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Posted to commits@taverna.apache.org by bu...@apache.org on 2015/03/12 17:42:02 UTC
svn commit: r943561 [2/2] - in /websites/staging/taverna/trunk: cgi-bin/
content/ content/documentation/scufl2/combined.html
Added: websites/staging/taverna/trunk/content/documentation/scufl2/combined.html
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--- websites/staging/taverna/trunk/content/documentation/scufl2/combined.html (added)
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+ <h1>SCUFL2 Taverna Language</h1>
+ </div>
+ <div>
+ <div class="row">
+ <div class="hidden-xs col-sm-3 col-md-2 col-lg-2">
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="/documentation/scufl2">Scufl2 home</a></li>
+ <li><a href="/documentation/scufl2/bundle">Workflow Bundle</a></li>
+ <li><a href="/documentation/scufl2/workflow">Workflow</a></li>
+ <li><a href="/documentation/scufl2/profile">Profile</a></li>
+ <li><a href="/documentation/scufl2/taverna_bundle">Taverna Bundle</a></li>
+ <li><a href="/documentation/scufl2/datalink">Datalink</a></li>
+ <li><a href="/documentation/scufl2/api">API</a></li>
+ <li><a href="/documentation/scufl2/language">Language</a></li>
+ <li class="dropdown"><a class="dropdown-toggle" data-toggle="dropdown" href="/ns">Namespace
+ <span class="caret"></span></a>
+ <ul class="dropdown-menu">
+ <li><a href="/ns">Namespace home</a></li>
+ <li><a href="/ns/2008/xml/t2flow/">t2flow</a></li>
+ <li><a href="/ns/2010/scufl2/">sculf2</a></li>
+ <li><a href="/ns/2010/taverna/">taverna</a></li>
+ <li><a href="/ns/2010/workflowBundle/">workflowBundle</a></li>
+ <li><a href="/ns/2011/data/">data</a></li>
+ <li><a href="/ns/2011/run/">run</a></li>
+ <li><a href="/ns/2012/component/">component</a></li>
+ <li><a href="/ns/2015/ore">ore</a></li>
+ </ul>
+ </li>
+ <li><a href="/documentation/scufl2/uris">URIs</a></li>
+ <li><a href="/documentation/scufl2/ontology">Ontology</a></li>
+ <li><a href="/download/scufl2">Download</a></li>
+</ul>
+
+ </div>
+ <div class="col-xs-12 col-sm-9 col-md-10 col-lg-10">
+ <div id="content"><p>SCUFL2 is the new (since Taverna 3) mechanism for specifying Taverna workflows.
+SCUFL2 defines a model, a workflow bundle file format (.wfbundle), and a Java API for working with workflow structures.
+SCUFL2 is the workflow language for Taverna 3, and replaces Taverna 2's t2flow format.</p>
+<h2 id="summary">Summary</h2>
+<p>SCUFL2 is the Taverna 3 mechanism for specifying Taverna workflows.
+SCUFL2 adopts Linked Data technology and preservation methodologies to create a platform-independent workflow language
+ that can be inspected, modified, created and executed.</p>
+<p>SCUFL2 comes with a <a href="/documentation/scufl2/api">Java API</a> that can be used for programmatic access to read and write SCUFL2
+ <a href="/documentation/scufl2/bundle">workflow bundles</a>.
+A workflow bundle is a structured ZIP file with the workflow definitions included as XML documents.
+Those workflow documents are described by an XML Schema and are also valid RDF/XML.
+The XML Schema allows tools to read and write SCUFL2 workflow definitions as regular structured XML.
+The RDF allows RDF-enabled tools to link workflow definitions with external resources.</p>
+<p>The workflow structure is defined using an <a href="/documentation/scufl2/ontology">OWL ontology</a>
+ and annotated with URIs so that third parties can form semantic statements about any component of a Scufl2 workflow,
+ for example to state that a particular service produces outputs of a certain type,
+ or that a data link was added by a specific researcher.</p>
+<p>Semantic annotations and a manifest for the bundle declare the purpose of,
+ and links between the different components forming a workflow.
+This allows third parties to extract and append annotations about data and services used by the workflow.</p>
+<h2 id="motivation">Motivation</h2>
+<p>The t2flow serialization format suffers from being very close to the Java object model,
+ and contains various items that are simply Java beans serialized using <em>XMLBeans</em>.
+As the t2flow format is very verbose, it can be difficult to deal with for third party software to do
+ <strong>inspection</strong> ("Which services does this workflow use?"), <strong>modification</strong>
+ ("Change all calls to <em>broken.com</em> to <em>fixed.com</em>") and <strong>generation</strong>
+ ("Build a custom workflow from a button").</p>
+<p>Developers have informed us that the old SCUFL format of Taverna 1 was significantly easier to work with.
+However, this format also has its caveats, like no schema,
+ unidentified ways to extend service definitions for Taverna plugins and
+ not supporting various new features in the Taverna 2 engine.</p>
+<p>We have therefore decided to form a new serialisation format for workflows, called <strong>SCUFL2</strong>.</p>
+<h2 id="overview">Overview</h2>
+<p>SCUFL2 consists of:</p>
+<ul>
+<li><a href="/documentation/scufl2/language">SCUFL2 language</a></li>
+<li>SCUFL2 <a href="/documentation/scufl2/bundle">Workflow Bundle</a> format</li>
+<li><a href="/documentation/scufl2/api">SCUFL2 API</a> for Java</li>
+</ul>
+<h1 id="scufl2-workflowbundle">Scufl2-WorkflowBundle</h1>
+<p>The entry point of the Taverna Workflow Bundle.</p>
+<p>Defines the <em>workflows</em> and <em>profiles</em> of a
+ <a href="/documentation/scufl2/taverna_bundle">Taverna Workflow Bundle</a>.
+The <em>main workflow</em> is also normally defined, which would be the top-level workflow to execute.
+The profiles defines how these workflows can be realised and <em>executed</em> on different environments,
+ one of which can be suggested as the <em>main profile</em>.</p>
+<h2 id="bundle-path-and-root-files">Bundle path and root files</h2>
+<p>The <strong>workflow bundle document</strong> in RDF/XML format <strong>should</strong> be in in <code>/workflowBundle.rdf</code> within the bundle archive.</p>
+<p>If the archive is a <a href="/documentation/scufl2/taverna_bundle">workflow bundle</a>,
+ i.e. <code>/mimetype</code> is <code>application/vnd.taverna.scufl2.workflow-bundle</code>,
+ then the <code>META-INF/container.xml</code> can define <strong>root files</strong> at alternative paths and media types.
+This specification requires that one of those formats is <code>application/rdf+xml</code> according to this specification. </p>
+<p>Example <code>META-INF/container.xml</code>: (may be outdated)</p>
+<div class="codehilite"><pre><span class="cp"><?xml version=&quot;1.0&quot;?></span>
+<span class="nt"><container</span> <span class="na">version=</span><span class="s">"1.0"</span>
+ <span class="na">xmlns=</span><span class="s">";urn:oasis:names:tc:opendocument:xmlns:container"</span><span class="nt">></span>
+ <span class="nt"><rootfiles></span>
+ <span class="nt"><rootfile</span> <span class="na">full-path=</span><span class="s">"workflowBundle.ttl"</span>
+ <span class="na">media-type=</span><span class="s">"text/turtle"</span> <span class="nt">/></span>
+ <span class="nt"><rootfile</span> <span class="na">full-path=</span><span class="s">"workflowBundle.rdf"</span>
+ <span class="na">media-type=</span><span class="s">"application/rdf+xml"</span> <span class="nt">/></span>
+ <span class="nt"></rootfiles></span>
+<span class="nt"></container></span>
+</pre></div>
+
+
+<p>This defines the RDF/XML root file to be <code>/workflowBundle.rdf</code> -
+ with <code>workflowBundle.ttl</code> being an alternate representation the resource in Turtle format.</p>
+<p>SCUFL2-compliant workflow bundle writers:</p>
+<ul>
+<li><strong>Must</strong> set the bundle <strong>mimetype</strong> to <code>application/vnd.taverna.scufl2.workflow-bundle</code></li>
+<li><strong>Must</strong> add a workflow bundle document in <code>application/rdf+xml</code> format</li>
+<li><strong>Should</strong> store the workflow bundle document in <code>/workflowBundle.rdf</code></li>
+<li><strong>Must not</strong> contain a resource <code>/workflowBundle.rdf</code> which is not the workflow bundle document</li>
+<li>If the <code>application/rdf+xml</code> representation is not in <code>/workflowBundle.rdf</code>,
+ the writer <strong>must</strong> include <code>META-INF/container.xml</code> with the required <code><rootfile></code> entries.</li>
+<li><code>META-INF/container.xml</code>, if present, <strong>must</strong> contain one and only one <code>rootfile</code> with the media-type
+ <code>application/rdf+xml</code>.
+ rootfiles of other media-types <strong>may</strong> be included, but their formats and restrictions are not defined by this specification.</li>
+<li><strong>May</strong> Add additional representation of the workflow bundle document (and other documents).
+ Alternates of the workflow bundle document <strong>should</strong> be included in the <code>META-INF/container.xml</code>,
+ but only if they can be considered to fully specify the workflow bundle as in the RDF/XML format.
+ (So for instance a <code>text/html</code> or <code>image/png</code> representation would not normally be considered a
+ <strong>rootfile</strong> if it does not include all the structural information from the RDF/XML representation as specified here)</li>
+</ul>
+<p>It is possible to include a workflow bundle document within a different kind of archive or bundle,
+ for instance in a data bundle.
+In this case the bundle is not considered an <code>application/vnd.taverna.scufl2.workflow-bundle</code> -
+ but producers of such archives:</p>
+<ul>
+<li><strong>Should</strong> store the workflow bundle document in <code>/workflowBundle.rdf</code>,
+ unless the workflow bundle is not to be considered to have a 'main' or 'prominent' role within the archive.
+ (For instance if the archive is a collection of workflow bundles).</li>
+<li><strong>Should</strong> have a <code>mimetype</code> and <code>META-INF/container.xml</code> resource which declares the archive's main entry point,
+ like the data bundle document.
+ The mime type <strong>must not</strong> be <code>application/vnd.taverna.scufl2.workflow-bundle</code> and
+ the root files <strong>should not</strong> be the workflow bundle document.</li></li>
+<li><strong>Should</strong> link to the workflow bundle document from a resource within the archive which (ultimately)
+ is linked to from one of the <code>rootfile</code> documents.
+ Such documents <strong>should</strong> be in RDF/XML format.</li>
+<li><strong>Should</strong> declare the media type of the RDF/XML workflow bundle document as <code>application/rdf+xml</code>
+ in its <code>META-INF/manifest.xml</code></li>
+</ul>
+<p>SCUFL2 compliant workflow bundle readers:</p>
+<ul>
+<li><strong>Should</strong> assume that <code>/workflowBundle.rdf</code> - if present -
+ is the root workflow bundle in the <code>application/rdf+xml</code> format specified here.</li>
+<li><strong>Should</strong> assume that if the archive's <code>mimetype</code> is <code>application/vnd.taverna.scufl2.workflow-bundle</code>,
+ then the <code>rootfile</code> in <code>META-INF/container.xml</code> with the media type {{application/rdf+xml})
+ is the root workflow bundle document.</li>
+<li><strong>May</strong> assume that any alternate formats listed as a <code>rootfile</code> in a <code>application/vnd.taverna.scufl2.workflow-bundle</code>
+ archive would fully cover the specification of the RDF/XML representation, and read such formats instead.</li>
+<li><strong>May</strong> assume that any <code>application/rdf+xml</code> document with a <code>xsi:type="WorkflowBundleDocument"</code>
+ can be parsed according to the Scufl2 XML schema</li>
+</ul>
+<h2 id="identifiers">Identifiers</h2>
+<p>Workflow bundles and their resources <strong>must</strong> be declared with relative identifiers within the archive.
+In a <code>application/vnd.taverna.scufl2.workflow-bundle</code> archive,
+ the workflow bundle <strong>must</strong> be identified as the root of the archive.
+If the Workflow Bundle document is in <code>workflowBundle.rdf</code> within the archive, the workflow identifier is <code>./</code>.<br />
+This <strong>should</strong> be achieved by setting <code>xml:base="./"</code> and <code>rdf:about=""</code>.</p>
+<p>This means that one can mint a URI to refer to resources within the bundle archive, including the workflow bundle,
+ workflows and representations.
+If <code>http://example.com/myWfBundle.scufl2</code> returns a <a href="/documentation/scufl2/taverna_bundle">Scufl2 workflow bundle</a>
+ archive of the content type <code>application/vnd.taverna.scufl2.workflow-bundle</code>,<br />
+ then (assuming default structure of the archive):</p>
+<ul>
+<li><code>http://example.com/myWfBundle.scufl2</code> identifies for the Workflow Bundle representation (the archive)</li>
+<li><code>http://example.com/myWfBundle.scufl2/</code> identifies the Workflow Bundle (as described here)</li>
+<li><code>http://example.com/myWfBundle.scufl2/workflowBundle.rdf</code> identifies the Workflow Bundle representation in RDF/XML</li>
+<li><code>http://example.com/myWfBundle.scufl2/workflow/HelloWorld/</code> identifies the "HelloWorld"
+ <a href="/documentation/scufl2/workflow">workflow</a> within the bundle</li>
+<li><code>http://example.com/myWfBundle.scufl2/workflow/HelloWorld.rdf</code> identifies the "HelloWorld" workflow representation in RDF/XML</li>
+<li><code>http://example.com/myWfBundle.scufl2/workflow/HelloWorld/processor/Hello/</code> identifies the "Hello"
+ processor within the "HelloWorld" workflow.</li>
+</ul>
+<h3 id="embedded-workflow-bundles">Embedded workflow bundles</h3>
+<p>If the archive is another type of bundle which includes the workflow bundle
+ (but is not primarily playing the role as the format for this workflow bundle),
+ the local workflow identifier <strong>should</strong> be unique within the archive.
+This is easiest achieved by using the same folder technique as for the workflow representations:</p>
+<ul>
+<li><code>workflowBundle1.rdf</code> can define <code>workflowBundle1/</code></li>
+<li><code>exampleWorkflowBundles/hello.rdf</code> defines <code>exampleWorkflowBundles/hello/</code></li>
+</ul>
+<p>Such embedded workflow bundles <strong>should</strong> include their constituent representations
+ (such as <code>workflow/HelloWorld.rdf</code>) within that folder,
+ for instance <code>exampleWorkflowBundles/hello/workflow/HelloWorld.rdf</code> to define
+ <code>exampleWorkflowBundles/hello/workflow/HelloWorld/</code> - but could also be shared among bundles,
+ for instance both <code>workflowBundle1.rdf</code> and <code>workflowBundle2.rdf</code> might refer to <code>workflow/Shared.rdf</code>.</p>
+<h3 id="global-workflow-bundle-identifiers">Global workflow bundle identifiers</h3>
+<p>Workflow bundles <strong>should</strong> declare a <strong>sameBaseAs</strong> reference to a globally unique non-informational URI.</p>
+<p>Anyone can generate such a URI using the form <code>http://ns.taverna.org.uk/2010/workflowBundle/UUID/</code> -
+ for instance <code>http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/</code> -
+ including the trailing slash.</p>
+<p>The semantics of <strong>sameBaseAs</strong> is a kind of recursive version of <strong>owl:sameAs</strong> -
+ so also resources which URI start with the same will be included.</p>
+<p>So if:</p>
+<div class="codehilite"><pre><span class="p">@</span><span class="n">prefix</span> <span class="p">:</span> <span class="o"><</span><span class="p">;</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">ns</span><span class="p">.</span><span class="n">taverna</span><span class="p">.</span><span class="n">org</span><span class="p">.</span><span class="n">uk</span><span class="o">/</span>2010<span class="o">/</span><span class="n">scufl2</span><span class="o">></span> <span class="p">.</span>
+<span class="p">@</span><span class="n">prefix</span> <span class="n">rdfs</span><span class="p">:</span> <span class="o"><</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">www</span><span class="p">.</span><span class="n">w3</span><span class="p">.</span><span class="n">org</span><span class="o">/</span>2000<span class="o">/</span>01<span class="o">/</span><span class="n">rdf</span><span class="o">-</span><span class="n">schema</span><span class="o">></span> <span class="p">.</span>
+
+<span class="o"><./></span> <span class="n">a</span> <span class="p">:</span><span class="n">WorkflowBundle</span><span class="p">;</span>
+ <span class="p">:</span><span class="n">name</span> "<span class="n">HelloWorld</span>"<span class="p">;</span>
+ <span class="p">:</span><span class="n">sameBaseAs</span> <span class="o"><</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">ns</span><span class="p">.</span><span class="n">taverna</span><span class="p">.</span><span class="n">org</span><span class="p">.</span><span class="n">uk</span><span class="o">/</span>2010<span class="o">/</span><span class="n">workflowBundle</span><span class="o">/</span>28<span class="n">f7c554</span><span class="o">-</span>4<span class="n">f35</span><span class="o">-</span>401<span class="n">f</span><span class="o">-</span><span class="n">b34b</span><span class="o">-</span>516<span class="n">e9a0ef731</span><span class="o">/></span><span class="p">;</span>
+ <span class="p">:</span><span class="n">mainWorkflow</span> <span class="o"><</span><span class="n">workflow</span><span class="o">/</span><span class="n">HelloWorld</span><span class="o">/></span><span class="p">;</span>
+ <span class="p">:</span><span class="n">workflow</span> <span class="o"><</span><span class="n">workflow</span><span class="o">/</span><span class="n">HelloWorld</span><span class="o">/></span><span class="p">;</span>
+
+<span class="o"><</span><span class="n">workflow</span><span class="o">/</span><span class="n">HelloWorld</span><span class="o">/></span> <span class="n">a</span> <span class="p">:</span><span class="n">Workflow</span><span class="p">;</span>
+ <span class="n">rdfs</span><span class="p">:</span><span class="n">seeAlso</span> <span class="o"><</span><span class="n">workflow</span><span class="o">/</span><span class="n">HelloWorld</span><span class="p">.</span><span class="n">ttl</span><span class="o">></span> <span class="p">.</span>
+</pre></div>
+
+
+<p>then also:</p>
+<p><code><./></code>= <code><http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/></code> <br />
+<code><workflow/HelloWorld/></code> = <code><http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/></code> <br />
+<code><workflow/HelloWorld.rdf></code> = <code><http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld.rdf></code></p>
+<p>This allows anyone to make a statement about any resource within the workflow bundle,
+ even if the URL of the workflow bundle representation itself might change,
+ be it on a local USB disk, DropBox folder, myExperiment, etc.</p>
+<h4 id="updating-the-uuid">Updating the UUID</h4>
+<p>It is up to the software editing or creating the workflow to assign a new UUID as soon as
+ any change has been done to any workflow, profile or workflow bundle,
+ as this is the globally unique identifier for this workflow archive,
+ and also the base URI for all the other resources in the archive.</p>
+<blockquote>
+<p><img alt="" src="/img/warning.png" /><strong>Not implemented by API</strong> Scufl2 API do not yet</p>
+<p>automatically update the workflow bundle identifier.
+<a href="http://www.mygrid.org.uk/dev/issues/browse/SCUFL2-41">SCUFL2-41</a></p>
+<p>To update the URI, use <code>workflowBundle.setSameBaseAs(WorkflowBundle.generateIdentifier())</code>.</p>
+</blockquote>
+<h2 id="example-representation-in-rdfxml">Example representation in RDF/XML</h2>
+<p>(may be outdated)</p>
+<div class="codehilite"><pre><span class="cp"><?xml version="1.0"?></span>
+<span class="nt"><rdf:RDF</span> <span class="na">xmlns=</span><span class="s">"http://ns.taverna.org.uk/2010/scufl2#"</span>
+ <span class="na">xmlns:rdf=</span><span class="s">"http://www.w3.org/1999/02/22-rdf-syntax-ns#"</span> <span class="na">xmlns:rdfs=</span><span class="s">"http://www.w3.org/2000/01/rdf-schema#"</span>
+ <span class="na">xmlns:xsi=</span><span class="s">"http://www.w3.org/2001/XMLSchema-instance"</span>
+ <span class="na">xsi:schemaLocation=</span><span class="s">"http://ns.taverna.org.uk/2010/scufl2# http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd http://www.w3.org/1999/02/22-rdf-syntax-ns# http://ns.taverna.org.uk/2010/scufl2/rdf.xsd"</span>
+ <span class="na">xsi:type=</span><span class="s">"WorkflowBundleDocument"</span> <span class="na">xml:base=</span><span class="s">"./"</span><span class="nt">></span>
+ <span class="nt"><WorkflowBundle</span> <span class="na">rdf:about=</span><span class="s">""</span><span class="nt">></span>
+ <span class="nt"><name></span>HelloWorld<span class="nt"></name></span>
+ <span class="nt"><sameBaseAs</span>
+ <span class="na">rdf:resource=</span><span class="s">"http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/"</span> <span class="nt">/></span>
+ <span class="nt"><mainWorkflow</span> <span class="na">rdf:resource=</span><span class="s">"workflow/HelloWorld/"</span> <span class="nt">/></span>
+ <span class="nt"><workflow></span>
+ <span class="nt"><Workflow</span> <span class="na">rdf:about=</span><span class="s">"workflow/HelloWorld/"</span><span class="nt">></span>
+ <span class="nt"><rdfs:seeAlso</span> <span class="na">rdf:resource=</span><span class="s">"workflow/HelloWorld.rdf"</span> <span class="nt">/></span>
+ <span class="nt"></Workflow></span>
+ <span class="nt"></workflow></span>
+ <span class="c"><!--</span>
+<span class="c"> <workflow></span>
+<span class="c"> <Workflow rdf:about="workflow/SomeNestedWorkflow/"></span>
+<span class="c"> <rdfs:seeAlso rdf:resource="workflow/SomeNestedWorkflow.rdf" /></span>
+<span class="c"> </Workflow></span>
+<span class="c"> </workflow></span>
+<span class="c"> --></span>
+ <span class="nt"><mainProfile</span> <span class="na">rdf:resource=</span><span class="s">"profile/tavernaWorkbench/"</span> <span class="nt">/></span>
+ <span class="nt"><profile></span>
+ <span class="nt"><Profile</span> <span class="na">rdf:about=</span><span class="s">"profile/tavernaServer/"</span><span class="nt">></span>
+ <span class="nt"><rdfs:seeAlso</span> <span class="na">rdf:resource=</span><span class="s">"profile/tavernaServer.rdf"</span> <span class="nt">/></span>
+ <span class="nt"></Profile></span>
+ <span class="nt"></profile></span>
+ <span class="nt"><profile></span>
+ <span class="nt"><Profile</span> <span class="na">rdf:about=</span><span class="s">"profile/tavernaWorkbench/"</span><span class="nt">></span>
+ <span class="nt"><rdfs:seeAlso</span> <span class="na">rdf:resource=</span><span class="s">"profile/tavernaWorkbench.rdf"</span> <span class="nt">/></span>
+ <span class="nt"></Profile></span>
+ <span class="nt"></profile></span>
+ <span class="nt"><rdfs:seeAlso</span> <span class="na">rdf:resource=</span><span class="s">"annotation/workflowBundle.rdf"</span> <span class="nt">/></span>
+ <span class="nt"></WorkflowBundle></span>
+<span class="nt"></rdf:RDF></span>
+</pre></div>
+
+
+<p>This example defines the workflow bundle "HelloWorld".
+It contains one workflow <code>workflow/HelloWorld</code>, which is also the <strong>main workflow</strong>.
+Any additional workflows are typically nested (and nested-nested, etc) workflows bound as activities in processors).
+Two execution profiles are provided, and <code>profile/tavernaWorkbench</code> is dedicated as the <strong>main profile</strong>.</p>
+<h2 id="properties">Properties</h2>
+<ul>
+<li><strong>name</strong> (required) gives the human readable title for this workflow archive.
+ This is a subproperty of <code>dc:title</code>.</li>
+<li><strong>sameBaseAs</strong> (optional) gives a unique URI which is <strong>owl:sameAs</strong> with this workflow bundle and its children.</li>
+<li><strong>workflow</strong> (required) All <a href="/documentation/scufl2/workflow">workflows</a> included in this bundle.
+ Each workflow must have an <strong>rdfs:seeAlso</strong> link to the bundle resource that defines the workflow,
+ typically <code>workflow/workflowName.rdf</code> corresponding to the non-information resource <code>workflow/workflowName/</code>.</li>
+<li><strong>mainWorkflow</strong> (optional) The reference to the top-level <a href="/documentation/scufl2/workflow">workflow</a> of this bundle.
+ It is valid to have a workflow bundle without a main workflow,
+ for instance if the bundled workflows are unconnected "workflow fragments".
+ If there is a <strong>mainProfile</strong> the workflow bundle must also have a <strong>mainWorkflow</strong>.
+ The main workflow must always be listed under <strong>workflow</strong>.</li>
+<li><strong>profile</strong> (optional) <a href="/wiki/display/developer/Scufl2-Profile">profiles</a> specifying how to <strong>execute</strong> the bundled workflows. In particular the profile provides a set of configured activities bound to the processors for a particular run environment. If no profiles are specified this is an abstract workflow bundle.</li></li>
+<li><strong>mainProfile</strong> (optional) the suggested <strong>main profile</strong>. Execution platforms unable to choose between the provided profiles can select this profile as a default. It is valid to have a workflow bundle without a main profile (even if it has other profiles), but any main profile must be listed under <strong>profile</strong>.</li></li>
+<li><strong>rdfs:seeAlso</strong> (optional) link to annotations about the workflow bundle and its content. Traditionally found in <code>annotation/workflowBundle.rdf</code>, which should contain further links to annotations from different sources, for instance <code>annotation/myExperiment.rdf</code> for annotations included from myExperiment.</li></li>
+</ul>
+<h2 id="bundle-links">Bundle links</h2>
+<p>The workflow bundle document is the starting point for finding all workflow bundle resources within the archive.
+Each of the workflows and profiles must therefore have a <strong>rdfs:seeAlso</strong> link to the bundle resource that defines it.</p>
+<p>If alternate formats other than the required RDF/XML format is included in the bundle,
+ these formats can therefore link to resources in other formats, for instance in an additional <code>workflowBundle.ttl</code>
+ (<a href="http://www.w3.org/TeamSubmission/turtle/">Turtle format</a>):</p>
+<div class="codehilite"><pre><span class="p">@</span><span class="n">prefix</span> <span class="p">:</span> <span class="o"><</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">ns</span><span class="p">.</span><span class="n">taverna</span><span class="p">.</span><span class="n">org</span><span class="p">.</span><span class="n">uk</span><span class="o">/</span>2010<span class="o">/</span><span class="n">scufl2</span>#<span class="o">></span> <span class="p">.</span>
+<span class="p">@</span><span class="n">prefix</span> <span class="n">rdfs</span><span class="p">:</span> <span class="o"><</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">www</span><span class="p">.</span><span class="n">w3</span><span class="p">.</span><span class="n">org</span><span class="o">/</span>2000<span class="o">/</span>01<span class="o">/</span><span class="n">rdf</span><span class="o">-</span><span class="n">schema</span>#<span class="o">></span> <span class="p">.</span>
+
+<span class="o"><./></span> <span class="n">a</span> <span class="p">:</span><span class="n">WorkflowBundle</span><span class="p">;</span>
+ <span class="p">:</span><span class="n">mainProfile</span> <span class="o"><</span><span class="n">profile</span><span class="o">/</span><span class="n">tavernaWorkbench</span><span class="o">/></span><span class="p">;</span>
+ <span class="p">:</span><span class="n">mainWorkflow</span> <span class="o"><</span><span class="n">workflow</span><span class="o">/</span><span class="n">HelloWorld</span><span class="o">/></span><span class="p">;</span>
+ <span class="p">:</span><span class="n">name</span> "<span class="n">HelloWorld</span>"<span class="p">;</span>
+ <span class="p">:</span><span class="n">profile</span> <span class="o"><</span><span class="n">profile</span><span class="o">/</span><span class="n">tavernaServer</span><span class="o">/></span><span class="p">,</span>
+ <span class="o"><</span><span class="n">profile</span><span class="o">/</span><span class="n">tavernaWorkbench</span><span class="o">/></span><span class="p">;</span>
+ <span class="p">:</span><span class="n">sameBaseAs</span> <span class="o"><</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">ns</span><span class="p">.</span><span class="n">taverna</span><span class="p">.</span><span class="n">org</span><span class="p">.</span><span class="n">uk</span><span class="o">/</span>2010<span class="o">/</span><span class="n">workflowBundle</span><span class="o">/</span>28<span class="n">f7c554</span><span class="o">-</span>4<span class="n">f35</span><span class="o">-</span>401<span class="n">f</span><span class="o">-</span><span class="n">b34b</span><span class="o">-</span>516<span class="n">e9a0ef731</span><span class="o">/></span><span class="p">;</span>
+ <span class="p">:</span><span class="n">workflow</span> <span class="o"><</span><span class="n">workflow</span><span class="o">/</span><span class="n">HelloWorld</span><span class="o">/></span><span class="p">;</span>
+ <span class="n">rdfs</span><span class="p">:</span><span class="n">seeAlso</span> <span class="o"><</span><span class="n">annotation</span><span class="o">/</span><span class="n">workflowBundle</span><span class="p">.</span><span class="n">ttl</span><span class="o">></span> <span class="p">.</span>
+
+<span class="o"><</span><span class="n">profile</span><span class="o">/</span><span class="n">tavernaServer</span><span class="o">/></span> <span class="n">a</span> <span class="p">:</span><span class="n">Profile</span><span class="p">;</span>
+ <span class="n">rdfs</span><span class="p">:</span><span class="n">seeAlso</span> <span class="o"><</span><span class="n">profile</span><span class="o">/</span><span class="n">tavernaServer</span><span class="p">.</span><span class="n">ttl</span><span class="o">></span> <span class="p">.</span>
+
+<span class="o"><</span><span class="n">profile</span><span class="o">/</span><span class="n">tavernaWorkbench</span><span class="o">/></span> <span class="n">a</span> <span class="p">:</span><span class="n">Profile</span><span class="p">;</span>
+ <span class="n">rdfs</span><span class="p">:</span><span class="n">seeAlso</span> <span class="o"><</span><span class="n">profile</span><span class="o">/</span><span class="n">tavernaWorkbench</span><span class="p">.</span><span class="n">ttl</span><span class="o">></span> <span class="p">.</span>
+
+<span class="o"><</span><span class="n">workflow</span><span class="o">/</span><span class="n">HelloWorld</span><span class="o">/></span> <span class="n">a</span> <span class="p">:</span><span class="n">Workflow</span><span class="p">;</span>
+ <span class="n">rdfs</span><span class="p">:</span><span class="n">seeAlso</span> <span class="o"><</span><span class="n">workflow</span><span class="o">/</span><span class="n">HelloWorld</span><span class="p">.</span><span class="n">ttl</span><span class="o">></span> <span class="p">.</span>
+</pre></div>
+
+
+<h2 id="parsingwriting">Parsing/writing</h2>
+<p>SCUFL2 compliant writers, when producing the workflow bundle document:</p>
+<ul>
+<li><strong>Should</strong> write the workflow bundle RDF/XML document according to the SCUFL2 XML schema,
+ use the default namespace <code>xmlns="http://ns.taverna.org.uk/2010/scufl2#"</code> and declare the
+ <code>xsi:type="WorkflowBundleDocument"</code></li>
+<li><strong>Must</strong> ensure the workflow bundle RDF/XML document is valid <a href="http://www.w3.org/TR/REC-rdf-syntax/">RDF/XML</a>
+ and includes the properties deemed required by this specification.
+ Conforming to the XML schema should ensure this.</li>
+<li><strong>Should</strong> set the <code>xml:base</code> property to<code>"./</code></li>
+<li><strong>Should</strong> set <strong>rdf:about</strong> to <code>""</code> (or <code>"./"' if</code>xml:base` is not set))</li>
+<li><strong>Should</strong> declare a <strong>mainWorkflow</strong> and <strong>mainProfile</strong></li>
+<li><strong>Must</strong>ensure that any <strong>workflow</strong>/<strong>profile</strong> has a relative <strong>rdfs:seeAlso</strong> link to a bundle resource in
+ <code>application/rdf+xml</code> which defines <br />
+ that <a href="/documentation/scufl2/workflow">workflow</a> / <a href="/documentation/scufl2/profile">profile</a>.</li>
+</ul>
+<p>SCUFL2 compliant readers, when parsing a workflow bundle document:</p>
+<p><strong>May</strong> assume that a declared workflow/profile is defined in the referenced representation.
+ For instance, if:</p>
+<div class="codehilite"><pre><span class="nt"><workflow></span>
+ <span class="nt"><Workflow</span> <span class="na">rdf:about=</span><span class="s">"workflow/SomeNestedWorkflow/"</span><span class="nt">></span>
+ <span class="nt"><rdfs:seeAlso</span> <span class="na">rdf:resource=</span><span class="s">"workflow/SomeNestedWorkflow.rdf"</span> <span class="nt">/></span>
+ <span class="nt"></Workflow></span>
+<span class="nt"></workflow></span>
+</pre></div>
+
+
+<p>then <code>workflow/SomeNestedWorkflow.rdf</code>> <strong>must</strong> contain a <a href="/documentation/scufl2/workflow">workflow definition</a>
+ for <code>workflow/SomeNestedWorkflow/</code>. <br />
+<strong>May</strong> parse the <code>/workflowBundle.rdf</code> as RDF/XML <br />
+<strong>May</strong> parse the {/workflowBundle.rdf}} according to the XML schema if the <code>xsi:type="WorkflowBundleDocument"</code>
+ is set on the <code>rdf:RDF</code> element.</p>
+<h1 id="scufl2-workflow">Scufl2-Workflow</h1>
+<p>The definition of a workflow, its processors, inputs/outputs and links.</p>
+<ul>
+<li>Bundle path: <code>/workflow/\$name.n3</code></li>
+</ul>
+<p>Each nested workflow (and nested nested workflows etc.) exists in a separate file within the <code>/workflow/</code> folder in the bundle.
+The bundle's <a href="/documentation/scufl2/bundle">research object</a> defines what is the top level workflow.</p>
+<h2 id="identifier">Identifier</h2>
+<p>Each workflow <strong>must</strong> have a unique name within the bundle's workflow files.
+The base part of the file name (excluding extension) <strong>must</strong> match the <strong>scufl2:name</strong> of the workflow.</p>
+<p>Workflows used in a particular research object are globally identified as
+ <code><http://ns.taverna.org.uk/2010/researchObject/$uuid/workflow/$workflowName/></code> -
+ for instance <code><http://ns.taverna.org.uk/2010/researchObject/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/Helloworld/></code>.</p>
+<p>As it can be useful to identify nested workflows included in several workflow bundles,
+ each workflow must also have a <em>scufl2:workflowIdentifier</em> property, which URI <strong>must</strong> be on the form
+ <code><http://ns.taverna.org.uk/2010/workflow/$uuid></code>, for example
+ <code><http://ns.taverna.org.uk/2010/workflow/efb1cdcd-1e19-408a-885a-303c6553a672/></code>.
+It is responsibility of the software creating or modifying the workflow to generate a new workflowcIdentifier
+ as soon as the workflow has changed.
+(The randomly generated UUID of the workflow must <strong>not</strong> match the UUID of a research object or any other workflow.)
+The owning <a href="/documentation/scufl2/bundle">research object</a> should then also be assigned a new UUID.
+(Note that editing metadata and bindings in other files don't update the workflow, but still update the research object.)</p>
+<p>The workflow file <strong>should</strong> set the @base to the form <code><workflow/$name></code>}
+ so that nested resources can be referenced relatively, like {{<processor/$processorName></code>.</p></p>
+<h2 id="example">Example</h2>
+<p>(Outdated)</p>
+<div class="codehilite"><pre><span class="p">@</span><span class="n">base</span> <span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="n">workflow</span><span class="o">/</span><span class="n">Helloworld</span><span class="o">/&</span><span class="n">gt</span><span class="p">;</span>
+<span class="p">@</span><span class="n">prefix</span> <span class="n">scufl2</span><span class="p">:</span> <span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">ns</span><span class="p">.</span><span class="n">taverna</span><span class="p">.</span><span class="n">org</span><span class="p">.</span><span class="n">uk</span><span class="o">/</span>2010<span class="o">/</span><span class="n">scufl2</span><span class="o">/</span><span class="n">ontology</span><span class="o">/&</span><span class="n">gt</span><span class="p">;</span> <span class="p">.</span>
+
+<span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="o">&</span><span class="n">gt</span><span class="p">;</span>
+ <span class="n">a</span> <span class="n">scufl2</span><span class="p">:</span><span class="n">Workflow</span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span class="n">name</span> <span class="o">&</span><span class="n">quot</span><span class="p">;</span><span class="n">Helloworld</span><span class="o">&</span><span class="n">quot</span><span class="p">;</span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span class="n">inputWorkflowPort</span> <span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="n">in</span><span class="o">/</span><span class="n">yourName</span><span class="o">&</span><span class="n">gt</span><span class="p">;</span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span class="n">outputWorkflowPort</span> <span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="n">out</span><span class="o">/</span><span class="n">results</span><span class="o">&</span><span class="n">gt</span><span class="p">;</span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span class="n">datalink</span> <span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="n">datalink</span><span class="o">/</span>1<span class="o">&</span><span class="n">gt</span><span class="p">;,</span> <span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="n">datalink</span><span class="o">/</span>2<span class="o">&</span><span class="n">gt</span><span class="p">;</span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span class="n">processor</span> <span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="n">processor</span><span class="o">/</span><span class="n">Hello</span><span class="o">&</span><span class="n">gt</span><span class="p">;</span> <span class="p">.</span>
+<span class="p">]]</span><span class="o">></span>
+</pre></div>
+
+
+<p>This example defines the workflow "HelloWorld".
+It contains one workflow input port and one workflow output port, in addition to a single processor and two datalinks.</p>
+<p>The nested resources for this workflow, such as InputWorkflowPort , OutputWorkflowPort,
+ <a href="/documentation/scufl2/datalink">DataLink</a>, Processor and their children <strong>should</strong> be described
+ in the same file as the workflow itself.
+Additional metadata should be added to an <code>/annotations/</code> file.</p>
+<h2 id="properties_1">Properties</h2>
+<ul>
+<li><strong>scufl2:name</strong> (required) gives the programmatic short-name for this workflow within this bundle.
+ This must be unique among the other workflows.</li>
+<li><strong>scufl2:workflowIdentifier</strong> (required) gives the globally unique URI defining this workflow.
+ See <em>Identifier</em> above.</li>
+<li><strong>scufl2:inputWorkflowPort</strong> (optional) All workflow input ports defined for this workflow.</li>
+<li><strong>scufl2:outputWorkflowPort</strong> (optional) All workflow output ports defined for this workflow.</li>
+<li><strong>scufl2:datalink</strong> (optional) All <a href="/documentation/scufl2/datalink">datalinks</a>
+ defined between workflow and processor ports in this workflow.
+ (Note that if this is a nested workflow, its outside links are defined in the parent workflow)</li>
+<li><strong>scufl2:processor</strong> (optional) All <a href="/documentation/scufl2/processors">processors</a> in this workflow.</li>
+</ul>
+<h2 id="bundle-links_1">Bundle links</h2>
+<p>All nested workflow resources should also be defined in the same archive file as this workflow.
+Their URIs <strong>must</strong> be relative to this workflow, their type and <strong>scufl2:name</strong>.
+So for instance <workflow/Helloworld/processor/Hello> is a <strong>scufl2:Processor</strong> in <workflow/Helloworld>,
+ and has a <strong>scufl2:name</strong> "Hello".</p>
+<h1 id="scufl2-profile">Scufl2 Profile</h1>
+<p>Details of the Scufl2 profile still to be added.</p>
+<h1 id="taverna-workflow-bundle">Taverna Workflow Bundle</h1>
+<p>The primary SCUFL2 file format is the Taverna <em>workflow bundle</em>.</p>
+<table><tbody>
+<tr>
+<th>Media type</th>
+<td><code>application/vnd.taverna.scufl2.workflow-bundle</code></td>
+</tr>
+<tr>
+<th>File extension</th>
+<td><code>.wfbundle</code></td>
+</tr>
+<tr>
+<th>File type</th>
+<td>Zip archive</td>
+</tr>
+</tbody></table>
+
+</div>
+
+<p>This file is a structured ZIP archive, based on the
+ <a href="http://livedocs.adobe.com/navigator/9/Navigator_SDK9_HTMLHelp/wwhelp/wwhimpl/common/html/wwhelp.htm?context=Navigator_SDK9_HTMLHelp&amp;file=Appx_Packaging.6.31.html">Adobe UCF</a>
+ format.
+This is similar to the structured ZIPs used by the OpenOffice format <a href="http://en.wikipedia.org/wiki/OpenDocument_technical_specification#Format_internals">ODF</a>.</p>
+<p>For a file to be a Taverna Workflow Bundle if it <strong>must</strong>:</p>
+<ul>
+<li>Is a valid <a href="http://livedocs.adobe.com/navigator/9/Navigator_SDK9_HTMLHelp/wwhelp/wwhimpl/common/html/wwhelp.htm?context=Navigator_SDK9_HTMLHelp&amp;file=Appx_Packaging.6.1.html#1522568">ZIP container</a></li>
+<li>Contains the file <code>mimetype</code> with the ASCII content <code>application/vnd.taverna.scufl2.workflow-bundle</code> (without LF/CR)</li>
+<li>Contains the file <code>workflowBundle.rdf</code> as a valid <a href="http://www.w3.org/TR/rdf-syntax-grammar/">RDF/XML</a>
+ document describing a <a href="/documentation/scufl2/bundle">workflow bundle</a></li>
+</ul>
+<p>To be fully compliant, the bundle <strong>should</strong> also:</p>
+<ul>
+<li>Contain a valid <code>META-INF/manifest.xml</code> file listing all files in the archive</li>
+<li>Contain a valid <code>META-INF/container.xml</code> file including an entry for <code>workflowBundle.rdf</code></li>
+</ul>
+<p>The <a href="/documentation/scufl2/bundle">workflow bundle document</a> is the top level entry point ("root file")
+ for the archive (think: <code>index.html</code>), and describes:</p>
+<ul>
+<li>Which workflows are included in the bundle under <code>workflow/</code></li>
+<li>Which profiles are included in the bundle under <code>profile/</code></li>
+<li>Which of the workflows is the suggested <em>main workflow</em></li>
+<li>Which of the profiles is the suggested <em>main profile</em></li>
+<li>What is the global workflow bundle identifier.</li>
+</ul>
+<p>A Workflow Bundle document can also be included as part of any other bundle,
+ archive or resource according to these specifications.
+In that case the resource name might or might not be <code>workflowBundle.rdf</code>,
+ this depends on the specification of that other format.</p>
+<h3 id="archive-directory-structure">Archive directory structure</h3>
+<table><tbody>
+<tr>
+<th>Path</th>
+<th>Type</th>
+<th>Description</th>
+</tr>
+<tr>
+<td>mimetype</td>
+<td>Text</td>
+<td>Mime type of bundle, ie. <code>application/vnd.taverna.scufl2.workflow-bundle</code></td>
+</tr>
+<tr>
+<td>META-INF/</td>
+<td>Folder</td>
+<td>Reserved folder for manifest </td>
+</tr>
+<tr>
+<td> META-INF/manifest.xml </td>
+<td> XML </td>
+<td> ODF 1.3-like manifest, listing each file, mime-type and file size </td>
+</tr>
+<tr>
+<td> META-INF/container.xml </td>
+<td> XML </td>
+<td>Adobe UCF/OEBPS list of <a href="http://livedocs.adobe.com/navigator/9/Navigator_SDK9_HTMLHelp/wwhelp/wwhimpl/common/html/wwhelp.htm?context=Navigator_SDK9_HTMLHelp&file=Appx_Packaging.6.31.html" class="external-link" rel="nofollow">root files</a> (ie. <code>workflowBundle.rdf</code>))</td>
+</tr>
+<tr>
+<td> workflowBundle.rdf </td>
+<td> RDF/XML </td>
+<td> <a href="/wiki/display/developer/Scufl2-WorkflowBundle">Workflow Bundle Document</a> </td>
+</tr>
+<tr>
+<td>vworkflow/ </td>
+<td> Folder </td>
+<td> Workflow definitions </td>
+</tr>
+<tr>
+<td> workflow/HelloWorld.rdf </td>
+<td> RDF/XML</td>
+<td> <a href="/documentation/scufl2/workflow">Workflow definition</a> for "HelloWorld" </p></td>
+</tr>
+<tr>
+<td>workflow/otherWorkflow.rdf</td>
+<td> RDF/XML</td>
+<td> Workflow definition for "otherWorkflow" </td>
+</tr>
+<tr>
+<td> profile/ </td>
+<td> Folder </td>
+<td> Execution <a href="/wiki/display/developer/Scufl2-Profile">Profile </a> definitions </td>
+</tr>
+<tr>
+<td> profile/someProfile.rdf </td>
+<td> RDF/XML</td>
+<td> Profile definition "someProfile" </td>
+</tr>
+<tr>
+<td> profile/other.rdf </td>
+<td> RDF/XML</td>
+<td> Profile definition "other"</td>
+</tr>
+</tbody></table>
+
+</div>
+
+<p>The archive must be a ZIP file, and should have the file extension <code>.wfbundle</code>.
+Some situations might require treating the workflow bundle as an unpacked set of folders.
+In this case the top folder should still have the file extension <code>.wfbundle</code>.</p>
+<p>According to the Adobe UCF specifications, the <code>mimetype</code> file must be the <em>first file</em> in the folder,
+ and must be stored without compression, encryption or permission attributes,
+ to support detection by mimemagic and similar.</p>
+<p>The file <code>META-INF/manifest.xml</code> - if present - must list every non-<code>META-INF</code> file and folder in the archive,
+ including the root folder.
+It should provide the mime-type - if known - for individual files.
+The root folder should have the same mime type as in the <code>mimetype</code> file - <code>application/vnd.taverna.scufl2.workflow-bundle</code>.</p>
+<p>The file <code>META-INF/container.xml</code> - if present - should point to the 'root' workflow bundle document.
+One and only one entry which must be of the mime type <code>application/rdf+xml</code>,
+ and this entry must be called <code>workflowBundle.rdf</code>.
+Alternative representation of the workflow bundle root document can be included in other formats,
+ there's no similar restriction on their filenames, although it is recommended they match the RDF/XML filename,
+ for instance <code>workflowBundle.html</code>, <code>workflowBundle.json</code>, etc.</p>
+<p>The folder <code>workflow</code> contain each of the workflow definitions as
+ <a href="/documentation/scufl2/workflow">Workflow Documents</a>.
+One of these is typically the <em>main workflow</em> while the others are <em>nested workflows</em>,
+ but there is no requirement that the workflows included are to be included as a nested workflow or a main workflow.
+Such 'dangling workflows' can be considered to be only <em>declared workflows</em> -
+ they might be there for historical reasons or because the workflow bundle is at an early stage of development
+ when there is no main workflow yet.</p>
+<p>The execution details of workflows (such as activity choice, configuration) are described in the <code>profile</code> folder,
+ one <a href="/documentation/scufl2/profile">Profile Document</a> per possible execution binding.
+(For instance, one profile for the graphical Workbench, one for the Taverna Server and one for the Taverna Portal.).
+One profile document can include execution details for several workflows,
+ but there could also be workflows which don't have any execution details in any profile -
+ these can be considered <em>abstract workflows</em>.</p>
+<h2 id="workflowbundlerdf">workflowBundle.rdf</h2>
+<p>The workflow bundle document <code>workflowBundle.rdf</code> should list each of these <em>workflows</em> and <em>profiles</em>,
+ and <strong>should</strong> suggest the <em>main workflow</em> and <em>main profile</em>. </p>
+<h2 id="mimetype">mimetype</h2>
+<p>This file is required, as a guide for mime magic and similar tools that guess the type of the archive.
+Therefore it must be added as the first file to the archive, uncompressed,
+ so that its content is available in cleartext in the first bytes of the ZIP archive.</p>
+<p>The file must be in ASCII and <strong>not</strong> contain any line feeds.
+If the archive is a Taverna Workflow Bundle, the mime type should be <code>application/vnd.taverna.scufl2.workflow-bundle</code>.
+If <code>META-INF/manifest.xml</code> is present, this mime type must match the mime type of <code>"/"</code> in the manifest.</p>
+<p>To add the file <code>mimetype</code> as the first uncompressed file, followed by the rest of the bundle (excluding the mimetype file),
+ try using InfoZip:</p>
+<div class="codehilite"><pre>$ <span class="n">zip</span> <span class="o">-</span>0 <span class="o">-</span><span class="n">X</span> <span class="p">.</span><span class="o">./</span><span class="n">example</span><span class="p">.</span><span class="n">wfbundle</span> <span class="n">mimetype</span>
+ <span class="n">adding</span><span class="p">:</span> <span class="n">mimetype</span> <span class="p">(</span><span class="n">stored</span> 0<span class="c">%)</span>
+
+$ <span class="n">zip</span> <span class="o">-</span><span class="n">X</span> <span class="o">-</span><span class="n">r</span> <span class="p">.</span><span class="o">./</span><span class="n">example</span><span class="p">.</span><span class="n">wfbundle</span> <span class="p">.</span> <span class="o">-</span><span class="n">x</span> <span class="n">mimetype</span>
+ <span class="n">adding</span><span class="p">:</span> <span class="n">workflowBundle</span><span class="p">.</span><span class="n">rdf</span> <span class="p">(</span><span class="n">deflated</span> 74<span class="c">%)</span>
+ <span class="n">adding</span><span class="p">:</span> <span class="n">workflow</span><span class="o">/</span> <span class="p">(</span><span class="n">stored</span> 0<span class="c">%)</span>
+ <span class="n">adding</span><span class="p">:</span> <span class="n">workflow</span><span class="o">/</span><span class="n">HelloWorld</span><span class="p">.</span><span class="n">rdf</span> <span class="p">(</span><span class="n">stored</span> 0<span class="c">%)</span>
+<span class="p">..</span>
+ <span class="n">adding</span><span class="p">:</span> <span class="n">META</span><span class="o">-</span><span class="n">INF</span><span class="o">/</span> <span class="p">(</span><span class="n">stored</span> 0<span class="c">%)</span>
+ <span class="n">adding</span><span class="p">:</span> <span class="n">META</span><span class="o">-</span><span class="n">INF</span><span class="o">/</span><span class="n">manifest</span><span class="p">.</span><span class="n">xml</span> <span class="p">(</span><span class="n">deflated</span> 78<span class="c">%)</span>
+ <span class="n">adding</span><span class="p">:</span> <span class="n">META</span><span class="o">-</span><span class="n">INF</span><span class="o">/</span><span class="n">container</span><span class="p">.</span><span class="n">xml</span> <span class="p">(</span><span class="n">deflated</span> 50<span class="c">%)</span>
+</pre></div>
+
+
+<p>To verify:</p>
+<div class="codehilite"><pre>$ <span class="n">unzip</span> <span class="o">-</span><span class="n">lv</span> <span class="p">.</span><span class="o">./</span><span class="n">example</span><span class="p">.</span><span class="n">wfbundle</span>
+<span class="n">Archive</span><span class="p">:</span> <span class="p">.</span><span class="o">./</span><span class="n">example</span><span class="p">.</span><span class="n">wfbundle</span>
+ <span class="n">Length</span> <span class="n">Method</span> <span class="n">Size</span> <span class="n">Cmpr</span> <span class="n">Date</span> <span class="n">Time</span> <span class="n">CRC</span><span class="o">-</span>32 <span class="n">Name</span>
+<span class="o">--------</span> <span class="o">------</span> <span class="o">-------</span> <span class="o">----</span> <span class="o">----------</span> <span class="o">-----</span> <span class="o">--------</span> <span class="o">----</span>
+ 35 <span class="n">Stored</span> 35 0<span class="c">% 2010-10-11 16:44 8373c7d8 mimetype</span>
+ 3047 <span class="n">Defl</span><span class="p">:</span><span class="n">N</span> 786 74<span class="c">% 2010-10-13 09:40 743ecfe4 workflowBundle.rdf</span>
+ 0 <span class="n">Stored</span> 0 0<span class="c">% 2010-10-06 14:57 00000000 workflow/</span>
+<span class="p">...</span>
+
+$ <span class="n">python</span> <span class="o">-</span><span class="n">c</span> <span class="o">&</span><span class="n">quot</span><span class="p">;</span><span class="n">print</span> <span class="n">open</span> <span class="p">(</span><span class="o">&</span>#39<span class="p">;.</span><span class="o">./</span><span class="n">example</span><span class="p">.</span><span class="n">wfbundle</span><span class="o">&</span>#39<span class="p">;).</span><span class="n">read</span><span class="p">(</span>128<span class="p">)[</span>38<span class="p">:</span>84<span class="p">]</span><span class="o">&</span><span class="n">quot</span><span class="p">;</span>
+<span class="n">print</span><span class="p">(</span>"<span class="n">code</span> <span class="n">sample</span>"<span class="p">);</span>`<span class="n">application</span><span class="o">/</span><span class="n">vnd</span><span class="p">.</span><span class="n">taverna</span><span class="p">.</span><span class="n">scufl2</span><span class="p">.</span><span class="n">workflow</span><span class="o">-</span><span class="n">bundle</span>
+</pre></div>
+
+
+<h2 id="meta-infmanifestxml">META-INF/manifest.xml</h2>
+<p>This file, if exists, should follow the OpenDocument container format,
+ and list every file in the bundle (except for the META-INF files).
+The main functionality provided by the manifest is to give the mime-type of additional resources.
+As a minimum the mime-type should distinguish between <code>text/plain</code> (UTF-8 text) and <code>application/octet-stream</code> (binary).
+If a mime-magick like tool has guessed a more detailed mime type, it can also be provided here.</p>
+<p>Additionally the manifest may specify the file sizes,
+cccin general this can be useful when inspecting a larger workflow bundle remotely (exposed as a RESTful folder or similar).</p>
+<p>The folder <code>/</code> represents the bundle itself, and must have the same mime type as in the file <code>mimetype</code>,
+ ie. <code>application/vnd.taverna.scufl2.workflow-bundle</code>.
+A different mime type might be used if the primary purpose of the archive is different from being a workflow bundle,
+ for instance being a Taverna Data Bundle.</p>
+<p>The <code>workflowBundle.rdf</code> file must be listed in the manifest, and it must be listed with the <code>application/rdf+xml</code> mime type.
+Any alternative representations must also be listed, and their mime type must match those in <code>META-INF/container.xml</code>
+ (see below).</p>
+<p>The other folders are not required to have a mimetype.</p>
+<p>If there is no manifest in the workflow bundle,
+ all data value files should be treated to be binary <code>application/octet-stream</code>,
+ unless they have one of these file extensions:</p></p>
+<ul>
+<li><code>*.txt</code> is <code>text/plain</code> in UTF-8 character set</li>
+<li><code>*.rdf</code> is <code>application/rdf+xml</code></li>
+</ul>
+<p>Example manifest:</p>
+<div class="codehilite"><pre><span class="cp"><?</span><span class="nx">xml</span> <span class="nx">version</span><span class="o">=</span><span class="s2">"1.0"</span> <span class="nx">encoding</span><span class="o">=</span><span class="s2">"UTF-8"</span><span class="cp">?></span>
+<span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">manifest</span> <span class="nx">xmlns</span><span class="o">:</span><span class="nx">manifest</span><span class="o">=</span><span class="s2">"urn:oasis:names:tc:opendocument:xmlns:manifest:1.0"</span><span class="o">></span>
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"application/vnd.taverna.scufl2.workflow-bundle"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"/"</span><span class="o">/></span>
+
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"application/rdf+xml"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"workflowBundle.rdf"</span><span class="o">/></span>
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"application/rdf+xml"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"workflow/HelloWorld.rdf"</span><span class="o">/></span>
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"application/rdf+xml"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"annotation/workflow/HelloWorld.rdf"</span><span class="o">/></span>
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"application/rdf+xml"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"annotation/workflowBundle.rdf"</span><span class="o">/></span>
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"application/rdf+xml"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"profile/tavernaWorkbench.rdf"</span><span class="o">/></span>
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"application/rdf+xml"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"profile/tavernaServer.rdf"</span><span class="o">/></span>
+
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"text/turtle"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"workflowBundle.ttl"</span><span class="o">/></span>
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"text/turtle"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"workflow/HelloWorld.ttl"</span><span class="o">/></span>
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"text/turtle"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"annotation/workflow/HelloWorld.ttl"</span><span class="o">/></span>
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"text/turtle"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"annotation/workflowBundle.ttl"</span><span class="o">/></span>
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"text/turtle"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"profile/tavernaWorkbench.ttl"</span><span class="o">/></span>
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"text/turtle"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"profile/tavernaServer.ttl"</span><span class="o">/></span>
+
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"image/svg+xml"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"Thumbnails/thumbnail.svg"</span><span class="o">/></span>
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"image/png"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"Thumbnails/thumbnail.png"</span><span class="o">/></span>
+
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"image/svg+xml"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"diagram/workflow/HelloWorld.svg"</span><span class="o">/></span>
+ <span class="o"><</span><span class="nx">manifest</span><span class="o">:</span><span class="nx">file</span><span class="o">-</span><span class="nx">entry</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">media</span><span class="o">-</span><span class="nx">type</span><span class="o">=</span><span class="s2">"image/png"</span> <span class="nx">manifest</span><span class="o">:</span><span class="nx">full</span><span class="o">-</span><span class="nx">path</span><span class="o">=</span><span class="s2">"diagram/workflow/HelloWorld.png"</span><span class="o">/></span>
+<span class="o"><</span><span class="err">/manifest:manifest></span>
+</pre></div>
+
+
+<h2 id="meta-infcontainerxml">META-INF/container.xml</h2>
+<p>This file, if present, should point to the root workflow bundle document,
+ which in an <code>application/vnd.taverna.scufl2.workflow-bundle</code> must be <code>workflowBundle.rdf</code>.
+Alternative representation of the same file are permitted,
+ but SCUFL2 compliant tools are only required to understand the <code>application/rdf+xml</code> representations described here.</p>
+<p>The Adobe UCF specification defines the
+ <a href="http://livedocs.adobe.com/navigator/9/Navigator_SDK9_HTMLHelp/wwhelp/wwhimpl/common/html/wwhelp.htm?context=Navigator_SDK9_HTMLHelp&amp;file=Appx_Packaging.6.31.html">format of this container file</a>.</p>
+<p><img alt="" src="//img/warning.png" /> <em>XML namespace in container.xml</em></p>
+<blockquote>
+<div class="codehilite"><pre><span class="n">Adobe</span> <span class="n">UCF</span> <span class="n">have</span> <span class="n">used</span> <span class="n">the</span> <span class="n">XML</span> <span class="n">namespace</span> `<span class="n">urn</span><span class="p">:</span><span class="n">oasis</span><span class="p">:</span><span class="n">names</span><span class="p">:</span><span class="n">tc</span><span class="p">:</span><span class="n">opendocument</span><span class="p">:</span><span class="n">xmlns</span><span class="p">:</span><span class="n">container</span>` <span class="n">although</span> <span class="n">this</span> <span class="n">format</span>
+</pre></div>
+
+
+<p>is not defined by OASIS or the Open Document specification. </p>
+<div class="codehilite"><pre><span class="n">SCUFL2</span> <span class="n">compliant</span> <span class="n">tools</span> <span class="n">should</span> <span class="n">therefore</span> <span class="n">parse</span> `<span class="n">container</span><span class="p">.</span><span class="n">xml</span>` <span class="n">ignoring</span> <span class="n">any</span> <span class="n">default</span> <span class="n">namespaces</span><span class="p">,</span> <span class="n">and</span> <span class="n">write</span> <span class="n">using</span> <span class="n">the</span> <span class="n">default</span> <span class="n">name</span>
+</pre></div>
+
+
+<p>space and <code><container
+xmlns="urn:oasis:names:tc:opendocument:xmlns:container"</code> as the root
+element.</p>
+</blockquote>
+<p>If the archive is of the mime type <code>application/vnd.taverna.scufl2.workflow-bundle</code>
+ and contains other representations of the workflow bundle (for instance: JSON,
+Turtle, t2flow) then the bundle <strong>must</strong> have a container file and list these representations in addition to
+ <code>workflowBundle.rdf</code>.
+Derived representations such as SVG diagrams and HTML reports should generally <strong>not</strong> be listed as 'root files'
+ unless they can be considered to 'fully represent the workflow bundle', for instance by using RDFa.</p>
+<p>A SCUFL2 compliant parser can assume that an archive which is <em>not</em> of the mime type
+ <code>application/vnd.taverna.scufl2.workflow-bundle</code>,
+ but does contain a <code>META-INF/container.xml</code>-listed root file named <code>workflowBundle.rdf</code>,
+ that file <strong>can</strong> be read as an RDF/XML representation of a workflow bundle document,
+ even if it is not declared as having the <code>application/rdf+xml</code> mime type.
+This enables any future extensions superseeding this <code>application/vnd.taverna.scufl2.workflow-bundle</code> format.</p>
+<p>All rootfiles must be equivalent and describe the same workflow structure,
+ although additional formats can include more or less information than the required format.
+There should be only one rootfile per media-type, and there must be a rootfile for the media type <code>application/rdf+xml</code>.</p>
+<p>Example:</p>
+<div class="codehilite"><pre><span class="cp"><?xml version="1.0"?></span>
+<span class="nt"><container</span> <span class="na">version=</span><span class="s">"1.0"</span>
+ <span class="na">xmlns=</span><span class="s">"urn:oasis:names:tc:opendocument:xmlns:container"</span><span class="nt">></span>
+ <span class="nt"><rootfiles></span>
+ <span class="nt"><rootfile</span> <span class="na">full-path=</span><span class="s">"workflowBundle.ttl"</span>
+ <span class="na">media-type=</span><span class="s">"text/turtle"</span> <span class="nt">/></span>
+ <span class="nt"><rootfile</span> <span class="na">full-path=</span><span class="s">"workflowBundle.rdf"</span>
+ <span class="na">media-type=</span><span class="s">"application/rdf+xml"</span> <span class="nt">/></span>
+ <span class="nt"></rootfiles></span>
+ <span class="nt"><relationships></span>
+ <span class="nt"><relationship</span> <span class="na">type=</span><span class="s">"metadata"</span> <span class="na">target=</span><span class="s">"/annotation/</span><span class="p">$</span><span class="nv">dir</span><span class="s">/</span><span class="p">$</span><span class="nv">filename</span><span class="s">.</span><span class="p">$</span><span class="nv">ext</span><span class="s">"</span> <span class="nt">/></span>
+ <span class="nt"></relationships></span>
+<span class="nt"></container></span>
+</pre></div>
+
+
+<h2 id="unknown-files-and-file-types">Unknown files and file types</h2>
+<p>Any other files in <code>workflow</code> and <code>profile</code> <strong>should</strong> be ignored by SCUFL2 compliant parsers,
+ regardless of if they have the <code>application/rdf+xml</code> mime type or not.
+When a SCUFL2 compliant tool has <em>modified</em> an existing Workflow Bundle,
+ it <strong>should</strong> remove such unknown files from <code>workflow</code> and <code>profile</code> when saving,
+ unless it has the capabilities to also update these.
+These files would typically be representations in other formats which would be out of date after the editing.
+On the other hand, if the tool has not structurally modified a workflow or profile,
+ the tool <strong>should not</strong> remove unknown files from <code>workflow</code> and <code>profile</code>.</p>
+<p>On removal of files, the tool should also remove them from <code>META-INF/manifest.xml</code> and if necessary from
+ <code>META-INF/container.xml</code>.</p>
+<h2 id="additional-resources">Additional resources</h2>
+<p>The workflow bundle format is an open-ended specification, so the archive can include additional resources not described here.</p>
+<p>For instance the bundle can include:</p>
+<ul>
+<li>Thumbnail of bundle (mini-diagram) (Recommendation: <code>META-INF/Thumbnails/thumbnail.png</code> and <code>Thumbnails/thumbnail.svg</code>)</li>
+<li>Ontologies referenced from RDF/XML files, in particular from configurations
+ (Recommendation: <code>ontology/taverna2.2/beanshell.rdf</code>)</li>
+<li>Diagrams of workflows (Recommendation: <code>diagram/workflow/HelloWorld.svg</code> and <code>.png</code>)</li>
+<li>Alternative representations (RDF, JSON) (Recommendation: Same naming conventions with different extensions)</li>
+<li>Annotations (Recommendation: under <code>annotations/</code> in RDF/XML format) -
+ one file per annotation source, like `myExperiment.rdf)</li>
+<li>Resources/binaries/data needed by workflow (Recommendation: under <code>resources/</code></li>
+<li>Example input and output data (Recommendation: as in data bundle)</li>
+<li>Provenance and data of one or more workflow runs (Recommendation: under <code>run/</code></li>
+</ul>
+<p>A workflow bundle can also play 'double roles' by being other bundles, like a data bundle.
+It is the <code>mimetype</code> and <em>root file</em> that determines what is the "main function" of the bundle,
+ suggesting which tool should primarily open the bundle.
+One can for instance imagine an UCF archive which primarily is an Adobe PDFXML file for a published paper
+ (see: <a href="http://labs.adobe.com/technologies/mars/">Mars project</a>) and should be opened in Adobe Acrobat Reader.
+However, it can also contain <code>workflowBundle.rdf</code>, <code>workflow/importantResearch.rdf</code>,
+ and could therefore also be opened using SCUFL2 tools. </p>
+<h1 id="scufl2-datalink">Scufl2-DataLink</h1>
+<p>The definition of a data link.</p>
+<div class="codehilite"><pre><span class="n">Bundle</span> <span class="n">path</span><span class="p">:</span> <span class="o">/</span><span class="n">workflow</span><span class="o">/\</span>$<span class="n">workflowName</span><span class="p">.</span><span class="n">n3</span>
+</pre></div>
+
+
+<p>Datalink should be described in the same file as their containing workflow.</p>
+<h2 id="identifier_1">Identifier</h2>
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