Developer:WorkflowsResource

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Index of workflow

URI: GET http://www.myexperiment.org/workflows.xml

Example output: 

<?xml version='1.0' encoding='UTF-8'?>
<workflows>
  <workflow uri='http://www.myexperiment.org/workflow.xml?id=4' resource='http://www.myexperiment.org/workflows/4'>EBI InterProScan</workflow>
  <workflow uri='http://www.myexperiment.org/workflow.xml?id=5' resource='http://www.myexperiment.org/workflows/5'>DOI2PMID</workflow>
  <workflow uri='http://www.myexperiment.org/workflow.xml?id=6' resource='http://www.myexperiment.org/workflows/6'>Genome annotation pipeline demonstrator workflow for Nucleic Acids Research</workflow>
  <workflow uri='http://www.myexperiment.org/workflow.xml?id=7' resource='http://www.myexperiment.org/workflows/7'>Fetch Dragon images from BioMoby v2</workflow>
  <workflow uri='http://www.myexperiment.org/workflow.xml?id=10' resource='http://www.myexperiment.org/workflows/10'>HUMAN Microarray CEL file to candidate pathways</workflow>
  ...
</workflows>


Create workflow

URL: POST http://www.myexperiment.org/workflow.xml

Example input: 

<?xml version="1.0"?>
<workflow>
  <title>Cove NetCDF visualization</title>
  <description>
    The Cove workflow reads oceanographic NetCDF data, does a simple processing
    step, writes the data out, then sends a web service message to the COVE
    visualization tool. It is a four step, sequential workflow.
  </description>
  <license-type>by-sa</license-type>
  <content-type>application/xaml+xml</content-type>
  <content encoding="base64" type="binary">
    PHdmOlNlcXVlbnRpYWxXb3JrZmxvd0FjdGl2aXR5DQogIHhtbG5zPSJodHRw
    Oi8vc2NoZW1hcy5taWNyb3NvZnQuY29tL3Jlc2VhcmNoLzIwMDcvU2NpZW50
    aWZpY1dvcmtmbG93Ig0KICB4bWxuczp3Zj0iaHR0cDovL3NjaGVtYXMubWlj
    ...
    eSBCYXkiIExpbms9Int3ZjpBY3Rpdml0eUJpbmQgV3JpdGUsUGF0aD1MaW5r
    fSIgSG9zdE5hbWU9ImxvY2FsaG9zdDoxMTIyMyIvPg0KPC93ZjpTZXF1ZW50
    aWFsV29ya2Zsb3dBY3Rpdml0eT4NCg==
  </content>
  <preview encoding="base64" type="binary">
    iVBORw0KGgoAAAANSUhEUgAAAo8AAADACAIAAADqYx68AACJH0lEQVR4nOyd
    B3gVxdqAZ+vZ089J772QQu9deq9SFBDsKF6xge23XRWvDXtBsQA2QIoiIAhI
    7ySUhJqQ3uup28s/exIQlatiEgyXfTkPz8lmM7s738xXZme+QRRFBn8V5S+f
    ...
    k+u2DMpAiPL8t7/F0YD1/PuY8IBq7R37O6uhVHvNGXmRonhPTbwKr7lUvApv
    uW7RSlvppXhNIWVVTkW07YOotZfcDwjvB10qiLukmikKwsupSr38P/JToTLY
    1NlZAAAAAElFTkSuQmCC
  </preview>
</workflow>

The full example input is over 800 lines long and is shown on a separate page for reference.

Example output: 

<?xml version="1.0" encoding="UTF-8"?>
<workflow uri="http://www.myexperiment.org/workflow.xml?id=635" resource="http://www.myexperiment.org/workflows/635" version="1">
  <title>Cove NetCDF visualization</title>
  <description>The Cove workflow reads oceanographic NetCDF data, does a simple processing step, writes the data out, then sends a web service message to the COVE visualization tool. It is a four step, sequential workflow.</description>
  <uploader uri="http://www.myexperiment.org/user.xml?id=22" resource="http://www.myexperiment.org/users/22">Don Cruickshank</uploader>
  <created-at>Wed Jan 21 15:56:19 +0000 2009</created-at>
  <preview>http://www.myexperiment.org/workflow/image/635/preview.png</preview>
  <license-type>by-sa</license-type>
  <content-uri>http://www.myexperiment.org/workflows/635/download/cove_netcdf_visualization_88240</content-uri>
  <content-type>application/xaml+xml</content-type>
  <tags/>
</workflow>

You can also set sharing permissions when uploading workflows via the REST API.


Read workflow

URL: GET http://www.myexperiment.org/workflow.xml?id=173

Example output: 

<?xml version="1.0" encoding="UTF-8" ?> 
<workflow uri="http://www.myexperiment.org/workflow.xml?id=173" resource="http://www.myexperiment.org/workflows/173" version="2">
  <title>Unique tags</title> 
  <description>This workflow takes a comma separated list of tags and removes duplicate entries. Tags may have multiple words in them. An example string is "carrots,handbags,carrots,cheese".</description> 
  <uploader uri="http://www.myexperiment.org/user.xml?id=22" resource="http://www.myexperiment.org/users/22">Don Cruickshank</uploader> 
  <created-at>Tue Mar 11 16:52:42 +0000 2008</created-at> 
  <preview>http://www.myexperiment.org/workflow/image/173/unique_tags_18054_2.png</preview> 
  <svg>http://www.myexperiment.org/workflow/svg/173/unique_tags_18054_2.svg</svg> 
  <license-type>by-sa</license-type> 
  <content-uri>http://www.myexperiment.org/workflows/173/download/unique_tags_18054.xml</content-uri> 
  <content-type>application/vnd.taverna.scufl+xml</content-type> 
  <tags>
    <tag uri="http://www.myexperiment.org/tag.xml?id=555" resource="http://www.myexperiment.org/tags/555">example</tag> 
    <tag uri="http://www.myexperiment.org/tag.xml?id=450" resource="http://www.myexperiment.org/tags/450">scampi</tag> 
    <tag uri="http://www.myexperiment.org/tag.xml?id=760" resource="http://www.myexperiment.org/tags/760">design pattern</tag> 
  </tags>
</workflow>


Update workflow

URL: PUT http://www.myexperiment.org/workflow.xml?id=173

Example input: 

<?xml version="1.0" encoding="UTF-8" ?> 
<workflow>
  <title>Unique tags (updated)</title> 
  <description>This workflow takes a comma separated list of tags and removes duplicate entries. Tags may have multiple words in them. An example string is "carrots,handbags,carrots,cheese".</description> 
  <license-type>by-sa</license-type> 
  <content-type>application/vnd.taverna.scufl+xml</content-type>  
</workflow>


Example output: 

<?xml version="1.0" encoding="UTF-8" ?> 
<workflow uri="http://www.myexperiment.org/workflow.xml?id=173" resource="http://www.myexperiment.org/workflows/173" version="2">
  <title>Unique tags (updated)</title> 
  <description>This workflow takes a comma separated list of tags and removes duplicate entries. Tags may have multiple words in them. An example string is "carrots,handbags,carrots,cheese".</description> 
  <uploader uri="http://www.myexperiment.org/user.xml?id=22" resource="http://www.myexperiment.org/users/22">Don Cruickshank</uploader> 
  <created-at>Tue Mar 11 16:52:42 +0000 2008</created-at> 
  <preview>http://www.myexperiment.org/workflow/image/173/unique_tags_18054_2.png</preview> 
  <svg>http://www.myexperiment.org/workflow/svg/173/unique_tags_18054_2.svg</svg> 
  <license-type>by-sa</license-type> 
  <content-uri>http://www.myexperiment.org/workflows/173/download/unique_tags_18054.xml</content-uri> 
  <content-type>application/vnd.taverna.scufl+xml</content-type> 
  <tags>
    <tag uri="http://www.myexperiment.org/tag.xml?id=555" resource="http://www.myexperiment.org/tags/555">example</tag> 
    <tag uri="http://www.myexperiment.org/tag.xml?id=450" resource="http://www.myexperiment.org/tags/450">scampi</tag> 
    <tag uri="http://www.myexperiment.org/tag.xml?id=760" resource="http://www.myexperiment.org/tags/760">design pattern</tag> 
  </tags>
</workflow>


Delete workflow

URL: DELETE http://www.myexperiment.org/workflow.xml?id=173

Example output: 

<?xml version="1.0" encoding="UTF-8" ?> 
<workflow uri="http://www.myexperiment.org/workflow.xml?id=173" resource="http://www.myexperiment.org/workflows/173" version="2">
  <title>Unique tags (updated)</title> 
  <description>This workflow takes a comma separated list of tags and removes duplicate entries. Tags may have multiple words in them. An example string is "carrots,handbags,carrots,cheese".</description> 
  <uploader uri="http://www.myexperiment.org/user.xml?id=22" resource="http://www.myexperiment.org/users/22">Don Cruickshank</uploader> 
  <created-at>Tue Mar 11 16:52:42 +0000 2008</created-at> 
  <preview>http://www.myexperiment.org/workflow/image/173/unique_tags_18054_2.png</preview> 
  <svg>http://www.myexperiment.org/workflow/svg/173/unique_tags_18054_2.svg</svg> 
  <license-type>by-sa</license-type> 
  <content-uri>http://www.myexperiment.org/workflows/173/download/unique_tags_18054.xml</content-uri> 
  <content-type>application/vnd.taverna.scufl+xml</content-type> 
  <tags>
    <tag uri="http://www.myexperiment.org/tag.xml?id=555" resource="http://www.myexperiment.org/tags/555">example</tag> 
    <tag uri="http://www.myexperiment.org/tag.xml?id=450" resource="http://www.myexperiment.org/tags/450">scampi</tag> 
    <tag uri="http://www.myexperiment.org/tag.xml?id=760" resource="http://www.myexperiment.org/tags/760">design pattern</tag> 
  </tags>
</workflow>


Elements for workflow

  • id - the id of the workflow
  • title - the title of the workflow
  • description - a description of the workflow
  • type - the content type resource that describes the type of the workflow
  • uploader - the user that uploaded the workflow
  • created-at - the date/time the workflow was created (uploaded)
  • updated-at - the date/time the workflow details were last modified
  • preview - a URL to a preview size image of the workflow
  • thumbnail - a URL to a thumbnail size image of the workflow
  • thumbnail-big - a URL to a big thumbnail size image of the workflow
  • svg - a URL to a SVG of the workflow
  • license-type - the license resource that describes the licensing of the workflow
  • content-uri - a URL to download the workflow file itself
  • content-type - the mime type of the workflow file
  • content - contents of the uploaded workflow file encoded in base64
  • tags - a list of tag resources describing the workflow
  • taggings - a list of tagging resources (i.e. resources that describe tag resources in the context of the workflow)
  • versions - a list of versions of the workflow that have been uploaded over time
  • reviews - a list of reviews of the workflow
  • comments - a list of comments on the workflow
  • ratings - a list of ratings for the workflow
  • credits - a list of users/groups credited for the creation (intellectual property) of the workflow
  • attributions - a list of workflows/files to which the workflow attributes its creation
  • citations - a list of citations resources that cite the workflow in some publication
  • components - the component elements that make up a workflow's dataflow (e.g. Taverna has sources, sinks, processors, links and coordinations)
  • privileges - a list of access privileges the user requesting the workflow has for the resource
  • statistics - total viewings and downloads for the workflow, including a further breakdown into those accessed directly from the site and those accessed in other ways (e.g. Taverna plugin)
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