1. Scufl2 – because a workflow is more than its definition
Scufl2 – because a workflow is more than its definition
Project site:
Source code:
License: GNU Lesser General Public License (LGPL) 2.1
Stian Soiland-Reyes, Alan R Williams, Stuart Owen, David Withers and Carole Goble School of Computer Science, University of Manchester, UK
{stian.soiland-reyes, alan.r.williams, stuart.owen, david.withers,
Taverna’s future workflow and data format
Goal: Simplify third-party reading, writing, annotating and extending
Scufl2: specification, schema, ontology, Java API and conversion tool
Alpha
“Structured” zip-file
(can be unpacked to be exposed on the web)
Self-documenting media type (OpenOffice ODF, ePub OCF, Adobe UCF) – for tools like file(1) and mime magic
Root file: Primary document of the bundle (ePub OCF/Adobe UCF). Alternative representations of same workflow bundle allowed (Turtle, JSON, HTML, etc)
the-workflow-bundle.scufl2
application/vnd.taverna.scufl2.workflow-bundle
mimetype
Manifest listing all resources in
bundle with media types
<manifest:manifest xmlns:manifest="urn:oasis:names:tc:opendocument:xmlns:manifest:1.0">
 <manifest:file-entry manifest:media-type="application/vnd.taverna.scufl2.workflow-bundle" manifest:full-path="/"/>
 <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="workflowBundle.rdf"/>
<!– Standard resources -->
 <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="workflow/HelloWorld.rdf"/>
 <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="profile/tavernaWorkbench.rdf"/>
 <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="profile/tavernaServer.rdf"/>
 <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="annotation/user_annotations.rdf"/>
<!– Any additional resources -->
 <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="annotation/myExperiment-wf-765.rdf"/> 
 <manifest:file-entry manifest:media-type="image/png" manifest:full-path="Thumbnails/thumbnail.png"/>
 <manifest:file-entry manifest:media-type="image/svg+xml" manifest:full-path="diagram/workflow/HelloWorld.svg"/>
</manifest:manifest>
META-INF/manifest.xml
META-INF/container.xml
    <rootfiles>
<container version="1.0“ xmlns="urn:oasis:names:tc:opendocument:xmlns:container">
        <!-- <rootfile full-path="workflowBundle.ttl"
        <rootfile full-path="workflowBundle.rdf" media-type="application/rdf+xml" />
    </rootfiles>
         media-type="text/turtle" /> Alternative repr. --> 
</container>
Unique identifier which can be used as prefix for all relative references in bundle
workflowBundle.rdf
Suggests main workflow and main profile, but executor could (e.g. by parameter) run a different workflow or profile
<rdf:RDF xmlns=" xmlns:rdf=".." xmlns:rdfs=".." xmlns:xsi=".." xsi:schemaLocation=" " xsi:type="WorkflowBundleDocument" xml:base="./">
          <sameBaseAs rdf:resource= "
          <name>HelloWorld</name>
      <WorkflowBundle rdf:about="">
          <workflow>
          <mainWorkflow rdf:resource="workflow/HelloWorld/" />
            <Workflow rdf:about="workflow/HelloWorld/">
              <rdfs:seeAlso rdf:resource="workflow/HelloWorld.rdf" />
          <mainProfile rdf:resource="profile/tavernaWorkbench/" />
          </workflow>
           </Workflow> <!-- plus each nested <Workflow> -->
           <Profile rdf:about="profile/tavernaWorkbench/">
          <profile>
          </profile>
            </Profile> <!– plus optional alternative <Profile>-->
             <rdfs:seeAlso rdf:resource="profile/tavernaWorkbench.rdf" />
      </WorkflowBundle>
          <rdfs:seeAlso rdf:resource="annotation/myExperiment-wf-765.rdf" />
          <rdfs:seeAlso rdf:resource="annotation/user_annotations.rdf" />
</rdf:RDF>
Definition of workflow structure. Nested workflows are separate resources.
Additional (non-executable) annotations and metadata
workflow/HelloWorld.rdf
<rdf:RDF xmlns="
      xsi:schemaLocation=" ..
      xmlns:rdf=".." xmlns:owl=".." xmlns:rdfs=".." xmlns:xsi=".."
  xsi:type="WorkflowDocument" xml:base="HelloWorld/">
<workflowIdentifier
<name>HelloWorld</name>
  <Workflow rdf:about="">
  <InputWorkflowPort rdf:about="in/yourName">
<inputWorkflowPort>
  rdf:resource="
<name>yourName</name>
</inputWorkflowPort>
  </InputWorkflowPort>
<portDepth>0</portDepth>
<Processor rdf:about="processor/Hello/">
<processor>
<outputWorkflowPort><! ></outputWorkflowPort>
<name>Hello</name>
  <OutputProcessorPort rdf:about="processor/Hello/out/greeting">
<outputProcessorPort>
<inputProcessorPort><! ></inputProcessorPort>
<name>greeting</name>
</OutputProcessorPort>
<granularPortDepth>0</granularPortDepth>
              <dispatchStack>
</outputProcessorPort>
                 <rdf:type rdf:resource="
               <DispatchStack rdf:about="processor/wait4me/dispatchStack/">
                </DispatchStack>
               <IterationStrategyStack rdf:about="processor/Hello/iterationstrategy/">
              <iterationStrategyStack>
              </dispatchStack>
                <iterationStrategies rdf:parseType="Collection">
                </IterationStrategyStack>
                  </iterationStrategies>
                     <CrossProduct> <!-- .. --></CrossProduct>
              </iterationStrategyStack>
        <datalink>
        </processor> <!-- plus other <processor>s -->
            </Processor>
         <DataLink rdf:about="datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0">
              <sendTo rdf:resource="out/results" />
           <receiveFrom rdf:resource="processor/Hello/out/greeting" />
              <mergePosition>0</mergePosition>
        <control>
        </datalink>  <!-- plus more <datalink>s -->      
          </DataLink>
         <Blocking rdf:about="control?block=processor/Hello/&untilFinished=processor/wait4me/">
           <block
                 <untilFinished rdf:resource="processor/wait4me/" />
           <block rdf:resource="processor/Hello/" />
    </Workflow>
        </control>
          </Blocking>
</rdf:RDF>
Profile gives implementation bindings, alternative profiles can customize execution of workflow steps for different environments (e.g. desktop, server, cloud)
profile/tavernaWorkbench.rdf
Every workflow part has a URI, allowing deep annotations
Relative references can also be made absolute using the sameBaseAs prefix, RDF clients resolving such URIs at workflowBundle/ can be redirected to a generated RDF resource stating what’s obvious from the URI.
<rdf:RDF xmlns=" xmlns:beanshell=" xmlns:owl=".." xmlns:rdf=".." xmlns:rdfs=".." xmlns:xsi=".."
      xsi:schemaLocation=" .."
      xsi:type="ProfileDocument" xml:base="tavernaWorkbench/">
            <processorBinding rdf:resource="processorbinding/Hello/" />
            <name>tavernaWorkbench</name>
      <Profile rdf:about="">
      </Profile>
            <activateConfiguration rdf:resource="configuration/Hello/" />
            <name>HelloScript</name>
            <rdf:type rdf:resource="
      <Activity rdf:about="activity/HelloScript/">
                  <InputActivityPort rdf:about="activity/HelloScript/in/personName">
            <inputActivityPort>
                  </InputActivityPort>
                        <portDepth>0</portDepth>
                        <name>personName</name>
      </Activity>
            <outputActivityPort><! ></outputActivityPort>
            </inputActivityPort>
            <bindActivity rdf:resource="activity/HelloScript/" />      
            <name>Hello</name>           
      <ProcessorBinding rdf:about="processorbinding/Hello/">
            <activityPosition>10</activityPosition>
            <bindProcessor rdf:resource="../../workflow/HelloWorld/processor/Hello/" />
         <bindInputActivityPort rdf:resource="activity/HelloScript/in/personName" />
                  <InputPortBinding rdf:about="processorbinding/Hello/in/name">
            <inputPortBinding>
         <bindInputProcessorPort rdf:resource="../../workflow/HelloWorld/processor/Hello/in/name" />
                  </InputPortBinding>
      </ProcessorBinding>
            <outputPortBinding><!-- --> </outputPortBinding>           
            </inputPortBinding>
            <rdf:type rdf:resource="
      <Configuration rdf:about="configuration/Hello/">
            <beanshell:script>hello = "Hello, " + personName;
            <configure rdf:resource="activity/HelloScript/" />
            <name>Hello</name>
</rdf:RDF>
      </Configuration>
JOptionPane.showMessageDialog(null, hello);</beanshell:script>
Hybrid of RDF/XML and XML schema - If the xsi:type is given, documents can be parsed and generated as regular XML, using xpath, etc.
The schema ensures the document can still be parsed as RDF/XML as well. Pure RDF writers can ommit the xsi:type
“Cool URI”-style relative references allow parsers to ‘cheat’ and pick out processor “Hello” and port “greeting” - but only if starts with the keyword paths out/ in/ or processor/
Annotations
Resources
Provenance
Inputs
Outputs
Binaries
The bundle (as a ZIP file) can be extended to include arbitrary resources. These could be referenced internally by workflow activities, it could be PDFs, spreadsheets, etc.
Wf4Ever: A Research Object (RO) captures enough data and provenance about results to make data and methods reproducible, verifiable, shareable, reusable and repeatable. The Scufl2 workflow run bundle forms such an RO for Taverna workflow results – with the goal of becoming an executable paper.
Embedding provenance, input and output data of a workflow run can provide example use and expected outputs. Changing the root-file to point to the provenance makes the bundle a workflow run bundle, where the workflow definition is secondary.
Similarly a data bundle represents primarily the data, but by including the workflow and the provenance also embed information on how it was generated.
Funded by: EPSRC EP/G026238/1; European Commission’s 7th FWP FP7-ICT ;  FP7-ICT