
- "org.apache.taverna.scufl2, scufl2-validation-correctness, 0.9.2",
- "org.apache.taverna.scufl2, scufl2-validation-structural, 0.9.2",
- "net.sf.taverna.t2, results, 2.0-SNAPSHOT",
- "net.sf.taverna.t2, baclava, 0.1-SNAPSHOT",
- // "net.sf.taverna.t2.taverna-commandline, taverna-commandline-common, 2.0-SNAPSHOT"
- };
- }
-
- protected void setup() throws Exception {
-
- if (masterPasswordProvider == null) {
- masterPasswordProvider = new MasterPasswordProvider() {
- public String getMasterPassword(boolean firstTime) {
- return "test";
- }
-
- public void setMasterPassword(String password) {
- }
-
- public int getProviderPriority() {
- return 0;
- }
- };
- bundleContext.registerService(
- "net.sf.taverna.t2.security.credentialmanager.MasterPasswordProvider",
- masterPasswordProvider, null);
- }
-
- if (credentialManager == null) {
- ServiceReference credentialManagerReference = bundleContext
- .getServiceReference("net.sf.taverna.t2.security.credentialmanager.CredentialManager");
- credentialManager = (CredentialManager) bundleContext
- .getService(credentialManagerReference);
- }
-
- if (workflowBundleReader == null) {
- ServiceReference[] workflowBundleReaderReferences = bundleContext.getServiceReferences(
- "org.apache.taverna.scufl2.api.io.WorkflowBundleReader", null);
- for (ServiceReference serviceReference : workflowBundleReaderReferences) {
- workflowBundleReader = (WorkflowBundleReader) bundleContext
- .getService(serviceReference);
- if (workflowBundleReader.getMediaTypes().contains(
- T2FlowReader.APPLICATION_VND_TAVERNA_T2FLOW_XML)) {
- break;
- }
- }
- }
-
- if (databaseConfiguration == null) {
- ServiceReference databaseConfigurationReference = bundleContext
- .getServiceReference("uk.org.taverna.configuration.database.DatabaseConfiguration");
- databaseConfiguration = (DatabaseConfiguration) bundleContext
- .getService(databaseConfigurationReference);
- ServiceReference jndiContextManagerReference = bundleContext
- .getServiceReference("org.osgi.service.jndi.JNDIContextManager");
- jndiContextManager = (JNDIContextManager) bundleContext
- .getService(jndiContextManagerReference);
- ServiceReference applicationConfigurationReference = bundleContext
- .getServiceReference("uk.org.taverna.configuration.app.ApplicationConfiguration");
- applicationConfiguration = (ApplicationConfiguration) bundleContext
- .getService(applicationConfigurationReference);
- }
-
- }
-
- public void testOsgiPlatformStarts() throws Exception {
- System.out.println(Constants.FRAMEWORK_VENDOR + " = "
- + bundleContext.getProperty(Constants.FRAMEWORK_VENDOR));
- System.out.println(Constants.FRAMEWORK_VERSION + " = "
- + bundleContext.getProperty(Constants.FRAMEWORK_VERSION));
- System.out.println(Constants.FRAMEWORK_EXECUTIONENVIRONMENT + " = "
- + bundleContext.getProperty(Constants.FRAMEWORK_EXECUTIONENVIRONMENT));
- System.out.println(Constants.OSGI_IMPL_VERSION_KEY + " = "
- + bundleContext.getProperty(Constants.OSGI_IMPL_VERSION_KEY));
- }
-
- public WorkflowBundle loadWorkflow(String t2FlowFile) throws Exception {
- URL wfResource = getClass().getResource(t2FlowFile);
- assertNotNull(wfResource);
- return workflowBundleReader.readBundle(wfResource.openStream(),
- T2FlowReader.APPLICATION_VND_TAVERNA_T2FLOW_XML);
- }
-
- public File loadFile(String fileName) throws IOException, FileNotFoundException {
- File file = File.createTempFile("platform-test", null);
- InputStream inputStream = getClass().getResource(fileName).openStream();
- OutputStream outputStream = new FileOutputStream(file);
- byte[] buffer = new byte[64];
- int length = -1;
- while ((length = inputStream.read(buffer)) >= 0) {
- outputStream.write(buffer, 0, length);
- }
- outputStream.flush();
- outputStream.close();
- return file;
- }
-
- public void printErrors(Data data) {
- ErrorDocument error = (ErrorDocument) data.getValue();
- String message = error.getMessage();
- if (message != null) {
- System.out.println(message);
- }
- String exceptionMessage = error.getExceptionMessage();
- if (exceptionMessage != null) {
- System.out.println(exceptionMessage);
- }
- for (StackTraceElementBean stackTraceElementBean : error.getStackTraceStrings()) {
- System.out.println(stackTraceElementBean.getClassName());
- System.out.println(stackTraceElementBean.getMethodName());
- System.out.println(stackTraceElementBean.getLineNumber());
- }
-// Set<T2Reference> errorReferences = error.getErrorReferences();
-// for (T2Reference t2Reference : errorReferences) {
-// printErrors(referenceService, t2Reference);
-// }
- }
-
- public boolean checkResult(Data result, String expectedResult) {
- if (result.isError()) {
- printErrors(result);
- return false;
- } else {
- Object resultObject = result.getValue();
- String resultValue = null;
- if (resultObject instanceof byte[]) {
- resultValue = new String((byte[]) resultObject);
- } else {
- resultValue = (String) resultObject;
- }
-
- if (resultValue.startsWith(expectedResult)) {
- return true;
- } else {
- System.out.println("Expected: " + expectedResult + ", Actual: " + resultValue);
- return false;
- }
- }
- }
-
- public boolean waitForState(WorkflowReport report, State state) throws InterruptedException {
- return waitForState(report, state, true);
- }
-
- public boolean waitForState(WorkflowReport report, State state, boolean printReport)
- throws InterruptedException {
- int wait = 0;
- while (!report.getState().equals(state) && wait++ < 30) {
- if (printReport)
- System.out.println(report);
- Thread.sleep(500);
- }
- return report.getState().equals(state);
- }
-
- public void waitForResults(Map<String, Data> results, WorkflowReport report, String... ports)
- throws InterruptedException {
- int wait = 0;
- while (!resultsReady(results, ports) && wait++ < 20) {
- System.out.println(report);
- Thread.sleep(500);
- }
- }
-
- private boolean resultsReady(Map<String, Data> results, String... ports) {
- for (String port : ports) {
- if (!results.containsKey(port)) {
- return false;
- }
- }
- return true;
- }
-
-}