http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-integration-tests/src/test/resources/t2flow/FetchTodaysXkcdComic.t2flow ---------------------------------------------------------------------- diff --git a/taverna-integration-tests/src/test/resources/t2flow/FetchTodaysXkcdComic.t2flow b/taverna-integration-tests/src/test/resources/t2flow/FetchTodaysXkcdComic.t2flow deleted file mode 100644 index 4aeef6f..0000000 --- a/taverna-integration-tests/src/test/resources/t2flow/FetchTodaysXkcdComic.t2flow +++ /dev/null @@ -1,343 +0,0 @@ -<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1" producedBy="taverna-2.3.0"><dataflow id="24e3ca77-bca1-47a6-8f5e-0549801eb27e" role="top"><name>Fetch_today_s_xkcd_comic</name><inputPorts /><outputPorts><port><name>todaysXkcd</name><annotations /></port></outputPorts><processors><processor><name>getPage</name><inputPorts><port><name>url</name><depth>0</depth></port></inputPorts><outputPorts><port><name>contents</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="url" to="url" /></inputMap><outputMap><map from="contents" to="contents" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns=""> - 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<name>contents</name> - <depth>0</depth> - <mimeTypes> - <string>'text/plain,text/html'</string> - </mimeTypes> - <granularDepth>0</granularDepth> - </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean> - </outputs> - <classLoaderSharing>workflow</classLoaderSharing> - <localDependencies /> - <artifactDependencies /> - <script>URL inputURL = null; -if (base != void) { - inputURL = new URL(new URL(base), url); -} -else { - inputURL = new URL(url); -} -URLConnection con = inputURL.openConnection(); -InputStream in = con.getInputStream(); - -InputStreamReader isr = new InputStreamReader(in); -Reader inReader = new BufferedReader(isr); - -StringBuffer buf = new StringBuffer(); -int ch; -while ((ch = inReader.read()) > -1) { - buf.append((char)ch); -} -inReader.close(); -contents = buf.toString(); - - -//String NEWLINE = System.getProperty("line.separator"); -// -//URL inputURL = null; -//if (base != void) { -// inputURL = new URL(new URL(base), url); -//} else { -// inputURL = new URL(url); -//} -//StringBuffer result = new StringBuffer(); -//BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream())); -//String line = null; -//while ((line = reader.readLine()) != null) { -// result.append(line); -// result.append(NEWLINE); -//} -// -//contents = result.toString(); -</script> - 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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="url" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>xkcdURL</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>http://xkcd.com/</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>getImageLinks</name><inputPorts><port><name>document</name><depth>0</depth></port></inputPorts><outputPorts><port><name>imagelinks</name><depth>1</depth><granularDepth>1</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="document" to="document" /></inputMap><outputMap><map from="imagelinks" to="imagelinks" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns=""> - <inputs> - <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> - <name>document</name> - <depth>0</depth> - <mimeTypes> - <string>'text/html'</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>imagelinks</name> - <depth>1</depth> - <mimeTypes> - <string>l('text/x-taverna-web-url')</string> - </mimeTypes> - <granularDepth>1</granularDepth> - </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean> - </outputs> - <classLoaderSharing>workflow</classLoaderSharing> - <localDependencies /> - <artifactDependencies /> - <script>String lowerCaseContent = document.toLowerCase(); -int index = 0; -List imagelinks = new ArrayList(); -while ((index = lowerCaseContent.indexOf("<img", index)) != -1) { - if ((index = lowerCaseContent.indexOf("src", index)) == -1) - break; - if ((index = lowerCaseContent.indexOf("=", index)) == -1) - break; - index++; - String remaining = document.substring(index); - StringTokenizer st = new StringTokenizer(remaining, "\t\n\r\">#"); - String strLink = st.nextToken(); - imagelinks.add(strLink); -} - -</script> - <dependencies /> - <localworkerName>org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks</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="document" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>findComicURL</name><inputPorts><port><name>regex</name><depth>0</depth></port><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>filteredlist</name><depth>1</depth><granularDepth>1</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="regex" to="regex" /><map from="stringlist" to="stringlist" /></inputMap><outputMap><map from="filteredlist" to="filteredlist" /></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>regex</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>filteredlist</name> - <depth>1</depth> - <mimeTypes> - <string>l('text/plain')</string> - </mimeTypes> - <granularDepth>1</granularDepth> - </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean> - </outputs> - <classLoaderSharing>workflow</classLoaderSharing> - <localDependencies /> - <artifactDependencies /> - <script>filteredlist = new ArrayList(); -for (Iterator i = stringlist.iterator(); i.hasNext();) { - String item = (String) i.next(); - if (item.matches(regex)) { - filteredlist.add(item); - } -} -</script> - <dependencies /> - <localworkerName>org.embl.ebi.escience.scuflworkers.java.FilterStringList</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=""> - 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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="regex" depth="0" /><port name="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>comicURLRegex</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>.*/comics/.*</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=" "> - 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<name>image</name> - <depth>0</depth> - <mimeTypes> - <string>'image/*'</string> - </mimeTypes> - <granularDepth>0</granularDepth> - </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean> - </outputs> - <classLoaderSharing>workflow</classLoaderSharing> - <localDependencies /> - <artifactDependencies /> - <script>URL inputURL = null; -if (base != void) { - inputURL = new URL(new URL(base), url); -} else { - inputURL = new URL(url); -} - -byte[] contents; -if (inputURL.openConnection().getContentLength() == -1) { - // Content size unknown, must read first... - byte[] buffer = new byte[1024]; - int bytesRead = 0; - int totalBytesRead = 0; - InputStream is = inputURL.openStream(); - while (bytesRead != -1) { - totalBytesRead += bytesRead; - bytesRead = is.read(buffer, 0, 1024); - } - contents = new byte[totalBytesRead]; -} else { - contents = new byte[inputURL.openConnection().getContentLength()]; -} -int bytesRead = 0; -int totalBytesRead = 0; -InputStream is = inputURL.openStream(); -while (bytesRead != -1) { - bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead); - totalBytesRead += bytesRead; - if (contents.length==totalBytesRead) break; -} - -image = contents; -</script> - <dependencies /> - <localworkerName>org.embl.ebi.escience.scuflworkers.java.WebImageFetcher</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="base" depth="0" /><port name="url" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>getPage</processor><port>url</port></sink><source type="processor"><processor>xkcdURL</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>getImageLinks</processor><port>document</port></sink><source type="processor"><processor>getPage</processor><port>contents</port></source></datalink><datali nk><sink type="processor"><processor>findComicURL</processor><port>regex</port></sink><source type="processor"><processor>comicURLRegex</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>findComicURL</processor><port>stringlist</port></sink><source type="processor"><processor>getImageLinks</processor><port>imagelinks</port></source></datalink><datalink><sink type="processor"><processor>getComicStrip</processor><port>base</port></sink><source type="processor"><processor>xkcdURL</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>getComicStrip</processor><port>url</port></sink><source type="processor"><processor>findComicURL</processor><port>filteredlist</port></source></datalink><datalink><sink type="dataflow"><port>todaysXkcd</port></sink><source type="processor"><processor>getComicStrip</processor><port>image</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>24e3ca77-bca1-47a6-8f5e-0549801eb27e</identification> - </annotationBean> - <date>2011-07-12 14:11:15.348 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>Fetch today's xkcd comic</text> - </annotationBean> - <date>2009-12-15 20:39:06.623 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>8b032490-948e-4983-b632-d16653755fcd</identification> - </annotationBean> - <date>2010-07-04 18:16:02.491 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>Use the local services and some filtering operations to fetch the comic strip image from http://xkcd.com/ - -Based on the FetchDailyDilbert workflow.</text> - </annotationBean> - <date>2011-07-12 14:11:12.608 BST</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>Tom Oinn, Stian Soiland-Reyes</text> - </annotationBean> - <date>2009-12-15 20:38:58.43 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-engine/blob/3ecb1291/taverna-integration-tests/src/test/resources/t2flow/GBSeqTest.t2flow ---------------------------------------------------------------------- diff --git a/taverna-integration-tests/src/test/resources/t2flow/GBSeqTest.t2flow b/taverna-integration-tests/src/test/resources/t2flow/GBSeqTest.t2flow deleted file mode 100644 index 196a4bc..0000000 --- a/taverna-integration-tests/src/test/resources/t2flow/GBSeqTest.t2flow +++ /dev/null @@ -1,518 +0,0 @@ -<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1" producedBy="taverna-2.3.0"><dataflow id="c00b121a-0114-471a-bd29-03597414879c" role="top"><name>GBSeq_test</name><inputPorts /><outputPorts><port><name>nuc_fasta</name><annotations /></port><port><name>nuc_xml</name><annotations /></port><port><name>nuc_insd</name><annotations /></port><port><name>nuc_tiny</name><annotations /></port><port><name>prot_fasta</name><annotations /></port><port><name>protein_xml</name><annotations /></port><port><name>prot_insd</name><annotations /></port><port><name>prot_tiny</name><annotations /></port></outputPorts><processors><processor><name>nuc_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>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.St ringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns=""> - <value>NM_000059</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>protein_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>1.3</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>NP_000050</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=" "> - 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<inputs> - <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> - <name>id</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>outputText</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>if ((id == void) || (id == null) || id.equals("")) { - throw new RunTimeException("port id must have a non-empty value"); -} - -URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&db=nucleotide&retmode=xml&id="; + id); - -BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream())); -StringWriter writer = new StringWriter(); - -char[] buffer = new char[1024]; - while (true) { - int r = reader.read(buffer); - if (r <= 0) { - break; - } - writer.write(buffer, 0, r); - } -outputText = writer.toString(); -</script> - <dependencies /> - <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker</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=""> - 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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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Nucleotide_FASTA</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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.LocalworkerActivit y</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns=""> - <inputs> - <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> - <name>id</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>outputText</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>if ((id == void) || (id == null) || id.equals("")) { - throw new RunTimeException("port id must have a non-empty value"); -} - -URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=nucleotide&retmode=text&id="; + id); - -BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream())); -StringWriter writer = new StringWriter(); - -char[] buffer = new char[1024]; - while (true) { - int r = reader.read(buffer); - if (r <= 0) { - break; - } - writer.write(buffer, 0, r); - } -outputText = writer.toString(); -</script> - <dependencies /> - <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker</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=""> - 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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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Get_Nucleotide_INSDSeq_XML</processor><port>id</port></sink><source type="processor"><processor>nuc_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Nucleotide_FASTA</processor><port>id</port></sink><source type="processor"><processor>nuc_id</processor><port>value</port></source></datalink><datalink><sink type="pr ocessor"><processor>Get_Nucleotide_GBSeq_XML</processor><port>id</port></sink><source type="processor"><processor>nuc_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Nucleotide_TinySeq_XML</processor><port>id</port></sink><source type="processor"><processor>nuc_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Protein_FASTA</processor><port>id</port></sink><source type="processor"><processor>protein_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Protein_INSDSeq_XML</processor><port>id</port></sink><source type="processor"><processor>protein_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Protein_TinySeq_XML</processor><port>id</port></sink><source type="processor"><processor>protein_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Ge t_Protein_GBSeq_XML</processor><port>id</port></sink><source type="processor"><processor>protein_id</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>nuc_fasta</port></sink><source type="processor"><processor>Get_Nucleotide_FASTA</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>nuc_xml</port></sink><source type="processor"><processor>Get_Nucleotide_GBSeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>nuc_insd</port></sink><source type="processor"><processor>Get_Nucleotide_INSDSeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>nuc_tiny</port></sink><source type="processor"><processor>Get_Nucleotide_TinySeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>prot_fasta</port></sink><source type="processor"><processor>Get_Protein_FASTA</processor><port>outputText</por t></source></datalink><datalink><sink type="dataflow"><port>protein_xml</port></sink><source type="processor"><processor>Get_Protein_GBSeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>prot_insd</port></sink><source type="processor"><processor>Get_Protein_INSDSeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>prot_tiny</port></sink><source type="processor"><processor>Get_Protein_TinySeq_XML</processor><port>outputText</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>GBSeq test</text> - </annotationBean> - <date>2009-12-15 20:30:12.959 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.FreeTextDescription"> - <text>This workflow retrieves nucleotide and protein sequences with the literature and references associated -to them given a protein and a nucleotide id.</text> - </annotationBean> - <date>2009-12-15 20:30:23.505 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>f0fac9a7-7943-4191-a0d3-7e8e09044e43</identification> - </annotationBean> - <date>2010-07-04 18:16:42.290 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>c00b121a-0114-471a-bd29-03597414879c</identification> - </annotationBean> - <date>2011-07-12 14:07:08.97 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>af08cba7-dd16-404c-b20b-fd3cb7ccf7aa</identification> - </annotationBean> - <date>2011-07-12 14:06:02.422 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>Franck Tanoh</text> - </annotationBean> - <date>2011-07-12 14:07:04.790 BST</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
