1.
http://www.taverna.org.uk/ Project site: Scufl2 – because a workflow http://www.taverna.org.uk/ Source code: is more than its definition https://github.com/mygrid/scufl2 Stian Soiland-Reyes, Alan R Williams, Stuart Owen, David Withers and Carole Goble http://taverna.googlecode.com/ School of Computer Science, University of Manchester, UK License: GNU Lesser General Public {stian.soiland-reyes, alan.r.williams, stuart.owen, david.withers, carole.a.goble}@manchester.ac.uk License (LGPL) 2.1 “Structured” zip-file • Taverna’s future workflow and data format Self-documenting media (can be unpacked to be • Goal: Simplify third-party reading, writing, exposed on the web) type (OpenOffice ODF, ePub OCF, Adobe UCF) – annotating and extending • for tools like file(1) and mime magic Scufl2: specification, schema, ontology, Java API and conversion tool the-workflow-bundle.scufl2 mimetype Manifest listing all resources in application/vnd.taverna.scufl2.workflow-bundle META-INF/manifest.xml bundle with media META-INF/container.xml types <manifest:manifest xmlns:manifest="urn:oasis:names:tc:opendocument:xmlns:manifest:1.0 "> <container version="1.0“ xmlns="urn:oasis:names:tc:opendocument:xmlns:container"> <manifest:file-entry manifest:media- <rootfiles> type="application/vnd.taverna.scufl2.workflow-bundle" <rootfile full-path="workflowBundle.rdf" media-type="application/rdf+xml" /> manifest:full-path="/"/> <!-- <rootfile full-path="workflowBundle.ttl" <!– Standard resources --> media-type="text/turtle" /> Alternative repr. --> <manifest:file-entry manifest:media-type="application/rdf+xml" </rootfiles> manifest:full-path="workflowBundle.rdf"/> </container> <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" workflowBundle.rdf manifest:full-path="profile/tavernaServer.rdf"/> <!– Any additional resources --> <manifest:file-entry manifest:media-type="application/rdf+xml" <rdf:RDF xmlns="http://ns.taverna.org.uk/2010/scufl2#" xmlns:rdf=".." manifest:full-path="annotation/user_annotations.rdf"/> xmlns:rdfs=".." xmlns:xsi=".." xsi:schemaLocation="http://ns.taverna.org.uk/2010/scufl2# <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="annotation/myExperiment-wf-765.rdf"/> Definition of <manifest:file-entry manifest:media-type="image/png" manifest:full- http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd .." xsi:type="WorkflowBundleDocument" xml:base="./"> path="Thumbnails/thumbnail.png"/> <manifest:file-entry manifest:media-type="image/svg+xml" manifest:full- workflow structure. <WorkflowBundle rdf:about=""> <name>HelloWorld</name> <sameBaseAs rdf:resource= path="diagram/workflow/HelloWorld.svg"/> </manifest:manifest> Nested workflows "http://ns.taverna.org.uk/2010/workflowBundle/28f7c..a0ef731/" /> <mainWorkflow rdf:resource="workflow/HelloWorld/" /> <workflow> are separate <Workflow rdf:about="workflow/HelloWorld/"> <rdfs:seeAlso rdf:resource="workflow/HelloWorld.rdf" /> resources. </Workflow> <!-- plus each nested <Workflow> --> </workflow> <mainProfile rdf:resource="profile/tavernaWorkbench/" /> workflow/HelloWorld.rdf <profile> <Profile rdf:about="profile/tavernaWorkbench/"> <rdfs:seeAlso rdf:resource="profile/tavernaWorkbench.rdf" /> <rdf:RDF xmlns="http://ns.taverna.org.uk/2010/scufl2#" </Profile> <!– plus optional alternative <Profile>--> xmlns:rdf=".." xmlns:owl=".." xmlns:rdfs=".." xmlns:xsi=".." xsi:schemaLocation="http://ns.taverna.org.uk/2010/scufl2# </profile> http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd .. <rdfs:seeAlso rdf:resource="annotation/user_annotations.rdf" />Profile gives implementation <rdfs:seeAlso rdf:resource="annotation/myExperiment-wf-765.rdf" /> xsi:type="WorkflowDocument" xml:base="HelloWorld/"> <Workflow rdf:about=""> </WorkflowBundle> <name>HelloWorld</name>bindings, alternative profiles </rdf:RDF> <workflowIdentifier rdf:resource="http://ns.taverna.org.uk/2010/workflow/006...c84e2ca/" />can customize execution of <inputWorkflowPort> <InputWorkflowPort rdf:about="in/yourName"> <name>yourName</name>workflow steps for differentenvironments (e.g. desktop, profile/tavernaWorkbench.rdf <portDepth>0</portDepth> </InputWorkflowPort> </inputWorkflowPort> Every workflow part <outputWorkflowPort><!-- .. --></outputWorkflowPort>server, cloud) <rdf:RDF xmlns="http://ns.taverna.org.uk/2010/scufl2#" xmlns:beanshell="http://ns.taverna.org.uk/2010/activity/beanshell#" xmlns:dc=".." <processor> <Processor rdf:about="processor/Hello/"> xmlns:owl=".." xmlns:rdf=".." xmlns:rdfs=".." xmlns:xsi=".." <name>Hello</name> xsi:schemaLocation="http://ns.taverna.org.uk/2010/scufl2# http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd .." xsi:type="ProfileDocument" xml:base="tavernaWorkbench/"> <inputProcessorPort><!-- .. --></inputProcessorPort> <outputProcessorPort> <OutputProcessorPort rdf:about="processor/Hello/out/greeting"> has a URI, allowing <Profile rdf:about=""> <name>greeting</name> <name>tavernaWorkbench</name> <processorBinding rdf:resource="processorbinding/Hello/" /> <portDepth>0</portDepth> <granularPortDepth>0</granularPortDepth> deep annotationsHybrid of RDF/XML and XML <activateConfiguration rdf:resource="configuration/Hello/" /> </Profile> </OutputProcessorPort> </outputProcessorPort> <Activity rdf:about="activity/HelloScript/"> <dispatchStack>schema - If the xsi:type is <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/beanshell" /> <name>HelloScript</name> <DispatchStack rdf:about="processor/wait4me/dispatchStack/"> <rdf:type Relative references can alsogiven, documents can be <inputActivityPort> <InputActivityPort rdf:about="activity/HelloScript/in/personName"> rdf:resource="http://ns.taverna.org.uk/2010/scufl2/taverna#defaultDispatchStack" /> </DispatchStack> be made absolute using the <name>personName</name> </dispatchStack>parsed and generated as <portDepth>0</portDepth> <iterationStrategyStack> sameBaseAs prefix, RDF clients </InputActivityPort> <IterationStrategyStack rdf:about="processor/Hello/iterationstrategy/">regular XML, using xpath, etc. </inputActivityPort> <outputActivityPort><!-- .. --></outputActivityPort> <iterationStrategies rdf:parseType="Collection"> <CrossProduct> <!-- .. --></CrossProduct> resolving such URIs at </Activity> </iterationStrategies> <ProcessorBinding rdf:about="processorbinding/Hello/"> </IterationStrategyStack> http://ns.taverna.org.uk/2010/ <name>Hello</name> </iterationStrategyStack>The schema ensures the <bindActivity rdf:resource="activity/HelloScript/" /> <bindProcessor rdf:resource="../../workflow/HelloWorld/processor/Hello/" /> </Processor> </processor> <!-- plus other <processor>s --> workflowBundle/can bedocument can still be parsed <activityPosition>10</activityPosition> <inputPortBinding> <datalink> <DataLink redirected to a generated RDF <InputPortBinding rdf:about="processorbinding/Hello/in/name"> rdf:about="datalink?from=processor/Hello/out/greeting&amp;to=out/results&amp;mergePositas RDF/XML as well. Pure RDF <bindInputActivityPort rdf:resource="activity/HelloScript/in/personName" /> ion=0"> resource stating what’s <bindInputProcessorPort <receiveFrom rdf:resource="processor/Hello/out/greeting" />writers can ommit the xsi:type rdf:resource="../../workflow/HelloWorld/processor/Hello/in/name" /> </InputPortBinding> <sendTo rdf:resource="out/results" /> <mergePosition>0</mergePosition> obvious from the URI. </inputPortBinding> </DataLink> <outputPortBinding><!-- --> </outputPortBinding> </datalink> <!-- plus more <datalink>s --> </ProcessorBinding> <Configuration rdf:about="configuration/Hello/"> <control> <Blocking “Cool URI”-style relative <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/beanshell#Config" /> rdf:about="control?block=processor/Hello/&amp;untilFinished=processor/wait4me/"> <block rdf:resource="processor/Hello/" /> references allow parsers to <name>Hello</name> <untilFinished rdf:resource="processor/wait4me/" /> <configure rdf:resource="activity/HelloScript/" /> <beanshell:script>hello = "Hello, " + personName; <block </Blocking> ‘cheat’ and pick out processor JOptionPane.showMessageDialog(null, hello);</beanshell:script> </Configuration> </control> </Workflow> “Hello” and port “greeting” - </rdf:RDF> </rdf:RDF> but only if starts with the keyword paths out/ in/ or processor/ Resources Annotations Binaries Provenance Inputs Outputs The bundle (as a ZIP file) can be extended to include Wf4Ever: A Research arbitrary resources. These could be referenced Object (RO) captures Embedding provenance, input and output data of a internally by workflow activities, it could be PDFs, enough data and workflow run can provide example use and spreadsheets, etc. provenance about results expected outputs. Changing the root-file to point to make data and methods to the provenance makes the bundle a workflow reproducible, verifiable, run bundle, where the workflow definition is shareable, reusable and secondary. repeatable. The Scufl2 workflow run bundle forms Similarly a data bundle represents primarily the such an RO for Taverna data, but by including the workflow and the workflow results – with the provenance also embed information on how it was http://www.wf4ever-project.org/ generated. goal of becoming an http://www.mygrid.org.uk/ executable paper. Funded by: EPSRC EP/G026238/1; European Commission’s 7th FWP FP7-ICT-2007-6 270192; FP7-ICT-2007-6 270137