workflow-to-galaxy 0.2.7 → 0.2.8

data/CHANGES

@@ -1,6 +1,10 @@
 = Changes log for the Taverna-Galaxy Gem
 
-== Version 0.2.7
+== Version 0.2.8
+* Clean up of documentation
+* Added rubyzip dependency to gemspec
+
 
-* A Galaxy tool can now also be created by provided a t2flow file with the --t2flow flag.
+== Version 0.2.7
+* A Galaxy tool can now also be created by providing a t2flow file with the --t2flow flag.
 

data/README

@@ -2,7 +2,7 @@
 
 
 Authors::     Konstantinos Karasavvas
-Gem Version:: 0.2.7
+Gem Version:: 0.2.8
 Contact::     mailto:kostas.karasavvas@nbic.nl
 Licence::     MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
 Copyright::   (c) 2010 Netherlands Bioinformatics Centre, The Netherlands
@@ -18,12 +18,12 @@ is used to access workflow information via its REST API but a workflow descripti
 from a file is also supported.
 
 The name is workflow-to-galaxy rather than t2-workflow-to-galaxy because it is
-possible that it will support other workflow management system's in the future.
+possible that it will support other workflow management systems in the future.
 
 
 == Installation
 
-[sudo] gem install workflow-to-galaxy
+  [sudo] gem install workflow-to-galaxy
 
 
 == Usage
@@ -36,11 +36,11 @@ the full URL of the workflow in the myExperiment website. Alternatively
 a t2flow file can be passed for workflows not in myExperiment. Available
 options are:
 
--o OUTPUT, --output=OUTPUT  The file name(s) of the generated tool. If it is not specified then the workflow's name will be used.
+  -o OUTPUT, --output=OUTPUT  The file name(s) of the generated tool. If it is not specified then the workflow's name will be used.
 
--s SERVER, --server=SERVER  The taverna server that the script will request execution from. If it is not specified then "http://localhost:8980/taverna-server" will be used.
+  -s SERVER, --server=SERVER  The taverna server that the script will request execution from. If it is not specified then "http://localhost:8980/taverna-server" will be used.
 
--t,        --t2flow         The workflow is a t2flow file.
+  -t,        --t2flow         The workflow is a t2flow file.
 
 
 == Example
@@ -48,13 +48,14 @@ options are:
 Let's say we want to install the taverna2 workflow http://www.myexperiment.org/workflows/74.html
 from myExperiment repository:
 
-<tt>$ workflow_to_galaxy  -s http://localhost:8980/taverna-server  http://www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_781733.t2flow?version=5</tt>
+  $ workflow_to_galaxy  -s http://localhost:8980/taverna-server  http://www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_781733.t2flow?version=5
 
 
 
 == References
 
-Galaxy::       http://galaxy.psu.edu
-Taverna2::     http://www.taverna.org.uk
-myExperiment:: http://www.myexperiment.org
+Taverna-Galaxy:: https://trac.nbic.nl/elabfactory/wiki/eGalaxy
+Galaxy::         http://galaxy.psu.edu
+Taverna2::       http://www.taverna.org.uk
+myExperiment::   http://www.myexperiment.org
 

data/Rakefile

@@ -6,13 +6,13 @@
 require 'rubygems'
 require 'rake'
 require 'rake/clean'
-require 'rake/gempackagetask'
-require 'rake/rdoctask'
 require 'rake/testtask'
+require 'rubygems/package_task'
+require 'rdoc/task'
 
 spec = Gem::Specification.new do |s|
   s.name = 'workflow-to-galaxy'
-  s.version = '0.2.7'
+  s.version = '0.2.8'
   s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
   s.summary = 'This script acquires information for a taverna 2 workflow from myExperiment (or from a file) and generates a Galaxy tool (.xml and .rb files).'
   s.description = s.summary
@@ -25,16 +25,17 @@ spec = Gem::Specification.new do |s|
   s.add_dependency 'myexperiment-rest', '>= 0.2.6'
   s.add_dependency 'taverna-t2flow', '>= 0.2.0'
   s.add_dependency 't2-server', '>= 0.5.3'
+  s.add_dependency 'rubyzip', '>= 0.9.4'
 end
 
-Rake::GemPackageTask.new(spec) do |p|
+Gem::PackageTask.new(spec) do |p|
   p.gem_spec = spec
   p.need_tar = true
   p.need_zip = true
 end
 
-Rake::RDocTask.new do |rdoc|
-  files =['README', 'LICENSE', 'lib/**/*.rb']
+RDoc::Task.new do |rdoc|
+  files =['README', 'LICENSE', 'CHANGES', 'lib/**/*.rb']
   rdoc.rdoc_files.add(files)
   rdoc.main = "README" # page to start on
   rdoc.title = "workflow-to-galaxy Docs"

data/doc/rdoc/CHANGES.html

@@ -0,0 +1,105 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
+
+  <title>File: CHANGES [workflow-to-galaxy Docs]</title>
+
+  <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
+
+  <script src="./js/jquery.js" type="text/javascript"
+    charset="utf-8"></script>
+  <script src="./js/thickbox-compressed.js" type="text/javascript"
+    charset="utf-8"></script>
+  <script src="./js/quicksearch.js" type="text/javascript"
+    charset="utf-8"></script>
+  <script src="./js/darkfish.js" type="text/javascript"
+    charset="utf-8"></script>
+</head>
+
+<body class="file">
+  <div id="metadata">
+    <div id="home-metadata">
+      <div id="home-section" class="section">
+        <h3 class="section-header">
+          <a href="./index.html">Home</a>
+          <a href="./index.html#classes">Classes</a>
+          <a href="./index.html#methods">Methods</a>
+        </h3>
+      </div>
+    </div>
+
+    <div id="project-metadata">
+      
+      
+      <div id="fileindex-section" class="section project-section">
+        <h3 class="section-header">Files</h3>
+        <ul>
+        
+          <li class="file"><a href="./CHANGES.html">CHANGES</a></li>
+        
+          <li class="file"><a href="./LICENSE.html">LICENSE</a></li>
+        
+          <li class="file"><a href="./README.html">README</a></li>
+        
+        </ul>
+      </div>
+      
+
+      <div id="classindex-section" class="section project-section">
+        <h3 class="section-header">Class Index
+          <span class="search-toggle"><img src="./images/find.png"
+            height="16" width="16" alt="[+]"
+            title="show/hide quicksearch" /></span></h3>
+        <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+        <fieldset>
+          <legend>Quicksearch</legend>
+          <input type="text" name="quicksearch" value=""
+            class="quicksearch-field" />
+        </fieldset>
+        </form>
+
+        <ul class="link-list">
+        
+          <li><a href="./Generator.html">Generator</a></li>
+        
+          <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
+        
+        </ul>
+        <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+      </div>
+
+      
+    </div>
+  </div>
+
+  <div id="documentation">
+    
+<h1>Changes log for the Taverna-Galaxy Gem</h1>
+
+<h2>Version 0.2.8</h2>
+<ul><li>
+<p>Clean up of documentation</p>
+</li><li>
+<p>Added rubyzip dependency to gemspec</p>
+</li></ul>
+
+<h2>Version 0.2.7</h2>
+<ul><li>
+<p>A Galaxy tool can now also be created by providing a t2flow file with the
+–t2flow flag.</p>
+</li></ul>
+
+  </div>
+
+  <div id="validator-badges">
+    <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+    <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+      Rdoc Generator</a> 2</small>.</p>
+  </div>
+</body>
+</html>
+

data/doc/rdoc/Generator.html

@@ -0,0 +1,262 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
+
+  <title>Module: Generator</title>
+
+  <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+  <script src="./js/jquery.js" type="text/javascript" charset="utf-8"></script>
+  <script src="./js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
+  <script src="./js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
+  <script src="./js/darkfish.js" type="text/javascript" charset="utf-8"></script>
+
+</head>
+<body id="top" class="module">
+
+  <div id="metadata">
+    <div id="home-metadata">
+      <div id="home-section" class="section">
+        <h3 class="section-header">
+          <a href="./index.html">Home</a>
+          <a href="./index.html#classes">Classes</a>
+          <a href="./index.html#methods">Methods</a>
+        </h3>
+      </div>
+    </div>
+
+    <div id="file-metadata">
+      <div id="file-list-section" class="section">
+        <h3 class="section-header">In Files</h3>
+        <div class="section-body">
+          <ul>
+          
+            <li><a href="./lib/workflow-to-galaxy/generator_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
+              class="thickbox" title="lib/workflow-to-galaxy/generator.rb">lib/workflow-to-galaxy/generator.rb</a></li>
+          
+          </ul>
+        </div>
+      </div>
+
+      
+    </div>
+
+    <div id="class-metadata">
+      
+
+      
+
+      
+
+      
+      <!-- Method Quickref -->
+      <div id="method-list-section" class="section">
+        <h3 class="section-header">Methods</h3>
+        <ul class="link-list">
+          
+          <li><a href="#method-i-generate_script">#generate_script</a></li>
+          
+          <li><a href="#method-i-generate_xml">#generate_xml</a></li>
+          
+        </ul>
+      </div>
+      
+
+      
+    </div>
+
+    <div id="project-metadata">
+      
+      
+      <div id="fileindex-section" class="section project-section">
+        <h3 class="section-header">Files</h3>
+        <ul>
+        
+          <li class="file"><a href="./CHANGES.html">CHANGES</a></li>
+        
+          <li class="file"><a href="./LICENSE.html">LICENSE</a></li>
+        
+          <li class="file"><a href="./README.html">README</a></li>
+        
+        </ul>
+      </div>
+      
+
+      <div id="classindex-section" class="section project-section">
+        <h3 class="section-header">Class/Module Index
+          <span class="search-toggle"><img src="./images/find.png"
+            height="16" width="16" alt="[+]"
+            title="show/hide quicksearch" /></span></h3>
+        <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+        <fieldset>
+          <legend>Quicksearch</legend>
+          <input type="text" name="quicksearch" value=""
+            class="quicksearch-field" />
+        </fieldset>
+        </form>
+
+        <ul class="link-list">
+        
+          <li><a href="./Generator.html">Generator</a></li>
+        
+          <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
+        
+        </ul>
+        <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+      </div>
+
+      
+    </div>
+  </div>
+
+  <div id="documentation">
+    <h1 class="module">Generator</h1>
+
+    <div id="description" class="description">
+      
+<p>The <a href="Generator.html">Generator</a> module contains two public
+methods that generate a Galaxy’s tool XML and script files</p>
+
+    </div><!-- description -->
+
+    
+    <div id="5Buntitled-5D" class="documentation-section">
+      
+
+      
+
+      
+
+      
+
+      <!-- Methods -->
+      
+      <div id="public-instance-method-details" class="method-section section">
+        <h3 class="section-header">Public Instance Methods</h3>
+
+      
+        <div id="generate_script-method" class="method-detail ">
+          <a name="method-i-generate_script"></a>
+
+          
+          
+          <div class="method-heading">
+            <span class="method-callseq">generate_script(my_exp_rest, t2_server, script_file) &rarr; nil</span>
+            
+            <span class="method-click-advice">click to toggle source</span>
+            
+          </div>
+          
+          
+
+          <div class="method-description">
+            
+            <p>Generates the Galaxy tool’s script file responsible for talking to the
+taverna server</p>
+<dl class="rdoc-list"><dt><tt>my_exp_rest</tt></dt>
+<dd>
+<p>a <em>Workflow</em> object as returned from
+<em>MyExperimentREST.ReadWorkflow.new(url)</em></p>
+</dd><dt><tt>t2_server</tt></dt>
+<dd>
+<p>a string containing the URL of the taverna 2 server</p>
+</dd><dt><tt>script_out</tt></dt>
+<dd>
+<p>the file handler to write the generated script code</p>
+</dd></dl>
+            
+
+            
+            <div class="method-source-code" id="generate_script-source">
+<pre>
+<span class="ruby-comment"># File lib/workflow-to-galaxy/generator.rb, line 487</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">generate_script</span>(<span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">t2_server</span>, <span class="ruby-identifier">script_out</span>)
+  <span class="ruby-identifier">script_preample</span>(<span class="ruby-identifier">script_out</span>)
+  <span class="ruby-identifier">script_util_methods</span>(<span class="ruby-identifier">script_out</span>)
+  <span class="ruby-identifier">script_create_t2_run</span>(<span class="ruby-identifier">script_out</span>, <span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">t2_server</span>)
+  <span class="ruby-identifier">script_init_inputs</span>(<span class="ruby-identifier">script_out</span>, <span class="ruby-identifier">t2_workflow</span>)
+  <span class="ruby-identifier">script_start_run</span>(<span class="ruby-identifier">script_out</span>)
+  <span class="ruby-identifier">script_get_outputs</span>(<span class="ruby-identifier">script_out</span>, <span class="ruby-identifier">t2_workflow</span>)
+  <span class="ruby-identifier">script_finish_run</span>(<span class="ruby-identifier">script_out</span>)
+<span class="ruby-keyword">end</span></pre>
+            </div><!-- generate_script-source -->
+            
+          </div>
+
+          
+
+          
+        </div><!-- generate_script-method -->
+
+      
+        <div id="generate_xml-method" class="method-detail ">
+          <a name="method-i-generate_xml"></a>
+
+          
+          
+          <div class="method-heading">
+            <span class="method-callseq">generate_xml(my_exp_rest, xml_file) &rarr; nil</span>
+            
+            <span class="method-click-advice">click to toggle source</span>
+            
+          </div>
+          
+          
+
+          <div class="method-description">
+            
+            <p>Generates the Galaxy tool’s xml file responsible for the UI.</p>
+<dl class="rdoc-list"><dt><tt>t2_workflow</tt></dt>
+<dd>
+<p>a <em>Workflow</em> object as returned from
+<em>MyExperimentREST::Workflows.new.read(url)</em></p>
+</dd><dt><tt>xml_file</tt></dt>
+<dd>
+<p>a string containing the name of the generated XML file</p>
+</dd><dt><tt>xml_out</tt></dt>
+<dd>
+<p>the file handler to write the generated XML tags</p>
+</dd></dl>
+            
+
+            
+            <div class="method-source-code" id="generate_xml-source">
+<pre>
+<span class="ruby-comment"># File lib/workflow-to-galaxy/generator.rb, line 468</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">generate_xml</span>(<span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">xml_file</span>, <span class="ruby-identifier">xml_out</span>)
+  <span class="ruby-identifier">tool_begin_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>.<span class="ruby-identifier">title</span>)
+  <span class="ruby-identifier">command_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">xml_file</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-string">'.xml'</span>, <span class="ruby-string">'.rb'</span>))
+  <span class="ruby-identifier">inputs_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>.<span class="ruby-identifier">inputs</span>)
+  <span class="ruby-identifier">outputs_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>.<span class="ruby-identifier">outputs</span>)
+  <span class="ruby-identifier">help_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>)
+  <span class="ruby-identifier">tool_end_tag</span>(<span class="ruby-identifier">xml_out</span>)
+<span class="ruby-keyword">end</span></pre>
+            </div><!-- generate_xml-source -->
+            
+          </div>
+
+          
+
+          
+        </div><!-- generate_xml-method -->
+
+      
+      </div><!-- public-instance-method-details -->
+    
+    </div><!-- 5Buntitled-5D -->
+  
+
+  </div><!-- documentation -->
+
+  <div id="validator-badges">
+    <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+    <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+      Rdoc Generator</a> 2</small>.</p>
+  </div>
+
+</body>
+</html>
+

data/doc/rdoc/LICENSE.html

@@ -0,0 +1,115 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
+
+  <title>File: LICENSE [workflow-to-galaxy Docs]</title>
+
+  <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
+
+  <script src="./js/jquery.js" type="text/javascript"
+    charset="utf-8"></script>
+  <script src="./js/thickbox-compressed.js" type="text/javascript"
+    charset="utf-8"></script>
+  <script src="./js/quicksearch.js" type="text/javascript"
+    charset="utf-8"></script>
+  <script src="./js/darkfish.js" type="text/javascript"
+    charset="utf-8"></script>
+</head>
+
+<body class="file">
+  <div id="metadata">
+    <div id="home-metadata">
+      <div id="home-section" class="section">
+        <h3 class="section-header">
+          <a href="./index.html">Home</a>
+          <a href="./index.html#classes">Classes</a>
+          <a href="./index.html#methods">Methods</a>
+        </h3>
+      </div>
+    </div>
+
+    <div id="project-metadata">
+      
+      
+      <div id="fileindex-section" class="section project-section">
+        <h3 class="section-header">Files</h3>
+        <ul>
+        
+          <li class="file"><a href="./CHANGES.html">CHANGES</a></li>
+        
+          <li class="file"><a href="./LICENSE.html">LICENSE</a></li>
+        
+          <li class="file"><a href="./README.html">README</a></li>
+        
+        </ul>
+      </div>
+      
+
+      <div id="classindex-section" class="section project-section">
+        <h3 class="section-header">Class Index
+          <span class="search-toggle"><img src="./images/find.png"
+            height="16" width="16" alt="[+]"
+            title="show/hide quicksearch" /></span></h3>
+        <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+        <fieldset>
+          <legend>Quicksearch</legend>
+          <input type="text" name="quicksearch" value=""
+            class="quicksearch-field" />
+        </fieldset>
+        </form>
+
+        <ul class="link-list">
+        
+          <li><a href="./Generator.html">Generator</a></li>
+        
+          <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
+        
+        </ul>
+        <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+      </div>
+
+      
+    </div>
+  </div>
+
+  <div id="documentation">
+    
+<h2>workflow-to-galaxy</h2>
+
+<p>The MIT License</p>
+
+<p>Copyright © 2010 - Netherlands Bioinformatics Centre</p>
+
+<p>Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the
+“Software”), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to permit
+persons to whom the Software is furnished to do so, subject to the
+following conditions:</p>
+
+<p>The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.</p>
+
+<p>THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS
+OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.</p>
+
+  </div>
+
+  <div id="validator-badges">
+    <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+    <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+      Rdoc Generator</a> 2</small>.</p>
+  </div>
+</body>
+</html>
+