Hi all,
I need your light about a problem I get. In workbench 2.2.1, I can
execute and get result of a simple workflow (one in attachment)
successfully - however moby data parser seems to not receive data at its
input port (in progress report tab), don't know if it is a bug or else,
anyway parsed result are clearly available in workflow swiss_prot_entry
output.
When using command line tool 2.2.0 the workflow is stopped and a Moby
exception is thrown as seen in swissprot_entry_moby output file:
<moby:MOBY xmlns:moby="http://www.biomoby.org/moby";>
<moby:mobyContent>
<moby:serviceNotes>
<moby:mobyException moby:refQueryID="a0">
<moby:exceptionCode>600</moby:exceptionCode>
<moby:exceptionMessage>Nothing was found for the given id
('P13637 ')</moby:exceptionMessage>
</moby:mobyException>
</moby:serviceNotes>
<moby:mobyData moby:queryID="a0" />
</moby:mobyContent>
</moby:MOBY>
Why is there a difference when calling the webservice whether I use the
workbench or command line tool? Is it a bug or did I miss something?
Thanks for your help.
--
Raphaël Flores
Téléphone : 01 69 33 23 56
UMR de Génétique Végétale, INRA, Univ. Paris-Sud, CNRS, AgroParisTech,
F-91190 Gif-sur-Yvette, France
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1"
producedBy="taverna-2.2.0"><dataflow id="70912376-9154-4126-9c11-23b2c2fbf9f0"
role="top"><name>Workflow22</name><inputPorts><port><name>accession</name><depth>0</depth><granularDepth>0</granularDepth><annotations
/></port></inputPorts><outputPorts><port><name>swissprot_entry</name><annotations
/></port><port><name>swissprot_entry_moby</name><annotations
/></port></outputPorts><processors><processor><name>namespace</name><inputPorts
/><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap
/><outputMap><map from="value" to="value" /></outputMap><configBean
encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean
xmlns="">
<value>UniProt</value>
</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean
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<maxJobs>1</maxJobs>
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<maxDelay>5000</maxDelay>
<maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean
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encoding="xstream"><net.sf.taverna.t2.activities.biomoby.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
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xmlns="">
<maxJobs>1</maxJobs>
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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="id" depth="0" /><port name="namespace" depth="0"
/></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>getEntryFromUniProt</name><inputPorts><port><name>Object(id)</name><depth>0</depth></port></inputPorts><outputPorts><port><name>SwissProt_Text(entry)</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.BiomobyActivity</class><inputMap><map
from="Object(id)" to="Object(id)" /></inputMap><outputMap><map
from="SwissProt_Text(entry)" to="SwissProt_Text(entry)"
/></outputMap><configBean
encoding="xstream"><net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean
xmlns="">
<mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</mobyEndpoint>
<serviceName>getEntryFromUniProt</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>
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/></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
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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(id)" depth="0"
/></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Parse
Moby
Data(SwissProt_Text)</name><inputPorts><port><name>mobyData('SwissProt_Text')</name><depth>0</depth></port></inputPorts><outputPorts><port><name>entry_'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.activities.biomoby.MobyParseDatatypeActivity</class><inputMap><map
from="mobyData('SwissProt_Text')" to="mobyData('SwissProt_Text')"
/></inputMap><outputMap><map from="entry_'content'" to="entry_'content'"
/></outputMap><configBean
encoding="xstream"><net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityConfigurationBean
xmlns="">
<datatypeName>SwissProt_Text</datatypeName>
<registryEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</registryEndpoint>
<articleNameUsedByService>entry</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="">
<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('SwissProt_Text')" depth="0"
/></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions
/><datalinks><datalink><sink
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encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean
class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>70912376-9154-4126-9c11-23b2c2fbf9f0</identification>
</annotationBean>
<date>2010-11-25 16:04:35.51 CET</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2
encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean
class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>d02e62e6-815d-4a6f-b5a1-5c6323fc7b1c</identification>
</annotationBean>
<date>2010-11-25 15:59:02.0 CET</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>------------------------------------------------------------------------------
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