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Hello Taverna 2 user/developer, Would any of you be able to try the enclosed workflows for me? It tests two operations of this service by Martijn Schuemie. The workflows are virtually identical, but one is in taverna 1 and the other in Taverna 2. In Taverna 1 is working, while in Taverna 2 the synonyms operation is not producing any results. Do you have a suggestion of what could be wrong? I wonder if there is a problem with the list depth of the operations' outputs. The two operations of the service return a different list depth, at least in Taverna 1. I understand Taverna 2 is less forgiving with respect to list depth anomalies (which is probably a good thing). Many thanks! Marco. -- Marco Roos Faculty of Science University of Amsterdam Kruislaan 403, room F1.02 1098 SJ Amsterdam tel. +31 (0) 20 525 7522 http://home.medewerker.uva.nl/m.roos1 (includes links to social networks) Note the change of e-mail address to [email protected] |
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1"><dataflow id="37c90a88-1c87-4c6b-b085-6fe17ce95ff1" role="top"><name>dataflow30</name><inputPorts /><outputPorts><port><name>synonym</name></port><port><name>uniprot</name></port></outputPorts><processors><processor><name>getSynsets</name><inputPorts><port><name>term</name><depth>0</depth></port></inputPorts><outputPorts><port><name>getSynsetsReturn</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="term" to="term" /></inputMap><outputMap><map from="getSynsetsReturn" to="getSynsetsReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns=""> <wsdl>http://bubbles.biosemantics.org:8180/axis/services/SynsetServer/SynsetServer.jws?wsdl</wsdl> <operation>getSynsets</operation> </net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="term" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>getUniprotID</name><inputPorts><port><name>term</name><depth>0</depth></port></inputPorts><outputPorts><port><name>getUniprotIDReturn</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="term" to="term" /></inputMap><outputMap><map from="getUniprotIDReturn" to="getUniprotIDReturn" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns=""> <wsdl>http://bubbles.biosemantics.org:8180/axis/services/SynsetServer/SynsetServer.jws?wsdl</wsdl> <operation>getUniprotID</operation> </net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="term" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>input</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>0.4</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>p53</value> </net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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><datalink><sink type="processor"><processor>getSynsets</processor><port>term</port></sink><source type="processor"><processor>input</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>getUniprotID</processor><port>term</port></sink><source type="processor"><processor>input</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>synonym</port></sink><source type="processor"><processor>getSynsets</processor><port>getSynsetsReturn</port></source></datalink><datalink><sink type="dataflow"><port>uniprot</port></sink><source type="processor"><processor>getUniprotID</processor><port>getUniprotIDReturn</port></source></datalink></datalinks><annotations /></dataflow></workflow>
<?xml version="1.0" encoding="UTF-8"?> <s:scufl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"; version="0.2" log="0"> <s:workflowdescription lsid="urn:lsid:net.sf.taverna:wfDefinition:ab898b4a-faca-4ad6-be9a-e2110a559097" author="" title="SynsetTest_taverna1" /> <s:processor name="getSynsets"> <s:arbitrarywsdl> <s:wsdl>http://bubbles.biosemantics.org:8180/axis/services/SynsetServer/SynsetServer.jws?wsdl</s:wsdl> <s:operation>getSynsets</s:operation> </s:arbitrarywsdl> </s:processor> <s:processor name="getUniprotID"> <s:arbitrarywsdl> <s:wsdl>http://bubbles.biosemantics.org:8180/axis/services/SynsetServer/SynsetServer.jws?wsdl</s:wsdl> <s:operation>getUniprotID</s:operation> </s:arbitrarywsdl> </s:processor> <s:processor name="input" boring="true"> <s:stringconstant>p53</s:stringconstant> </s:processor> <s:link source="input:value" sink="getSynsets:term" /> <s:link source="input:value" sink="getUniprotID:term" /> <s:link source="getSynsets:getSynsetsReturn" sink="synonym" /> <s:link source="getUniprotID:getUniprotIDReturn" sink="uniprot" /> <s:sink name="synonym" /> <s:sink name="uniprot" /> </s:scufl>
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