Hi Alan, Here I've attached the rat.txt file. Yes of course. I'd like to work on this. :-)
On 5 March 2015 at 00:54, Alan Williams <[email protected]> wrote: > On 04-Mar-15 18:41, Menaka Madushanka wrote: > >> I'm trying to build the Taverna, but ended up with this error. :( >> > > Hello, > > Can you send the rat.txt it generated ? I think (for you) it is in: > > /Extra/GSOC'15/incubator-taverna-language-master/target/rat.txt > > Thanks, > > Alan > > P.S. Were you interested in a particular GSOC project? >
***************************************************** Summary ------- Generated at: 2015-03-04T23:58:39+05:30 Notes: 1 Binaries: 0 Archives: 0 Standards: 38 Apache Licensed: 27 Generated Documents: 0 JavaDocs are generated and so license header is optional Generated files do not required license headers 11 Unknown Licenses ******************************* Unapproved licenses: taverna-scufl2-wfdesc/src/test/resources/nested.t2flow taverna-scufl2-wfdesc/src/test/resources/enm-v21.t2flow taverna-scufl2-wfdesc/src/test/resources/rdf-in-example-annotation.t2flow taverna-scufl2-wfdesc/src/test/resources/valid_component_imagemagickconvert.t2flow taverna-scufl2-wfdesc/src/test/resources/helloworld.wfdesc.ttl taverna-scufl2-wfdesc/src/test/resources/localdependency.t2flow taverna-scufl2-wfdesc/src/main/resources/org/w3/prov-o.ttl taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfprov.ttl taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wf4ever.ttl taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/roterms.ttl ******************************* Archives: ***************************************************** Files with Apache License headers will be marked AL Binary files (which do not require AL headers) will be marked B Compressed archives will be marked A Notices, licenses etc will be marked N N LICENSE AL .travis.yml AL pom.xml AL taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestConvertToWfdesc.java AL taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestWfdescReader.java AL taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestAnnotationQuoting.java AL taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestWfdescWriter.java AL taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestNested.java AL taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestRoEvoSerializer.java AL taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestSemanticAnnotations.java AL taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestAllTypes.java AL taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestInvalidURITemplate.java AL taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestLocalDependency.java !????? taverna-scufl2-wfdesc/src/test/resources/nested.t2flow !????? taverna-scufl2-wfdesc/src/test/resources/enm-v21.t2flow !????? taverna-scufl2-wfdesc/src/test/resources/rdf-in-example-annotation.t2flow !????? taverna-scufl2-wfdesc/src/test/resources/valid_component_imagemagickconvert.t2flow !????? taverna-scufl2-wfdesc/src/test/resources/helloworld.wfdesc.ttl AL taverna-scufl2-wfdesc/src/test/resources/helloanyone.t2flow !????? taverna-scufl2-wfdesc/src/test/resources/localdependency.t2flow AL taverna-scufl2-wfdesc/src/test/resources/helloworld.t2flow AL taverna-scufl2-wfdesc/src/test/resources/T3-1226-annotations-with-quotes.t2flow AL taverna-scufl2-wfdesc/src/test/resources/allTypes.t2flow AL taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ConvertToWfdesc.java AL taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescWriter.java AL taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/TurtleWriterWithBase.java AL taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java AL taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/Labelled.java AL taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescReader.java AL taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescSerialiser.java AL taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescAgent.java !????? taverna-scufl2-wfdesc/src/main/resources/org/w3/prov-o.ttl !????? taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl !????? taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfprov.ttl !????? taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wf4ever.ttl !????? taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/roterms.ttl AL taverna-scufl2-wfdesc/src/main/resources/META-INF/spring/scufl2-wfdesc-context.xml AL taverna-scufl2-wfdesc/src/main/resources/META-INF/spring/scufl2-wfdesc-context-osgi.xml AL taverna-scufl2-wfdesc/pom.xml ***************************************************** Printing headers for files without AL header... ======================================================================= ==taverna-scufl2-wfdesc/src/test/resources/nested.t2flow ======================================================================= <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; 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Coehoorngracht - Vlissingen",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778547,52.29,5.0211,,,,NL,,,"1.9km n Veltersloot PEN",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53779121,52.8983,4.9392,,,,NL,,,"Westerland - thv rioolgemaal - nabij split",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53789607,52.9051,5.0504,,,,NL,,,HOOGE KWELSLOOT KRUISING SLUITGATWEG,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784133,52.7322,5.1419,,,,NL,,,"NARREVLIET NOORDZIJDE VOKKOMMENWEG THV",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53787081,52.4203,4.6714,,,,NL,,,BIJ GEMAAL TEN WESTEN VAN SPAARNDAM,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781688,52.9149,5.5534,,,,NL,,,"HET ZWIN -Oudega 2 toevoer",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53780907,52.572,4.7471,,,,NL,,,Noordhollands Kanaal pontveer Akersloot,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53776376,51.8116,4.3068,,,,NL,,,hoofdwatergang-bij gemaal De Biersum/Sch,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781036,52.0009,4.2744,,,,NL,,,Oude en Nieuwe Broekpolder gemaal,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778324,52.7992,4.6939,,,,NL,,,"SLOOT TOV WESTERDUINWEG NOORDZIJDE PA",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778293,53.019,4.8036,,,,NL,,,toevoerkanaal gemaal Prins Hendrikpolder,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53786744,52.0056,4.3975,,,,NL,,,"Zuidpld van Delfgauw - Ecoplas uitlaat",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781220,52.8342,4.8113,,,,NL,,,"Oudesluis - tpv brug tussen de Ruigweg en",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53779200,52.5271,5.9158,,,,NL,,,Natuurgebied De Enk,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784321,52.2917,4.9313,,,,NL,,,OUDERKERKERPLAS MIDDEN OP DE PLAS,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53786909,52.3024,5.1151,,,,NL,,,Naardermeer(Groote meer),,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784041,52.8432,5.5714,,,,NL,,,"poldervaart HUITEBUURSTERPOLDER - gemaal",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53783983,52.9344,4.7627,,,,NL,,,"SLOOT HALF-GEISOL - TWV STATION DEN HELDE",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53783445,52.2415,4.4736,,,,NL,,,Vogelsloot - t.O.v. Leeweg tussen weg en,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53787106,52.2133,4.7239,,,,NL,,,Drecht t.h.v. de brug in Bilderdam,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53779219,52.4276,5.0186,,,,NL,,,Bozen meertje,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53783911,52.006,4.9585,,,,NL,,,eb13 Benschopperwetering brug huisnr. 32,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53783572,52.8387,4.7211,,,,NL,,,"SLOOT BIJ DUIKER TNV KRUIS - UITLANDER",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778356,52.7451,4.7979,,,,NL,,,"Harenkarspel - waterb 400m N gem Woudmeer",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,, ======================================================================= ==taverna-scufl2-wfdesc/src/test/resources/rdf-in-example-annotation.t2flow ======================================================================= <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1" producedBy="taverna-core-2.5.0"><dataflow id="b9ca25c7-f594-47c1-af62-af9d380002c8" role="top"><name>Workflow4</name><inputPorts><port><name>example</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>@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix skos: <http://www.w3.org/2004/02/skos/core#> . @prefix dct: <http://purl.org/dc/terms/> . </text> </annotationBean> <date>2014-04-30 09:48:34.212 UTC</date> <creators /> <curationEventList /> </net.sf.taverna.t2.annotation.AnnotationAssertionImpl> </annotationAssertions> </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts /><processors /><conditions /><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>b9ca25c7-f594-47c1-af62-af9d380002c8</identification> </annotationBean> <date>2014-04-30 09:48:41.168 UTC</date> <creators /> <curationEventList /> </net.sf.taverna.t2.annotation.AnnotationAssertionImpl> </annotationAssertions> </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow> ======================================================================= ==taverna-scufl2-wfdesc/src/test/resources/valid_component_imagemagickconvert.t2flow ======================================================================= <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1" producedBy="taverna-2.4.0"><dataflow id="8d2f9ef0-09ca-4103-b4fd-0ee0a40d8263" role="top"><name>Imagemagick_convert_</name><inputPorts><port><name>from_uri</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>in.tiff</text> </annotationBean> <date>2013-03-06 15:58:34.431 UTC</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>URI to the input object</text> </annotationBean> <date>2013-03-06 15:58:35.192 UTC</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.SemanticAnnotation"> <mimeType>text/rdf+n3</mimeType> <content><> <http://purl.org/DP/components#portType> <http://purl.org/DP/components#FromURIPort> . </content> </annotationBean> <date>2013-03-06 15:36:17.856 UTC</date> <creators /> <curationEventList /> </net.sf.taverna.t2.annotation.AnnotationAssertionImpl> </annotationAssertions> </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></port><port><name>to_uri</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>out.tiff</text> </annotationBean> <date>2013-03-06 15:58:28.756 UTC</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> ======================================================================= ==taverna-scufl2-wfdesc/src/test/resources/helloworld.wfdesc.ttl ======================================================================= @base <http://ns.taverna.org.uk/2010/workflowBundle/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/workflow/Hello_World/> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix prov: <http://www.w3.org/ns/prov#> . @prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> . @prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> . @prefix roterms: <http://purl.org/wf4ever/roterms#> . @prefix dc: <http://purl.org/dc/elements/1.1/> . @prefix dcterms: <http://purl.org/dc/terms/> . @prefix comp: <http://purl.org/DP/components#> . @prefix dep: <http://scape.keep.pt/vocab/dependencies#> . @prefix biocat: <http://biocatalogue.org/attribute/> . @prefix : <#> . <datalink?from=processor/hello/out/value&to=out/greeting> a wfdesc:DataLink ; wfdesc:hasSource <processor/hello/out/value> ; wfdesc:hasSink <out/greeting> . <> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process ; dc:creator "Stian Soiland-Reyes" ; dcterms:description "One of the simplest workflows possible. No workflow input ports, a single workflow output port \"greeting\", outputting \"Hello, world!\" as produced by the String Constant \"hello\"." ; dcterms:title "Hello World" ; rdfs:label "Hello_World" ; wfdesc:hasOutput <out/greeting> ; wfdesc:hasSubProcess <processor/hello/> ; wfdesc:hasDataLink <datalink?from=processor/hello/out/value&to=out/greeting> . <out/greeting> a wfdesc:Output , wfdesc:Description , wfdesc:Input ; rdfs:label "greeting" . <processor/hello/> a wfdesc:Process , wfdesc:Description ; rdfs:label "hello" ; wfdesc:hasOutput <processor/hello/out/value> . <processor/hello/out/value> a wfdesc:Output , wfdesc:Description ; rdfs:label "value" . ======================================================================= ==taverna-scufl2-wfdesc/src/test/resources/localdependency.t2flow ======================================================================= <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1" producedBy="taverna-2.4.0"><dataflow id="024011b4-bc92-4836-8043-6e787cfc72b7" role="top"><name>Workflow1</name><inputPorts /><outputPorts /><processors><processor><name>Beanshell</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns=""> <inputs /> <outputs /> <classLoaderSharing>workflow</classLoaderSharing> <localDependencies> <string>hello.jar</string> </localDependencies> <artifactDependencies /> <script>// depends on hello.jar</script> <dependencies /> </net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</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>1.4</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks /><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>024011b4-bc92-4836-8043-6e787cfc72b7</identification> </annotationBean> <date>2014-03-02 23:55:26.534 UTC</date> <creators /> <curationEventList /> </net.sf.taverna.t2.annotation.AnnotationAssertionImpl> </annotationAssertions> </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow> ======================================================================= ==taverna-scufl2-wfdesc/src/main/resources/org/w3/prov-o.ttl ======================================================================= @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix : <http://www.w3.org/ns/prov#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . rdfs:comment a owl:AnnotationProperty ; rdfs:comment ""@en ; rdfs:isDefinedBy <http://www.w3.org/ns/prov-o#> . rdfs:isDefinedBy a owl:AnnotationProperty . rdfs:label a owl:AnnotationProperty ; rdfs:comment ""@en ; rdfs:isDefinedBy <http://www.w3.org/ns/prov-o#> . rdfs:seeAlso a owl:AnnotationProperty ; rdfs:comment ""@en . owl:Thing a owl:Class . owl:versionInfo a owl:AnnotationProperty . <http://www.w3.org/ns/prov#> a owl:Ontology . :Activity a owl:Class ; rdfs:isDefinedBy <http://www.w3.org/ns/prov-o#> ; rdfs:label "Activity" ; owl:disjointWith :Entity ; :category "starting-point" ; :component "entities-activities" ; :constraints "http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig"^^xsd:anyURI ; :definition "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; :dm "http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Activity"^^xsd:anyURI ; :n "http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Activity"^^xsd:anyURI . :ActivityInfluence a owl:Class ; rdfs:comment "ActivityInfluence provides additional descriptions of an Activity's binary influence upon any other kind of resource. Instances of ActivityInfluence use the prov:activity property to cite the influencing Activity."@en, "It is not recommended that the type ActivityInfluence be asserted without also asserting one of its more specific subclasses."@en ; rdfs:isDefinedBy <http://www.w3.org/ns/prov-o#> ; rdfs:label "ActivityInfluence" ; rdfs:seeAlso :activity ; ======================================================================= ==taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl ======================================================================= @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . @prefix parrot: <http://vocab.ctic.es/parrot#> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix : <http://www.semanticweb.org/owl/owlapi/turtle#> . @prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> . @prefix xml: <http://www.w3.org/XML/1998/namespace> . @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix skos: <http://www.w3.org/2004/02/skos/core#> . @base <http://purl.org/wf4ever/wfdesc> . <http://purl.org/wf4ever/wfdesc> rdf:type owl:Ontology ; rdfs:comment """This ontology (\"wfdesc\") describes an abstract workflow description structure, which on the top level is defined as a wfdesc:Workflow. A wfdesc:Workflow contains several wfdesc:Process instances, associated using the wfdesc:hasSubProcess property. Each of these (and the workflow itself) wfdesc:hasInput and wfdesc:hasOutput some wfdesc:Parameter (wfdesc:Input or wfdesc:Output). An wfdesc:Artifact is associated with a wfdesc:Parameter using wfdesc:hasArtifact. The wfdesc:Workflow also wfdesc:hasDataLink several wfdesc:DataLink instances, which forms the connection between parameters. Thus this ontology allows the description a direct acyclic graph, or a dataflow. This ontology is meant as an upper ontology for more specific workflow definitions, and as a way to express abstract workflows. The wfprov ontology shows how to link these descriptions to a provenance trace of a workflow execution."""@en ; owl:versionIRI <https://raw.github.com/wf4ever/ro/master/wfdesc.owl> ; parrot:hasPrologue <index.html#ro> . ################################################################# # # Annotation properties # ################################################################# rdfs:comment rdf:type owl:AnnotationProperty . ################################################################# # # Datatypes # ################################################################# ################################################################# # ======================================================================= ==taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfprov.ttl ======================================================================= @prefix wfprov: <http://purl.org/wf4ever/wfprov#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix : <http://www.semanticweb.org/owl/owlapi/turtle#> . @prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> . @prefix xml: <http://www.w3.org/XML/1998/namespace> . @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix ro: <http://purl.org/wf4ever/ro#> . @base <http://purl.org/wf4ever/wfprov> . <http://purl.org/wf4ever/wfprov> rdf:type owl:Ontology ; owl:versionIRI <https://raw.github.com/wf4ever/ro/master/wfprov.owl> ; rdfs:comment """The wfprov ontology shows how to express minimal provenance information about the execution of a workflow described using the wf ontology. Here the concern is mainly the provenance which affects the research object, so in particular how some ro:Resource's might have been generated or used by the execution of a wfdesc:Workflow. The main class here is a wfprov:WorkflowRun which shows how wfprov:Artifact instances (the data) wfprov:wasOutputFrom a wfprov:ProcessRun for generated artifacts, or wfprov:usedInput for consumed artifacts. The WorkflowRun is also a ProcessRun, and so the overall inputs and outputs of thw workflow execution can be described in the same manner. These provenance details are linked to the corresponding wfdesc descriptions using wfdesc:describedbyProcess, wfdesc:describedByWorkflow and wfdesc:describedByParameter. This ontology can be further linked to more specific provenance ontologies like OPM-V or W3C PROV-O, but this should be done separately."""@en ; rdfs:seeAlso <http://purl.org/wf4ever/ro> ; owl:imports <http://purl.org/wf4ever/wfdesc> , <http://xmlns.com/foaf/0.1/> . ################################################################# # # Annotation properties # ################################################################# ################################################################# # # Datatypes # ################################################################# ################################################################# # ======================================================================= ==taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wf4ever.ttl ======================================================================= @prefix wfprov: <http://purl.org/wf4ever/wfprov#> . @prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix ore: <http://www.openarchives.org/ore/terms/> . @prefix : <http://purl.org/wf4ever/wf4ever#> . @prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> . @prefix xml: <http://www.w3.org/XML/1998/namespace> . @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix skos: <http://www.w3.org/2004/02/skos/core#> . @prefix ro: <http://purl.org/wf4ever/ro#> . @base <http://purl.org/wf4ever/wf4ever> . <http://purl.org/wf4ever/wf4ever> rdf:type owl:Ontology ; rdfs:comment """The wf4ever ontology. This is based on the wf4ever ontologies ro, wf and wfdesc- but adds custom classes like wf4ever:Image and wf4ever:WebServiceProcess"""@en ; owl:imports <http://purl.org/wf4ever/ro> , <http://purl.org/wf4ever/wfdesc> , <http://purl.org/wf4ever/wfprov> ; owl:versionIRI <https://raw.github.com/wf4ever/ro/master/wf4ever.owl> . ################################################################# # # Annotation properties # ################################################################# ################################################################# # # Datatypes # ################################################################# ################################################################# # # Data properties # ################################################################# ======================================================================= ==taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/roterms.ttl ======================================================================= @prefix : <http://purl.org/wf4ever/roterms> . @prefix co: <http://purl.org/co/> . @prefix dc: <http://purl.org/dc/elements/1.1/> . @prefix ro: <http://purl.org/wf4ever/ro#> . @prefix cnt: <http://www.w3.org/2011/content#> . @prefix ore: <http://www.openarchives.org/ore/terms/> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix pav: <http://purl.org/pav/> . @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix xml: <http://www.w3.org/XML/1998/namespace> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . @prefix dcat: <http://www.w3.org/ns/dcat#> . @prefix foaf: <http://xmlns.com/foaf/0.1/> . @prefix prov: <http://www.w3.org/ns/prov#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix skos: <http://www.w3.org/2004/02/skos/core#> . @prefix terms: <http://purl.org/dc/terms/> . @prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> . @prefix wfprov: <http://purl.org/wf4ever/wfprov#> . @prefix roterms: <http://purl.org/wf4ever/roterms#> . @prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> . @base <http://purl.org/wf4ever/roterms#> . <http://purl.org/wf4ever/roterms#> rdf:type owl:Ontology ; rdfs:label "RO terms"@en ; owl:versionInfo "0.1.0"^^xsd:string ; dc:contributor "Graham Klyne"@en , "Khalid Belhajjame"@en ; dc:creator "Stian Soiland-Reyes"@en ; rdfs:comment """The Research Object vocabularies are built on existing popular vocabularies and standards, such as ORE, DC terms, PROV, to cite a few. In addition to terms that we borrowed and adapted from such vocabularies, we defined new terms under the name space roterms. These new terms serve two main purposes. They are used to specify annotations that are, to our knowledge, not catered for by existing ontologies, e.g., roterms:Hypothesis and roterms:exampleValue. ii) They are also used to specify shortcuts that make the ontology easy to use and more accessible. For example, roterms:inputSelected associates a wfdesc:WorkflowDefinition to a ro:Resource to state that a file is meant to be used with a given workflow definition, without specifying at which input port or in which workflow run. """@en ; owl:imports <http://purl.org/co> , <http://purl.org/wf4ever/wf4ever> , <http://www.w3.org/2011/content> , <http://www.w3.org/ns/dcat> ; owl:versionIRI <https://github.com/wf4ever/ro/blob/master/roterms.owl> . ################################################################# # # Annotation properties
