myGrid
  1. myGrid
  2. TAV-706

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.

      1. e_Search_Test.xml
        5 kB
        Stuart Owen
      2. pauls_workflow.xml
        10 kB
        Stuart Owen
      3. pauls_workflow-inner.xml
        5 kB
        Stuart Owen
      4. phenotype_to_pubmed.xml
        10 kB
        Stuart Owen

        Activity

        Stuart Owen made changes -
        Field Original Value New Value
        Attachment phenotype_to_pubmed.xml [ 10093 ]
        Stuart Owen made changes -
        Attachment e_Search_Test.xml [ 10094 ]
        Stuart Owen made changes -
        Description When running the attached workflow (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.
        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.
        Alan Williams made changes -
        Assignee Alan Williams [ awilliams ] David Withers [ witherd5 ]
        Stuart Owen made changes -
        Attachment pauls_workflow.xml [ 10095 ]
        Stuart Owen made changes -
        Attachment pauls_workflow-inner.xml [ 10096 ]
        Stuart Owen made changes -
        Status Open [ 1 ] Closed [ 6 ]
        Assignee David Withers [ witherd5 ] Alan Williams [ awilliams ]
        Resolution Not A Bug [ 6 ]

          People

          • Assignee:
            Alan Williams
            Reporter:
            Stuart Owen
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            Dates

            • Created:
              Updated:
              Resolved: