Web services package

• Assigned to Tommy
• Now using SUDS library
  • Emanuele's pointers:
    • It is important to have in mind that we need to create Modules for methods and types on the fly. ZSI provided a way to generate class stubs for all methods and types in a wsdl file and VisTrails used those to create the Modules. I believe the other libraries can't do that so we might have to do that ourselves.
    • Potential library: SUDS
      • Simple interface
      • The WSDL can be cached in different ways.
      • Complex types can be stored as dict's.
    • This page on stackoverflow can also be useful: What's the best SOAP client library for Python, and where is the documentation for it?
    • Here's how Taverna handles Web Services:
      • http://www.taverna.org.uk/introduction/services-in-taverna/ the model is that any "plain" SOAP service can be used immediately, given the URL of its WSDL specification, while some special collections like caGrid, Biomoby and other services need a Taverna plugin to be used, due to their specific requirements (regarding security, for example).
      • They use Axis 1 to parse WSDLs and call web services, but built an overlay on top of Axis1 to do higher-level support, for instance caching of XSDs and header support.
      • REST support is currently under development with an alpha due out in September.
  • Status of Web Service examples in vistrails
    • chebi_webservice: OK
    • chembiogrid_webservice: There are no namespaces in the .vt file that indicates where to find the wsdl file. Namespace bug?
    • DataTransformation_webservice: Methods not available but at least a nice message: "This service was terminated. Thank you for your access."
    • DDBJ_webService: "Pipeline cannot be instantiated: Output port 'Result' has bad specification in module edu.utah.sci.vistrails.basic of package PythonSource" signature="(edu.utah.sci.vistrails.control_flow:ListOfElements)". Is this related to the removed ListOfElements type?
    • EMBOSS_webservices: OK
    • EntrezGeneToKEGG Pathway: OK
    • KEGGPathway: OK
    • KEGG_SearchEntities_webservice: OK
    • KEGG_webservices: OK
    • noaa_webservices: "1" has Been appended to method names. Bug/change in wsdl file? (looks like bug) OK (works now)
    • protein_visualization: OK
    • structure_or_id_webservice: OK
  • Status of translating examples to the new WebService package
    • chebi_webservice: OK
    • chembiogrid_webservice: Cannot construct (original broken)
    • DataTransformation_webservice: OK (But service terminated)
    • DDBJ_webService: Cannot construct (original broken)
    • EMBOSS_webservices: OK (had to handle base64 encoding and add an enum module)
    • EntrezGeneToKEGG Pathway: OK (Identical to KEGGPathway)
    • KEGGPathway: OK
    • KEGG_SearchEntities_webservice: OK
    • KEGG_webservices: OK
    • noaa_webservices: OK
    • protein_visualization: OK
    • structure_or_id_webservice: OK
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  • Related tickets
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