Author: buildbot
Date: Mon Mar 9 12:53:44 2015
New Revision: 943005
Log:
Staging update by buildbot for taverna
Added:
websites/staging/taverna/trunk/content/documentation/scufl2/DataLink.html
Modified:
websites/staging/taverna/trunk/cgi-bin/ (props changed)
websites/staging/taverna/trunk/content/ (props changed)
Propchange: websites/staging/taverna/trunk/cgi-bin/
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@@ -1 +1 @@
-1665201
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Propchange: websites/staging/taverna/trunk/content/
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--- cms:source-revision (original)
+++ cms:source-revision Mon Mar 9 12:53:44 2015
@@ -1 +1 @@
-1665201
+1665217
Added: websites/staging/taverna/trunk/content/documentation/scufl2/DataLink.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/scufl2/DataLink.html
(added)
+++ websites/staging/taverna/trunk/content/documentation/scufl2/DataLink.html
Mon Mar 9 12:53:44 2015
@@ -0,0 +1,329 @@
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+ <meta http-equiv="X-UA-Compatible" content="IE=edge">
+ <meta name="viewport" content="width=device-width, initial-scale=1">
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+
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+
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+
+ <!-- JSON-LD markup for Google Structured Data -->
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+ <!-- generic JSON-LD for this page -->
+ <script type="application/ld+json">
+ {
+ "@context" : "http://schema.org";,
+ "@type" : ["CreativeWork"],
+ "@id": "",
+ "name" : "Scufl2-DataLink",
+ "publisher" : {
+ "@type" : "Organization",
+ "url" : "http://www.apache.org/";,
+ "name" : "The Apache Software Foundation (ASF)"
+ },
+ "license": {
+ "@type": "CreativeWork",
+ "@id":
"http://www.apache.org/licenses/LICENSE-2.0";,
+ "url":
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+
+ <div id="page" class="container">
+ <h1>Scufl2-DataLink</h1>
+ <div class="alert alert-info" role="alert"><p><span class="glyphicon
glyphicon-info-sign" aria-hidden="true"></span>
+
+Taverna is transitioning to the Apache Incubator.
+This webpage reflects material not yet released under Apache Incubator.
+Instead it shows <a class="alert-link"
href="http://www.taverna.org.uk/";>taverna2</a> material that is expected to
become part of the Apache Incubator project in the future.
+</div>
+
+
+ <div id="content"><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>$<span
class="n">workflowName</span><span class="p">.</span><span class="n">n3</span>
+</pre></div>
+
+
+<p>Datalink should be described in the same file as their containing
workflow.</p>
+<h2 id="identifier">Identifier</h2>
+<p>Each datalink is uniquely identified by their source and destination ports,
in addition to the optional merge position.</p>
+<p>Datalinks are globally identified as <a
href="http://ns.taverna.org.uk/2010/researchObject/$researchObjectUUID/workflow/$workflow/datalink?from=$fromPort&to=$toPort&mergePosition=$mergePosition";>http://ns.taverna.org.uk/2010/researchObject/$researchObjectUUID/workflow/$workflow/datalink?from=$fromPort&to=$toPort&mergePosition=$mergePosition</a>
- for instance <a
href="http://ns.taverna.org.uk/2010/researchObject/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/datalink?from=processor/A/out/result&to=processor/B/in/db";>http://ns.taverna.org.uk/2010/researchObject/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/datalink?from=processor/A/out/result&to=processor/B/in/db</a>
defines the link in workflow "HelloWorld" from the output port "result" in the
processor "A" going to the input port "db" for the processor "B". As there is
no mergePosition there can't be any other links going to the "db" port.</p>
+<p>As these URIs can be tricky to construct or maintain, feel free to use
anonymous nodes, or construct alterative URIs as <datalink/$number>, the number
here would not have any semantic meaning except it must be unique per datalink
in that workflow.</p>
+<h2 id="example">Example</h2>
+<p>workflow/Helloworld.n3: (out of Date)</p>
+<div class="codehilite"><pre><span class="p">@</span><span
class="n">base</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">prefix</span> <span
class="n">scufl2</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="n">ontology</span><span class="o">/></span> <span class="p">.</span>
+<span class="p">@</span><span class="n">prefix</span> <span
class="n">dc</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">purl</span><span class="p">.</span><span class="n">org</span><span
class="o">/</span><span class="n">dc</span><span class="o">/</span><span
class="n">elements</span><span class="o">/</span>1<span
class="p">.</span>1<span class="o">/></span> <span class="p">.</span>
+
+<span class="o"><></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="n">Helloworld</span>" <span
class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">workflowIdentifier</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">workflow</span><span class="o">/</span>00626652<span
class="o">-</span>55<span class="n">ae</span><span class="o">-</span>4<span
class="n">a9e</span><span class="o">-</span>80<span class="n">d4</span><span
class="o">-</span><span class="n">c8e9ac84e2ca</span><span
class="o">/></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">in</span><span class="o">/</span><span class="n">yourName</span><span
class="o">></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">out</span><span class="o">/</span><span class="n">results</span><span
class="o">></span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">datalink</span> <span class="n">_</span><span class="p">:</span><span
class="n">datalink1</span><span class="p">,</span> <span
class="o"><</span><span class="n">datalink</span><span
class="o">/</span>5<span class="o">></span><span class="p">,</span> <span
class="o"><</span><span class="n">datalink</span>?<span
class="n">from</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">out</span><span
class="o">/</span><span class="n">greeting</span><span
class="o">&</span><span class="n">to</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">mergePosition</span><span
class="p">=</span>0<span class="o">></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">processor</span><span class="o">/</span><span
class="n">Hello</span><span class="o">></span> <span class="p">.</span>
+
+<span class="o"><</span><span class="n">in</span><span
class="o">/</span><span class="n">yourName</span><span class="o">></span>
<span class="n">a</span> <span class="n">scufl2</span><span
class="p">:</span><span class="n">InputWorkflowPort</span> <span
class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">name</span> "<span class="n">yourName</span>" <span
class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">portDepth</span> 0 <span class="p">.</span>
+
+<span class="o"><</span><span class="n">out</span><span
class="o">/</span><span class="n">results</span><span class="o">></span>
<span class="n">a</span> <span class="n">scufl2</span><span
class="p">:</span><span class="n">OutputWorkflowPort</span> <span
class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">name</span> "<span class="n">results</span>" <span
class="p">.</span>
+
+<span class="n">_</span><span class="p">:</span><span
class="n">datalink1</span> <span class="n">a</span> <span
class="n">scufl2</span><span class="p">:</span><span class="n">DataLink</span>
<span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">receivesFrom</span> <span class="o"><</span><span
class="n">in</span><span class="o">/</span><span class="n">yourName</span><span
class="o">></span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">sendsTo</span> <span class="o"><</span><span
class="n">processor</span><span class="o">/</span><span
class="n">Hello</span><span class="o">/</span><span class="n">in</span><span
class="o">/</span><span class="n">name</span><span class="o">></span> <span
class="p">.</span>
+
+<span class="o"><</span><span class="n">datalink</span><span
class="o">/</span>5<span class="o">></span> <span class="n">a</span> <span
class="n">scufl2</span><span class="p">:</span><span class="n">DataLink</span>
<span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">receivesFrom</span> <span class="o"><</span><span
class="n">in</span><span class="o">/</span><span class="n">yourName</span><span
class="o">></span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">sendsTo</span> <span class="o"><</span><span
class="n">out</span><span class="o">/</span><span class="n">results</span><span
class="o">></span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">mergePosition</span> 1 <span class="p">.</span>
+
+<span class="o"><</span><span class="n">datalink</span>?<span
class="n">from</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">out</span><span
class="o">/</span><span class="n">greeting</span><span
class="o">&</span><span class="n">to</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">mergePosition</span><span
class="p">=</span>0<span class="o">></span> <span class="n">a</span> <span
class="n">scufl2</span><span class="p">:</span><span class="n">DataLink</span>
<span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">receivesFrom</span> <span class="o"><</span><span
class="n">processor</span><span class="o">/</span><span
class="n">Hello</span><span class="o">/</span><span class="n">out</span><span
class="o">/</span><span class="n">greeting</span><span class="o">></span>
<span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">sendsTo</span> <span class="o"><</span><span
class="n">out</span><span class="o">/</span><span class="n">results</span><span
class="o">></span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">mergePosition</span> 0 <span class="p">.</span>
+</pre></div>
+
+
+<p>This example defines three datalinks.</p>
+<p>The first link <code>_:datalink1</code> is just an anonymous node without
an identifier. It defines a data link from the input port "yourName" to the
processor input port "name". This link could also have been written embedded
with the workflow:</p>
+<div class="codehilite"><pre><span class="o"><></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="p">...</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">datalink</span> <span class="p">[</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">receivesFrom</span> <span class="o"><</span><span
class="n">in</span><span class="o">/</span><span class="n">yourName</span><span
class="o">></span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span
class="n">sendsTo</span> <span class="o"><</span><span
class="n">processor</span><span class="o">/</span><span
class="n">Hello</span><span class="o">/</span><span class="n">in</span><span
class="o">/</span><span class="n">name</span><span class="o">></span>
+ <span class="p">]</span> <span class="p">.</span>
+</pre></div>
+
+
+<p>The second datalink <code><datalink/5>></code> defines a link
directly from the workflow input port "yourName" to the output port "results".
+Links must go from a scufl2:SendingPort sending to a scufl2:ReceivingPort,
+ meaning from a workflow input port or processor output port, going to
either a workflow output port or processor input port.
+Several links can receive from the same sending port.
+ Merges</p>
+<blockquote>
+<p>Merges is a way Taverna allows you to connect several links to the
+same scufl2:ReceivingPort, that is to a processor input port or
+workflow output port. When executing, values from each link will be
+inserted into the specified scufl2:mergePosition in a new list.</p>
+<p>You only need to specify scufl2:mergePosition if more than one link is
+connected to the same processor input port or workflow output port. If
+there is more than one link connected to the same receiving port, all
+of them need to specify a unique mergePosition, starting from 0, with
+no gaps. If you specify a single link to the port with a mergePosition
+of 0, that port input would still be wrapped in a list.</p>
+</blockquote>
+<p>The third datalink, specified using the 'full' URI
<code><datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0></code>,
+ defines the link from the output port "out" in processor "Hello", linking to
the workflow output port "results".
+As now two links go to that receiving port, they both need to specify a unique
mergePosition.
+The second link specifies position 1, and the third position 0.
+That means that the output port will receive a list Scufl2-DataLink.
+The second element 'yourName' would arrive first (as it is sent before "Hello"
produces "greeting"),
+ but it would be arriving in position 1 rather than 0.</p>
+<blockquote>
+<p>URI templates not enough</p>
+<p>The full URIs such as
+<a
href="http://ns.taverna.org.uk/2010/researchObject/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/datalink?from=processor/A/out/result&to=processor/B/in/db";>http://ns.taverna.org.uk/2010/researchObject/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/datalink?from=processor/A/out/result&to=processor/B/in/db</a>
+are meant to be helpful, not defining. The workflow definitions should
+be complete without having to be parse these URIs. Such URIs are
+however useful to be able to annotate or talk about workflow elements
+outside of the workflow definition.</p>
+<p>Although a resource is specified using a full URI which uniquely
+identifies it, such as in the datalink above, the resource must still
+be defined, such as the datalink must define the properties
+scufl2:receivesFrom, scufl2:sendsTo (and optionally)
+scufl2:mergePosition. Similarly the input port <in/yourName> must
+still be defined with a scufl2:name "yourName".</p>
+</blockquote>
+<p>The nested resources for this workflow, such as InputProcessorPort ,
+OutputProcessorPort, DispatchStack, IterationStrategyStack and their
+children should be described in the same file as owning workflow
+itself. Additional metadata should be added to an /annotations/ file.</p>
+<h2 id="properties">Properties</h2>
+<ul>
+<li><em>scufl2:receivesFrom</em> (required) The <em>scufl2:SendingPort</em>
this link is receiving data from.
+ The port must be in the same workflow as the link.</li>
+<li><em>scufl2:sendsTo</em> (required) The <em>scufl2:ReceivingPort</em> this
link is sending data to.
+ The port must be in the same workflow as the link.</li>
+<li><em>scufl2:mergePosition</em> (optional) An integer, starting from 0.
+ Must be set where more than one datalinks <em>sendsTo</em> the same
ReceivingPort.
+ The positions for a port must be sequentially assigned from 0 without
gaps.</li>
+</ul></div>
+
+ </div>
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