[Taverna-users] JDOMParseException: Error in building: FWK005 parse may not be called while parsing

Markus Plangg Mon, 16 Jan 2012 14:58:40 -0800

Hi,

I noticed that I sometimes get the following exception when running a
workflow:


ERROR 2012-01-16 23:43:33,915
(net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator:33)
- Null invocation
org.jdom.input.JDOMParseException: Error in building: FWK005 parse may
not be called while parsing.: FWK005 parse may not be called while parsing.
    at org.jdom.input.SAXBuilder.build(SAXBuilder.java:473)
    at org.jdom.input.SAXBuilder.build(SAXBuilder.java:851)
    at
net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator.convert(MechanismCreator.java:31)
    at
net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean.convertDetailsToMechanism(ExternalToolActivityConfigurationBean.java:143)
    at
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity.recreateMechanism(ExternalToolActivity.java:207)
    at
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity$1.run(ExternalToolActivity.java:227)
    at java.lang.Thread.run(Thread.java:679)
Caused by: org.xml.sax.SAXException: FWK005 parse may not be called
while parsing.
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
    at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown
Source)
    at org.jdom.input.SAXBuilder.build(SAXBuilder.java:453)
    ... 6 more
Caused by: org.xml.sax.SAXException: FWK005 parse may not be called
while parsing.
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
    at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown
Source)
    at org.jdom.input.SAXBuilder.build(SAXBuilder.java:453)
    at org.jdom.input.SAXBuilder.build(SAXBuilder.java:851)
    at
net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator.convert(MechanismCreator.java:31)
    at
net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean.convertDetailsToMechanism(ExternalToolActivityConfigurationBean.java:143)
    at
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity.recreateMechanism(ExternalToolActivity.java:207)
    at
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity$1.run(ExternalToolActivity.java:227)
    at java.lang.Thread.run(Thread.java:679)
WARN  2012-01-16 23:43:33,915
(net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke:234) -
Failed (INVOCATION) invoking
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity@31eded5e
for job DispatchJobEvent
facade503:Workflow85:Nested_workflow_3:invocation981:facade506:Workflow1:Tool[]:
Uncaught exception while invoking
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity@31eded5e
java.lang.IllegalStateException: Root element not set
    at org.jdom.Document.getRootElement(Document.java:218)
    at
net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator.convert(MechanismCreator.java:39)
    at
net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean.convertDetailsToMechanism(ExternalToolActivityConfigurationBean.java:143)
    at
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity.recreateMechanism(ExternalToolActivity.java:207)
    at
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity$1.run(ExternalToolActivity.java:227)
    at java.lang.Thread.run(Thread.java:679)
WARN  2012-01-16 23:43:33,918
(net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke:234) -
Failed (INVOCATION) invoking
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity@7118867f
for job DispatchJobEvent
facade503:Workflow85:Nested_workflow_6:invocation979:facade504:Workflow1:Tool[]:
Uncaught exception while invoking
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity@7118867f
java.lang.NullPointerException
    at
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity.getInvocation(ExternalToolActivity.java:286)
    at
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity.access$100(ExternalToolActivity.java:63)
    at
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity$1.run(ExternalToolActivity.java:227)
    at java.lang.Thread.run(Thread.java:679)

I figured this may be, because multiple tool services are started at the
exact same moment. I have attached a sample workflow where the issue
_sometimes_ occurs. Maybe this is also related to
http://sourceforge.net/mailarchive/message.php?msg_id=28660209 since the
tools are located within nested workflows and the
SQLIntegrityConstraintViolationException as described in the message is
thrown as well.

Regards,

Markus

<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1" 
producedBy="taverna-2.3.0"><dataflow id="0c8e0b43-b5a1-484c-96be-19e4a136faa8" 
role="top"><name>Workflow85</name><inputPorts /><outputPorts 
/><processors><processor><name>Nested_workflow</name><inputPorts /><outputPorts 
/><annotations 
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap
 /><outputMap /><configBean encoding="dataflow"><dataflow 
ref="18c60bb8-36fb-4d83-8adb-77908e063119" /></configBean><annotations 
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean
 
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 encoding="xstream"><null xmlns="" 
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 encoding="xstream"><null xmlns="" 
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 encoding="xstream"><null xmlns="" 
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 encoding="xstream"><null xmlns="" 
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  <maxRetries>0</maxRetries>
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 encoding="xstream"><null xmlns="" 
/></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy
 
/></iteration></iterationStrategyStack></processor><processor><name>Nested_workflow_7</name><inputPorts
 /><outputPorts /><annotations 
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap
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encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
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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>1.3</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>1.3</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>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean
 
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control="String_constant" target="Nested_workflow_3" /><condition 
control="String_constant" target="Nested_workflow" /><condition 
control="String_constant" target="Nested_workflow_8" /><condition 
control="String_constant" target="Nested_workflow_5" /><condition 
control="String_constant" target="Nested_workflow_7" /><condition 
control="String_constant" target="Nested_workflow_2" /></conditions><datalinks 
/><annotations><annotation_chain_2_2 
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      <date>2012-01-16 23:43:08.887 CET</date>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow
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/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity</class><inputMap
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  <mechanismName>default local</mechanismName>
  <mechanismXML>&lt;?xml version="1.0" encoding="UTF-8"?&gt;&#xD;
&lt;localInvocation&gt;&lt;shellPrefix&gt;/bin/sh 
-c&lt;/shellPrefix&gt;&lt;linkCommand&gt;/bin/ln -s %%PATH_TO_ORIGINAL%% 
%%TARGET_NAME%%&lt;/linkCommand&gt;&lt;/localInvocation&gt;&#xD;
</mechanismXML>
  <externaltoolid>61ca5050-a4d8-4a71-ae94-73fba7d4296c</externaltoolid>
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    <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
    <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
    <tags />
    <REs />
    <queue__preferred />
    <queue__deny />
    <static__inputs />
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    <includeStdIn>false</includeStdIn>
    <includeStdOut>true</includeStdOut>
    <includeStdErr>true</includeStdErr>
    <validReturnCodes>
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  </useCaseDescription>
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</net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean><annotations
 
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean
 
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/></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy
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class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2
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class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>

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