myGrid

T2 XMLInputSplitterActivity problem

Details

  • Type: Bug Bug
  • Status: Closed Closed
  • Priority: Major Major
  • Resolution: Not A Bug
  • Affects Version/s: 1.7
  • Fix Version/s: 1.7.1
  • Component/s: None
  • Labels:
    None

Description

When running the attached workflow (Phenotype to pubmed - provided by Paul, bear in mind it takes a while to load) with the input "african trypanosomiasis AND mouse" then the following error occurs:

ERROR 2008-01-11 10:20:54,325 net.sf.taverna.t2.workflowmodel.processor.dispatch.impl.DispatchStackImpl (DispatchStackImpl$1:156) Error received in dispatch stack on owningProcess:facade0:dataflow2:parametersXML_eSearch, msg:Error in XMLInputSplitterActivity
java.lang.IllegalStateException: Invalid directory/Users/sowen/Library/Application Support/Taverna-1.7.0/t2-datamanager/a34b5427-25a8-4039-b471-ffe69a6aa16a/blob/fa
at net.sf.taverna.t2.cloudone.datamanager.file.FileBlobStore.parentDirectory(FileBlobStore.java:317)
at net.sf.taverna.t2.cloudone.datamanager.file.FileBlobStore.fileById(FileBlobStore.java:285)
at net.sf.taverna.t2.cloudone.datamanager.file.FileBlobStore.storeFromStream(FileBlobStore.java:245)
at net.sf.taverna.t2.cloudone.datamanager.file.FileBlobStore.storeFromString(FileBlobStore.java:276)
at net.sf.taverna.t2.cloudone.datamanager.DataFacade.register(DataFacade.java:260)
at net.sf.taverna.t2.cloudone.datamanager.DataFacade.register(DataFacade.java:151)
at net.sf.taverna.t2.cloudone.datamanager.DataFacade.register(DataFacade.java:103)
at net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity$1.createOutputData(XMLInputSplitterActivity.java:81)
at net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity$1.run(XMLInputSplitterActivity.java:69)
at java.lang.Thread.run(Thread.java:613)

i.e. there is a problem with the splitter at the top of the workflow.
The workflow passes all health checks, and runs successfully with the T1 enactor.

Attachments

  1. XML File
    e_Search_Test.xml
    2008-01-11 10:41
    5 kB
    Stuart Owen
  2. XML File
    pauls_workflow.xml
    2008-01-23 14:02
    10 kB
    Stuart Owen
  3. XML File
    pauls_workflow-inner.xml
    2008-01-23 14:02
    5 kB
    Stuart Owen
  4. XML File
    phenotype_to_pubmed.xml
    2008-01-11 10:31
    10 kB
    Stuart Owen

Activity

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Stuart Owen added a comment - 2008-01-11 10:31

an example input is "african trypanosomiasis AND mouse" (without the quotes)

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Stuart Owen added a comment - 2008-01-11 10:31 an example input is "african trypanosomiasis AND mouse" (without the quotes)
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Stuart Owen added a comment - 2008-01-11 10:41

I've also attached a workflow that contains just the call to esearch, plus the upstream splitter fed with string constants just as in Pauls workflow. However, this works.

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Stuart Owen added a comment - 2008-01-11 10:41 I've also attached a workflow that contains just the call to esearch, plus the upstream splitter fed with string constants just as in Pauls workflow. However, this works.
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Alan Williams added a comment - 2008-01-11 11:07

I think this comes under session management

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Alan Williams added a comment - 2008-01-11 11:07 I think this comes under session management
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Stuart Owen added a comment - 2008-01-23 14:02

It seems resaving the workflow to create the attached workflow (to overcome path issues with pauls nested workflows) fixes the above problem. However, the workflow still doesn't complete for other reasons - yet to be determined.

The problem reported here still remains an issue though and I'll attach the original workflows. The outer workflow is pauls_workflow.xml and the inner nested workflow is pauls_workflow-inner.xml . The outer workflow scufl will need editing to correct the path to the inner workflow, which is currently set to:

<s:workflow>
<s:xscufllocation>file:/Users/sowen/tmp/pauls_workflow-inner.xml</s:xscufllocation>
</s:workflow>

Show
Stuart Owen added a comment - 2008-01-23 14:02 It seems resaving the workflow to create the attached workflow (to overcome path issues with pauls nested workflows) fixes the above problem. However, the workflow still doesn't complete for other reasons - yet to be determined. The problem reported here still remains an issue though and I'll attach the original workflows. The outer workflow is pauls_workflow.xml and the inner nested workflow is pauls_workflow-inner.xml . The outer workflow scufl will need editing to correct the path to the inner workflow, which is currently set to: <s:workflow> <s:xscufllocation>file:/Users/sowen/tmp/pauls_workflow-inner.xml</s:xscufllocation> </s:workflow>
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Stuart Owen added a comment - 2008-01-23 14:41

Closing this as its not a bug specific to the XML splitter. It seems to be a general enactment/error handling error.

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Stuart Owen added a comment - 2008-01-23 14:41 Closing this as its not a bug specific to the XML splitter. It seems to be a general enactment/error handling error.

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Dates

  • Created:
    2008-01-11 10:30
    Updated:
    2008-01-23 14:41
    Resolved:
    2008-01-23 14:41
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