Author: buildbot
Date: Thu Jul 14 00:24:57 2016
New Revision: 992764
Log:
Staging update by buildbot for taverna
Modified:
websites/staging/taverna/trunk/cgi-bin/ (props changed)
websites/staging/taverna/trunk/content/ (props changed)
websites/staging/taverna/trunk/content/documentation/components/index.html
Propchange: websites/staging/taverna/trunk/cgi-bin/
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--- cms:source-revision (original)
+++ cms:source-revision Thu Jul 14 00:24:57 2016
@@ -1 +1 @@
-1752572
+1752573
Propchange: websites/staging/taverna/trunk/content/
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--- cms:source-revision (original)
+++ cms:source-revision Thu Jul 14 00:24:57 2016
@@ -1 +1 @@
-1752572
+1752573
Modified:
websites/staging/taverna/trunk/content/documentation/components/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/components/index.html
(original)
+++ websites/staging/taverna/trunk/content/documentation/components/index.html
Thu Jul 14 00:24:57 2016
@@ -200,20 +200,20 @@ h2:hover > .headerlink, h3:hover > .head
<li><a href="#requirements">Requirements</a></li>
<li><a href="#workflows">Workflows</a><ul>
<li><a href="#example-workflow-with-components">Example workflow with
components</a></li>
-</ul>
-</li>
<li><a href="#including-a-component-in-a-workflow">Including a component in a
workflow</a></li>
<li><a href="#executing-a-component-in-a-workflow-run">Executing a component
in a workflow run</a></li>
-<li><a href="#components">Components</a><ul>
-<li><a href="#component-creation">Component creation</a></li>
</ul>
</li>
+<li><a href="#components">Components</a><ul>
+<li><a href="#component-creation">Component creation</a></li>
<li><a href="#component-profile">Component profile</a></li>
<li><a href="#component-creation-against-a-profile">Component creation against
a profile</a></li>
<li><a href="#checking-a-component-against-a-profile">Checking a component
against a profile</a></li>
<li><a href="#publishing-a-component">Publishing a component</a></li>
<li><a href="#discovering-a-component">Discovering a component</a></li>
</ul>
+</li>
+</ul>
</div>
<h2 id="overview">Overview<a class="headerlink" href="#overview"
title="Permanent link">¶</a></h2>
<p>Taverna Workflow Components are a system for creating shareable, reusable,
@@ -248,7 +248,7 @@ Workflow components within a given compo
width="679" height="294" /></p>
<p>Without components, using the same view, it would instead look like
this:</p>
<p><a
href="http://www.taverna.org.uk/pages/wp-content/uploads/2013/05/component_c.png";><img
class="aligncenter" title="Un-componentized Workflow"
src="/img/component_c.png" alt="" width="245" height="526" /></a></p>
-<h2 id="including-a-component-in-a-workflow">Including a component in a
workflow<a class="headerlink" href="#including-a-component-in-a-workflow"
title="Permanent link">¶</a></h2>
+<h3 id="including-a-component-in-a-workflow">Including a component in a
workflow<a class="headerlink" href="#including-a-component-in-a-workflow"
title="Permanent link">¶</a></h3>
<p>A component can be added into a Taverna workflow in the same way as an
ordinary service:
by dragging it from the service panel of the workbench into the workflow
design view.
<em>Although it may be realized internally as a workflow,
@@ -257,7 +257,7 @@ Workflow components within a given compo
<p>It is intended that there will be consistency checks to ensure components
are only plugged
together in a sensible manner, and for the discovery of (and connection to)
suitable components
based upon existing workflow structure.</p>
-<h2 id="executing-a-component-in-a-workflow-run">Executing a component in a
workflow run<a class="headerlink"
href="#executing-a-component-in-a-workflow-run" title="Permanent
link">¶</a></h2>
+<h3 id="executing-a-component-in-a-workflow-run">Executing a component in a
workflow run<a class="headerlink"
href="#executing-a-component-in-a-workflow-run" title="Permanent
link">¶</a></h3>
<p>When a component is invoked during a workflow run, the underlying workflow
is called with the
corresponding data.
The results of the workflow are used as the output data for the component
invocation.
@@ -275,7 +275,7 @@ The results of the workflow are used as
This allows complex internal component functionality and removes the need for
extensive new
software to design components.</p>
<p><img class="aligncenter" src="/img/arch1.png" alt="" width="340"
height="433" /></p>
-<h2 id="component-profile">Component profile<a class="headerlink"
href="#component-profile" title="Permanent link">¶</a></h2>
+<h3 id="component-profile">Component profile<a class="headerlink"
href="#component-profile" title="Permanent link">¶</a></h3>
<p>A specification of the format for the component profile has been agreed.
The format is in XML and an XML schema (xsd) has been created.
An example <a
href="http://www.myexperiment.org/files/905/versions/1/download/Characterisation%20Component.xml";>component
profile</a>
@@ -290,7 +290,7 @@ A <a href="/documentation/components/com
<p>The SCAPE project has an
<a href="https://github.com/openpreserve/scape-component-profiles";>extended
discussion of component profiles</a>
available.</p>
-<h2 id="component-creation-against-a-profile">Component creation against a
profile<a class="headerlink" href="#component-creation-against-a-profile"
title="Permanent link">¶</a></h2>
+<h3 id="component-creation-against-a-profile">Component creation against a
profile<a class="headerlink" href="#component-creation-against-a-profile"
title="Permanent link">¶</a></h3>
<p>In order to conform to a component profile, it can be necessary to make
semantic annotations
parts of the corresponding workflow.
For example, the annotation of the type of format in which data is output by a
port or
@@ -298,7 +298,7 @@ For example, the annotation of the type
<p>The component profile specifies the ontologies that will be used for the
components within the
family, the correspondence between object classes within a workflow
(input port, service etc.) and the concepts within the ontologies.</p>
-<h2 id="checking-a-component-against-a-profile">Checking a component against a
profile<a class="headerlink" href="#checking-a-component-against-a-profile"
title="Permanent link">¶</a></h2>
+<h3 id="checking-a-component-against-a-profile">Checking a component against a
profile<a class="headerlink" href="#checking-a-component-against-a-profile"
title="Permanent link">¶</a></h3>
<p>Although the components will be modified using a chosen profile,
it is unlikely that the components can be assured as being âcorrect by
constructionâ.
For this reason, a separate
@@ -306,7 +306,7 @@ For this reason, a separate
is being implemented.
The component validator is included within
<a href="http://www.myexperiment.org";>myExperiment</a>.</p>
-<h2 id="publishing-a-component">Publishing a component<a class="headerlink"
href="#publishing-a-component" title="Permanent link">¶</a></h2>
+<h3 id="publishing-a-component">Publishing a component<a class="headerlink"
href="#publishing-a-component" title="Permanent link">¶</a></h3>
<p>Since components are realized as âextensionsâ to Taverna workflows,
it was decided that rather than using a separate component repository,
the extensive capabilities of myExperiment would be used.
@@ -317,7 +317,7 @@ The components themselves are items with
machine.</p>
<p>When a user publishes a component either to myExperiment or to their local
file system,
their service panel is updated to reflect the new component.</p>
-<h2 id="discovering-a-component">Discovering a component<a class="headerlink"
href="#discovering-a-component" title="Permanent link">¶</a></h2>
+<h3 id="discovering-a-component">Discovering a component<a class="headerlink"
href="#discovering-a-component" title="Permanent link">¶</a></h3>
<p>Since component families are realized as packs on myExperiment
(or by analogous structures in the userâs file system),
we use the existing Taverna code to talk to the myExperiment REST interface
to give users
![http://www.taverna.org.uk/pages/wp-content/uploads/2013/05/component_c.png"](http://www.taverna.org.uk/pages/wp-content/uploads/2013/05/component_c.png"){kind=link}