EMBL-EBI Web Services

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====== Triana ======

===== Introduction =====

[[http://www.trianacode.org/|Triana]] is a workflow development and execution tool developed at Cardiff University.

===== Using Triana with EMBL-EBI Web Services =====

The following information refers to Triana 3.2.3, which has the required web service support.

==== Importing a WSDL ====

To access a SOAP based web service, the WSDL describing the service interface needs to be imported. To do this:
  - Click the "Services" -> "Import Service..."
  - Copy/paste or type the WSDL URL (e.g. http://www.ebi.ac.uk/Tools/webservices/wsdl/WSDbfetch.wsdl for [[:services:dbfetch|WSDbfetch]]) into the "Service location?" field
  - Click the "OK" button

A "WebServices" folder should now appear in the toolbox (the tree of components and services on the left), in this folder the imported services appear. In the case of WSDbfetch a sub-folder called "WSDbfetch" appears containing components that can be added to the workflow for each of the operations provided by the service.

**Note**: services are not automatically imported when a workflow depending on them is loaded, so when using workflows which use remote services be sure to import the required WSDL descriptions before attempting to execute the workflow.

==== Using Service Operations ====

Service operations can be used the same way as any other component in Triana. For example building a workflow which uses WSDbfetch to retrieve the UniProtKB WAP_RAT entry in fasta format can be done as follows:
  - Import the WSDL for [[:services:dbfetch|WSDbfetch]] as [[#importing_a_wsdl|described above]].
  - Create an new workflow using "File" -> "New...", ctrl-N or the toolbar icon.
  - Add the component to fetch the data from the service:
    - Open the "WebServices" -> "WSDbfetch" folder in the tool box.
    - Drag the "fetchData" component from the tool box into the workflow.
  - Add the component to display the resulting data:
    - Open the "Common" -> "String" folder in the tool box.
    - Drag the "StringViewer" component from the tool box into the workflow.
  - Add the component to provide the input to the service operation and configure the input parameters:
    - Using a generated type interface ("WSTypeGen"):
      - Open the "Common" -> "WebServices" folder in the tool box.
      - Drag the "WSTypeGen" component from the tool box into the workflow.
      - Double-click the "WSTypeGen" component
      - In the dialog fill-in the data for the parameters, these are in the order specified in the WSDL: query, format and style
        - "UNIPROT:WAP_RAT"
        - "fasta"
        - "raw"
      - Click "OK"
    - Specifying the parameters individually:
      - Open the "Common" -> "String"
      - Drag the "StringGen" component from the tool box into the workflow, this adds a component called "StringGen".
      - Drag the "StringGen" component from the tool box into the workflow, this adds a component called "StringGen1".
      - Drag the "StringGen" component from the tool box into the workflow, this adds a component called "StringGen2".
      - The inputs on the "fetchData" component are in order, so the "StringGen" connected to the top input is //query//, the middle one is //format// and the bottom one is //query//, so rename the "StringGen" components (right-click on the component and select "Rename...") to reflect this.
      - Set the string for each of the inputs by double-clicking on the component, typing the string in the box and clicking "OK"
        - //query//: "UNIPROT:WAP_RAT"
        - //format//: "fasta"
        - //style//: "raw"
  - Execute the workflow, using the "Run" -> "Run" menu item or the icon on the tool bar.
  - View the result: double-click on the "StringViewer" component to see the result.

===== Examples =====

  * [[:services:dbfetch|WSDbfetch]] (SOAP):
    * [[http://www.ebi.ac.uk/Tools/webservices/downloads/workflows/triana/EBI_dbfetch_fetchData.xml|EBI_dbfetch_fetchData.xml]]
    * [[http://www.ebi.ac.uk/Tools/webservices/downloads/workflows/triana/EBI_dbfetch_fetchBatch.xml|EBI_dbfetch_fetchBatch.xml]]
  * [[:services:archive:pfa:WSInterProScan]]: [[http://www.ebi.ac.uk/Tools/webservices/downloads/workflows/triana/EBI_InterProScan.xml|EBI_InterProScan.xml]]

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