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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:17:23 UTC
[07/52] [abbrv] incubator-taverna-language git commit: Removed
duplicate workflows (See scufl2-examples)
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomartandembossanalysis_904962.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomartandembossanalysis_904962.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomartandembossanalysis_904962.t2flow
deleted file mode 100644
index e94384f..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomartandembossanalysis_904962.t2flow
+++ /dev/null
@@ -1,370 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="2f216461-50f5-45be-a2d2-49c84b1fce5e" role="top"><name>BiomartAndEMBOSSAnalysis</name><inputPorts /><outputPorts><port><name>outputPlot</name><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.MimeType">
- <text>image/png</text>
- </annotationBean>
- <date>2009-12-15 21:49:47.668 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.MimeType">
- <text>application/octet-stream</text>
- </annotationBean>
- <date>2009-12-15 21:49:47.668 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>HSapIDs</name><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.MimeType">
- <text>text/plain</text>
- </annotationBean>
- <date>2009-12-15 21:49:47.668 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>MMusIDs</name><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.MimeType">
- <text>text/plain</text>
- </annotationBean>
- <date>2009-12-15 21:49:47.668 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>RNorIDs</name><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.MimeType">
- <text>text/plain</text>
- </annotationBean>
- <date>2009-12-15 21:49:47.668 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></outputPorts><processors><processor><name>GetUniqueHomolog</name><inputPorts><port><name>HSGeneIDs</name><depth>1</depth></port><port><name>RatGeneIDs</name><depth>1</depth></port><port><name>MouseGeneIDs</name><depth>1</depth></port></inputPorts><outputPorts><port><name>MouseOut</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>HSOut</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>RatOut</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="HSGeneIDs" to="HSGeneIDs" /><map from="RatGeneIDs" to="RatGeneIDs" /><map from="MouseGeneIDs" to="MouseGeneIDs" /></inputMap><outputMap><map f
rom="RatOut" to="RatOut" /><map from="HSOut" to="HSOut" /><map from="MouseOut" to="MouseOut" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>List HSOut = new ArrayList();
-List RatOut = new ArrayList();
-List MouseOut = new ArrayList();
-
-Map hsToMouse = new HashMap();
-Iterator j = MouseGeneIDs.iterator();
-for (Iterator i = HSGeneIDs.iterator(); i.hasNext();) {
- String id = (String)i.next();
- hsToMouse.put(id, j.next());
-}
-Map hsToRat = new HashMap();
-j = RatGeneIDs.iterator();
-for (Iterator i = HSGeneIDs.iterator(); i.hasNext();) {
- String id = (String)i.next();
- hsToRat.put(id, j.next());
-}
-
-// Build the unique outputs
-for (Iterator i = hsToRat.keySet().iterator(); i.hasNext();) {
- String hsID = (String)i.next();
- String ratID = (String)hsToRat.get(hsID);
- // Remove version number
- // ratID = (ratID.split("."))[0];
- String mouseID = (String)hsToMouse.get(hsID);
- // Remove version number
- //mouseId = (mouseID.split("."))[0];
- if (ratID != null && mouseID != null && ratID.equals("")==false && mouseID.equals("")==false) {
- HSOut.add(hsID);
- RatOut.add(ratID.split("\\.")[0]);
- MouseOut.add(mouseID.split("\\.")[0]);
- }
-}</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>HSGeneIDs</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('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>MouseGeneIDs</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('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>RatGeneIDs</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('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>HSOut</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>RatOut</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>MouseOut</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </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>0</initialDelay>
- <maxDelay>0</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="RatGeneIDs" depth="1" /><port name="MouseGeneIDs" depth="1" /><port name="HSGeneIDs" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>hsapiensGeneEnsembl</name><inputPorts /><outputPorts><port><name>hsapiens_gene_ensembl.mouse_ensembl_gene</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>hsapiens_gene_ensembl.ensembl_gene_id</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>hsapiens_gene_ensembl.rat_ensembl_gene</name><depth>1</depth
><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomart-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.biomart.BiomartActivity</class><inputMap /><outputMap><map from="hsapiens_gene_ensembl.rat_ensembl_gene" to="hsapiens_gene_ensembl.rat_ensembl_gene" /><map from="hsapiens_gene_ensembl.ensembl_gene_id" to="hsapiens_gene_ensembl.ensembl_gene_id" /><map from="hsapiens_gene_ensembl.mouse_ensembl_gene" to="hsapiens_gene_ensembl.mouse_ensembl_gene" /></outputMap><configBean encoding="jdomxml"><MartQuery xmlns=""><MartService location="http://www.biomart.org/biomart/martservice" /><MartDataset displayName="Homo sapiens genes (GRCh37)" name="hsapiens_gene_ensembl" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2009-07-15 14:24:08"><MartURLLocation database="ensembl_mart_55" default="1" dis
playName="ENSEMBL 55 GENES (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="0" softwareVersion="0.7" requestId="taverna"><Dataset name="hsapiens_gene_ensembl"><Attribute name="ensembl_gene_id" /><Attribute name="mouse_ensembl_gene" /><Attribute name="rat_ensembl_gene" /><Filter name="chromosome_name" value="22" /><Filter name="with_mmusculus_homolog" excluded="0" /></Dataset></Query></MartQuery></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.Paralle
lizeConfig 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>0</initialDelay>
- <maxDelay>0</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 /></strategy></iteration></iterationStrategyStack></processor><processor><name>getHSapSequence</name><inputPorts><port><name>hsapiens_gene_ensembl.ensembl_gene_id_filter</name><depth>1</depth></port></inputPorts><outputPorts><port><name>hsapiens_gene_ensembl.ensembl_gene_id</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>hsapiens_gene_ensembl.coding_gene_flank</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</
group><artifact>biomart-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.biomart.BiomartActivity</class><inputMap><map from="hsapiens_gene_ensembl.ensembl_gene_id_filter" to="hsapiens_gene_ensembl.ensembl_gene_id_filter" /></inputMap><outputMap><map from="hsapiens_gene_ensembl.coding_gene_flank" to="hsapiens_gene_ensembl.coding_gene_flank" /><map from="hsapiens_gene_ensembl.ensembl_gene_id" to="hsapiens_gene_ensembl.ensembl_gene_id" /></outputMap><configBean encoding="jdomxml"><MartQuery xmlns=""><MartService location="http://www.biomart.org/biomart/martservice" /><MartDataset displayName="Homo sapiens genes (GRCh37)" name="hsapiens_gene_ensembl" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2009-07-15 14:24:08"><MartURLLocation database="ensembl_mart_55" default="1" displayName="ENSEMBL 55 GENES (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="0" softwareVersion="0.7" requestId="taverna"><Dataset name="hsapiens_gene_ensembl"><Attribute name="coding_gene_flank" /><Attribute name="ensembl_gene_id" /><Filter name="ensembl_gene_id" value="" list="true" /><Filter name="upstream_flank" value="100" /></Dataset></Query></MartQuery></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>0</initialDelay>
- <maxDelay>0</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="hsapiens_gene_ensembl.ensembl_gene_id_filter" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>CreateFasta</name><inputPorts><port><name>hsSeq</name><depth>0</depth></port><port><name>rnSeq</name><depth>0</depth></port><port><name>mmSeq</name><depth>0</depth></port></inputPorts><outputPorts><port><name>fasta</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>be
anshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="hsSeq" to="hsSeq" /><map from="rnSeq" to="rnSeq" /><map from="mmSeq" to="mmSeq" /></inputMap><outputMap><map from="fasta" to="fasta" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>fasta = ">Human\n"+hsSeq+"\n>Mouse\n"+mmSeq+"\n>Rat\n"+rnSeq;</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>hsSeq</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>mmSeq</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>rnSeq</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>fasta</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.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>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
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">
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- <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="">
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- <initialDelay>0</initialDelay>
- <maxDelay>0</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="sequences_direct_data" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>emma</name><inputPorts><port><name>sequence_direct_data</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outseq</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>dendoutfile_url</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>dendoutfile</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>outseq_url</name><depth>0</depth><g
ranularDepth>0</granularDepth></port><port><name>report</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="sequence_direct_data" to="sequence_direct_data" /></inputMap><outputMap><map from="outseq_url" to="outseq_url" /><map from="dendoutfile" to="dendoutfile" /><map from="dendoutfile_url" to="dendoutfile_url" /><map from="report" to="report" /><map from="outseq" to="outseq" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
- <endpoint>http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.emma</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="">
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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>1.2</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="
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- <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_direct_data" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>GetUniqueHomolog</processor><port>HSGeneIDs</port></sink><source type="processor"><processor>hsapiensGeneEnsembl</processor><port>hsapiens_gene_ensembl.ensembl_gene_id</port></source></datalink><datalink><sink type="processor"><processor>GetUniqueHomolog</processor><port>RatGeneIDs</port></sink><source type="processor"><processor>hsapiensGeneEnse
mbl</processor><port>hsapiens_gene_ensembl.rat_ensembl_gene</port></source></datalink><datalink><sink type="processor"><processor>GetUniqueHomolog</processor><port>MouseGeneIDs</port></sink><source type="processor"><processor>hsapiensGeneEnsembl</processor><port>hsapiens_gene_ensembl.mouse_ensembl_gene</port></source></datalink><datalink><sink type="processor"><processor>getHSapSequence</processor><port>hsapiens_gene_ensembl.ensembl_gene_id_filter</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>HSOut</port></source></datalink><datalink><sink type="processor"><processor>CreateFasta</processor><port>hsSeq</port></sink><source type="processor"><processor>getHSapSequence</processor><port>hsapiens_gene_ensembl.coding_gene_flank</port></source></datalink><datalink><sink type="processor"><processor>CreateFasta</processor><port>rnSeq</port></sink><source type="processor"><processor>getRNorSequence</processor><port>rnorvegicus_gene_ensembl.coding_gene_flank
</port></source></datalink><datalink><sink type="processor"><processor>CreateFasta</processor><port>mmSeq</port></sink><source type="processor"><processor>getMMusSequence</processor><port>mmusculus_gene_ensembl.coding_gene_flank</port></source></datalink><datalink><sink type="processor"><processor>getRNorSequence</processor><port>rnorvegicus_gene_ensembl.ensembl_gene_id_filter</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>RatOut</port></source></datalink><datalink><sink type="processor"><processor>getMMusSequence</processor><port>mmusculus_gene_ensembl.ensembl_gene_id_filter</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>MouseOut</port></source></datalink><datalink><sink type="processor"><processor>FlattenImageList</processor><port>inputlist</port></sink><source type="processor"><processor>plot</processor><port>Graphics_in_PNG</port></source></datalink><datalink><sink type="processor"><processor>seqret</process
or><port>sequence_direct_data</port></sink><source type="processor"><processor>CreateFasta</processor><port>fasta</port></source></datalink><datalink><sink type="processor"><processor>plot</processor><port>sequences_direct_data</port></sink><source type="processor"><processor>emma</processor><port>outseq</port></source></datalink><datalink><sink type="processor"><processor>emma</processor><port>sequence_direct_data</port></sink><source type="processor"><processor>seqret</processor><port>outseq</port></source></datalink><datalink><sink type="dataflow"><port>outputPlot</port></sink><source type="processor"><processor>FlattenImageList</processor><port>outputlist</port></source></datalink><datalink><sink type="dataflow"><port>HSapIDs</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>HSOut</port></source></datalink><datalink><sink type="dataflow"><port>MMusIDs</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>MouseOut</por
t></source></datalink><datalink><sink type="dataflow"><port>RNorIDs</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>RatOut</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>BiomartAndEMBOSSAnalysis</text>
- </annotationBean>
- <date>2009-12-15 21:49:49.57 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>Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.</text>
- </annotationBean>
- <date>2009-12-15 21:49:49.57 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>2f216461-50f5-45be-a2d2-49c84b1fce5e</identification>
- </annotationBean>
- <date>2010-07-04 18:05:56.821 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 />
- </annotationBean>
- <date>2009-12-15 21:49:49.57 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-language/blob/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomoby_tutorial_workflow_877727.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomoby_tutorial_workflow_877727.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomoby_tutorial_workflow_877727.t2flow
deleted file mode 100644
index edd0848..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomoby_tutorial_workflow_877727.t2flow
+++ /dev/null
@@ -1,247 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="fb218d56-b901-42bd-b3d1-ba8d44445818" role="top"><name>BioMoby_tutorial_workflow</name><inputPorts><port><name>namespace</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>NCBI_gi</text>
- </annotationBean>
- <date>2010-07-04 17:44:30.945 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.FreeTextDescription">
- <text>The namespace of the identifier</text>
- </annotationBean>
- <date>2010-07-04 17:43:33.391 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>id</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>656461</text>
- </annotationBean>
- <date>2010-07-04 17:43:21.263 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.FreeTextDescription">
- <text>An gene identifier</text>
- </annotationBean>
- <date>2010-07-04 17:43:16.581 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.FreeTextDescription">
- <text>A list of </text>
- </annotationBean>
- <date>2010-07-04 17:41:21.191 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.FreeTextDescription">
- <text>An id</text>
- </annotationBean>
- <date>2010-07-04 17:42:57.232 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>fasta_out</name><annotations /></port><port><name>moby_blast_ids</name><annotations /></port><port><name>restrict_out</name><annotations /></port></outputPorts><processors><processor><name>Object</name><inputPorts><port><name>namespace</name><depth>0</depth></port><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>mobyData</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity</class><inputMap><map from="id" to="id" /><map from="namespace" to="namespace" /></inputMap><outputMap><map from="mobyData" to="mobyData" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.biom
oby.BiomobyObjectActivityConfigurationBean xmlns="">
- <mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</mobyEndpoint>
- <serviceName>Object</serviceName>
- <authorityName>openinformatics.com</authorityName>
-</net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean></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="namespace" depth="0" /><port name="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>getGenBankFasta</name><inputPorts><port><name>Object(identifier)</name><depth>0</depth></port></inputPorts><outputPorts><port><name>FASTA(fasta)</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.
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- <mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</mobyEndpoint>
- <serviceName>getGenBankFasta</serviceName>
- <authorityName>bioinfo.icapture.ubc.ca</authorityName>
- <category />
- <serviceType />
- <secondaries />
-</net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean></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="Object(identifier)" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Parse Moby Data(FASTA)</name><inputPorts><port><name>mobyData('FASTA')</name><depth>0</depth></port></inputPorts><outputPorts><port><name>fasta_'content'</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activit
ies.biomoby.MobyParseDatatypeActivity</class><inputMap><map from="mobyData('FASTA')" to="mobyData('FASTA')" /></inputMap><outputMap><map from="fasta_'content'" to="fasta_'content'" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityConfigurationBean xmlns="">
- <datatypeName>FASTA</datatypeName>
- <registryEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</registryEndpoint>
- <articleNameUsedByService>fasta</articleNameUsedByService>
-</net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityConfigurationBean></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="
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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>1.2</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="mobyData('FASTA')" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>parseDragonDBBlastText</name><inputPorts><port><name>NCBI_BLAST_Text(blastreport)</name><depth>0</depth></port></inputPorts><outputPorts><port><name>Object(Collection - 'hit_ids')</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>
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- <mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</mobyEndpoint>
- <serviceName>parseDragonDBBlastText</serviceName>
- <authorityName>antirrhinum.net</authorityName>
- <category />
- <serviceType />
- <secondaries />
-</net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean></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><cross><port name="NCBI_BLAST_Text(blastreport)" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>getDragonBlastText</name><inputPorts><port><name>FASTA(sequence)</name><depth>0</depth></port></inputPorts><outputPorts><port><name>NCBI_BLAST_Text(blast)</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>net.sf.taverna
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- <pollingInterval>0</pollingInterval>
- <pollingBackoff>1.0</pollingBackoff>
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- <identification>fb218d56-b901-42bd-b3d1-ba8d44445818</identification>
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- <date>2010-07-04 17:44:45.645 BST</date>
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- <annotationAssertions>
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- <date>2010-07-04 17:39:12.485 BST</date>
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <date>2010-07-04 17:39:27.212 BST</date>
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- <date>2010-07-04 17:39:46.556 BST</date>
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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