workflow-to-galaxy 0.2.8 → 0.2.9

data/CHANGES

@@ -1,5 +1,10 @@
 = Changes log for the Taverna-Galaxy Gem
 
+== Version 0.2.9
+* Fixed minor bug when workflow had empty description
+* Added instructions to generated scripts on how to run them without Galaxy.
+
+
 == Version 0.2.8
 * Clean up of documentation
 * Added rubyzip dependency to gemspec

data/README

@@ -2,7 +2,7 @@
 
 
 Authors::     Konstantinos Karasavvas
-Gem Version:: 0.2.8
+Gem Version:: 0.2.9
 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

data/Rakefile

@@ -12,7 +12,7 @@ require 'rdoc/task'
 
 spec = Gem::Specification.new do |s|
   s.name = 'workflow-to-galaxy'
-  s.version = '0.2.8'
+  s.version = '0.2.9'
   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

data/doc/rdoc/CHANGES.html

@@ -66,6 +66,8 @@
         
           <li><a href="./Generator.html">Generator</a></li>
         
+          <li><a href="./Object.html">Object</a></li>
+        
           <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
         
         </ul>
@@ -80,6 +82,13 @@
     
 <h1>Changes log for the Taverna-Galaxy Gem</h1>
 
+<h2>Version 0.2.9</h2>
+<ul><li>
+<p>Fixed minor bug when workflow had empty description</p>
+</li><li>
+<p>Added instructions to generated scripts on how to run them without Galaxy.</p>
+</li></ul>
+
 <h2>Version 0.2.8</h2>
 <ul><li>
 <p>Clean up of documentation</p>

data/doc/rdoc/Generator.html

@@ -34,6 +34,9 @@
         <div class="section-body">
           <ul>
           
+            <li><a href="./lib/generator_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
+              class="thickbox" title="lib/generator.rb">lib/generator.rb</a></li>
+          
             <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>
           
@@ -102,6 +105,8 @@
         
           <li><a href="./Generator.html">Generator</a></li>
         
+          <li><a href="./Object.html">Object</a></li>
+        
           <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
         
         </ul>
@@ -117,6 +122,9 @@
 
     <div id="description" class="description">
       
+<p>Contains code to generate the Galaxy’s tool xml and script files</p>
+<hr style="height: 1px">
+
 <p>The <a href="Generator.html">Generator</a> module contains two public
 methods that generate a Galaxy’s tool XML and script files</p>
 
@@ -129,6 +137,19 @@ methods that generate a Galaxy’s tool XML and script files</p>
       
 
       
+      <!-- Constants -->
+      <div id="constants-list" class="section">
+        <h3 class="section-header">Constants</h3>
+        <dl>
+        
+          <dt><a name="INDENT">INDENT</a></dt>
+          
+          <dd class="description"></dd>
+          
+        
+        </dl>
+      </div>
+      
 
       
 
@@ -142,45 +163,33 @@ methods that generate a Galaxy’s tool XML and script files</p>
           <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-name">generate_script</span><span
+              class="method-args">(me_rest, t2_server, script_file)</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-comment"># File lib/generator.rb, line 253</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">generate_script</span>(<span class="ruby-identifier">me_rest</span>, <span class="ruby-identifier">t2_server</span>, <span class="ruby-identifier">script_file</span>)
+  <span class="ruby-identifier">out</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">script_file</span>, <span class="ruby-string">&quot;w&quot;</span>)
+  <span class="ruby-identifier">script_preample</span>(<span class="ruby-identifier">out</span>)
+  <span class="ruby-identifier">script_util_methods</span>(<span class="ruby-identifier">out</span>)
+  <span class="ruby-identifier">script_create_t2_run</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>.<span class="ruby-identifier">uri</span>, <span class="ruby-identifier">t2_server</span>)
+  <span class="ruby-identifier">script_init_inputs</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>)
+  <span class="ruby-identifier">script_start_run</span>(<span class="ruby-identifier">out</span>)
+  <span class="ruby-identifier">script_get_outputs</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>)
+  <span class="ruby-identifier">script_finish_run</span>(<span class="ruby-identifier">out</span>)
+  <span class="ruby-identifier">out</span>.<span class="ruby-identifier">close</span>
 <span class="ruby-keyword">end</span></pre>
             </div><!-- generate_script-source -->
             
@@ -196,43 +205,31 @@ taverna server</p>
           <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-name">generate_xml</span><span
+              class="method-args">(me_rest, xml_file)</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-comment"># File lib/generator.rb, line 238</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">generate_xml</span>(<span class="ruby-identifier">me_rest</span>, <span class="ruby-identifier">xml_file</span>)
+  <span class="ruby-identifier">out</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">xml_file</span>, <span class="ruby-string">&quot;w&quot;</span>)
+  <span class="ruby-identifier">tool_b</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>.<span class="ruby-identifier">workflow</span>.<span class="ruby-identifier">title</span>)
+  <span class="ruby-identifier">command_be</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</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_be</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>.<span class="ruby-identifier">workflow</span>.<span class="ruby-identifier">inputs</span>)
+  <span class="ruby-identifier">outputs_be</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>.<span class="ruby-identifier">workflow</span>.<span class="ruby-identifier">outputs</span>)
+  <span class="ruby-identifier">help_be</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>)
+  <span class="ruby-identifier">tool_e</span>(<span class="ruby-identifier">out</span>)
+  <span class="ruby-identifier">out</span>.<span class="ruby-identifier">close</span>
 <span class="ruby-keyword">end</span></pre>
             </div><!-- generate_xml-source -->
             

data/doc/rdoc/LICENSE.html

@@ -66,6 +66,8 @@
         
           <li><a href="./Generator.html">Generator</a></li>
         
+          <li><a href="./Object.html">Object</a></li>
+        
           <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
         
         </ul>

data/doc/rdoc/Object.html

@@ -0,0 +1,161 @@
+<?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>Class: Object</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="class">
+
+  <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_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
+              class="thickbox" title="lib/workflow_to_galaxy.rb">lib/workflow_to_galaxy.rb</a></li>
+          
+          </ul>
+        </div>
+      </div>
+
+      
+    </div>
+
+    <div id="class-metadata">
+      
+      <!-- Parent Class -->
+      <div id="parent-class-section" class="section">
+        <h3 class="section-header">Parent</h3>
+        
+        <p class="link"></p>
+        
+      </div>
+      
+
+      
+
+      
+
+      
+
+      
+      <!-- Included Modules -->
+      <div id="includes-section" class="section">
+        <h3 class="section-header">Included Modules</h3>
+        <ul class="link-list">
+        
+        
+          <li><span class="include">MyExperimentREST</span></li>
+        
+        
+        
+          <li><a class="include" href="Generator.html">Generator</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="./Object.html">Object</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="class">Object</h1>
+
+    <div id="description" class="description">
+      
+    </div><!-- description -->
+
+    
+    <div id="5Buntitled-5D" class="documentation-section">
+      
+
+      
+
+      
+
+      
+
+      <!-- Methods -->
+      
+    </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/README.html

@@ -66,6 +66,8 @@
         
           <li><a href="./Generator.html">Generator</a></li>
         
+          <li><a href="./Object.html">Object</a></li>
+        
           <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
         
         </ul>
@@ -84,7 +86,7 @@
 <p>Konstantinos Karasavvas</p>
 </td></tr><tr><td class="rdoc-term"><p>Gem Version</p></td>
 <td>
-<p>0.2.8</p>
+<p>0.2.9</p>
 </td></tr><tr><td class="rdoc-term"><p>Contact</p></td>
 <td>
 <p><a href="mailto:kostas.karasavvas@nbic.nl">kostas.karasavvas@nbic.nl</a></p>

data/doc/rdoc/WorkflowToGalaxy.html

@@ -90,6 +90,8 @@
         
           <li><a href="./Generator.html">Generator</a></li>
         
+          <li><a href="./Object.html">Object</a></li>
+        
           <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
         
         </ul>

data/doc/rdoc/created.rid

@@ -1,6 +1,8 @@
-Fri, 22 Jul 2011 15:00:07 +0200
-lib/workflow-to-galaxy.rb	Mon, 13 Dec 2010 15:22:40 +0100
-LICENSE	Wed, 06 Apr 2011 16:41:53 +0200
-README	Fri, 22 Jul 2011 14:51:41 +0200
-CHANGES	Fri, 22 Jul 2011 14:46:31 +0200
-lib/workflow-to-galaxy/generator.rb	Mon, 04 Jul 2011 16:13:08 +0200
+Tue, 26 Jul 2011 16:38:29 +0200
+lib/generator.rb	Tue, 26 Jul 2011 16:35:55 +0200
+lib/workflow-to-galaxy.rb	Tue, 26 Jul 2011 16:35:55 +0200
+LICENSE	Tue, 26 Jul 2011 16:35:55 +0200
+lib/workflow_to_galaxy.rb	Tue, 26 Jul 2011 16:35:55 +0200
+README	Tue, 26 Jul 2011 16:35:55 +0200
+CHANGES	Tue, 26 Jul 2011 16:35:55 +0200
+lib/workflow-to-galaxy/generator.rb	Tue, 26 Jul 2011 16:35:55 +0200

data/doc/rdoc/index.html

@@ -29,7 +29,7 @@
 <p>Konstantinos Karasavvas</p>
 </td></tr><tr><td class="rdoc-term"><p>Gem Version</p></td>
 <td>
-<p>0.2.8</p>
+<p>0.2.9</p>
 </td></tr><tr><td class="rdoc-term"><p>Contact</p></td>
 <td>
 <p><a href="mailto:kostas.karasavvas@nbic.nl">kostas.karasavvas@nbic.nl</a></p>
@@ -122,6 +122,8 @@ href="https://trac.nbic.nl/elabfactory/wiki/eGalaxy">trac.nbic.nl/elabfactory/wi
     
     <li class="module"><a href="Generator.html">Generator</a></li>
     
+    <li class="class"><a href="Object.html">Object</a></li>
+    
     <li class="module"><a href="WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
     
   </ul>

data/doc/rdoc/lib/generator_rb.html

@@ -0,0 +1,54 @@
+<?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: generator.rb [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 file-popup">
+  <div id="metadata">
+    <dl>
+      <dt class="modified-date">Last Modified</dt>
+      <dd class="modified-date">Tue Jul 26 16:35:55 +0200 2011</dd>
+
+      
+      <dt class="requires">Requires</dt>
+      <dd class="requires">
+        <ul>
+        
+        </ul>
+      </dd>
+      
+
+      
+    </dl>
+  </div>
+
+  <div id="documentation">
+    
+    <div class="description">
+      <h2>Description</h2>
+      
+<p>Contains code to generate the Galaxy’s tool xml and script files</p>
+
+    </div>
+    
+  </div>
+</body>
+</html>
+

data/doc/rdoc/lib/workflow-to-galaxy/generator_rb.html

@@ -24,7 +24,7 @@
   <div id="metadata">
     <dl>
       <dt class="modified-date">Last Modified</dt>
-      <dd class="modified-date">Mon Jul 04 16:13:08 +0200 2011</dd>
+      <dd class="modified-date">Tue Jul 26 16:35:55 +0200 2011</dd>
 
       
       <dt class="requires">Requires</dt>

data/doc/rdoc/lib/workflow-to-galaxy_rb.html

@@ -24,7 +24,7 @@
   <div id="metadata">
     <dl>
       <dt class="modified-date">Last Modified</dt>
-      <dd class="modified-date">Mon Dec 13 15:22:40 +0100 2010</dd>
+      <dd class="modified-date">Tue Jul 26 16:35:55 +0200 2011</dd>
 
       
       <dt class="requires">Requires</dt>

data/doc/rdoc/lib/workflow_to_galaxy_rb.html

@@ -0,0 +1,60 @@
+<?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: workflow_to_galaxy.rb [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 file-popup">
+  <div id="metadata">
+    <dl>
+      <dt class="modified-date">Last Modified</dt>
+      <dd class="modified-date">Tue Jul 26 16:35:55 +0200 2011</dd>
+
+      
+      <dt class="requires">Requires</dt>
+      <dd class="requires">
+        <ul>
+        
+          <li>rubygems</li>
+        
+          <li>optparse</li>
+        
+          <li>myexperiment-rest</li>
+        
+          <li>generator</li>
+        
+        </ul>
+      </dd>
+      
+
+      
+    </dl>
+  </div>
+
+  <div id="documentation">
+    
+    <div class="description">
+      <h2>Description</h2>
+      
+    </div>
+    
+  </div>
+</body>
+</html>
+

data/lib/generator.rb

@@ -0,0 +1,265 @@
+
+# Contains code to generate the Galaxy's tool xml and script files
+module Generator
+
+  INDENT = "  "
+
+
+  # private methods
+  private
+
+  def tool_b(out, name)
+    out.write("<tool id=\"#{name}_id\" name=\"#{name}\">\n")
+  end
+
+  def command_be(out, me_rest, script)
+    out.write "#{INDENT}<command interpreter=\"ruby\">"
+    out.write script + " "
+    me_rest.workflow.inputs.each do |i|
+      out.write "\"$#{i.name}\" "
+    end
+    me_rest.workflow.outputs.each do |o|
+      out.write "$#{o.name} "
+    end
+    out.write "</command>\n"
+  end
+
+  def inputs_be(out, inputs)
+    out.write "#{INDENT}<inputs>\n"
+    if inputs.size >= 1
+      inputs.each do |i|
+        2.times { out.write "#{INDENT}" }
+        out.write "<param name=\"#{i.name}\" type=\"text\" size=\"30\" "
+        if i.examples.size >= 1
+          # escape double quotes characters for galaxy's xml file
+          ex = i.examples[0].to_s.gsub('"', '&quot;')
+          out.write "value=\"#{ex}\" "
+        end
+        out.write "label=\"Enter #{i.name}\"/>\n"
+      end
+    else
+      2.times { out.write "#{INDENT}" }
+      out.write "<param name=\"input\" type=\"select\" display=\"radio\" size=\"250\" label=\"This workflow has no inputs\" />\n"
+    end  
+    out.write "#{INDENT}</inputs>\n"
+  end
+
+  def outputs_be(out, outputs)
+    out.write "#{INDENT}<outputs>\n"
+    outputs.each do |o|
+      2.times { out.write "#{INDENT}" }
+      out.write "<data format=\"tabular\" name=\"#{o.name}\" label=\"#{o.name}\"/>\n"
+    end
+    out.write "#{INDENT}</outputs>\n"
+  end
+
+  def help_be(out, me_rest)
+    out.write "#{INDENT}<help>\n"
+    out.write "**What it does**\n\n"
+
+    # Sometimes the workflow description contains HTML tags that are not allowed
+    # in Galaxy's xml interface specification and thus are removed! Same for
+    # HTML entities!
+    out.write me_rest.workflow.description.gsub(/<.*?>|&.*?;/, '') + "\n\n"
+
+    if me_rest.workflow.inputs.size >= 1
+      out.write "-----\n\n"
+      out.write "**Inputs**\n\n"
+      me_rest.workflow.inputs.each do |i|
+        out.write "- **#{i.name}** "
+        if i.descriptions.size >= 1
+          i.descriptions.each do |desc|
+            out.write desc.to_s + " "
+          end
+        end
+        if i.examples.size >= 1
+          out.write "Examples include:\n\n"
+          i.examples.each do |ex|
+            out.write "  - " + ex.to_s + "\n"
+          end
+        end
+        out.write "\n"
+      end
+      out.write "\n"
+    end
+
+    # TODO this code is identical to the inputs code above -- method?
+    if me_rest.workflow.outputs.size >= 1
+      out.write "-----\n\n"
+      out.write "**Outputs**\n\n"
+      me_rest.workflow.outputs.each do |o|
+        out.write "- **#{o.name}** "
+        if o.descriptions.size >= 1
+          o.descriptions.each do |desc|
+            out.write desc.to_s + " "
+          end
+        end
+        if o.examples.size >= 1
+          out.write "Examples include:\n\n"
+          o.examples.each do |ex|
+            out.write "  - " + ex.to_s + "\n"
+          end
+        end
+        out.write "\n"
+      end
+      out.write "\n"
+    end
+
+
+    out.write "-----\n\n"
+    out.write "For more information on that workflow please visit #{me_rest.uri.gsub(/(.*workflows\/\d+)[\/.].*/, '\1')}.\n"
+
+    out.write "#{INDENT}</help>\n"
+  end
+
+  def tool_e(out)
+    out.write("</tool>\n")
+  end
+
+
+
+
+  def script_preample(out)
+    out.write("#!/usr/bin/env ruby\n\n")
+    out.write("require 'rubygems'\n")
+    out.write("require 't2-server'\n")
+    out.write("require 'open-uri'\n\n")
+  end
+
+  def script_util_methods(out)
+
+    out.write <<UTIL_METHODS
+    
+  # method that flattens the list of list of list ... result of get_output
+  def print_flattened_result(out, data_lists)
+    data_lists.each do |l|
+      if l.instance_of? Array
+        print_flattened_result(out, l)
+      else
+        out.puts l
+      end
+    end
+  end
+
+
+  # method that acquires all the results of the specified output
+  def get_outputs(run, refs, outfile, dir)
+    data_lists = run.get_output(dir, refs)
+    print_flattened_result(outfile, data_lists)
+  end
+
+
+  #
+  # Sanitize single and double quotes in str. E.g. galaxy substitures them to
+  # __sq__ and __dq__ respectively. This methods turns them back to their
+  # original values before using them
+  #
+  def sanitize(string)
+    string.gsub(/(__sq__|__dq__|__at__)/) do
+      if $1 == '__sq__'
+        "'"
+      elsif $1 == '__dq__'
+        '\\\"'
+      else
+        '@'
+      end
+    end
+  end
+
+UTIL_METHODS
+
+  end
+
+
+  def script_create_t2_run(out, wkf_uri, t2_uri)
+    out.write <<CREATE_T2_RUN
+
+# use the uri reference to download the workflow locally
+wkf_file = URI.parse('#{wkf_uri}')
+in_wkf = open(wkf_file)
+wkf = in_wkf.read()
+
+# create run
+begin
+  run = T2Server::Run.create('#{t2_uri}', wkf)
+rescue T2Server::T2ServerError => e
+  exit 1
+end
+
+CREATE_T2_RUN
+
+  end
+
+
+  def script_init_inputs(out, me_rest)
+    out.write "# get input arguments\n"
+    0.upto(me_rest.workflow.inputs.size-1) do |i|
+      out.write "input#{i}_arg = ARGV[#{i}].chomp\n"
+      out.write "run.set_input('" + me_rest.workflow.inputs[i].name.to_s + "', sanitize(input#{i}_arg))\n"
+    end
+
+  end
+
+
+  def script_start_run(out)
+    out.write <<START_RUN
+
+# start run and wait until it is finished
+run.start
+run.wait(:progress => true)
+
+START_RUN
+  end
+
+
+  def script_get_outputs(out, me_rest)
+    outputs_start_index = me_rest.workflow.inputs.size
+    outputs_end_index = outputs_start_index + me_rest.workflow.outputs.size - 1
+    out.write "# get output arguments and associated them with a file\n"
+    outputs_start_index.upto(outputs_end_index) do |o|
+      out.write "output#{o} = File.open(ARGV[#{o}], \"w\")\n"
+      out.write "get_outputs(run, false, output#{o}, '" + me_rest.workflow.outputs[o - outputs_start_index].name.to_s + "')\n"
+    end
+
+  end
+
+
+  def script_finish_run(out)
+    out.write "\n# delete run\n"
+    out.write "run.delete\n"
+  end
+
+
+
+  # public methods from here onwards
+  public
+
+  # Generates the Galaxy tool's xml file responsible for the UI.
+  def generate_xml(me_rest, xml_file)
+    out = File.open(xml_file, "w")
+    tool_b(out, me_rest.workflow.title)
+    command_be(out, me_rest, xml_file.gsub('.xml', '.rb'))
+    inputs_be(out, me_rest.workflow.inputs)
+    outputs_be(out, me_rest.workflow.outputs)
+    help_be(out, me_rest)
+    tool_e(out)
+    out.close
+  end
+
+  #
+  # Generates the Galaxy tool's script file responsible for talking to the
+  # taverna server
+  #
+  def generate_script(me_rest, t2_server, script_file)
+    out = File.open(script_file, "w")
+    script_preample(out)
+    script_util_methods(out)
+    script_create_t2_run(out, me_rest.uri, t2_server)
+    script_init_inputs(out, me_rest)
+    script_start_run(out)
+    script_get_outputs(out, me_rest)
+    script_finish_run(out)
+    out.close
+  end
+
+end

data/lib/workflow-to-galaxy/generator.rb

@@ -1,7 +1,8 @@
 #
 # The Generator module contains two public methods that generate a Galaxy's tool
 # XML and script files
-#
+#--
+# Add appropriate requires here. Currently they are all in the executable!
 module Generator
 
   # private methods
@@ -106,27 +107,30 @@ module Generator
   # Galaxy's XML help tag
   def help_tag(out, t2_workflow)
     out.write indent(1) + "<help>\n"
-    out.write "**What it does**\n\n"
 
-    description = t2_workflow.description + "\n\n"
+    if t2_workflow.description
+      out.write "**What it does**\n\n"
 
-    # Sometimes the workflow description contains HTML tags that are not allowed
-    # in Galaxy's xml interface specification and thus are removed! Same for
-    # HTML entities!
-    # TODO go through tags and find Galaxy's equivalent to include
-    description.gsub!(/<.*?>|&.*?;/, '')
+      description = t2_workflow.description + "\n\n"
 
-    # To remove ^M (cntl-v + cntl-m) characters that DOS files might have
-    description.gsub!(/\r/, '')
-    
-    # TODO that works as a literal too but font changes to courier!
-    #out.write "::\n\n"   # Start Galaxy's literal block to ignore indendation
+      # Sometimes the workflow description contains HTML tags that are not allowed
+      # in Galaxy's xml interface specification and thus are removed! Same for
+      # HTML entities!
+      # TODO go through tags and find Galaxy's equivalent to include
+      description.gsub!(/<.*?>|&.*?;/, '')
+
+      # To remove ^M (cntl-v + cntl-m) characters that DOS files might have
+      description.gsub!(/\r/, '')
+
+      # TODO that works as a literal too but font changes to courier!
+      #out.write "::\n\n"   # Start Galaxy's literal block to ignore indendation
 
-    # remove indendation from all description lines since Galaxy is confused by it
-    description.split(/[\n]/).each { |l| out.write "#{l.gsub(/^\s+/, '')}\n" }
+      # remove indendation from all description lines since Galaxy is confused by it
+      description.split(/[\n]/).each { |l| out.write "#{l.gsub(/^\s+/, '')}\n" }
 
-    # endline makes the following be parsed as a Galaxy GUI construct
-    out.write "\n"       
+      # endline makes the following be parsed as a Galaxy GUI construct
+      out.write "\n"
+    end
 
     # if at least one input add it to tool's UI help description
     if t2_workflow.inputs.size >= 1
@@ -218,6 +222,16 @@ module Generator
   # Galaxy's script preample
   def script_preample(out)
     out.write("#!/usr/bin/env ruby\n\n")
+
+    out.write("# This script can be tested without Galaxy. You can run from the shell as follows:\n#\n")
+    out.write("#   $ script_name.rb <input1> true|false <input2> true|false  yes|no  <output1> <output2>\n#\n")
+    out.write("# After each input value a boolean specifies if the value is literal (false) or if\n")
+    out.write("# it specifies a file name to read as input.\n#\n")
+    out.write("# After all workflow inputs a yes or no input specifies if we also want our results zipped.\n#\n")
+    out.write("# Finally, all the output files follow. Note that if you selected to also get a zip\n")
+    out.write("# then you need to specify an additional output in the end after the normal workflow\n")
+    out.write("# outputs.\n\n")
+
     out.write("require 'rubygems'\n")
     out.write("require 't2-server'\n")
     out.write("require 'open-uri'\n")

data/lib/workflow_to_galaxy.rb

@@ -0,0 +1,65 @@
+#!/usr/bin/env ruby
+
+require 'rubygems'
+require 'optparse'
+require 'myexperiment-rest'
+require 'generator'
+
+include MyExperimentREST
+include Generator
+
+
+# Set up and parse arguments
+out_file = ""
+t2_server = ""
+opts = OptionParser.new do |opt|
+  opt.banner = "Usage: workflow_to_galaxy [options] <myExperiement-workflow>"
+  opt.separator ""
+  opt.separator "Generates a Galaxy tool (a UI xml definition plus a script) for the "
+  opt.separator "specified Taverna2 workflow, where <myExperiment-workflow> is "
+  opt.separator "the full URL of the workflow in the myExperiment website. Available "
+  opt.separator "options are:"
+
+  opt.on("-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.") do |val|
+    out_file = val if val != nil
+  end
+
+  opt.on("-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.") do |val|
+    t2_server = val if val != nil
+  end
+end
+
+opts.parse!
+
+# Read and check workflow URL
+url = ARGV.shift
+if url == nil
+  puts opts
+  exit 1
+end
+
+# Get workflow data from myexperiment
+me_rest = ReadWorkflow.new(url)
+
+# Set output files
+if out_file != ""
+  xml_file = "#{out_file}.xml"
+  script_file = "#{out_file}.rb"
+else
+  xml_file = "#{me_rest.workflow.title}".gsub(/\W/, '') + ".xml"
+  script_file = "#{me_rest.workflow.title}".gsub(/\W/, '') + ".rb"
+end
+
+# Set taverna server
+if t2_server == ""
+  t2_server = "http://localhost:8980/taverna-server"
+end
+
+
+
+generate_xml(me_rest, xml_file)
+generate_script(me_rest, t2_server, script_file)
+
+

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: workflow-to-galaxy
 version: !ruby/object:Gem::Version 
-  hash: 7
+  hash: 5
   prerelease: 
   segments: 
   - 0
   - 2
-  - 8
-  version: 0.2.8
+  - 9
+  version: 0.2.9
 platform: ruby
 authors: 
 - Kostas Karasavvas
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-07-22 00:00:00 Z
+date: 2011-07-26 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: myexperiment-rest
@@ -97,6 +97,8 @@ files:
 - CHANGES
 - Rakefile
 - bin/workflow_to_galaxy.rb
+- lib/workflow_to_galaxy.rb
+- lib/generator.rb
 - lib/workflow-to-galaxy/generator.rb
 - lib/workflow-to-galaxy.rb
 - doc/rdoc/WorkflowToGalaxy.html
@@ -109,7 +111,10 @@ files:
 - doc/rdoc/js/darkfish.js
 - doc/rdoc/js/quicksearch.js
 - doc/rdoc/README.html
+- doc/rdoc/Object.html
+- doc/rdoc/lib/workflow_to_galaxy_rb.html
 - doc/rdoc/lib/workflow-to-galaxy_rb.html
+- doc/rdoc/lib/generator_rb.html
 - doc/rdoc/lib/workflow-to-galaxy/generator_rb.html
 - doc/rdoc/created.rid
 - doc/rdoc/CHANGES.html