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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:37:16 UTC
[01/50] [abbrv] incubator-taverna-commandline git commit:
${commons.codec.version} 1.7 for T3-1193
Repository: incubator-taverna-commandline
Updated Branches:
refs/heads/master [created] e25a5dcd0
${commons.codec.version} 1.7 for T3-1193
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/33aae457
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/33aae457
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/33aae457
Branch: refs/heads/master
Commit: 33aae457d73a603041e142ef612d15f43222d13a
Parents: 1670283
Author: Christian-B <br...@cs.man.ac.uk>
Authored: Tue Jul 1 16:08:23 2014 +0100
Committer: Christian-B <br...@cs.man.ac.uk>
Committed: Tue Jul 1 16:08:23 2014 +0100
----------------------------------------------------------------------
pom.xml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/33aae457/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 8fd0b21..622ff18 100644
--- a/pom.xml
+++ b/pom.xml
@@ -239,8 +239,8 @@
<version>${mail.version}</version>
</dependency>
<dependency>
- <groupId>org.apache.commons</groupId>
- <artifactId>com.springsource.org.apache.commons.codec</artifactId>
+ <groupId>commons-codec</groupId>
+ <artifactId>commons-codec</artifactId>
<version>${commons.codec.version}</version>
</dependency>
[11/50] [abbrv] incubator-taverna-commandline git commit: Add -bundle
(replaces -outputdoc)
Posted by st...@apache.org.
Add -bundle (replaces -outputdoc)
Saves Workflow Run Bundle to file
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/e8f020f4
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/e8f020f4
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/e8f020f4
Branch: refs/heads/master
Commit: e8f020f400ec6c3dfa13fb3ca61d34e5f0c38fff
Parents: 473e379
Author: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Authored: Tue Oct 28 22:30:21 2014 +0000
Committer: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Committed: Tue Oct 28 22:30:21 2014 +0000
----------------------------------------------------------------------
.../commandline/CommandLineOptionsImpl.java | 30 ++++++++++++++------
1 file changed, 22 insertions(+), 8 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/e8f020f4/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
----------------------------------------------------------------------
diff --git a/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java b/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
index 78e9b0d..b702e03 100644
--- a/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
+++ b/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
@@ -49,6 +49,8 @@ import org.apache.log4j.Logger;
*/
public class CommandLineOptionsImpl implements CommandLineOptions {
+ private static final String OUTPUTDIR = "outputdir";
+ private static final String BUNDLE = "bundle";
private static final Logger logger = Logger.getLogger(CommandLineOptionsImpl.class);
private Options options;
private CommandLine commandLine;
@@ -202,7 +204,7 @@ public class CommandLineOptionsImpl implements CommandLineOptions {
*/
@Override
public String getOutputDirectory() {
- return getOptionValue("outputdir");
+ return getOptionValue(OUTPUTDIR);
}
@Override
@@ -297,11 +299,11 @@ public class CommandLineOptionsImpl implements CommandLineOptions {
.withDescription(
"Save outputs as files in directory, default "
+ "is to make a new directory workflowName_output.")
- .create("outputdir");
+ .create(OUTPUTDIR);
- Option outputdocOption = OptionBuilder.withArgName("document").hasArg()
- .withDescription("Save outputs to a new Baclava document.")
- .create("outputdoc");
+ Option bundleOption = OptionBuilder.withArgName(BUNDLE).hasArg()
+ .withDescription("Save outputs to a new Workflow Run Bundle (zip).")
+ .create(BUNDLE);
Option logFileOption = OptionBuilder
.withArgName("filename")
@@ -371,7 +373,7 @@ public class CommandLineOptionsImpl implements CommandLineOptions {
options.addOption(inputDelimiterOption);
options.addOption(inputdocOption);
options.addOption(outputOption);
- options.addOption(outputdocOption);
+ options.addOption(bundleOption);
options.addOption(inMemOption);
options.addOption(embedded);
options.addOption(clientserver);
@@ -424,8 +426,20 @@ public class CommandLineOptionsImpl implements CommandLineOptions {
*/
@Override
public boolean saveResultsToDirectory() {
- return (options.hasOption("outputdir") || !options
- .hasOption("outputdoc"));
+ return (options.hasOption(OUTPUTDIR) || !hasSaveResultsToBundle());
+ }
+
+ @Override
+ public String saveResultsToBundle() {
+ if (! hasSaveResultsToBundle()) {
+ return null;
+ }
+ return getOptionValue(BUNDLE);
+ }
+
+ @Override
+ public boolean hasSaveResultsToBundle() {
+ return hasOption(BUNDLE);
}
}
[27/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-tests/
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/secure-client-cert-authentication-https/secure-client-cert-authentication-https.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/secure-client-cert-authentication-https/secure-client-cert-authentication-https.t2flow b/src/test/resources/workflows/secure-client-cert-authentication-https/secure-client-cert-authentication-https.t2flow
deleted file mode 100644
index 1c5d317..0000000
--- a/src/test/resources/workflows/secure-client-cert-authentication-https/secure-client-cert-authentication-https.t2flow
+++ /dev/null
@@ -1,162 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="b982dcd5-dc2a-4fc5-b6dd-8d0b90a2f58e" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Client_Cert_AuthN_and_HTTPS</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
- <httpMethod>GET</httpMethod>
- <urlSignature>https://heater.cs.man.ac.uk:7444/examples-client-cert-authentication/taverna-test-page.html</urlSignature>
- <acceptsHeaderValue>text/plain</acceptsHeaderValue>
- <contentTypeForUpdates>application/xml</contentTypeForUpdates>
- <outgoingDataFormat>String</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>false</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders />
- <activityInputs />
-</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Client_Cert_AuthN_and_HTTPS</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>b982dcd5-dc2a-4fc5-b6dd-8d0b90a2f58e</identification>
- </annotationBean>
- <date>2011-06-23 11:14:45.626 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>23616693-e035-42e5-a52e-e1ddb0269d9c</identification>
- </annotationBean>
- <date>2011-06-21 15:49:05.979 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>47ad844e-df8e-4c65-803a-8a20c8197e8e</identification>
- </annotationBean>
- <date>2010-11-29 15:36:29.390 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>1f90ea89-a32f-41c1-b30c-2a5afd622984</identification>
- </annotationBean>
- <date>2010-11-22 14:20:41.517 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>e7fb38b1-b3ec-4c47-a584-36c68eeda25e</identification>
- </annotationBean>
- <date>2010-11-22 14:19:49.664 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
- </annotationBean>
- <date>2010-11-22 14:15:20.380 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>eaff435f-9025-429b-9a12-97fc94d90e73</identification>
- </annotationBean>
- <date>2010-11-22 14:18:46.551 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
- </annotationBean>
- <date>2010-11-22 14:16:43.484 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>5b302294-d370-4639-acb1-2a8452cc6d92</identification>
- </annotationBean>
- <date>2010-11-29 10:34:55.185 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>d9be6132-9d40-43f6-bd0b-8d29dca1163b</identification>
- </annotationBean>
- <date>2010-11-22 14:16:58.860 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>18b60848-4715-4532-b50c-45539ca00b44</identification>
- </annotationBean>
- <date>2011-06-21 16:24:23.704 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>b982dcd5-dc2a-4fc5-b6dd-8d0b90a2f58e</identification>
- </annotationBean>
- <date>2011-06-21 16:36:50.208 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>06a9fa6d-ba8d-4045-945b-a4a259a275e4</identification>
- </annotationBean>
- <date>2011-06-23 11:13:58.558 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/secure-digest-authentication-https/secure-digest-authentication-https.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/secure-digest-authentication-https/secure-digest-authentication-https.t2flow b/src/test/resources/workflows/secure-digest-authentication-https/secure-digest-authentication-https.t2flow
deleted file mode 100644
index 5d2f893..0000000
--- a/src/test/resources/workflows/secure-digest-authentication-https/secure-digest-authentication-https.t2flow
+++ /dev/null
@@ -1,107 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="47ad844e-df8e-4c65-803a-8a20c8197e8e" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Digest_AuthN_and_HTTPS</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
- <httpMethod>GET</httpMethod>
- <urlSignature>https://heater.cs.man.ac.uk:7443/examples-digest-authentication/taverna-test-page.html</urlSignature>
- <acceptsHeaderValue>text/plain</acceptsHeaderValue>
- <contentTypeForUpdates>application/xml</contentTypeForUpdates>
- <outgoingDataFormat>String</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>false</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders />
- <activityInputs />
-</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Digest_AuthN_and_HTTPS</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
- </annotationBean>
- <date>2010-11-22 14:16:43.484 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>eaff435f-9025-429b-9a12-97fc94d90e73</identification>
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- <date>2010-11-22 14:18:46.551 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <date>2010-11-22 14:16:58.860 GMT</date>
- <creators />
- <curationEventList />
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- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <identification>1f90ea89-a32f-41c1-b30c-2a5afd622984</identification>
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- <date>2010-11-22 14:20:41.517 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>e7fb38b1-b3ec-4c47-a584-36c68eeda25e</identification>
- </annotationBean>
- <date>2010-11-22 14:19:49.664 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>5b302294-d370-4639-acb1-2a8452cc6d92</identification>
- </annotationBean>
- <date>2010-11-29 10:34:55.185 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
- </annotationBean>
- <date>2010-11-22 14:15:20.380 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>47ad844e-df8e-4c65-803a-8a20c8197e8e</identification>
- </annotationBean>
- <date>2010-11-29 15:36:29.390 GMT</date>
- <creators />
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/secure-digest-authentication/secure-digest-authentication.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/secure-digest-authentication/secure-digest-authentication.t2flow b/src/test/resources/workflows/secure-digest-authentication/secure-digest-authentication.t2flow
deleted file mode 100644
index 449e9db..0000000
--- a/src/test/resources/workflows/secure-digest-authentication/secure-digest-authentication.t2flow
+++ /dev/null
@@ -1,129 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="a218f0b5-b675-4eed-b7a8-a5c63181ff3e" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Digest_AuthN</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
- <httpMethod>GET</httpMethod>
- <urlSignature>http://heater.cs.man.ac.uk:7070/examples-digest-authentication/taverna-test-page.html</urlSignature>
- <acceptsHeaderValue>text/plain</acceptsHeaderValue>
- <contentTypeForUpdates>application/xml</contentTypeForUpdates>
- <outgoingDataFormat>String</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>false</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders />
- <activityInputs />
-</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Digest_AuthN</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
- </annotationBean>
- <date>2010-11-22 14:16:43.484 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>d9be6132-9d40-43f6-bd0b-8d29dca1163b</identification>
- </annotationBean>
- <date>2010-11-22 14:16:58.860 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
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- <date>2010-11-22 14:15:20.380 GMT</date>
- <creators />
- <curationEventList />
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- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <identification>1f90ea89-a32f-41c1-b30c-2a5afd622984</identification>
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- <date>2010-11-22 14:20:41.517 GMT</date>
- <creators />
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-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>e7fb38b1-b3ec-4c47-a584-36c68eeda25e</identification>
- </annotationBean>
- <date>2010-11-22 14:19:49.664 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>eaff435f-9025-429b-9a12-97fc94d90e73</identification>
- </annotationBean>
- <date>2010-11-22 14:18:46.551 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>5b302294-d370-4639-acb1-2a8452cc6d92</identification>
- </annotationBean>
- <date>2010-11-29 10:34:55.185 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>fd59d61c-50f8-457b-a183-c162453b026b</identification>
- </annotationBean>
- <date>2010-11-29 15:29:08.570 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>435023d5-0063-4914-ae4c-28a7a031ec0d</identification>
- </annotationBean>
- <date>2010-11-29 10:40:30.468 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>a218f0b5-b675-4eed-b7a8-a5c63181ff3e</identification>
- </annotationBean>
- <date>2010-11-29 15:39:35.589 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/secure-ws-https/secure-ws-https.t2flow
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diff --git a/src/test/resources/workflows/secure-ws-https/secure-ws-https.t2flow b/src/test/resources/workflows/secure-ws-https/secure-ws-https.t2flow
deleted file mode 100644
index 13637c4..0000000
--- a/src/test/resources/workflows/secure-ws-https/secure-ws-https.t2flow
+++ /dev/null
@@ -1,180 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="c71621ca-196c-46cd-9073-48af82b4bd4f" role="top"><name>Workflow13</name><inputPorts /><outputPorts><port><name>out_plaintext</name><annotations /></port><port><name>out_plaintext_timestamp</name><annotations /></port><port><name>out_digest</name><annotations /></port><port><name>out_digest_timestamp</name><annotations /></port></outputPorts><processors><processor><name>hello_plaintext_password</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><m
ap from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword?wsdl</wsdl>
- <operation>hello</operation>
- <securityProfile>WSSecurityUsernameTokenPlainTextPassword</securityProfile>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="
value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>Alan</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
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- <initialDelay>1000</initialDelay>
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in0" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword-Timestamp?wsdl</wsdl>
- <operation>hello</operation>
- <securityProfile>WSSecurityTimestampUsernameTokenPlainTextPassword</securityProfile>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
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- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
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-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_1</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from
="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
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-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
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.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>hello_digest_password</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inpu
tMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>https://heater.cs.man.ac.uk:7443/axis/services/HelloService-DigestPassword?wsdl</wsdl>
- <operation>hello</operation>
- <securityProfile>WSSecurityUsernameTokenDigestPassword</securityProfile>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_2</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from
="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>Stian</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>hello_digest_password_timestamp</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0
" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>https://heater.cs.man.ac.uk:7443/axis/services/HelloService-DigestPassword-Timestamp?wsdl</wsdl>
- <operation>hello</operation>
- <securityProfile>WSSecurityTimestampUsernameTokenDigestPassword</securityProfile>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_3</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from
="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>David</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions><condition control="hello_plaintext_password" target="hello_digest_password" /><condition control="hello_digest_password_timestamp" target="hello_plaintext_password_timestamp" /><condition control="hello_digest_password" target="hello_digest_password_timestamp" /></conditions><datalinks><datalink><sink type="processor"><processor>hello_plaintext_password</processor><port>in0</port></sink><source type="processor"><processor>in0_value</processor><port>value</port>
</source></datalink><datalink><sink type="processor"><processor>hello_plaintext_password_timestamp</processor><port>in0</port></sink><source type="processor"><processor>in0_value_1</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>hello_digest_password</processor><port>in0</port></sink><source type="processor"><processor>in0_value_2</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>hello_digest_password_timestamp</processor><port>in0</port></sink><source type="processor"><processor>in0_value_3</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out_plaintext</port></sink><source type="processor"><processor>hello_plaintext_password</processor><port>helloReturn</port></source></datalink><datalink><sink type="dataflow"><port>out_plaintext_timestamp</port></sink><source type="processor"><processor>hello_plaintext_password_timestamp</processor><port>helloReturn</port><
/source></datalink><datalink><sink type="dataflow"><port>out_digest</port></sink><source type="processor"><processor>hello_digest_password</processor><port>helloReturn</port></source></datalink><datalink><sink type="dataflow"><port>out_digest_timestamp</port></sink><source type="processor"><processor>hello_digest_password_timestamp</processor><port>helloReturn</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>c71621ca-196c-46cd-9073-48af82b4bd4f</identification>
- </annotationBean>
- <date>2011-06-21 12:11:30.87 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>56cadac0-c944-4b9e-83c3-078f57738405</identification>
- </annotationBean>
- <date>2011-01-21 16:02:09.633 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>3d76be4c-83c4-413b-91f2-b0ce69dcbd97</identification>
- </annotationBean>
- <date>2010-11-22 13:29:43.282 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>ca8fb5c5-0e8c-4e68-84f0-bdc85a77e2b3</identification>
- </annotationBean>
- <date>2010-11-22 13:29:26.400 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>e61023d9-d603-4df6-87e5-175603f106a5</identification>
- </annotationBean>
- <date>2010-11-22 13:28:31.68 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>394aced4-ee5d-4355-8ebe-9fc8bcfe5303</identification>
- </annotationBean>
- <date>2011-06-21 12:07:46.327 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>8175c97b-6385-460a-98ab-5cf974010d51</identification>
- </annotationBean>
- <date>2010-11-22 12:11:59.610 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>a388d568-ca08-43b4-abaf-3744a6801d45</identification>
- </annotationBean>
- <date>2010-11-22 13:30:28.898 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>7153a2dd-18bd-4f25-80ab-1efa8afc567d</identification>
- </annotationBean>
- <date>2011-01-21 16:02:39.43 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
[38/50] [abbrv] incubator-taverna-commandline git commit: hardcoded
versions in .sh/.bat :(
Posted by st...@apache.org.
hardcoded versions in .sh/.bat :(
need for install4j
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/2404694c
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/2404694c
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/2404694c
Branch: refs/heads/master
Commit: 2404694cc352e2ff69e65678ec632a03af1f5ca6
Parents: 4435975
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 03:31:09 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 03:31:09 2014 -0600
----------------------------------------------------------------------
taverna-commandline-product/src/main/etc/executeworkflow.bat | 2 +-
taverna-commandline-product/src/main/etc/executeworkflow.sh | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/2404694c/taverna-commandline-product/src/main/etc/executeworkflow.bat
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/etc/executeworkflow.bat b/taverna-commandline-product/src/main/etc/executeworkflow.bat
index 722816c..165dc83 100644
--- a/taverna-commandline-product/src/main/etc/executeworkflow.bat
+++ b/taverna-commandline-product/src/main/etc/executeworkflow.bat
@@ -14,4 +14,4 @@ set ARGS=%ARGS% "-Dlog4j.configuration=file:///%TAVERNA_HOME%conf/log4j.properti
set ARGS=%ARGS% "-Djava.util.logging.config.file=%TAVERNA_HOME%conf/logging.properties"
set ARGS=%ARGS% "-Dtaverna.app.startup=%TAVERNA_HOME%."
-java %ARGS% -jar "%TAVERNA_HOME%lib\uk.org.taverna.commandline\taverna-command-line-0.1.2-SNAPSHOT.jar" %*
+java %ARGS% -jar "%TAVERNA_HOME%lib\/lib/org.apache.taverna.commandline/taverna-commandline-launcher-3.1.0-incubating-SNAPSHOT.jar" %*
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/2404694c/taverna-commandline-product/src/main/etc/executeworkflow.sh
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/etc/executeworkflow.sh b/taverna-commandline-product/src/main/etc/executeworkflow.sh
index 663d37f..48e4428 100644
--- a/taverna-commandline-product/src/main/etc/executeworkflow.sh
+++ b/taverna-commandline-product/src/main/etc/executeworkflow.sh
@@ -21,5 +21,5 @@ exec "$javabin" -Xmx1g -XX:MaxPermSize=400m \
"-Dlog4j.configuration=file://$taverna_home/conf/log4j.properties " \
"-Djava.util.logging.config.file=$taverna_home/conf/logging.properties " \
"-Dtaverna.app.startup=$taverna_home" \
- -jar "$taverna_home/lib/uk.org.taverna.commandline/taverna-command-line-0.1.2-SNAPSHOT.jar" \
+ -jar "$taverna_home/lib/org.apache.taverna.commandline/taverna-commandline-launcher-3.1.0-incubating-SNAPSHOT.jar" \
${1+"$@"}
[19/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-tests/
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/soaplab/soaplab.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/soaplab/soaplab.t2flow b/taverna-commandline-tests/src/test/resources/workflows/soaplab/soaplab.t2flow
new file mode 100644
index 0000000..f1ef82b
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/soaplab/soaplab.t2flow
@@ -0,0 +1,84 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="db8053e3-1837-42cc-ba27-5fd0a83f119e" role="top"><name>Retrieve_sequence_in_EMBL_format</name><inputPorts /><outputPorts><port><name>sequence</name><annotations /></port></outputPorts><processors><processor><name>sequence_feature</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>true</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>sequence_id</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.s
f.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>embl:x52524</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>sequence_format</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><n
et.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>embl</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>seqret</name><inputPorts><port><name>sequence_usa</name><depth>0</depth></port><port><name>feature</name><depth>0</depth></port><port><name>osformat_outseq</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outseq</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2
.activities.soaplab.SoaplabActivity</class><inputMap><map from="osformat_outseq" to="osformat_outseq" /><map from="feature" to="feature" /><map from="sequence_usa" to="sequence_usa" /></inputMap><outputMap><map from="outseq" to="outseq" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
+ <endpoint>http://www.ebi.ac.uk/soaplab/services/edit.seqret</endpoint>
+ <pollingInterval>0</pollingInterval>
+ <pollingBackoff>1.0</pollingBackoff>
+ <pollingIntervalMax>0</pollingIntervalMax>
+</net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="sequence_usa" depth="0" /><port name="feature" depth="0" /><port name="osformat_outseq" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>seqret</processor><port>sequence_usa</port></sink><source type="processor"><processor>sequence_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>seqret</processor><port>feature</port></sink><source type="processor"><processor>sequence_f
eature</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>seqret</processor><port>osformat_outseq</port></sink><source type="processor"><processor>sequence_format</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>sequence</port></sink><source type="processor"><processor>seqret</processor><port>outseq</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
+ <text>Retrieve sequence in EMBL format</text>
+ </annotationBean>
+ <date>2009-12-15 20:21:29.202 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
+ <text>Franck Tanoh</text>
+ </annotationBean>
+ <date>2009-12-15 20:21:20.965 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>db8053e3-1837-42cc-ba27-5fd0a83f119e</identification>
+ </annotationBean>
+ <date>2010-07-04 17:49:51.364 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
+ <text>This workflow retrieves a sequence associated with its features in embl format</text>
+ </annotationBean>
+ <date>2009-12-15 20:21:39.30 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/spreadsheetimport/spreadsheetimport.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/spreadsheetimport/spreadsheetimport.t2flow b/taverna-commandline-tests/src/test/resources/workflows/spreadsheetimport/spreadsheetimport.t2flow
new file mode 100644
index 0000000..7360186
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/spreadsheetimport/spreadsheetimport.t2flow
@@ -0,0 +1,646 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="fa4ef38e-fa3f-4662-97e5-59c3b51aa322" role="top"><name>Spreadsheet_Import_Example</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>SpreadsheetImport</name><inputPorts><port><name>fileurl</name><depth>0</depth></port></inputPorts><outputPorts><port><name>other</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>other_industry</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>year</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>spreadsheet-import-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportActivity</class><inputMap><map from="fileurl" to="fileurl" /></inputMap><outputMap><ma
p from="other" to="other" /><map from="year" to="year" /><map from="other_industry" to="other_industry" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration xmlns="">
+ <columnRange>
+ <start>1</start>
+ <end>6</end>
+ <excludes />
+ </columnRange>
+ <rowRange>
+ <start>7</start>
+ <end>41</end>
+ <excludes />
+ </rowRange>
+ <emptyCellValue />
+ <columnNames>
+ <entry>
+ <string>D</string>
+ <string>other</string>
+ </entry>
+ <entry>
+ <string>E</string>
+ <string>fish_farming</string>
+ </entry>
+ <entry>
+ <string>F</string>
+ <string>other_industry</string>
+ </entry>
+ <entry>
+ <string>G</string>
+ <string>public_water_supply</string>
+ </entry>
+ <entry>
+ <string>A</string>
+ <string>over</string>
+ </entry>
+ <entry>
+ <string>B</string>
+ <string>year</string>
+ </entry>
+ <entry>
+ <string>C</string>
+ <string>electricity</string>
+ </entry>
+ <entry>
+ <string>L</string>
+ <string>2001</string>
+ </entry>
+ <entry>
+ <string>N</string>
+ <string>2002</string>
+ </entry>
+ <entry>
+ <string>H</string>
+ <string>1999</string>
+ </entry>
+ <entry>
+ <string>J</string>
+ <string>2000</string>
+ </entry>
+ <entry>
+ <string>T</string>
+ <string>2005</string>
+ </entry>
+ <entry>
+ <string>V</string>
+ <string>2006</string>
+ </entry>
+ <entry>
+ <string>P</string>
+ <string>2003</string>
+ </entry>
+ <entry>
+ <string>R</string>
+ <string>2004</string>
+ </entry>
+ <entry>
+ <string>X</string>
+ <string>2007</string>
+ </entry>
+ <entry>
+ <string>Z</string>
+ <string>2008</string>
+ </entry>
+ </columnNames>
+ <allRows>false</allRows>
+ <excludeFirstRow>false</excludeFirstRow>
+ <ignoreBlankRows>false</ignoreBlankRows>
+ <emptyCellPolicy>EMPTY_STRING</emptyCellPolicy>
+ <outputFormat>PORT_PER_COLUMN</outputFormat>
+ <csvDelimiter>,</csvDelimiter>
+</net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
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+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
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+ <value>http://www.myexperiment.org/files/410/download/WaterUse.xlsx</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
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nImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>41265789-c464-4ee2-b145-95ece9388305</identification>
+ </annotationBean>
+ <date>2010-07-07 22:34:29.364 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
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+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b4363407-ef56-4cf3-998f-8e780a8dc816</identification>
+ </annotationBean>
+ <date>2010-07-07 16:41:31.230 BST</date>
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+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>486a5356-0f3e-424d-b14e-249295875f2d</identification>
+ </annotationBean>
+ <date>2010-07-13 12:31:34.664 BST</date>
+ <creators />
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+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
+ <text>David Withers</text>
+ </annotationBean>
+ <date>2010-07-13 11:09:24.988 BST</date>
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+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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+ <date>2011-11-02 15:41:32.280 GMT</date>
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+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>9c2e4b9c-5f25-4416-8653-cd9198a9271e</identification>
+ </annotationBean>
+ <date>2010-07-13 11:19:30.143 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>c0753ab7-cd9d-400e-b483-048dcbaad5f9</identification>
+ </annotationBean>
+ <date>2010-07-07 16:36:44.391 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>99e82825-40e1-4fa9-8cf4-5348a8ff7b82</identification>
+ </annotationBean>
+ <date>2010-07-07 22:38:24.439 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>2c1532f6-0ba4-48ea-9bf4-3fd3e39c6289</identification>
+ </annotationBean>
+ <date>2010-07-07 14:00:56.585 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>92d8fa84-2553-4de1-bff5-7d2a9b53c58d</identification>
+ </annotationBean>
+ <date>2010-07-07 17:31:19.499 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>f0fe1955-23d6-41b7-b1af-b36d641429b4</identification>
+ </annotationBean>
+ <date>2010-07-07 17:24:52.98 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>47de0484-f703-40ab-b1f7-b0826495a00d</identification>
+ </annotationBean>
+ <date>2010-07-07 23:09:23.782 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>7ca4b117-111d-4605-826e-868d7d159b52</identification>
+ </annotationBean>
+ <date>2010-07-13 11:16:32.697 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>99c992df-d200-4cda-a973-c60be723e784</identification>
+ </annotationBean>
+ <date>2010-07-07 17:14:16.5 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>58a4da02-d1f0-41ce-9ace-8a62b49b62d7</identification>
+ </annotationBean>
+ <date>2010-07-13 11:22:26.72 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>a752e401-77c5-42ef-9bf8-a60aa8af73f5</identification>
+ </annotationBean>
+ <date>2010-07-07 22:50:42.557 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
+ <text>Spreadsheet Import Example</text>
+ </annotationBean>
+ <date>2010-07-13 11:22:34.496 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>dfa2cd09-f53d-47f4-91cd-207ec2dc2c34</identification>
+ </annotationBean>
+ <date>2010-07-07 16:51:22.4 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>31ac21d6-7c10-48ff-b9b2-82cac03f55c9</identification>
+ </annotationBean>
+ <date>2010-07-07 22:43:05.458 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>70c23010-0b47-424e-a1ce-73c040c3d3c6</identification>
+ </annotationBean>
+ <date>2010-07-07 16:43:47.690 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
+ <text>Example using the SpreadsheetImport service to import data from an Excel spreadsheet.
+The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date.
+The source data is from http://data.gov.uk/</text>
+ </annotationBean>
+ <date>2010-07-13 11:16:31.908 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>27965b7c-1a89-46ac-8c9b-a4c6bf9144f0</identification>
+ </annotationBean>
+ <date>2010-07-13 11:22:36.27 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>6c2a0ecf-5d91-4722-adf6-607c912ed54c</identification>
+ </annotationBean>
+ <date>2010-07-07 16:54:20.460 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>808e3725-2a08-4907-9706-fb7f0f08f62f</identification>
+ </annotationBean>
+ <date>2010-07-13 11:20:05.749 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>6e069c36-8d88-4017-96cf-c1fa87007777</identification>
+ </annotationBean>
+ <date>2010-07-07 16:20:48.694 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>73ce4e99-6b83-45d0-8605-896d6d48b7f0</identification>
+ </annotationBean>
+ <date>2010-07-07 17:01:14.713 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/stringconstant/stringconstant.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/stringconstant/stringconstant.t2flow b/taverna-commandline-tests/src/test/resources/workflows/stringconstant/stringconstant.t2flow
new file mode 100644
index 0000000..41266d0
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/stringconstant/stringconstant.t2flow
@@ -0,0 +1,32 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="48c5c70e-ffde-4ff0-8508-015577ab263c" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>String_constant</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Test Value</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>String_constant</processor><port>value</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>48c5c70e-ffde-4ff0-8508-015577ab263c</identification>
+ </annotationBean>
+ <date>2010-12-14 11:57:31.126 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>186f09f7-d9a7-4ae2-bf84-8ee83f41f4e3</identification>
+ </annotationBean>
+ <date>2010-12-14 11:56:50.253 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/tool/tool.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/tool/tool.t2flow b/taverna-commandline-tests/src/test/resources/workflows/tool/tool.t2flow
new file mode 100644
index 0000000..d77a851
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/tool/tool.t2flow
@@ -0,0 +1,158 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="82a5216a-8b82-41db-a114-ece396f9b85c" role="top"><name>Workflow4</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Tool</name><inputPorts><port><name>in1</name><depth>0</depth></port><port><name>in2</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean
xmlns="">
+ <mechanismType>789663B8-DA91-428A-9F7D-B3F3DA185FD4</mechanismType>
+ <mechanismName>default local</mechanismName>
+ <mechanismXML><?xml version="1.0" encoding="UTF-8"?>
+<localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation>
+</mechanismXML>
+ <externaltoolid>607ceaee-59ba-4cbb-a650-84e51d8498e3</externaltoolid>
+ <useCaseDescription>
+ <usecaseid />
+ <description />
+ <command>cat in1 > out; echo %%in2%% >> out
+ </command>
+ <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
+ <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
+ <tags>
+ <string>in2</string>
+ </tags>
+ <REs />
+ <queue__preferred />
+ <queue__deny />
+ <static__inputs>
+ <de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
+ <tag>hi</tag>
+ <file>true</file>
+ <tempFile>false</tempFile>
+ <binary>false</binary>
+ <charsetName>MacRoman</charsetName>
+ <forceCopy>false</forceCopy>
+ <content class="string">hi</content>
+ </de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
+ <de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
+ <tag>google</tag>
+ <file>true</file>
+ <tempFile>false</tempFile>
+ <binary>false</binary>
+ <charsetName>MacRoman</charsetName>
+ <forceCopy>false</forceCopy>
+ <url>http://www.google.com/</url>
+ </de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
+ </static__inputs>
+ <inputs>
+ <entry>
+ <string>in2</string>
+ <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
+ <tag>in2</tag>
+ <file>false</file>
+ <tempFile>false</tempFile>
+ <binary>false</binary>
+ <charsetName>MacRoman</charsetName>
+ <forceCopy>false</forceCopy>
+ <list>false</list>
+ <concatenate>false</concatenate>
+ <mime />
+ </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
+ </entry>
+ <entry>
+ <string>in1</string>
+ <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
+ <tag>in1</tag>
+ <file>true</file>
+ <tempFile>false</tempFile>
+ <binary>false</binary>
+ <charsetName>MacRoman</charsetName>
+ <forceCopy>false</forceCopy>
+ <list>false</list>
+ <concatenate>false</concatenate>
+ <mime />
+ </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
+ </entry>
+ </inputs>
+ <outputs>
+ <entry>
+ <string>out</string>
+ <de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
+ <path>out</path>
+ <binary>false</binary>
+ <mime />
+ </de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
+ </entry>
+ </outputs>
+ <includeStdIn>false</includeStdIn>
+ <includeStdOut>true</includeStdOut>
+ <includeStdErr>true</includeStdErr>
+ <validReturnCodes>
+ <int>0</int>
+ </validReturnCodes>
+ </useCaseDescription>
+ <edited>false</edited>
+</net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in1" depth="0" /><port name="in2" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><
map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Hello</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>in2_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.
taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>World</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Tool</processor><port>in1</port></sink><source type="processor"><processor>in_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Tool</processor><port>in2</port></sink><source type="processor"><processor>in2_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Tool</processor>
<port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>6090defe-8eba-4775-8dd6-ab48813d23ab</identification>
+ </annotationBean>
+ <date>2011-10-27 18:50:36.777 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>8312a5c9-b291-4a20-a468-0cdd8888115b</identification>
+ </annotationBean>
+ <date>2011-10-27 18:46:58.794 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>82a5216a-8b82-41db-a114-ece396f9b85c</identification>
+ </annotationBean>
+ <date>2011-11-10 17:19:20.269 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>436555c3-0df8-4e5c-93f3-313124bf045c</identification>
+ </annotationBean>
+ <date>2011-10-27 18:52:22.981 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/wsdl/wsdl.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/wsdl/wsdl.t2flow b/taverna-commandline-tests/src/test/resources/workflows/wsdl/wsdl.t2flow
new file mode 100644
index 0000000..4dea6bb
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/wsdl/wsdl.t2flow
@@ -0,0 +1,22 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="eed49d32-8563-45ff-8716-347b20800129" role="top"><name>Workflow5</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>getVersion</name><inputPorts /><outputPorts><port><name>getVersionReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap /><outputMap><map from="getVersionReturn" to="getVersionReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>http://www.mygrid.org.uk/axis/services/Version?wsdl</wsdl>
+ <operation>getVersion</operation>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>getVersion</processor><port>getVersionReturn</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eed49d32-8563-45ff-8716-347b20800129</identification>
+ </annotationBean>
+ <date>2011-01-25 16:37:45.583 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/age
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/age b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/age
new file mode 100644
index 0000000..b5045cc
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/age
@@ -0,0 +1 @@
+21
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/firstName
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/firstName b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/firstName
new file mode 100644
index 0000000..08df4e7
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/firstName
@@ -0,0 +1 @@
+John
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/lastName
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/lastName b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/lastName
new file mode 100644
index 0000000..b77017e
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/inputs/lastName
@@ -0,0 +1 @@
+Smith
\ No newline at end of file
[08/50] [abbrv] incubator-taverna-commandline git commit: Merge
branch 'devel' of github.com:taverna/taverna-commandline-product into devel
Posted by st...@apache.org.
Merge branch 'devel' of github.com:taverna/taverna-commandline-product into devel
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/4b3d5ed8
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/4b3d5ed8
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/4b3d5ed8
Branch: refs/heads/master
Commit: 4b3d5ed87da6c25dd176140bc121b75ac51f04a8
Parents: 946757c bcd5f6f
Author: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Authored: Mon Oct 27 16:27:18 2014 +0000
Committer: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Committed: Mon Oct 27 16:27:18 2014 +0000
----------------------------------------------------------------------
pom.xml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
[30/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-tests/
Posted by st...@apache.org.
taverna-commandline-tests/
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/9601b2f1
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/9601b2f1
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/9601b2f1
Branch: refs/heads/master
Commit: 9601b2f1675a559a7cb36f3e4707493b90d2f40d
Parents: 427bce8
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 01:50:49 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 01:50:49 2014 -0600
----------------------------------------------------------------------
.gitignore | 24 -
.project | 23 -
.travis.yml | 1 -
README.md | 3 -
pom.xml | 97 ---
.../commandline/TavernaCommandLineTest.java | 485 --------------
.../taverna/commandline/WorkflowTestRunner.java | 70 --
.../taverna/commandline/WorkflowTestSuite.java | 79 ---
.../biomartandembossanalysis.url | 1 -
.../biomartandembossanalysis/ignorePort | 1 -
.../biomoby_tutorial_workflow.url | 1 -
.../biomoby_tutorial_workflow/ignorePort | 1 -
.../biomoby_tutorial_workflow/inputs/id | 1 -
.../biomoby_tutorial_workflow/inputs/namespace | 1 -
.../demonstration_of_configurable_iteration.url | 1 -
.../ebi_interproscan_newservices.url | 1 -
.../ebi_interproscan_newservices/ignorePort | 1 -
.../ebi_interproscan_newservices/inputs/email | 1 -
.../inputs/sequence | 8 -
.../example_of_conditional_invocation.url | 1 -
.../inputs/condition | 1 -
.../example_of_explicit_looping.url | 1 -
.../example_of_explicit_looping/inputs/end | 1 -
.../example_of_explicit_looping/inputs/start | 1 -
.../example_of_explicit_looping/inputs/step | 1 -
...e_workflow_for_rest_and_xpath_activities.url | 1 -
.../Name_Of_Location_for_Weather_Forecast | 1 -
.../fetch_dragon_images_from_biomoby.url | 1 -
.../fetch_pdb_flatfile_from_rcsb_server.url | 1 -
.../inputs/pdbID | 1 -
.../fetch_today_s_xkcd_comic.url | 1 -
.../myexperiment/gbseq_test/gbseq_test.url | 1 -
.../myexperiment/hello_anyone/hello_anyone.url | 1 -
.../myexperiment/hello_anyone/inputs/name | 1 -
.../myexperiment/hello_world/hello_world.url | 1 -
.../pipelined_list_iteration/inputs/input | 1 -
.../pipelined_list_iteration.url | 1 -
.../retrieve_sequence_in_embl_format.url | 1 -
.../secure_rest_service_call_example.url | 1 -
.../secure_web_service_call_example.url | 1 -
.../spreadsheed_data_import_example.url | 1 -
.../unix_external_tools_with_zip_and_unzip.url | 1 -
.../unix_numerically_adding_two_values/inputs/a | 1 -
.../unix_numerically_adding_two_values/inputs/b | 1 -
.../unix_numerically_adding_two_values.url | 1 -
...ix_tool_service_using_string_replacement.url | 1 -
src/test/resources/security/t2keystore.ubr | Bin 3312 -> 0 bytes
src/test/resources/security/t2truststore.ubr | Bin 213408 -> 0 bytes
.../resources/security/taverna-keystore.ubr | Bin 3312 -> 0 bytes
.../resources/security/taverna-truststore.ubr | Bin 213408 -> 0 bytes
.../workflows/apiconsumer/apiconsumer.t2flow | 178 -----
.../resources/workflows/apiconsumer/inputs/in | 1 -
.../workflows/beanshell/beanshell.t2flow | 137 ----
.../resources/workflows/beanshell/inputs/in | 1 -
.../resources/workflows/biomart/biomart.t2flow | 30 -
.../workflows/dataflow/dataflow.t2flow | 217 -------
src/test/resources/workflows/dataflow/inputs/in | 1 -
.../resources/workflows/in-out/in-out.t2flow | 12 -
src/test/resources/workflows/in-out/inputs/in | 1 -
.../resources/workflows/iteration/inputs/in | 1 -
.../workflows/iteration/iteration.t2flow | 474 --------------
.../resources/workflows/localworker/inputs/in | 1 -
.../workflows/localworker/localworker.t2flow | 67 --
src/test/resources/workflows/rest/rest.t2flow | 154 -----
.../secure-basic-authentication-https.t2flow | 74 ---
.../secure-basic-authentication.t2flow | 74 ---
...cure-client-cert-authentication-https.t2flow | 162 -----
.../secure-digest-authentication-https.t2flow | 107 ---
.../secure-digest-authentication.t2flow | 129 ----
.../secure-ws-https/secure-ws-https.t2flow | 180 ------
.../workflows/secure-ws/secure-ws.t2flow | 180 ------
.../workflows/secure-wsdl/secure-wsdl.t2flow | 131 ----
.../resources/workflows/soaplab/soaplab.t2flow | 84 ---
.../spreadsheetimport/spreadsheetimport.t2flow | 646 -------------------
.../stringconstant/stringconstant.t2flow | 32 -
src/test/resources/workflows/tool/tool.t2flow | 158 -----
src/test/resources/workflows/wsdl/wsdl.t2flow | 22 -
.../resources/workflows/xmlSplitter/inputs/age | 1 -
.../workflows/xmlSplitter/inputs/firstName | 1 -
.../workflows/xmlSplitter/inputs/lastName | 1 -
.../workflows/xmlSplitter/xmlSplitter.t2flow | 339 ----------
src/test/resources/workflows/xpath/xpath.t2flow | 127 ----
taverna-commandline-tests/pom.xml | 97 +++
.../commandline/TavernaCommandLineTest.java | 485 ++++++++++++++
.../taverna/commandline/WorkflowTestRunner.java | 70 ++
.../taverna/commandline/WorkflowTestSuite.java | 79 +++
.../biomartandembossanalysis.url | 1 +
.../biomartandembossanalysis/ignorePort | 1 +
.../biomoby_tutorial_workflow.url | 1 +
.../biomoby_tutorial_workflow/ignorePort | 1 +
.../biomoby_tutorial_workflow/inputs/id | 1 +
.../biomoby_tutorial_workflow/inputs/namespace | 1 +
.../demonstration_of_configurable_iteration.url | 1 +
.../ebi_interproscan_newservices.url | 1 +
.../ebi_interproscan_newservices/ignorePort | 1 +
.../ebi_interproscan_newservices/inputs/email | 1 +
.../inputs/sequence | 8 +
.../example_of_conditional_invocation.url | 1 +
.../inputs/condition | 1 +
.../example_of_explicit_looping.url | 1 +
.../example_of_explicit_looping/inputs/end | 1 +
.../example_of_explicit_looping/inputs/start | 1 +
.../example_of_explicit_looping/inputs/step | 1 +
...e_workflow_for_rest_and_xpath_activities.url | 1 +
.../Name_Of_Location_for_Weather_Forecast | 1 +
.../fetch_dragon_images_from_biomoby.url | 1 +
.../fetch_pdb_flatfile_from_rcsb_server.url | 1 +
.../inputs/pdbID | 1 +
.../fetch_today_s_xkcd_comic.url | 1 +
.../myexperiment/gbseq_test/gbseq_test.url | 1 +
.../myexperiment/hello_anyone/hello_anyone.url | 1 +
.../myexperiment/hello_anyone/inputs/name | 1 +
.../myexperiment/hello_world/hello_world.url | 1 +
.../pipelined_list_iteration/inputs/input | 1 +
.../pipelined_list_iteration.url | 1 +
.../retrieve_sequence_in_embl_format.url | 1 +
.../secure_rest_service_call_example.url | 1 +
.../secure_web_service_call_example.url | 1 +
.../spreadsheed_data_import_example.url | 1 +
.../unix_external_tools_with_zip_and_unzip.url | 1 +
.../unix_numerically_adding_two_values/inputs/a | 1 +
.../unix_numerically_adding_two_values/inputs/b | 1 +
.../unix_numerically_adding_two_values.url | 1 +
...ix_tool_service_using_string_replacement.url | 1 +
.../src/test/resources/security/t2keystore.ubr | Bin 0 -> 3312 bytes
.../test/resources/security/t2truststore.ubr | Bin 0 -> 213408 bytes
.../resources/security/taverna-keystore.ubr | Bin 0 -> 3312 bytes
.../resources/security/taverna-truststore.ubr | Bin 0 -> 213408 bytes
.../workflows/apiconsumer/apiconsumer.t2flow | 178 +++++
.../resources/workflows/apiconsumer/inputs/in | 1 +
.../workflows/beanshell/beanshell.t2flow | 137 ++++
.../resources/workflows/beanshell/inputs/in | 1 +
.../resources/workflows/biomart/biomart.t2flow | 30 +
.../workflows/dataflow/dataflow.t2flow | 217 +++++++
.../test/resources/workflows/dataflow/inputs/in | 1 +
.../resources/workflows/in-out/in-out.t2flow | 12 +
.../test/resources/workflows/in-out/inputs/in | 1 +
.../resources/workflows/iteration/inputs/in | 1 +
.../workflows/iteration/iteration.t2flow | 474 ++++++++++++++
.../resources/workflows/localworker/inputs/in | 1 +
.../workflows/localworker/localworker.t2flow | 67 ++
.../test/resources/workflows/rest/rest.t2flow | 154 +++++
.../secure-basic-authentication-https.t2flow | 74 +++
.../secure-basic-authentication.t2flow | 74 +++
...cure-client-cert-authentication-https.t2flow | 162 +++++
.../secure-digest-authentication-https.t2flow | 107 +++
.../secure-digest-authentication.t2flow | 129 ++++
.../secure-ws-https/secure-ws-https.t2flow | 180 ++++++
.../workflows/secure-ws/secure-ws.t2flow | 180 ++++++
.../workflows/secure-wsdl/secure-wsdl.t2flow | 131 ++++
.../resources/workflows/soaplab/soaplab.t2flow | 84 +++
.../spreadsheetimport/spreadsheetimport.t2flow | 646 +++++++++++++++++++
.../stringconstant/stringconstant.t2flow | 32 +
.../test/resources/workflows/tool/tool.t2flow | 158 +++++
.../test/resources/workflows/wsdl/wsdl.t2flow | 22 +
.../resources/workflows/xmlSplitter/inputs/age | 1 +
.../workflows/xmlSplitter/inputs/firstName | 1 +
.../workflows/xmlSplitter/inputs/lastName | 1 +
.../workflows/xmlSplitter/xmlSplitter.t2flow | 339 ++++++++++
.../test/resources/workflows/xpath/xpath.t2flow | 127 ++++
160 files changed, 4499 insertions(+), 4550 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/.gitignore
----------------------------------------------------------------------
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index ebe0e5b..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,24 +0,0 @@
-# ignore project files #
-.classpath
-.project
-.settings/
-catalog-v001.xml
-
-# ignore target files #
-target/
-bin/
-build/
-dist/
-apidoc/
-*.swp
-
-# ignore svn files if there
-.svn
-
-# ignore log files #
-*.log
-/logs/*
-*/logs/*
-
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/.project
----------------------------------------------------------------------
diff --git a/.project b/.project
deleted file mode 100644
index 339aa3c..0000000
--- a/.project
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>taverna-command-line-tests</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.m2e.core.maven2Builder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jdt.core.javanature</nature>
- <nature>org.eclipse.m2e.core.maven2Nature</nature>
- </natures>
-</projectDescription>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/.travis.yml
----------------------------------------------------------------------
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index dff5f3a..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1 +0,0 @@
-language: java
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
deleted file mode 100644
index a5d02e1..0000000
--- a/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-Taverna 3 command line tests
-
-This code was previously hosted at http://taverna.googlecode.com/svn/taverna/command-line-tests/
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
deleted file mode 100644
index 9b33bea..0000000
--- a/pom.xml
+++ /dev/null
@@ -1,97 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <!-- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>parent</artifactId>
- <version>0.2.2011-02-17</version>
- </parent> -->
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>uk.org.taverna.commandline</groupId>
- <artifactId>taverna-command-line-tests</artifactId>
- <version>0.1.0-SNAPSHOT</version>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-surefire-plugin</artifactId>
- <version>2.12</version>
- <configuration>
- <systemPropertyVariables>
- <buildDirectory>${project.build.directory}</buildDirectory>
- </systemPropertyVariables>
- </configuration>
- </plugin>
- </plugins>
- </build>
- <dependencies>
- <dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-t2flow</artifactId>
- <version>${scufl2.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-rdfxml</artifactId>
- <version>${scufl2.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>4.8.1</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <version>2.2</version>
- <scope>test</scope>
- </dependency>
- <!-- Optional for scufl2-xdfxml -->
- <dependency>
- <groupId>com.sun.xml.bind</groupId>
- <artifactId>jaxb-impl</artifactId>
- <version>2.2.4-1</version>
- <scope>test</scope>
- </dependency>
- <!-- Required by scufl2-xdfxml, see SCUFL2-122 -->
- <dependency>
- <groupId>org.jdom</groupId>
- <artifactId>com.springsource.org.jdom</artifactId>
- <version>1.1.0</version>
- <scope>test</scope>
- </dependency>
- <!-- <dependency>
- <groupId>org.jdom</groupId>
- <artifactId>jdom</artifactId>
- <version>1.1.2</version>
- <scope>test</scope>
- </dependency> -->
- </dependencies>
- <repositories>
- <repository>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- </repository>
- <repository>
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- </repository>
- </repositories>
-</project>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java
----------------------------------------------------------------------
diff --git a/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java b/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java
deleted file mode 100644
index 07df1c3..0000000
--- a/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java
+++ /dev/null
@@ -1,485 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2012 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.commandline;
-
-import static org.junit.Assert.assertArrayEquals;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.junit.Assume.assumeTrue;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.PrintStream;
-import java.net.URI;
-import java.net.URL;
-import java.text.MessageFormat;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipFile;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.io.comparator.NameFileComparator;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-
-import uk.org.taverna.commandline.WorkflowTestSuite.Workflows;
-import uk.org.taverna.scufl2.api.container.WorkflowBundle;
-import uk.org.taverna.scufl2.api.io.WorkflowBundleIO;
-import uk.org.taverna.scufl2.rdfxml.RDFXMLReader;
-
-/**
- * Regression tests for Taverna Command Line Tool.
- *
- * @author David Withers
- */
-@RunWith(WorkflowTestSuite.class)
-public class TavernaCommandLineTest {
-
- private static String baseVersion = "2.4.0";
- private static boolean baseVersionReleased = true;
-
- private static String testVersion = "3.0.1-SNAPSHOT";
- private static boolean testVersionReleased = false;
- private static boolean testVersionSupportsScufl2 = true;
-
- private static String script = "executeworkflow.sh";
- private static String baseName = "taverna-commandline-" + baseVersion;
- private static String testName = "taverna-command-line-" + testVersion;
- private static String releasedLocation = "https://launchpad.net/taverna/t2/";
- private static String unreleasedLocation = "http://build.mygrid.org.uk/ci/job/t3-taverna-commandline-product/lastSuccessfulBuild/net.sf.taverna.t2$taverna-commandline/artifact/net.sf.taverna.t2/taverna-commandline/";
-
- private static String baseVersionLocation = (baseVersionReleased ? releasedLocation
- : unreleasedLocation) + baseVersion + "/+download/" + baseName + ".zip";
- private static String testVersionLocation = (testVersionReleased ? releasedLocation
- : unreleasedLocation)
- + testVersion
- + "/"
- + testName
- + (testVersionReleased ? ".zip" : "-bin.zip");
-
- private static String baseCommand;
- private static String testCommand;
-
- private static File buildDirectory;
-
- private File workflowDirectory;
- private File baseOutput;
- private File testOutput;
- private boolean secure;
- private List<File> inputs;
- private String ignorePort;
- private String message;
-
- public TavernaCommandLineTest(File workflowDirectory) throws Exception {
- this.workflowDirectory = workflowDirectory;
- if (buildDirectory == null) {
- String buildDirectoryLocation = System.getProperty("buildDirectory");
- if (buildDirectoryLocation == null) {
- buildDirectoryLocation = System.getProperty("user.dir")
- + System.getProperty("file.separator") + "target";
- }
- buildDirectory = new File(buildDirectoryLocation);
- buildDirectory.mkdirs();
- }
- if (baseCommand == null) {
- File commandDirectory = new File(buildDirectory, baseName);
- if (!commandDirectory.exists()) {
- System.out.println("Fetching " + baseName);
- fetchTaverna(baseVersionLocation, baseName);
- }
- baseCommand = new File(baseName, script).getPath();
- }
- if (testCommand == null) {
- File commandDirectory = new File(buildDirectory, testName);
- if (!commandDirectory.exists()) {
- System.out.println("Fetching " + testName);
- fetchTaverna(testVersionLocation, testName);
- }
- testCommand = new File(testName, script).getPath();
- }
- File outputsDirectory = new File(buildDirectory, "test-outputs");
- baseOutput = new File(outputsDirectory, workflowDirectory.getName() + "-" + baseVersion);
- testOutput = new File(outputsDirectory, workflowDirectory.getName() + "-" + testVersion);
- secure = workflowDirectory.getName().startsWith("secure");
- inputs = getInputs();
- ignorePort = getIgnorePort();
- message = "Running {0} with version {1}";
- }
-
- @Workflows
- public static List<File> workflows() {
- List<File> workflows = new ArrayList<File>();
- for (File workflowDirectory : getResources("workflows")) {
- workflows.add(workflowDirectory);
- }
- for (File workflowDirectory : getResources("myexperiment")) {
- workflows.add(workflowDirectory);
- }
- return workflows;
- }
-
- @Before
- public void setup() throws Exception {
- if (!baseOutput.exists()) {
- if (baseVersion.equals("2.3.0") && workflowDirectory.getName().equals("tool"))
- return;// version 2.3.0 is missing tool plugin
- String workflow = getWorkflow().toASCIIString();
- System.out.println(MessageFormat.format(message, workflow, baseVersion)
- + (inputs.size() > 0 ? " using input values" : ""));
- runWorkflow(baseCommand, workflow, baseOutput, true, secure, false);
- assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
- baseOutput.exists());
- }
- }
-
- public boolean testExcluded() {
- // version 3.0.0 is missing biomoby activity
- if (testVersion.startsWith("3.") && workflowDirectory.getName().contains("biomoby"))
- return true;
- // version 3.0.0 is missing tool activity
- if (testVersion.startsWith("3.")
- && workflowDirectory.getName().equals("unix_external_tools_with_zip_and_unzip"))
- return true;
- if (testVersion.startsWith("3.")
- && workflowDirectory.getName().equals("unix_numerically_adding_two_values"))
- return true;
- if (testVersion.startsWith("3.")
- && workflowDirectory.getName().equals("unix_tool_service_using_string_replacement"))
- return true;
- // version 3.0.0 is missing looping configuration
- if (testVersion.startsWith("3.")
- && workflowDirectory.getName().equals("ebi_interproscan_newservices"))
- return true;
- if (testVersion.startsWith("3.")
- && workflowDirectory.getName().equals("biomartandembossanalysis"))
- return true;
- return false;
- }
-
- @Test
- public void testWorkflowWithoutInputs() throws Exception {
- assumeTrue(!testExcluded());
- assumeTrue(baseOutput.exists());
- assumeTrue(inputs.isEmpty());
- FileUtils.deleteDirectory(testOutput);
- String workflow = getWorkflow().toASCIIString();
- System.out.println(MessageFormat.format(message, workflow, testVersion));
- runWorkflow(testCommand, workflow, testOutput, true, secure, false);
- assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
- testOutput.exists());
- assertOutputsEquals(baseOutput, testOutput);
- }
-
- @Test
- public void testWorkflowWithInputValues() throws Exception {
- assumeTrue(!testExcluded());
- assumeTrue(baseOutput.exists());
- assumeTrue(inputs.size() > 0);
- FileUtils.deleteDirectory(testOutput);
- String workflow = getWorkflow().toASCIIString();
- System.out.println(MessageFormat.format(message, workflow, testVersion)
- + " using input values");
- runWorkflow(testCommand, workflow, testOutput, true, secure, false);
- assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
- testOutput.exists());
- assertOutputsEquals(baseOutput, testOutput);
- }
-
- @Test
- public void testWorkflowWithInputFiles() throws Exception {
- assumeTrue(!testExcluded());
- assumeTrue(baseOutput.exists());
- assumeTrue(inputs.size() > 0);
- FileUtils.deleteDirectory(testOutput);
- String workflow = getWorkflow().toASCIIString();
- System.out.println(MessageFormat.format(message, workflow, testVersion)
- + " using input files");
- runWorkflow(testCommand, workflow, testOutput, false, secure, false);
- assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
- testOutput.exists());
- assertOutputsEquals(baseOutput, testOutput);
- }
-
- @Test
- @Ignore
- public void testWorkflowWithDatabase() throws Exception {
- assumeTrue(!testExcluded());
- assumeTrue(baseOutput.exists());
- assumeTrue(inputs.size() > 0);
- FileUtils.deleteDirectory(testOutput);
- String workflow = getWorkflow().toASCIIString();
- System.out
- .println(MessageFormat.format(message, workflow, testVersion) + " using database");
- runWorkflow(testCommand, workflow, testOutput, true, secure, true);
- assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
- testOutput.exists());
- assertOutputsEquals(baseOutput, testOutput);
- }
-
- @Test
- public void testScufl2Workflow() throws Exception {
- assumeTrue(!testExcluded());
- assumeTrue(baseOutput.exists());
- assumeTrue(testVersionSupportsScufl2);
-
- FileUtils.deleteDirectory(testOutput);
- String workflow = getScufl2Workflow().toASCIIString();
- System.out.println(MessageFormat.format(message, workflow, testVersion)
- + (inputs.size() > 0 ? " using input values" : ""));
- runWorkflow(testCommand, workflow, testOutput, true, secure, true);
- assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
- testOutput.exists());
- assertOutputsEquals(baseOutput, testOutput);
- }
-
- private synchronized void runWorkflow(String command, String workflow, File outputsDirectory,
- boolean inputValues, boolean secure, boolean database) throws Exception {
- ProcessBuilder processBuilder = new ProcessBuilder("sh", command);
- processBuilder.redirectErrorStream(true);
- processBuilder.directory(buildDirectory);
- List<String> args = processBuilder.command();
- for (File input : inputs) {
- if (inputValues) {
- args.add("-inputvalue");
- args.add(input.getName());
- args.add(IOUtils.toString(new FileReader(input)));
- } else {
- args.add("-inputfile");
- args.add(input.getName());
- args.add(input.getAbsolutePath());
- }
- }
- args.add("-outputdir");
- args.add(outputsDirectory.getPath());
- if (secure) {
- args.add("-cmdir");
- args.add(getClass().getResource("/security").getFile());
- args.add("-cmpassword");
- }
- if (database) {
- args.add("-embedded");
- }
- args.add(workflow);
- Process process = processBuilder.start();
- if (secure) {
- PrintStream outputStream = new PrintStream(process.getOutputStream());
- outputStream.println("test");
- outputStream.flush();
- }
- waitFor(process);
- }
-
- private URI getWorkflow() throws Exception {
- File workflow = new File(workflowDirectory, workflowDirectory.getName() + ".t2flow");
- if (!workflow.exists()) {
- workflow = new File(workflowDirectory, workflowDirectory.getName() + ".url");
- return new URI(IOUtils.toString(new FileReader(workflow)));
- }
- return workflow.toURI();
- }
-
- private URI getScufl2Workflow() throws Exception {
- File workflow = new File(buildDirectory, workflowDirectory.getName() + ".wfbundle");
- // if (!workflow.exists()) {
- WorkflowBundleIO workflowBundleIO = new WorkflowBundleIO();
- WorkflowBundle bundle = workflowBundleIO.readBundle(getWorkflow().toURL(), null);
- workflowBundleIO.writeBundle(bundle, workflow,
- RDFXMLReader.APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE);
- // }
- return workflow.toURI();
- }
-
- private synchronized int waitFor(Process process) throws IOException {
- while (true) {
- try {
- wait(500);
- } catch (InterruptedException e) {
- }
- IOUtils.copy(process.getInputStream(), System.out);
- try {
- return process.exitValue();
- } catch (IllegalThreadStateException e) {
- }
- }
- }
-
- private void assertOutputsEquals(File directory1, File directory2) {
- File[] directory1Files = directory1.listFiles();
- File[] directory2Files = directory2.listFiles();
- // assert directories contain same number of files
- assertEquals(String.format("%s has %s files but %s has %s files", directory1.getName(),
- directory1Files.length, directory2.getName(), directory2Files.length),
- directory1Files.length, directory2Files.length);
- // sort files in directory
- Arrays.sort(directory1Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
- Arrays.sort(directory2Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
- for (int i = 0; i < directory1Files.length; i++) {
- assertFilesEqual(directory1Files[i], directory2Files[i], !directory1Files[i].getName()
- .equals(ignorePort));
- }
- }
-
- private void assertDirectoriesEquals(File directory1, File directory2, boolean checkFileContents) {
- if (directory1.exists()) {
- assertTrue(String.format("%s exists but %s does not", directory1, directory2),
- directory2.exists());
- } else {
- assertFalse(String.format("%s does not exists but %s does", directory1, directory2),
- directory2.exists());
- }
- File[] directory1Files = directory1.listFiles();
- File[] directory2Files = directory2.listFiles();
- // assert directories contain same number of files
- assertEquals(String.format("%s has %s files but %s has %s files", directory1.getName(),
- directory1Files.length, directory2.getName(), directory2Files.length),
- directory1Files.length, directory2Files.length);
- // sort files in directory
- Arrays.sort(directory1Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
- Arrays.sort(directory2Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
- for (int i = 0; i < directory1Files.length; i++) {
- assertFilesEqual(directory1Files[i], directory2Files[i], checkFileContents);
- }
- }
-
- private void assertFilesEqual(File file1, File file2, boolean checkFileContents) {
- if (file1.isHidden()) {
- assertTrue(String.format("%s is hidden but %s is not", file1, file2), file2.isHidden());
- } else {
- assertFalse(String.format("%s is not hidden but %s is", file1, file2), file2.isHidden());
- assertEquals(file1.getName(), file2.getName());
- if (file1.isDirectory()) {
- assertTrue(String.format("%s is a directory but %s is not", file1, file2),
- file2.isDirectory());
- assertDirectoriesEquals(file1, file2, checkFileContents);
- } else {
- assertFalse(String.format("%s is not a directory but %s is", file1, file2),
- file2.isDirectory());
- if (isZipFile(file1)) {
- assertZipFilesEqual(file1, file2);
- } else if (checkFileContents) {
- assertEquals(String.format("%s is a different length to %s", file1, file2),
- file1.length(), file2.length());
- try {
- byte[] byteArray1 = IOUtils.toByteArray(new FileReader(file1));
- byte[] byteArray2 = IOUtils.toByteArray(new FileReader(file2));
- assertArrayEquals(String.format("%s != %s", file1, file2), byteArray1,
- byteArray2);
- } catch (FileNotFoundException e) {
- fail(e.getMessage());
- } catch (IOException e) {
- fail(e.getMessage());
- }
- }
- }
- }
- }
-
- private void assertZipFilesEqual(File file1, File file2) {
- ZipFile zipFile1 = null;
- ZipFile zipFile2 = null;
- try {
- zipFile1 = new ZipFile(file1);
- zipFile2 = new ZipFile(file2);
- } catch (Exception e) {
- assertTrue(String.format("%s and %s are not both zip files"), zipFile1 == null);
- }
- if (zipFile1 != null && zipFile2 != null) {
- Enumeration<? extends ZipEntry> entries1 = zipFile1.entries();
- Enumeration<? extends ZipEntry> entries2 = zipFile2.entries();
- while (entries1.hasMoreElements()) {
- assertTrue(entries2.hasMoreElements());
- ZipEntry zipEntry1 = entries1.nextElement();
- ZipEntry zipEntry2 = entries2.nextElement();
- assertEquals(
- String.format("%s and %s are not both directories", zipEntry1, zipEntry2),
- zipEntry1.isDirectory(), zipEntry2.isDirectory());
- assertEquals(String.format("%s and %s have different names", zipEntry1, zipEntry2),
- zipEntry1.getName(), zipEntry2.getName());
- assertEquals(String.format("%s and %s have different sizes", zipEntry1, zipEntry2),
- zipEntry1.getSize(), zipEntry2.getSize());
- try {
- byte[] byteArray1 = IOUtils.toByteArray(zipFile1.getInputStream(zipEntry1));
- byte[] byteArray2 = IOUtils.toByteArray(zipFile2.getInputStream(zipEntry2));
- assertArrayEquals(String.format("%s != %s", zipEntry1, zipEntry2), byteArray1,
- byteArray2);
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
- assertFalse(entries2.hasMoreElements());
- }
- }
-
- private boolean isZipFile(File file) {
- try {
- new ZipFile(file);
- return true;
- } catch (Exception e) {
- return false;
- }
- }
-
- private static File[] getResources(String directory) {
- return new File(TavernaCommandLineTest.class.getResource("/" + directory).getFile())
- .listFiles();
- }
-
- private List<File> getInputs() {
- File inputsDirectory = new File(workflowDirectory, "inputs");
- if (inputsDirectory.exists() && inputsDirectory.isDirectory()) {
- return Arrays.asList(inputsDirectory.listFiles());
- }
- return Collections.emptyList();
- }
-
- private String getIgnorePort() throws Exception {
- File ignorePort = new File(workflowDirectory, "ignorePort");
- if (ignorePort.exists()) {
- return IOUtils.toString(new FileReader(ignorePort));
- }
- return "";
- }
-
- private void fetchTaverna(String location, String name) throws Exception {
- File zipFile = new File(buildDirectory, name + ".zip");
- IOUtils.copy(new URL(location).openStream(), new FileOutputStream(zipFile));
- ProcessBuilder processBuilder = new ProcessBuilder("unzip", "-q", name);
- processBuilder.redirectErrorStream(true);
- processBuilder.directory(buildDirectory);
- System.out.println(processBuilder.command());
- Process process = processBuilder.start();
- waitFor(process);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java
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diff --git a/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java b/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java
deleted file mode 100644
index 56ed82d..0000000
--- a/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2012 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.commandline;
-
-import java.io.File;
-import java.util.List;
-
-import org.junit.runner.notification.RunNotifier;
-import org.junit.runners.BlockJUnit4ClassRunner;
-import org.junit.runners.model.FrameworkMethod;
-import org.junit.runners.model.InitializationError;
-import org.junit.runners.model.Statement;
-
-/**
- * Test runner for running workflows.
- *
- * @author David Withers
- */
-public class WorkflowTestRunner extends BlockJUnit4ClassRunner {
- private File workflow;
-
- public WorkflowTestRunner(Class<?> type, File workflow) throws InitializationError {
- super(type);
- this.workflow = workflow;
- }
-
- @Override
- public Object createTest() throws Exception {
- return getTestClass().getOnlyConstructor().newInstance(workflow);
- }
-
- @Override
- protected String getName() {
- return String.format("[%s]", workflow.getName());
- }
-
- @Override
- protected String testName(final FrameworkMethod method) {
- return String.format("%s[%s]", method.getName(), workflow.getName());
- }
-
- @Override
- protected void validateConstructor(List<Throwable> errors) {
- validateOnlyOneConstructor(errors);
- }
-
- @Override
- protected Statement classBlock(RunNotifier notifier) {
- return childrenInvoker(notifier);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java
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diff --git a/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java b/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java
deleted file mode 100644
index 140dec6..0000000
--- a/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java
+++ /dev/null
@@ -1,79 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2012 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.commandline;
-
-import java.io.File;
-import java.lang.annotation.ElementType;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
-import java.lang.reflect.Modifier;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import org.junit.runner.Runner;
-import org.junit.runners.Suite;
-import org.junit.runners.model.FrameworkMethod;
-import org.junit.runners.model.TestClass;
-
-/**
- * Test suite for running workflows specified by a method annotated by @Workflows.
- *
- * @author David Withers
- */
-public class WorkflowTestSuite extends Suite {
-
- @Retention(RetentionPolicy.RUNTIME)
- @Target(ElementType.METHOD)
- public static @interface Workflows {}
-
- private ArrayList<Runner> runners = new ArrayList<Runner>();
-
- public WorkflowTestSuite(Class<?> klass) throws Throwable {
- super(klass, Collections.<Runner>emptyList());
- for (File workflow : getWorkflows(getTestClass())) {
- runners.add(new WorkflowTestRunner(getTestClass().getJavaClass(), workflow));
- }
- }
-
- @Override
- protected List<Runner> getChildren() {
- return runners;
- }
-
- @SuppressWarnings("unchecked")
- private List<File> getWorkflows(TestClass klass) throws Throwable {
- return (List<File>) getWorkflowsMethod(klass).invokeExplosively(null);
- }
-
- public FrameworkMethod getWorkflowsMethod(TestClass testClass) throws Exception {
- List<FrameworkMethod> methods = testClass.getAnnotatedMethods(Workflows.class);
- for (FrameworkMethod method : methods) {
- int modifiers = method.getMethod().getModifiers();
- if (Modifier.isStatic(modifiers) && Modifier.isPublic(modifiers)) {
- return method;
- }
- }
- throw new Exception("No public static Workflows annotated method on class " + testClass.getName());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url
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diff --git a/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url b/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url
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--- a/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url
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-http://www.myexperiment.org/workflows/1794/download/biomartandembossanalysis_457009.t2flow?version=4
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/biomartandembossanalysis/ignorePort
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diff --git a/src/test/resources/myexperiment/biomartandembossanalysis/ignorePort b/src/test/resources/myexperiment/biomartandembossanalysis/ignorePort
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--- a/src/test/resources/myexperiment/biomartandembossanalysis/ignorePort
+++ /dev/null
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-outputPlot
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/biomoby_tutorial_workflow/biomoby_tutorial_workflow.url
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diff --git a/src/test/resources/myexperiment/biomoby_tutorial_workflow/biomoby_tutorial_workflow.url b/src/test/resources/myexperiment/biomoby_tutorial_workflow/biomoby_tutorial_workflow.url
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index a73b8c4..0000000
--- a/src/test/resources/myexperiment/biomoby_tutorial_workflow/biomoby_tutorial_workflow.url
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-http://www.myexperiment.org/workflows/1366/download/biomoby_tutorial_workflow_877727.t2flow?version=1
\ No newline at end of file
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diff --git a/src/test/resources/myexperiment/biomoby_tutorial_workflow/ignorePort b/src/test/resources/myexperiment/biomoby_tutorial_workflow/ignorePort
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index f8e22dd..0000000
--- a/src/test/resources/myexperiment/biomoby_tutorial_workflow/ignorePort
+++ /dev/null
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-restrict_out
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/id
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index 1dfd176..0000000
--- a/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/id
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-656461
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/namespace
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diff --git a/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/namespace b/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/namespace
deleted file mode 100644
index c188363..0000000
--- a/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/namespace
+++ /dev/null
@@ -1 +0,0 @@
-NCBI_gi
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/demonstration_of_configurable_iteration/demonstration_of_configurable_iteration.url
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diff --git a/src/test/resources/myexperiment/demonstration_of_configurable_iteration/demonstration_of_configurable_iteration.url b/src/test/resources/myexperiment/demonstration_of_configurable_iteration/demonstration_of_configurable_iteration.url
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index 38abe3a..0000000
--- a/src/test/resources/myexperiment/demonstration_of_configurable_iteration/demonstration_of_configurable_iteration.url
+++ /dev/null
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-http://www.myexperiment.org/workflows/1367/download/demonstration_of_configurable_iteration_114130.t2flow?version=1
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/ebi_interproscan_newservices/ebi_interproscan_newservices.url
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diff --git a/src/test/resources/myexperiment/ebi_interproscan_newservices/ebi_interproscan_newservices.url b/src/test/resources/myexperiment/ebi_interproscan_newservices/ebi_interproscan_newservices.url
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--- a/src/test/resources/myexperiment/ebi_interproscan_newservices/ebi_interproscan_newservices.url
+++ /dev/null
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-http://www.myexperiment.org/workflows/1767/download/ebi_interproscan_newservices_421482.t2flow?version=2
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/ebi_interproscan_newservices/ignorePort
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diff --git a/src/test/resources/myexperiment/ebi_interproscan_newservices/ignorePort b/src/test/resources/myexperiment/ebi_interproscan_newservices/ignorePort
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--- a/src/test/resources/myexperiment/ebi_interproscan_newservices/ignorePort
+++ /dev/null
@@ -1 +0,0 @@
-Graphical_output
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/email
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diff --git a/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/email b/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/email
deleted file mode 100644
index 38133d0..0000000
--- a/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/email
+++ /dev/null
@@ -1 +0,0 @@
-test@mygrid.org.uk
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/sequence
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diff --git a/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/sequence b/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/sequence
deleted file mode 100644
index 19a43dd..0000000
--- a/src/test/resources/myexperiment/ebi_interproscan_newservices/inputs/sequence
+++ /dev/null
@@ -1,8 +0,0 @@
->sp|Q9BTV4|TMM43_HUMAN Transmembrane protein 43 OS=Homo sapiens GN=TMEM43 PE=1 SV=1
-MAANYSSTSTRREHVKVKTSSQPGFLERLSETSGGMFVGLMAFLLSFYLIFTNEGRALKT
-ATSLAEGLSLVVSPDSIHSVAPENEGRLVHIIGALRTSKLLSDPNYGVHLPAVKLRRHVE
-MYQWVETEESREYTEDGQVKKETRYSYNTEWRSEIINSKNFDREIGHKNPSAMAVESFMA
-TAPFVQIGRFFLSSGLIDKVDNFKSLSLSKLEDPHVDIIRRGDFFYHSENPKYPEVGDLR
-VSFSYAGLSGDDPDLGPAHVVTVIARQRGDQLVPFSTKSGDTLLLLHHGDFSAEEVFHRE
-LRSNSMKTWGLRAAGWMAMFMGLNLMTRILYTLVDWFPVFRDLVNIGLKAFAFCVATSLT
-LLTVAAGWLFYRPLWALLIAGLALVPILVARTRVPAKKLE
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/example_of_conditional_invocation/example_of_conditional_invocation.url
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diff --git a/src/test/resources/myexperiment/example_of_conditional_invocation/example_of_conditional_invocation.url b/src/test/resources/myexperiment/example_of_conditional_invocation/example_of_conditional_invocation.url
deleted file mode 100644
index 350a27f..0000000
--- a/src/test/resources/myexperiment/example_of_conditional_invocation/example_of_conditional_invocation.url
+++ /dev/null
@@ -1 +0,0 @@
-http://www.myexperiment.org/workflows/2561/download/example_of_conditional_invocation_369634.t2flow?version=1
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/example_of_conditional_invocation/inputs/condition
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diff --git a/src/test/resources/myexperiment/example_of_conditional_invocation/inputs/condition b/src/test/resources/myexperiment/example_of_conditional_invocation/inputs/condition
deleted file mode 100644
index f32a580..0000000
--- a/src/test/resources/myexperiment/example_of_conditional_invocation/inputs/condition
+++ /dev/null
@@ -1 +0,0 @@
-true
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/example_of_explicit_looping/example_of_explicit_looping.url
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diff --git a/src/test/resources/myexperiment/example_of_explicit_looping/example_of_explicit_looping.url b/src/test/resources/myexperiment/example_of_explicit_looping/example_of_explicit_looping.url
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-http://www.myexperiment.org/workflows/2562/download/example_of_explicit_looping_785852.t2flow?version=1
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/example_of_explicit_looping/inputs/end
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diff --git a/src/test/resources/myexperiment/example_of_explicit_looping/inputs/end b/src/test/resources/myexperiment/example_of_explicit_looping/inputs/end
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+++ /dev/null
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-14
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/example_of_explicit_looping/inputs/start
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diff --git a/src/test/resources/myexperiment/example_of_explicit_looping/inputs/start b/src/test/resources/myexperiment/example_of_explicit_looping/inputs/start
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--- a/src/test/resources/myexperiment/example_of_explicit_looping/inputs/start
+++ /dev/null
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--3
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/example_of_explicit_looping/inputs/step
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diff --git a/src/test/resources/myexperiment/example_of_explicit_looping/inputs/step b/src/test/resources/myexperiment/example_of_explicit_looping/inputs/step
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--- a/src/test/resources/myexperiment/example_of_explicit_looping/inputs/step
+++ /dev/null
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-3
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/example_workflow_for_rest_and_xpath_activities.url
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diff --git a/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/example_workflow_for_rest_and_xpath_activities.url b/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/example_workflow_for_rest_and_xpath_activities.url
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index bd3ff3d..0000000
--- a/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/example_workflow_for_rest_and_xpath_activities.url
+++ /dev/null
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-http://www.myexperiment.org/workflows/1510/download/example_workflow_for_rest_and_xpath_activities_650957.t2flow?version=1
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/inputs/Name_Of_Location_for_Weather_Forecast
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diff --git a/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/inputs/Name_Of_Location_for_Weather_Forecast b/src/test/resources/myexperiment/example_workflow_for_rest_and_xpath_activities/inputs/Name_Of_Location_for_Weather_Forecast
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- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="object" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>String</processor><port>string</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>toUpperCase</processor><port>object</port></sink><source type="processor"><processor>String</processor><port>object</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="proc
essor"><processor>toUpperCase</processor><port>result</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>483d65c6-98c1-4b94-b628-d5bcbf351e97</identification>
- </annotationBean>
- <date>2011-05-16 13:07:03.385 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>d460e60a-43bb-47fc-a9f4-89e15274b100</identification>
- </annotationBean>
- <date>2011-11-02 12:43:09.911 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>0d977496-aa5d-4274-9827-85400d5f13a2</identification>
- </annotationBean>
- <date>2011-05-16 13:06:33.69 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>8bf2b5e5-a3e0-4fbd-bfd2-aefc7b2a6b8a</identification>
- </annotationBean>
- <date>2011-11-02 12:46:41.313 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>58f30a52-57df-46ce-b1bb-b9533984f8dd</identification>
- </annotationBean>
- <date>2011-11-02 12:29:15.575 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>c2693c41-1373-48cf-afbe-d8bbe0ea9e35</identification>
- </annotationBean>
- <date>2011-11-02 12:31:01.678 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>1ce7f3a0-71f4-4794-8bbd-dbb6de42442d</identification>
- </annotationBean>
- <date>2011-05-16 12:57:01.975 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>4c2b6995-eecb-47a7-b72c-63cfb96b6852</identification>
- </annotationBean>
- <date>2011-11-02 12:43:51.355 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>225db881-4e07-4cdb-920c-343dc1536edc</identification>
- </annotationBean>
- <date>2011-05-16 13:10:54.588 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>404e203c-ce51-4a9f-907c-1dab7f2eaaa2</identification>
- </annotationBean>
- <date>2011-05-16 12:44:02.533 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>0b6881f1-aa8d-483e-a7bb-7ad38b1da778</identification>
- </annotationBean>
- <date>2011-05-16 12:26:38.721 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/apiconsumer/inputs/in
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/apiconsumer/inputs/in b/src/test/resources/workflows/apiconsumer/inputs/in
deleted file mode 100644
index fede229..0000000
--- a/src/test/resources/workflows/apiconsumer/inputs/in
+++ /dev/null
@@ -1 +0,0 @@
-test-input
\ No newline at end of file
[36/50] [abbrv] incubator-taverna-commandline git commit: using
Apache Taverna dependencies
Posted by st...@apache.org.
using Apache Taverna dependencies
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/f6985f0c
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/f6985f0c
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/f6985f0c
Branch: refs/heads/master
Commit: f6985f0c1c2149170b6900583df5f8ce439f4948
Parents: 9a15408
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 02:26:45 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 02:26:45 2014 -0600
----------------------------------------------------------------------
pom.xml | 4 ++-
taverna-commandline-api/pom.xml | 2 +-
taverna-commandline-common/pom.xml | 52 +++++++++++++++----------------
taverna-commandline-launcher/pom.xml | 18 +++++------
taverna-commandline-product/pom.xml | 2 +-
taverna-commandline-tests/pom.xml | 34 +++++---------------
6 files changed, 47 insertions(+), 65 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/f6985f0c/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 7b5a7b3..0045712 100644
--- a/pom.xml
+++ b/pom.xml
@@ -10,7 +10,7 @@
<artifactId>taverna-commandline</artifactId>
<version>3.1.0-incubating-SNAPSHOT</version>
<packaging>pom</packaging>
- <name>Apache Taverna Engine and Platform</name>
+ <name>Apache Taverna Command Line</name>
<properties>
<taverna.language.version>0.15.0-incubating-SNAPSHOT</taverna.language.version>
<taverna.osgi.version>0.2.0-incubating-SNAPSHOT</taverna.osgi.version>
@@ -21,7 +21,9 @@
<module>taverna-commandline-common</module>
<module>taverna-commandline-launcher</module>
<module>taverna-commandline-product</module>
+ <!--
<module>taverna-commandline-tests</module>
+ -->
</modules>
<repositories>
<repository>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/f6985f0c/taverna-commandline-api/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/pom.xml b/taverna-commandline-api/pom.xml
index 36f73a6..ab49d38 100644
--- a/taverna-commandline-api/pom.xml
+++ b/taverna-commandline-api/pom.xml
@@ -8,5 +8,5 @@
</parent>
<packaging>bundle</packaging>
<artifactId>taverna-commandline-api</artifactId>
- <name>Apache Taverna Command Line API</name>
+ <name>Apache Taverna Commandline API</name>
</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/f6985f0c/taverna-commandline-common/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/pom.xml b/taverna-commandline-common/pom.xml
index 4230b99..ee2ffce 100644
--- a/taverna-commandline-common/pom.xml
+++ b/taverna-commandline-common/pom.xml
@@ -11,59 +11,59 @@
<name>Apache Taverna Commandline Common</name>
<dependencies>
<dependency>
- <groupId>net.sf.taverna.t2.taverna-commandline</groupId>
+ <groupId>${project.parent.groupId}</groupId>
<artifactId>taverna-commandline-api</artifactId>
- <version>${project.version}</version>
+ <version>${project.parent.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.platform</groupId>
+ <groupId>org.apache.taverna.engine</groupId>
<artifactId>taverna-run-api</artifactId>
- <version>${platform.version}</version>
+ <version>${taverna.engine.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.configuration</groupId>
+ <groupId>org.apache.taverna.engine</groupId>
<artifactId>taverna-database-configuration-api</artifactId>
- <version>${taverna.configuration.version}</version>
+ <version>${taverna.engine.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-api</artifactId>
- <version>${scufl2.version}</version>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-api</artifactId>
+ <version>${taverna.language.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-validation</artifactId>
- <version>${scufl2.version}</version>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-validation</artifactId>
+ <version>${taverna.language.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-validation-structural</artifactId>
- <version>${scufl2.version}</version>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-validation-structural</artifactId>
+ <version>${taverna.language.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-validation-correctness</artifactId>
- <version>${scufl2.version}</version>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-validation-correctness</artifactId>
+ <version>${taverna.language.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.databundle</groupId>
- <artifactId>databundle</artifactId>
- <version>${taverna.databundle.version}</version>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-databundle</artifactId>
+ <version>${taverna.language.version}</version>
</dependency>
<!--
<dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
+ <groupId>org.apache.taverna.engine</groupId>
<artifactId>provenanceconnector</artifactId>
- <version>${t2.core.provenanceconnector.version}</version>
+ <version>${taverna.engine.version}</version>
</dependency>
-->
<dependency>
- <groupId>net.sf.taverna.t2.security</groupId>
- <artifactId>credential-manager</artifactId>
- <version>${t2.security.version}</version>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-credential-manager</artifactId>
+ <version>${taverna.engine.version}</version>
</dependency>
<dependency>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/f6985f0c/taverna-commandline-launcher/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/pom.xml b/taverna-commandline-launcher/pom.xml
index 340c70a..5aad907 100644
--- a/taverna-commandline-launcher/pom.xml
+++ b/taverna-commandline-launcher/pom.xml
@@ -7,7 +7,7 @@
<version>3.1.0-incubating-SNAPSHOT</version>
</parent>
<artifactId>taverna-commandline-launcher</artifactId>
- <name>Apache Taverna Command Line Launcher</name>
+ <name>Apache Taverna Commandline Launcher</name>
<build>
<plugins>
<plugin>
@@ -29,19 +29,19 @@
</build>
<dependencies>
<dependency>
- <groupId>net.sf.taverna.t2.taverna-commandline</groupId>
+ <groupId>${project.parent.groupId}</groupId>
<artifactId>taverna-commandline-api</artifactId>
- <version>${t2.taverna-commandline.version}</version>
+ <version>${project.parent.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.osgi</groupId>
+ <groupId>org.apache.taverna.osgi</groupId>
<artifactId>osgi-launcher</artifactId>
- <version>${osgi.launcher.version}</version>
+ <version>${taverna.osgi.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.configuration</groupId>
+ <groupId>org.apache.taverna.osgi</groupId>
<artifactId>taverna-app-configuration-impl</artifactId>
- <version>${taverna.configuration.version}</version>
+ <version>${taverna.osgi.version}</version>
</dependency>
<dependency>
@@ -51,8 +51,8 @@
</dependency>
<dependency>
<groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <version>${commons.io.version}</version>
+ <artifactId>commons-io</artifactId>
+ <version>${commons.io.version}</version>
</dependency>
<dependency>
<groupId>org.apache.log4j</groupId>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/f6985f0c/taverna-commandline-product/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/pom.xml b/taverna-commandline-product/pom.xml
index 3518d1a..e563167 100644
--- a/taverna-commandline-product/pom.xml
+++ b/taverna-commandline-product/pom.xml
@@ -8,7 +8,7 @@
<version>3.1.0-incubating-SNAPSHOT</version>
</parent>
<artifactId>taverna-command-line-product</artifactId>
- <name>Apache Taverna Command Line Product</name>
+ <name>Apache Taverna Commandline Product</name>
<packaging>taverna-application</packaging>
<profiles>
<profile>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/f6985f0c/taverna-commandline-tests/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/pom.xml b/taverna-commandline-tests/pom.xml
index 26789fe..e28c4a0 100644
--- a/taverna-commandline-tests/pom.xml
+++ b/taverna-commandline-tests/pom.xml
@@ -7,7 +7,7 @@
<version>3.1.0-incubating-SNAPSHOT</version>
</parent>
<artifactId>taverna-command-line-tests</artifactId>
- <name>Apache Taverna Command Line Tests</name>
+ <name>Apache Taverna Commandline Tests</name>
<build>
<plugins>
<plugin>
@@ -24,15 +24,15 @@
</build>
<dependencies>
<dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-t2flow</artifactId>
- <version>${scufl2.version}</version>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-t2flow</artifactId>
+ <version>${taverna.language.version}</version>
<scope>test</scope>
</dependency>
<dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-rdfxml</artifactId>
- <version>${scufl2.version}</version>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-rdfxml</artifactId>
+ <version>${taverna.language.version}</version>
<scope>test</scope>
</dependency>
<dependency>
@@ -68,24 +68,4 @@
<scope>test</scope>
</dependency> -->
</dependencies>
- <repositories>
- <repository>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- </repository>
- <repository>
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- </repository>
- </repositories>
</project>
[20/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-tests/
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/secure-ws-https/secure-ws-https.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-ws-https/secure-ws-https.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-ws-https/secure-ws-https.t2flow
new file mode 100644
index 0000000..13637c4
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-ws-https/secure-ws-https.t2flow
@@ -0,0 +1,180 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="c71621ca-196c-46cd-9073-48af82b4bd4f" role="top"><name>Workflow13</name><inputPorts /><outputPorts><port><name>out_plaintext</name><annotations /></port><port><name>out_plaintext_timestamp</name><annotations /></port><port><name>out_digest</name><annotations /></port><port><name>out_digest_timestamp</name><annotations /></port></outputPorts><processors><processor><name>hello_plaintext_password</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><m
ap from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityUsernameTokenPlainTextPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="
value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Alan</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>hello_plaintext_password_timestamp</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="
in0" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword-Timestamp?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityTimestampUsernameTokenPlainTextPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_1</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from
="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Alex</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>hello_digest_password</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inpu
tMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>https://heater.cs.man.ac.uk:7443/axis/services/HelloService-DigestPassword?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityUsernameTokenDigestPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_2</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from
="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Stian</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>hello_digest_password_timestamp</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0
" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>https://heater.cs.man.ac.uk:7443/axis/services/HelloService-DigestPassword-Timestamp?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityTimestampUsernameTokenDigestPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_3</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from
="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>David</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions><condition control="hello_plaintext_password" target="hello_digest_password" /><condition control="hello_digest_password_timestamp" target="hello_plaintext_password_timestamp" /><condition control="hello_digest_password" target="hello_digest_password_timestamp" /></conditions><datalinks><datalink><sink type="processor"><processor>hello_plaintext_password</processor><port>in0</port></sink><source type="processor"><processor>in0_value</processor><port>value</port>
</source></datalink><datalink><sink type="processor"><processor>hello_plaintext_password_timestamp</processor><port>in0</port></sink><source type="processor"><processor>in0_value_1</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>hello_digest_password</processor><port>in0</port></sink><source type="processor"><processor>in0_value_2</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>hello_digest_password_timestamp</processor><port>in0</port></sink><source type="processor"><processor>in0_value_3</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out_plaintext</port></sink><source type="processor"><processor>hello_plaintext_password</processor><port>helloReturn</port></source></datalink><datalink><sink type="dataflow"><port>out_plaintext_timestamp</port></sink><source type="processor"><processor>hello_plaintext_password_timestamp</processor><port>helloReturn</port><
/source></datalink><datalink><sink type="dataflow"><port>out_digest</port></sink><source type="processor"><processor>hello_digest_password</processor><port>helloReturn</port></source></datalink><datalink><sink type="dataflow"><port>out_digest_timestamp</port></sink><source type="processor"><processor>hello_digest_password_timestamp</processor><port>helloReturn</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>c71621ca-196c-46cd-9073-48af82b4bd4f</identification>
+ </annotationBean>
+ <date>2011-06-21 12:11:30.87 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>56cadac0-c944-4b9e-83c3-078f57738405</identification>
+ </annotationBean>
+ <date>2011-01-21 16:02:09.633 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>3d76be4c-83c4-413b-91f2-b0ce69dcbd97</identification>
+ </annotationBean>
+ <date>2010-11-22 13:29:43.282 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ca8fb5c5-0e8c-4e68-84f0-bdc85a77e2b3</identification>
+ </annotationBean>
+ <date>2010-11-22 13:29:26.400 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>e61023d9-d603-4df6-87e5-175603f106a5</identification>
+ </annotationBean>
+ <date>2010-11-22 13:28:31.68 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>394aced4-ee5d-4355-8ebe-9fc8bcfe5303</identification>
+ </annotationBean>
+ <date>2011-06-21 12:07:46.327 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>8175c97b-6385-460a-98ab-5cf974010d51</identification>
+ </annotationBean>
+ <date>2010-11-22 12:11:59.610 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>a388d568-ca08-43b4-abaf-3744a6801d45</identification>
+ </annotationBean>
+ <date>2010-11-22 13:30:28.898 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>7153a2dd-18bd-4f25-80ab-1efa8afc567d</identification>
+ </annotationBean>
+ <date>2011-01-21 16:02:39.43 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/secure-ws/secure-ws.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-ws/secure-ws.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-ws/secure-ws.t2flow
new file mode 100644
index 0000000..764b810
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-ws/secure-ws.t2flow
@@ -0,0 +1,180 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="c71621ca-196c-46cd-9073-48af82b4bd4f" role="top"><name>Workflow13</name><inputPorts /><outputPorts><port><name>out_plaintext</name><annotations /></port><port><name>out_plaintext_timestamp</name><annotations /></port><port><name>out_digest</name><annotations /></port><port><name>out_digest_timestamp</name><annotations /></port></outputPorts><processors><processor><name>hello_plaintext_password</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><m
ap from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityUsernameTokenPlainTextPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="
value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Alan</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>hello_plaintext_password_timestamp</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="
in0" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword-Timestamp?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityTimestampUsernameTokenPlainTextPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_1</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from
="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Alex</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>hello_digest_password</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inpu
tMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>http://heater.cs.man.ac.uk:7070/axis/services/HelloService-DigestPassword?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityUsernameTokenDigestPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_2</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from
="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Stian</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>hello_digest_password_timestamp</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0
" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>http://heater.cs.man.ac.uk:7070/axis/services/HelloService-DigestPassword-Timestamp?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityTimestampUsernameTokenDigestPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value_3</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from
="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>David</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions><condition control="hello_plaintext_password" target="hello_digest_password" /><condition control="hello_digest_password_timestamp" target="hello_plaintext_password_timestamp" /><condition control="hello_digest_password" target="hello_digest_password_timestamp" /></conditions><datalinks><datalink><sink type="processor"><processor>hello_plaintext_password</processor><port>in0</port></sink><source type="processor"><processor>in0_value</processor><port>value</port>
</source></datalink><datalink><sink type="processor"><processor>hello_plaintext_password_timestamp</processor><port>in0</port></sink><source type="processor"><processor>in0_value_1</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>hello_digest_password</processor><port>in0</port></sink><source type="processor"><processor>in0_value_2</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>hello_digest_password_timestamp</processor><port>in0</port></sink><source type="processor"><processor>in0_value_3</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out_plaintext</port></sink><source type="processor"><processor>hello_plaintext_password</processor><port>helloReturn</port></source></datalink><datalink><sink type="dataflow"><port>out_plaintext_timestamp</port></sink><source type="processor"><processor>hello_plaintext_password_timestamp</processor><port>helloReturn</port><
/source></datalink><datalink><sink type="dataflow"><port>out_digest</port></sink><source type="processor"><processor>hello_digest_password</processor><port>helloReturn</port></source></datalink><datalink><sink type="dataflow"><port>out_digest_timestamp</port></sink><source type="processor"><processor>hello_digest_password_timestamp</processor><port>helloReturn</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>c71621ca-196c-46cd-9073-48af82b4bd4f</identification>
+ </annotationBean>
+ <date>2011-06-21 12:11:30.87 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>56cadac0-c944-4b9e-83c3-078f57738405</identification>
+ </annotationBean>
+ <date>2011-01-21 16:02:09.633 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>3d76be4c-83c4-413b-91f2-b0ce69dcbd97</identification>
+ </annotationBean>
+ <date>2010-11-22 13:29:43.282 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ca8fb5c5-0e8c-4e68-84f0-bdc85a77e2b3</identification>
+ </annotationBean>
+ <date>2010-11-22 13:29:26.400 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>e61023d9-d603-4df6-87e5-175603f106a5</identification>
+ </annotationBean>
+ <date>2010-11-22 13:28:31.68 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>394aced4-ee5d-4355-8ebe-9fc8bcfe5303</identification>
+ </annotationBean>
+ <date>2011-06-21 12:07:46.327 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>8175c97b-6385-460a-98ab-5cf974010d51</identification>
+ </annotationBean>
+ <date>2010-11-22 12:11:59.610 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>a388d568-ca08-43b4-abaf-3744a6801d45</identification>
+ </annotationBean>
+ <date>2010-11-22 13:30:28.898 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>7153a2dd-18bd-4f25-80ab-1efa8afc567d</identification>
+ </annotationBean>
+ <date>2011-01-21 16:02:39.43 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/secure-wsdl/secure-wsdl.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-wsdl/secure-wsdl.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-wsdl/secure-wsdl.t2flow
new file mode 100644
index 0000000..4db4ad5
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-wsdl/secure-wsdl.t2flow
@@ -0,0 +1,131 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="b23a2149-976e-4e98-b120-e5b8580839ef" role="top"><name>Workflow13</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>hello_plaintext_password</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl</wsdl>
+ <operation>hello</operation>
+ <securityProfile>WSSecurityUsernameTokenPlainTextPassword</securityProfile>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value"
/></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Alan</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>hello_plaintext_password</processor><port>in0</port></sink><source type="processor"><processor>in0_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>hello_plaintext_password</processor><port>helloReturn</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotati
on.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ca8fb5c5-0e8c-4e68-84f0-bdc85a77e2b3</identification>
+ </annotationBean>
+ <date>2010-11-22 13:29:26.400 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>7153a2dd-18bd-4f25-80ab-1efa8afc567d</identification>
+ </annotationBean>
+ <date>2011-01-21 16:02:39.43 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>394aced4-ee5d-4355-8ebe-9fc8bcfe5303</identification>
+ </annotationBean>
+ <date>2011-06-21 12:07:46.327 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>c71621ca-196c-46cd-9073-48af82b4bd4f</identification>
+ </annotationBean>
+ <date>2011-06-21 12:11:30.87 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>8175c97b-6385-460a-98ab-5cf974010d51</identification>
+ </annotationBean>
+ <date>2010-11-22 12:11:59.610 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>56cadac0-c944-4b9e-83c3-078f57738405</identification>
+ </annotationBean>
+ <date>2011-01-21 16:02:09.633 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>a388d568-ca08-43b4-abaf-3744a6801d45</identification>
+ </annotationBean>
+ <date>2010-11-22 13:30:28.898 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b23a2149-976e-4e98-b120-e5b8580839ef</identification>
+ </annotationBean>
+ <date>2011-08-23 13:40:15.238 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>3d76be4c-83c4-413b-91f2-b0ce69dcbd97</identification>
+ </annotationBean>
+ <date>2010-11-22 13:29:43.282 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>e61023d9-d603-4df6-87e5-175603f106a5</identification>
+ </annotationBean>
+ <date>2010-11-22 13:28:31.68 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
[43/50] [abbrv] incubator-taverna-commandline git commit:
htmlparser.version
Posted by st...@apache.org.
htmlparser.version
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/bf51ad1b
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/bf51ad1b
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/bf51ad1b
Branch: refs/heads/master
Commit: bf51ad1bb040d9e4b1502e401a4bb92cfb9a190e
Parents: 505d947
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Jan 6 13:06:36 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Jan 6 13:06:36 2015 +0000
----------------------------------------------------------------------
taverna-commandline-product/pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/bf51ad1b/taverna-commandline-product/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/pom.xml b/taverna-commandline-product/pom.xml
index 41e73e6..63f73f6 100644
--- a/taverna-commandline-product/pom.xml
+++ b/taverna-commandline-product/pom.xml
@@ -514,7 +514,7 @@
<dependency>
<groupId>nu.validator.htmlparser</groupId>
<artifactId>htmlparser</artifactId>
- <version>1.4</version>
+ <version>${htmlparser.version}</version>
</dependency>
</dependencies>
[35/50] [abbrv] incubator-taverna-commandline git commit:
org.apache.taverna.commandline pom.xml (first cut)
Posted by st...@apache.org.
org.apache.taverna.commandline pom.xml (first cut)
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/9a15408d
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/9a15408d
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/9a15408d
Branch: refs/heads/master
Commit: 9a15408d4c6d16ff85bf8ee2c99aabd6e9489306
Parents: 101439b
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 02:15:07 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 02:15:07 2014 -0600
----------------------------------------------------------------------
taverna-commandline-api/pom.xml | 28 +++----------------
taverna-commandline-common/pom.xml | 29 +++-----------------
taverna-commandline-launcher/pom.xml | 33 +++++------------------
taverna-commandline-product/pom.xml | 45 +++++++++----------------------
taverna-commandline-tests/pom.xml | 16 ++++-------
5 files changed, 31 insertions(+), 120 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9a15408d/taverna-commandline-api/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/pom.xml b/taverna-commandline-api/pom.xml
index 54fdd7f..36f73a6 100644
--- a/taverna-commandline-api/pom.xml
+++ b/taverna-commandline-api/pom.xml
@@ -2,31 +2,11 @@
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
- <groupId>net.sf.taverna.t2.taverna-commandline</groupId>
+ <groupId>org.apache.taverna.commandline</groupId>
<artifactId>taverna-commandline</artifactId>
- <version>2.0.1-SNAPSHOT</version>
+ <version>3.1.0-incubating-SNAPSHOT</version>
</parent>
<packaging>bundle</packaging>
<artifactId>taverna-commandline-api</artifactId>
- <name>Taverna Commandline API</name>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
-</project>
\ No newline at end of file
+ <name>Apache Taverna Command Line API</name>
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9a15408d/taverna-commandline-common/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/pom.xml b/taverna-commandline-common/pom.xml
index 7abb64f..4230b99 100644
--- a/taverna-commandline-common/pom.xml
+++ b/taverna-commandline-common/pom.xml
@@ -2,13 +2,13 @@
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
- <groupId>net.sf.taverna.t2.taverna-commandline</groupId>
+ <groupId>org.apache.taverna.commandline</groupId>
<artifactId>taverna-commandline</artifactId>
- <version>2.0.1-SNAPSHOT</version>
+ <version>3.1.0-incubating-SNAPSHOT</version>
</parent>
<artifactId>taverna-commandline-common</artifactId>
<packaging>bundle</packaging>
- <name>Taverna Commandline Common</name>
+ <name>Apache Taverna Commandline Common</name>
<dependencies>
<dependency>
<groupId>net.sf.taverna.t2.taverna-commandline</groupId>
@@ -53,7 +53,7 @@
<version>${taverna.databundle.version}</version>
</dependency>
-<!--
+<!--
<dependency>
<groupId>net.sf.taverna.t2.core</groupId>
<artifactId>provenanceconnector</artifactId>
@@ -85,25 +85,4 @@
</dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
-
</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9a15408d/taverna-commandline-launcher/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/pom.xml b/taverna-commandline-launcher/pom.xml
index ad8330e..340c70a 100644
--- a/taverna-commandline-launcher/pom.xml
+++ b/taverna-commandline-launcher/pom.xml
@@ -2,13 +2,12 @@
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
+ <groupId>org.apache.taverna.commandline</groupId>
+ <artifactId>taverna-commandline</artifactId>
+ <version>3.1.0-incubating-SNAPSHOT</version>
</parent>
- <groupId>uk.org.taverna.commandline</groupId>
- <artifactId>taverna-command-line</artifactId>
- <version>0.1.2-SNAPSHOT</version>
+ <artifactId>taverna-commandline-launcher</artifactId>
+ <name>Apache Taverna Command Line Launcher</name>
<build>
<plugins>
<plugin>
@@ -73,24 +72,4 @@
<scope>test</scope>
</dependency>
</dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
-</project>
\ No newline at end of file
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9a15408d/taverna-commandline-product/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/pom.xml b/taverna-commandline-product/pom.xml
index d67a916..3518d1a 100644
--- a/taverna-commandline-product/pom.xml
+++ b/taverna-commandline-product/pom.xml
@@ -3,13 +3,12 @@
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
+ <groupId>org.apache.taverna.commandline</groupId>
+ <artifactId>taverna-commandline</artifactId>
+ <version>3.1.0-incubating-SNAPSHOT</version>
</parent>
- <groupId>uk.org.taverna.workbench</groupId>
<artifactId>taverna-command-line-product</artifactId>
- <name>Taverna Command Line</name>
+ <name>Apache Taverna Command Line Product</name>
<packaging>taverna-application</packaging>
<profiles>
<profile>
@@ -215,7 +214,7 @@
<version>${activation.version}</version>
</dependency>
<!-- The bundle "com.springsource.bsh_2.0.0.b4 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.servlet; version="[2.5.0,3.0.0)" -->
- <dependency>
+ <dependency>
<groupId>javax.servlet</groupId>
<artifactId>com.springsource.javax.servlet</artifactId>
<version>2.5.0</version>
@@ -520,22 +519,23 @@
<!-- The bundle "org.purl.wf4ever.robundle_0.3.1 " could not be resolved. Reason: Missing Constraint: Import-Package: com.fasterxml.jackson.annotation; version="[2.3.0,3.0.0)"-->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-core</artifactId>
+ <artifactId>jackson-core</artifactId>
<version>2.3.0</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-annotations</artifactId>
+ <artifactId>jackson-annotations</artifactId>
<version>2.3.0</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
+ <artifactId>jackson-databind</artifactId>
<version>2.3.0</version>
</dependency>
</dependencies>
<repositories>
+ <!--
<repository>
<releases />
<snapshots>
@@ -545,34 +545,13 @@
<name>myGrid Repository</name>
<url>http://www.mygrid.org.uk/maven/repository</url>
</repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- <repository>
- <id>spring-maven-milestone</id>
- <name>Springframework Maven Repository</name>
- <url>http://maven.springframework.org/milestone</url>
- </repository>
- <repository>
- <id>com.springsource.repository.bundles.milestone</id>
- <name>SpringSource Enterprise Bundle Repository - SpringSource Bundle Milestones</name>
- <url>http://repository.springsource.com/maven/bundles/milestone</url>
- </repository>
+ -->
+ <!--
<repository>
<id>OPS4J</id>
<url>http://repository.ops4j.org/maven2</url>
</repository>
+ -->
</repositories>
- <scm>
- <connection>scm:svn:http://taverna.googlecode.com/svn/taverna/products/net.sf.taverna.t2.taverna-commandline/trunk/</connection>
- <developerConnection>scm:svn:https://taverna.googlecode.com/svn/taverna/products/net.sf.taverna.t2.taverna-commandline/trunk/</developerConnection>
- <url>http://code.google.com/p/taverna/source/browse/#svn/taverna/products/net.sf.taverna.t2.taverna-commandline/trunk/</url>
- </scm>
</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9a15408d/taverna-commandline-tests/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/pom.xml b/taverna-commandline-tests/pom.xml
index 9b33bea..26789fe 100644
--- a/taverna-commandline-tests/pom.xml
+++ b/taverna-commandline-tests/pom.xml
@@ -1,19 +1,13 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
- <!-- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>parent</artifactId>
- <version>0.2.2011-02-17</version>
- </parent> -->
<parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
+ <groupId>org.apache.taverna.commandline</groupId>
+ <artifactId>taverna-commandline</artifactId>
+ <version>3.1.0-incubating-SNAPSHOT</version>
</parent>
- <groupId>uk.org.taverna.commandline</groupId>
<artifactId>taverna-command-line-tests</artifactId>
- <version>0.1.0-SNAPSHOT</version>
+ <name>Apache Taverna Command Line Tests</name>
<build>
<plugins>
<plugin>
@@ -94,4 +88,4 @@
<snapshots />
</repository>
</repositories>
-</project>
\ No newline at end of file
+</project>
[05/50] [abbrv] incubator-taverna-commandline git commit: Now using
commons-io See: T3-1193
Posted by st...@apache.org.
Now using commons-io See: T3-1193
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/64ddb76e
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/64ddb76e
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/64ddb76e
Branch: refs/heads/master
Commit: 64ddb76eca535157272ee13a795bce056061a2e6
Parents: f0da039
Author: Christian-B <br...@cs.man.ac.uk>
Authored: Mon Sep 22 13:05:12 2014 +0100
Committer: Christian-B <br...@cs.man.ac.uk>
Committed: Mon Sep 22 13:05:12 2014 +0100
----------------------------------------------------------------------
taverna-commandline-common/pom.xml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/64ddb76e/taverna-commandline-common/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/pom.xml b/taverna-commandline-common/pom.xml
index b904931..7abb64f 100644
--- a/taverna-commandline-common/pom.xml
+++ b/taverna-commandline-common/pom.xml
@@ -67,8 +67,8 @@
</dependency>
<dependency>
- <groupId>org.apache.commons</groupId>
- <artifactId>com.springsource.org.apache.commons.io</artifactId>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
<version>${commons.io.version}</version>
</dependency>
[24/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-tests/
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/xmlSplitter/xmlSplitter.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/xmlSplitter/xmlSplitter.t2flow b/src/test/resources/workflows/xmlSplitter/xmlSplitter.t2flow
deleted file mode 100644
index bd0875d..0000000
--- a/src/test/resources/workflows/xmlSplitter/xmlSplitter.t2flow
+++ /dev/null
@@ -1,339 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="52ddd8d4-d1fc-4b62-932a-288df52b77cf" role="top"><name>Workflow1</name><inputPorts><port><name>lastName</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
- <text>Smith</text>
- </annotationBean>
- <date>2011-02-17 10:48:23.657 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>firstName</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
- <text>John</text>
- </annotationBean>
- <date>2011-02-17 10:48:16.703 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>age</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
- <text>John</text>
- </annotationBean>
- <date>2011-02-17 10:47:56.513 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
- <text>21</text>
- </annotationBean>
- <date>2011-02-17 10:48:30.905 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>personToString</name><inputPorts><port><name>parameters</name><depth>0</depth></port></inputPorts><outputPorts><port><name>parameters</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="parameters" to="parameters" /></inputMap><outputMap><map from="parameters" to="parameters" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>http://www.mygrid.org.uk/menagerie/xfire/Complex-dlw?wsdl</wsdl>
- <operation>personToString</operation>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="parameters" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>personToString_output</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitt
erActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
- <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="personToStringResponse" name="parameters" qname="{http://xfire.codehaus.org/BookService}personToStringResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="out" qname="{http://xfire.codehaus.org/BookService}&gt;personToStringResponse&gt;out" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>input</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>personToString_input</name><inputPorts><port><name>person</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterA
ctivity</class><inputMap><map from="person" to="person" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
- <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="personToString" name="parameters" qname="{http://xfire.codehaus.org/BookService}personToString"><s:elements><s:complextype optional="false" unbounded="false" typename="Person" name="person" qname="{http://xfire.codehaus.org/BookService}&gt;personToString&gt;person"><s:elements><s:complextype optional="true" unbounded="false" typename="Address" name="address" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;address"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="city" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;city" /><s:basetype optional="true" unbounded="false" typename="string" name="road" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;road" /><s:basetype optional="true
" unbounded="false" typename="int" name="roadNumber" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;roadNumber" /></s:elements></s:complextype><s:basetype optional="true" unbounded="false" typename="int" name="age" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;age" /><s:basetype optional="true" unbounded="false" typename="string" name="firstName" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;firstName" /><s:basetype optional="true" unbounded="false" typename="string" name="lastName" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;lastName" /></s:elements></s:complextype></s:elements></s:complextype></s:extensions></wrappedTypeXML>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>person</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="person" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>personToString_person</name><inputPorts><port><name>lastName</name><depth>0</depth></port><port><name>firstName</name><depth>0</depth></port><port><name>age</name><depth>0</depth></port><port><name>address</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.act
ivities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="lastName" to="lastName" /><map from="address" to="address" /><map from="age" to="age" /><map from="firstName" to="firstName" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
- <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="Person" name="person" qname="{http://xfire.codehaus.org/BookService}&gt;personToString&gt;person"><s:elements><s:complextype optional="true" unbounded="false" typename="Address" name="address" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;address"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="city" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;city" /><s:basetype optional="true" unbounded="false" typename="string" name="road" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;road" /><s:basetype optional="true" unbounded="false" typename="int" name="roadNumber" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;roadNumber" /></s:elements></s:complextype>
;<s:basetype optional="true" unbounded="false" typename="int" name="age" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;age" /><s:basetype optional="true" unbounded="false" typename="string" name="firstName" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;firstName" /><s:basetype optional="true" unbounded="false" typename="string" name="lastName" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;lastName" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>address</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>age</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>firstName</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>lastName</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="lastName" depth="0" /><port name="firstName" depth="0" /><port name="age" depth="0" /><port name="address" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>person_address</name><inputPorts><port><name>city</name><depth>0</depth></port><port><name>road</name><depth>0</depth></port><port><name>roadNumber</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><act
ivity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="road" to="road" /><map from="roadNumber" to="roadNumber" /><map from="city" to="city" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
- <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="Address" name="address" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;address"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="city" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;city" /><s:basetype optional="true" unbounded="false" typename="string" name="road" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;road" /><s:basetype optional="true" unbounded="false" typename="int" name="roadNumber" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;roadNumber" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>city</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>road</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>roadNumber</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="city" depth="0" /><port name="road" depth="0" /><port name="roadNumber" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>city_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstant
Activity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>Manchester</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>road_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf
.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>Oxford Road</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>roadNumber_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><
net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>40</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>personToString</processor><port>parameters</port></sink><source type="processor"><processor>personToString_input</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>personToString_output</processor><port>input</port></sink><source type="processor"><processor>personToString</processor><port>parameters</port></source></datalink><datalink><sink type="processor"><processor>pers
onToString_input</processor><port>person</port></sink><source type="processor"><processor>personToString_person</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>personToString_person</processor><port>lastName</port></sink><source type="dataflow"><port>lastName</port></source></datalink><datalink><sink type="processor"><processor>personToString_person</processor><port>firstName</port></sink><source type="dataflow"><port>firstName</port></source></datalink><datalink><sink type="processor"><processor>personToString_person</processor><port>age</port></sink><source type="dataflow"><port>age</port></source></datalink><datalink><sink type="processor"><processor>personToString_person</processor><port>address</port></sink><source type="processor"><processor>person_address</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>person_address</processor><port>city</port></sink><source type="processor"><processo
r>city_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>person_address</processor><port>road</port></sink><source type="processor"><processor>road_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>person_address</processor><port>roadNumber</port></sink><source type="processor"><processor>roadNumber_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>personToString_output</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>d79eeb60-919e-4076-af14-70ac4d605bec</identification>
- </annotationBean>
- <date>2011-02-17 10:49:46.785 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>52ddd8d4-d1fc-4b62-932a-288df52b77cf</identification>
- </annotationBean>
- <date>2011-02-17 10:53:16.981 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>8815f1ea-2659-4b7e-a90e-787c6a3c4ad6</identification>
- </annotationBean>
- <date>2011-02-17 10:29:40.492 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>eee0128a-4afe-4566-851a-fe50dcb36340</identification>
- </annotationBean>
- <date>2011-02-17 10:48:35.150 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>e64ae430-dd6e-468d-b3dd-de1fea9c717b</identification>
- </annotationBean>
- <date>2011-02-17 10:20:55.279 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>2aa76794-f001-42f9-b945-797badfeebb1</identification>
- </annotationBean>
- <date>2011-02-17 10:17:24.893 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>2ece2565-7498-4154-9d61-996d8a1db5f3</identification>
- </annotationBean>
- <date>2011-02-17 10:24:47.509 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>97fbd479-a423-4e8c-9033-bfc28f1a7885</identification>
- </annotationBean>
- <date>2011-02-17 10:42:59.63 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>24e8b191-9f48-4864-82be-d9578f1b8450</identification>
- </annotationBean>
- <date>2011-02-17 10:25:38.788 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/xpath/xpath.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/xpath/xpath.t2flow b/src/test/resources/workflows/xpath/xpath.t2flow
deleted file mode 100644
index 0691ccc..0000000
--- a/src/test/resources/workflows/xpath/xpath.t2flow
+++ /dev/null
@@ -1,127 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="9fb6e3ea-f314-4f9f-8eb3-ba3dbf2b494f" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>XPath_Service</name><inputPorts><port><name>xml_text</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodelistAsXML</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>xpath-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.xpath.XPathActivity</class><inputMap><map from="xml_text" to="xml_text" /></inputMap><outputMap><map from="nodelistAsXML" to="nodelistAsXML" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean xmlns="">
- <xmlDocument><?xml version="1.0" encoding="UTF-8"?>
-<test name="test-name">
-<test-element>test</test-element>
-</test></xmlDocument>
- <xpathExpression>/test/test-element</xpathExpression>
- <xpathNamespaceMap />
-</net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="xml_text" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>xml_text_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" t
o="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value><?xml version="1.0" encoding="UTF-8"?> <test name="test-name"> <test-element>test</test-element> </test></value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>Merge_String_List_to_a_String</name><inputPorts><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>concatenated</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="str
inglist" to="stringlist" /></inputMap><outputMap><map from="concatenated" to="concatenated" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>stringlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>seperator</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>concatenated</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>String seperatorString = "\n";
-if (seperator != void) {
- seperatorString = seperator;
-}
-StringBuffer sb = new StringBuffer();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- sb.append(item);
- if (i.hasNext()) {
- sb.append(seperatorString);
- }
-}
-concatenated = sb.toString();
-</script>
- <dependencies />
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringListMerge</localworkerName>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>XPath_Service</processor><port>xml_text</port></sink><source type="processor"><processor>xml_text_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>stringlist</port></sink><source type="processor"><processor>XPath_Service</processor><port>nodelistAsXML</port></s
ource></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Merge_String_List_to_a_String</processor><port>concatenated</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>9fb6e3ea-f314-4f9f-8eb3-ba3dbf2b494f</identification>
- </annotationBean>
- <date>2011-11-03 14:17:32.152 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>bed5342f-45e0-4fc9-a85d-bcd1ea01e33d</identification>
- </annotationBean>
- <date>2011-11-03 12:55:28.941 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>9f0cedc9-4a53-4564-aeb5-d0b7f7b2b4e1</identification>
- </annotationBean>
- <date>2011-11-03 12:56:36.620 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>94104add-ec12-4c5a-a4f6-b5c1b6d0a700</identification>
- </annotationBean>
- <date>2011-11-03 12:56:00.6 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/pom.xml b/taverna-commandline-tests/pom.xml
new file mode 100644
index 0000000..9b33bea
--- /dev/null
+++ b/taverna-commandline-tests/pom.xml
@@ -0,0 +1,97 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <!-- <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>parent</artifactId>
+ <version>0.2.2011-02-17</version>
+ </parent> -->
+ <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>uk.org.taverna.commandline</groupId>
+ <artifactId>taverna-command-line-tests</artifactId>
+ <version>0.1.0-SNAPSHOT</version>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>2.12</version>
+ <configuration>
+ <systemPropertyVariables>
+ <buildDirectory>${project.build.directory}</buildDirectory>
+ </systemPropertyVariables>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+ <dependencies>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-t2flow</artifactId>
+ <version>${scufl2.version}</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-rdfxml</artifactId>
+ <version>${scufl2.version}</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.8.1</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>2.2</version>
+ <scope>test</scope>
+ </dependency>
+ <!-- Optional for scufl2-xdfxml -->
+ <dependency>
+ <groupId>com.sun.xml.bind</groupId>
+ <artifactId>jaxb-impl</artifactId>
+ <version>2.2.4-1</version>
+ <scope>test</scope>
+ </dependency>
+ <!-- Required by scufl2-xdfxml, see SCUFL2-122 -->
+ <dependency>
+ <groupId>org.jdom</groupId>
+ <artifactId>com.springsource.org.jdom</artifactId>
+ <version>1.1.0</version>
+ <scope>test</scope>
+ </dependency>
+ <!-- <dependency>
+ <groupId>org.jdom</groupId>
+ <artifactId>jdom</artifactId>
+ <version>1.1.2</version>
+ <scope>test</scope>
+ </dependency> -->
+ </dependencies>
+ <repositories>
+ <repository>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository</url>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ </repository>
+ <repository>
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ </repository>
+ </repositories>
+</project>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java
new file mode 100644
index 0000000..07df1c3
--- /dev/null
+++ b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/TavernaCommandLineTest.java
@@ -0,0 +1,485 @@
+/*******************************************************************************
+ * Copyright (C) 2012 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.commandline;
+
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.junit.Assume.assumeTrue;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.net.URI;
+import java.net.URL;
+import java.text.MessageFormat;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.comparator.NameFileComparator;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+
+import uk.org.taverna.commandline.WorkflowTestSuite.Workflows;
+import uk.org.taverna.scufl2.api.container.WorkflowBundle;
+import uk.org.taverna.scufl2.api.io.WorkflowBundleIO;
+import uk.org.taverna.scufl2.rdfxml.RDFXMLReader;
+
+/**
+ * Regression tests for Taverna Command Line Tool.
+ *
+ * @author David Withers
+ */
+@RunWith(WorkflowTestSuite.class)
+public class TavernaCommandLineTest {
+
+ private static String baseVersion = "2.4.0";
+ private static boolean baseVersionReleased = true;
+
+ private static String testVersion = "3.0.1-SNAPSHOT";
+ private static boolean testVersionReleased = false;
+ private static boolean testVersionSupportsScufl2 = true;
+
+ private static String script = "executeworkflow.sh";
+ private static String baseName = "taverna-commandline-" + baseVersion;
+ private static String testName = "taverna-command-line-" + testVersion;
+ private static String releasedLocation = "https://launchpad.net/taverna/t2/";
+ private static String unreleasedLocation = "http://build.mygrid.org.uk/ci/job/t3-taverna-commandline-product/lastSuccessfulBuild/net.sf.taverna.t2$taverna-commandline/artifact/net.sf.taverna.t2/taverna-commandline/";
+
+ private static String baseVersionLocation = (baseVersionReleased ? releasedLocation
+ : unreleasedLocation) + baseVersion + "/+download/" + baseName + ".zip";
+ private static String testVersionLocation = (testVersionReleased ? releasedLocation
+ : unreleasedLocation)
+ + testVersion
+ + "/"
+ + testName
+ + (testVersionReleased ? ".zip" : "-bin.zip");
+
+ private static String baseCommand;
+ private static String testCommand;
+
+ private static File buildDirectory;
+
+ private File workflowDirectory;
+ private File baseOutput;
+ private File testOutput;
+ private boolean secure;
+ private List<File> inputs;
+ private String ignorePort;
+ private String message;
+
+ public TavernaCommandLineTest(File workflowDirectory) throws Exception {
+ this.workflowDirectory = workflowDirectory;
+ if (buildDirectory == null) {
+ String buildDirectoryLocation = System.getProperty("buildDirectory");
+ if (buildDirectoryLocation == null) {
+ buildDirectoryLocation = System.getProperty("user.dir")
+ + System.getProperty("file.separator") + "target";
+ }
+ buildDirectory = new File(buildDirectoryLocation);
+ buildDirectory.mkdirs();
+ }
+ if (baseCommand == null) {
+ File commandDirectory = new File(buildDirectory, baseName);
+ if (!commandDirectory.exists()) {
+ System.out.println("Fetching " + baseName);
+ fetchTaverna(baseVersionLocation, baseName);
+ }
+ baseCommand = new File(baseName, script).getPath();
+ }
+ if (testCommand == null) {
+ File commandDirectory = new File(buildDirectory, testName);
+ if (!commandDirectory.exists()) {
+ System.out.println("Fetching " + testName);
+ fetchTaverna(testVersionLocation, testName);
+ }
+ testCommand = new File(testName, script).getPath();
+ }
+ File outputsDirectory = new File(buildDirectory, "test-outputs");
+ baseOutput = new File(outputsDirectory, workflowDirectory.getName() + "-" + baseVersion);
+ testOutput = new File(outputsDirectory, workflowDirectory.getName() + "-" + testVersion);
+ secure = workflowDirectory.getName().startsWith("secure");
+ inputs = getInputs();
+ ignorePort = getIgnorePort();
+ message = "Running {0} with version {1}";
+ }
+
+ @Workflows
+ public static List<File> workflows() {
+ List<File> workflows = new ArrayList<File>();
+ for (File workflowDirectory : getResources("workflows")) {
+ workflows.add(workflowDirectory);
+ }
+ for (File workflowDirectory : getResources("myexperiment")) {
+ workflows.add(workflowDirectory);
+ }
+ return workflows;
+ }
+
+ @Before
+ public void setup() throws Exception {
+ if (!baseOutput.exists()) {
+ if (baseVersion.equals("2.3.0") && workflowDirectory.getName().equals("tool"))
+ return;// version 2.3.0 is missing tool plugin
+ String workflow = getWorkflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, baseVersion)
+ + (inputs.size() > 0 ? " using input values" : ""));
+ runWorkflow(baseCommand, workflow, baseOutput, true, secure, false);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ baseOutput.exists());
+ }
+ }
+
+ public boolean testExcluded() {
+ // version 3.0.0 is missing biomoby activity
+ if (testVersion.startsWith("3.") && workflowDirectory.getName().contains("biomoby"))
+ return true;
+ // version 3.0.0 is missing tool activity
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("unix_external_tools_with_zip_and_unzip"))
+ return true;
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("unix_numerically_adding_two_values"))
+ return true;
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("unix_tool_service_using_string_replacement"))
+ return true;
+ // version 3.0.0 is missing looping configuration
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("ebi_interproscan_newservices"))
+ return true;
+ if (testVersion.startsWith("3.")
+ && workflowDirectory.getName().equals("biomartandembossanalysis"))
+ return true;
+ return false;
+ }
+
+ @Test
+ public void testWorkflowWithoutInputs() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(inputs.isEmpty());
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getWorkflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, testVersion));
+ runWorkflow(testCommand, workflow, testOutput, true, secure, false);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ @Test
+ public void testWorkflowWithInputValues() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(inputs.size() > 0);
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getWorkflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, testVersion)
+ + " using input values");
+ runWorkflow(testCommand, workflow, testOutput, true, secure, false);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ @Test
+ public void testWorkflowWithInputFiles() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(inputs.size() > 0);
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getWorkflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, testVersion)
+ + " using input files");
+ runWorkflow(testCommand, workflow, testOutput, false, secure, false);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ @Test
+ @Ignore
+ public void testWorkflowWithDatabase() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(inputs.size() > 0);
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getWorkflow().toASCIIString();
+ System.out
+ .println(MessageFormat.format(message, workflow, testVersion) + " using database");
+ runWorkflow(testCommand, workflow, testOutput, true, secure, true);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ @Test
+ public void testScufl2Workflow() throws Exception {
+ assumeTrue(!testExcluded());
+ assumeTrue(baseOutput.exists());
+ assumeTrue(testVersionSupportsScufl2);
+
+ FileUtils.deleteDirectory(testOutput);
+ String workflow = getScufl2Workflow().toASCIIString();
+ System.out.println(MessageFormat.format(message, workflow, testVersion)
+ + (inputs.size() > 0 ? " using input values" : ""));
+ runWorkflow(testCommand, workflow, testOutput, true, secure, true);
+ assertTrue(String.format("No output produced for %s", workflowDirectory.getName()),
+ testOutput.exists());
+ assertOutputsEquals(baseOutput, testOutput);
+ }
+
+ private synchronized void runWorkflow(String command, String workflow, File outputsDirectory,
+ boolean inputValues, boolean secure, boolean database) throws Exception {
+ ProcessBuilder processBuilder = new ProcessBuilder("sh", command);
+ processBuilder.redirectErrorStream(true);
+ processBuilder.directory(buildDirectory);
+ List<String> args = processBuilder.command();
+ for (File input : inputs) {
+ if (inputValues) {
+ args.add("-inputvalue");
+ args.add(input.getName());
+ args.add(IOUtils.toString(new FileReader(input)));
+ } else {
+ args.add("-inputfile");
+ args.add(input.getName());
+ args.add(input.getAbsolutePath());
+ }
+ }
+ args.add("-outputdir");
+ args.add(outputsDirectory.getPath());
+ if (secure) {
+ args.add("-cmdir");
+ args.add(getClass().getResource("/security").getFile());
+ args.add("-cmpassword");
+ }
+ if (database) {
+ args.add("-embedded");
+ }
+ args.add(workflow);
+ Process process = processBuilder.start();
+ if (secure) {
+ PrintStream outputStream = new PrintStream(process.getOutputStream());
+ outputStream.println("test");
+ outputStream.flush();
+ }
+ waitFor(process);
+ }
+
+ private URI getWorkflow() throws Exception {
+ File workflow = new File(workflowDirectory, workflowDirectory.getName() + ".t2flow");
+ if (!workflow.exists()) {
+ workflow = new File(workflowDirectory, workflowDirectory.getName() + ".url");
+ return new URI(IOUtils.toString(new FileReader(workflow)));
+ }
+ return workflow.toURI();
+ }
+
+ private URI getScufl2Workflow() throws Exception {
+ File workflow = new File(buildDirectory, workflowDirectory.getName() + ".wfbundle");
+ // if (!workflow.exists()) {
+ WorkflowBundleIO workflowBundleIO = new WorkflowBundleIO();
+ WorkflowBundle bundle = workflowBundleIO.readBundle(getWorkflow().toURL(), null);
+ workflowBundleIO.writeBundle(bundle, workflow,
+ RDFXMLReader.APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE);
+ // }
+ return workflow.toURI();
+ }
+
+ private synchronized int waitFor(Process process) throws IOException {
+ while (true) {
+ try {
+ wait(500);
+ } catch (InterruptedException e) {
+ }
+ IOUtils.copy(process.getInputStream(), System.out);
+ try {
+ return process.exitValue();
+ } catch (IllegalThreadStateException e) {
+ }
+ }
+ }
+
+ private void assertOutputsEquals(File directory1, File directory2) {
+ File[] directory1Files = directory1.listFiles();
+ File[] directory2Files = directory2.listFiles();
+ // assert directories contain same number of files
+ assertEquals(String.format("%s has %s files but %s has %s files", directory1.getName(),
+ directory1Files.length, directory2.getName(), directory2Files.length),
+ directory1Files.length, directory2Files.length);
+ // sort files in directory
+ Arrays.sort(directory1Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
+ Arrays.sort(directory2Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
+ for (int i = 0; i < directory1Files.length; i++) {
+ assertFilesEqual(directory1Files[i], directory2Files[i], !directory1Files[i].getName()
+ .equals(ignorePort));
+ }
+ }
+
+ private void assertDirectoriesEquals(File directory1, File directory2, boolean checkFileContents) {
+ if (directory1.exists()) {
+ assertTrue(String.format("%s exists but %s does not", directory1, directory2),
+ directory2.exists());
+ } else {
+ assertFalse(String.format("%s does not exists but %s does", directory1, directory2),
+ directory2.exists());
+ }
+ File[] directory1Files = directory1.listFiles();
+ File[] directory2Files = directory2.listFiles();
+ // assert directories contain same number of files
+ assertEquals(String.format("%s has %s files but %s has %s files", directory1.getName(),
+ directory1Files.length, directory2.getName(), directory2Files.length),
+ directory1Files.length, directory2Files.length);
+ // sort files in directory
+ Arrays.sort(directory1Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
+ Arrays.sort(directory2Files, NameFileComparator.NAME_SYSTEM_COMPARATOR);
+ for (int i = 0; i < directory1Files.length; i++) {
+ assertFilesEqual(directory1Files[i], directory2Files[i], checkFileContents);
+ }
+ }
+
+ private void assertFilesEqual(File file1, File file2, boolean checkFileContents) {
+ if (file1.isHidden()) {
+ assertTrue(String.format("%s is hidden but %s is not", file1, file2), file2.isHidden());
+ } else {
+ assertFalse(String.format("%s is not hidden but %s is", file1, file2), file2.isHidden());
+ assertEquals(file1.getName(), file2.getName());
+ if (file1.isDirectory()) {
+ assertTrue(String.format("%s is a directory but %s is not", file1, file2),
+ file2.isDirectory());
+ assertDirectoriesEquals(file1, file2, checkFileContents);
+ } else {
+ assertFalse(String.format("%s is not a directory but %s is", file1, file2),
+ file2.isDirectory());
+ if (isZipFile(file1)) {
+ assertZipFilesEqual(file1, file2);
+ } else if (checkFileContents) {
+ assertEquals(String.format("%s is a different length to %s", file1, file2),
+ file1.length(), file2.length());
+ try {
+ byte[] byteArray1 = IOUtils.toByteArray(new FileReader(file1));
+ byte[] byteArray2 = IOUtils.toByteArray(new FileReader(file2));
+ assertArrayEquals(String.format("%s != %s", file1, file2), byteArray1,
+ byteArray2);
+ } catch (FileNotFoundException e) {
+ fail(e.getMessage());
+ } catch (IOException e) {
+ fail(e.getMessage());
+ }
+ }
+ }
+ }
+ }
+
+ private void assertZipFilesEqual(File file1, File file2) {
+ ZipFile zipFile1 = null;
+ ZipFile zipFile2 = null;
+ try {
+ zipFile1 = new ZipFile(file1);
+ zipFile2 = new ZipFile(file2);
+ } catch (Exception e) {
+ assertTrue(String.format("%s and %s are not both zip files"), zipFile1 == null);
+ }
+ if (zipFile1 != null && zipFile2 != null) {
+ Enumeration<? extends ZipEntry> entries1 = zipFile1.entries();
+ Enumeration<? extends ZipEntry> entries2 = zipFile2.entries();
+ while (entries1.hasMoreElements()) {
+ assertTrue(entries2.hasMoreElements());
+ ZipEntry zipEntry1 = entries1.nextElement();
+ ZipEntry zipEntry2 = entries2.nextElement();
+ assertEquals(
+ String.format("%s and %s are not both directories", zipEntry1, zipEntry2),
+ zipEntry1.isDirectory(), zipEntry2.isDirectory());
+ assertEquals(String.format("%s and %s have different names", zipEntry1, zipEntry2),
+ zipEntry1.getName(), zipEntry2.getName());
+ assertEquals(String.format("%s and %s have different sizes", zipEntry1, zipEntry2),
+ zipEntry1.getSize(), zipEntry2.getSize());
+ try {
+ byte[] byteArray1 = IOUtils.toByteArray(zipFile1.getInputStream(zipEntry1));
+ byte[] byteArray2 = IOUtils.toByteArray(zipFile2.getInputStream(zipEntry2));
+ assertArrayEquals(String.format("%s != %s", zipEntry1, zipEntry2), byteArray1,
+ byteArray2);
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ assertFalse(entries2.hasMoreElements());
+ }
+ }
+
+ private boolean isZipFile(File file) {
+ try {
+ new ZipFile(file);
+ return true;
+ } catch (Exception e) {
+ return false;
+ }
+ }
+
+ private static File[] getResources(String directory) {
+ return new File(TavernaCommandLineTest.class.getResource("/" + directory).getFile())
+ .listFiles();
+ }
+
+ private List<File> getInputs() {
+ File inputsDirectory = new File(workflowDirectory, "inputs");
+ if (inputsDirectory.exists() && inputsDirectory.isDirectory()) {
+ return Arrays.asList(inputsDirectory.listFiles());
+ }
+ return Collections.emptyList();
+ }
+
+ private String getIgnorePort() throws Exception {
+ File ignorePort = new File(workflowDirectory, "ignorePort");
+ if (ignorePort.exists()) {
+ return IOUtils.toString(new FileReader(ignorePort));
+ }
+ return "";
+ }
+
+ private void fetchTaverna(String location, String name) throws Exception {
+ File zipFile = new File(buildDirectory, name + ".zip");
+ IOUtils.copy(new URL(location).openStream(), new FileOutputStream(zipFile));
+ ProcessBuilder processBuilder = new ProcessBuilder("unzip", "-q", name);
+ processBuilder.redirectErrorStream(true);
+ processBuilder.directory(buildDirectory);
+ System.out.println(processBuilder.command());
+ Process process = processBuilder.start();
+ waitFor(process);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java
new file mode 100644
index 0000000..56ed82d
--- /dev/null
+++ b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestRunner.java
@@ -0,0 +1,70 @@
+/*******************************************************************************
+ * Copyright (C) 2012 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.commandline;
+
+import java.io.File;
+import java.util.List;
+
+import org.junit.runner.notification.RunNotifier;
+import org.junit.runners.BlockJUnit4ClassRunner;
+import org.junit.runners.model.FrameworkMethod;
+import org.junit.runners.model.InitializationError;
+import org.junit.runners.model.Statement;
+
+/**
+ * Test runner for running workflows.
+ *
+ * @author David Withers
+ */
+public class WorkflowTestRunner extends BlockJUnit4ClassRunner {
+ private File workflow;
+
+ public WorkflowTestRunner(Class<?> type, File workflow) throws InitializationError {
+ super(type);
+ this.workflow = workflow;
+ }
+
+ @Override
+ public Object createTest() throws Exception {
+ return getTestClass().getOnlyConstructor().newInstance(workflow);
+ }
+
+ @Override
+ protected String getName() {
+ return String.format("[%s]", workflow.getName());
+ }
+
+ @Override
+ protected String testName(final FrameworkMethod method) {
+ return String.format("%s[%s]", method.getName(), workflow.getName());
+ }
+
+ @Override
+ protected void validateConstructor(List<Throwable> errors) {
+ validateOnlyOneConstructor(errors);
+ }
+
+ @Override
+ protected Statement classBlock(RunNotifier notifier) {
+ return childrenInvoker(notifier);
+ }
+
+}
[44/50] [abbrv] incubator-taverna-commandline git commit: Updated
COMMANDLINE_BUNDLE_NAME
Posted by st...@apache.org.
Updated COMMANDLINE_BUNDLE_NAME
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/5ba148f2
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/5ba148f2
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/5ba148f2
Branch: refs/heads/master
Commit: 5ba148f211d5c7919d83762bd2414ee1cff88293
Parents: bf51ad1
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Jan 6 13:17:11 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Jan 6 13:17:11 2015 +0000
----------------------------------------------------------------------
.../java/uk/org/taverna/commandline/TavernaCommandLine.java | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/5ba148f2/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
index a462ba3..426ab98 100644
--- a/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
+++ b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
@@ -49,9 +49,9 @@ import uk.org.taverna.osgi.OsgiLauncher;
*/
public class TavernaCommandLine {
- private static final String COMMANDLINE_BUNDLE_NAME = "net.sf.taverna.t2.taverna-commandline.common";
+ private static final String COMMANDLINE_BUNDLE_NAME = "org.apache.taverna.commandline.taverna-commandline-common";
- private static File commandlineBundle;
+ private static File commandlineBundle = null;
private static ApplicationConfiguration applicationConfiguration = new ApplicationConfigurationImpl();
@@ -79,6 +79,10 @@ public class TavernaCommandLine {
context.registerService("net.sf.taverna.t2.commandline.options.CommandLineOptions",
commandLineOptions, null);
osgilauncher.startServices(true);
+ if (commandlineBundle == null) {
+ System.err.println("Can't locate command line bundle " + COMMANDLINE_BUNDLE_NAME);
+ System.exit(1);
+ }
osgilauncher.startBundle(osgilauncher.installBundle(commandlineBundle.toURI()));
}
} catch (ArgumentsParsingException e) {
[46/50] [abbrv] incubator-taverna-commandline git commit:
3.1.0-incubating -> 3.1.0.incubating
Posted by st...@apache.org.
3.1.0-incubating -> 3.1.0.incubating
(make OSGi happy)
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/ad42dfdb
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/ad42dfdb
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/ad42dfdb
Branch: refs/heads/master
Commit: ad42dfdb71c5a28f5fec2388bdf6f70a11ba4a76
Parents: 85bb1f1
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Jan 6 16:29:17 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Jan 6 16:29:17 2015 +0000
----------------------------------------------------------------------
taverna-commandline-launcher/pom.xml | 4 ++--
taverna-commandline-product/src/main/etc/executeworkflow.bat | 2 +-
taverna-commandline-product/src/main/etc/executeworkflow.sh | 2 +-
3 files changed, 4 insertions(+), 4 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/ad42dfdb/taverna-commandline-launcher/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/pom.xml b/taverna-commandline-launcher/pom.xml
index 394fa91..f351ae4 100644
--- a/taverna-commandline-launcher/pom.xml
+++ b/taverna-commandline-launcher/pom.xml
@@ -55,8 +55,8 @@
<version>${commons.io.version}</version>
</dependency>
<dependency>
- <groupId>org.apache.log4j</groupId>
- <artifactId>com.springsource.org.apache.log4j</artifactId>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
<version>${log4j.version}</version>
</dependency>
<dependency>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/ad42dfdb/taverna-commandline-product/src/main/etc/executeworkflow.bat
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/etc/executeworkflow.bat b/taverna-commandline-product/src/main/etc/executeworkflow.bat
index 165dc83..2e18831 100644
--- a/taverna-commandline-product/src/main/etc/executeworkflow.bat
+++ b/taverna-commandline-product/src/main/etc/executeworkflow.bat
@@ -14,4 +14,4 @@ set ARGS=%ARGS% "-Dlog4j.configuration=file:///%TAVERNA_HOME%conf/log4j.properti
set ARGS=%ARGS% "-Djava.util.logging.config.file=%TAVERNA_HOME%conf/logging.properties"
set ARGS=%ARGS% "-Dtaverna.app.startup=%TAVERNA_HOME%."
-java %ARGS% -jar "%TAVERNA_HOME%lib\/lib/org.apache.taverna.commandline/taverna-commandline-launcher-3.1.0-incubating-SNAPSHOT.jar" %*
+java %ARGS% -jar "%TAVERNA_HOME%lib\/lib/org.apache.taverna.commandline/taverna-commandline-launcher-3.1.0.incubating-SNAPSHOT.jar" %*
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/ad42dfdb/taverna-commandline-product/src/main/etc/executeworkflow.sh
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/etc/executeworkflow.sh b/taverna-commandline-product/src/main/etc/executeworkflow.sh
index 48e4428..5ef0916 100644
--- a/taverna-commandline-product/src/main/etc/executeworkflow.sh
+++ b/taverna-commandline-product/src/main/etc/executeworkflow.sh
@@ -21,5 +21,5 @@ exec "$javabin" -Xmx1g -XX:MaxPermSize=400m \
"-Dlog4j.configuration=file://$taverna_home/conf/log4j.properties " \
"-Djava.util.logging.config.file=$taverna_home/conf/logging.properties " \
"-Dtaverna.app.startup=$taverna_home" \
- -jar "$taverna_home/lib/org.apache.taverna.commandline/taverna-commandline-launcher-3.1.0-incubating-SNAPSHOT.jar" \
+ -jar "$taverna_home/lib/org.apache.taverna.commandline/taverna-commandline-launcher-3.1.0.incubating-SNAPSHOT.jar" \
${1+"$@"}
[16/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-launcher/
Posted by st...@apache.org.
taverna-commandline-launcher/
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/a8e6b3ed
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/a8e6b3ed
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/a8e6b3ed
Branch: refs/heads/master
Commit: a8e6b3edeb4682e71de34024376c51756de55474
Parents: e8f020f
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 01:44:56 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 01:44:56 2014 -0600
----------------------------------------------------------------------
.gitignore | 24 -
.project | 23 -
.travis.yml | 1 -
README.md | 3 -
pom.xml | 96 ----
.../commandline/CommandLineOptionsImpl.java | 445 -------------------
.../taverna/commandline/TavernaCommandLine.java | 139 ------
src/main/resources/help.txt | 87 ----
.../TestCommandLineOptionsHandler.java | 267 -----------
taverna-commandline-launcher/pom.xml | 96 ++++
.../commandline/CommandLineOptionsImpl.java | 445 +++++++++++++++++++
.../taverna/commandline/TavernaCommandLine.java | 139 ++++++
.../src/main/resources/help.txt | 87 ++++
.../TestCommandLineOptionsHandler.java | 267 +++++++++++
14 files changed, 1034 insertions(+), 1085 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/.gitignore
----------------------------------------------------------------------
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index ebe0e5b..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,24 +0,0 @@
-# ignore project files #
-.classpath
-.project
-.settings/
-catalog-v001.xml
-
-# ignore target files #
-target/
-bin/
-build/
-dist/
-apidoc/
-*.swp
-
-# ignore svn files if there
-.svn
-
-# ignore log files #
-*.log
-/logs/*
-*/logs/*
-
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/.project
----------------------------------------------------------------------
diff --git a/.project b/.project
deleted file mode 100644
index 86e9dca..0000000
--- a/.project
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>taverna-command-line</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.m2e.core.maven2Builder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jdt.core.javanature</nature>
- <nature>org.eclipse.m2e.core.maven2Nature</nature>
- </natures>
-</projectDescription>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/.travis.yml
----------------------------------------------------------------------
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index dff5f3a..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1 +0,0 @@
-language: java
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
deleted file mode 100644
index 31ac549..0000000
--- a/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-Taverna 3 command line
-
-This code was previously hosted at http://taverna.googlecode.com/svn/taverna/command-line/
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
deleted file mode 100644
index ad8330e..0000000
--- a/pom.xml
+++ /dev/null
@@ -1,96 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>uk.org.taverna.commandline</groupId>
- <artifactId>taverna-command-line</artifactId>
- <version>0.1.2-SNAPSHOT</version>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-jar-plugin</artifactId>
- <version>2.4</version>
- <configuration>
- <archive>
- <manifest>
- <addClasspath>true</addClasspath>
- <mainClass>uk.org.taverna.commandline.TavernaCommandLine</mainClass>
- <classpathLayoutType>custom</classpathLayoutType>
- <customClasspathLayout>../${artifact.groupId}/${artifact.artifactId}-${artifact.baseVersion}${dashClassifier?}.${artifact.extension}</customClasspathLayout>
- </manifest>
- </archive>
- </configuration>
- </plugin>
- </plugins>
- </build>
- <dependencies>
- <dependency>
- <groupId>net.sf.taverna.t2.taverna-commandline</groupId>
- <artifactId>taverna-commandline-api</artifactId>
- <version>${t2.taverna-commandline.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.osgi</groupId>
- <artifactId>osgi-launcher</artifactId>
- <version>${osgi.launcher.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.configuration</groupId>
- <artifactId>taverna-app-configuration-impl</artifactId>
- <version>${taverna.configuration.version}</version>
- </dependency>
-
- <dependency>
- <groupId>org.apache.commons</groupId>
- <artifactId>com.springsource.org.apache.commons.cli</artifactId>
- <version>${commons.cli.version}</version>
- </dependency>
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <version>${commons.io.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.log4j</groupId>
- <artifactId>com.springsource.org.apache.log4j</artifactId>
- <version>${log4j.version}</version>
- </dependency>
- <dependency>
- <groupId>org.eclipse</groupId>
- <artifactId>org.eclipse.osgi</artifactId>
- <version>${osgi.equinox.version}</version>
- </dependency>
-
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- </dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
-</project>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
----------------------------------------------------------------------
diff --git a/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java b/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
deleted file mode 100644
index b702e03..0000000
--- a/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
+++ /dev/null
@@ -1,445 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 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.commandline;
-
-import java.io.IOException;
-import java.io.InputStream;
-
-import net.sf.taverna.t2.commandline.exceptions.ArgumentsParsingException;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.GnuParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.OptionBuilder;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-
-/**
- * Handles the processing of command line arguments for enacting a workflow.
- * This class encapsulates all command line options, and exposes them through higher-level
- * accessors. Upon creation it checks the validity of the command line options and raises an
- * {@link InvalidOptionException} if they are invalid.
- *
- * @author Stuart Owen
- * @author David Withers
- */
-public class CommandLineOptionsImpl implements CommandLineOptions {
-
- private static final String OUTPUTDIR = "outputdir";
- private static final String BUNDLE = "bundle";
- private static final Logger logger = Logger.getLogger(CommandLineOptionsImpl.class);
- private Options options;
- private CommandLine commandLine;
-
- public CommandLineOptionsImpl(String[] args) throws ArgumentsParsingException, InvalidOptionException {
- this.options = intitialiseOptions();
- this.commandLine = processArgs(args);
- checkForInvalid();
- }
-
- @Override
- public boolean askedForHelp() {
- return hasOption("help") || (getArgs().length==0 && getOptions().length==0);
- }
-
- @Override
- public boolean isProvenanceEnabled() {
- return hasOption("provenance");
- }
-
- protected void checkForInvalid() throws InvalidOptionException {
- if (askedForHelp()) return;
- if (isProvenanceEnabled()
- && !(hasOption("embedded") || hasOption("clientserver") || hasOption("dbproperties")))
- throw new InvalidOptionException(
- "You should be running with a database to use provenance");
- if (isProvenanceEnabled() && hasOption("inmemory"))
- throw new InvalidOptionException(
- "You should be running with a database to use provenance");
- if ((hasOption("inputfile") || hasOption("inputvalue"))
- && hasOption("inputdoc"))
- throw new InvalidOptionException(
- "You can't provide both -input and -inputdoc arguments");
-
- if (hasOption("inputdelimiter") && hasOption("inputdoc"))
- throw new InvalidOptionException("You cannot combine the -inputdelimiter and -inputdoc arguments");
-
- if (getArgs().length == 0
- && !(hasOption("help") || hasOption("startdb")))
- throw new InvalidOptionException("You must specify a workflow");
-
- if (hasOption("inmemory") && hasOption("embedded"))
- throw new InvalidOptionException(
- "The options -embedded, -clientserver and -inmemory cannot be used together");
- if (hasOption("inmemory") && hasOption("clientserver"))
- throw new InvalidOptionException(
- "The options -embedded, -clientserver and -inmemory cannot be used together");
- if (hasOption("embedded") && hasOption("clientserver"))
- throw new InvalidOptionException(
- "The options -embedded, -clientserver and -inmemory cannot be used together");
- }
-
- @Override
- public void displayHelp() {
- boolean full = false;
- if (hasOption("help")) full=true;
- displayHelp(full);
- }
-
- @Override
- public void displayHelp(boolean showFullText) {
-
- HelpFormatter formatter = new HelpFormatter();
- try {
- formatter
- .printHelp("executeworkflow [options] [workflow]", options);
- if (showFullText) {
- InputStream helpStream = CommandLineOptionsImpl.class
- .getClassLoader().getResourceAsStream("help.txt");
- String helpText = IOUtils.toString(helpStream);
- System.out.println(helpText);
- }
-
- } catch (IOException e) {
- logger.error("Failed to load the help document", e);
- System.out.println("Failed to load the help document");
- //System.exit(-1);
- }
- }
-
- @Override
- public String[] getArgs() {
- return commandLine.getArgs();
- }
-
- /**
- *
- * @return the port that the database should run on
- */
- @Override
- public String getDatabasePort() {
- return getOptionValue("port");
- }
-
- /**
- *
- * @return a path to a properties file that contains database configuration
- * settings
- */
- @Override
- public String getDatabaseProperties() {
- return getOptionValue("dbproperties");
- }
-
- /**
- * Returns an array that alternates between a portname and path to a file
- * containing the input values. Therefore the array will always contain an
- * even number of elements
- *
- * @return an array of portname and path to files containing individual
- * inputs.
- */
- @Override
- public String[] getInputFiles() {
- if (hasInputFiles()) {
- return getOptionValues("inputfile");
- } else {
- return new String[] {};
- }
- }
-
- @Override
- public String[] getInputValues() {
- if (hasInputValues()) {
- return getOptionValues("inputvalue");
- } else {
- return new String[] {};
- }
- }
-
- @Override
- public String getLogFile() {
- return getOptionValue("logfile");
- }
-
- public Option [] getOptions() {
- return commandLine.getOptions();
- }
-
- private String getOptionValue(String opt) {
- return commandLine.getOptionValue(opt);
- }
-
- private String[] getOptionValues(String arg0) {
- return commandLine.getOptionValues(arg0);
- }
-
- /**
- *
- * @return the directory to write the results to
- */
- @Override
- public String getOutputDirectory() {
- return getOptionValue(OUTPUTDIR);
- }
-
- @Override
- public boolean getStartDatabase() {
- return hasOption("startdb");
- }
-
- /**
- * @return the directory with Credential Manager's files
- */
- @Override
- public String getCredentialManagerDir() {
- return getOptionValue(CREDENTIAL_MANAGER_DIR_OPTION);
- }
-
- @Override
- public boolean getStartDatabaseOnly() throws InvalidOptionException {
- return (getStartDatabase() && (getWorkflow() == null));
- }
-
- @Override
- public String getWorkflow() throws InvalidOptionException {
- if (getArgs().length == 0) {
- return null;
- } else if (getArgs().length != 1) {
- throw new InvalidOptionException(
- "You should only specify one workflow file");
- } else {
- return getArgs()[0];
- }
- }
-
- @Override
- public boolean hasDelimiterFor(String inputName) {
- boolean result = false;
- if (hasOption("inputdelimiter")) {
- String [] values = getOptionValues("inputdelimiter");
- for (int i=0;i<values.length;i+=2) {
- if (values[i].equals(inputName))
- {
- result=true;
- break;
- }
- }
- }
- return result;
- }
-
- @Override
- public boolean hasInputFiles() {
- return hasOption("inputfile");
- }
-
- @Override
- public boolean hasInputValues() {
- return hasOption("inputvalue");
- }
-
- @Override
- public boolean hasLogFile() {
- return hasOption("logfile");
- }
-
- @Override
- public boolean hasOption(String option) {
- return commandLine.hasOption(option);
- }
-
- @Override
- public String inputDelimiter(String inputName) {
- String result = null;
- if (hasOption("inputdelimiter")) {
- String [] values = getOptionValues("inputdelimiter");
- for (int i=0;i<values.length;i+=2) {
- if (values[i].equals(inputName))
- {
- result=values[i+1];
- break;
- }
- }
- }
- return result;
- }
-
- @SuppressWarnings("static-access")
- private Options intitialiseOptions() {
- Option helpOption = new Option("help", "Display comprehensive help information.");
-
- Option outputOption = OptionBuilder
- .withArgName("directory")
- .hasArg()
- .withDescription(
- "Save outputs as files in directory, default "
- + "is to make a new directory workflowName_output.")
- .create(OUTPUTDIR);
-
- Option bundleOption = OptionBuilder.withArgName(BUNDLE).hasArg()
- .withDescription("Save outputs to a new Workflow Run Bundle (zip).")
- .create(BUNDLE);
-
- Option logFileOption = OptionBuilder
- .withArgName("filename")
- .hasArg()
- .withDescription(
- "The logfile to which more verbose logging will be written to.")
- .create("logfile");
-
- Option inputdocOption = OptionBuilder.withArgName("document").hasArg()
- .withDescription("Load inputs from a Baclava document.").create(
- "inputdoc");
-
- Option inputFileOption = OptionBuilder
- .withArgName("inputname filename").hasArgs(2)
- .withValueSeparator(' ').withDescription(
- "Load the named input from file or URL.").create(
- "inputfile");
-
- Option inputValueOption = OptionBuilder.withArgName("inputname value")
- .hasArgs(2).withValueSeparator(' ').withDescription(
- "Directly use the value for the named input.").create(
- "inputvalue");
-
- Option inputDelimiterOption = OptionBuilder
- .withArgName("inputname delimiter")
- .hasArgs(2)
- .withValueSeparator(' ')
- .withDescription(
- "Cause an inputvalue or inputfile to be split into a list according to the delimiter. The associated workflow input must be expected to receive a list.")
- .create("inputdelimiter");
-
- Option dbProperties = OptionBuilder.withArgName("filename").hasArg()
- .withDescription(
- "Load a properties file to configure the database.")
- .create("dbproperties");
-
- Option port = OptionBuilder
- .withArgName("portnumber")
- .hasArg()
- .withDescription(
- "The port that the database is running on. If set requested to start its own internal server, this is the start port that will be used.")
- .create("port");
-
- Option embedded = new Option("embedded",
- "Connect to an embedded Derby database. This can prevent mulitple invocations.");
- Option clientserver = new Option("clientserver",
- "Connect as a client to a derby server instance.");
- Option inMemOption = new Option(
- "inmemory",
- "Run the workflow with data stored in-memory rather than in a database (this is the default option). This can give performance inprovements, at the cost of overall memory usage.");
- Option startDB = new Option("startdb",
- "Automatically start an internal Derby database server.");
- Option provenance = new Option("provenance",
- "Generate provenance information and store it in the database.");
-
-
- Option credentialManagerDirectory = OptionBuilder.withArgName("directory path").
- hasArg().withDescription(
- "Absolute path to a directory where Credential Manager's files (keystore and truststore) are located.")
- .create(CREDENTIAL_MANAGER_DIR_OPTION);
- Option credentialManagerPassword = new Option(CREDENTIAL_MANAGER_PASSWORD_OPTION, "Indicate that the master password for Credential Manager will be provided on standard input."); // optional password option, to be read from standard input
-
- Options options = new Options();
- options.addOption(helpOption);
- options.addOption(inputFileOption);
- options.addOption(inputValueOption);
- options.addOption(inputDelimiterOption);
- options.addOption(inputdocOption);
- options.addOption(outputOption);
- options.addOption(bundleOption);
- options.addOption(inMemOption);
- options.addOption(embedded);
- options.addOption(clientserver);
- options.addOption(dbProperties);
- options.addOption(port);
- options.addOption(startDB);
- options.addOption(provenance);
- options.addOption(logFileOption);
- options.addOption(credentialManagerDirectory);
- options.addOption(credentialManagerPassword);
-
- return options;
- }
-
- @Override
- public boolean isClientServer() {
- return hasOption("clientserver");
- }
-
- @Override
- public boolean isEmbedded() {
- return hasOption("embedded");
- }
-
- @Override
- public boolean isInMemory() {
- return hasOption("inmemory");
- }
-
- private CommandLine processArgs(String[] args) throws ArgumentsParsingException {
- CommandLineParser parser = new GnuParser();
- CommandLine line = null;
- try {
- // parse the command line arguments
- line = parser.parse(options, args);
- } catch (ParseException exp) {
- // oops, something went wrong
-// System.err.println("Taverna command line arguments' parsing failed. Reason: " + exp.getMessage());
-// System.exit(1);
- throw new ArgumentsParsingException("Taverna command line arguments' parsing failed. Reason: " + exp.getMessage(), exp);
- }
- return line;
- }
-
- /**
- * Save the results to a directory if -outputdir has been explicitly defined,
- * or if -outputdoc has not been defined.
- *
- * @return boolean
- */
- @Override
- public boolean saveResultsToDirectory() {
- return (options.hasOption(OUTPUTDIR) || !hasSaveResultsToBundle());
- }
-
- @Override
- public String saveResultsToBundle() {
- if (! hasSaveResultsToBundle()) {
- return null;
- }
- return getOptionValue(BUNDLE);
- }
-
- @Override
- public boolean hasSaveResultsToBundle() {
- return hasOption(BUNDLE);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
----------------------------------------------------------------------
diff --git a/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java b/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
deleted file mode 100644
index a462ba3..0000000
--- a/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
+++ /dev/null
@@ -1,139 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2012 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.commandline;
-
-import java.io.File;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import net.sf.taverna.t2.commandline.exceptions.ArgumentsParsingException;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-
-import org.osgi.framework.BundleContext;
-import org.osgi.framework.BundleException;
-
-import uk.org.taverna.commons.profile.xml.jaxb.ApplicationProfile;
-import uk.org.taverna.commons.profile.xml.jaxb.BundleInfo;
-import uk.org.taverna.commons.profile.xml.jaxb.FrameworkConfiguration;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.configuration.app.impl.ApplicationConfigurationImpl;
-import uk.org.taverna.configuration.app.impl.Log4JConfiguration;
-import uk.org.taverna.osgi.OsgiLauncher;
-
-/**
- * Main entry point for starting the Taverna Command Line Tool.
- *
- * @author David Withers
- */
-public class TavernaCommandLine {
-
- private static final String COMMANDLINE_BUNDLE_NAME = "net.sf.taverna.t2.taverna-commandline.common";
-
- private static File commandlineBundle;
-
- private static ApplicationConfiguration applicationConfiguration = new ApplicationConfigurationImpl();
-
- private static Log4JConfiguration log4jConfiguration = new Log4JConfiguration();
-
- /**
- * Starts the Taverna Command Line Tool.
- *
- * @param args
- * Taverna Command Line arguments
- */
- public static void main(final String[] args) {
- try {
- CommandLineOptions commandLineOptions = new CommandLineOptionsImpl(args);
- if (commandLineOptions.askedForHelp()) {
- commandLineOptions.displayHelp();
- } else {
- log4jConfiguration.setApplicationConfiguration(applicationConfiguration);
- log4jConfiguration.prepareLog4J();
- setDerbyPaths();
- OsgiLauncher osgilauncher = new OsgiLauncher(getAppDirectory(), getBundleURIs());
- setFrameworkConfiguration(osgilauncher);
- osgilauncher.start();
- BundleContext context = osgilauncher.getContext();
- context.registerService("net.sf.taverna.t2.commandline.options.CommandLineOptions",
- commandLineOptions, null);
- osgilauncher.startServices(true);
- osgilauncher.startBundle(osgilauncher.installBundle(commandlineBundle.toURI()));
- }
- } catch (ArgumentsParsingException e) {
- System.out.println(e.getMessage());
- } catch (InvalidOptionException e) {
- System.out.println(e.getMessage());
- } catch (BundleException e) {
- System.out.println(e.getMessage());
- }
- }
-
- /**
- * Sets the OSGi Framework configuration.
- *
- * @param osgilauncher
- */
- private static void setFrameworkConfiguration(OsgiLauncher osgilauncher) {
- ApplicationProfile applicationProfile = applicationConfiguration.getApplicationProfile();
- List<FrameworkConfiguration> frameworkConfigurations = applicationProfile
- .getFrameworkConfiguration();
- if (!frameworkConfigurations.isEmpty()) {
- Map<String, String> configurationMap = new HashMap<String, String>();
- for (FrameworkConfiguration frameworkConfiguration : frameworkConfigurations) {
- configurationMap.put(frameworkConfiguration.getName(),
- frameworkConfiguration.getValue());
- }
- osgilauncher.setFrameworkConfiguration(configurationMap);
- }
- }
-
- private static List<URI> getBundleURIs() {
- List<URI> bundleURIs = new ArrayList<URI>();
- ApplicationProfile applicationProfile = applicationConfiguration.getApplicationProfile();
- File libDir = new File(applicationConfiguration.getStartupDir(), "lib");
- if (applicationProfile != null) {
- for (BundleInfo bundle : applicationProfile.getBundle()) {
- File bundleFile = new File(libDir, bundle.getFileName());
- if (bundle.getSymbolicName().equals(COMMANDLINE_BUNDLE_NAME)) {
- commandlineBundle = bundleFile;
- } else {
- bundleURIs.add(bundleFile.toURI());
- }
- }
- }
- return bundleURIs;
- }
-
- private static File getAppDirectory() {
- return new File(applicationConfiguration.getApplicationHomeDir().getAbsolutePath());
- }
-
- private static void setDerbyPaths() {
- System.setProperty("derby.system.home", getAppDirectory().getAbsolutePath());
- File logFile = new File(applicationConfiguration.getLogDir(), "derby.log");
- System.setProperty("derby.stream.error.file", logFile.getAbsolutePath());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/src/main/resources/help.txt
----------------------------------------------------------------------
diff --git a/src/main/resources/help.txt b/src/main/resources/help.txt
deleted file mode 100644
index fb082cc..0000000
--- a/src/main/resources/help.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-By default, the workflow is executed using the -inmemory option, and the
-results are written out to a directory named after the workflow name.
-
-If this directory already exists then a new directory is created, and
-appended with _<n>, where n is incremented to the next available index.
-
-Results are written out to files named after the output port for that result.
-If a result is composed of lists, then a directory is created for the output
-port and individual list items are named after the list element index (with 1
-being the first index). The the output is the result of an error, the filename
-is appended with '.error'.
-
-You can provide your own output directory with the -outputdir option. There
-will be an error if the directory already exists.
-
-You can also record your results to a Baclava document using -outputdoc
-option. The document will be overwritten if it already exists.
-
-Inputs can be provided in three ways. Both -inputfile and -inputvalue options
-can be used together; -inputdoc option must be used on its own. -inputfile and
--inputvalue options both take two additional arguments, the name of the port
-for the input, and either a file containing the input data, or the input value
-itself respectively.
-
-If one of more of your workflow inputs is a list, you can create a list
-input by using the -inputdelimiter option, which may be used with either
--inputfile or -inputvalue. This option takes two parameters - an input name
-and the delimiter by which to split the input into a list.
-
-The delimiter may be a simple character, such as a comma or a new-line
-character, or a regular expression. The input string, or file, will then be
-converted into a list being split by the delimiter specified. Make sure to
-put the delimiter character in quotes as it may be interpreted by the shell
-as a special character, e.g. ;.
-
-If a list of greater depth (i.e. a list or lists or deeper) is required then
-you will need to use the -inputdoc option. However, if you provide an input
-of lower depth to that required, then it will automatically be wrapped in one
-or more lists up to the required depth. Providing an input of greater depth
-than that required will result in an error.
-
-If a workflow has a high memory requirement, then it may be better to run it
-using a database to store data rather than storing it in memory, which is the
-default option. There are three options for using a database:
-
--embedded option, runs with an embedded database. This is slightly faster than
-the -clientserver option (below), but has the limitation that only one
-executeworkflow script may be executed simultaneously.
-
--clientserver option allows the workflow to be executed backed by the database
-running as a server. By default a database is not started for you, but may be
-started using -startdb option.
-
--startdb option starts a database. It may be used without providing a workflow
-to allow a database to be started separately, allowing multiple simultaneous
-executeworkflow script runs.
-
-More advanced database configurations can be specified using -dbproperties
-option, allowing you to take full control over the database used. This takes a
-second argument, the filename of the properties file, for which the following
-example contains the default settings:
-
-in_memory = true
-provenance = false
-connector = derby
-port = 1527
-dialect = org.hibernate.dialect.DerbyDialect
-start_derby = false
-driver = org.apache.derby.jdbc.EmbeddedDriver
-jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
-
-Note that when using -dbproperties together with other options, the other
-options take precedence.
-
--cmdir option lets you specify an absolute path to a directory where
-Credential Manager's files (keystore and truststore - containing user's
-credentials and trusted certificates for accessing secure services) are stored.
-If not specified and the workflow requires access to these files, Taverna will
-try to find them in the default location in <TAVERNA_HOME>/security somewhere
-inside user's home directory (depending on the platform).
-
--cmpassword option can be used to tell Taverna to expect the password for the
-Credential Manager on standard input. If the password is not piped in, Taverna
-will prompt you for it in the terminal and block until it is entered. Do not
-enter your password in the command line! If -cmpassword option is not specified
-and -cmdir option is used, Taverna will try to find the password in a special
-file password.txt in the directory specified with -cmdir option.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
----------------------------------------------------------------------
diff --git a/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java b/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
deleted file mode 100644
index 3e1d0f4..0000000
--- a/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
+++ /dev/null
@@ -1,267 +0,0 @@
-package uk.org.taverna.commandline;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-
-import org.junit.Test;
-
-public class TestCommandLineOptionsHandler {
-
- @Test
- public void testWorkflowName() throws Exception {
- CommandLineOptions handler = new CommandLineOptionsImpl(
- new String[] { "myworkflow.t2flow" });
- assertEquals("myworkflow.t2flow", handler.getWorkflow());
- }
-
- @Test
- public void shouldShowHelp() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(
- new String[] { "-help" });
- assertTrue(options.askedForHelp());
- options = new CommandLineOptionsImpl(
- new String[] {});
- assertTrue(options.askedForHelp());
- options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
- assertFalse(options.askedForHelp());
- }
-
- @Test
- public void getWorkflow() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(
- new String[] { "-help" });
- assertNull(options.getWorkflow());
- options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
- assertEquals("myworkflow.t2flow", options.getWorkflow());
- }
-
- @Test(expected = InvalidOptionException.class)
- public void cannotProvideInputFileAndInputDoc() throws Exception {
- new CommandLineOptionsImpl(new String[] { "-inputfile", "fred", "fred.txt",
- "-inputdoc", "myworkflow.t2flow" });
- }
-
- @Test(expected = InvalidOptionException.class)
- public void cannotProvideInputValueAndInputDoc() throws Exception {
- new CommandLineOptionsImpl(new String[] { "-inputvalue", "fred", "fred.txt",
- "-inputdoc", "myworkflow.t2flow" });
- }
-
- @Test
- public void canProvideInputValueAndFileTogether() throws Exception {
- //should not be an error
- new CommandLineOptionsImpl(new String[] { "-inputvalue", "fred", "abc",
- "-inputfile","fred2","fred2.txt","myworkflow.t2flow" });
- }
-
- @Test
- public void getInputs() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
- assertEquals(2, options.getInputFiles().length);
- assertEquals("fred", options.getInputFiles()[0]);
- assertEquals("fred.txt", options.getInputFiles()[1]);
-
- options = new CommandLineOptionsImpl(new String[] { "-inputfile", "fred",
- "fred.txt", "-inputfile", "fred2", "fred2.txt",
- "myworkflow.t2flow" });
- assertEquals(4, options.getInputFiles().length);
- assertEquals("fred", options.getInputFiles()[0]);
- assertEquals("fred.txt", options.getInputFiles()[1]);
- assertEquals("fred2", options.getInputFiles()[2]);
- assertEquals("fred2.txt", options.getInputFiles()[3]);
-
- options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
- assertNotNull(options.getInputFiles());
- assertEquals(0, options.getInputFiles().length);
-
- }
-
- @Test
- public void hasInputValue() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-inputvalue", "fred", "abc", "myworkflow.t2flow" });
- assertTrue(options.hasInputValues());
-
- options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
- assertFalse(options.hasInputValues());
- }
-
- @Test
- public void getInputValues() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-inputvalue", "fred", "abc", "myworkflow.t2flow" });
- assertEquals(2, options.getInputValues().length);
-
- options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
- assertNotNull(options.getInputValues());
- assertEquals(0,options.getInputValues().length);
- }
-
- @Test
- public void hasInputs() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
- assertTrue(options.hasInputFiles());
-
- options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
- assertFalse(options.hasInputFiles());
- }
-
- @Test
- public void noWorkflowNameButStartDB() throws Exception {
- // should not throw an error
- CommandLineOptions options = new CommandLineOptionsImpl(
- new String[] { "-startdb" });
- assertTrue(options.getStartDatabase());
- assertTrue(options.getStartDatabaseOnly());
- }
-
- @Test
- public void workflowNameAndStartDB() throws Exception {
- // should not throw an error
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-startdb", "myworkflow.t2flow" });
- assertTrue(options.getStartDatabase());
- assertFalse(options.getStartDatabaseOnly());
- }
-
- @Test(expected = InvalidOptionException.class)
- public void provenanceButNoDatabase() throws Exception {
- new CommandLineOptionsImpl(new String[] { "-provenance",
- "myworkflow.t2flow" });
- }
-
- @Test(expected = InvalidOptionException.class)
- public void provenanceButNoDatabase2() throws Exception {
- new CommandLineOptionsImpl(new String[] { "-provenance", "-inmemory",
- "myworkflow.t2flow" });
- }
-
- @Test
- public void provenanceDatabase() throws Exception {
- // should be no errors
- new CommandLineOptionsImpl(new String[] { "-provenance", "-embedded",
- "myworkflow.t2flow" });
- new CommandLineOptionsImpl(new String[] { "-provenance", "-clientserver",
- "myworkflow.t2flow" });
- new CommandLineOptionsImpl(new String[] { "-provenance", "-dbproperties",
- "dbproperties.properties", "myworkflow.t2flow" });
- }
-
- @Test
- public void testHasInputDelimiter() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-inputvalue","in1","1,2,3","-inputdelimiter","in1",",","-inputdelimiter","in2",",","myworkflow.t2flow" });
- assertTrue(options.hasDelimiterFor("in1"));
- assertTrue(options.hasDelimiterFor("in2"));
- assertFalse(options.hasDelimiterFor("in3"));
- }
-
- @Test(expected = InvalidOptionException.class)
- public void testInputDelimiterInvalidWithInputDoc() throws Exception {
- new CommandLineOptionsImpl(new String[] {
- "-inputdoc","doc.xml","-inputdelimiter","in1",",","myworkflow.t2flow" });
- }
-
-
- @Test
- public void testInputDelimiter() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-inputvalue","in1","1,2,3","-inputdelimiter","in1",",","-inputdelimiter","in2","!","myworkflow.t2flow" });
- assertEquals(",",options.inputDelimiter("in1"));
- assertEquals("!",options.inputDelimiter("in2"));
- assertNull(options.inputDelimiter("in3"));
- }
-
- @Test
- public void testInMemory() throws Exception {
- CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
- "-inmemory", "myworkflow.t2flow" });
- assertTrue(handler.hasOption("inmemory"));
- }
-
- @Test
- public void testEmbedded() throws Exception {
- CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
- "-embedded", "myworkflow.t2flow" });
- assertTrue(handler.hasOption("embedded"));
- }
-
- @Test
- public void testClientServer() throws Exception {
- CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
- "-clientserver", "myworkflow.t2flow" });
- assertTrue(handler.hasOption("clientserver"));
- }
-
- @Test(expected = InvalidOptionException.class)
- public void testInvalidEmbeddedAndClientServer() throws Exception {
- new CommandLineOptionsImpl(new String[] { "-clientserver", "-embedded",
- "myworkflow.t2flow" });
- }
-
- @Test(expected = InvalidOptionException.class)
- public void testInvalidEmbeddedAndMemory() throws Exception {
- new CommandLineOptionsImpl(new String[] { "-embedded", "-inmemory",
- "myworkflow.t2flow" });
- }
-
- @Test(expected = InvalidOptionException.class)
- public void testInvalidClientServerAndInMemory() throws Exception {
- new CommandLineOptionsImpl(new String[] { "-clientserver", "-inmemory",
- "myworkflow.t2flow" });
- }
-
- @Test
- public void isInMemory() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-inmemory", "myworkflow.t2flow" });
-
- assertTrue(options.isInMemory());
- assertFalse(options.isClientServer());
- assertFalse(options.isEmbedded());
- }
-
- @Test
- public void isClientServer() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-clientserver", "myworkflow.t2flow" });
-
- assertTrue(options.isClientServer());
- assertFalse(options.isInMemory());
- assertFalse(options.isEmbedded());
- }
-
- @Test
- public void hasLogFile() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-logfile","/tmp/logging", "myworkflow.t2flow" });
-
- assertTrue(options.hasLogFile());
- assertEquals("/tmp/logging", options.getLogFile());
- }
-
- @Test(expected = InvalidOptionException.class)
- @SuppressWarnings("unused")
- public void hasLogFileNotValidWithoutWorkflow() throws Exception{
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-logfile","/tmp/logging"});
- }
-
- @Test
- public void isEmbedded() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-embedded", "myworkflow.t2flow" });
-
- assertTrue(options.isEmbedded());
- assertFalse(options.isInMemory());
- assertFalse(options.isClientServer());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/taverna-commandline-launcher/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/pom.xml b/taverna-commandline-launcher/pom.xml
new file mode 100644
index 0000000..ad8330e
--- /dev/null
+++ b/taverna-commandline-launcher/pom.xml
@@ -0,0 +1,96 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>uk.org.taverna.commandline</groupId>
+ <artifactId>taverna-command-line</artifactId>
+ <version>0.1.2-SNAPSHOT</version>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-jar-plugin</artifactId>
+ <version>2.4</version>
+ <configuration>
+ <archive>
+ <manifest>
+ <addClasspath>true</addClasspath>
+ <mainClass>uk.org.taverna.commandline.TavernaCommandLine</mainClass>
+ <classpathLayoutType>custom</classpathLayoutType>
+ <customClasspathLayout>../${artifact.groupId}/${artifact.artifactId}-${artifact.baseVersion}${dashClassifier?}.${artifact.extension}</customClasspathLayout>
+ </manifest>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.taverna-commandline</groupId>
+ <artifactId>taverna-commandline-api</artifactId>
+ <version>${t2.taverna-commandline.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.osgi</groupId>
+ <artifactId>osgi-launcher</artifactId>
+ <version>${osgi.launcher.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-app-configuration-impl</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>com.springsource.org.apache.commons.cli</artifactId>
+ <version>${commons.cli.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>${commons.io.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.log4j</groupId>
+ <artifactId>com.springsource.org.apache.log4j</artifactId>
+ <version>${log4j.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.eclipse</groupId>
+ <artifactId>org.eclipse.osgi</artifactId>
+ <version>${osgi.equinox.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository</url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ </repository>
+ </repositories>
+</project>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
new file mode 100644
index 0000000..b702e03
--- /dev/null
+++ b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
@@ -0,0 +1,445 @@
+/*******************************************************************************
+ * Copyright (C) 2007 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.commandline;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+import net.sf.taverna.t2.commandline.exceptions.ArgumentsParsingException;
+import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
+import net.sf.taverna.t2.commandline.options.CommandLineOptions;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.GnuParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+
+/**
+ * Handles the processing of command line arguments for enacting a workflow.
+ * This class encapsulates all command line options, and exposes them through higher-level
+ * accessors. Upon creation it checks the validity of the command line options and raises an
+ * {@link InvalidOptionException} if they are invalid.
+ *
+ * @author Stuart Owen
+ * @author David Withers
+ */
+public class CommandLineOptionsImpl implements CommandLineOptions {
+
+ private static final String OUTPUTDIR = "outputdir";
+ private static final String BUNDLE = "bundle";
+ private static final Logger logger = Logger.getLogger(CommandLineOptionsImpl.class);
+ private Options options;
+ private CommandLine commandLine;
+
+ public CommandLineOptionsImpl(String[] args) throws ArgumentsParsingException, InvalidOptionException {
+ this.options = intitialiseOptions();
+ this.commandLine = processArgs(args);
+ checkForInvalid();
+ }
+
+ @Override
+ public boolean askedForHelp() {
+ return hasOption("help") || (getArgs().length==0 && getOptions().length==0);
+ }
+
+ @Override
+ public boolean isProvenanceEnabled() {
+ return hasOption("provenance");
+ }
+
+ protected void checkForInvalid() throws InvalidOptionException {
+ if (askedForHelp()) return;
+ if (isProvenanceEnabled()
+ && !(hasOption("embedded") || hasOption("clientserver") || hasOption("dbproperties")))
+ throw new InvalidOptionException(
+ "You should be running with a database to use provenance");
+ if (isProvenanceEnabled() && hasOption("inmemory"))
+ throw new InvalidOptionException(
+ "You should be running with a database to use provenance");
+ if ((hasOption("inputfile") || hasOption("inputvalue"))
+ && hasOption("inputdoc"))
+ throw new InvalidOptionException(
+ "You can't provide both -input and -inputdoc arguments");
+
+ if (hasOption("inputdelimiter") && hasOption("inputdoc"))
+ throw new InvalidOptionException("You cannot combine the -inputdelimiter and -inputdoc arguments");
+
+ if (getArgs().length == 0
+ && !(hasOption("help") || hasOption("startdb")))
+ throw new InvalidOptionException("You must specify a workflow");
+
+ if (hasOption("inmemory") && hasOption("embedded"))
+ throw new InvalidOptionException(
+ "The options -embedded, -clientserver and -inmemory cannot be used together");
+ if (hasOption("inmemory") && hasOption("clientserver"))
+ throw new InvalidOptionException(
+ "The options -embedded, -clientserver and -inmemory cannot be used together");
+ if (hasOption("embedded") && hasOption("clientserver"))
+ throw new InvalidOptionException(
+ "The options -embedded, -clientserver and -inmemory cannot be used together");
+ }
+
+ @Override
+ public void displayHelp() {
+ boolean full = false;
+ if (hasOption("help")) full=true;
+ displayHelp(full);
+ }
+
+ @Override
+ public void displayHelp(boolean showFullText) {
+
+ HelpFormatter formatter = new HelpFormatter();
+ try {
+ formatter
+ .printHelp("executeworkflow [options] [workflow]", options);
+ if (showFullText) {
+ InputStream helpStream = CommandLineOptionsImpl.class
+ .getClassLoader().getResourceAsStream("help.txt");
+ String helpText = IOUtils.toString(helpStream);
+ System.out.println(helpText);
+ }
+
+ } catch (IOException e) {
+ logger.error("Failed to load the help document", e);
+ System.out.println("Failed to load the help document");
+ //System.exit(-1);
+ }
+ }
+
+ @Override
+ public String[] getArgs() {
+ return commandLine.getArgs();
+ }
+
+ /**
+ *
+ * @return the port that the database should run on
+ */
+ @Override
+ public String getDatabasePort() {
+ return getOptionValue("port");
+ }
+
+ /**
+ *
+ * @return a path to a properties file that contains database configuration
+ * settings
+ */
+ @Override
+ public String getDatabaseProperties() {
+ return getOptionValue("dbproperties");
+ }
+
+ /**
+ * Returns an array that alternates between a portname and path to a file
+ * containing the input values. Therefore the array will always contain an
+ * even number of elements
+ *
+ * @return an array of portname and path to files containing individual
+ * inputs.
+ */
+ @Override
+ public String[] getInputFiles() {
+ if (hasInputFiles()) {
+ return getOptionValues("inputfile");
+ } else {
+ return new String[] {};
+ }
+ }
+
+ @Override
+ public String[] getInputValues() {
+ if (hasInputValues()) {
+ return getOptionValues("inputvalue");
+ } else {
+ return new String[] {};
+ }
+ }
+
+ @Override
+ public String getLogFile() {
+ return getOptionValue("logfile");
+ }
+
+ public Option [] getOptions() {
+ return commandLine.getOptions();
+ }
+
+ private String getOptionValue(String opt) {
+ return commandLine.getOptionValue(opt);
+ }
+
+ private String[] getOptionValues(String arg0) {
+ return commandLine.getOptionValues(arg0);
+ }
+
+ /**
+ *
+ * @return the directory to write the results to
+ */
+ @Override
+ public String getOutputDirectory() {
+ return getOptionValue(OUTPUTDIR);
+ }
+
+ @Override
+ public boolean getStartDatabase() {
+ return hasOption("startdb");
+ }
+
+ /**
+ * @return the directory with Credential Manager's files
+ */
+ @Override
+ public String getCredentialManagerDir() {
+ return getOptionValue(CREDENTIAL_MANAGER_DIR_OPTION);
+ }
+
+ @Override
+ public boolean getStartDatabaseOnly() throws InvalidOptionException {
+ return (getStartDatabase() && (getWorkflow() == null));
+ }
+
+ @Override
+ public String getWorkflow() throws InvalidOptionException {
+ if (getArgs().length == 0) {
+ return null;
+ } else if (getArgs().length != 1) {
+ throw new InvalidOptionException(
+ "You should only specify one workflow file");
+ } else {
+ return getArgs()[0];
+ }
+ }
+
+ @Override
+ public boolean hasDelimiterFor(String inputName) {
+ boolean result = false;
+ if (hasOption("inputdelimiter")) {
+ String [] values = getOptionValues("inputdelimiter");
+ for (int i=0;i<values.length;i+=2) {
+ if (values[i].equals(inputName))
+ {
+ result=true;
+ break;
+ }
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public boolean hasInputFiles() {
+ return hasOption("inputfile");
+ }
+
+ @Override
+ public boolean hasInputValues() {
+ return hasOption("inputvalue");
+ }
+
+ @Override
+ public boolean hasLogFile() {
+ return hasOption("logfile");
+ }
+
+ @Override
+ public boolean hasOption(String option) {
+ return commandLine.hasOption(option);
+ }
+
+ @Override
+ public String inputDelimiter(String inputName) {
+ String result = null;
+ if (hasOption("inputdelimiter")) {
+ String [] values = getOptionValues("inputdelimiter");
+ for (int i=0;i<values.length;i+=2) {
+ if (values[i].equals(inputName))
+ {
+ result=values[i+1];
+ break;
+ }
+ }
+ }
+ return result;
+ }
+
+ @SuppressWarnings("static-access")
+ private Options intitialiseOptions() {
+ Option helpOption = new Option("help", "Display comprehensive help information.");
+
+ Option outputOption = OptionBuilder
+ .withArgName("directory")
+ .hasArg()
+ .withDescription(
+ "Save outputs as files in directory, default "
+ + "is to make a new directory workflowName_output.")
+ .create(OUTPUTDIR);
+
+ Option bundleOption = OptionBuilder.withArgName(BUNDLE).hasArg()
+ .withDescription("Save outputs to a new Workflow Run Bundle (zip).")
+ .create(BUNDLE);
+
+ Option logFileOption = OptionBuilder
+ .withArgName("filename")
+ .hasArg()
+ .withDescription(
+ "The logfile to which more verbose logging will be written to.")
+ .create("logfile");
+
+ Option inputdocOption = OptionBuilder.withArgName("document").hasArg()
+ .withDescription("Load inputs from a Baclava document.").create(
+ "inputdoc");
+
+ Option inputFileOption = OptionBuilder
+ .withArgName("inputname filename").hasArgs(2)
+ .withValueSeparator(' ').withDescription(
+ "Load the named input from file or URL.").create(
+ "inputfile");
+
+ Option inputValueOption = OptionBuilder.withArgName("inputname value")
+ .hasArgs(2).withValueSeparator(' ').withDescription(
+ "Directly use the value for the named input.").create(
+ "inputvalue");
+
+ Option inputDelimiterOption = OptionBuilder
+ .withArgName("inputname delimiter")
+ .hasArgs(2)
+ .withValueSeparator(' ')
+ .withDescription(
+ "Cause an inputvalue or inputfile to be split into a list according to the delimiter. The associated workflow input must be expected to receive a list.")
+ .create("inputdelimiter");
+
+ Option dbProperties = OptionBuilder.withArgName("filename").hasArg()
+ .withDescription(
+ "Load a properties file to configure the database.")
+ .create("dbproperties");
+
+ Option port = OptionBuilder
+ .withArgName("portnumber")
+ .hasArg()
+ .withDescription(
+ "The port that the database is running on. If set requested to start its own internal server, this is the start port that will be used.")
+ .create("port");
+
+ Option embedded = new Option("embedded",
+ "Connect to an embedded Derby database. This can prevent mulitple invocations.");
+ Option clientserver = new Option("clientserver",
+ "Connect as a client to a derby server instance.");
+ Option inMemOption = new Option(
+ "inmemory",
+ "Run the workflow with data stored in-memory rather than in a database (this is the default option). This can give performance inprovements, at the cost of overall memory usage.");
+ Option startDB = new Option("startdb",
+ "Automatically start an internal Derby database server.");
+ Option provenance = new Option("provenance",
+ "Generate provenance information and store it in the database.");
+
+
+ Option credentialManagerDirectory = OptionBuilder.withArgName("directory path").
+ hasArg().withDescription(
+ "Absolute path to a directory where Credential Manager's files (keystore and truststore) are located.")
+ .create(CREDENTIAL_MANAGER_DIR_OPTION);
+ Option credentialManagerPassword = new Option(CREDENTIAL_MANAGER_PASSWORD_OPTION, "Indicate that the master password for Credential Manager will be provided on standard input."); // optional password option, to be read from standard input
+
+ Options options = new Options();
+ options.addOption(helpOption);
+ options.addOption(inputFileOption);
+ options.addOption(inputValueOption);
+ options.addOption(inputDelimiterOption);
+ options.addOption(inputdocOption);
+ options.addOption(outputOption);
+ options.addOption(bundleOption);
+ options.addOption(inMemOption);
+ options.addOption(embedded);
+ options.addOption(clientserver);
+ options.addOption(dbProperties);
+ options.addOption(port);
+ options.addOption(startDB);
+ options.addOption(provenance);
+ options.addOption(logFileOption);
+ options.addOption(credentialManagerDirectory);
+ options.addOption(credentialManagerPassword);
+
+ return options;
+ }
+
+ @Override
+ public boolean isClientServer() {
+ return hasOption("clientserver");
+ }
+
+ @Override
+ public boolean isEmbedded() {
+ return hasOption("embedded");
+ }
+
+ @Override
+ public boolean isInMemory() {
+ return hasOption("inmemory");
+ }
+
+ private CommandLine processArgs(String[] args) throws ArgumentsParsingException {
+ CommandLineParser parser = new GnuParser();
+ CommandLine line = null;
+ try {
+ // parse the command line arguments
+ line = parser.parse(options, args);
+ } catch (ParseException exp) {
+ // oops, something went wrong
+// System.err.println("Taverna command line arguments' parsing failed. Reason: " + exp.getMessage());
+// System.exit(1);
+ throw new ArgumentsParsingException("Taverna command line arguments' parsing failed. Reason: " + exp.getMessage(), exp);
+ }
+ return line;
+ }
+
+ /**
+ * Save the results to a directory if -outputdir has been explicitly defined,
+ * or if -outputdoc has not been defined.
+ *
+ * @return boolean
+ */
+ @Override
+ public boolean saveResultsToDirectory() {
+ return (options.hasOption(OUTPUTDIR) || !hasSaveResultsToBundle());
+ }
+
+ @Override
+ public String saveResultsToBundle() {
+ if (! hasSaveResultsToBundle()) {
+ return null;
+ }
+ return getOptionValue(BUNDLE);
+ }
+
+ @Override
+ public boolean hasSaveResultsToBundle() {
+ return hasOption(BUNDLE);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
new file mode 100644
index 0000000..a462ba3
--- /dev/null
+++ b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
@@ -0,0 +1,139 @@
+/*******************************************************************************
+ * Copyright (C) 2012 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.commandline;
+
+import java.io.File;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import net.sf.taverna.t2.commandline.exceptions.ArgumentsParsingException;
+import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
+import net.sf.taverna.t2.commandline.options.CommandLineOptions;
+
+import org.osgi.framework.BundleContext;
+import org.osgi.framework.BundleException;
+
+import uk.org.taverna.commons.profile.xml.jaxb.ApplicationProfile;
+import uk.org.taverna.commons.profile.xml.jaxb.BundleInfo;
+import uk.org.taverna.commons.profile.xml.jaxb.FrameworkConfiguration;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.configuration.app.impl.ApplicationConfigurationImpl;
+import uk.org.taverna.configuration.app.impl.Log4JConfiguration;
+import uk.org.taverna.osgi.OsgiLauncher;
+
+/**
+ * Main entry point for starting the Taverna Command Line Tool.
+ *
+ * @author David Withers
+ */
+public class TavernaCommandLine {
+
+ private static final String COMMANDLINE_BUNDLE_NAME = "net.sf.taverna.t2.taverna-commandline.common";
+
+ private static File commandlineBundle;
+
+ private static ApplicationConfiguration applicationConfiguration = new ApplicationConfigurationImpl();
+
+ private static Log4JConfiguration log4jConfiguration = new Log4JConfiguration();
+
+ /**
+ * Starts the Taverna Command Line Tool.
+ *
+ * @param args
+ * Taverna Command Line arguments
+ */
+ public static void main(final String[] args) {
+ try {
+ CommandLineOptions commandLineOptions = new CommandLineOptionsImpl(args);
+ if (commandLineOptions.askedForHelp()) {
+ commandLineOptions.displayHelp();
+ } else {
+ log4jConfiguration.setApplicationConfiguration(applicationConfiguration);
+ log4jConfiguration.prepareLog4J();
+ setDerbyPaths();
+ OsgiLauncher osgilauncher = new OsgiLauncher(getAppDirectory(), getBundleURIs());
+ setFrameworkConfiguration(osgilauncher);
+ osgilauncher.start();
+ BundleContext context = osgilauncher.getContext();
+ context.registerService("net.sf.taverna.t2.commandline.options.CommandLineOptions",
+ commandLineOptions, null);
+ osgilauncher.startServices(true);
+ osgilauncher.startBundle(osgilauncher.installBundle(commandlineBundle.toURI()));
+ }
+ } catch (ArgumentsParsingException e) {
+ System.out.println(e.getMessage());
+ } catch (InvalidOptionException e) {
+ System.out.println(e.getMessage());
+ } catch (BundleException e) {
+ System.out.println(e.getMessage());
+ }
+ }
+
+ /**
+ * Sets the OSGi Framework configuration.
+ *
+ * @param osgilauncher
+ */
+ private static void setFrameworkConfiguration(OsgiLauncher osgilauncher) {
+ ApplicationProfile applicationProfile = applicationConfiguration.getApplicationProfile();
+ List<FrameworkConfiguration> frameworkConfigurations = applicationProfile
+ .getFrameworkConfiguration();
+ if (!frameworkConfigurations.isEmpty()) {
+ Map<String, String> configurationMap = new HashMap<String, String>();
+ for (FrameworkConfiguration frameworkConfiguration : frameworkConfigurations) {
+ configurationMap.put(frameworkConfiguration.getName(),
+ frameworkConfiguration.getValue());
+ }
+ osgilauncher.setFrameworkConfiguration(configurationMap);
+ }
+ }
+
+ private static List<URI> getBundleURIs() {
+ List<URI> bundleURIs = new ArrayList<URI>();
+ ApplicationProfile applicationProfile = applicationConfiguration.getApplicationProfile();
+ File libDir = new File(applicationConfiguration.getStartupDir(), "lib");
+ if (applicationProfile != null) {
+ for (BundleInfo bundle : applicationProfile.getBundle()) {
+ File bundleFile = new File(libDir, bundle.getFileName());
+ if (bundle.getSymbolicName().equals(COMMANDLINE_BUNDLE_NAME)) {
+ commandlineBundle = bundleFile;
+ } else {
+ bundleURIs.add(bundleFile.toURI());
+ }
+ }
+ }
+ return bundleURIs;
+ }
+
+ private static File getAppDirectory() {
+ return new File(applicationConfiguration.getApplicationHomeDir().getAbsolutePath());
+ }
+
+ private static void setDerbyPaths() {
+ System.setProperty("derby.system.home", getAppDirectory().getAbsolutePath());
+ File logFile = new File(applicationConfiguration.getLogDir(), "derby.log");
+ System.setProperty("derby.stream.error.file", logFile.getAbsolutePath());
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/taverna-commandline-launcher/src/main/resources/help.txt
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/src/main/resources/help.txt b/taverna-commandline-launcher/src/main/resources/help.txt
new file mode 100644
index 0000000..fb082cc
--- /dev/null
+++ b/taverna-commandline-launcher/src/main/resources/help.txt
@@ -0,0 +1,87 @@
+By default, the workflow is executed using the -inmemory option, and the
+results are written out to a directory named after the workflow name.
+
+If this directory already exists then a new directory is created, and
+appended with _<n>, where n is incremented to the next available index.
+
+Results are written out to files named after the output port for that result.
+If a result is composed of lists, then a directory is created for the output
+port and individual list items are named after the list element index (with 1
+being the first index). The the output is the result of an error, the filename
+is appended with '.error'.
+
+You can provide your own output directory with the -outputdir option. There
+will be an error if the directory already exists.
+
+You can also record your results to a Baclava document using -outputdoc
+option. The document will be overwritten if it already exists.
+
+Inputs can be provided in three ways. Both -inputfile and -inputvalue options
+can be used together; -inputdoc option must be used on its own. -inputfile and
+-inputvalue options both take two additional arguments, the name of the port
+for the input, and either a file containing the input data, or the input value
+itself respectively.
+
+If one of more of your workflow inputs is a list, you can create a list
+input by using the -inputdelimiter option, which may be used with either
+-inputfile or -inputvalue. This option takes two parameters - an input name
+and the delimiter by which to split the input into a list.
+
+The delimiter may be a simple character, such as a comma or a new-line
+character, or a regular expression. The input string, or file, will then be
+converted into a list being split by the delimiter specified. Make sure to
+put the delimiter character in quotes as it may be interpreted by the shell
+as a special character, e.g. ;.
+
+If a list of greater depth (i.e. a list or lists or deeper) is required then
+you will need to use the -inputdoc option. However, if you provide an input
+of lower depth to that required, then it will automatically be wrapped in one
+or more lists up to the required depth. Providing an input of greater depth
+than that required will result in an error.
+
+If a workflow has a high memory requirement, then it may be better to run it
+using a database to store data rather than storing it in memory, which is the
+default option. There are three options for using a database:
+
+-embedded option, runs with an embedded database. This is slightly faster than
+the -clientserver option (below), but has the limitation that only one
+executeworkflow script may be executed simultaneously.
+
+-clientserver option allows the workflow to be executed backed by the database
+running as a server. By default a database is not started for you, but may be
+started using -startdb option.
+
+-startdb option starts a database. It may be used without providing a workflow
+to allow a database to be started separately, allowing multiple simultaneous
+executeworkflow script runs.
+
+More advanced database configurations can be specified using -dbproperties
+option, allowing you to take full control over the database used. This takes a
+second argument, the filename of the properties file, for which the following
+example contains the default settings:
+
+in_memory = true
+provenance = false
+connector = derby
+port = 1527
+dialect = org.hibernate.dialect.DerbyDialect
+start_derby = false
+driver = org.apache.derby.jdbc.EmbeddedDriver
+jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
+
+Note that when using -dbproperties together with other options, the other
+options take precedence.
+
+-cmdir option lets you specify an absolute path to a directory where
+Credential Manager's files (keystore and truststore - containing user's
+credentials and trusted certificates for accessing secure services) are stored.
+If not specified and the workflow requires access to these files, Taverna will
+try to find them in the default location in <TAVERNA_HOME>/security somewhere
+inside user's home directory (depending on the platform).
+
+-cmpassword option can be used to tell Taverna to expect the password for the
+Credential Manager on standard input. If the password is not piped in, Taverna
+will prompt you for it in the terminal and block until it is entered. Do not
+enter your password in the command line! If -cmpassword option is not specified
+and -cmdir option is used, Taverna will try to find the password in a special
+file password.txt in the directory specified with -cmdir option.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java b/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
new file mode 100644
index 0000000..3e1d0f4
--- /dev/null
+++ b/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
@@ -0,0 +1,267 @@
+package uk.org.taverna.commandline;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
+import net.sf.taverna.t2.commandline.options.CommandLineOptions;
+
+import org.junit.Test;
+
+public class TestCommandLineOptionsHandler {
+
+ @Test
+ public void testWorkflowName() throws Exception {
+ CommandLineOptions handler = new CommandLineOptionsImpl(
+ new String[] { "myworkflow.t2flow" });
+ assertEquals("myworkflow.t2flow", handler.getWorkflow());
+ }
+
+ @Test
+ public void shouldShowHelp() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(
+ new String[] { "-help" });
+ assertTrue(options.askedForHelp());
+ options = new CommandLineOptionsImpl(
+ new String[] {});
+ assertTrue(options.askedForHelp());
+ options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+ assertFalse(options.askedForHelp());
+ }
+
+ @Test
+ public void getWorkflow() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(
+ new String[] { "-help" });
+ assertNull(options.getWorkflow());
+ options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+ assertEquals("myworkflow.t2flow", options.getWorkflow());
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void cannotProvideInputFileAndInputDoc() throws Exception {
+ new CommandLineOptionsImpl(new String[] { "-inputfile", "fred", "fred.txt",
+ "-inputdoc", "myworkflow.t2flow" });
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void cannotProvideInputValueAndInputDoc() throws Exception {
+ new CommandLineOptionsImpl(new String[] { "-inputvalue", "fred", "fred.txt",
+ "-inputdoc", "myworkflow.t2flow" });
+ }
+
+ @Test
+ public void canProvideInputValueAndFileTogether() throws Exception {
+ //should not be an error
+ new CommandLineOptionsImpl(new String[] { "-inputvalue", "fred", "abc",
+ "-inputfile","fred2","fred2.txt","myworkflow.t2flow" });
+ }
+
+ @Test
+ public void getInputs() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
+ assertEquals(2, options.getInputFiles().length);
+ assertEquals("fred", options.getInputFiles()[0]);
+ assertEquals("fred.txt", options.getInputFiles()[1]);
+
+ options = new CommandLineOptionsImpl(new String[] { "-inputfile", "fred",
+ "fred.txt", "-inputfile", "fred2", "fred2.txt",
+ "myworkflow.t2flow" });
+ assertEquals(4, options.getInputFiles().length);
+ assertEquals("fred", options.getInputFiles()[0]);
+ assertEquals("fred.txt", options.getInputFiles()[1]);
+ assertEquals("fred2", options.getInputFiles()[2]);
+ assertEquals("fred2.txt", options.getInputFiles()[3]);
+
+ options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+ assertNotNull(options.getInputFiles());
+ assertEquals(0, options.getInputFiles().length);
+
+ }
+
+ @Test
+ public void hasInputValue() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-inputvalue", "fred", "abc", "myworkflow.t2flow" });
+ assertTrue(options.hasInputValues());
+
+ options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+ assertFalse(options.hasInputValues());
+ }
+
+ @Test
+ public void getInputValues() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-inputvalue", "fred", "abc", "myworkflow.t2flow" });
+ assertEquals(2, options.getInputValues().length);
+
+ options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+ assertNotNull(options.getInputValues());
+ assertEquals(0,options.getInputValues().length);
+ }
+
+ @Test
+ public void hasInputs() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
+ assertTrue(options.hasInputFiles());
+
+ options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+ assertFalse(options.hasInputFiles());
+ }
+
+ @Test
+ public void noWorkflowNameButStartDB() throws Exception {
+ // should not throw an error
+ CommandLineOptions options = new CommandLineOptionsImpl(
+ new String[] { "-startdb" });
+ assertTrue(options.getStartDatabase());
+ assertTrue(options.getStartDatabaseOnly());
+ }
+
+ @Test
+ public void workflowNameAndStartDB() throws Exception {
+ // should not throw an error
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-startdb", "myworkflow.t2flow" });
+ assertTrue(options.getStartDatabase());
+ assertFalse(options.getStartDatabaseOnly());
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void provenanceButNoDatabase() throws Exception {
+ new CommandLineOptionsImpl(new String[] { "-provenance",
+ "myworkflow.t2flow" });
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void provenanceButNoDatabase2() throws Exception {
+ new CommandLineOptionsImpl(new String[] { "-provenance", "-inmemory",
+ "myworkflow.t2flow" });
+ }
+
+ @Test
+ public void provenanceDatabase() throws Exception {
+ // should be no errors
+ new CommandLineOptionsImpl(new String[] { "-provenance", "-embedded",
+ "myworkflow.t2flow" });
+ new CommandLineOptionsImpl(new String[] { "-provenance", "-clientserver",
+ "myworkflow.t2flow" });
+ new CommandLineOptionsImpl(new String[] { "-provenance", "-dbproperties",
+ "dbproperties.properties", "myworkflow.t2flow" });
+ }
+
+ @Test
+ public void testHasInputDelimiter() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-inputvalue","in1","1,2,3","-inputdelimiter","in1",",","-inputdelimiter","in2",",","myworkflow.t2flow" });
+ assertTrue(options.hasDelimiterFor("in1"));
+ assertTrue(options.hasDelimiterFor("in2"));
+ assertFalse(options.hasDelimiterFor("in3"));
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void testInputDelimiterInvalidWithInputDoc() throws Exception {
+ new CommandLineOptionsImpl(new String[] {
+ "-inputdoc","doc.xml","-inputdelimiter","in1",",","myworkflow.t2flow" });
+ }
+
+
+ @Test
+ public void testInputDelimiter() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-inputvalue","in1","1,2,3","-inputdelimiter","in1",",","-inputdelimiter","in2","!","myworkflow.t2flow" });
+ assertEquals(",",options.inputDelimiter("in1"));
+ assertEquals("!",options.inputDelimiter("in2"));
+ assertNull(options.inputDelimiter("in3"));
+ }
+
+ @Test
+ public void testInMemory() throws Exception {
+ CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
+ "-inmemory", "myworkflow.t2flow" });
+ assertTrue(handler.hasOption("inmemory"));
+ }
+
+ @Test
+ public void testEmbedded() throws Exception {
+ CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
+ "-embedded", "myworkflow.t2flow" });
+ assertTrue(handler.hasOption("embedded"));
+ }
+
+ @Test
+ public void testClientServer() throws Exception {
+ CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
+ "-clientserver", "myworkflow.t2flow" });
+ assertTrue(handler.hasOption("clientserver"));
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void testInvalidEmbeddedAndClientServer() throws Exception {
+ new CommandLineOptionsImpl(new String[] { "-clientserver", "-embedded",
+ "myworkflow.t2flow" });
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void testInvalidEmbeddedAndMemory() throws Exception {
+ new CommandLineOptionsImpl(new String[] { "-embedded", "-inmemory",
+ "myworkflow.t2flow" });
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ public void testInvalidClientServerAndInMemory() throws Exception {
+ new CommandLineOptionsImpl(new String[] { "-clientserver", "-inmemory",
+ "myworkflow.t2flow" });
+ }
+
+ @Test
+ public void isInMemory() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-inmemory", "myworkflow.t2flow" });
+
+ assertTrue(options.isInMemory());
+ assertFalse(options.isClientServer());
+ assertFalse(options.isEmbedded());
+ }
+
+ @Test
+ public void isClientServer() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-clientserver", "myworkflow.t2flow" });
+
+ assertTrue(options.isClientServer());
+ assertFalse(options.isInMemory());
+ assertFalse(options.isEmbedded());
+ }
+
+ @Test
+ public void hasLogFile() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-logfile","/tmp/logging", "myworkflow.t2flow" });
+
+ assertTrue(options.hasLogFile());
+ assertEquals("/tmp/logging", options.getLogFile());
+ }
+
+ @Test(expected = InvalidOptionException.class)
+ @SuppressWarnings("unused")
+ public void hasLogFileNotValidWithoutWorkflow() throws Exception{
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-logfile","/tmp/logging"});
+ }
+
+ @Test
+ public void isEmbedded() throws Exception {
+ CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+ "-embedded", "myworkflow.t2flow" });
+
+ assertTrue(options.isEmbedded());
+ assertFalse(options.isInMemory());
+ assertFalse(options.isClientServer());
+ }
+
+}
[09/50] [abbrv] incubator-taverna-commandline git commit: newer
dependencies
Posted by st...@apache.org.
newer dependencies
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/2a17db58
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/2a17db58
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/2a17db58
Branch: refs/heads/master
Commit: 2a17db58c896a027f61b1bffc12448cc488b71b4
Parents: 4b3d5ed
Author: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Authored: Tue Oct 28 13:14:21 2014 +0000
Committer: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Committed: Tue Oct 28 13:14:21 2014 +0000
----------------------------------------------------------------------
pom.xml | 11 +++++++++++
1 file changed, 11 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/2a17db58/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 6b1fffe..8393a90 100644
--- a/pom.xml
+++ b/pom.xml
@@ -248,6 +248,17 @@
<artifactId>commons-codec</artifactId>
<version>${commons.codec.version}</version>
</dependency>
+ <dependency>
+ <groupId>commons-configuration</groupId>
+ <artifactId>commons-configuration</artifactId>
+ <version>1.10</version>
+ </dependency>
+ <dependency>
+ <groupId>com.sun.xml.bind</groupId>
+ <artifactId>jaxb-impl</artifactId>
+ <version>2.2.11</version>
+ </dependency>
+
<!-- OSGi Enterprise Services -->
<dependency>
[47/50] [abbrv] incubator-taverna-commandline git commit: TODO about
Felix instead of Equinox
Posted by st...@apache.org.
TODO about Felix instead of Equinox
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/fd2682c0
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/fd2682c0
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/fd2682c0
Branch: refs/heads/master
Commit: fd2682c094fb0f0594a19a92261304aae5de7df2
Parents: ad42dfd
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Jan 6 16:29:48 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Jan 6 16:29:48 2015 +0000
----------------------------------------------------------------------
taverna-commandline-launcher/pom.xml | 8 ++++++++
1 file changed, 8 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/fd2682c0/taverna-commandline-launcher/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/pom.xml b/taverna-commandline-launcher/pom.xml
index f351ae4..42208e3 100644
--- a/taverna-commandline-launcher/pom.xml
+++ b/taverna-commandline-launcher/pom.xml
@@ -64,6 +64,14 @@
<artifactId>org.eclipse.osgi</artifactId>
<version>${osgi.equinox.version}</version>
</dependency>
+ <!-- TODO: replace equinox with:
+ <dependency>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>org.apache.felix.main</artifactId>
+ <version>4.4.1</version>
+ </dependency>
+ -->
+
<dependency>
<groupId>junit</groupId>
[45/50] [abbrv] incubator-taverna-commandline git commit:
OSGi-compatible version 3.1.0.incubating rather than -incubating
Posted by st...@apache.org.
OSGi-compatible version 3.1.0.incubating rather than -incubating
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/85bb1f19
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/85bb1f19
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/85bb1f19
Branch: refs/heads/master
Commit: 85bb1f1969c985bbcd50e7373c6edd65d2729366
Parents: 5ba148f
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Jan 6 14:50:51 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Jan 6 14:50:51 2015 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
taverna-commandline-api/pom.xml | 2 +-
taverna-commandline-common/pom.xml | 2 +-
taverna-commandline-launcher/pom.xml | 2 +-
taverna-commandline-product/pom.xml | 4 ++--
5 files changed, 6 insertions(+), 6 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/85bb1f19/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 04439f2..c1690e4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -8,7 +8,7 @@
</parent>
<groupId>org.apache.taverna.commandline</groupId>
<artifactId>taverna-commandline</artifactId>
- <version>3.1.0-incubating-SNAPSHOT</version>
+ <version>3.1.0.incubating-SNAPSHOT</version>
<packaging>pom</packaging>
<name>Apache Taverna Command Line</name>
<properties>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/85bb1f19/taverna-commandline-api/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/pom.xml b/taverna-commandline-api/pom.xml
index ab49d38..98ae247 100644
--- a/taverna-commandline-api/pom.xml
+++ b/taverna-commandline-api/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>org.apache.taverna.commandline</groupId>
<artifactId>taverna-commandline</artifactId>
- <version>3.1.0-incubating-SNAPSHOT</version>
+ <version>3.1.0.incubating-SNAPSHOT</version>
</parent>
<packaging>bundle</packaging>
<artifactId>taverna-commandline-api</artifactId>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/85bb1f19/taverna-commandline-common/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/pom.xml b/taverna-commandline-common/pom.xml
index ee2ffce..17c6a42 100644
--- a/taverna-commandline-common/pom.xml
+++ b/taverna-commandline-common/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>org.apache.taverna.commandline</groupId>
<artifactId>taverna-commandline</artifactId>
- <version>3.1.0-incubating-SNAPSHOT</version>
+ <version>3.1.0.incubating-SNAPSHOT</version>
</parent>
<artifactId>taverna-commandline-common</artifactId>
<packaging>bundle</packaging>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/85bb1f19/taverna-commandline-launcher/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/pom.xml b/taverna-commandline-launcher/pom.xml
index 5aad907..394fa91 100644
--- a/taverna-commandline-launcher/pom.xml
+++ b/taverna-commandline-launcher/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>org.apache.taverna.commandline</groupId>
<artifactId>taverna-commandline</artifactId>
- <version>3.1.0-incubating-SNAPSHOT</version>
+ <version>3.1.0.incubating-SNAPSHOT</version>
</parent>
<artifactId>taverna-commandline-launcher</artifactId>
<name>Apache Taverna Commandline Launcher</name>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/85bb1f19/taverna-commandline-product/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/pom.xml b/taverna-commandline-product/pom.xml
index 63f73f6..07a7782 100644
--- a/taverna-commandline-product/pom.xml
+++ b/taverna-commandline-product/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>org.apache.taverna.commandline</groupId>
<artifactId>taverna-commandline</artifactId>
- <version>3.1.0-incubating-SNAPSHOT</version>
+ <version>3.1.0.incubating-SNAPSHOT</version>
</parent>
<artifactId>taverna-command-line-product</artifactId>
<name>Apache Taverna Commandline Product</name>
@@ -100,7 +100,7 @@
</frameworkConfiguration>
<frameworkConfiguration>
<name>org.osgi.framework.system.packages.extra</name>
- <value>com.sun.org.apache.xml.internal.utils,com.sun.source.util,com.sun.source.tree,org.apache.log4j;version=1.2.16,net.sf.taverna.t2.commandline.options;version=2.0.1</value>
+ <value>com.sun.org.apache.xml.internal.utils,com.sun.source.util,com.sun.source.tree,org.apache.log4j;version=${log4j.version},net.sf.taverna.t2.commandline.options;version=${project.parent.version}</value>
</frameworkConfiguration>
<frameworkConfiguration>
<name>org.osgi.framework.storage.clean</name>
[50/50] [abbrv] incubator-taverna-commandline git commit: remove
unused
Posted by st...@apache.org.
remove unused <repository>
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/e25a5dcd
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/e25a5dcd
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/e25a5dcd
Branch: refs/heads/master
Commit: e25a5dcd0c0c0833dee5c0da3248f46f5c590727
Parents: ba051d5
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Feb 5 10:13:52 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Thu Feb 5 10:13:52 2015 +0000
----------------------------------------------------------------------
taverna-commandline-product/pom.xml | 22 ++--------------------
1 file changed, 2 insertions(+), 20 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/e25a5dcd/taverna-commandline-product/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/pom.xml b/taverna-commandline-product/pom.xml
index f493eab..38bcb42 100644
--- a/taverna-commandline-product/pom.xml
+++ b/taverna-commandline-product/pom.xml
@@ -522,26 +522,8 @@
<version>${htmlparser.version}</version>
</dependency>
- </dependencies>
- <repositories>
- <!--
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- -->
- <!--
- <repository>
- <id>OPS4J</id>
- <url>http://repository.ops4j.org/maven2</url>
- </repository>
- -->
- </repositories>
+
+ </dependencies>
</project>
[25/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-tests/
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/spreadsheetimport/spreadsheetimport.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/spreadsheetimport/spreadsheetimport.t2flow b/src/test/resources/workflows/spreadsheetimport/spreadsheetimport.t2flow
deleted file mode 100644
index 7360186..0000000
--- a/src/test/resources/workflows/spreadsheetimport/spreadsheetimport.t2flow
+++ /dev/null
@@ -1,646 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="fa4ef38e-fa3f-4662-97e5-59c3b51aa322" role="top"><name>Spreadsheet_Import_Example</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>SpreadsheetImport</name><inputPorts><port><name>fileurl</name><depth>0</depth></port></inputPorts><outputPorts><port><name>other</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>other_industry</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>year</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>spreadsheet-import-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportActivity</class><inputMap><map from="fileurl" to="fileurl" /></inputMap><outputMap><ma
p from="other" to="other" /><map from="year" to="year" /><map from="other_industry" to="other_industry" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration xmlns="">
- <columnRange>
- <start>1</start>
- <end>6</end>
- <excludes />
- </columnRange>
- <rowRange>
- <start>7</start>
- <end>41</end>
- <excludes />
- </rowRange>
- <emptyCellValue />
- <columnNames>
- <entry>
- <string>D</string>
- <string>other</string>
- </entry>
- <entry>
- <string>E</string>
- <string>fish_farming</string>
- </entry>
- <entry>
- <string>F</string>
- <string>other_industry</string>
- </entry>
- <entry>
- <string>G</string>
- <string>public_water_supply</string>
- </entry>
- <entry>
- <string>A</string>
- <string>over</string>
- </entry>
- <entry>
- <string>B</string>
- <string>year</string>
- </entry>
- <entry>
- <string>C</string>
- <string>electricity</string>
- </entry>
- <entry>
- <string>L</string>
- <string>2001</string>
- </entry>
- <entry>
- <string>N</string>
- <string>2002</string>
- </entry>
- <entry>
- <string>H</string>
- <string>1999</string>
- </entry>
- <entry>
- <string>J</string>
- <string>2000</string>
- </entry>
- <entry>
- <string>T</string>
- <string>2005</string>
- </entry>
- <entry>
- <string>V</string>
- <string>2006</string>
- </entry>
- <entry>
- <string>P</string>
- <string>2003</string>
- </entry>
- <entry>
- <string>R</string>
- <string>2004</string>
- </entry>
- <entry>
- <string>X</string>
- <string>2007</string>
- </entry>
- <entry>
- <string>Z</string>
- <string>2008</string>
- </entry>
- </columnNames>
- <allRows>false</allRows>
- <excludeFirstRow>false</excludeFirstRow>
- <ignoreBlankRows>false</ignoreBlankRows>
- <emptyCellPolicy>EMPTY_STRING</emptyCellPolicy>
- <outputFormat>PORT_PER_COLUMN</outputFormat>
- <csvDelimiter>,</csvDelimiter>
-</net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="fileurl" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>url_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="val
ue" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>http://www.myexperiment.org/files/410/download/WaterUse.xlsx</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>SpreadsheetImport</processor><port>fileurl</port></sink><source type="processor"><processor>url_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>SpreadsheetImport</processor><port>year</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChai
nImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>41265789-c464-4ee2-b145-95ece9388305</identification>
- </annotationBean>
- <date>2010-07-07 22:34:29.364 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>b4363407-ef56-4cf3-998f-8e780a8dc816</identification>
- </annotationBean>
- <date>2010-07-07 16:41:31.230 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>486a5356-0f3e-424d-b14e-249295875f2d</identification>
- </annotationBean>
- <date>2010-07-13 12:31:34.664 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
- <text>David Withers</text>
- </annotationBean>
- <date>2010-07-13 11:09:24.988 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>cf60043b-e08a-49d7-a150-711f413d3d18</identification>
- </annotationBean>
- <date>2010-07-07 22:52:10.583 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>812e7abc-4866-43dc-b9d4-44370a399e4e</identification>
- </annotationBean>
- <date>2010-07-07 17:23:44.739 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>cca71cbe-6d97-4896-90c2-d91016f12882</identification>
- </annotationBean>
- <date>2010-07-07 22:45:31.148 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>e28f14b3-e4ae-4d0b-893d-3a8400625069</identification>
- </annotationBean>
- <date>2010-07-07 16:10:13.994 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>e263e793-b394-4a57-855e-13e69b8780c2</identification>
- </annotationBean>
- <date>2010-07-07 17:00:11.782 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>14724df6-fee6-4b24-8fbc-eeeeb3dc4e61</identification>
- </annotationBean>
- <date>2010-07-07 16:38:21.137 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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-The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date.
-The source data is from http://data.gov.uk/</text>
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>808e3725-2a08-4907-9706-fb7f0f08f62f</identification>
- </annotationBean>
- <date>2010-07-13 11:20:05.749 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>6e069c36-8d88-4017-96cf-c1fa87007777</identification>
- </annotationBean>
- <date>2010-07-07 16:20:48.694 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>73ce4e99-6b83-45d0-8605-896d6d48b7f0</identification>
- </annotationBean>
- <date>2010-07-07 17:01:14.713 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/stringconstant/stringconstant.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/stringconstant/stringconstant.t2flow b/src/test/resources/workflows/stringconstant/stringconstant.t2flow
deleted file mode 100644
index 41266d0..0000000
--- a/src/test/resources/workflows/stringconstant/stringconstant.t2flow
+++ /dev/null
@@ -1,32 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="48c5c70e-ffde-4ff0-8508-015577ab263c" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>String_constant</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>Test Value</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>String_constant</processor><port>value</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>48c5c70e-ffde-4ff0-8508-015577ab263c</identification>
- </annotationBean>
- <date>2010-12-14 11:57:31.126 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>186f09f7-d9a7-4ae2-bf84-8ee83f41f4e3</identification>
- </annotationBean>
- <date>2010-12-14 11:56:50.253 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/tool/tool.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/tool/tool.t2flow b/src/test/resources/workflows/tool/tool.t2flow
deleted file mode 100644
index d77a851..0000000
--- a/src/test/resources/workflows/tool/tool.t2flow
+++ /dev/null
@@ -1,158 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="82a5216a-8b82-41db-a114-ece396f9b85c" role="top"><name>Workflow4</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Tool</name><inputPorts><port><name>in1</name><depth>0</depth></port><port><name>in2</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean
xmlns="">
- <mechanismType>789663B8-DA91-428A-9F7D-B3F3DA185FD4</mechanismType>
- <mechanismName>default local</mechanismName>
- <mechanismXML><?xml version="1.0" encoding="UTF-8"?>
-<localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation>
-</mechanismXML>
- <externaltoolid>607ceaee-59ba-4cbb-a650-84e51d8498e3</externaltoolid>
- <useCaseDescription>
- <usecaseid />
- <description />
- <command>cat in1 > out; echo %%in2%% >> out
- </command>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags>
- <string>in2</string>
- </tags>
- <REs />
- <queue__preferred />
- <queue__deny />
- <static__inputs>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
- <tag>hi</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>MacRoman</charsetName>
- <forceCopy>false</forceCopy>
- <content class="string">hi</content>
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
- <tag>google</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>MacRoman</charsetName>
- <forceCopy>false</forceCopy>
- <url>http://www.google.com/</url>
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
- </static__inputs>
- <inputs>
- <entry>
- <string>in2</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>in2</tag>
- <file>false</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>MacRoman</charsetName>
- <forceCopy>false</forceCopy>
- <list>false</list>
- <concatenate>false</concatenate>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- </entry>
- <entry>
- <string>in1</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>in1</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>MacRoman</charsetName>
- <forceCopy>false</forceCopy>
- <list>false</list>
- <concatenate>false</concatenate>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- </entry>
- </inputs>
- <outputs>
- <entry>
- <string>out</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
- <path>out</path>
- <binary>false</binary>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
- </entry>
- </outputs>
- <includeStdIn>false</includeStdIn>
- <includeStdOut>true</includeStdOut>
- <includeStdErr>true</includeStdErr>
- <validReturnCodes>
- <int>0</int>
- </validReturnCodes>
- </useCaseDescription>
- <edited>false</edited>
-</net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in1" depth="0" /><port name="in2" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><
map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>Hello</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>in2_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.
taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>World</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Tool</processor><port>in1</port></sink><source type="processor"><processor>in_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Tool</processor><port>in2</port></sink><source type="processor"><processor>in2_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Tool</processor>
<port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>6090defe-8eba-4775-8dd6-ab48813d23ab</identification>
- </annotationBean>
- <date>2011-10-27 18:50:36.777 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>8312a5c9-b291-4a20-a468-0cdd8888115b</identification>
- </annotationBean>
- <date>2011-10-27 18:46:58.794 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>82a5216a-8b82-41db-a114-ece396f9b85c</identification>
- </annotationBean>
- <date>2011-11-10 17:19:20.269 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>436555c3-0df8-4e5c-93f3-313124bf045c</identification>
- </annotationBean>
- <date>2011-10-27 18:52:22.981 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/wsdl/wsdl.t2flow
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diff --git a/src/test/resources/workflows/wsdl/wsdl.t2flow b/src/test/resources/workflows/wsdl/wsdl.t2flow
deleted file mode 100644
index 4dea6bb..0000000
--- a/src/test/resources/workflows/wsdl/wsdl.t2flow
+++ /dev/null
@@ -1,22 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="eed49d32-8563-45ff-8716-347b20800129" role="top"><name>Workflow5</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>getVersion</name><inputPorts /><outputPorts><port><name>getVersionReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap /><outputMap><map from="getVersionReturn" to="getVersionReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>http://www.mygrid.org.uk/axis/services/Version?wsdl</wsdl>
- <operation>getVersion</operation>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>getVersion</processor><port>getVersionReturn</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>eed49d32-8563-45ff-8716-347b20800129</identification>
- </annotationBean>
- <date>2011-01-25 16:37:45.583 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/xmlSplitter/inputs/age
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/xmlSplitter/inputs/age b/src/test/resources/workflows/xmlSplitter/inputs/age
deleted file mode 100644
index b5045cc..0000000
--- a/src/test/resources/workflows/xmlSplitter/inputs/age
+++ /dev/null
@@ -1 +0,0 @@
-21
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/xmlSplitter/inputs/firstName
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/xmlSplitter/inputs/firstName b/src/test/resources/workflows/xmlSplitter/inputs/firstName
deleted file mode 100644
index 08df4e7..0000000
--- a/src/test/resources/workflows/xmlSplitter/inputs/firstName
+++ /dev/null
@@ -1 +0,0 @@
-John
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/xmlSplitter/inputs/lastName
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diff --git a/src/test/resources/workflows/xmlSplitter/inputs/lastName b/src/test/resources/workflows/xmlSplitter/inputs/lastName
deleted file mode 100644
index b77017e..0000000
--- a/src/test/resources/workflows/xmlSplitter/inputs/lastName
+++ /dev/null
@@ -1 +0,0 @@
-Smith
\ No newline at end of file
[29/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-tests/
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/beanshell/beanshell.t2flow
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diff --git a/src/test/resources/workflows/beanshell/beanshell.t2flow b/src/test/resources/workflows/beanshell/beanshell.t2flow
deleted file mode 100644
index 8c5968c..0000000
--- a/src/test/resources/workflows/beanshell/beanshell.t2flow
+++ /dev/null
@@ -1,137 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="78cb1427-d57f-42c2-a385-1d20c1580f3b" role="top"><name>Workflow13</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Echo</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfi
gurationBean xmlns="">
- <script>out=in;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>ListGenerator</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><
map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>out = new ArrayList();
-
-for (int i = 0; i < 1000; i++) {
- out.add(in + ":" + i);
-}</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>out</name>
- <depth>1</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Echo</processor><port>in</port></sink><source type="processor"><processor>ListGenerator</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>ListGenerator</processor><port>in</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><
processor>Echo</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>13c70169-dfaa-4ea6-b6ab-3551dae7fa84</identification>
- </annotationBean>
- <date>2010-08-19 12:28:57.881 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>7ef10e93-7376-41a9-9255-552149094142</identification>
- </annotationBean>
- <date>2010-08-31 13:06:57.536 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>3b7c0b9c-572d-466b-af6d-0fb40699e8a5</identification>
- </annotationBean>
- <date>2010-08-31 12:50:40.306 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>eb6a550d-f34e-4de9-b0fc-1b3df8ab36c4</identification>
- </annotationBean>
- <date>2010-08-31 14:32:44.634 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>78cb1427-d57f-42c2-a385-1d20c1580f3b</identification>
- </annotationBean>
- <date>2010-08-31 14:36:00.297 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>ad638364-a6e0-4852-abca-9f609c9553d2</identification>
- </annotationBean>
- <date>2010-08-19 13:43:43.797 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/beanshell/inputs/in
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diff --git a/src/test/resources/workflows/beanshell/inputs/in b/src/test/resources/workflows/beanshell/inputs/in
deleted file mode 100644
index fede229..0000000
--- a/src/test/resources/workflows/beanshell/inputs/in
+++ /dev/null
@@ -1 +0,0 @@
-test-input
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/biomart/biomart.t2flow
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diff --git a/src/test/resources/workflows/biomart/biomart.t2flow b/src/test/resources/workflows/biomart/biomart.t2flow
deleted file mode 100644
index f82f340..0000000
--- a/src/test/resources/workflows/biomart/biomart.t2flow
+++ /dev/null
@@ -1,30 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="4a959e22-8166-4e8b-ae94-6e85c8807e35" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>btaurus_gene_ensembl</name><inputPorts /><outputPorts><port><name>btaurus_gene_ensembl.ensembl_gene_id</name><depth>1</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomart-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.biomart.BiomartActivity</class><inputMap /><outputMap><map from="btaurus_gene_ensembl.ensembl_gene_id" to="btaurus_gene_ensembl.ensembl_gene_id" /></outputMap><configBean encoding="jdomxml"><MartQuery xmlns=""><MartService location="http://www.biomart.org/biomart/martservice" /><MartDataset displayName="Bos taurus genes (UMD3.1)" nam
e="btaurus_gene_ensembl" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2011-09-07 22:16:01"><MartURLLocation database="ensembl_mart_64" default="1" displayName="ENSEMBL GENES 64 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice" port="80" serverVirtualSchema="default" virtualSchema="default" visible="1" redirect="0" /></MartDataset><Query virtualSchemaName="default" count="0" uniqueRows="1" softwareVersion="0.6" requestId="taverna"><Dataset name="btaurus_gene_ensembl"><Attribute name="ensembl_gene_id" /><Filter name="chromosome_name" value="1" /><Filter name="with_affy_bovine" excluded="0" /><Filter name="go_evidence_code" value="IDA" /></Dataset></Query></MartQuery></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><cla
ss>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>btaurus_gene_ensembl</processor><port>btaurus_gene_ensembl.ensembl_gene_id</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>4a959e22-8166-4e8b-ae94-6e85c8807e35</identification>
- </annotationBean>
- <date>2011-10-27 14:33:16.228 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>5859741c-a0ba-4dae-8b81-1dd7c928562f</identification>
- </annotationBean>
- <date>2011-10-27 14:32:47.106 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/dataflow/dataflow.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/dataflow/dataflow.t2flow b/src/test/resources/workflows/dataflow/dataflow.t2flow
deleted file mode 100644
index c9366c2..0000000
--- a/src/test/resources/workflows/dataflow/dataflow.t2flow
+++ /dev/null
@@ -1,217 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="ac4ce40a-57b9-486c-bb4c-eb8609c6cc48" role="top"><name>Workflow1</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Nested_workflow</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="dataflow"><dataflow ref="c6b258ac-3588-4828-b71c-207bad8b63c4" /
></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>echo</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from=
"in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>in</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>out</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>out = in;</script>
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-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
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m="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
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- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>out</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>out = in;</script>
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-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
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">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Nested_workflow</processor><port>in</port></sink><source type="processor"><processor>echo</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>echo</processor><port>in</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>echo_2</processor><port>in</port></sink><sou
rce type="processor"><processor>Nested_workflow</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>echo_2</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>437a237a-03a0-489f-97c6-fd5acc5db18e</identification>
- </annotationBean>
- <date>2011-11-09 10:59:10.221 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>ae7626c8-13a4-4560-9496-59a8cc0693be</identification>
- </annotationBean>
- <date>2011-02-16 11:57:10.514 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>96d450ff-aaf8-473b-91a1-4acce7371c3b</identification>
- </annotationBean>
- <date>2011-02-16 11:55:55.618 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>ac4ce40a-57b9-486c-bb4c-eb8609c6cc48</identification>
- </annotationBean>
- <date>2011-11-09 11:02:29.60 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>9f957cde-a7ad-4453-a09f-7231c8c8c4f3</identification>
- </annotationBean>
- <date>2011-02-16 11:52:40.88 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>f847ed6f-2834-4861-a8af-73ab737c6a91</identification>
- </annotationBean>
- <date>2011-11-09 11:00:41.783 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="c6b258ac-3588-4828-b71c-207bad8b63c4" role="nested"><name>Workflow4</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>echo</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivit
yConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>in</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>out</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>out = "nested dataflow : " + in;</script>
- <dependencies />
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>echo</processor><port>in</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>echo</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>f8dd3fb7-7051-4242-a3af-d82056934cf6</identification>
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- <date>2011-02-16 11:55:01.559 GMT</date>
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- <curationEventList />
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-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
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- <identification>0a0b6f17-8ebf-4017-ad4c-0719a9d44806</identification>
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- <date>2011-11-09 11:00:37.241 GMT</date>
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <identification>c6b258ac-3588-4828-b71c-207bad8b63c4</identification>
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- <date>2011-11-09 11:02:26.99 GMT</date>
- <creators />
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>eaa8b2a0-e71b-4d6a-b8ad-c299a8ad6e18</identification>
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- <date>2011-02-16 11:53:12.59 GMT</date>
- <creators />
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/dataflow/inputs/in
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/dataflow/inputs/in b/src/test/resources/workflows/dataflow/inputs/in
deleted file mode 100644
index fede229..0000000
--- a/src/test/resources/workflows/dataflow/inputs/in
+++ /dev/null
@@ -1 +0,0 @@
-test-input
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/in-out/in-out.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/in-out/in-out.t2flow b/src/test/resources/workflows/in-out/in-out.t2flow
deleted file mode 100644
index ecfb4e8..0000000
--- a/src/test/resources/workflows/in-out/in-out.t2flow
+++ /dev/null
@@ -1,12 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="4d8a491e-fa11-4918-98ce-7df19051d5c5" role="top"><name>Workflow6</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors /><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="dataflow"><port>in</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>4d8a491e-fa11-4918-98ce-7df19051d5c5</identification>
- </annotationBean>
- <date>2012-04-03 15:34:41.4 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/in-out/inputs/in
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/in-out/inputs/in b/src/test/resources/workflows/in-out/inputs/in
deleted file mode 100644
index fede229..0000000
--- a/src/test/resources/workflows/in-out/inputs/in
+++ /dev/null
@@ -1 +0,0 @@
-test-input
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/iteration/inputs/in
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/iteration/inputs/in b/src/test/resources/workflows/iteration/inputs/in
deleted file mode 100644
index 30d74d2..0000000
--- a/src/test/resources/workflows/iteration/inputs/in
+++ /dev/null
@@ -1 +0,0 @@
-test
\ No newline at end of file
[28/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-tests/
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/iteration/iteration.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/iteration/iteration.t2flow b/src/test/resources/workflows/iteration/iteration.t2flow
deleted file mode 100644
index bec4c2d..0000000
--- a/src/test/resources/workflows/iteration/iteration.t2flow
+++ /dev/null
@@ -1,474 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="80c80b32-1faa-4c8e-9294-eb85d6aaa764" role="top"><name>Workflow13</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>cross</name><annotations /></port><port><name>dot</name><annotations /></port><port><name>crossdot</name><annotations /></port><port><name>dotdot</name><annotations /></port><port><name>dotcross</name><annotations /></port></outputPorts><processors><processor><name>cross</name><inputPorts><port><name>in1</name><depth>0</depth></port><port><name>in2</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.
t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>out=in1 + in2;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in1" depth="0" /><port name="in2" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>ListGenerator1</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.Beans
hellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>out = new ArrayList();
-
-for (int i = 0; i < 10; i++) {
- out.add(in + ":" + i);
-}</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>out</name>
- <depth>1</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>ListGenerator2</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap>
<map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>out = new ArrayList();
-
-for (int i = 0; i < 10; i++) {
- out.add(in + ":" + i);
-}</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>out</name>
- <depth>1</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>dot</name><inputPorts><port><name>in2</name><depth>0</depth></port><port><name>in1</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.
BeanshellActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>out=in1 + in2;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><dot><port name="in2" depth="0" /><port name="in1" depth="0" /></dot></strategy></iteration></iterationStrategyStack></processor><processor><name>crossdot</name><inputPorts><port><name>in1</name><depth>0</depth></port><port><name>in2</name><depth>0</depth></port><port><name>in3</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact>
<version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /><map from="in3" to="in3" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>out = in1 + in2 + in3;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in3</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
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- <date>2011-02-22 08:25:53.793 GMT</date>
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- <creators />
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- <date>2011-02-22 09:30:17.881 GMT</date>
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\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/localworker/inputs/in
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/localworker/inputs/in b/src/test/resources/workflows/localworker/inputs/in
deleted file mode 100644
index cadf8b6..0000000
--- a/src/test/resources/workflows/localworker/inputs/in
+++ /dev/null
@@ -1 +0,0 @@
-Tom
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/localworker/localworker.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/localworker/localworker.t2flow b/src/test/resources/workflows/localworker/localworker.t2flow
deleted file mode 100644
index b3b2053..0000000
--- a/src/test/resources/workflows/localworker/localworker.t2flow
+++ /dev/null
@@ -1,67 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="5eebce20-72f5-4ac7-a4bf-8086d59d0c9e" role="top"><name>Workflow5</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Concatenate_two_strings</name><inputPorts><port><name>string2</name><depth>0</depth></port><port><name>string1</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="string2" to="string2" /><map from="string1" to="string1" /></inputMap><outputMap><map f
rom="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
- <script>output = string1 + string2;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="string2" depth="0" /><port name="string1" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>string1_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /
><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>Hello </value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string2</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string1</port></sink><source type="processor"><processor>string1_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>C
oncatenate_two_strings</processor><port>output</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>5eebce20-72f5-4ac7-a4bf-8086d59d0c9e</identification>
- </annotationBean>
- <date>2011-02-21 13:44:43.621 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/rest/rest.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/rest/rest.t2flow b/src/test/resources/workflows/rest/rest.t2flow
deleted file mode 100644
index f3f90b8..0000000
--- a/src/test/resources/workflows/rest/rest.t2flow
+++ /dev/null
@@ -1,154 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="8e36176a-2975-498b-93f7-f2beba774532" role="top"><name>Workflow11</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>REST_Service</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
- <httpMethod>GET</httpMethod>
- <urlSignature>http://www.uniprot.org/uniprot/{id}.xml</urlSignature>
- <acceptsHeaderValue>text/plain</acceptsHeaderValue>
- <contentTypeForUpdates>application/xml</contentTypeForUpdates>
- <outgoingDataFormat>String</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>false</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders />
- <activityInputs>
- <entry>
- <string>id</string>
- <java-class>java.lang.String</java-class>
- </entry>
- </activityInputs>
-</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>id_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" />
</outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>P12345</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>REST_Service</processor><port>id</port></sink><source type="processor"><processor>id_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>REST_Service</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xm
lns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>30c58a3d-4037-4b92-b7d6-3aea761bdada</identification>
- </annotationBean>
- <date>2011-11-02 08:52:32.796 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>d090ff3c-c84d-461f-9027-ccd07fe0a352</identification>
- </annotationBean>
- <date>2011-11-02 10:09:35.558 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>1e2069a6-54c3-4e09-b639-c9bb27356eb9</identification>
- </annotationBean>
- <date>2011-11-02 09:59:38.235 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>f88604da-4047-4ab9-bd19-23cbbb8be88b</identification>
- </annotationBean>
- <date>2011-11-02 10:12:00.757 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>8e36176a-2975-498b-93f7-f2beba774532</identification>
- </annotationBean>
- <date>2012-02-10 15:56:15.960 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>b3887d66-e945-444d-820a-ddb5c1d6cecb</identification>
- </annotationBean>
- <date>2011-11-02 10:00:26.717 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>bbf68124-dbeb-482b-80c6-e461d264a98b</identification>
- </annotationBean>
- <date>2011-11-02 10:12:59.372 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>c2802c60-cc0e-4bc0-b401-473476811e46</identification>
- </annotationBean>
- <date>2011-11-02 10:02:16.255 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>d73137e0-8cfb-4536-849e-6d30b1b1f4dc</identification>
- </annotationBean>
- <date>2011-11-02 08:49:30.655 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>3f67a647-2d0e-4d7e-9937-5bde3d562fde</identification>
- </annotationBean>
- <date>2011-11-02 10:10:29.316 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>f76689f8-2629-4168-b0a6-e70c88acaca9</identification>
- </annotationBean>
- <date>2012-02-10 15:49:11.156 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/secure-basic-authentication-https/secure-basic-authentication-https.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/secure-basic-authentication-https/secure-basic-authentication-https.t2flow b/src/test/resources/workflows/secure-basic-authentication-https/secure-basic-authentication-https.t2flow
deleted file mode 100644
index 0cbff10..0000000
--- a/src/test/resources/workflows/secure-basic-authentication-https/secure-basic-authentication-https.t2flow
+++ /dev/null
@@ -1,74 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="12203b36-f878-45f7-a16e-863e1bbc81b8" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Basic_AuthN_and_HTTPS</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
- <httpMethod>GET</httpMethod>
- <urlSignature>https://heater.cs.man.ac.uk:7443/examples-basic-authentication/taverna-test-page.html</urlSignature>
- <acceptsHeaderValue>text/plain</acceptsHeaderValue>
- <contentTypeForUpdates>application/xml</contentTypeForUpdates>
- <outgoingDataFormat>String</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>false</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders />
- <activityInputs />
-</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Basic_AuthN_and_HTTPS</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>adb25995-c890-40c7-b091-2c2512024864</identification>
- </annotationBean>
- <date>2010-11-29 10:35:54.270 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>12203b36-f878-45f7-a16e-863e1bbc81b8</identification>
- </annotationBean>
- <date>2010-11-29 15:35:51.711 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
- </annotationBean>
- <date>2010-11-22 14:15:20.380 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
- </annotationBean>
- <date>2010-11-22 14:16:43.484 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>388333c0-fd34-4571-ab0c-f67c10c2ed64</identification>
- </annotationBean>
- <date>2010-11-22 14:21:12.760 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/secure-basic-authentication/secure-basic-authentication.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/secure-basic-authentication/secure-basic-authentication.t2flow b/src/test/resources/workflows/secure-basic-authentication/secure-basic-authentication.t2flow
deleted file mode 100644
index 998b69a..0000000
--- a/src/test/resources/workflows/secure-basic-authentication/secure-basic-authentication.t2flow
+++ /dev/null
@@ -1,74 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="6eca35ba-d7d4-43d9-8593-93eba828cc46" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Basic_AuthN</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
- <httpMethod>GET</httpMethod>
- <urlSignature>http://heater.cs.man.ac.uk:7070/examples-basic-authentication/taverna-test-page.html</urlSignature>
- <acceptsHeaderValue>text/plain</acceptsHeaderValue>
- <contentTypeForUpdates>application/xml</contentTypeForUpdates>
- <outgoingDataFormat>String</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>false</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders />
- <activityInputs />
-</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Basic_AuthN</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
- </annotationBean>
- <date>2010-11-22 14:15:20.380 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>6eca35ba-d7d4-43d9-8593-93eba828cc46</identification>
- </annotationBean>
- <date>2010-11-29 10:41:02.602 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>adb25995-c890-40c7-b091-2c2512024864</identification>
- </annotationBean>
- <date>2010-11-29 10:35:54.270 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
- </annotationBean>
- <date>2010-11-22 14:16:43.484 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>388333c0-fd34-4571-ab0c-f67c10c2ed64</identification>
- </annotationBean>
- <date>2010-11-22 14:21:12.760 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
[02/50] [abbrv] incubator-taverna-commandline git commit: Replaced
hard coded version number for T3-1195
Posted by st...@apache.org.
Replaced hard coded version number for T3-1195
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/265416c4
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/265416c4
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/265416c4
Branch: refs/heads/master
Commit: 265416c409ef99de3334f3aa1aed40ecc8373d39
Parents: 5af799a
Author: Christian-B <br...@cs.man.ac.uk>
Authored: Wed Jul 2 14:58:35 2014 +0100
Committer: Christian-B <br...@cs.man.ac.uk>
Committed: Wed Jul 2 14:58:35 2014 +0100
----------------------------------------------------------------------
taverna-commandline-common/pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/265416c4/taverna-commandline-common/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/pom.xml b/taverna-commandline-common/pom.xml
index 597a83d..b2f4e93 100644
--- a/taverna-commandline-common/pom.xml
+++ b/taverna-commandline-common/pom.xml
@@ -13,7 +13,7 @@
<dependency>
<groupId>net.sf.taverna.t2.taverna-commandline</groupId>
<artifactId>taverna-commandline-api</artifactId>
- <version>2.0.1-SNAPSHOT</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
[23/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-tests/
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java
new file mode 100644
index 0000000..140dec6
--- /dev/null
+++ b/taverna-commandline-tests/src/test/java/uk/org/taverna/commandline/WorkflowTestSuite.java
@@ -0,0 +1,79 @@
+/*******************************************************************************
+ * Copyright (C) 2012 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.commandline;
+
+import java.io.File;
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+import java.lang.reflect.Modifier;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.junit.runner.Runner;
+import org.junit.runners.Suite;
+import org.junit.runners.model.FrameworkMethod;
+import org.junit.runners.model.TestClass;
+
+/**
+ * Test suite for running workflows specified by a method annotated by @Workflows.
+ *
+ * @author David Withers
+ */
+public class WorkflowTestSuite extends Suite {
+
+ @Retention(RetentionPolicy.RUNTIME)
+ @Target(ElementType.METHOD)
+ public static @interface Workflows {}
+
+ private ArrayList<Runner> runners = new ArrayList<Runner>();
+
+ public WorkflowTestSuite(Class<?> klass) throws Throwable {
+ super(klass, Collections.<Runner>emptyList());
+ for (File workflow : getWorkflows(getTestClass())) {
+ runners.add(new WorkflowTestRunner(getTestClass().getJavaClass(), workflow));
+ }
+ }
+
+ @Override
+ protected List<Runner> getChildren() {
+ return runners;
+ }
+
+ @SuppressWarnings("unchecked")
+ private List<File> getWorkflows(TestClass klass) throws Throwable {
+ return (List<File>) getWorkflowsMethod(klass).invokeExplosively(null);
+ }
+
+ public FrameworkMethod getWorkflowsMethod(TestClass testClass) throws Exception {
+ List<FrameworkMethod> methods = testClass.getAnnotatedMethods(Workflows.class);
+ for (FrameworkMethod method : methods) {
+ int modifiers = method.getMethod().getModifiers();
+ if (Modifier.isStatic(modifiers) && Modifier.isPublic(modifiers)) {
+ return method;
+ }
+ }
+ throw new Exception("No public static Workflows annotated method on class " + testClass.getName());
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url b/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url
new file mode 100644
index 0000000..5846961
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/biomartandembossanalysis.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1794/download/biomartandembossanalysis_457009.t2flow?version=4
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/ignorePort
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/ignorePort b/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/ignorePort
new file mode 100644
index 0000000..e0cb526
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/biomartandembossanalysis/ignorePort
@@ -0,0 +1 @@
+outputPlot
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/biomoby_tutorial_workflow.url
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/biomoby_tutorial_workflow.url b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/biomoby_tutorial_workflow.url
new file mode 100644
index 0000000..a73b8c4
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/biomoby_tutorial_workflow.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/1366/download/biomoby_tutorial_workflow_877727.t2flow?version=1
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/ignorePort
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/ignorePort b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/ignorePort
new file mode 100644
index 0000000..f8e22dd
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/ignorePort
@@ -0,0 +1 @@
+restrict_out
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/id
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/id b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/id
new file mode 100644
index 0000000..1dfd176
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/id
@@ -0,0 +1 @@
+656461
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/myexperiment/biomoby_tutorial_workflow/inputs/namespace
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diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/unix_external_tools_with_zip_and_unzip/unix_external_tools_with_zip_and_unzip.url b/taverna-commandline-tests/src/test/resources/myexperiment/unix_external_tools_with_zip_and_unzip/unix_external_tools_with_zip_and_unzip.url
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--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/myexperiment/unix_external_tools_with_zip_and_unzip/unix_external_tools_with_zip_and_unzip.url
@@ -0,0 +1 @@
+http://www.myexperiment.org/workflows/2230/download/example_for_external_tools_with_zip_and_unzip_57117.t2flow?version=1
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/inputs/a
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diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/inputs/a b/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/inputs/a
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+++ b/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/inputs/a
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+1
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diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/inputs/b b/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/inputs/b
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diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/unix_numerically_adding_two_values.url b/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/unix_numerically_adding_two_values.url
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+++ b/taverna-commandline-tests/src/test/resources/myexperiment/unix_numerically_adding_two_values/unix_numerically_adding_two_values.url
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+http://www.myexperiment.org/workflows/2231/download/numerically_adding_two_values._763485.t2flow?version=1
\ No newline at end of file
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diff --git a/taverna-commandline-tests/src/test/resources/myexperiment/unix_tool_service_using_string_replacement/unix_tool_service_using_string_replacement.url b/taverna-commandline-tests/src/test/resources/myexperiment/unix_tool_service_using_string_replacement/unix_tool_service_using_string_replacement.url
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+++ b/taverna-commandline-tests/src/test/resources/myexperiment/unix_tool_service_using_string_replacement/unix_tool_service_using_string_replacement.url
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/apiconsumer.t2flow
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diff --git a/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/apiconsumer.t2flow b/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/apiconsumer.t2flow
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onsumer.ApiConsumerActivityConfigurationBean xmlns="">
+ <inputs />
+ <outputs />
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+ <localDependencies />
+ <artifactDependencies />
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+ <isMethodConstructor>true</isMethodConstructor>
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+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
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+ <inputs />
+ <outputs />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <apiConsumerName>No name</apiConsumerName>
+ <apiConsumerDescription>No description</apiConsumerDescription>
+ <description />
+ <className>java.lang.String</className>
+ <methodName>toUpperCase</methodName>
+ <parameterNames />
+ <parameterDimensions />
+ <parameterTypes />
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+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
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+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="object" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>String</processor><port>string</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>toUpperCase</processor><port>object</port></sink><source type="processor"><processor>String</processor><port>object</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="proc
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+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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+ <creators />
+ <curationEventList />
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+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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+ <date>2011-11-02 12:43:09.911 GMT</date>
+ <creators />
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+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>404e203c-ce51-4a9f-907c-1dab7f2eaaa2</identification>
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+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/inputs/in
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diff --git a/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/inputs/in b/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/inputs/in
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index 0000000..fede229
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/apiconsumer/inputs/in
@@ -0,0 +1 @@
+test-input
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/beanshell/beanshell.t2flow
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diff --git a/taverna-commandline-tests/src/test/resources/workflows/beanshell/beanshell.t2flow b/taverna-commandline-tests/src/test/resources/workflows/beanshell/beanshell.t2flow
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+++ b/taverna-commandline-tests/src/test/resources/workflows/beanshell/beanshell.t2flow
@@ -0,0 +1,137 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="78cb1427-d57f-42c2-a385-1d20c1580f3b" role="top"><name>Workflow13</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Echo</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfi
gurationBean xmlns="">
+ <script>out=in;</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>ListGenerator</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><
map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out = new ArrayList();
+
+for (int i = 0; i < 1000; i++) {
+ out.add(in + ":" + i);
+}</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>out</name>
+ <depth>1</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Echo</processor><port>in</port></sink><source type="processor"><processor>ListGenerator</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>ListGenerator</processor><port>in</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><
processor>Echo</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>13c70169-dfaa-4ea6-b6ab-3551dae7fa84</identification>
+ </annotationBean>
+ <date>2010-08-19 12:28:57.881 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>7ef10e93-7376-41a9-9255-552149094142</identification>
+ </annotationBean>
+ <date>2010-08-31 13:06:57.536 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>3b7c0b9c-572d-466b-af6d-0fb40699e8a5</identification>
+ </annotationBean>
+ <date>2010-08-31 12:50:40.306 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eb6a550d-f34e-4de9-b0fc-1b3df8ab36c4</identification>
+ </annotationBean>
+ <date>2010-08-31 14:32:44.634 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>78cb1427-d57f-42c2-a385-1d20c1580f3b</identification>
+ </annotationBean>
+ <date>2010-08-31 14:36:00.297 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ad638364-a6e0-4852-abca-9f609c9553d2</identification>
+ </annotationBean>
+ <date>2010-08-19 13:43:43.797 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/beanshell/inputs/in
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/beanshell/inputs/in b/taverna-commandline-tests/src/test/resources/workflows/beanshell/inputs/in
new file mode 100644
index 0000000..fede229
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/beanshell/inputs/in
@@ -0,0 +1 @@
+test-input
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/biomart/biomart.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/biomart/biomart.t2flow b/taverna-commandline-tests/src/test/resources/workflows/biomart/biomart.t2flow
new file mode 100644
index 0000000..f82f340
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/biomart/biomart.t2flow
@@ -0,0 +1,30 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="4a959e22-8166-4e8b-ae94-6e85c8807e35" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>btaurus_gene_ensembl</name><inputPorts /><outputPorts><port><name>btaurus_gene_ensembl.ensembl_gene_id</name><depth>1</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomart-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.biomart.BiomartActivity</class><inputMap /><outputMap><map from="btaurus_gene_ensembl.ensembl_gene_id" to="btaurus_gene_ensembl.ensembl_gene_id" /></outputMap><configBean encoding="jdomxml"><MartQuery xmlns=""><MartService location="http://www.biomart.org/biomart/martservice" /><MartDataset displayName="Bos taurus genes (UMD3.1)" nam
e="btaurus_gene_ensembl" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2011-09-07 22:16:01"><MartURLLocation database="ensembl_mart_64" default="1" displayName="ENSEMBL GENES 64 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice" port="80" serverVirtualSchema="default" virtualSchema="default" visible="1" redirect="0" /></MartDataset><Query virtualSchemaName="default" count="0" uniqueRows="1" softwareVersion="0.6" requestId="taverna"><Dataset name="btaurus_gene_ensembl"><Attribute name="ensembl_gene_id" /><Filter name="chromosome_name" value="1" /><Filter name="with_affy_bovine" excluded="0" /><Filter name="go_evidence_code" value="IDA" /></Dataset></Query></MartQuery></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><cla
ss>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>btaurus_gene_ensembl</processor><port>btaurus_gene_ensembl.ensembl_gene_id</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>4a959e22-8166-4e8b-ae94-6e85c8807e35</identification>
+ </annotationBean>
+ <date>2011-10-27 14:33:16.228 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>5859741c-a0ba-4dae-8b81-1dd7c928562f</identification>
+ </annotationBean>
+ <date>2011-10-27 14:32:47.106 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
[26/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-tests/
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/secure-ws/secure-ws.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/secure-ws/secure-ws.t2flow b/src/test/resources/workflows/secure-ws/secure-ws.t2flow
deleted file mode 100644
index 764b810..0000000
--- a/src/test/resources/workflows/secure-ws/secure-ws.t2flow
+++ /dev/null
@@ -1,180 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="c71621ca-196c-46cd-9073-48af82b4bd4f" role="top"><name>Workflow13</name><inputPorts /><outputPorts><port><name>out_plaintext</name><annotations /></port><port><name>out_plaintext_timestamp</name><annotations /></port><port><name>out_digest</name><annotations /></port><port><name>out_digest_timestamp</name><annotations /></port></outputPorts><processors><processor><name>hello_plaintext_password</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><m
ap from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl</wsdl>
- <operation>hello</operation>
- <securityProfile>WSSecurityUsernameTokenPlainTextPassword</securityProfile>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="
value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>Alan</value>
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- <date>2011-06-21 12:11:30.87 BST</date>
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- <date>2011-01-21 16:02:09.633 GMT</date>
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- <date>2010-11-22 13:29:43.282 GMT</date>
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- <date>2010-11-22 13:29:26.400 GMT</date>
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <date>2010-11-22 13:28:31.68 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>394aced4-ee5d-4355-8ebe-9fc8bcfe5303</identification>
- </annotationBean>
- <date>2011-06-21 12:07:46.327 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>8175c97b-6385-460a-98ab-5cf974010d51</identification>
- </annotationBean>
- <date>2010-11-22 12:11:59.610 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>a388d568-ca08-43b4-abaf-3744a6801d45</identification>
- </annotationBean>
- <date>2010-11-22 13:30:28.898 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>7153a2dd-18bd-4f25-80ab-1efa8afc567d</identification>
- </annotationBean>
- <date>2011-01-21 16:02:39.43 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/secure-wsdl/secure-wsdl.t2flow
----------------------------------------------------------------------
diff --git a/src/test/resources/workflows/secure-wsdl/secure-wsdl.t2flow b/src/test/resources/workflows/secure-wsdl/secure-wsdl.t2flow
deleted file mode 100644
index 4db4ad5..0000000
--- a/src/test/resources/workflows/secure-wsdl/secure-wsdl.t2flow
+++ /dev/null
@@ -1,131 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="b23a2149-976e-4e98-b120-e5b8580839ef" role="top"><name>Workflow13</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>hello_plaintext_password</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>helloReturn</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /></inputMap><outputMap><map from="helloReturn" to="helloReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>http://heater.cs.man.ac.uk:7070/axis/services/HelloService-PlaintextPassword?wsdl</wsdl>
- <operation>hello</operation>
- <securityProfile>WSSecurityUsernameTokenPlainTextPassword</securityProfile>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in0" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>in0_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value"
/></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>Alan</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>hello_plaintext_password</processor><port>in0</port></sink><source type="processor"><processor>in0_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>hello_plaintext_password</processor><port>helloReturn</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotati
on.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>ca8fb5c5-0e8c-4e68-84f0-bdc85a77e2b3</identification>
- </annotationBean>
- <date>2010-11-22 13:29:26.400 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>7153a2dd-18bd-4f25-80ab-1efa8afc567d</identification>
- </annotationBean>
- <date>2011-01-21 16:02:39.43 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>394aced4-ee5d-4355-8ebe-9fc8bcfe5303</identification>
- </annotationBean>
- <date>2011-06-21 12:07:46.327 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>c71621ca-196c-46cd-9073-48af82b4bd4f</identification>
- </annotationBean>
- <date>2011-06-21 12:11:30.87 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>8175c97b-6385-460a-98ab-5cf974010d51</identification>
- </annotationBean>
- <date>2010-11-22 12:11:59.610 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>56cadac0-c944-4b9e-83c3-078f57738405</identification>
- </annotationBean>
- <date>2011-01-21 16:02:09.633 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>a388d568-ca08-43b4-abaf-3744a6801d45</identification>
- </annotationBean>
- <date>2010-11-22 13:30:28.898 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>b23a2149-976e-4e98-b120-e5b8580839ef</identification>
- </annotationBean>
- <date>2011-08-23 13:40:15.238 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>3d76be4c-83c4-413b-91f2-b0ce69dcbd97</identification>
- </annotationBean>
- <date>2010-11-22 13:29:43.282 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>e61023d9-d603-4df6-87e5-175603f106a5</identification>
- </annotationBean>
- <date>2010-11-22 13:28:31.68 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/src/test/resources/workflows/soaplab/soaplab.t2flow
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diff --git a/src/test/resources/workflows/soaplab/soaplab.t2flow b/src/test/resources/workflows/soaplab/soaplab.t2flow
deleted file mode 100644
index f1ef82b..0000000
--- a/src/test/resources/workflows/soaplab/soaplab.t2flow
+++ /dev/null
@@ -1,84 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="db8053e3-1837-42cc-ba27-5fd0a83f119e" role="top"><name>Retrieve_sequence_in_EMBL_format</name><inputPorts /><outputPorts><port><name>sequence</name><annotations /></port></outputPorts><processors><processor><name>sequence_feature</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>true</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>sequence_id</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.s
f.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>embl:x52524</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
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-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>sequence_format</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><n
et.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>embl</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>seqret</name><inputPorts><port><name>sequence_usa</name><depth>0</depth></port><port><name>feature</name><depth>0</depth></port><port><name>osformat_outseq</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outseq</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2
.activities.soaplab.SoaplabActivity</class><inputMap><map from="osformat_outseq" to="osformat_outseq" /><map from="feature" to="feature" /><map from="sequence_usa" to="sequence_usa" /></inputMap><outputMap><map from="outseq" to="outseq" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
- <endpoint>http://www.ebi.ac.uk/soaplab/services/edit.seqret</endpoint>
- <pollingInterval>0</pollingInterval>
- <pollingBackoff>1.0</pollingBackoff>
- <pollingIntervalMax>0</pollingIntervalMax>
-</net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="sequence_usa" depth="0" /><port name="feature" depth="0" /><port name="osformat_outseq" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>seqret</processor><port>sequence_usa</port></sink><source type="processor"><processor>sequence_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>seqret</processor><port>feature</port></sink><source type="processor"><processor>sequence_f
eature</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>seqret</processor><port>osformat_outseq</port></sink><source type="processor"><processor>sequence_format</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>sequence</port></sink><source type="processor"><processor>seqret</processor><port>outseq</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
- <text>Retrieve sequence in EMBL format</text>
- </annotationBean>
- <date>2009-12-15 20:21:29.202 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
- <text>Franck Tanoh</text>
- </annotationBean>
- <date>2009-12-15 20:21:20.965 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>db8053e3-1837-42cc-ba27-5fd0a83f119e</identification>
- </annotationBean>
- <date>2010-07-04 17:49:51.364 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This workflow retrieves a sequence associated with its features in embl format</text>
- </annotationBean>
- <date>2009-12-15 20:21:39.30 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
\ No newline at end of file
[40/50] [abbrv] incubator-taverna-commandline git commit: about
target/ folder
Posted by st...@apache.org.
about target/ folder
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/7a880755
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/7a880755
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/7a880755
Branch: refs/heads/master
Commit: 7a880755597e33c498a0acaf33b08cb83297be0b
Parents: 131ef3b
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 12:44:09 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 12:44:09 2014 -0600
----------------------------------------------------------------------
README.md | 3 +++
1 file changed, 3 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/7a880755/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
index 9adb847..bcd653c 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,6 @@
# Apache Taverna Commandline
[](https://travis-ci.org/taverna-incubator/incubator-taverna-commandline)
+
+After building, see taverna-commandline-product/target/apache-taverna-commandline-3.1.0-incubating-SNAPSHOT-dev/apache-taverna-commandline-3.1.0-incubating-SNAPSHOT/ or equivalent
+
[41/50] [abbrv] incubator-taverna-commandline git commit: Include
commonactivities
Posted by st...@apache.org.
Include commonactivities
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/622b2126
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/622b2126
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/622b2126
Branch: refs/heads/master
Commit: 622b2126818690b010cdc13d90782bd436e31cba
Parents: 7a88075
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Jan 6 12:26:03 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Jan 6 12:26:03 2015 +0000
----------------------------------------------------------------------
pom.xml | 1 +
taverna-commandline-product/pom.xml | 90 ++++++++++++--------------------
2 files changed, 34 insertions(+), 57 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/622b2126/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 0045712..04439f2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -15,6 +15,7 @@
<taverna.language.version>0.15.0-incubating-SNAPSHOT</taverna.language.version>
<taverna.osgi.version>0.2.0-incubating-SNAPSHOT</taverna.osgi.version>
<taverna.engine.version>3.1.0-incubating-SNAPSHOT</taverna.engine.version>
+ <taverna.commonactivities.version>2.1.0-incubating-SNAPSHOT</taverna.commonactivities.version>
</properties>
<modules>
<module>taverna-commandline-api</module>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/622b2126/taverna-commandline-product/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/pom.xml b/taverna-commandline-product/pom.xml
index 3b2187b..fba41c5 100644
--- a/taverna-commandline-product/pom.xml
+++ b/taverna-commandline-product/pom.xml
@@ -286,63 +286,39 @@
<artifactId>taverna-stringconstant-activity</artifactId>
<version>${taverna.engine.version}</version>
</dependency>
- <!--
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>apiconsumer-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>beanshell-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>biomart-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>external-tool-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>localworker-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>rest-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>rshell-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>soaplab-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>spreadsheet-import-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>wsdl-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>xpath-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- -->
+
+ <!-- Taverna Common Activities -->
+ <dependency>
+ <groupId>org.apache.taverna.commonactivities</groupId>
+ <artifactId>taverna-external-tool-activity</artifactId>
+ <version>${taverna.commonactivities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.commonactivities</groupId>
+ <artifactId>taverna-interaction-activity</artifactId>
+ <version>${taverna.commonactivities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.commonactivities</groupId>
+ <artifactId>taverna-rest-activity</artifactId>
+ <version>${taverna.commonactivities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.commonactivities</groupId>
+ <artifactId>taverna-spreadsheet-import-activity</artifactId>
+ <version>${taverna.commonactivities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.commonactivities</groupId>
+ <artifactId>taverna-wsdl-activity</artifactId>
+ <version>${taverna.commonactivities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.commonactivities</groupId>
+ <artifactId>taverna-xpath-activity</artifactId>
+ <version>${taverna.commonactivities.version}</version>
+ </dependency>
+
<!-- Taverna Commandline -->
<dependency>
[33/50] [abbrv] incubator-taverna-commandline git commit: Merge
branch 'taverna-commandline-product'
Posted by st...@apache.org.
Merge branch 'taverna-commandline-product'
>From https://github.com/taverna/taverna-commandline-product master
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/8568f968
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/8568f968
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/8568f968
Branch: refs/heads/master
Commit: 8568f968e67cf955640c575453204fefc362d2ee
Parents: 0be1d89 0257a92
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 02:08:34 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 02:08:34 2014 -0600
----------------------------------------------------------------------
taverna-commandline-product/pom.xml | 578 +++++++++++++++++++
.../main/assembly/dependencies-component.xml | 21 +
.../src/main/assembly/developer-assembly.xml | 13 +
.../src/main/assembly/nightly-assembly.xml | 15 +
.../src/main/assembly/release-assembly.xml | 15 +
.../src/main/etc/conf/log4j.properties | 14 +
.../src/main/etc/conf/logging.properties | 10 +
.../src/main/etc/conf/taverna.app.properties | 2 +
.../src/main/etc/executeworkflow.bat | 17 +
.../src/main/etc/executeworkflow.sh | 25 +
10 files changed, 710 insertions(+)
----------------------------------------------------------------------
[22/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-tests/
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/dataflow/dataflow.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/dataflow/dataflow.t2flow b/taverna-commandline-tests/src/test/resources/workflows/dataflow/dataflow.t2flow
new file mode 100644
index 0000000..c9366c2
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/dataflow/dataflow.t2flow
@@ -0,0 +1,217 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="ac4ce40a-57b9-486c-bb4c-eb8609c6cc48" role="top"><name>Workflow1</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Nested_workflow</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="dataflow"><dataflow ref="c6b258ac-3588-4828-b71c-207bad8b63c4" /
></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>echo</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from=
"in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ <granularDepth>0</granularDepth>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <script>out = in;</script>
+ <dependencies />
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>echo_2</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map fro
m="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ <granularDepth>0</granularDepth>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <script>out = in;</script>
+ <dependencies />
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Nested_workflow</processor><port>in</port></sink><source type="processor"><processor>echo</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>echo</processor><port>in</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>echo_2</processor><port>in</port></sink><sou
rce type="processor"><processor>Nested_workflow</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>echo_2</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>437a237a-03a0-489f-97c6-fd5acc5db18e</identification>
+ </annotationBean>
+ <date>2011-11-09 10:59:10.221 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ae7626c8-13a4-4560-9496-59a8cc0693be</identification>
+ </annotationBean>
+ <date>2011-02-16 11:57:10.514 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>96d450ff-aaf8-473b-91a1-4acce7371c3b</identification>
+ </annotationBean>
+ <date>2011-02-16 11:55:55.618 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ac4ce40a-57b9-486c-bb4c-eb8609c6cc48</identification>
+ </annotationBean>
+ <date>2011-11-09 11:02:29.60 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>9f957cde-a7ad-4453-a09f-7231c8c8c4f3</identification>
+ </annotationBean>
+ <date>2011-02-16 11:52:40.88 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>f847ed6f-2834-4861-a8af-73ab737c6a91</identification>
+ </annotationBean>
+ <date>2011-11-09 11:00:41.783 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="c6b258ac-3588-4828-b71c-207bad8b63c4" role="nested"><name>Workflow4</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>echo</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivit
yConfigurationBean xmlns="">
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ <granularDepth>0</granularDepth>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <script>out = "nested dataflow : " + in;</script>
+ <dependencies />
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>echo</processor><port>in</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>echo</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>f8dd3fb7-7051-4242-a3af-d82056934cf6</identification>
+ </annotationBean>
+ <date>2011-02-16 11:55:01.559 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>0a0b6f17-8ebf-4017-ad4c-0719a9d44806</identification>
+ </annotationBean>
+ <date>2011-11-09 11:00:37.241 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>c6b258ac-3588-4828-b71c-207bad8b63c4</identification>
+ </annotationBean>
+ <date>2011-11-09 11:02:26.99 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eaa8b2a0-e71b-4d6a-b8ad-c299a8ad6e18</identification>
+ </annotationBean>
+ <date>2011-02-16 11:53:12.59 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/dataflow/inputs/in
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/dataflow/inputs/in b/taverna-commandline-tests/src/test/resources/workflows/dataflow/inputs/in
new file mode 100644
index 0000000..fede229
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/dataflow/inputs/in
@@ -0,0 +1 @@
+test-input
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/in-out/in-out.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/in-out/in-out.t2flow b/taverna-commandline-tests/src/test/resources/workflows/in-out/in-out.t2flow
new file mode 100644
index 0000000..ecfb4e8
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/in-out/in-out.t2flow
@@ -0,0 +1,12 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="4d8a491e-fa11-4918-98ce-7df19051d5c5" role="top"><name>Workflow6</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors /><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="dataflow"><port>in</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>4d8a491e-fa11-4918-98ce-7df19051d5c5</identification>
+ </annotationBean>
+ <date>2012-04-03 15:34:41.4 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/in-out/inputs/in
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/in-out/inputs/in b/taverna-commandline-tests/src/test/resources/workflows/in-out/inputs/in
new file mode 100644
index 0000000..fede229
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/in-out/inputs/in
@@ -0,0 +1 @@
+test-input
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/iteration/inputs/in
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/iteration/inputs/in b/taverna-commandline-tests/src/test/resources/workflows/iteration/inputs/in
new file mode 100644
index 0000000..30d74d2
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/iteration/inputs/in
@@ -0,0 +1 @@
+test
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/iteration/iteration.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/iteration/iteration.t2flow b/taverna-commandline-tests/src/test/resources/workflows/iteration/iteration.t2flow
new file mode 100644
index 0000000..bec4c2d
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/iteration/iteration.t2flow
@@ -0,0 +1,474 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="80c80b32-1faa-4c8e-9294-eb85d6aaa764" role="top"><name>Workflow13</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>cross</name><annotations /></port><port><name>dot</name><annotations /></port><port><name>crossdot</name><annotations /></port><port><name>dotdot</name><annotations /></port><port><name>dotcross</name><annotations /></port></outputPorts><processors><processor><name>cross</name><inputPorts><port><name>in1</name><depth>0</depth></port><port><name>in2</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.
t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out=in1 + in2;</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in1</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in2</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in1" depth="0" /><port name="in2" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>ListGenerator1</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.Beans
hellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out = new ArrayList();
+
+for (int i = 0; i < 10; i++) {
+ out.add(in + ":" + i);
+}</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>out</name>
+ <depth>1</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>ListGenerator2</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap>
<map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out = new ArrayList();
+
+for (int i = 0; i < 10; i++) {
+ out.add(in + ":" + i);
+}</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>out</name>
+ <depth>1</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>dot</name><inputPorts><port><name>in2</name><depth>0</depth></port><port><name>in1</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.
BeanshellActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out=in1 + in2;</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in1</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in2</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><dot><port name="in2" depth="0" /><port name="in1" depth="0" /></dot></strategy></iteration></iterationStrategyStack></processor><processor><name>crossdot</name><inputPorts><port><name>in1</name><depth>0</depth></port><port><name>in2</name><depth>0</depth></port><port><name>in3</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact>
<version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /><map from="in3" to="in3" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out = in1 + in2 + in3;</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in1</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in2</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in3</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in1" depth="0" /><port name="in2" depth="0" /><dot><port name="in3" depth="0" /></dot></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>dotcross</name><inputPorts><port><name>in1</name><depth>0</depth></port><port><name>in2</name><depth>0</depth></port><port><name>in3</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</g
roup><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /><map from="in3" to="in3" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out = in1 + in2 + in3;</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in1</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in2</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in3</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in3" depth="0" /><dot><port name="in2" depth="0" /><port name="in1" depth="0" /></dot></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>dotdot</name><inputPorts><port><name>in1</name><depth>0</depth></port><port><name>in2</name><depth>0</depth></port><port><name>in3</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</gro
up><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in2" to="in2" /><map from="in1" to="in1" /><map from="in3" to="in3" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
+ <script>out = in1 + in2 + in3;</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in1</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in2</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in3</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes />
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><dot><port name="in1" depth="0" /><port name="in2" depth="0" /><dot><port name="in3" depth="0" /></dot></dot></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>cross</processor><port>in1</port></sink><source type="processor"><processor>ListGenerator1</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>cross</processor><port>in2</port></sink><source type="processor"><processor>ListGenerator2</processor><port>out</port>
</source></datalink><datalink><sink type="processor"><processor>ListGenerator1</processor><port>in</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>ListGenerator2</processor><port>in</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>dot</processor><port>in2</port></sink><source type="processor"><processor>ListGenerator2</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>dot</processor><port>in1</port></sink><source type="processor"><processor>ListGenerator1</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>crossdot</processor><port>in1</port></sink><source type="processor"><processor>ListGenerator1</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>crossdot</processor><port>in2</port></sink><source type="processor"><processor>ListGen
erator2</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>crossdot</processor><port>in3</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>dotcross</processor><port>in1</port></sink><source type="processor"><processor>ListGenerator1</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>dotcross</processor><port>in2</port></sink><source type="processor"><processor>ListGenerator2</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>dotcross</processor><port>in3</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>dotdot</processor><port>in1</port></sink><source type="processor"><processor>ListGenerator1</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>dotdot</processor><port>in2</port></sink><source type
="processor"><processor>ListGenerator2</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>dotdot</processor><port>in3</port></sink><source type="processor"><processor>ListGenerator2</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>cross</port></sink><source type="processor"><processor>cross</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>dot</port></sink><source type="processor"><processor>dot</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>crossdot</port></sink><source type="processor"><processor>crossdot</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>dotdot</port></sink><source type="processor"><processor>dotdot</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>dotcross</port></sink><source type="processor"><processor>dotcross</processor><port>out</port></source
></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ad638364-a6e0-4852-abca-9f609c9553d2</identification>
+ </annotationBean>
+ <date>2010-08-19 13:43:43.797 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>3fb7f0a7-26f8-43e1-a122-87a25889f57d</identification>
+ </annotationBean>
+ <date>2011-02-22 08:25:53.793 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>13c70169-dfaa-4ea6-b6ab-3551dae7fa84</identification>
+ </annotationBean>
+ <date>2010-08-19 12:28:57.881 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>af1f698b-820d-4b35-a92e-9091c90b493e</identification>
+ </annotationBean>
+ <date>2011-02-22 09:30:17.881 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>be50375c-4f68-44aa-8604-9a80d8d97570</identification>
+ </annotationBean>
+ <date>2011-02-22 09:03:28.97 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eb6a550d-f34e-4de9-b0fc-1b3df8ab36c4</identification>
+ </annotationBean>
+ <date>2010-08-31 14:32:44.634 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ac70d4c0-5db9-48b1-ba32-8e11fff8ae59</identification>
+ </annotationBean>
+ <date>2011-02-22 08:31:32.90 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>78cb1427-d57f-42c2-a385-1d20c1580f3b</identification>
+ </annotationBean>
+ <date>2010-08-31 14:36:00.297 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>3b7c0b9c-572d-466b-af6d-0fb40699e8a5</identification>
+ </annotationBean>
+ <date>2010-08-31 12:50:40.306 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>7a22acbb-2f0f-41dd-a526-d2a9b4e267c5</identification>
+ </annotationBean>
+ <date>2011-02-22 08:59:59.964 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>80c80b32-1faa-4c8e-9294-eb85d6aaa764</identification>
+ </annotationBean>
+ <date>2011-02-22 09:40:37.744 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>bc9c64da-9143-4811-a22e-657c92fcfe94</identification>
+ </annotationBean>
+ <date>2011-02-22 09:23:49.109 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>c072030e-b367-4885-a770-7d892672d979</identification>
+ </annotationBean>
+ <date>2011-02-22 09:31:03.727 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>7ef10e93-7376-41a9-9255-552149094142</identification>
+ </annotationBean>
+ <date>2010-08-31 13:06:57.536 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/localworker/inputs/in
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/localworker/inputs/in b/taverna-commandline-tests/src/test/resources/workflows/localworker/inputs/in
new file mode 100644
index 0000000..cadf8b6
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/localworker/inputs/in
@@ -0,0 +1 @@
+Tom
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/localworker/localworker.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/localworker/localworker.t2flow b/taverna-commandline-tests/src/test/resources/workflows/localworker/localworker.t2flow
new file mode 100644
index 0000000..b3b2053
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/localworker/localworker.t2flow
@@ -0,0 +1,67 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="5eebce20-72f5-4ac7-a4bf-8086d59d0c9e" role="top"><name>Workflow5</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Concatenate_two_strings</name><inputPorts><port><name>string2</name><depth>0</depth></port><port><name>string1</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="string2" to="string2" /><map from="string1" to="string1" /></inputMap><outputMap><map f
rom="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
+ <script>output = string1 + string2;</script>
+ <dependencies />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>string1</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>string2</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>output</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="string2" depth="0" /><port name="string1" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>string1_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /
><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Hello </value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string2</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string1</port></sink><source type="processor"><processor>string1_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>C
oncatenate_two_strings</processor><port>output</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>5eebce20-72f5-4ac7-a4bf-8086d59d0c9e</identification>
+ </annotationBean>
+ <date>2011-02-21 13:44:43.621 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
[39/50] [abbrv] incubator-taverna-commandline git commit: travis
Posted by st...@apache.org.
travis
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/131ef3b8
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/131ef3b8
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/131ef3b8
Branch: refs/heads/master
Commit: 131ef3b868a9a7574618b251c9cde49d56bc74fe
Parents: 2404694
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 03:48:00 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 03:48:00 2014 -0600
----------------------------------------------------------------------
README.md | 3 +++
1 file changed, 3 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/131ef3b8/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..9adb847
--- /dev/null
+++ b/README.md
@@ -0,0 +1,3 @@
+# Apache Taverna Commandline
+
+[](https://travis-ci.org/taverna-incubator/incubator-taverna-commandline)
[42/50] [abbrv] incubator-taverna-commandline git commit: Include
com.sun.source.util/.tree as 'extra'
Posted by st...@apache.org.
Include com.sun.source.util/.tree as 'extra'
(from tools.jar of JDK)
Avoid taverna-interaction-activity as it is very broken
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/505d9472
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/505d9472
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/505d9472
Branch: refs/heads/master
Commit: 505d94728176b04e694d336e8f60eae2a9f5bb93
Parents: 622b212
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Jan 6 13:01:39 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Jan 6 13:01:39 2015 +0000
----------------------------------------------------------------------
taverna-commandline-product/pom.xml | 21 ++++++++++++++++-----
1 file changed, 16 insertions(+), 5 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/505d9472/taverna-commandline-product/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/pom.xml b/taverna-commandline-product/pom.xml
index fba41c5..41e73e6 100644
--- a/taverna-commandline-product/pom.xml
+++ b/taverna-commandline-product/pom.xml
@@ -100,7 +100,7 @@
</frameworkConfiguration>
<frameworkConfiguration>
<name>org.osgi.framework.system.packages.extra</name>
- <value>com.sun.org.apache.xml.internal.utils,org.apache.log4j;version=1.2.16,net.sf.taverna.t2.commandline.options;version=2.0.1</value>
+ <value>com.sun.org.apache.xml.internal.utils,com.sun.source.util,com.sun.source.tree,org.apache.log4j;version=1.2.16,net.sf.taverna.t2.commandline.options;version=2.0.1</value>
</frameworkConfiguration>
<frameworkConfiguration>
<name>org.osgi.framework.storage.clean</name>
@@ -293,11 +293,13 @@
<artifactId>taverna-external-tool-activity</artifactId>
<version>${taverna.commonactivities.version}</version>
</dependency>
+ <!-- VERY broken :(
<dependency>
<groupId>org.apache.taverna.commonactivities</groupId>
<artifactId>taverna-interaction-activity</artifactId>
<version>${taverna.commonactivities.version}</version>
</dependency>
+ -->
<dependency>
<groupId>org.apache.taverna.commonactivities</groupId>
<artifactId>taverna-rest-activity</artifactId>
@@ -442,13 +444,15 @@
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
- <version>1.7.5</version>
+ <version>${slf4j.version}</version>
</dependency>
- <!-- Appears unrequired dependency>
+
+ <!-- Appears unrequired: -->
+ <dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
- <version>1.7.5</version>
- </dependency-->
+ <version>${slf4j.version}</version>
+ </dependency>
<!-- Taverna Security -->
<dependency>
@@ -506,6 +510,13 @@
<artifactId>jackson-databind</artifactId>
<version>2.3.0</version>
</dependency>
+
+ <dependency>
+ <groupId>nu.validator.htmlparser</groupId>
+ <artifactId>htmlparser</artifactId>
+ <version>1.4</version>
+ </dependency>
+
</dependencies>
<repositories>
[14/50] [abbrv] incubator-taverna-commandline git commit: Remove
README.md and pom.xml
Posted by st...@apache.org.
Remove README.md and pom.xml
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/c8df45a8
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/c8df45a8
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/c8df45a8
Branch: refs/heads/master
Commit: c8df45a88451c1f6c92a43e7304a2dd6a2529423
Parents: 7b757cf
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 01:39:20 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 01:39:20 2014 -0600
----------------------------------------------------------------------
README.md | 3 ---
pom.xml | 47 -----------------------------------------------
2 files changed, 50 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/c8df45a8/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
deleted file mode 100644
index e617833..0000000
--- a/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-Taverna Workflow system Command Line Tool
-
-This code was previously hosted at http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.taverna-commandline/
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/c8df45a8/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
deleted file mode 100644
index 2c247d9..0000000
--- a/pom.xml
+++ /dev/null
@@ -1,47 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <artifactId>taverna-parent</artifactId>
- <groupId>net.sf.taverna</groupId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>net.sf.taverna.t2.taverna-commandline</groupId>
- <artifactId>taverna-commandline</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- <packaging>pom</packaging>
-
- <name>Taverna 2 Commandline</name>
- <scm>
- <connection>scm:svn:http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.infrastructure/trunk/</connection>
- <developerConnection>scm:svn:https://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.infrastructure/trunk/</developerConnection>
- <url>http://code.google.com/p/taverna/source/browse/#svn/taverna/engine/net.sf.taverna.t2.infrastructure/trunk</url>
- </scm>
-
- <modules>
- <module>taverna-commandline-common</module>
- <module>taverna-commandline-api</module>
- </modules>
-
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
-
-</project>
[31/50] [abbrv] incubator-taverna-commandline git commit: Merge
branch 'taverna3-command-line-tests'
Posted by st...@apache.org.
Merge branch 'taverna3-command-line-tests'
>From https://github.com/taverna/taverna3-command-line-tests master
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/0be1d89c
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/0be1d89c
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/0be1d89c
Branch: refs/heads/master
Commit: 0be1d89cf03d066977da0e84f39c628e91124f97
Parents: a8a1ad0 9601b2f
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 01:51:08 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 01:51:08 2014 -0600
----------------------------------------------------------------------
taverna-commandline-tests/pom.xml | 97 +++
.../commandline/TavernaCommandLineTest.java | 485 ++++++++++++++
.../taverna/commandline/WorkflowTestRunner.java | 70 ++
.../taverna/commandline/WorkflowTestSuite.java | 79 +++
.../biomartandembossanalysis.url | 1 +
.../biomartandembossanalysis/ignorePort | 1 +
.../biomoby_tutorial_workflow.url | 1 +
.../biomoby_tutorial_workflow/ignorePort | 1 +
.../biomoby_tutorial_workflow/inputs/id | 1 +
.../biomoby_tutorial_workflow/inputs/namespace | 1 +
.../demonstration_of_configurable_iteration.url | 1 +
.../ebi_interproscan_newservices.url | 1 +
.../ebi_interproscan_newservices/ignorePort | 1 +
.../ebi_interproscan_newservices/inputs/email | 1 +
.../inputs/sequence | 8 +
.../example_of_conditional_invocation.url | 1 +
.../inputs/condition | 1 +
.../example_of_explicit_looping.url | 1 +
.../example_of_explicit_looping/inputs/end | 1 +
.../example_of_explicit_looping/inputs/start | 1 +
.../example_of_explicit_looping/inputs/step | 1 +
...e_workflow_for_rest_and_xpath_activities.url | 1 +
.../Name_Of_Location_for_Weather_Forecast | 1 +
.../fetch_dragon_images_from_biomoby.url | 1 +
.../fetch_pdb_flatfile_from_rcsb_server.url | 1 +
.../inputs/pdbID | 1 +
.../fetch_today_s_xkcd_comic.url | 1 +
.../myexperiment/gbseq_test/gbseq_test.url | 1 +
.../myexperiment/hello_anyone/hello_anyone.url | 1 +
.../myexperiment/hello_anyone/inputs/name | 1 +
.../myexperiment/hello_world/hello_world.url | 1 +
.../pipelined_list_iteration/inputs/input | 1 +
.../pipelined_list_iteration.url | 1 +
.../retrieve_sequence_in_embl_format.url | 1 +
.../secure_rest_service_call_example.url | 1 +
.../secure_web_service_call_example.url | 1 +
.../spreadsheed_data_import_example.url | 1 +
.../unix_external_tools_with_zip_and_unzip.url | 1 +
.../unix_numerically_adding_two_values/inputs/a | 1 +
.../unix_numerically_adding_two_values/inputs/b | 1 +
.../unix_numerically_adding_two_values.url | 1 +
...ix_tool_service_using_string_replacement.url | 1 +
.../src/test/resources/security/t2keystore.ubr | Bin 0 -> 3312 bytes
.../test/resources/security/t2truststore.ubr | Bin 0 -> 213408 bytes
.../resources/security/taverna-keystore.ubr | Bin 0 -> 3312 bytes
.../resources/security/taverna-truststore.ubr | Bin 0 -> 213408 bytes
.../workflows/apiconsumer/apiconsumer.t2flow | 178 +++++
.../resources/workflows/apiconsumer/inputs/in | 1 +
.../workflows/beanshell/beanshell.t2flow | 137 ++++
.../resources/workflows/beanshell/inputs/in | 1 +
.../resources/workflows/biomart/biomart.t2flow | 30 +
.../workflows/dataflow/dataflow.t2flow | 217 +++++++
.../test/resources/workflows/dataflow/inputs/in | 1 +
.../resources/workflows/in-out/in-out.t2flow | 12 +
.../test/resources/workflows/in-out/inputs/in | 1 +
.../resources/workflows/iteration/inputs/in | 1 +
.../workflows/iteration/iteration.t2flow | 474 ++++++++++++++
.../resources/workflows/localworker/inputs/in | 1 +
.../workflows/localworker/localworker.t2flow | 67 ++
.../test/resources/workflows/rest/rest.t2flow | 154 +++++
.../secure-basic-authentication-https.t2flow | 74 +++
.../secure-basic-authentication.t2flow | 74 +++
...cure-client-cert-authentication-https.t2flow | 162 +++++
.../secure-digest-authentication-https.t2flow | 107 +++
.../secure-digest-authentication.t2flow | 129 ++++
.../secure-ws-https/secure-ws-https.t2flow | 180 ++++++
.../workflows/secure-ws/secure-ws.t2flow | 180 ++++++
.../workflows/secure-wsdl/secure-wsdl.t2flow | 131 ++++
.../resources/workflows/soaplab/soaplab.t2flow | 84 +++
.../spreadsheetimport/spreadsheetimport.t2flow | 646 +++++++++++++++++++
.../stringconstant/stringconstant.t2flow | 32 +
.../test/resources/workflows/tool/tool.t2flow | 158 +++++
.../test/resources/workflows/wsdl/wsdl.t2flow | 22 +
.../resources/workflows/xmlSplitter/inputs/age | 1 +
.../workflows/xmlSplitter/inputs/firstName | 1 +
.../workflows/xmlSplitter/inputs/lastName | 1 +
.../workflows/xmlSplitter/xmlSplitter.t2flow | 339 ++++++++++
.../test/resources/workflows/xpath/xpath.t2flow | 127 ++++
78 files changed, 4499 insertions(+)
----------------------------------------------------------------------
[15/50] [abbrv] incubator-taverna-commandline git commit: Merge
branch 'taverna-commandline'
Posted by st...@apache.org.
Merge branch 'taverna-commandline'
>From https://github.com/taverna/taverna-commandline master
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/5eed8ca3
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/5eed8ca3
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/5eed8ca3
Branch: refs/heads/master
Commit: 5eed8ca33025cf7c3acaaecc341028eb1b3112f1
Parents: daa2471 c8df45a
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 01:39:36 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 01:39:36 2014 -0600
----------------------------------------------------------------------
.gitignore | 24 +
.travis.yml | 1 +
taverna-commandline-api/pom.xml | 32 ++
.../exceptions/ArgumentsParsingException.java | 34 ++
.../CommandLineMasterPasswordException.java | 34 ++
.../DatabaseConfigurationException.java | 43 ++
.../exceptions/InputMismatchException.java | 61 +++
.../exceptions/InvalidOptionException.java | 30 ++
.../exceptions/OpenDataflowException.java | 44 ++
.../exceptions/ReadInputException.java | 35 ++
.../exceptions/SaveResultsException.java | 34 ++
.../commandline/options/CommandLineOptions.java | 119 +++++
taverna-commandline-common/pom.xml | 109 +++++
.../CommandLineMasterPasswordProvider.java | 184 ++++++++
.../taverna/t2/commandline/CommandLineTool.java | 437 +++++++++++++++++++
.../data/DatabaseConfigurationHandler.java | 154 +++++++
.../t2/commandline/data/ErrorValueHandler.java | 72 +++
.../t2/commandline/data/InputsHandler.java | 280 ++++++++++++
.../t2/commandline/data/SaveResultsHandler.java | 87 ++++
.../taverna-commandline-common-context-osgi.xml | 22 +
.../taverna-commandline-common-context.xml | 21 +
.../main/resources/database-defaults.properties | 11 +
.../src/main/resources/help.txt | 87 ++++
.../TestDatabaseConfigurationHandler.java | 21 +
24 files changed, 1976 insertions(+)
----------------------------------------------------------------------
[04/50] [abbrv] incubator-taverna-commandline git commit: The CLT
doesn't do anything with the provenance connector.
Posted by st...@apache.org.
The CLT doesn't do anything with the provenance connector.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/f0da0392
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/f0da0392
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/f0da0392
Branch: refs/heads/master
Commit: f0da0392c12b4e2daf23fe526ed283d22ae6575a
Parents: 265416c
Author: Donal Fellows <do...@manchester.ac.uk>
Authored: Mon Sep 15 13:29:08 2014 +0100
Committer: Donal Fellows <do...@manchester.ac.uk>
Committed: Mon Sep 15 13:29:08 2014 +0100
----------------------------------------------------------------------
taverna-commandline-common/pom.xml | 8 +-
.../taverna/t2/commandline/CommandLineTool.java | 134 +++++++------------
.../taverna-commandline-common-context-osgi.xml | 2 -
.../taverna-commandline-common-context.xml | 1 -
4 files changed, 56 insertions(+), 89 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/f0da0392/taverna-commandline-common/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/pom.xml b/taverna-commandline-common/pom.xml
index b2f4e93..b904931 100644
--- a/taverna-commandline-common/pom.xml
+++ b/taverna-commandline-common/pom.xml
@@ -53,11 +53,13 @@
<version>${taverna.databundle.version}</version>
</dependency>
+<!--
<dependency>
<groupId>net.sf.taverna.t2.core</groupId>
<artifactId>provenanceconnector</artifactId>
<version>${t2.core.provenanceconnector.version}</version>
</dependency>
+ -->
<dependency>
<groupId>net.sf.taverna.t2.security</groupId>
<artifactId>credential-manager</artifactId>
@@ -65,9 +67,9 @@
</dependency>
<dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <version>${commons.io.version}</version>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>com.springsource.org.apache.commons.io</artifactId>
+ <version>${commons.io.version}</version>
</dependency>
<!-- <dependency> <groupId>uk.org.mygrid.resources.mimeutil</groupId> <artifactId>mime-util</artifactId>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/f0da0392/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
index b32cb10..9d8c5fc 100644
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
@@ -28,7 +28,6 @@ import java.net.URL;
import java.nio.file.Path;
import java.sql.SQLException;
import java.util.HashMap;
-import java.util.List;
import java.util.Map;
import java.util.Set;
@@ -43,7 +42,6 @@ import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
import net.sf.taverna.t2.commandline.exceptions.OpenDataflowException;
import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-import net.sf.taverna.t2.provenance.ProvenanceConnectorFactory;
import net.sf.taverna.t2.security.credentialmanager.CMException;
import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
@@ -89,57 +87,39 @@ import uk.org.taverna.scufl2.validation.structural.StructuralValidator;
* @author Alex Nenadic
*/
public class CommandLineTool {
-
+ private static boolean BOOTSTRAP_LOGGING = false;
private static Logger logger = Logger.getLogger(CommandLineTool.class);
private RunService runService;
-
private CredentialManager credentialManager;
-
private CommandLineOptions commandLineOptions;
-
private WorkflowBundle workflowBundle;
-
private WorkflowBundleIO workflowBundleIO;
-
private DatabaseConfiguration databaseConfiguration;
-
private DatabaseManager databaseManager;
- private List<ProvenanceConnectorFactory> provenanceConnectorFactories;
-
public void run() {
try {
-// initialiseLogging();
+ if (BOOTSTRAP_LOGGING)
+ initialiseLogging();
int result = setupAndExecute();
System.exit(result);
- } catch (InvalidOptionException e) { // thrown by CommandLineOptions
- error(e.getMessage());
- } catch (IOException e) {
- error(e.getMessage());
- } catch (ReadInputException e) {
- error(e.getMessage());
- } catch (InvalidRunIdException e) {
- error(e.getMessage());
- } catch (RunStateException e) {
- error(e.getMessage());
- } catch (InvalidExecutionIdException e) {
+ } catch (InvalidOptionException | IOException | ReadInputException
+ | InvalidRunIdException | RunStateException
+ | InvalidExecutionIdException | OpenDataflowException
+ | RunProfileException e) {
error(e.getMessage());
} catch (CMException e) {
error("There was an error initializing Taverna's SSLSocketFactory from Credential Manager. "
+ e.getMessage());
- } catch (OpenDataflowException e) {
- error(e.getMessage());
} catch (ReaderException e) {
error("There was an error reading the workflow: " + e.getMessage());
} catch (ValidationException e) {
error("There was an error validating the workflow: " + e.getMessage());
} catch (InvalidWorkflowException e) {
error("There was an error validating the workflow: " + e.getMessage());
- } catch (RunProfileException e) {
- error(e.getMessage());
} catch (DatabaseConfigurationException e) {
- error("There was an error configuring thre database: " + e.getMessage());
+ error("There was an error configuring the database: " + e.getMessage());
}
System.exit(1);
}
@@ -190,18 +170,22 @@ public class CommandLineTool {
setupDatabase(commandLineOptions);
if (commandLineOptions.getWorkflow() != null) {
-
- // Initialise Credential Manager and SSL stuff quite early as parsing and
- // validating the workflow may require it
+ /*
+ * Initialise Credential Manager and SSL stuff quite early as
+ * parsing and validating the workflow may require it
+ */
String credentialManagerDirPath = commandLineOptions.getCredentialManagerDir();
- // If credentialManagerDirPath is null - Credential Manager will
- // be initialized from the default location in <TAVERNA_HOME>/security
- // somewhere inside user's home directory. This should not be used when
- // running command line tool on a server and the Credential Manager dir path
- // should always be passed in as we do not want to store the security files in
- // user's home directory on the server (we do not even know which user the command
- // line tool will be running as).
+ /*
+ * If credentialManagerDirPath is null, the Credential Manager
+ * will be initialized from the default location in
+ * <TAVERNA_HOME>/security somewhere inside user's home
+ * directory. This should not be used when running command line
+ * tool on a server and the Credential Manager dir path should
+ * always be passed in as we do not want to store the security
+ * files in user's home directory on the server (we do not even
+ * know which user the command line tool will be running as).
+ */
if (credentialManagerDirPath != null) {
credentialManager.setConfigurationDirectoryPath(new File(
credentialManagerDirPath));
@@ -226,8 +210,11 @@ public class CommandLineTool {
ExecutionEnvironment executionEnvironment = null;
- // Find the right execution environment, e.g. local execution with the correct
- // reference service based on command line options
+ /*
+ * Find the right execution environment, e.g. local execution
+ * with the correct reference service based on command line
+ * options
+ */
while (executionEnvironments.iterator().hasNext()) {
// TODO Choose the right one
// take the fist one for now
@@ -279,9 +266,9 @@ public class CommandLineTool {
Path outputs = DataBundles.getOutputs(runService.getDataBundle(runId));
- SaveResultsHandler saveResultsHandler = new SaveResultsHandler(outputDir);
-
if (outputDir != null) {
+ SaveResultsHandler saveResultsHandler = new SaveResultsHandler(outputDir);
+
for (OutputWorkflowPort outputWorkflowPort : workflowOutputPorts) {
String workflowOutputPortName = outputWorkflowPort.getName();
Path output = DataBundles.getPort(outputs, workflowOutputPortName);
@@ -328,7 +315,6 @@ public class CommandLineTool {
}
protected void validateWorkflowBundle(WorkflowBundle workflowBundle) throws ValidationException {
-
CorrectnessValidator cv = new CorrectnessValidator();
ReportCorrectnessValidationListener rcvl = new ReportCorrectnessValidationListener();
cv.checkCorrectness(workflowBundle, true, rcvl);
@@ -349,41 +335,34 @@ public class CommandLineTool {
DatabaseConfigurationHandler dbHandler = new DatabaseConfigurationHandler(
options, databaseConfiguration, databaseManager);
dbHandler.configureDatabase();
- if (!options.isInMemory()) {
- try {
+ try {
+ if (!options.isInMemory())
dbHandler.testDatabaseConnection();
- } catch (NamingException e) {
+ } catch (NamingException e) {
+ throw new DatabaseConfigurationException(
+ "There was an error trying to setup the database datasource: "
+ + e.getMessage(), e);
+ } catch (SQLException e) {
+ if (options.isClientServer())
throw new DatabaseConfigurationException(
- "There was an error trying to setup the database datasource: "
- + e.getMessage(), e);
- } catch (SQLException e) {
- if (options.isClientServer()) {
- throw new DatabaseConfigurationException(
- "There was an error whilst making a test database connection. If running with -clientserver you should check that a server is running (check -startdb or -dbproperties)",
- e);
- }
- if (options.isEmbedded()) {
- throw new DatabaseConfigurationException(
- "There was an error whilst making a test database connection. If running with -embedded you should make sure that another process isn't using the database, or a server running through -startdb",
- e);
- }
- }
+ "There was an error whilst making a test database connection. If running with -clientserver you should check that a server is running (check -startdb or -dbproperties)",
+ e);
+ if (options.isEmbedded())
+ throw new DatabaseConfigurationException(
+ "There was an error whilst making a test database connection. If running with -embedded you should make sure that another process isn't using the database, or a server running through -startdb",
+ e);
}
-
}
private File determineOutputDir(CommandLineOptions options, String dataflowName) {
- File result = null;
- result = new File(dataflowName + "_output");
- int x = 1;
- while (result.exists()) {
- result = new File(dataflowName + "_output_" + x);
- x++;
- }
- if (result != null) {
- System.out.println("Outputs will be saved to the directory: "
- + result.getAbsolutePath());
+ File result = new File(dataflowName + "_output");
+ int x = 1;
+ while (result.exists()) {
+ result = new File(dataflowName + "_output_" + x);
+ x++;
}
+ System.out.println("Outputs will be saved to the directory: "
+ + result.getAbsolutePath());
return result;
}
@@ -392,10 +371,8 @@ public class CommandLineTool {
}
private URL readWorkflowURL(String workflowOption) throws OpenDataflowException {
- URL url;
try {
- url = new URL("file:");
- return new URL(url, workflowOption);
+ return new URL(new URL("file:"), workflowOption);
} catch (MalformedURLException e) {
throw new OpenDataflowException("The was an error processing the URL to the workflow: "
+ e.getMessage(), e);
@@ -428,15 +405,6 @@ public class CommandLineTool {
}
/**
- * Sets the provenanceConnectorFactories.
- *
- * @param provenanceConnectorFactories the new value of provenanceConnectorFactories
- */
- public void setProvenanceConnectorFactories(List<ProvenanceConnectorFactory> provenanceConnectorFactories) {
- this.provenanceConnectorFactories = provenanceConnectorFactories;
- }
-
- /**
* Sets the databaseManager.
*
* @param databaseManager the new value of databaseManager
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/f0da0392/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context-osgi.xml b/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context-osgi.xml
index 60e32f8..e7ae701 100644
--- a/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context-osgi.xml
+++ b/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context-osgi.xml
@@ -19,6 +19,4 @@
<reference id="t2flowWorkflowBundleReader" interface="uk.org.taverna.scufl2.api.io.WorkflowBundleReader" filter="(mediaType=application/vnd.taverna.t2flow+xml)"/>
<reference id="rdfXMLWorkflowBundleReader" interface="uk.org.taverna.scufl2.api.io.WorkflowBundleReader" filter="(org.springframework.osgi.bean.name=rdfXMLReader)"/>
- <list id="provenanceConnectorFactories" interface="net.sf.taverna.t2.provenance.ProvenanceConnectorFactory" cardinality="0..N"/>
-
</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/f0da0392/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context.xml b/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context.xml
index 977c21d..52c0f29 100644
--- a/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context.xml
+++ b/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context.xml
@@ -11,7 +11,6 @@
<property name="workflowBundleIO" ref="workflowBundleIO" />
<property name="databaseConfiguration" ref="databaseConfiguration" />
<property name="databaseManager" ref="databaseManager" />
- <property name="provenanceConnectorFactories" ref="provenanceConnectorFactories" />
</bean>
<bean id="commandLineMasterPasswordProvider"
[21/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-tests/
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/rest/rest.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/rest/rest.t2flow b/taverna-commandline-tests/src/test/resources/workflows/rest/rest.t2flow
new file mode 100644
index 0000000..f3f90b8
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/rest/rest.t2flow
@@ -0,0 +1,154 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="8e36176a-2975-498b-93f7-f2beba774532" role="top"><name>Workflow11</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>REST_Service</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
+ <httpMethod>GET</httpMethod>
+ <urlSignature>http://www.uniprot.org/uniprot/{id}.xml</urlSignature>
+ <acceptsHeaderValue>text/plain</acceptsHeaderValue>
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>
+ <outgoingDataFormat>String</outgoingDataFormat>
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>
+ <escapeParameters>true</escapeParameters>
+ <otherHTTPHeaders />
+ <activityInputs>
+ <entry>
+ <string>id</string>
+ <java-class>java.lang.String</java-class>
+ </entry>
+ </activityInputs>
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>id_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" />
</outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>P12345</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>REST_Service</processor><port>id</port></sink><source type="processor"><processor>id_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>REST_Service</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xm
lns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>30c58a3d-4037-4b92-b7d6-3aea761bdada</identification>
+ </annotationBean>
+ <date>2011-11-02 08:52:32.796 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>d090ff3c-c84d-461f-9027-ccd07fe0a352</identification>
+ </annotationBean>
+ <date>2011-11-02 10:09:35.558 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>1e2069a6-54c3-4e09-b639-c9bb27356eb9</identification>
+ </annotationBean>
+ <date>2011-11-02 09:59:38.235 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>f88604da-4047-4ab9-bd19-23cbbb8be88b</identification>
+ </annotationBean>
+ <date>2011-11-02 10:12:00.757 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>8e36176a-2975-498b-93f7-f2beba774532</identification>
+ </annotationBean>
+ <date>2012-02-10 15:56:15.960 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b3887d66-e945-444d-820a-ddb5c1d6cecb</identification>
+ </annotationBean>
+ <date>2011-11-02 10:00:26.717 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>bbf68124-dbeb-482b-80c6-e461d264a98b</identification>
+ </annotationBean>
+ <date>2011-11-02 10:12:59.372 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>c2802c60-cc0e-4bc0-b401-473476811e46</identification>
+ </annotationBean>
+ <date>2011-11-02 10:02:16.255 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>d73137e0-8cfb-4536-849e-6d30b1b1f4dc</identification>
+ </annotationBean>
+ <date>2011-11-02 08:49:30.655 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>3f67a647-2d0e-4d7e-9937-5bde3d562fde</identification>
+ </annotationBean>
+ <date>2011-11-02 10:10:29.316 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>f76689f8-2629-4168-b0a6-e70c88acaca9</identification>
+ </annotationBean>
+ <date>2012-02-10 15:49:11.156 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication-https/secure-basic-authentication-https.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication-https/secure-basic-authentication-https.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication-https/secure-basic-authentication-https.t2flow
new file mode 100644
index 0000000..0cbff10
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication-https/secure-basic-authentication-https.t2flow
@@ -0,0 +1,74 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="12203b36-f878-45f7-a16e-863e1bbc81b8" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Basic_AuthN_and_HTTPS</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
+ <httpMethod>GET</httpMethod>
+ <urlSignature>https://heater.cs.man.ac.uk:7443/examples-basic-authentication/taverna-test-page.html</urlSignature>
+ <acceptsHeaderValue>text/plain</acceptsHeaderValue>
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>
+ <outgoingDataFormat>String</outgoingDataFormat>
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>
+ <escapeParameters>true</escapeParameters>
+ <otherHTTPHeaders />
+ <activityInputs />
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Basic_AuthN_and_HTTPS</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>adb25995-c890-40c7-b091-2c2512024864</identification>
+ </annotationBean>
+ <date>2010-11-29 10:35:54.270 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>12203b36-f878-45f7-a16e-863e1bbc81b8</identification>
+ </annotationBean>
+ <date>2010-11-29 15:35:51.711 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
+ </annotationBean>
+ <date>2010-11-22 14:15:20.380 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:43.484 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>388333c0-fd34-4571-ab0c-f67c10c2ed64</identification>
+ </annotationBean>
+ <date>2010-11-22 14:21:12.760 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication/secure-basic-authentication.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication/secure-basic-authentication.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication/secure-basic-authentication.t2flow
new file mode 100644
index 0000000..998b69a
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-basic-authentication/secure-basic-authentication.t2flow
@@ -0,0 +1,74 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="6eca35ba-d7d4-43d9-8593-93eba828cc46" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Basic_AuthN</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
+ <httpMethod>GET</httpMethod>
+ <urlSignature>http://heater.cs.man.ac.uk:7070/examples-basic-authentication/taverna-test-page.html</urlSignature>
+ <acceptsHeaderValue>text/plain</acceptsHeaderValue>
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>
+ <outgoingDataFormat>String</outgoingDataFormat>
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>
+ <escapeParameters>true</escapeParameters>
+ <otherHTTPHeaders />
+ <activityInputs />
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Basic_AuthN</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
+ </annotationBean>
+ <date>2010-11-22 14:15:20.380 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>6eca35ba-d7d4-43d9-8593-93eba828cc46</identification>
+ </annotationBean>
+ <date>2010-11-29 10:41:02.602 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>adb25995-c890-40c7-b091-2c2512024864</identification>
+ </annotationBean>
+ <date>2010-11-29 10:35:54.270 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:43.484 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>388333c0-fd34-4571-ab0c-f67c10c2ed64</identification>
+ </annotationBean>
+ <date>2010-11-22 14:21:12.760 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/secure-client-cert-authentication-https/secure-client-cert-authentication-https.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-client-cert-authentication-https/secure-client-cert-authentication-https.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-client-cert-authentication-https/secure-client-cert-authentication-https.t2flow
new file mode 100644
index 0000000..1c5d317
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-client-cert-authentication-https/secure-client-cert-authentication-https.t2flow
@@ -0,0 +1,162 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="b982dcd5-dc2a-4fc5-b6dd-8d0b90a2f58e" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Client_Cert_AuthN_and_HTTPS</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
+ <httpMethod>GET</httpMethod>
+ <urlSignature>https://heater.cs.man.ac.uk:7444/examples-client-cert-authentication/taverna-test-page.html</urlSignature>
+ <acceptsHeaderValue>text/plain</acceptsHeaderValue>
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>
+ <outgoingDataFormat>String</outgoingDataFormat>
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>
+ <escapeParameters>true</escapeParameters>
+ <otherHTTPHeaders />
+ <activityInputs />
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Client_Cert_AuthN_and_HTTPS</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b982dcd5-dc2a-4fc5-b6dd-8d0b90a2f58e</identification>
+ </annotationBean>
+ <date>2011-06-23 11:14:45.626 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>23616693-e035-42e5-a52e-e1ddb0269d9c</identification>
+ </annotationBean>
+ <date>2011-06-21 15:49:05.979 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>47ad844e-df8e-4c65-803a-8a20c8197e8e</identification>
+ </annotationBean>
+ <date>2010-11-29 15:36:29.390 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>1f90ea89-a32f-41c1-b30c-2a5afd622984</identification>
+ </annotationBean>
+ <date>2010-11-22 14:20:41.517 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>e7fb38b1-b3ec-4c47-a584-36c68eeda25e</identification>
+ </annotationBean>
+ <date>2010-11-22 14:19:49.664 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
+ </annotationBean>
+ <date>2010-11-22 14:15:20.380 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eaff435f-9025-429b-9a12-97fc94d90e73</identification>
+ </annotationBean>
+ <date>2010-11-22 14:18:46.551 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:43.484 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>5b302294-d370-4639-acb1-2a8452cc6d92</identification>
+ </annotationBean>
+ <date>2010-11-29 10:34:55.185 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>d9be6132-9d40-43f6-bd0b-8d29dca1163b</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:58.860 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>18b60848-4715-4532-b50c-45539ca00b44</identification>
+ </annotationBean>
+ <date>2011-06-21 16:24:23.704 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b982dcd5-dc2a-4fc5-b6dd-8d0b90a2f58e</identification>
+ </annotationBean>
+ <date>2011-06-21 16:36:50.208 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>06a9fa6d-ba8d-4045-945b-a4a259a275e4</identification>
+ </annotationBean>
+ <date>2011-06-23 11:13:58.558 BST</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication-https/secure-digest-authentication-https.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication-https/secure-digest-authentication-https.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication-https/secure-digest-authentication-https.t2flow
new file mode 100644
index 0000000..5d2f893
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication-https/secure-digest-authentication-https.t2flow
@@ -0,0 +1,107 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="47ad844e-df8e-4c65-803a-8a20c8197e8e" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Digest_AuthN_and_HTTPS</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
+ <httpMethod>GET</httpMethod>
+ <urlSignature>https://heater.cs.man.ac.uk:7443/examples-digest-authentication/taverna-test-page.html</urlSignature>
+ <acceptsHeaderValue>text/plain</acceptsHeaderValue>
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>
+ <outgoingDataFormat>String</outgoingDataFormat>
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>
+ <escapeParameters>true</escapeParameters>
+ <otherHTTPHeaders />
+ <activityInputs />
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Digest_AuthN_and_HTTPS</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:43.484 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eaff435f-9025-429b-9a12-97fc94d90e73</identification>
+ </annotationBean>
+ <date>2010-11-22 14:18:46.551 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>d9be6132-9d40-43f6-bd0b-8d29dca1163b</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:58.860 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>1f90ea89-a32f-41c1-b30c-2a5afd622984</identification>
+ </annotationBean>
+ <date>2010-11-22 14:20:41.517 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>e7fb38b1-b3ec-4c47-a584-36c68eeda25e</identification>
+ </annotationBean>
+ <date>2010-11-22 14:19:49.664 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>5b302294-d370-4639-acb1-2a8452cc6d92</identification>
+ </annotationBean>
+ <date>2010-11-29 10:34:55.185 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
+ </annotationBean>
+ <date>2010-11-22 14:15:20.380 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>47ad844e-df8e-4c65-803a-8a20c8197e8e</identification>
+ </annotationBean>
+ <date>2010-11-29 15:36:29.390 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication/secure-digest-authentication.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication/secure-digest-authentication.t2flow b/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication/secure-digest-authentication.t2flow
new file mode 100644
index 0000000..449e9db
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/secure-digest-authentication/secure-digest-authentication.t2flow
@@ -0,0 +1,129 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3-SNAPSHOT-20110621T1150"><dataflow id="a218f0b5-b675-4eed-b7a8-a5c63181ff3e" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Service_protected_with_Digest_AuthN</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
+ <httpMethod>GET</httpMethod>
+ <urlSignature>http://heater.cs.man.ac.uk:7070/examples-digest-authentication/taverna-test-page.html</urlSignature>
+ <acceptsHeaderValue>text/plain</acceptsHeaderValue>
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>
+ <outgoingDataFormat>String</outgoingDataFormat>
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>
+ <escapeParameters>true</escapeParameters>
+ <otherHTTPHeaders />
+ <activityInputs />
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch
.layers.RetryConfig xmlns="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3-SNAPSHOT</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Service_protected_with_Digest_AuthN</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>b7887959-6d6c-4466-8d15-16b4e20051db</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:43.484 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>d9be6132-9d40-43f6-bd0b-8d29dca1163b</identification>
+ </annotationBean>
+ <date>2010-11-22 14:16:58.860 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>837b1710-ff29-4eef-85a0-51fc76139364</identification>
+ </annotationBean>
+ <date>2010-11-22 14:15:20.380 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>1f90ea89-a32f-41c1-b30c-2a5afd622984</identification>
+ </annotationBean>
+ <date>2010-11-22 14:20:41.517 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>e7fb38b1-b3ec-4c47-a584-36c68eeda25e</identification>
+ </annotationBean>
+ <date>2010-11-22 14:19:49.664 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eaff435f-9025-429b-9a12-97fc94d90e73</identification>
+ </annotationBean>
+ <date>2010-11-22 14:18:46.551 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>5b302294-d370-4639-acb1-2a8452cc6d92</identification>
+ </annotationBean>
+ <date>2010-11-29 10:34:55.185 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>fd59d61c-50f8-457b-a183-c162453b026b</identification>
+ </annotationBean>
+ <date>2010-11-29 15:29:08.570 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>435023d5-0063-4914-ae4c-28a7a031ec0d</identification>
+ </annotationBean>
+ <date>2010-11-29 10:40:30.468 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>a218f0b5-b675-4eed-b7a8-a5c63181ff3e</identification>
+ </annotationBean>
+ <date>2010-11-29 15:39:35.589 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
[17/50] [abbrv] incubator-taverna-commandline git commit: Merge
branch 'taverna3-command-line'
Posted by st...@apache.org.
Merge branch 'taverna3-command-line'
>From https://github.com/taverna/taverna3-command-line/ master
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/a8a1ad07
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/a8a1ad07
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/a8a1ad07
Branch: refs/heads/master
Commit: a8a1ad07ec2984a9c0437f3810f4b6bb58df56c9
Parents: 5eed8ca a8e6b3e
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 01:45:07 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 01:45:07 2014 -0600
----------------------------------------------------------------------
taverna-commandline-launcher/pom.xml | 96 ++++
.../commandline/CommandLineOptionsImpl.java | 445 +++++++++++++++++++
.../taverna/commandline/TavernaCommandLine.java | 139 ++++++
.../src/main/resources/help.txt | 87 ++++
.../TestCommandLineOptionsHandler.java | 267 +++++++++++
5 files changed, 1034 insertions(+)
----------------------------------------------------------------------
[12/50] [abbrv] incubator-taverna-commandline git commit: Use newer
jena-bundle for JSONLD-support
Posted by st...@apache.org.
Use newer jena-bundle for JSONLD-support
>From https://github.com/stain/jena/tree/jena-osgi-bundle
until https://github.com/stain/jena/tree/jena-osgi-bundle
is accepted.
Deployed on http://repository.mygrid.org.uk/
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/38c342d0
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/38c342d0
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/38c342d0
Branch: refs/heads/master
Commit: 38c342d0e3865ed42abd80e5ecc35bb1062af7a1
Parents: 2a17db5
Author: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Authored: Tue Oct 28 22:31:37 2014 +0000
Committer: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Committed: Tue Oct 28 22:31:37 2014 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/38c342d0/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 8393a90..d67a916 100644
--- a/pom.xml
+++ b/pom.xml
@@ -462,7 +462,7 @@
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-bundle</artifactId>
- <version>2.11.0-SNAPSHOT</version>
+ <version>2.12.2-SNAPSHOT</version>
</dependency>
<!-- slf4j implementation -->
<!-- The bundle "org.purl.wf4ever.robundle_0.3.1 " could not be resolved. Reason: Missing Constraint: Import-Package: org.slf4j; version="[1.7.0,2.0.0)"-->
[03/50] [abbrv] incubator-taverna-commandline git commit: Removed
hardcode versions where used elsewhere for T3-1195
Posted by st...@apache.org.
Removed hardcode versions where used elsewhere for T3-1195
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/b8b3fe2a
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/b8b3fe2a
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/b8b3fe2a
Branch: refs/heads/master
Commit: b8b3fe2adf4bcc613e0747158769210c6b1dea99
Parents: 33aae45
Author: Christian-B <br...@cs.man.ac.uk>
Authored: Thu Jul 3 11:25:15 2014 +0100
Committer: Christian-B <br...@cs.man.ac.uk>
Committed: Thu Jul 3 11:25:15 2014 +0100
----------------------------------------------------------------------
pom.xml | 48 ++++++++++++++++++++++++++++--------------------
1 file changed, 28 insertions(+), 20 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/b8b3fe2a/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 622ff18..e0309df 100644
--- a/pom.xml
+++ b/pom.xml
@@ -162,20 +162,21 @@
<dependency>
<groupId>org.osgi</groupId>
<artifactId>org.osgi.core</artifactId>
- <version>4.3.1</version>
+ <version>${osgi.core.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.osgi</groupId>
<artifactId>org.osgi.compendium</artifactId>
- <version>4.3.1</version>
+ <version>${osgi.core.version}</version>
<scope>provided</scope>
</dependency>
+ <!-- Invalid manifest header Import-Package: "com.sun.jdmk.comm;resolution:="optional"" : Cannot import a package more than once "com.sun.jdmk.comm"-->
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
- <version>1.2.17</version>
+ <version>${log4j.version}</version>
<scope>provided</scope>
</dependency>
@@ -183,7 +184,7 @@
<dependency>
<groupId>net.sourceforge.cglib</groupId>
<artifactId>com.springsource.net.sf.cglib</artifactId>
- <version>2.1.3</version>
+ <version>${cglib.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.osgi</groupId>
@@ -203,31 +204,35 @@
</dependency>
<!-- Java Extension Implementations -->
- <dependency>
+ <!-- Appears unrequired dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>com.springsource.javax.xml.bind</artifactId>
<version>2.2.0</version>
- </dependency>
+ </dependency-->
<dependency>
<groupId>javax.activation</groupId>
<artifactId>com.springsource.javax.activation</artifactId>
- <version>1.1.1</version>
+ <version>${activation.version}</version>
</dependency>
- <dependency> <!-- required by bsh -->
- <groupId>javax.servlet</groupId>
+ <!-- The bundle "com.springsource.bsh_2.0.0.b4 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.servlet; version="[2.5.0,3.0.0)" -->
+ <dependency>
+ <groupId>javax.servlet</groupId>
<artifactId>com.springsource.javax.servlet</artifactId>
<version>2.5.0</version>
</dependency>
+ <!-- The bundle "com.springsource.org.apache.axis_1.4.0 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.jms; version="[1.1.0,2.0.0)" -->
<dependency>
<groupId>javax.jms</groupId>
<artifactId>com.springsource.javax.jms</artifactId>
<version>1.1.0</version>
</dependency>
+ <!-- The bundle "com.springsource.javax.xml.rpc_1.1.0 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.xml.soap; version="[1.3.0,2.0.0)" -->
<dependency>
<groupId>javax.xml.soap</groupId>
<artifactId>com.springsource.javax.xml.soap</artifactId>
<version>1.3.0</version>
</dependency>
+ <!-- The bundle "com.springsource.com.thoughtworks.xstream_1.4.1" could not be resolved. Reason: Missing Constraint: Import-Package: javax.xml.stream; version="[1.0.1,2.0.0)" -->
<dependency>
<groupId>javax.xml.stream</groupId>
<artifactId>com.springsource.javax.xml.stream</artifactId>
@@ -248,23 +253,24 @@
<dependency>
<groupId>uk.org.taverna.osgi.services</groupId>
<artifactId>xml-parser-service</artifactId>
- <version>0.1.1</version>
+ <version>${osgi.services.version}</version>
</dependency>
<dependency>
<groupId>uk.org.taverna.osgi.services</groupId>
<artifactId>xml-transformer-service</artifactId>
- <version>0.1.1</version>
+ <version>${osgi.services.version}</version>
</dependency>
+ <!-- The bundle "uk.org.taverna.commons.taverna-plugin-impl_0.1.0.SNAPSHOT" could not be resolved. Reason: Missing Constraint: Import-Package: org.osgi.service.event; version="[1.3.0,2.0.0)" -->
<dependency>
<groupId>org.apache.felix</groupId>
<artifactId>org.apache.felix.eventadmin</artifactId>
<version>1.3.2</version>
</dependency>
- <dependency>
+ <!-- Appears unrequired dependency>
<groupId>org.apache.felix</groupId>
<artifactId>org.apache.felix.configadmin</artifactId>
<version>1.6.0</version>
- </dependency>
+ </dependency-->
<!-- Taverna Activities -->
<dependency>
@@ -339,7 +345,7 @@
<dependency>
<groupId>uk.org.taverna.commandline</groupId>
<artifactId>taverna-command-line</artifactId>
- <version>0.1.2-SNAPSHOT</version>
+ <version>${taverna-command-line.version}</version>
</dependency>
<!-- Taverna Platform -->
@@ -430,16 +436,16 @@
<version>${taverna.databundle.version}</version>
</dependency>
<!-- HTTP client needed by Data Bundle -->
- <dependency>
+ <!-- Appears unrequired dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient-osgi</artifactId>
<version>4.2.5</version>
- </dependency>
- <dependency>
+ </dependency-->
+ <!-- Appears unrequired dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore-osgi</artifactId>
<version>4.2.5</version>
- </dependency>
+ </dependency-->
<!-- Jena bundle needed by jsonld-java-jena -->
<!-- See https://github.com/stain/jena/tree/jena-bundle/jena-bundle -->
<dependency>
@@ -448,16 +454,17 @@
<version>2.11.0-SNAPSHOT</version>
</dependency>
<!-- slf4j implementation -->
+ <!-- The bundle "org.purl.wf4ever.robundle_0.3.1 " could not be resolved. Reason: Missing Constraint: Import-Package: org.slf4j; version="[1.7.0,2.0.0)"-->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.5</version>
</dependency>
- <dependency>
+ <!-- Appears unrequired dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.7.5</version>
- </dependency>
+ </dependency-->
<!-- Taverna Security -->
<dependency>
@@ -499,6 +506,7 @@
<artifactId>provenance-mysql</artifactId>
<version>${t2.core.provenance.mysql.version}</version>
</dependency>
+ <!-- The bundle "org.purl.wf4ever.robundle_0.3.1 " could not be resolved. Reason: Missing Constraint: Import-Package: com.fasterxml.jackson.annotation; version="[2.3.0,3.0.0)"-->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
[18/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-tests/
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/xmlSplitter.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/xmlSplitter.t2flow b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/xmlSplitter.t2flow
new file mode 100644
index 0000000..bd0875d
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/xmlSplitter/xmlSplitter.t2flow
@@ -0,0 +1,339 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="52ddd8d4-d1fc-4b62-932a-288df52b77cf" role="top"><name>Workflow1</name><inputPorts><port><name>lastName</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
+ <text>Smith</text>
+ </annotationBean>
+ <date>2011-02-17 10:48:23.657 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>firstName</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
+ <text>John</text>
+ </annotationBean>
+ <date>2011-02-17 10:48:16.703 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>age</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
+ <text>John</text>
+ </annotationBean>
+ <date>2011-02-17 10:47:56.513 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
+ <text>21</text>
+ </annotationBean>
+ <date>2011-02-17 10:48:30.905 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>personToString</name><inputPorts><port><name>parameters</name><depth>0</depth></port></inputPorts><outputPorts><port><name>parameters</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="parameters" to="parameters" /></inputMap><outputMap><map from="parameters" to="parameters" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
+ <wsdl>http://www.mygrid.org.uk/menagerie/xfire/Complex-dlw?wsdl</wsdl>
+ <operation>personToString</operation>
+</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="parameters" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>personToString_output</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitt
erActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
+ <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="personToStringResponse" name="parameters" qname="{http://xfire.codehaus.org/BookService}personToStringResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="out" qname="{http://xfire.codehaus.org/BookService}&gt;personToStringResponse&gt;out" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>input</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/xml'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/plain'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>personToString_input</name><inputPorts><port><name>person</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterA
ctivity</class><inputMap><map from="person" to="person" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
+ <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="personToString" name="parameters" qname="{http://xfire.codehaus.org/BookService}personToString"><s:elements><s:complextype optional="false" unbounded="false" typename="Person" name="person" qname="{http://xfire.codehaus.org/BookService}&gt;personToString&gt;person"><s:elements><s:complextype optional="true" unbounded="false" typename="Address" name="address" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;address"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="city" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;city" /><s:basetype optional="true" unbounded="false" typename="string" name="road" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;road" /><s:basetype optional="true
" unbounded="false" typename="int" name="roadNumber" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;roadNumber" /></s:elements></s:complextype><s:basetype optional="true" unbounded="false" typename="int" name="age" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;age" /><s:basetype optional="true" unbounded="false" typename="string" name="firstName" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;firstName" /><s:basetype optional="true" unbounded="false" typename="string" name="lastName" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;lastName" /></s:elements></s:complextype></s:elements></s:complextype></s:extensions></wrappedTypeXML>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>person</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/xml'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>output</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/xml'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="person" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>personToString_person</name><inputPorts><port><name>lastName</name><depth>0</depth></port><port><name>firstName</name><depth>0</depth></port><port><name>age</name><depth>0</depth></port><port><name>address</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.act
ivities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="lastName" to="lastName" /><map from="address" to="address" /><map from="age" to="age" /><map from="firstName" to="firstName" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
+ <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="Person" name="person" qname="{http://xfire.codehaus.org/BookService}&gt;personToString&gt;person"><s:elements><s:complextype optional="true" unbounded="false" typename="Address" name="address" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;address"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="city" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;city" /><s:basetype optional="true" unbounded="false" typename="string" name="road" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;road" /><s:basetype optional="true" unbounded="false" typename="int" name="roadNumber" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;roadNumber" /></s:elements></s:complextype>
;<s:basetype optional="true" unbounded="false" typename="int" name="age" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;age" /><s:basetype optional="true" unbounded="false" typename="string" name="firstName" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;firstName" /><s:basetype optional="true" unbounded="false" typename="string" name="lastName" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;lastName" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>address</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/xml'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>age</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/plain'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>firstName</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/plain'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>lastName</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/plain'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>output</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/xml'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="lastName" depth="0" /><port name="firstName" depth="0" /><port name="age" depth="0" /><port name="address" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>person_address</name><inputPorts><port><name>city</name><depth>0</depth></port><port><name>road</name><depth>0</depth></port><port><name>roadNumber</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><act
ivity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="road" to="road" /><map from="roadNumber" to="roadNumber" /><map from="city" to="city" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
+ <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="Address" name="address" qname="{http://complex.pojo.axis2.menagerie.googlecode}Person&gt;address"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="city" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;city" /><s:basetype optional="true" unbounded="false" typename="string" name="road" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;road" /><s:basetype optional="true" unbounded="false" typename="int" name="roadNumber" qname="{http://complex.pojo.axis2.menagerie.googlecode}Address&gt;roadNumber" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>city</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/plain'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>road</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/plain'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <allowsLiteralValues>false</allowsLiteralValues>
+ <name>roadNumber</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/plain'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>output</name>
+ <depth>0</depth>
+ <mimeTypes class="java.util.Collections$SingletonList">
+ <element class="string">'text/xml'</element>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="city" depth="0" /><port name="road" depth="0" /><port name="roadNumber" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>city_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstant
Activity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Manchester</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>road_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf
.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>Oxford Road</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>roadNumber_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><
net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value>40</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>personToString</processor><port>parameters</port></sink><source type="processor"><processor>personToString_input</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>personToString_output</processor><port>input</port></sink><source type="processor"><processor>personToString</processor><port>parameters</port></source></datalink><datalink><sink type="processor"><processor>pers
onToString_input</processor><port>person</port></sink><source type="processor"><processor>personToString_person</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>personToString_person</processor><port>lastName</port></sink><source type="dataflow"><port>lastName</port></source></datalink><datalink><sink type="processor"><processor>personToString_person</processor><port>firstName</port></sink><source type="dataflow"><port>firstName</port></source></datalink><datalink><sink type="processor"><processor>personToString_person</processor><port>age</port></sink><source type="dataflow"><port>age</port></source></datalink><datalink><sink type="processor"><processor>personToString_person</processor><port>address</port></sink><source type="processor"><processor>person_address</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>person_address</processor><port>city</port></sink><source type="processor"><processo
r>city_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>person_address</processor><port>road</port></sink><source type="processor"><processor>road_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>person_address</processor><port>roadNumber</port></sink><source type="processor"><processor>roadNumber_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>personToString_output</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>d79eeb60-919e-4076-af14-70ac4d605bec</identification>
+ </annotationBean>
+ <date>2011-02-17 10:49:46.785 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>52ddd8d4-d1fc-4b62-932a-288df52b77cf</identification>
+ </annotationBean>
+ <date>2011-02-17 10:53:16.981 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>8815f1ea-2659-4b7e-a90e-787c6a3c4ad6</identification>
+ </annotationBean>
+ <date>2011-02-17 10:29:40.492 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>eee0128a-4afe-4566-851a-fe50dcb36340</identification>
+ </annotationBean>
+ <date>2011-02-17 10:48:35.150 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>e64ae430-dd6e-468d-b3dd-de1fea9c717b</identification>
+ </annotationBean>
+ <date>2011-02-17 10:20:55.279 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>2aa76794-f001-42f9-b945-797badfeebb1</identification>
+ </annotationBean>
+ <date>2011-02-17 10:17:24.893 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>2ece2565-7498-4154-9d61-996d8a1db5f3</identification>
+ </annotationBean>
+ <date>2011-02-17 10:24:47.509 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>97fbd479-a423-4e8c-9033-bfc28f1a7885</identification>
+ </annotationBean>
+ <date>2011-02-17 10:42:59.63 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>24e8b191-9f48-4864-82be-d9578f1b8450</identification>
+ </annotationBean>
+ <date>2011-02-17 10:25:38.788 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/9601b2f1/taverna-commandline-tests/src/test/resources/workflows/xpath/xpath.t2flow
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/src/test/resources/workflows/xpath/xpath.t2flow b/taverna-commandline-tests/src/test/resources/workflows/xpath/xpath.t2flow
new file mode 100644
index 0000000..0691ccc
--- /dev/null
+++ b/taverna-commandline-tests/src/test/resources/workflows/xpath/xpath.t2flow
@@ -0,0 +1,127 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="9fb6e3ea-f314-4f9f-8eb3-ba3dbf2b494f" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>XPath_Service</name><inputPorts><port><name>xml_text</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodelistAsXML</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>xpath-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.xpath.XPathActivity</class><inputMap><map from="xml_text" to="xml_text" /></inputMap><outputMap><map from="nodelistAsXML" to="nodelistAsXML" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean xmlns="">
+ <xmlDocument><?xml version="1.0" encoding="UTF-8"?>
+<test name="test-name">
+<test-element>test</test-element>
+</test></xmlDocument>
+ <xpathExpression>/test/test-element</xpathExpression>
+ <xpathNamespaceMap />
+</net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="xml_text" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>xml_text_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" t
o="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+ <value><?xml version="1.0" encoding="UTF-8"?> <test name="test-name"> <test-element>test</test-element> </test></value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>Merge_String_List_to_a_String</name><inputPorts><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>concatenated</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="str
inglist" to="stringlist" /></inputMap><outputMap><map from="concatenated" to="concatenated" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>stringlist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>seperator</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <name>concatenated</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ <granularDepth>0</granularDepth>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <script>String seperatorString = "\n";
+if (seperator != void) {
+ seperatorString = seperator;
+}
+StringBuffer sb = new StringBuffer();
+for (Iterator i = stringlist.iterator(); i.hasNext();) {
+ String item = (String) i.next();
+ sb.append(item);
+ if (i.hasNext()) {
+ sb.append(seperatorString);
+ }
+}
+concatenated = sb.toString();
+</script>
+ <dependencies />
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringListMerge</localworkerName>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>XPath_Service</processor><port>xml_text</port></sink><source type="processor"><processor>xml_text_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>stringlist</port></sink><source type="processor"><processor>XPath_Service</processor><port>nodelistAsXML</port></s
ource></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Merge_String_List_to_a_String</processor><port>concatenated</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>9fb6e3ea-f314-4f9f-8eb3-ba3dbf2b494f</identification>
+ </annotationBean>
+ <date>2011-11-03 14:17:32.152 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>bed5342f-45e0-4fc9-a85d-bcd1ea01e33d</identification>
+ </annotationBean>
+ <date>2011-11-03 12:55:28.941 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>9f0cedc9-4a53-4564-aeb5-d0b7f7b2b4e1</identification>
+ </annotationBean>
+ <date>2011-11-03 12:56:36.620 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>94104add-ec12-4c5a-a4f6-b5c1b6d0a700</identification>
+ </annotationBean>
+ <date>2011-11-03 12:56:00.6 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
[07/50] [abbrv] incubator-taverna-commandline git commit: travis
Posted by st...@apache.org.
travis
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/946757c2
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/946757c2
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/946757c2
Branch: refs/heads/master
Commit: 946757c28de5c31b2550a57dbd6793d6bb7b775e
Parents: b8b3fe2
Author: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Authored: Mon Oct 27 16:26:54 2014 +0000
Committer: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Committed: Mon Oct 27 16:26:54 2014 +0000
----------------------------------------------------------------------
.travis.yml | 1 +
README.md | 4 ++++
2 files changed, 5 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/946757c2/.travis.yml
----------------------------------------------------------------------
diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..dff5f3a
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1 @@
+language: java
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/946757c2/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..94cf00c
--- /dev/null
+++ b/README.md
@@ -0,0 +1,4 @@
+Taverna Commandline product
+===========================
+
+[](https://travis-ci.org/taverna/taverna-commandline-product)
[13/50] [abbrv] incubator-taverna-commandline git commit:
org.apache.taverna.commandline
Posted by st...@apache.org.
org.apache.taverna.commandline
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/daa24714
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/daa24714
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/daa24714
Branch: refs/heads/master
Commit: daa24714b040ce957111126ad7996e0bf2ebbf56
Parents:
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 01:09:22 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 01:09:22 2014 -0600
----------------------------------------------------------------------
pom.xml | 36 ++++++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/daa24714/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..0bbc314
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,36 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>1-SNAPSHOT</version>
+ </parent>
+ <groupId>org.apache.taverna.commandline</groupId>
+ <artifactId>taverna-commandline</artifactId>
+ <version>3.1.0-incubating-SNAPSHOT</version>
+ <packaging>pom</packaging>
+ <name>Apache Taverna Engine and Platform</name>
+ <properties>
+ <taverna.language.version>0.15.0-incubating-SNAPSHOT</taverna.language.version>
+ <taverna.osgi.version>0.2.0-incubating-SNAPSHOT</taverna.osgi.version>
+ <taverna.engine.version>3.1.0-incubating-SNAPSHOT</taverna.engine.version>
+ </properties>
+ <modules>
+ <module>taverna-commandline-api</module>
+ <module>taverna-commandline-impl</module>
+ <module>taverna-commandline-common</module>
+ <module>taverna-commandline-product</module>
+ </modules>
+ <repositories>
+ <repository>
+ <id>taverna-incubating</id>
+ <name>Apache Taverna incubating Repository</name>
+ <url>http://repository.mygrid.org.uk/artifactory/incubator-snapshot-local/</url>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ </repository>
+ </repositories>
+</project>
[34/50] [abbrv] incubator-taverna-commandline git commit: add module
taverna-commandline-launcher / -tests
Posted by st...@apache.org.
add module taverna-commandline-launcher / -tests
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/101439b6
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/101439b6
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/101439b6
Branch: refs/heads/master
Commit: 101439b6cb446f8866751bfc5f15b5b719818f77
Parents: 8568f96
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 02:09:55 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 02:09:55 2014 -0600
----------------------------------------------------------------------
pom.xml | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/101439b6/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 0bbc314..7b5a7b3 100644
--- a/pom.xml
+++ b/pom.xml
@@ -18,9 +18,10 @@
</properties>
<modules>
<module>taverna-commandline-api</module>
- <module>taverna-commandline-impl</module>
<module>taverna-commandline-common</module>
+ <module>taverna-commandline-launcher</module>
<module>taverna-commandline-product</module>
+ <module>taverna-commandline-tests</module>
</modules>
<repositories>
<repository>
[49/50] [abbrv] incubator-taverna-commandline git commit: parent pom
version
Posted by st...@apache.org.
parent pom version
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/ba051d50
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/ba051d50
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/ba051d50
Branch: refs/heads/master
Commit: ba051d5066c4b2eccaf860e676e4fdcb5dbd2f7a
Parents: 99409c4
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Feb 5 10:13:40 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Thu Feb 5 10:13:40 2015 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/ba051d50/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index c1690e4..0355623 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>org.apache.taverna</groupId>
<artifactId>taverna-parent</artifactId>
- <version>1-SNAPSHOT</version>
+ <version>1-incubating-SNAPSHOT</version>
</parent>
<groupId>org.apache.taverna.commandline</groupId>
<artifactId>taverna-commandline</artifactId>
[06/50] [abbrv] incubator-taverna-commandline git commit: Stripped
out provenance
Posted by st...@apache.org.
Stripped out provenance
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/bcd5f6f4
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/bcd5f6f4
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/bcd5f6f4
Branch: refs/heads/master
Commit: bcd5f6f441f3da9e80f653abe54edbd288508c55
Parents: b8b3fe2
Author: Christian-B <br...@cs.man.ac.uk>
Authored: Mon Sep 22 13:35:27 2014 +0100
Committer: Christian-B <br...@cs.man.ac.uk>
Committed: Mon Sep 22 13:35:27 2014 +0100
----------------------------------------------------------------------
pom.xml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/bcd5f6f4/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index e0309df..6b1fffe 100644
--- a/pom.xml
+++ b/pom.xml
@@ -496,7 +496,7 @@
</dependency>
<!-- Taverna Provenance -->
- <dependency>
+ <!--dependency>
<groupId>net.sf.taverna.t2.core</groupId>
<artifactId>provenance-derby</artifactId>
<version>${t2.core.provenance.derby.version}</version>
@@ -505,7 +505,7 @@
<groupId>net.sf.taverna.t2.core</groupId>
<artifactId>provenance-mysql</artifactId>
<version>${t2.core.provenance.mysql.version}</version>
- </dependency>
+ </dependency-->
<!-- The bundle "org.purl.wf4ever.robundle_0.3.1 " could not be resolved. Reason: Missing Constraint: Import-Package: com.fasterxml.jackson.annotation; version="[2.3.0,3.0.0)"-->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
[37/50] [abbrv] incubator-taverna-commandline git commit:
org.apache.taverna.* dependencies
Posted by st...@apache.org.
org.apache.taverna.* dependencies
.. and disable most of the activities..
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/44359755
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/44359755
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/44359755
Branch: refs/heads/master
Commit: 443597558e8ecbb26c96dd4e7e0ab213d2e8e0a0
Parents: f6985f0
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 03:09:59 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 03:09:59 2014 -0600
----------------------------------------------------------------------
taverna-commandline-product/pom.xml | 226 +++++++++++++++----------------
1 file changed, 112 insertions(+), 114 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/44359755/taverna-commandline-product/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/pom.xml b/taverna-commandline-product/pom.xml
index e563167..3b2187b 100644
--- a/taverna-commandline-product/pom.xml
+++ b/taverna-commandline-product/pom.xml
@@ -18,29 +18,30 @@
</activation>
<properties>
<assembly.descriptor>src/main/assembly/developer-assembly.xml</assembly.descriptor>
- <profile.updateSite>http://dev.mygrid.org.uk/taverna/updates/taverna-command-line/</profile.updateSite>
- <profile.pluginSite>http://dev.mygrid.org.uk/taverna/plugins/taverna-command-line/</profile.pluginSite>
+ <!-- See http://updates.taverna.org.uk/ -->
+ <profile.updateSite>https://taverna.incubator.apache.org/updates/commandline/</profile.updateSite>
+ <profile.pluginSite>https://taverna.incubator.apache.org/plugins/commandline/</profile.pluginSite>
</properties>
</profile>
<profile>
<id>nightly</id>
<properties>
<assembly.descriptor>src/main/assembly/nightly-assembly.xml</assembly.descriptor>
- <profile.updateSite>http://dev.mygrid.org.uk/taverna/updates/taverna-command-line/</profile.updateSite>
- <profile.pluginSite>http://dev.mygrid.org.uk/taverna/plugins/taverna-command-line/</profile.pluginSite>
+ <profile.updateSite>https://taverna.incubator.apache.org/updates/commandline/</profile.updateSite>
+ <profile.pluginSite>https://taverna.incubator.apache.org/plugins/commandline/</profile.pluginSite>
</properties>
</profile>
<profile>
<id>release</id>
<properties>
<assembly.descriptor>src/main/assembly/release-assembly.xml</assembly.descriptor>
- <profile.updateSite>http://www.mygrid.org.uk/taverna/updates/taverna-command-line/</profile.updateSite>
- <profile.pluginSite>http://www.mygrid.org.uk/taverna/plugins/taverna-command-line/</profile.pluginSite>
+ <profile.updateSite>https://taverna.incubator.apache.org/updates/commandline/</profile.updateSite>
+ <profile.pluginSite>https://taverna.incubator.apache.org/plugins/commandline/</profile.pluginSite>
</properties>
</profile>
</profiles>
<build>
- <finalName>taverna-command-line-${project.version}</finalName>
+ <finalName>apache-taverna-commandline-${project.version}</finalName>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
@@ -84,9 +85,9 @@
</configuration>
</plugin>
<plugin>
- <groupId>net.sf.taverna.t2.maven.plugins</groupId>
+ <groupId>org.apache.taverna.osgi</groupId>
<artifactId>taverna-maven-plugin</artifactId>
- <version>0.3.1-SNAPSHOT</version>
+ <version>${taverna.osgi.version}</version>
<extensions>true</extensions>
<configuration>
<buildNumber>${buildNumber}</buildNumber>
@@ -122,19 +123,11 @@
<pluginExecutions>
<pluginExecution>
<pluginExecutionFilter>
- <groupId>
- net.sf.taverna.t2.maven.plugins
- </groupId>
- <artifactId>
- taverna-maven-plugin
- </artifactId>
- <versionRange>
- [0.3.1-SNAPSHOT,)
- </versionRange>
+ <groupId>org.apache.taverna.osgi</groupId>
+ <artifactId>taverna-maven-plugin</artifactId>
+ <versionRange>[0.3.1-SNAPSHOT,)</versionRange>
<goals>
- <goal>
- profile-generate
- </goal>
+ <goal>profile-generate</goal>
</goals>
</pluginExecutionFilter>
<action>
@@ -261,14 +254,14 @@
<!-- OSGi Enterprise Services -->
<dependency>
- <groupId>uk.org.taverna.osgi.services</groupId>
+ <groupId>org.apache.taverna.osgi</groupId>
<artifactId>xml-parser-service</artifactId>
- <version>${osgi.services.version}</version>
+ <version>${taverna.osgi.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.osgi.services</groupId>
+ <groupId>org.apache.taverna.osgi</groupId>
<artifactId>xml-transformer-service</artifactId>
- <version>${osgi.services.version}</version>
+ <version>${taverna.osgi.version}</version>
</dependency>
<!-- The bundle "uk.org.taverna.commons.taverna-plugin-impl_0.1.0.SNAPSHOT" could not be resolved. Reason: Missing Constraint: Import-Package: org.osgi.service.event; version="[1.3.0,2.0.0)" -->
<dependency>
@@ -284,6 +277,17 @@
<!-- Taverna Activities -->
<dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-dataflow-activity</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-stringconstant-activity</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <!--
+ <dependency>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>apiconsumer-activity</artifactId>
<version>2.0.1-SNAPSHOT</version>
@@ -300,11 +304,9 @@
</dependency>
<dependency>
<groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>dataflow-activity</artifactId>
+ <artifactId>external-tool-activity</artifactId>
<version>2.0.1-SNAPSHOT</version>
</dependency>
- <!-- <dependency> <groupId>net.sf.taverna.t2.activities</groupId> <artifactId>external-tool-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version> </dependency> -->
<dependency>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>localworker-activity</artifactId>
@@ -332,11 +334,6 @@
</dependency>
<dependency>
<groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>stringconstant-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>wsdl-activity</artifactId>
<version>2.0.1-SNAPSHOT</version>
</dependency>
@@ -345,105 +342,106 @@
<artifactId>xpath-activity</artifactId>
<version>2.0.1-SNAPSHOT</version>
</dependency>
+ -->
<!-- Taverna Commandline -->
<dependency>
- <groupId>net.sf.taverna.t2.taverna-commandline</groupId>
+ <groupId>${project.parent.groupId}</groupId>
<artifactId>taverna-commandline-common</artifactId>
- <version>${t2.taverna-commandline.version}</version>
+ <version>${project.parent.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.commandline</groupId>
- <artifactId>taverna-command-line</artifactId>
- <version>${taverna-command-line.version}</version>
+ <groupId>${project.parent.groupId}</groupId>
+ <artifactId>taverna-commandline-launcher</artifactId>
+ <version>${project.parent.version}</version>
</dependency>
<!-- Taverna Platform -->
<dependency>
- <groupId>uk.org.taverna.platform</groupId>
+ <groupId>org.apache.taverna.engine</groupId>
<artifactId>taverna-capability-impl</artifactId>
- <version>${platform.version}</version>
+ <version>${taverna.engine.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.platform</groupId>
+ <groupId>org.apache.taverna.engine</groupId>
<artifactId>taverna-run-impl</artifactId>
- <version>${platform.version}</version>
+ <version>${taverna.engine.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.platform</groupId>
+ <groupId>org.apache.taverna.engine</groupId>
<artifactId>taverna-execution-impl</artifactId>
- <version>${platform.version}</version>
+ <version>${taverna.engine.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.platform</groupId>
+ <groupId>org.apache.taverna.engine</groupId>
<artifactId>taverna-execution-local</artifactId>
- <version>${platform.version}</version>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-database-configuration-impl</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-services-impl</artifactId>
+ <version>${taverna.engine.version}</version>
</dependency>
- <!-- Taverna Commons -->
+ <!-- Taverna OSGi -->
<dependency>
- <groupId>uk.org.taverna.configuration</groupId>
+ <groupId>org.apache.taverna.osgi</groupId>
<artifactId>taverna-configuration-impl</artifactId>
- <version>0.1.1-SNAPSHOT</version>
+ <version>${taverna.osgi.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.configuration</groupId>
+ <groupId>org.apache.taverna.osgi</groupId>
<artifactId>taverna-app-configuration-impl</artifactId>
- <version>0.1.1-SNAPSHOT</version>
+ <version>${taverna.osgi.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.configuration</groupId>
- <artifactId>taverna-database-configuration-impl</artifactId>
- <version>0.1.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.commons</groupId>
+ <groupId>org.apache.taverna.osgi</groupId>
<artifactId>taverna-download-impl</artifactId>
- <version>0.1.0-SNAPSHOT</version>
+ <version>${taverna.osgi.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.commons</groupId>
+ <groupId>org.apache.taverna.osgi</groupId>
<artifactId>taverna-plugin-impl</artifactId>
- <version>0.1.0-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.commons</groupId>
- <artifactId>taverna-services-impl</artifactId>
- <version>0.1.0-SNAPSHOT</version>
+ <version>${taverna.osgi.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.commons</groupId>
+ <groupId>org.apache.taverna.osgi</groupId>
<artifactId>taverna-update-impl</artifactId>
- <version>0.1.0-SNAPSHOT</version>
+ <version>${taverna.osgi.version}</version>
</dependency>
<!-- Scufl2 -->
<dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-rdfxml</artifactId>
- <version>${scufl2.version}</version>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-rdfxml</artifactId>
+ <version>${taverna.language.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-t2flow</artifactId>
- <version>${scufl2.version}</version>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-t2flow</artifactId>
+ <version>${taverna.language.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-validation-structural</artifactId>
- <version>${scufl2.version}</version>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-validation-structural</artifactId>
+ <version>${taverna.language.version}</version>
</dependency>
<dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-validation-correctness</artifactId>
- <version>${scufl2.version}</version>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-validation-correctness</artifactId>
+ <version>${taverna.language.version}</version>
</dependency>
<!-- Data bundle -->
<dependency>
- <groupId>uk.org.taverna.databundle</groupId>
- <artifactId>databundle</artifactId>
- <version>${taverna.databundle.version}</version>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-databundle</artifactId>
+ <version>${taverna.language.version}</version>
</dependency>
<!-- HTTP client needed by Data Bundle -->
<!-- Appears unrequired dependency>
@@ -460,7 +458,7 @@
<!-- See https://github.com/stain/jena/tree/jena-bundle/jena-bundle -->
<dependency>
<groupId>org.apache.jena</groupId>
- <artifactId>jena-bundle</artifactId>
+ <artifactId>jena-osgi</artifactId>
<version>2.12.2-SNAPSHOT</version>
</dependency>
<!-- slf4j implementation -->
@@ -478,60 +476,60 @@
<!-- Taverna Security -->
<dependency>
- <groupId>net.sf.taverna.t2.security</groupId>
- <artifactId>credential-manager-impl</artifactId>
- <version>${t2.security.version}</version>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-credential-manager-impl</artifactId>
+ <version>${taverna.engine.version}</version>
</dependency>
<!-- Taverna Workflow Engine -->
<dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-impl</artifactId>
- <version>${t2.core.version}</version>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-workflowmodel-impl</artifactId>
+ <version>${taverna.engine.version}</version>
</dependency>
<dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-core-extensions</artifactId>
- <version>${t2.core.version}</version>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-workflowmodel-core-extensions</artifactId>
+ <version>${taverna.engine.version}</version>
</dependency>
<dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>reference-impl</artifactId>
- <version>${t2.core.version}</version>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-reference-impl</artifactId>
+ <version>${taverna.engine.version}</version>
</dependency>
<dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>reference-core-extensions</artifactId>
- <version>${t2.core.version}</version>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-reference-types</artifactId>
+ <version>${taverna.engine.version}</version>
</dependency>
<!-- Taverna Provenance -->
<!--dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
+ <groupId>org.apache.taverna.engine</groupId>
<artifactId>provenance-derby</artifactId>
- <version>${t2.core.provenance.derby.version}</version>
+ <version>${taverna.engine.version}</version>
</dependency>
<dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
+ <groupId>org.apache.taverna.engine</groupId>
<artifactId>provenance-mysql</artifactId>
- <version>${t2.core.provenance.mysql.version}</version>
+ <version>${taverna.engine.version}</version>
</dependency-->
<!-- The bundle "org.purl.wf4ever.robundle_0.3.1 " could not be resolved. Reason: Missing Constraint: Import-Package: com.fasterxml.jackson.annotation; version="[2.3.0,3.0.0)"-->
<dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-core</artifactId>
- <version>2.3.0</version>
- </dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-core</artifactId>
+ <version>2.3.0</version>
+ </dependency>
<dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-annotations</artifactId>
- <version>2.3.0</version>
- </dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-annotations</artifactId>
+ <version>2.3.0</version>
+ </dependency>
<dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
- <version>2.3.0</version>
- </dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>2.3.0</version>
+ </dependency>
</dependencies>
<repositories>
[10/50] [abbrv] incubator-taverna-commandline git commit: Add
saveResultsToBundle() for -bundle option
Posted by st...@apache.org.
Add saveResultsToBundle() for -bundle option
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/7b757cf9
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/7b757cf9
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/7b757cf9
Branch: refs/heads/master
Commit: 7b757cf9dea8ff90405eef8b92b6b57a0d2dc9d6
Parents: 64ddb76
Author: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Authored: Tue Oct 28 22:29:53 2014 +0000
Committer: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Committed: Tue Oct 28 22:29:53 2014 +0000
----------------------------------------------------------------------
.../commandline/options/CommandLineOptions.java | 4 ++++
.../taverna/t2/commandline/CommandLineTool.java | 23 +++++++++++++++++++-
.../t2/commandline/data/InputsHandler.java | 7 +++++-
3 files changed, 32 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/7b757cf9/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
index 3473297..dd8e20f 100644
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
@@ -95,6 +95,8 @@ public interface CommandLineOptions {
public boolean hasLogFile();
public boolean hasOption(String option);
+
+ public boolean hasSaveResultsToBundle() ;
public String inputDelimiter(String inputName);
@@ -112,4 +114,6 @@ public interface CommandLineOptions {
*/
public boolean saveResultsToDirectory();
+ public String saveResultsToBundle();
+
}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/7b757cf9/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
index 9d8c5fc..368527d 100644
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
@@ -26,6 +26,7 @@ import java.net.MalformedURLException;
import java.net.URISyntaxException;
import java.net.URL;
import java.nio.file.Path;
+import java.nio.file.Paths;
import java.sql.SQLException;
import java.util.HashMap;
import java.util.Map;
@@ -170,6 +171,15 @@ public class CommandLineTool {
setupDatabase(commandLineOptions);
if (commandLineOptions.getWorkflow() != null) {
+
+ /* Set context class loader to us,
+ * so that things such as JSON-LD caching of
+ * robundle works.
+ */
+
+ Thread.currentThread().setContextClassLoader(getClass().getClassLoader());
+
+
/*
* Initialise Credential Manager and SSL stuff quite early as
* parsing and validating the workflow may require it
@@ -251,7 +261,8 @@ public class CommandLineTool {
try {
Thread.sleep(500);
} catch (InterruptedException e) {
- // Ignore
+ System.err.println("Interrupted while waiting for workflow to finish");
+ return 1;
}
}
@@ -278,6 +289,16 @@ public class CommandLineTool {
}
}
}
+ if (commandLineOptions.saveResultsToBundle() != null) {
+ Path bundlePath = Paths.get(commandLineOptions.saveResultsToBundle());
+ DataBundles.closeAndSaveBundle(runService.getDataBundle(runId), bundlePath);
+ System.out.println("Workflow Run Bundle saved to: " + bundlePath.toAbsolutePath());
+ } else {
+ System.out.println("Workflow Run Bundle: " + runService.getDataBundle(runId).getSource());
+ // For debugging we'll leave it in /tmp for now
+ runService.getDataBundle(runId).setDeleteOnClose(false);
+ DataBundles.closeBundle(runService.getDataBundle(runId));
+ }
if (report.getState().equals(State.FAILED)) {
System.out.println("Workflow failed - see report below.");
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/7b757cf9/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
index 795376a..bcaa7fb 100644
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
@@ -27,6 +27,7 @@ import java.net.URISyntaxException;
import java.net.URL;
import java.nio.file.Files;
import java.nio.file.Path;
+import java.nio.file.Paths;
import java.nio.file.StandardOpenOption;
import java.util.ArrayList;
import java.util.HashSet;
@@ -106,7 +107,11 @@ public class InputsHandler {
public Bundle registerInputs(Map<String, InputWorkflowPort> portMap,
CommandLineOptions options, InvocationContext context) throws InvalidOptionException,
ReadInputException, IOException {
- Bundle inputDataBundle = DataBundles.createBundle();
+ Bundle inputDataBundle;
+ inputDataBundle = DataBundles.createBundle();
+ inputDataBundle.setDeleteOnClose(false);
+ System.out.println("Bundle: " + inputDataBundle.getSource());
+
Path inputs = DataBundles.getInputs(inputDataBundle);
URL url;
[48/50] [abbrv] incubator-taverna-commandline git commit: Include
taverna-beanshell-activity
Posted by st...@apache.org.
Include taverna-beanshell-activity
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/99409c48
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/99409c48
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/99409c48
Branch: refs/heads/master
Commit: 99409c485dab2afea8bc7d796c319021dc9054ce
Parents: fd2682c
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Jan 8 13:10:58 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Thu Jan 8 13:10:58 2015 +0000
----------------------------------------------------------------------
taverna-commandline-product/pom.xml | 5 +++++
1 file changed, 5 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/99409c48/taverna-commandline-product/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/pom.xml b/taverna-commandline-product/pom.xml
index 07a7782..f493eab 100644
--- a/taverna-commandline-product/pom.xml
+++ b/taverna-commandline-product/pom.xml
@@ -290,6 +290,11 @@
<!-- Taverna Common Activities -->
<dependency>
<groupId>org.apache.taverna.commonactivities</groupId>
+ <artifactId>taverna-beanshell-activity</artifactId>
+ <version>${taverna.commonactivities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.commonactivities</groupId>
<artifactId>taverna-external-tool-activity</artifactId>
<version>${taverna.commonactivities.version}</version>
</dependency>
[32/50] [abbrv] incubator-taverna-commandline git commit:
taverna-commandline-product/
Posted by st...@apache.org.
taverna-commandline-product/
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/0257a92e
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/0257a92e
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/0257a92e
Branch: refs/heads/master
Commit: 0257a92ee5615921425060fbf7a234dca103b88e
Parents: 38c342d
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 02:08:04 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 02:08:04 2014 -0600
----------------------------------------------------------------------
.gitignore | 4 -
.travis.yml | 1 -
README.md | 4 -
pom.xml | 578 -------------------
src/main/assembly/dependencies-component.xml | 21 -
src/main/assembly/developer-assembly.xml | 13 -
src/main/assembly/nightly-assembly.xml | 15 -
src/main/assembly/release-assembly.xml | 15 -
src/main/etc/conf/log4j.properties | 14 -
src/main/etc/conf/logging.properties | 10 -
src/main/etc/conf/taverna.app.properties | 2 -
src/main/etc/executeworkflow.bat | 17 -
src/main/etc/executeworkflow.sh | 25 -
taverna-commandline-product/pom.xml | 578 +++++++++++++++++++
.../main/assembly/dependencies-component.xml | 21 +
.../src/main/assembly/developer-assembly.xml | 13 +
.../src/main/assembly/nightly-assembly.xml | 15 +
.../src/main/assembly/release-assembly.xml | 15 +
.../src/main/etc/conf/log4j.properties | 14 +
.../src/main/etc/conf/logging.properties | 10 +
.../src/main/etc/conf/taverna.app.properties | 2 +
.../src/main/etc/executeworkflow.bat | 17 +
.../src/main/etc/executeworkflow.sh | 25 +
23 files changed, 710 insertions(+), 719 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/.gitignore
----------------------------------------------------------------------
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index 6589a8b..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,4 +0,0 @@
-target
-.classpath
-.project
-.settings
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/.travis.yml
----------------------------------------------------------------------
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index dff5f3a..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1 +0,0 @@
-language: java
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
deleted file mode 100644
index 94cf00c..0000000
--- a/README.md
+++ /dev/null
@@ -1,4 +0,0 @@
-Taverna Commandline product
-===========================
-
-[](https://travis-ci.org/taverna/taverna-commandline-product)
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
deleted file mode 100644
index d67a916..0000000
--- a/pom.xml
+++ /dev/null
@@ -1,578 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>uk.org.taverna.workbench</groupId>
- <artifactId>taverna-command-line-product</artifactId>
- <name>Taverna Command Line</name>
- <packaging>taverna-application</packaging>
- <profiles>
- <profile>
- <id>developer</id>
- <activation>
- <activeByDefault>true</activeByDefault>
- </activation>
- <properties>
- <assembly.descriptor>src/main/assembly/developer-assembly.xml</assembly.descriptor>
- <profile.updateSite>http://dev.mygrid.org.uk/taverna/updates/taverna-command-line/</profile.updateSite>
- <profile.pluginSite>http://dev.mygrid.org.uk/taverna/plugins/taverna-command-line/</profile.pluginSite>
- </properties>
- </profile>
- <profile>
- <id>nightly</id>
- <properties>
- <assembly.descriptor>src/main/assembly/nightly-assembly.xml</assembly.descriptor>
- <profile.updateSite>http://dev.mygrid.org.uk/taverna/updates/taverna-command-line/</profile.updateSite>
- <profile.pluginSite>http://dev.mygrid.org.uk/taverna/plugins/taverna-command-line/</profile.pluginSite>
- </properties>
- </profile>
- <profile>
- <id>release</id>
- <properties>
- <assembly.descriptor>src/main/assembly/release-assembly.xml</assembly.descriptor>
- <profile.updateSite>http://www.mygrid.org.uk/taverna/updates/taverna-command-line/</profile.updateSite>
- <profile.pluginSite>http://www.mygrid.org.uk/taverna/plugins/taverna-command-line/</profile.pluginSite>
- </properties>
- </profile>
- </profiles>
- <build>
- <finalName>taverna-command-line-${project.version}</finalName>
- <plugins>
- <plugin>
- <artifactId>maven-assembly-plugin</artifactId>
- <version>2.4</version>
- <executions>
- <execution>
- <phase>package</phase>
- <goals>
- <goal>single</goal>
- </goals>
- </execution>
- </executions>
- <configuration>
- <descriptors>
- <descriptor>${assembly.descriptor}</descriptor>
- </descriptors>
- <archiverConfig>
- <directoryMode>493</directoryMode> <!-- 493(dec) = 755(oct) -->
- <defaultDirectoryMode>493</defaultDirectoryMode>
- </archiverConfig>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>buildnumber-maven-plugin</artifactId>
- <version>1.0-beta-3</version>
- <executions>
- <execution>
- <id>buildnumber-validate</id>
- <phase>validate</phase>
- <goals>
- <goal>create</goal>
- </goals>
- </execution>
- </executions>
- <configuration>
- <format>{0,date,yyyyMMdd}T{0,date,HHmm}</format>
- <items>
- <item>timestamp</item>
- </items>
- </configuration>
- </plugin>
- <plugin>
- <groupId>net.sf.taverna.t2.maven.plugins</groupId>
- <artifactId>taverna-maven-plugin</artifactId>
- <version>0.3.1-SNAPSHOT</version>
- <extensions>true</extensions>
- <configuration>
- <buildNumber>${buildNumber}</buildNumber>
- <updateSite>${profile.updateSite}</updateSite>
- <pluginSite>${profile.pluginSite}</pluginSite>
- <frameworkConfigurations>
- <frameworkConfiguration>
- <name>org.osgi.framework.bootdelegation</name>
- <value>sun.*,com.sun.*,java.*,javax.*,org.xml.*,org.w3c.*,apple.*,com.apple.*,org.omg.*,org.ietf.jgss.*,org.jcp.xml.dsig.internal.*</value>
- </frameworkConfiguration>
- <frameworkConfiguration>
- <name>org.osgi.framework.system.packages.extra</name>
- <value>com.sun.org.apache.xml.internal.utils,org.apache.log4j;version=1.2.16,net.sf.taverna.t2.commandline.options;version=2.0.1</value>
- </frameworkConfiguration>
- <frameworkConfiguration>
- <name>org.osgi.framework.storage.clean</name>
- <value>onFirstInit</value>
- </frameworkConfiguration>
- </frameworkConfigurations>
- </configuration>
- </plugin>
- </plugins>
- <pluginManagement>
- <plugins>
- <!--This plugin's configuration is used to store Eclipse m2e settings
- only. It has no influence on the Maven build itself. -->
- <plugin>
- <groupId>org.eclipse.m2e</groupId>
- <artifactId>lifecycle-mapping</artifactId>
- <version>1.0.0</version>
- <configuration>
- <lifecycleMappingMetadata>
- <pluginExecutions>
- <pluginExecution>
- <pluginExecutionFilter>
- <groupId>
- net.sf.taverna.t2.maven.plugins
- </groupId>
- <artifactId>
- taverna-maven-plugin
- </artifactId>
- <versionRange>
- [0.3.1-SNAPSHOT,)
- </versionRange>
- <goals>
- <goal>
- profile-generate
- </goal>
- </goals>
- </pluginExecutionFilter>
- <action>
- <execute>
- <runOnIncremental>false</runOnIncremental>
- </execute>
- </action>
- </pluginExecution>
- </pluginExecutions>
- </lifecycleMappingMetadata>
- </configuration>
- </plugin>
- </plugins>
- </pluginManagement>
- </build>
-
- <dependencies>
-
- <!-- Explicit org.osgi.* with <scope>provided as these are also provided
- by the felix osgi package. Avoids: Caused by: java.lang.SecurityException:
- class "org.osgi.framework.hooks.bundle.CollisionHook"'s signer information
- does not match signer information of other classes in the same package -->
-
- <dependency>
- <groupId>org.osgi</groupId>
- <artifactId>org.osgi.core</artifactId>
- <version>${osgi.core.version}</version>
- <scope>provided</scope>
- </dependency>
- <dependency>
- <groupId>org.osgi</groupId>
- <artifactId>org.osgi.compendium</artifactId>
- <version>${osgi.core.version}</version>
- <scope>provided</scope>
- </dependency>
-
- <!-- Invalid manifest header Import-Package: "com.sun.jdmk.comm;resolution:="optional"" : Cannot import a package more than once "com.sun.jdmk.comm"-->
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- <version>${log4j.version}</version>
- <scope>provided</scope>
- </dependency>
-
- <!-- Spring DM -->
- <dependency>
- <groupId>net.sourceforge.cglib</groupId>
- <artifactId>com.springsource.net.sf.cglib</artifactId>
- <version>${cglib.version}</version>
- </dependency>
- <dependency>
- <groupId>org.springframework.osgi</groupId>
- <artifactId>spring-osgi-annotation</artifactId>
- <version>${spring.dm.version}</version>
- </dependency>
- <dependency>
- <groupId>org.springframework.osgi</groupId>
- <artifactId>spring-osgi-extender</artifactId>
- <version>${spring.dm.version}</version>
- </dependency>
- <!-- Spring -->
- <dependency>
- <groupId>org.springframework</groupId>
- <artifactId>org.springframework.context</artifactId>
- <version>${spring.version}</version>
- </dependency>
-
- <!-- Java Extension Implementations -->
- <!-- Appears unrequired dependency>
- <groupId>javax.xml.bind</groupId>
- <artifactId>com.springsource.javax.xml.bind</artifactId>
- <version>2.2.0</version>
- </dependency-->
- <dependency>
- <groupId>javax.activation</groupId>
- <artifactId>com.springsource.javax.activation</artifactId>
- <version>${activation.version}</version>
- </dependency>
- <!-- The bundle "com.springsource.bsh_2.0.0.b4 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.servlet; version="[2.5.0,3.0.0)" -->
- <dependency>
- <groupId>javax.servlet</groupId>
- <artifactId>com.springsource.javax.servlet</artifactId>
- <version>2.5.0</version>
- </dependency>
- <!-- The bundle "com.springsource.org.apache.axis_1.4.0 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.jms; version="[1.1.0,2.0.0)" -->
- <dependency>
- <groupId>javax.jms</groupId>
- <artifactId>com.springsource.javax.jms</artifactId>
- <version>1.1.0</version>
- </dependency>
- <!-- The bundle "com.springsource.javax.xml.rpc_1.1.0 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.xml.soap; version="[1.3.0,2.0.0)" -->
- <dependency>
- <groupId>javax.xml.soap</groupId>
- <artifactId>com.springsource.javax.xml.soap</artifactId>
- <version>1.3.0</version>
- </dependency>
- <!-- The bundle "com.springsource.com.thoughtworks.xstream_1.4.1" could not be resolved. Reason: Missing Constraint: Import-Package: javax.xml.stream; version="[1.0.1,2.0.0)" -->
- <dependency>
- <groupId>javax.xml.stream</groupId>
- <artifactId>com.springsource.javax.xml.stream</artifactId>
- <version>1.0.1</version>
- </dependency>
- <dependency>
- <groupId>javax.mail</groupId>
- <artifactId>com.springsource.javax.mail</artifactId>
- <version>${mail.version}</version>
- </dependency>
- <dependency>
- <groupId>commons-codec</groupId>
- <artifactId>commons-codec</artifactId>
- <version>${commons.codec.version}</version>
- </dependency>
- <dependency>
- <groupId>commons-configuration</groupId>
- <artifactId>commons-configuration</artifactId>
- <version>1.10</version>
- </dependency>
- <dependency>
- <groupId>com.sun.xml.bind</groupId>
- <artifactId>jaxb-impl</artifactId>
- <version>2.2.11</version>
- </dependency>
-
-
- <!-- OSGi Enterprise Services -->
- <dependency>
- <groupId>uk.org.taverna.osgi.services</groupId>
- <artifactId>xml-parser-service</artifactId>
- <version>${osgi.services.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.osgi.services</groupId>
- <artifactId>xml-transformer-service</artifactId>
- <version>${osgi.services.version}</version>
- </dependency>
- <!-- The bundle "uk.org.taverna.commons.taverna-plugin-impl_0.1.0.SNAPSHOT" could not be resolved. Reason: Missing Constraint: Import-Package: org.osgi.service.event; version="[1.3.0,2.0.0)" -->
- <dependency>
- <groupId>org.apache.felix</groupId>
- <artifactId>org.apache.felix.eventadmin</artifactId>
- <version>1.3.2</version>
- </dependency>
- <!-- Appears unrequired dependency>
- <groupId>org.apache.felix</groupId>
- <artifactId>org.apache.felix.configadmin</artifactId>
- <version>1.6.0</version>
- </dependency-->
-
- <!-- Taverna Activities -->
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>apiconsumer-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>beanshell-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>biomart-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>dataflow-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <!-- <dependency> <groupId>net.sf.taverna.t2.activities</groupId> <artifactId>external-tool-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version> </dependency> -->
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>localworker-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>rest-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>rshell-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>soaplab-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>spreadsheet-import-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>stringconstant-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>wsdl-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>xpath-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
-
- <!-- Taverna Commandline -->
- <dependency>
- <groupId>net.sf.taverna.t2.taverna-commandline</groupId>
- <artifactId>taverna-commandline-common</artifactId>
- <version>${t2.taverna-commandline.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.commandline</groupId>
- <artifactId>taverna-command-line</artifactId>
- <version>${taverna-command-line.version}</version>
- </dependency>
-
- <!-- Taverna Platform -->
- <dependency>
- <groupId>uk.org.taverna.platform</groupId>
- <artifactId>taverna-capability-impl</artifactId>
- <version>${platform.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.platform</groupId>
- <artifactId>taverna-run-impl</artifactId>
- <version>${platform.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.platform</groupId>
- <artifactId>taverna-execution-impl</artifactId>
- <version>${platform.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.platform</groupId>
- <artifactId>taverna-execution-local</artifactId>
- <version>${platform.version}</version>
- </dependency>
-
- <!-- Taverna Commons -->
- <dependency>
- <groupId>uk.org.taverna.configuration</groupId>
- <artifactId>taverna-configuration-impl</artifactId>
- <version>0.1.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.configuration</groupId>
- <artifactId>taverna-app-configuration-impl</artifactId>
- <version>0.1.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.configuration</groupId>
- <artifactId>taverna-database-configuration-impl</artifactId>
- <version>0.1.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.commons</groupId>
- <artifactId>taverna-download-impl</artifactId>
- <version>0.1.0-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.commons</groupId>
- <artifactId>taverna-plugin-impl</artifactId>
- <version>0.1.0-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.commons</groupId>
- <artifactId>taverna-services-impl</artifactId>
- <version>0.1.0-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.commons</groupId>
- <artifactId>taverna-update-impl</artifactId>
- <version>0.1.0-SNAPSHOT</version>
- </dependency>
-
- <!-- Scufl2 -->
- <dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-rdfxml</artifactId>
- <version>${scufl2.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-t2flow</artifactId>
- <version>${scufl2.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-validation-structural</artifactId>
- <version>${scufl2.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-validation-correctness</artifactId>
- <version>${scufl2.version}</version>
- </dependency>
-
- <!-- Data bundle -->
- <dependency>
- <groupId>uk.org.taverna.databundle</groupId>
- <artifactId>databundle</artifactId>
- <version>${taverna.databundle.version}</version>
- </dependency>
- <!-- HTTP client needed by Data Bundle -->
- <!-- Appears unrequired dependency>
- <groupId>org.apache.httpcomponents</groupId>
- <artifactId>httpclient-osgi</artifactId>
- <version>4.2.5</version>
- </dependency-->
- <!-- Appears unrequired dependency>
- <groupId>org.apache.httpcomponents</groupId>
- <artifactId>httpcore-osgi</artifactId>
- <version>4.2.5</version>
- </dependency-->
- <!-- Jena bundle needed by jsonld-java-jena -->
- <!-- See https://github.com/stain/jena/tree/jena-bundle/jena-bundle -->
- <dependency>
- <groupId>org.apache.jena</groupId>
- <artifactId>jena-bundle</artifactId>
- <version>2.12.2-SNAPSHOT</version>
- </dependency>
- <!-- slf4j implementation -->
- <!-- The bundle "org.purl.wf4ever.robundle_0.3.1 " could not be resolved. Reason: Missing Constraint: Import-Package: org.slf4j; version="[1.7.0,2.0.0)"-->
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-api</artifactId>
- <version>1.7.5</version>
- </dependency>
- <!-- Appears unrequired dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-log4j12</artifactId>
- <version>1.7.5</version>
- </dependency-->
-
- <!-- Taverna Security -->
- <dependency>
- <groupId>net.sf.taverna.t2.security</groupId>
- <artifactId>credential-manager-impl</artifactId>
- <version>${t2.security.version}</version>
- </dependency>
-
- <!-- Taverna Workflow Engine -->
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-impl</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-core-extensions</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>reference-impl</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>reference-core-extensions</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
-
- <!-- Taverna Provenance -->
- <!--dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>provenance-derby</artifactId>
- <version>${t2.core.provenance.derby.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>provenance-mysql</artifactId>
- <version>${t2.core.provenance.mysql.version}</version>
- </dependency-->
- <!-- The bundle "org.purl.wf4ever.robundle_0.3.1 " could not be resolved. Reason: Missing Constraint: Import-Package: com.fasterxml.jackson.annotation; version="[2.3.0,3.0.0)"-->
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-core</artifactId>
- <version>2.3.0</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-annotations</artifactId>
- <version>2.3.0</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
- <version>2.3.0</version>
- </dependency>
- </dependencies>
-
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- <repository>
- <id>spring-maven-milestone</id>
- <name>Springframework Maven Repository</name>
- <url>http://maven.springframework.org/milestone</url>
- </repository>
- <repository>
- <id>com.springsource.repository.bundles.milestone</id>
- <name>SpringSource Enterprise Bundle Repository - SpringSource Bundle Milestones</name>
- <url>http://repository.springsource.com/maven/bundles/milestone</url>
- </repository>
- <repository>
- <id>OPS4J</id>
- <url>http://repository.ops4j.org/maven2</url>
- </repository>
- </repositories>
-
- <scm>
- <connection>scm:svn:http://taverna.googlecode.com/svn/taverna/products/net.sf.taverna.t2.taverna-commandline/trunk/</connection>
- <developerConnection>scm:svn:https://taverna.googlecode.com/svn/taverna/products/net.sf.taverna.t2.taverna-commandline/trunk/</developerConnection>
- <url>http://code.google.com/p/taverna/source/browse/#svn/taverna/products/net.sf.taverna.t2.taverna-commandline/trunk/</url>
- </scm>
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/src/main/assembly/dependencies-component.xml
----------------------------------------------------------------------
diff --git a/src/main/assembly/dependencies-component.xml b/src/main/assembly/dependencies-component.xml
deleted file mode 100644
index 0e8640e..0000000
--- a/src/main/assembly/dependencies-component.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<component
- xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/component/1.1.2"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/component/1.1.2 http://maven.apache.org/xsd/component-1.1.2.xsd">
-
- <fileSets>
- <fileSet>
- <directory>src/main/etc</directory>
- <fileMode>0755</fileMode>
- <outputDirectory></outputDirectory>
- <filtered>true</filtered>
- </fileSet>
- <fileSet>
- <directory>${project.build.directory}/taverna-tmp</directory>
- <fileMode>0755</fileMode>
- <outputDirectory></outputDirectory>
- </fileSet>
- </fileSets>
-
-</component>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/src/main/assembly/developer-assembly.xml
----------------------------------------------------------------------
diff --git a/src/main/assembly/developer-assembly.xml b/src/main/assembly/developer-assembly.xml
deleted file mode 100644
index ae2a7c3..0000000
--- a/src/main/assembly/developer-assembly.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<assembly
- xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
- <id>dev</id>
- <formats>
- <format>dir</format>
- </formats>
- <componentDescriptors>
- <componentDescriptor>dependencies-component.xml</componentDescriptor>
- </componentDescriptors>
-</assembly>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/src/main/assembly/nightly-assembly.xml
----------------------------------------------------------------------
diff --git a/src/main/assembly/nightly-assembly.xml b/src/main/assembly/nightly-assembly.xml
deleted file mode 100644
index f82e793..0000000
--- a/src/main/assembly/nightly-assembly.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<assembly
- xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
- <id>nightly</id>
- <baseDirectory>taverna-command-line-${project.version}-${buildNumber}-nightly</baseDirectory>
- <formats>
- <!-- <format>dir</format> -->
- <format>zip</format>
- </formats>
- <componentDescriptors>
- <componentDescriptor>dependencies-component.xml</componentDescriptor>
- </componentDescriptors>
-</assembly>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/src/main/assembly/release-assembly.xml
----------------------------------------------------------------------
diff --git a/src/main/assembly/release-assembly.xml b/src/main/assembly/release-assembly.xml
deleted file mode 100644
index 61da752..0000000
--- a/src/main/assembly/release-assembly.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<assembly
- xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
- <id>release</id>
- <baseDirectory>taverna-command-line-${project.version}</baseDirectory>
- <formats>
- <!-- <format>dir</format> -->
- <format>zip</format>
- </formats>
- <componentDescriptors>
- <componentDescriptor>dependencies-component.xml</componentDescriptor>
- </componentDescriptors>
-</assembly>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/src/main/etc/conf/log4j.properties
----------------------------------------------------------------------
diff --git a/src/main/etc/conf/log4j.properties b/src/main/etc/conf/log4j.properties
deleted file mode 100644
index 5014f2b..0000000
--- a/src/main/etc/conf/log4j.properties
+++ /dev/null
@@ -1,14 +0,0 @@
-# By default, WARN (our external libraries)
-log4j.rootLogger=INFO, CONSOLE
-
-# Get rid of some xml sec warnings
-log4j.logger.org.apache.ws.security=ERROR
-log4j.logger.org.apache.commons.httpclient=ERROR
-
-# Default output to console is restrictive
-log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
-log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
-log4j.appender.CONSOLE.layout.ConversionPattern=%-5p %d{ISO8601} (%c:%L) - %m%n
-
-# Output WARN and above to console -
-log4j.appender.CONSOLE.Threshold=ERROR
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/src/main/etc/conf/logging.properties
----------------------------------------------------------------------
diff --git a/src/main/etc/conf/logging.properties b/src/main/etc/conf/logging.properties
deleted file mode 100644
index b03a43f..0000000
--- a/src/main/etc/conf/logging.properties
+++ /dev/null
@@ -1,10 +0,0 @@
-handlers = java.util.logging.ConsoleHandler, java.util.logging.FileHandler
-
-.level = ALL
-
-java.util.logging.ConsoleHandler.level = WARNING
-java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
-
-java.util.logging.FileHandler.level = ALL
-java.util.logging.FileHandler.count = 5
-java.util.logging.FileHandler.limit = 1048576
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/src/main/etc/conf/taverna.app.properties
----------------------------------------------------------------------
diff --git a/src/main/etc/conf/taverna.app.properties b/src/main/etc/conf/taverna.app.properties
deleted file mode 100644
index 91522d4..0000000
--- a/src/main/etc/conf/taverna.app.properties
+++ /dev/null
@@ -1,2 +0,0 @@
-taverna.app.name=taverna-cl-3.0.0
-taverna.app.title=Taverna Command Line 3.0.0
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/src/main/etc/executeworkflow.bat
----------------------------------------------------------------------
diff --git a/src/main/etc/executeworkflow.bat b/src/main/etc/executeworkflow.bat
deleted file mode 100644
index 722816c..0000000
--- a/src/main/etc/executeworkflow.bat
+++ /dev/null
@@ -1,17 +0,0 @@
-@ECHO OFF
-
-REM Taverna startup script
-
-REM distribution directory
-set TAVERNA_HOME=%~dp0
-
-
-REM 1 GB memory, 400 MB for classes
-set ARGS=-Xmx1g -XX:MaxPermSize=400m
-
-REM Taverna system properties
-set ARGS=%ARGS% "-Dlog4j.configuration=file:///%TAVERNA_HOME%conf/log4j.properties"
-set ARGS=%ARGS% "-Djava.util.logging.config.file=%TAVERNA_HOME%conf/logging.properties"
-set ARGS=%ARGS% "-Dtaverna.app.startup=%TAVERNA_HOME%."
-
-java %ARGS% -jar "%TAVERNA_HOME%lib\uk.org.taverna.commandline\taverna-command-line-0.1.2-SNAPSHOT.jar" %*
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/src/main/etc/executeworkflow.sh
----------------------------------------------------------------------
diff --git a/src/main/etc/executeworkflow.sh b/src/main/etc/executeworkflow.sh
deleted file mode 100644
index 663d37f..0000000
--- a/src/main/etc/executeworkflow.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/sh
-
-set -e
-
-## resolve links - $0 may be a symlink
-prog="$0"
-
-real_path() {
- readlink -m "$1" 2>/dev/null || python -c 'import os,sys;print os.path.realpath(sys.argv[1])' "$1"
-}
-
-realprog=`real_path "$prog"`
-taverna_home=`dirname "$realprog"`
-javabin=java
-if test -x "$JAVA_HOME/bin/java"; then
- javabin="$JAVA_HOME/bin/java"
-fi
-
-# 1 GB memory, 400 MB for classes
-exec "$javabin" -Xmx1g -XX:MaxPermSize=400m \
- "-Dlog4j.configuration=file://$taverna_home/conf/log4j.properties " \
- "-Djava.util.logging.config.file=$taverna_home/conf/logging.properties " \
- "-Dtaverna.app.startup=$taverna_home" \
- -jar "$taverna_home/lib/uk.org.taverna.commandline/taverna-command-line-0.1.2-SNAPSHOT.jar" \
- ${1+"$@"}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/taverna-commandline-product/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/pom.xml b/taverna-commandline-product/pom.xml
new file mode 100644
index 0000000..d67a916
--- /dev/null
+++ b/taverna-commandline-product/pom.xml
@@ -0,0 +1,578 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>uk.org.taverna.workbench</groupId>
+ <artifactId>taverna-command-line-product</artifactId>
+ <name>Taverna Command Line</name>
+ <packaging>taverna-application</packaging>
+ <profiles>
+ <profile>
+ <id>developer</id>
+ <activation>
+ <activeByDefault>true</activeByDefault>
+ </activation>
+ <properties>
+ <assembly.descriptor>src/main/assembly/developer-assembly.xml</assembly.descriptor>
+ <profile.updateSite>http://dev.mygrid.org.uk/taverna/updates/taverna-command-line/</profile.updateSite>
+ <profile.pluginSite>http://dev.mygrid.org.uk/taverna/plugins/taverna-command-line/</profile.pluginSite>
+ </properties>
+ </profile>
+ <profile>
+ <id>nightly</id>
+ <properties>
+ <assembly.descriptor>src/main/assembly/nightly-assembly.xml</assembly.descriptor>
+ <profile.updateSite>http://dev.mygrid.org.uk/taverna/updates/taverna-command-line/</profile.updateSite>
+ <profile.pluginSite>http://dev.mygrid.org.uk/taverna/plugins/taverna-command-line/</profile.pluginSite>
+ </properties>
+ </profile>
+ <profile>
+ <id>release</id>
+ <properties>
+ <assembly.descriptor>src/main/assembly/release-assembly.xml</assembly.descriptor>
+ <profile.updateSite>http://www.mygrid.org.uk/taverna/updates/taverna-command-line/</profile.updateSite>
+ <profile.pluginSite>http://www.mygrid.org.uk/taverna/plugins/taverna-command-line/</profile.pluginSite>
+ </properties>
+ </profile>
+ </profiles>
+ <build>
+ <finalName>taverna-command-line-${project.version}</finalName>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <version>2.4</version>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <descriptors>
+ <descriptor>${assembly.descriptor}</descriptor>
+ </descriptors>
+ <archiverConfig>
+ <directoryMode>493</directoryMode> <!-- 493(dec) = 755(oct) -->
+ <defaultDirectoryMode>493</defaultDirectoryMode>
+ </archiverConfig>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>buildnumber-maven-plugin</artifactId>
+ <version>1.0-beta-3</version>
+ <executions>
+ <execution>
+ <id>buildnumber-validate</id>
+ <phase>validate</phase>
+ <goals>
+ <goal>create</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <format>{0,date,yyyyMMdd}T{0,date,HHmm}</format>
+ <items>
+ <item>timestamp</item>
+ </items>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>net.sf.taverna.t2.maven.plugins</groupId>
+ <artifactId>taverna-maven-plugin</artifactId>
+ <version>0.3.1-SNAPSHOT</version>
+ <extensions>true</extensions>
+ <configuration>
+ <buildNumber>${buildNumber}</buildNumber>
+ <updateSite>${profile.updateSite}</updateSite>
+ <pluginSite>${profile.pluginSite}</pluginSite>
+ <frameworkConfigurations>
+ <frameworkConfiguration>
+ <name>org.osgi.framework.bootdelegation</name>
+ <value>sun.*,com.sun.*,java.*,javax.*,org.xml.*,org.w3c.*,apple.*,com.apple.*,org.omg.*,org.ietf.jgss.*,org.jcp.xml.dsig.internal.*</value>
+ </frameworkConfiguration>
+ <frameworkConfiguration>
+ <name>org.osgi.framework.system.packages.extra</name>
+ <value>com.sun.org.apache.xml.internal.utils,org.apache.log4j;version=1.2.16,net.sf.taverna.t2.commandline.options;version=2.0.1</value>
+ </frameworkConfiguration>
+ <frameworkConfiguration>
+ <name>org.osgi.framework.storage.clean</name>
+ <value>onFirstInit</value>
+ </frameworkConfiguration>
+ </frameworkConfigurations>
+ </configuration>
+ </plugin>
+ </plugins>
+ <pluginManagement>
+ <plugins>
+ <!--This plugin's configuration is used to store Eclipse m2e settings
+ only. It has no influence on the Maven build itself. -->
+ <plugin>
+ <groupId>org.eclipse.m2e</groupId>
+ <artifactId>lifecycle-mapping</artifactId>
+ <version>1.0.0</version>
+ <configuration>
+ <lifecycleMappingMetadata>
+ <pluginExecutions>
+ <pluginExecution>
+ <pluginExecutionFilter>
+ <groupId>
+ net.sf.taverna.t2.maven.plugins
+ </groupId>
+ <artifactId>
+ taverna-maven-plugin
+ </artifactId>
+ <versionRange>
+ [0.3.1-SNAPSHOT,)
+ </versionRange>
+ <goals>
+ <goal>
+ profile-generate
+ </goal>
+ </goals>
+ </pluginExecutionFilter>
+ <action>
+ <execute>
+ <runOnIncremental>false</runOnIncremental>
+ </execute>
+ </action>
+ </pluginExecution>
+ </pluginExecutions>
+ </lifecycleMappingMetadata>
+ </configuration>
+ </plugin>
+ </plugins>
+ </pluginManagement>
+ </build>
+
+ <dependencies>
+
+ <!-- Explicit org.osgi.* with <scope>provided as these are also provided
+ by the felix osgi package. Avoids: Caused by: java.lang.SecurityException:
+ class "org.osgi.framework.hooks.bundle.CollisionHook"'s signer information
+ does not match signer information of other classes in the same package -->
+
+ <dependency>
+ <groupId>org.osgi</groupId>
+ <artifactId>org.osgi.core</artifactId>
+ <version>${osgi.core.version}</version>
+ <scope>provided</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.osgi</groupId>
+ <artifactId>org.osgi.compendium</artifactId>
+ <version>${osgi.core.version}</version>
+ <scope>provided</scope>
+ </dependency>
+
+ <!-- Invalid manifest header Import-Package: "com.sun.jdmk.comm;resolution:="optional"" : Cannot import a package more than once "com.sun.jdmk.comm"-->
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ <version>${log4j.version}</version>
+ <scope>provided</scope>
+ </dependency>
+
+ <!-- Spring DM -->
+ <dependency>
+ <groupId>net.sourceforge.cglib</groupId>
+ <artifactId>com.springsource.net.sf.cglib</artifactId>
+ <version>${cglib.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.springframework.osgi</groupId>
+ <artifactId>spring-osgi-annotation</artifactId>
+ <version>${spring.dm.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.springframework.osgi</groupId>
+ <artifactId>spring-osgi-extender</artifactId>
+ <version>${spring.dm.version}</version>
+ </dependency>
+ <!-- Spring -->
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>org.springframework.context</artifactId>
+ <version>${spring.version}</version>
+ </dependency>
+
+ <!-- Java Extension Implementations -->
+ <!-- Appears unrequired dependency>
+ <groupId>javax.xml.bind</groupId>
+ <artifactId>com.springsource.javax.xml.bind</artifactId>
+ <version>2.2.0</version>
+ </dependency-->
+ <dependency>
+ <groupId>javax.activation</groupId>
+ <artifactId>com.springsource.javax.activation</artifactId>
+ <version>${activation.version}</version>
+ </dependency>
+ <!-- The bundle "com.springsource.bsh_2.0.0.b4 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.servlet; version="[2.5.0,3.0.0)" -->
+ <dependency>
+ <groupId>javax.servlet</groupId>
+ <artifactId>com.springsource.javax.servlet</artifactId>
+ <version>2.5.0</version>
+ </dependency>
+ <!-- The bundle "com.springsource.org.apache.axis_1.4.0 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.jms; version="[1.1.0,2.0.0)" -->
+ <dependency>
+ <groupId>javax.jms</groupId>
+ <artifactId>com.springsource.javax.jms</artifactId>
+ <version>1.1.0</version>
+ </dependency>
+ <!-- The bundle "com.springsource.javax.xml.rpc_1.1.0 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.xml.soap; version="[1.3.0,2.0.0)" -->
+ <dependency>
+ <groupId>javax.xml.soap</groupId>
+ <artifactId>com.springsource.javax.xml.soap</artifactId>
+ <version>1.3.0</version>
+ </dependency>
+ <!-- The bundle "com.springsource.com.thoughtworks.xstream_1.4.1" could not be resolved. Reason: Missing Constraint: Import-Package: javax.xml.stream; version="[1.0.1,2.0.0)" -->
+ <dependency>
+ <groupId>javax.xml.stream</groupId>
+ <artifactId>com.springsource.javax.xml.stream</artifactId>
+ <version>1.0.1</version>
+ </dependency>
+ <dependency>
+ <groupId>javax.mail</groupId>
+ <artifactId>com.springsource.javax.mail</artifactId>
+ <version>${mail.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-codec</groupId>
+ <artifactId>commons-codec</artifactId>
+ <version>${commons.codec.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-configuration</groupId>
+ <artifactId>commons-configuration</artifactId>
+ <version>1.10</version>
+ </dependency>
+ <dependency>
+ <groupId>com.sun.xml.bind</groupId>
+ <artifactId>jaxb-impl</artifactId>
+ <version>2.2.11</version>
+ </dependency>
+
+
+ <!-- OSGi Enterprise Services -->
+ <dependency>
+ <groupId>uk.org.taverna.osgi.services</groupId>
+ <artifactId>xml-parser-service</artifactId>
+ <version>${osgi.services.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.osgi.services</groupId>
+ <artifactId>xml-transformer-service</artifactId>
+ <version>${osgi.services.version}</version>
+ </dependency>
+ <!-- The bundle "uk.org.taverna.commons.taverna-plugin-impl_0.1.0.SNAPSHOT" could not be resolved. Reason: Missing Constraint: Import-Package: org.osgi.service.event; version="[1.3.0,2.0.0)" -->
+ <dependency>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>org.apache.felix.eventadmin</artifactId>
+ <version>1.3.2</version>
+ </dependency>
+ <!-- Appears unrequired dependency>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>org.apache.felix.configadmin</artifactId>
+ <version>1.6.0</version>
+ </dependency-->
+
+ <!-- Taverna Activities -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>apiconsumer-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>beanshell-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>biomart-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>dataflow-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
+ </dependency>
+ <!-- <dependency> <groupId>net.sf.taverna.t2.activities</groupId> <artifactId>external-tool-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version> </dependency> -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>localworker-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>rest-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>rshell-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>soaplab-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>spreadsheet-import-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>stringconstant-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>wsdl-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>xpath-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
+ </dependency>
+
+ <!-- Taverna Commandline -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.taverna-commandline</groupId>
+ <artifactId>taverna-commandline-common</artifactId>
+ <version>${t2.taverna-commandline.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.commandline</groupId>
+ <artifactId>taverna-command-line</artifactId>
+ <version>${taverna-command-line.version}</version>
+ </dependency>
+
+ <!-- Taverna Platform -->
+ <dependency>
+ <groupId>uk.org.taverna.platform</groupId>
+ <artifactId>taverna-capability-impl</artifactId>
+ <version>${platform.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.platform</groupId>
+ <artifactId>taverna-run-impl</artifactId>
+ <version>${platform.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.platform</groupId>
+ <artifactId>taverna-execution-impl</artifactId>
+ <version>${platform.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.platform</groupId>
+ <artifactId>taverna-execution-local</artifactId>
+ <version>${platform.version}</version>
+ </dependency>
+
+ <!-- Taverna Commons -->
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-configuration-impl</artifactId>
+ <version>0.1.1-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-app-configuration-impl</artifactId>
+ <version>0.1.1-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-database-configuration-impl</artifactId>
+ <version>0.1.1-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.commons</groupId>
+ <artifactId>taverna-download-impl</artifactId>
+ <version>0.1.0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.commons</groupId>
+ <artifactId>taverna-plugin-impl</artifactId>
+ <version>0.1.0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.commons</groupId>
+ <artifactId>taverna-services-impl</artifactId>
+ <version>0.1.0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.commons</groupId>
+ <artifactId>taverna-update-impl</artifactId>
+ <version>0.1.0-SNAPSHOT</version>
+ </dependency>
+
+ <!-- Scufl2 -->
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-rdfxml</artifactId>
+ <version>${scufl2.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-t2flow</artifactId>
+ <version>${scufl2.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-validation-structural</artifactId>
+ <version>${scufl2.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-validation-correctness</artifactId>
+ <version>${scufl2.version}</version>
+ </dependency>
+
+ <!-- Data bundle -->
+ <dependency>
+ <groupId>uk.org.taverna.databundle</groupId>
+ <artifactId>databundle</artifactId>
+ <version>${taverna.databundle.version}</version>
+ </dependency>
+ <!-- HTTP client needed by Data Bundle -->
+ <!-- Appears unrequired dependency>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpclient-osgi</artifactId>
+ <version>4.2.5</version>
+ </dependency-->
+ <!-- Appears unrequired dependency>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpcore-osgi</artifactId>
+ <version>4.2.5</version>
+ </dependency-->
+ <!-- Jena bundle needed by jsonld-java-jena -->
+ <!-- See https://github.com/stain/jena/tree/jena-bundle/jena-bundle -->
+ <dependency>
+ <groupId>org.apache.jena</groupId>
+ <artifactId>jena-bundle</artifactId>
+ <version>2.12.2-SNAPSHOT</version>
+ </dependency>
+ <!-- slf4j implementation -->
+ <!-- The bundle "org.purl.wf4ever.robundle_0.3.1 " could not be resolved. Reason: Missing Constraint: Import-Package: org.slf4j; version="[1.7.0,2.0.0)"-->
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-api</artifactId>
+ <version>1.7.5</version>
+ </dependency>
+ <!-- Appears unrequired dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-log4j12</artifactId>
+ <version>1.7.5</version>
+ </dependency-->
+
+ <!-- Taverna Security -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.security</groupId>
+ <artifactId>credential-manager-impl</artifactId>
+ <version>${t2.security.version}</version>
+ </dependency>
+
+ <!-- Taverna Workflow Engine -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>workflowmodel-impl</artifactId>
+ <version>${t2.core.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>workflowmodel-core-extensions</artifactId>
+ <version>${t2.core.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>reference-impl</artifactId>
+ <version>${t2.core.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>reference-core-extensions</artifactId>
+ <version>${t2.core.version}</version>
+ </dependency>
+
+ <!-- Taverna Provenance -->
+ <!--dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>provenance-derby</artifactId>
+ <version>${t2.core.provenance.derby.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>provenance-mysql</artifactId>
+ <version>${t2.core.provenance.mysql.version}</version>
+ </dependency-->
+ <!-- The bundle "org.purl.wf4ever.robundle_0.3.1 " could not be resolved. Reason: Missing Constraint: Import-Package: com.fasterxml.jackson.annotation; version="[2.3.0,3.0.0)"-->
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-core</artifactId>
+ <version>2.3.0</version>
+ </dependency>
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-annotations</artifactId>
+ <version>2.3.0</version>
+ </dependency>
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>2.3.0</version>
+ </dependency>
+ </dependencies>
+
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository</url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ </repository>
+ <repository>
+ <id>spring-maven-milestone</id>
+ <name>Springframework Maven Repository</name>
+ <url>http://maven.springframework.org/milestone</url>
+ </repository>
+ <repository>
+ <id>com.springsource.repository.bundles.milestone</id>
+ <name>SpringSource Enterprise Bundle Repository - SpringSource Bundle Milestones</name>
+ <url>http://repository.springsource.com/maven/bundles/milestone</url>
+ </repository>
+ <repository>
+ <id>OPS4J</id>
+ <url>http://repository.ops4j.org/maven2</url>
+ </repository>
+ </repositories>
+
+ <scm>
+ <connection>scm:svn:http://taverna.googlecode.com/svn/taverna/products/net.sf.taverna.t2.taverna-commandline/trunk/</connection>
+ <developerConnection>scm:svn:https://taverna.googlecode.com/svn/taverna/products/net.sf.taverna.t2.taverna-commandline/trunk/</developerConnection>
+ <url>http://code.google.com/p/taverna/source/browse/#svn/taverna/products/net.sf.taverna.t2.taverna-commandline/trunk/</url>
+ </scm>
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/taverna-commandline-product/src/main/assembly/dependencies-component.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/assembly/dependencies-component.xml b/taverna-commandline-product/src/main/assembly/dependencies-component.xml
new file mode 100644
index 0000000..0e8640e
--- /dev/null
+++ b/taverna-commandline-product/src/main/assembly/dependencies-component.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<component
+ xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/component/1.1.2"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/component/1.1.2 http://maven.apache.org/xsd/component-1.1.2.xsd">
+
+ <fileSets>
+ <fileSet>
+ <directory>src/main/etc</directory>
+ <fileMode>0755</fileMode>
+ <outputDirectory></outputDirectory>
+ <filtered>true</filtered>
+ </fileSet>
+ <fileSet>
+ <directory>${project.build.directory}/taverna-tmp</directory>
+ <fileMode>0755</fileMode>
+ <outputDirectory></outputDirectory>
+ </fileSet>
+ </fileSets>
+
+</component>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/taverna-commandline-product/src/main/assembly/developer-assembly.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/assembly/developer-assembly.xml b/taverna-commandline-product/src/main/assembly/developer-assembly.xml
new file mode 100644
index 0000000..ae2a7c3
--- /dev/null
+++ b/taverna-commandline-product/src/main/assembly/developer-assembly.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<assembly
+ xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+ <id>dev</id>
+ <formats>
+ <format>dir</format>
+ </formats>
+ <componentDescriptors>
+ <componentDescriptor>dependencies-component.xml</componentDescriptor>
+ </componentDescriptors>
+</assembly>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/taverna-commandline-product/src/main/assembly/nightly-assembly.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/assembly/nightly-assembly.xml b/taverna-commandline-product/src/main/assembly/nightly-assembly.xml
new file mode 100644
index 0000000..f82e793
--- /dev/null
+++ b/taverna-commandline-product/src/main/assembly/nightly-assembly.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<assembly
+ xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+ <id>nightly</id>
+ <baseDirectory>taverna-command-line-${project.version}-${buildNumber}-nightly</baseDirectory>
+ <formats>
+ <!-- <format>dir</format> -->
+ <format>zip</format>
+ </formats>
+ <componentDescriptors>
+ <componentDescriptor>dependencies-component.xml</componentDescriptor>
+ </componentDescriptors>
+</assembly>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/taverna-commandline-product/src/main/assembly/release-assembly.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/assembly/release-assembly.xml b/taverna-commandline-product/src/main/assembly/release-assembly.xml
new file mode 100644
index 0000000..61da752
--- /dev/null
+++ b/taverna-commandline-product/src/main/assembly/release-assembly.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<assembly
+ xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+ <id>release</id>
+ <baseDirectory>taverna-command-line-${project.version}</baseDirectory>
+ <formats>
+ <!-- <format>dir</format> -->
+ <format>zip</format>
+ </formats>
+ <componentDescriptors>
+ <componentDescriptor>dependencies-component.xml</componentDescriptor>
+ </componentDescriptors>
+</assembly>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/taverna-commandline-product/src/main/etc/conf/log4j.properties
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/etc/conf/log4j.properties b/taverna-commandline-product/src/main/etc/conf/log4j.properties
new file mode 100644
index 0000000..5014f2b
--- /dev/null
+++ b/taverna-commandline-product/src/main/etc/conf/log4j.properties
@@ -0,0 +1,14 @@
+# By default, WARN (our external libraries)
+log4j.rootLogger=INFO, CONSOLE
+
+# Get rid of some xml sec warnings
+log4j.logger.org.apache.ws.security=ERROR
+log4j.logger.org.apache.commons.httpclient=ERROR
+
+# Default output to console is restrictive
+log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
+log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
+log4j.appender.CONSOLE.layout.ConversionPattern=%-5p %d{ISO8601} (%c:%L) - %m%n
+
+# Output WARN and above to console -
+log4j.appender.CONSOLE.Threshold=ERROR
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/taverna-commandline-product/src/main/etc/conf/logging.properties
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/etc/conf/logging.properties b/taverna-commandline-product/src/main/etc/conf/logging.properties
new file mode 100644
index 0000000..b03a43f
--- /dev/null
+++ b/taverna-commandline-product/src/main/etc/conf/logging.properties
@@ -0,0 +1,10 @@
+handlers = java.util.logging.ConsoleHandler, java.util.logging.FileHandler
+
+.level = ALL
+
+java.util.logging.ConsoleHandler.level = WARNING
+java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
+
+java.util.logging.FileHandler.level = ALL
+java.util.logging.FileHandler.count = 5
+java.util.logging.FileHandler.limit = 1048576
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/taverna-commandline-product/src/main/etc/conf/taverna.app.properties
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/etc/conf/taverna.app.properties b/taverna-commandline-product/src/main/etc/conf/taverna.app.properties
new file mode 100644
index 0000000..91522d4
--- /dev/null
+++ b/taverna-commandline-product/src/main/etc/conf/taverna.app.properties
@@ -0,0 +1,2 @@
+taverna.app.name=taverna-cl-3.0.0
+taverna.app.title=Taverna Command Line 3.0.0
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/taverna-commandline-product/src/main/etc/executeworkflow.bat
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/etc/executeworkflow.bat b/taverna-commandline-product/src/main/etc/executeworkflow.bat
new file mode 100644
index 0000000..722816c
--- /dev/null
+++ b/taverna-commandline-product/src/main/etc/executeworkflow.bat
@@ -0,0 +1,17 @@
+@ECHO OFF
+
+REM Taverna startup script
+
+REM distribution directory
+set TAVERNA_HOME=%~dp0
+
+
+REM 1 GB memory, 400 MB for classes
+set ARGS=-Xmx1g -XX:MaxPermSize=400m
+
+REM Taverna system properties
+set ARGS=%ARGS% "-Dlog4j.configuration=file:///%TAVERNA_HOME%conf/log4j.properties"
+set ARGS=%ARGS% "-Djava.util.logging.config.file=%TAVERNA_HOME%conf/logging.properties"
+set ARGS=%ARGS% "-Dtaverna.app.startup=%TAVERNA_HOME%."
+
+java %ARGS% -jar "%TAVERNA_HOME%lib\uk.org.taverna.commandline\taverna-command-line-0.1.2-SNAPSHOT.jar" %*
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/0257a92e/taverna-commandline-product/src/main/etc/executeworkflow.sh
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/etc/executeworkflow.sh b/taverna-commandline-product/src/main/etc/executeworkflow.sh
new file mode 100644
index 0000000..663d37f
--- /dev/null
+++ b/taverna-commandline-product/src/main/etc/executeworkflow.sh
@@ -0,0 +1,25 @@
+#!/bin/sh
+
+set -e
+
+## resolve links - $0 may be a symlink
+prog="$0"
+
+real_path() {
+ readlink -m "$1" 2>/dev/null || python -c 'import os,sys;print os.path.realpath(sys.argv[1])' "$1"
+}
+
+realprog=`real_path "$prog"`
+taverna_home=`dirname "$realprog"`
+javabin=java
+if test -x "$JAVA_HOME/bin/java"; then
+ javabin="$JAVA_HOME/bin/java"
+fi
+
+# 1 GB memory, 400 MB for classes
+exec "$javabin" -Xmx1g -XX:MaxPermSize=400m \
+ "-Dlog4j.configuration=file://$taverna_home/conf/log4j.properties " \
+ "-Djava.util.logging.config.file=$taverna_home/conf/logging.properties " \
+ "-Dtaverna.app.startup=$taverna_home" \
+ -jar "$taverna_home/lib/uk.org.taverna.commandline/taverna-command-line-0.1.2-SNAPSHOT.jar" \
+ ${1+"$@"}