HI
I was trying to create a workflow to implement the ebi emboss fproml
service but it seems that i had a problem, could you tell me what is wrong
with this workflow (attach) in the status check process,
taverna gives me this error:
ERROR 2009-07-24 12:03:12,392 Failure while executing task Fail_if_false
uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException:
Test matches, aborting downstream processors
at
org.embl.ebi.escience.scuflworkers.java.FailIfTrue.execute(FailIfTrue.java:51)
at
org.embl.ebi.escience.scuflworkers.java.LocalServiceTask.execute(LocalServiceTask.java:31)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:585)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:524)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:443)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithoutIteration(ProcessorTask.java:652)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:356)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:282)
at
uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)
thanks
cheers
<?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:fe578ddc-d9ba-43b4-af18-a9db63875282" author="" title="ebi_fproml" />
<s:processor name="sequenceXML">
<s:local>
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
<s:extensions>
<s:complextype optional="false" unbounded="false" typename="sequenceInput" name="sequence" qname="appInputs>sequence">
<s:elements>
<s:basetype optional="true" unbounded="false" typename="string" name="direct_data" qname="sequenceInput>direct_data" />
<s:basetype optional="true" unbounded="false" typename="string" name="usa" qname="sequenceInput>usa" />
<s:basetype optional="true" unbounded="false" typename="string" name="sformat" qname="sequenceInput>sformat" />
<s:basetype optional="true" unbounded="false" typename="long" name="sbegin" qname="sequenceInput>sbegin" />
<s:basetype optional="true" unbounded="false" typename="long" name="send" qname="sequenceInput>send" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="sprotein" qname="sequenceInput>sprotein" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="snucleotide" qname="sequenceInput>snucleotide" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="sreverse" qname="sequenceInput>sreverse" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="slower" qname="sequenceInput>slower" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="supper" qname="sequenceInput>supper" />
</s:elements>
</s:complextype>
</s:extensions>
</s:local>
</s:processor>
<s:processor name="jobIdXML">
<s:local>
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
<s:extensions>
<s:complextype optional="false" unbounded="false" typename="getResults" name="jobId" qname="{http://soaplab.org/typedws}getResults";>
<s:elements>
<s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname="getResultsRequest>jobId" />
</s:elements>
</s:complextype>
</s:extensions>
</s:local>
</s:processor>
<s:processor name="runXML">
<s:local>
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
<s:extensions>
<s:complextype optional="false" unbounded="false" typename="run" name="run" qname="{http://ebi.ac.uk/fproml}run";>
<s:elements>
<s:complextype optional="false" unbounded="false" typename="sequenceInput" name="sequence" qname="appInputs>sequence">
<s:elements>
<s:basetype optional="true" unbounded="false" typename="string" name="direct_data" qname="sequenceInput>direct_data" />
<s:basetype optional="true" unbounded="false" typename="string" name="usa" qname="sequenceInput>usa" />
<s:basetype optional="true" unbounded="false" typename="string" name="sformat" qname="sequenceInput>sformat" />
<s:basetype optional="true" unbounded="false" typename="long" name="sbegin" qname="sequenceInput>sbegin" />
<s:basetype optional="true" unbounded="false" typename="long" name="send" qname="sequenceInput>send" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="sprotein" qname="sequenceInput>sprotein" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="snucleotide" qname="sequenceInput>snucleotide" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="sreverse" qname="sequenceInput>sreverse" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="slower" qname="sequenceInput>slower" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="supper" qname="sequenceInput>supper" />
</s:elements>
</s:complextype>
<s:basetype optional="true" unbounded="false" typename="string" name="intreefile_direct_data" qname="appInputs>intreefile_direct_data" />
<s:basetype optional="true" unbounded="false" typename="string" name="intreefile_url" qname="appInputs>intreefile_url" />
<s:basetype optional="true" unbounded="false" typename="long" name="ncategories" qname="appInputs>ncategories" />
<s:basetype optional="true" unbounded="false" typename="string" name="rate" qname="appInputs>rate" />
<s:basetype optional="true" unbounded="false" typename="string" name="categories_direct_data" qname="appInputs>categories_direct_data" />
<s:basetype optional="true" unbounded="false" typename="string" name="categories_url" qname="appInputs>categories_url" />
<s:basetype optional="true" unbounded="false" typename="string" name="weights_direct_data" qname="appInputs>weights_direct_data" />
<s:basetype optional="true" unbounded="false" typename="string" name="weights_url" qname="appInputs>weights_url" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="lengths" qname="appInputs>lengths" />
<s:basetype optional="true" unbounded="false" typename="string" name="model" qname="appInputs>model" />
<s:basetype optional="true" unbounded="false" typename="string" name="gamma" qname="appInputs>gamma" />
<s:basetype optional="true" unbounded="false" typename="float" name="gammacoefficient" qname="appInputs>gammacoefficient" />
<s:basetype optional="true" unbounded="false" typename="long" name="ngammacat" qname="appInputs>ngammacat" />
<s:basetype optional="true" unbounded="false" typename="float" name="invarcoefficient" qname="appInputs>invarcoefficient" />
<s:basetype optional="true" unbounded="false" typename="long" name="ninvarcat" qname="appInputs>ninvarcat" />
<s:basetype optional="true" unbounded="false" typename="float" name="invarfrac" qname="appInputs>invarfrac" />
<s:basetype optional="true" unbounded="false" typename="long" name="nhmmcategories" qname="appInputs>nhmmcategories" />
<s:basetype optional="true" unbounded="false" typename="string" name="hmmrates" qname="appInputs>hmmrates" />
<s:basetype optional="true" unbounded="false" typename="string" name="hmmprobabilities" qname="appInputs>hmmprobabilities" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="adjsite" qname="appInputs>adjsite" />
<s:basetype optional="true" unbounded="false" typename="float" name="lambda" qname="appInputs>lambda" />
<s:basetype optional="true" unbounded="false" typename="long" name="njumble" qname="appInputs>njumble" />
<s:basetype optional="true" unbounded="false" typename="long" name="seed" qname="appInputs>seed" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="global" qname="appInputs>global" />
<s:basetype optional="true" unbounded="false" typename="long" name="outgrno" qname="appInputs>outgrno" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="rough" qname="appInputs>rough" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="trout" qname="appInputs>trout" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="printdata" qname="appInputs>printdata" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="progress" qname="appInputs>progress" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="treeprint" qname="appInputs>treeprint" />
<s:basetype optional="true" unbounded="false" typename="boolean" name="hypstate" qname="appInputs>hypstate" />
</s:elements>
</s:complextype>
</s:extensions>
</s:local>
</s:processor>
<s:processor name="appResultsXML">
<s:local>
org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter
<s:extensions>
<s:complextype optional="false" unbounded="false" typename="getResultsResponse" name="appResults" qname="{http://ebi.ac.uk/fproml}getResultsResponse";>
<s:elements>
<s:basetype optional="true" unbounded="false" typename="string" name="report" qname="appResults>report" />
<s:basetype optional="true" unbounded="false" typename="long" name="detailed_status" qname="appResults>detailed_status" />
<s:basetype optional="true" unbounded="false" typename="string" name="outfile" qname="appResults>outfile" />
<s:basetype optional="true" unbounded="false" typename="string" name="outfile_url" qname="appResults>outfile_url" />
<s:basetype optional="true" unbounded="false" typename="string" name="outtreefile" qname="appResults>outtreefile" />
<s:basetype optional="true" unbounded="false" typename="string" name="outtreefile_url" qname="appResults>outtreefile_url" />
</s:elements>
</s:complextype>
</s:extensions>
</s:local>
</s:processor>
<s:processor name="getResults">
<s:description>returns all results of a given job</s:description>
<s:arbitrarywsdl>
<s:wsdl>http://www.ebi.ac.uk/soaplab/typed/services/phylogeny_molecular_sequence.fproml?wsdl</s:wsdl>
<s:operation>getResults</s:operation>
</s:arbitrarywsdl>
</s:processor>
<s:processor name="run">
<s:description>starts a job and returns its job identifier that
can be used by the getStatus and the getResults methods</s:description>
<s:arbitrarywsdl>
<s:wsdl>http://www.ebi.ac.uk/soaplab/typed/services/phylogeny_molecular_sequence.fproml?wsdl</s:wsdl>
<s:operation>run</s:operation>
</s:arbitrarywsdl>
</s:processor>
<s:processor name="Nested_Workflow">
<s:workflow maxretries="30" retrydelay="15000" critical="true">
<s:scufl version="0.2" log="0">
<s:workflowdescription lsid="urn:lsid:net.sf.taverna:wfDefinition:9c1beb9f-709b-4e1e-a79f-5d4dc87384d5" author="" title="ebi_fproml_poll" />
<s:processor name="Fail_if_false">
<s:local critical="true">org.embl.ebi.escience.scuflworkers.java.FailIfFalse</s:local>
</s:processor>
<s:processor name="Beanshell">
<s:beanshell>
<s:scriptvalue>if(job_status.equals("DONE")) {
is_done = "true";
} else {
is_done = "false";
}</s:scriptvalue>
<s:beanshellinputlist>
<s:beanshellinput s:syntactictype="'text/plain'">job_status</s:beanshellinput>
</s:beanshellinputlist>
<s:beanshelloutputlist>
<s:beanshelloutput s:syntactictype="'text/plain'">is_done</s:beanshelloutput>
</s:beanshelloutputlist>
<s:dependencies s:classloader="iteration" />
</s:beanshell>
</s:processor>
<s:processor name="jobIdXML">
<s:local>
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
<s:extensions>
<s:complextype optional="false" unbounded="false" typename="getStatus" name="jobId" qname="{http://soaplab.org/typedws}getStatus";>
<s:elements>
<s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname="getStatusRequest>jobId" />
</s:elements>
</s:complextype>
</s:extensions>
</s:local>
</s:processor>
<s:processor name="getStatus">
<s:description>returns status of a given job</s:description>
<s:arbitrarywsdl>
<s:wsdl>http://www.ebi.ac.uk/soaplab/typed/services/phylogeny_molecular_sequence.fproml?wsdl</s:wsdl>
<s:operation>getStatus</s:operation>
</s:arbitrarywsdl>
</s:processor>
<s:link source="Beanshell:is_done" sink="Fail_if_false:test" />
<s:link source="getStatus:jobStatus" sink="Beanshell:job_status" />
<s:link source="j" sink="jobIdXML:jobId" />
<s:link source="getStatus:jobStatus" sink="job_ID" />
<s:link source="jobIdXML:output" sink="getStatus:jobId" />
<s:source name="j" />
<s:sink name="job_ID" />
</s:scufl>
</s:workflow>
</s:processor>
<s:link source="i" sink="sequenceXML:direct_data" />
<s:link source="getResults:appResults" sink="appResultsXML:input" />
<s:link source="jobIdXML:output" sink="getResults:jobId" />
<s:link source="run:runResponse" sink="Nested_Workflow:j" />
<s:link source="run:runResponse" sink="jobIdXML:jobId" />
<s:link source="runXML:output" sink="run:run" />
<s:link source="sequenceXML:output" sink="runXML:sequence" />
<s:link source="Nested_Workflow:job_ID" sink="hgfd" />
<s:link source="appResultsXML:outfile" sink="o" />
<s:link source="appResultsXML:outtreefile" sink="p" />
<s:source name="i">
<s:metadata>
<s:mimeTypes>
<s:mimeType>text/xml</s:mimeType>
</s:mimeTypes>
</s:metadata>
</s:source>
<s:sink name="o" />
<s:sink name="p" />
<s:sink name="hgfd" />
<s:coordination name="getResults_BLOCKON_Nested_Workflow">
<s:condition>
<s:state>Completed</s:state>
<s:target>Nested_Workflow</s:target>
</s:condition>
<s:action>
<s:target>getResults</s:target>
<s:statechange>
<s:from>Scheduled</s:from>
<s:to>Running</s:to>
</s:statechange>
</s:action>
</s:coordination>
</s:scufl>
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