Test Scufl workflows for Ambit web service

Brief outline of Scufl workflows and operations tested. All have default parameters using a Scufl string constant processor.

• testAmbitTermIndex.xml:
  • getTermIndex
  • getTermSubIndex

• testAmbitProteinAndSpeciesIndicies.xml:
  • getProteinIndex
  • getProteinSubIndex
  • getSpeciesIndex
  • getSpeciesSubIndex

• testAmbitMakeIndex.xml:
  • makeIndex

• testAmbitInfoLectin.xml:
  • getTitlebyText
  • listByTagged
  • getPapersByTag

• testAmbitInfoAuthor.xml:
  • listByAuthor
  • getTitleByAuthor

• testAmbitGetPaper.xml:
  • getPaper

Issues

Error Handling

The Ambit interface document describe that 0 is returned when there are no matches in the database. This means that the service does not match its WSDL description, which states that the response will be an array. (ArrayOfArrayOf_xsd_string in http://don.dcs.shef.ac.uk/axis/services/ambit?wsdl )

The following test workflow has a valid PubMed ID, but one that is not known to Ambit.

• testAmbitGetPaper_ERROR.xml: PubMed ID unknown to Ambit

The following error appears in the provenance log

<p:exceptionClass>uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException</p:exceptionClass>
    <p:exceptionMessage>Error occured during invocation Attempt to create a null data object, definitely not allowed!</p:exceptionMessage>

Large Data Volume in Results

There can be problems if the data returned is very large. An attempt to call listTerms appeared to complete, but the results were never displayed. (Similarly calling makeIndex with input gly did not display the results)

Notes

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Search&DB=PubMed can be used to test for valid PubMed ids.

-- MarkGreenwood - 04 Nov 2003

• testAmbitTermIndex.xml: testAmbitTermIndex
• testAmbitProteinAndSpeciesIndicies.xml:
• testAmbitInfoLectin.xml:
• testAmbitMakeIndex.xml:
• testAmbitInfoAuthor.xml:
• testAmbitGetPaper.xml:
• testAmbitGetPaper_ERROR.xml: PubMed ID unknown to Ambit