Author: buildbot
Date: Wed Mar 11 08:37:10 2015
New Revision: 943303
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/404.html
websites/staging/taverna/trunk/content/documentation/api-consumer-tool/index.html
websites/staging/taverna/trunk/content/documentation/command-line-tool/index.html
websites/staging/taverna/trunk/content/documentation/command-line/index.html
websites/staging/taverna/trunk/content/documentation/components/component-profile-editor.html
websites/staging/taverna/trunk/content/documentation/components/component-validator.html
websites/staging/taverna/trunk/content/documentation/components/index.html
websites/staging/taverna/trunk/content/documentation/dataviewer-tool/index.html
websites/staging/taverna/trunk/content/documentation/example-workflows/index.html
websites/staging/taverna/trunk/content/documentation/glossary/index.html
websites/staging/taverna/trunk/content/documentation/index.html
websites/staging/taverna/trunk/content/documentation/interaction/index.html
websites/staging/taverna/trunk/content/documentation/online.html
websites/staging/taverna/trunk/content/documentation/plugins/index.html
websites/staging/taverna/trunk/content/documentation/provenance/index.html
websites/staging/taverna/trunk/content/documentation/quick-start-guide/index.html
websites/staging/taverna/trunk/content/documentation/scufl2/api.html
websites/staging/taverna/trunk/content/documentation/scufl2/bundle.html
websites/staging/taverna/trunk/content/documentation/scufl2/datalink.html
websites/staging/taverna/trunk/content/documentation/scufl2/index.html
websites/staging/taverna/trunk/content/documentation/scufl2/processors.html
websites/staging/taverna/trunk/content/documentation/scufl2/uris.html
websites/staging/taverna/trunk/content/documentation/scufl2/workflow.html
websites/staging/taverna/trunk/content/documentation/server/index.html
websites/staging/taverna/trunk/content/documentation/service-sets/index.html
websites/staging/taverna/trunk/content/documentation/taverna-galaxy/index.html
websites/staging/taverna/trunk/content/documentation/taverna-player/index.html
websites/staging/taverna/trunk/content/documentation/training-and-workshops/index.html
websites/staging/taverna/trunk/content/documentation/tutorials/index.html
websites/staging/taverna/trunk/content/documentation/videos/index.html
websites/staging/taverna/trunk/content/documentation/web-service-developers/index.html
websites/staging/taverna/trunk/content/introduction/chemistry-web-services.html
websites/staging/taverna/trunk/content/introduction/how-can-taverna-help-me.html
websites/staging/taverna/trunk/content/introduction/index.html
websites/staging/taverna/trunk/content/introduction/related-projects.html
websites/staging/taverna/trunk/content/introduction/roadmap.html
websites/staging/taverna/trunk/content/introduction/services-in-taverna.html
websites/staging/taverna/trunk/content/introduction/taverna-features.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/annotation.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/arts.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/astronomy.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/biodiversity.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/bioinformatics.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/biology.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/chemistry.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/data-and-text-mining.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/databases.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/disease-research.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/document-analysis.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/education.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/engineering.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/genome-and-gene-expression/index.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/geoinformatics.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/index.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/information-quality.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/medicine.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/multimedia.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/natural-language-processing.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/other.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/protein-and-proteomics.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/service-provision.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/service-testing.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/social-sciences.html
websites/staging/taverna/trunk/content/introduction/taverna-in-use/systems-biology.html
websites/staging/taverna/trunk/content/introduction/what-is-a-workflow-management-system.html
websites/staging/taverna/trunk/content/introduction/what-is-in-silico-experimentation.html
websites/staging/taverna/trunk/content/introduction/why-use-workflows.html
websites/staging/taverna/trunk/content/introduction/works-with.html
Propchange: websites/staging/taverna/trunk/cgi-bin/
------------------------------------------------------------------------------
--- cms:source-revision (original)
+++ cms:source-revision Wed Mar 11 08:37:10 2015
@@ -1 +1 @@
-1665796
+1665797
Propchange: websites/staging/taverna/trunk/content/
------------------------------------------------------------------------------
--- cms:source-revision (original)
+++ cms:source-revision Wed Mar 11 08:37:10 2015
@@ -1 +1 @@
-1665796
+1665797
Modified: websites/staging/taverna/trunk/content/documentation/404.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/404.html (original)
+++ websites/staging/taverna/trunk/content/documentation/404.html Wed Mar 11
08:37:10 2015
@@ -104,118 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>Directory Under Development</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>Thank you for your interest in Taverna.</p>
-<p>The documentation page is currently under development.</p>
-<p>You are seeing this message as the requested page has not yet been copied
from:
-<a href="http://www.taverna.org.uk/documentation/taverna-2-x/";>the previous
Taverna website</a></p></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation,
Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0";>Apache
License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache
Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified:
websites/staging/taverna/trunk/content/documentation/api-consumer-tool/index.html
==============================================================================
---
websites/staging/taverna/trunk/content/documentation/api-consumer-tool/index.html
(original)
+++
websites/staging/taverna/trunk/content/documentation/api-consumer-tool/index.html
Wed Mar 11 08:37:10 2015
@@ -104,266 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>API Consumer Tool</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>This page contains information:</p>
-<ul>
-<li>for <a href="#api_developers">developers who want to use the API Consumer
Tool</a> to wrap their Java
- API for the subsequent use in Taverna workflows, and</li>
-<li>for <a href="#api_users">users who want to use the wrapped Java API</a>
inside their workflows.</li>
-</ul>
-<p><a name="api_developers"></a></p>
-<h2 id="api-consumer-tool">API Consumer Tool</h2>
-<p>Current version of the tool is 1.1.
-You can get it from the old
- <a
href="http://www.taverna.org.uk/download/associated-tools/api-consumer-tool";>download
pages</a>.
-Please also refer to the
- <a
href="http://www.mygrid.org.uk/dev/wiki/display/taverna/API+Consumer+Tool";>API
Consumer Tool section on the User Manual</a>.</p>
-<p>The API Consumer Tool allows the selection of subsets of Java APIs which
may then be imported
- into Taverna Workbench and used as services in workflows.
-This tool is intended for API developers rather than end-users.
-It produces an XML API definition file which Taverna imports - this is file
that you distribute
- alongside your API to âTaverna enableâ it.</p>
-<h3 id="prerequisites">Prerequisites</h3>
-<p>The API Consumer Tool is a Java Doclet and uses Ant to launch; you must
therefore have Java and
- Ant installed and available on the path.
-The Tool has been tested on Java 1.6; use other versions at your own risk.</p>
-<h3 id="setup">Setup</h3>
-<p>Before running the API Consumer Tool you need to place source files of your
API within the
- âtargetâ directory and any supporting libraries (i.e. dependencies)
required in the
- âlibâ directory.
-This is particularly important - if your API includes methods which consume or
return a type
- that is not available to the API Consumer Tool, the definitions it
generates will be invalid.
-For example, if your API contains a method âvoid foo(MagicClass bar)â and
the MagicClass is in
- some random package in a third party jar file that you have not included
there is no way for
- the Doclet to know the fully qualified classname of MagicClass.
-As Taverna requires full classnames, this will result in an API that cannot be
invoked from
- workflows.
-You can normally trap these issues by watching for the standard JavaDoc
warning messages in the
- console.</p>
-<h3 id="usage">Usage</h3>
-<p>Once your source and any supporting files are present as described above,
- from the API Consumer Tool directory you can either run the
- ârunme.batâ/ârunme.sh script or call Ant directly (just type
âantâ on
- the command line).
-The API Consumer Tool itself will be built from source and applied to the
target source files
- of your API.
-After some slight delay for this process (longer for very complex APIs) you
should see a screen
- such as the following:</p>
-<p><img alt="API Consumer" src="/img/APIConsumer-InitialWindow.png" /></p>
-<p>The tree on the left hand side of the window shows the available classes
(including inner
- classes where present) along with a search box - the right hand side
currently shows nothing.
-Selecting a class from the tree produces a display like the following, this
should be clearly
- similar to the information produced by the standard JavaDoc tool:</p>
-<p><img alt="API Consumer" src="/img/APIConsumer-SummaryDisplay.png" /></p>
-<p>In the case of large APIs the search box can be used to display a subset of
the complete class
- tree - enter a pattern to match and hit return in this text box and the
tree will be
- expanded to show all matching nodes.
-To return to the view with all nodes expanded clear the text in this box and
hit return.</p>
-<h3 id="adding-methods-to-the-api-definition">Adding methods to the API
definition</h3>
-<p>The next step is to select methods to add to the API definition - these
methods
- (static, instance or constructors) will appear as services within Taverna
Workbench's
- <a href="/documentation/glossary#service_panel">Service Panel</a> when the
definition file is imported.</p>
-<h4 id="using-graphical-interface">Using graphical interface</h4>
-<p>Methods can be manually added by choosing the class, opening the
âMethodsâ tab and either
- selecting individual methods or using the âSelect allâ and âClear
allâ boxes:</p>
-<p><img alt="API Consumer - methods" src="/img/APIConsumer-Methods.png" /></p>
-<h4 id="using-javadoc-tags">Using JavaDoc tags</h4>
-<p>For APIs under your direct control there is an alternative based on JavaDoc
tags.
-By adding the tag â@taverna.consumeâ to either classes or individual
methods you can
- automatically have these methods selected in the API consumer when it first
scans the source
- files.
-In the case of the tag at a class or interface level all constructors and
methods will be
- selected.</p>
-<h3 id="api-level-metadata">API level metadata</h3>
-<p>To aid use of your exported API you can select the âAPI Descriptionâ
tab and use it to provide
- a name and description for the entire API subset:</p>
-<p><img alt="API Consumer - description"
src="/img/APIConsumer-Description.png" /></p>
-<h3 id="saving-the-api-definition-file">Saving the API definition file</h3>
-<p>To save the API definition select the &âFileâ -> âSave as
XMLâ.
-This should bring up a standard save dialogue, choose a filename and save.
-This is the file that is then imported into Taverna Workbench's Service Panel
by selecting
- âImport new servicesâ -> âAPI Consumer servicesâ¦â.</p>
-<p><a name="api_users"></a></p>
-<h2 id="using-api-consumer-services-in-workflows">Using API Consumer Services
in Workflows</h2>
-<p>Please also refer to
- <a
href="http://www.mygrid.org.uk/dev/wiki/display/taverna/API+Consumer";>the API
Consumer section of the User Manual</a>.</p>
-<p>In order to use the API Consumer services in Taverna workflows, you need
the XML API Consumer
- definition (of the Java library) XML file generated from the API Consumer
tool,
- the library to be used (compiled and packaged as a <code>jar</code>file)
and any
- dependencies of the library as well (i.e. their <code>jar</code> files).</p>
-<p>To import the API Consumer definition file into Taverna, click on
- <strong>âImport new servicesâ -> âAPI Consumer servicesâ¦â
</strong> in the Service Panel.
-Select the API Consumer XML definition file.
-A new branch should be added to the Service Panel, showing the class names and
methods that
- have been selected for inclusion using the API Consumer Tool.
-<img alt="API Consumer - service panel"
src="/img/APIConsumer-ServicePanel.png" /></p>
-<p>In this lightweight example, our exposed API only has a constructor and a
single method.
-Using the API Consumer you have to build up the calls to the API as part of
your workflow,
- so as <code>sayHello()</code> is a method on the <code>HelloWorld</code>
instance,
- we first have to call the constructor <code>HelloWorld</code>,
- and then call the method on the returned object.
-We will add both API Consumer services to the workflow.
-Each parameter of the method is exposed as an input port, and the return value
is shown as an
- output port.
-In our example, our methods do not take any parameters except the implicit
object reference
- <code>this</code>, which we will have to provide by connecting the
<code>object</code>
- output of the constructor <code>HelloWorld</code> to the
<code>object</code> input of the
- method <code>sayHello</code>.</p>
-<p><img alt="API Consumer - workflow" src="/img/APIConsumer-workflow.png"
/></p>
-<p>As a convenience, methods also return the very same object in the output
port
- <code>object</code>, so that methods that needs to be run in a particular
sequence can be
- chained to pass their object reference, in effect preventing execution of
the second method
- before the first method is returning its result and object reference.</p>
-<blockquote>
-<p>Note that the Java objects can only be passed to other API Consumer
-services (and only if they are <strong>serializable</strong>); if you
-want any useful inputs and outputs to interact with your workflow you
-need to use basic types such as <code>String</code>. In our example,
-<code>sayHello()</code> returns a <code>String</code> that is
-connected to the workflow output called <code>sayHello_Result</code></p>
-</blockquote>
-<p>Static methods do not need the <code>object</code> reference, and hence do
not need the
- constructor call, unless you need to pass an instantiated object as a
normal argument.</p>
-<p>Before you can run the workflow you also need to copy the <code>jar</code>
file of the
- <code>HelloWorld</code> library and its dependencies in the
<code>lib</code> directory of
- your <a
href="http://dev.mygrid.org.uk/wiki/display/taverna/Taverna+home+directory";>TAVERNA_HOME
directory</a>.
-After copying the jar files, you need to specify which dependencies to use for
every API
- Consumer service in a workflow.
-To do so, right-click on the service and select <strong>âConfigure API
Consumerâ¦â</strong>.
-The default classloader sharing is âShared for whole workflowâ, so you
only need to tick of
- the dependency <code>jar</code> files on one of services using the same API
Consumer,
- for example the constructor.</p>
-<blockquote>
-<p>If your API is using JNI, or one of its dependencies uses JNI, which
-is a native library with binding for Java, you need to take some
-special considerations, as explained in the section on <a
-href="http://www.mygrid.org.uk/dev/wiki/display/taverna/Beanshell#Beanshell-JNIbasednativelibraries";
-target="_blank">JNI-based native libraries</a> under Beanshell
-services in the User Manual. In particular, you need to select the
-System classloader sharing for all your services and modify the
-Taverna startup scripts.</p>
-</blockquote>
-<h3 id="a-word-of-advice">A word of advice</h3>
-<p>Depending on the complexity of your API, building workflows in this way can
turn out to be
- very a cumbersome way to do graphical Java programming in a workflow.
-In many cases, writing a <a
href="/documentation/glossary#beanshell">Beanshell</a> script using the same
- dependency mechanism can give you most of the benefits in a smaller amount
of time.
-However, the API Consumer gives you one major advantage - the workflow
designer do not need to
- know much about Java and they will see a browsable structure of your API in
the
- Service Panel, just like the bundled services. The workflow designer does
need to know how
- to use your API though, but if you have explicitly designed it to be easy
to use from
- Taverna that barrier can be lowered significantly.</p>
-<p>An API that is useful for many people could also be wrapped as a
- <a href="/documentation/glossary#wsdl">WSDL Web service</a>, which would
make it usable from any
- Taverna Workbench without requiring installation of your JAR and API
Consumer XML definition
- files.</p></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation,
Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0";>Apache
License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache
Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified:
websites/staging/taverna/trunk/content/documentation/command-line-tool/index.html
==============================================================================
---
websites/staging/taverna/trunk/content/documentation/command-line-tool/index.html
(original)
+++
websites/staging/taverna/trunk/content/documentation/command-line-tool/index.html
Wed Mar 11 08:37:10 2015
@@ -104,127 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>Command Line Tool</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>Taverna 2 Command Line Tool is a script
that runs Taverna 2.x workflows from a terminal.
-It comes in a form of a command line script <em>executeworkflow</em>
(<em>executeworkflow.bat</em> on
- Windows and <em>executeworkflow.sh</em> on Linux/UNIX).</p>
-<h2 id="latest-none-apache-release">Latest None Apache Release</h2>
-<ul>
-<li>Documentation for the <a
href="http://dev.mygrid.org.uk/wiki/display/taverna/Command+Line+Tool";>Taverna
Command Line Tool 2.5</a></li>
-</ul>
-<h2 id="previous-releases">Previous Releases</h2>
-<ul>
-<li>Documentation for the <a
href="http://dev.mygrid.org.uk/wiki/display/taverna24/Command+Line+Tool";>Taverna
Command Line Tool 2.4</a></li>
-<li>Documentation for the <a
href="http://dev.mygrid.org.uk/wiki/display/taverna23/Command+Line+Tool";>Taverna
Command Line Tool 2.3</a></li>
-<li>Documentation for the <a
href="http://dev.mygrid.org.uk/wiki/display/taverna22/Command+Line+Tool";>Taverna
Command Line Tool 2.2</a></li>
-</ul></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation,
Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0";>Apache
License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache
Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified:
websites/staging/taverna/trunk/content/documentation/command-line/index.html
==============================================================================
---
websites/staging/taverna/trunk/content/documentation/command-line/index.html
(original)
+++
websites/staging/taverna/trunk/content/documentation/command-line/index.html
Wed Mar 11 08:37:10 2015
@@ -104,393 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>Command Line Tool</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>Command Line Tool is a script that runs
Taverna workflows from a terminal.
-It comes in a form of a command line script called <em>executeworkflow</em>
- (<em>executeworkflow.bat</em> on Windows and <em>executeworkflow.sh</em> on
Linux/UNIX).</p>
-<p>You can <a href="/download/command-line-tool">download the Command Line
Tool</a> from the Taverna Web site
- or use the <em>executeworkflow.sh</em> or <em>executeworkflow.bat</em> that
comes
- bundled with the Taverna Workbench installation.</p>
-<ul>
-<li><a
href="http://dev.mygrid.org.uk/wiki/display/tav250/Extended+version";>Extended
version</a></li>
-</ul>
-<h2
id="what-is-the-difference-between-the-bundled-and-standalone-executeworkflow"><img
alt="" src="/img/information.png" />What is the difference between the bundled
and standalone executeworkflow?</h2>
-<ul>
-<li>
-<p>The standalone command line tool has a <strong>separate
configuration</strong>
- <a
href="http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+home+directory";>home
directory</a>,
- called <em>taverna-cmdline-2.x.x</em> - while the bundled tool uses the
same configuration from
- <em>taverna</em> as the Taverna Workbench.</p>
-</li>
-<li>
-<p>Any <a
href="http://dev.mygrid.org.uk/wiki/display/tav250/HTTP+proxy+preferences";>proxy
settings</a>
- have to be configured manually - copy
- <em>conf/HttpProxy-B307A902-F292-4D2F-B8E7-00CC983982B6.config</em>
from a configured
- Workbench home directory.</p>
-</li>
-<li>
-<p>The bundled tool will load all the <strong>plugins</strong> installed for
the workbench,
- including third-party plugins.
- However it will also load various GUI-supporting functions which might
consume extra memory.</p>
-</li>
-<li>
-<p>To install service plugins for the command line tool, one will have to
manually edit the
- <em>plugins/plugins.xml</em> of the installation or home directory.
- The <em><plugin>... </plugin></em> block can be copied from the
<em>plugins/plugins.xml</em> from
- the <a
href="http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+home+directory";>home
directory</a>
- of a Workbench installation where the plugin is installed.</p>
-</li>
-<li>
-<p>The standalone installation and download is smaller than the workbench -
but keeping both
- installed will use more disk space.
- (Note: the command line tool could use the {repository}} folder from the
workbench using
- symlinks or modifiying <em>plugins/plugins.xml</em></p>
-</li>
-<li>
-<p>The standalone tool can easily be installed and used on remote servers
without GUI access.</p>
-</li>
-<li>
-<p>Running the embedded tool with the database and provenance enabled allows
the command line
- runs to show up in the workbench
- "<a
href="http://dev.mygrid.org.uk/wiki/display/tav250/Result+Perspective";>Workflow
runs</a>".</p>
-</li>
-<li>
-<p>On the other hand the tool will have to use <em>-clientserver</em> if the
workbench is already
- running, or if shut down either a standalone <em>-startdb</em> database
server process or
- <em>-embedded</em>.</p>
-</li>
-<li>
-<p>The standalone tool would not be in conflict with the database of the
workbench
- (as it's in a different home directory) - but could be in conflict with
parallel runs of
- the command line tool - in which case a separate <em>-startdb</em>
process should be started with
- the other calls using <em>-clientserver</em> - see
- <a href="#CommandLineTool-Runningthescriptwithdatabase">#Running the
script with database</a></p>
-</li>
-</ul>
-<p><a name="CommandLineTool-ExecuteworkflowScript"></a></p>
-<h2 id="executeworkflow-script">Executeworkflow Script</h2>
-<p>To get help and a full set of options for the executeworkflow script type
the following in the
- command prompt:</p>
-<blockquote>
-<p>$ sh executeworkflow.sh -help</p>
-</blockquote>
-<p>It will give the following usage options:</p>
-<pre>usage: executeworkflow [options] [workflow]
- -clientserver connects as a client to a
- derby server instance.
- -cmdir <Credential Manager's directory path> Absolute path to the
- directory on the disk
- where Credential Manager's
- files are located
- -cmpassword Indicates that the master
- password for Credential
- Manager will be provided
- on standard input
- -dbproperties <filename> loads a properties file
to
- configure the database
- -embedded connects to an embedded
- Derby database. This can
- prevent mulitple
- invocations
- -help displays comprehensive
- help information
- -inmemory runs the workflow with
- data stored in-memory
- rather than in a database.
- This can give performance
- inprovements, at the cost
- of overall memory usage
- -inputdelimiter <inputname delimiter> causes an inputvalue or
- inputfile to be split into
- a list according to the
- delimiter. The associated
- workflow input must be
- expected to receive a list
- -inputdoc <document> load inputs from a
Baclava
- document
- -inputfile <inputname filename> load the named input from
- file or URL
- -inputvalue <inputname value> directly use the value
for
- the named input
- -janus <file> saves Janus RDF/XML trace
- of execution to FILE or
- 'provenance-janus.rdf'
- -logfile <filename> the logfile to which more
- verbose logging will be
- written to
- -opm <file> saves Open Provenance
- Model (OPM) RDF/XML trace
- of execution to FILE or
- 'provenance-opm.rdf'
- -outputdir <directory> save outputs as files in
- directory, default is to
- make a new directory
- workflowName_output
- -outputdoc <document> save outputs to a new
- Baclava document
- -port <portnumber> the port that the
database
- is running on. If set
- requested to start its own
- internal server, this is
- the start port that will
- be used.
- -provenance generates provenance
- information and stores it
- in the database.
- -startdb automatically starts an
- internal Derby database
- server.
-
-(..)
-
-</pre>
-
-<p>If this directory already exists then an new directory is created, and
appended with
- <em>_<n></em>, where <em>n</em> is incremented to the next available
index.</p>
-<p>Results are written out to files named after the output port for that
result.
-If a result is composed of lists, then a directory is created for the output
port and
- individual list items are named after the list element index (with 1 being
the first index).
-The the output is the result of an error, the filename is appended with
â.errorâ.</p>
-<p>You can provide your own output directory with the <em>-outputdir</em>
option.
-There will be an error if the directory already exists.</p>
-<p>You can
- <a
href="http://dev.mygrid.org.uk//wiki/display/tav250/Provenance+export+to+OPM+and+Janus";>export
the provenance</a>
- using the <em>-opm</em> or <em>-janus</em> options.</p>
-<p>You can also record your results to a Baclava document using
<em>-outputdoc</em> option.
-The document will be overwritten if it already exists.
-You can use the <a
href="http://dev.mygrid.org.uk/wiki/display/tav250/DataViewer+Tool";>DataViewer
Tool</a>
- to view Baclava files.</p>
-<p>Inputs can be provided in three ways.
-Both <em>-inputfile</em> and <em>-inputvalue</em> options can be used
together; <em>-inputdoc</em> option must be
- used on its own.
-<em>-inputfile</em> and <em>-inputvalue</em> options both take two additional
arguments, the name of the port
- for the input, and either a file containing the input data, or the input
value itself
- respectively.</p>
-<p>If one of more of you workflow inputs is described as a list, you can
create a list by using
- the <em>-inputdelimiter</em> option, which may be used with either
<em>-inputfile</em> or
- <em>-inputvalue</em>.
-This option takes two parameters â an input name and the delimiter by which
to split the input
- into a list.</p>
-<p>The delimiter may be a simple character, such as a comma or a new-line
character,
- or a regular expression.
-The input string, or file, will then be converted into a list being split by
the delimiter
- specified. </p>
-<p>If a list of greater depth (i.e. a list or lists or deeper) is required
then you will need to
- use the <em>-inputdocoption</em> to pass data from a Baclava file.
-However, if you provide an input of lower depth to that required, then it will
automatically be
- wrapped in one or more lists up to the required depth.
-Providing an input of greater depth than that required will result in an
error. </p>
-<p><a name"CommandLineTool-Runningthescriptwithdatabase"></a></p>
-<h3 id="running-the-script-with-database">Running the script with database</h3>
-<p>If a workflow has a high memory requirement, then it may be better to run
it using a database
- to store data rather than storing it in memory, which is the default
option.
-There are three options for using a database: </p>
-<ul>
-<li><em>-embedded</em> option, runs with an embedded database.
- This is slightly faster than -clientserver option (below), but has the
limitation that only
- one <em>executeworkflow</em> script may be executed simultaneously.</li>
-<li><em>-clientserver</em> option allows the workflow to be executed backed by
the database running as
- a server.
- By default a database is not started for you, but may be started using
<em>-startdb</em> option.</li>
-<li><em>-startdb</em> option starts a database. It may be used without
providing a workflow to allow
- a database to be started separately, allowing multiple simultaneous
<em>executeworkflow</em>
- script runs.</li>
-</ul>
-<p>More advanced database configurations can be specified using
<em>-dbproperties</em> option,
- allowing you to take full control over the database used.
-This takes a second argument, the filename of the propeties file, for which
the following
- example contains the default settings used: </p>
-<pre>
-in_memory = true
-provenance = false
-connector = derby
-port = 1527
-dialect = org.hibernate.dialect.DerbyDialect
-start_derby = false
-driver = org.apache.derby.jdbc.EmbeddedDriver
-jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
-</pre>
-
-<p>If you want to run the Derby database with client/server setting instead of
with the embedded
- driver, change the properties in the <em>-dbproperties</em> file (described
above) as follows:</p>
-<pre>
-driver=org.apache.derby.jdbc.ClientDriver
-start_derby=true
-</pre>
-
-<p>If you wish to run your own separate Derby server instance, then do not
define the
- <em>start_derby</em> option and define the port on which you are running
you Derby server as
- <em>port=<port></em>. </p>
-<p>If you want to use MySQL database rather than Derby, first you need to drop
the
- mysql-connector-java-5.1.5.jar file from the
- <a href="http://dev.mysql.com/downloads/connector/j/";>mySQL</a> website
into the lib folder of the
- Taverna installation directory (Taverna installation directory if where you
are running the
- script from). </p>
-<p>You need to edit the <em>-dbproperties</em> file as follows: </p>
-<pre>
-connector=mysql
-jdbcuri=jdbc:mysql://localhost/T2Provenance
-dialect=org.hibernate.dialect.MySQLDialect
-driver=com.mysql.jdbc.Driver
-username=<username>
-password=<password>
-port=<port>
-</pre>
-
-<p>It is essential that the database name in the <em>jdbcuri</em> property is
T2Provenance,
- as this database is hard-coded into the MySQL provenance SQL queries. </p>
-<p>If you do not specify the port, the script will try to connect to the
default port for MySQL
- server, which is 3306. </p>
-<blockquote>
-<p><img alt="" src="/img/warning.png" /> When using <em>-dbproperties</em>
together with other
-options, the other options take precedence.</p>
-</blockquote>
-<p><a name=CommandLineTool-Examples"></a></p>
-<h2 id="examples">Examples</h2>
-<p>Some examples on how the script can be invoked are shown below. </p>
-<blockquote>
-<p>$ sh executeworkflow.sh "/Users/alex/Taverna
-Workflows/wf-1.t2flow"</p>
-</blockquote>
-<p>The above line executes the workflow located in <em>/Users/alex/Taverna
Workflows/wf-1.t2flow</em>
- that has no inputs and uses the memory for data storage (the default
option).
-Make sure to enclose the file path in quotes if it contains spaces.
-The <em><workflowName>_outputdirectory</em> will be created in the
current directory and outputs
- will be written to it. </p>
-<blockquote>
-<p>$ sh executeworkflow.sh -embedded -inputvalue in1 aaa -inputvalue in2
-"bb b" -outputdir /tmp/wf-2/ wf-2.t2flow</p>
-</blockquote>
-<p>The above line executes the workflow <em>wf-2.t2flow</em> from the current
directory passing the value
- âaaaâ to the input port <em>in1</em> and value âbb bâ to the input
port <em>in2</em>.
-If input values contain spaces make sure to enclose them in quotes.
-Uses the embedded Derby database to store the data.
-Outputs will be written to the <em>/tmp/wf-2/</em> directory. </p>
-<blockquote>
-<p>$ sh executeworkflow.sh -inputvalue in1 aaa -inputfile in2 input2.txt
--inputdelimiter in2 "\n" wf-3.t2flow</p>
-</blockquote>
-<p>The above line executes the workflow <em>wf-3.t2flow</em> from the current
directory passing the value
- âaaaâ to the input port <em>in1</em> and splitting the content of file
<em>input2.txt</em> using â\nâ
- (new line character) as the delimiter and passing the resulting list to the
input port <em>in2</em>.
-Make sure to out the delimiter in quotes, even if it is just a single
character, like â;â.
-The <em><workflowName>_outputdirectory</em> will be created in the
current directory and outputs
- will be written to it. </p>
-<blockquote>
-<p>$ sh executeworkflow.sh -inputdoc /tmp/input-doc.xml -outputdoc
-/tmp/output-doc.xml "/Users/alex/Taverna
-Workflows/wf-4.t2flow"</p>
-</blockquote>
-<p>The above line executes the workflow <em>/Users/alex/Taverna
Workflows/wf-4.t2flow</em>, loading
- inputs from the Baclava document in <em>/tmp/input-doc.xml</em>, and
writing the outputs to a
- Baclava document <em>/tmp/output-doc.xml</em>. </p></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation,
Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0";>Apache
License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache
Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified:
websites/staging/taverna/trunk/content/documentation/components/component-profile-editor.html
==============================================================================
---
websites/staging/taverna/trunk/content/documentation/components/component-profile-editor.html
(original)
+++
websites/staging/taverna/trunk/content/documentation/components/component-profile-editor.html
Wed Mar 11 08:37:10 2015
@@ -104,121 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>Component profile editor</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 Taverna Component Profile Editor is a
simple tool for editing and creating profiles for
- [Taverna Components[(/documentation/components).
-Component profiles define the required and supported interface of components;
- they are not intended to be easily edited by normal users.
-The editor guides an expert user as they define a profile,
- showing features that they may use and providing assistance for defining
semantic annotation requirements.</p>
-<div align="center"><img src="/img/component-profile-editor.png"
alt="Component Profile Editor" width="600" /></div></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation,
Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0";>Apache
License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache
Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified:
websites/staging/taverna/trunk/content/documentation/components/component-validator.html
==============================================================================
---
websites/staging/taverna/trunk/content/documentation/components/component-validator.html
(original)
+++
websites/staging/taverna/trunk/content/documentation/components/component-validator.html
Wed Mar 11 08:37:10 2015
@@ -104,123 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>Component validator</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 Taverna Component Validator is a tool
and library for checking whether a
- <a href="/documentation/components">Taverna Component</a> satisfies the
component profile defined by the family of which it is a member.
-It applies a number of checks to the component such that when they are all
satisfied,
- the component can be considered to be a high-quality member of the
component family,
- and provides human-readable descriptions of the conditions that are checked
and whether they were satisfied or not.</p>
-<p><img alt="Summary of validity of a component, from myExperiment"
src="/img/ComponentValiditySummary.png" /></p>
-<p>We currently have the validator deployed on
- <a href="http://www.myexperiment.org";>myExperiment.org</a> as an integrated
feature of the metadata displayed about components.</p>
-<p><img alt="Detail of validity of a component, from myExperiment"
src="/img/ComponentValidityDetails.png" /></p></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation,
Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0";>Apache
License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache
Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
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
Wed Mar 11 08:37:10 2015
@@ -104,221 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>Components</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>Taverna Workflow Components are a system
for creating shareable, reusable,
- encapsulated sub-workflows that perform clearly defined tasks while
abstracting away from
- the details of how those tasks are performed.
-They are an integrated feature of Taverna Since Workbench 2.5.0 and Server
2.5.4.</p>
-<p>As part of the BioVeL and SCAPE projects,
- we have developed a system of service components for Taverna.
-This consists of tools for the creation, management and use of workflow
components,
- and a repository for the storage and sharing of those components.
-Workflow components within a given component family will work together
cleanly,
- for example by adhering to a tidy type system and being well described.</p>
-<p>A set of minimal functional requirements for service component management
has been developed
- based upon previous component-related work carried out as part of the
e-Lico project and
- also an examination of the needs of BioVeL and SCAPE.</p>
-<p>These requirements include:</p>
-<ul>
-<li>The ability to create components</li>
-<li>The specification of the characteristics that are necessary for a set of
components to
- âplayâ together â called a âcomponent profileâ</li>
-<li>Creating a component so it complies with a given profile</li>
-<li>Checking that a component complies with a given profile</li>
-<li>Publishing a component</li>
-<li>Discovering a component</li>
-<li>Including a component in a workflow</li>
-<li>Executing the component within a workflow run</li>
-</ul>
-<p><img class="aligncenter" title="The Model of Components"
src="/img/registry.png" alt=""
- width="433" height="251" /></p>
-<h2 id="example">Example</h2>
-<p>This is an example workflow that includes components, with internal ports
hidden for simplicity:</p>
-<p><img class="alignnone" title="Componentized Workflow"
src="/img/component_b_1.png" alt=""
- 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</h2>
-<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.
- Note that although it may be realized internally as a workflow,
- a user sees it as a âblack boxâ and cannot (normally) edit the
componentâs workflow.</p>
-<p><img class="aligncenter" src="/img/arch3.png" alt="" width="500"
height="401" /></p>
-<p>It is intended that there will be consistency checks to ensure that
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</h2>
-<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.
-Note that the user sees the component invocation as a âblack boxâ and
cannot see details of
- what happens inside.</p>
-<p>Note that if you publish a workflow containing a component, you
<em>need</em> to make sure that the
- component is publicly readable in a globally-accessible component registry;
- myExperiment is such a suitable registry.</p>
-<h2 id="component-creation">Component creation</h2>
-<p>It was decided that the majority of the information necessary for a
component will be specified
- as a Taverna workflow.
-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</h2>
-<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>
- is available.
-Components that share a profile will be collected together into component
families.
-A <a href="/documentation/components/component-profile-editor">component
profile editor</a>
- is being developed.</p>
-<p style="text-align: center;">
-<img class="aligncenter" src="img/arch2.png" alt="" width="359" height="412" />
-</p>
-
-<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</h2>
-<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
- a service with the task it performs.</p>
-<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</h2>
-<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
- <a href="/documentation/components/component-validator">component
validator</a>
- 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</h2>
-<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.
-Thus a component is currently published and shared on myExperiment as (a pack
containing)
- a workflow.
-The components themselves are items within a pack corresponding to the
component family.</p>
-<p>To facilitate the development of components, a workflow can also be saved
to the userâs local
- 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</h2>
-<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
- access to families of components.
-Users can then see the discovered families of components via the Taverna
Workbench service
- panel, and the components within those families.
-A component can then be added to a workflow.</p></div>
-
- </div>
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