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  1. Apache Taverna
  2. TAVERNA-172

XML splitter problem

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Details

    • Bug
    • Status: To Do
    • Minor
    • Resolution: Unresolved
    • None
    • None

    Description

      The workflow causing the problem takes a gene or protein id (e.g. a uniprot id) and calls the 'findPathwaysByXref' function on WikiPathways to find all pathways that contain this protein. To extract the pathway url from the xml response, an xml splitter is used several times, but this doesn't seem to read the values from the xml correctly.

      Reproduceable in Taverna 2.1 as well (empty strings on all the value-output ports like 2_results_name, but not on deeper nested outputs like 2_result_fields), so moved to project Taverna 2.

      Workflow attached in Taverna 1 version (outdated) and Taverna 2 version (updated to new WSDL).

      Attachments

        1. wikipathways-xmlsplitters.t2flow
          34 kB
          Stian Soiland-Reyes
        2. emptyOutputs.xml
          201 kB
          Stian Soiland-Reyes
        3. a.xml
          6 kB
          Stian Soiland-Reyes

        Activity

          People

            Unassigned Unassigned
            stain Stian Soiland-Reyes
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            Dates

              Created:
              Updated: