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
  • Description:
    Hide

    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.

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

Activity

Ascending order - Click to sort in descending order
Hide
Permalink
Stuart Owen added a comment - 2008-01-11 10:31

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

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

Show
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.
Hide
Permalink
Alan Williams added a comment - 2008-01-11 11:07

I think this comes under session management

Show
Alan Williams added a comment - 2008-01-11 11:07 I think this comes under session management
Hide
Permalink
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>
Hide
Permalink
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.

Show
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.

People

Dates

  • Created:
    2008-01-11 10:30
    Updated:
    2008-01-23 14:41
    Resolved:
    2008-01-23 14:41
Atlassian JIRA (v4.1.1#522) | Report a problem | Request a feature | Contact administrators
Powered by a free Atlassian JIRA open source license for myGrid. Try JIRA - bug tracking software for your team.