workflow-to-galaxy 0.3.1 → 0.3.3

data/CHANGES

@@ -1,8 +1,22 @@
 = Changes log for the Taverna-Galaxy Gem
 
+== Version 0.3.3
+* Multiline output examples are now displayed better in HTML/Galaxy (similar to inputs)
+* Updated wkf 74 test
+* Fixed default values for output files and taverna server
+* Added an optional parameter (:response) to the config in case we already have the myExp wkf
+  - was needed by myExperiment in order to call the myExp REST API beforehand for auth
+
+
+== Version 0.3.2
+* Automatic filename creation is more robust (all special chars are removed)
+* More workflow tests
+
+
 == Version 0.3.1
-* Use semver formally... (tag: v0.3.1 semver !!) ????
-* For safety default file names substiture ' ' with '_'
+* Used semver formally (taged: v0.3.1 semver)
+* For safety default wkf title substitutes ' ' with '_'
+* Extended workflow tests
 
 
 == Version 0.3.0

data/README

@@ -2,7 +2,7 @@
 
 
 Authors::     Konstantinos Karasavvas
-Gem Version:: 0.3.0
+Gem Version:: 0.3.3
 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

@@ -7,7 +7,7 @@ require 'rdoc/task'
 
 spec = Gem::Specification.new do |s|
   s.name = 'workflow-to-galaxy'
-  s.version = '0.3.1'
+  s.version = '0.3.3'
   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/bin/workflow_to_galaxy.rb

@@ -9,8 +9,8 @@ include WorkflowToGalaxy
 
 
 # Set up and parse arguments
-out_file = ""
-t2_server = ""
+out_file = nil
+t2_server = nil
 options = {}
 opts = OptionParser.new do |opt|
   opt.banner = "Usage: workflow_to_galaxy [options] <myExperiment-workflow> | <t2flow-file>"
@@ -49,7 +49,7 @@ if url == nil
 end
 
 # Set taverna server if not specified
-t2_server ||= "http://localhost:8080/taverna-server"
+t2_server ||= 'http://localhost:8080/taverna-server'
 
 
 #if options[:t2flow]
@@ -59,7 +59,7 @@ t2_server ||= "http://localhost:8080/taverna-server"
 #end
 
 # create file handlers
-if out_file != ""
+if out_file != nil
   xml_out = open("#{out_file}.xml", "w")
   rb_out = open("#{out_file}.rb", "w")
 end
@@ -68,7 +68,7 @@ end
 # create generator or wrapper (could have used url for t2flow key to avoid
 # if/else but future sources would still need them)
 if options[:t2flow]
-  if out_file != ""
+  if out_file != nil
     wkf = GalaxyTool.new(:wkf_source => Workflows::T2FLOW,
                          :params => {:t2_server => t2_server,
                                      :t2flow => url,
@@ -80,7 +80,7 @@ if options[:t2flow]
                                      :t2flow => url } )
   end
 else
-  if out_file != ""
+  if out_file != nil
     wkf = GalaxyTool.new(:wkf_source => Workflows::MYEXPERIMENT_TAVERNA2,
                          :params => {:t2_server => t2_server,
                                      :url => url,
@@ -94,7 +94,7 @@ else
 end
 
 # close file handlers
-if out_file != ""
+if out_file != nil
   xml_out.close
   rb_out.close
 end

data/doc/rdoc/CHANGES.html

@@ -70,6 +70,8 @@
         
           <li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
         
+          <li><a href="./String.html">String</a></li>
+        
         </ul>
         <div id="no-class-search-results" style="display: none;">No matching classes.</div>
       </div>
@@ -82,11 +84,37 @@
     
 <h1>Changes log for the Taverna-Galaxy Gem</h1>
 
+<h2>Version 0.3.3</h2>
+<ul><li>
+<p>Multiline output examples are now displayed better in HTML/Galaxy (similar
+to inputs)</p>
+</li><li>
+<p>Updated wkf 74 test</p>
+</li><li>
+<p>Fixed default values for output files and taverna server</p>
+</li><li>
+<p>Added an optional parameter (:response) to the config in case we already
+have the myExp wkf</p>
+<ul><li>
+<p>was needed by myExperiment in order to call the myExp REST API beforehand
+for auth</p>
+</li></ul>
+</li></ul>
+
+<h2>Version 0.3.2</h2>
+<ul><li>
+<p>Automatic filename creation is more robust (all special chars are removed)</p>
+</li><li>
+<p>More workflow tests</p>
+</li></ul>
+
 <h2>Version 0.3.1</h2>
 <ul><li>
-<p>Use semver formally… (tag: v0.3.1 semver !!) ????</p>
+<p>Used semver formally (taged: v0.3.1 semver)</p>
+</li><li>
+<p>For safety default wkf title substitutes ‘ ’ with ‘_’</p>
 </li><li>
-<p>For safety default file names substiture ‘ ’ with ‘_’</p>
+<p>Extended workflow tests</p>
 </li></ul>
 
 <h2>Version 0.3.0</h2>

data/doc/rdoc/LICENSE.html

@@ -70,6 +70,8 @@
         
           <li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
         
+          <li><a href="./String.html">String</a></li>
+        
         </ul>
         <div id="no-class-search-results" style="display: none;">No matching classes.</div>
       </div>

data/doc/rdoc/README.html

@@ -70,6 +70,8 @@
         
           <li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
         
+          <li><a href="./String.html">String</a></li>
+        
         </ul>
         <div id="no-class-search-results" style="display: none;">No matching classes.</div>
       </div>
@@ -86,7 +88,7 @@
 <p>Konstantinos Karasavvas</p>
 </td></tr><tr><td class="rdoc-term"><p>Gem Version</p></td>
 <td>
-<p>0.3.0</p>
+<p>0.3.3</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/String.html

@@ -0,0 +1,203 @@
+<?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: String</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">Object</p>
+        
+      </div>
+      
+
+      
+
+      
+
+      
+      <!-- Method Quickref -->
+      <div id="method-list-section" class="section">
+        <h3 class="section-header">Methods</h3>
+        <ul class="link-list">
+          
+          <li><a href="#method-i-to_filename">#to_filename</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="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
+        
+          <li><a href="./WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
+        
+          <li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
+        
+          <li><a href="./String.html">String</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">String</h1>
+
+    <div id="description" class="description">
+      
+<p>Add methods to the <a href="String.html">String</a> class to operate on
+file paths.</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="to_filename-method" class="method-detail ">
+          <a name="method-i-to_filename"></a>
+
+          
+          
+          <div class="method-heading">
+            <span class="method-callseq">to_filename &rarr; string</span>
+            
+            <span class="method-click-advice">click to toggle source</span>
+            
+          </div>
+          
+          
+
+          <div class="method-description">
+            
+            <p>Returns a new <a href="String.html">String</a> with spaces substituted by
+underscores and removes all special characters.</p>
+            
+
+            
+            <div class="method-source-code" id="to_filename-source">
+<pre>
+<span class="ruby-comment"># File lib/workflow-to-galaxy.rb, line 17</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">to_filename</span>
+  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-regexp">/ /</span>, <span class="ruby-string">'_'</span>).<span class="ruby-identifier">gsub</span>(<span class="ruby-regexp">/[^A-Za-z0-9_]/</span>, <span class="ruby-string">''</span>)
+<span class="ruby-keyword">end</span></pre>
+            </div><!-- to_filename-source -->
+            
+          </div>
+
+          
+
+          
+        </div><!-- to_filename-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/WorkflowToGalaxy.html

@@ -124,6 +124,8 @@
         
           <li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
         
+          <li><a href="./String.html">String</a></li>
+        
         </ul>
         <div id="no-class-search-results" style="display: none;">No matching classes.</div>
       </div>

data/doc/rdoc/WorkflowToGalaxy/GalaxyTool.html

@@ -114,6 +114,8 @@
         
           <li><a href="../WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
         
+          <li><a href="../String.html">String</a></li>
+        
         </ul>
         <div id="no-class-search-results" style="display: none;">No matching classes.</div>
       </div>
@@ -217,7 +219,7 @@ the workflow object that will be used to generate the galaxy tool</p>
             
             <div class="method-source-code" id="new-source">
 <pre>
-<span class="ruby-comment"># File lib/workflow-to-galaxy/galaxy.rb, line 39</span>
+<span class="ruby-comment"># File lib/workflow-to-galaxy/galaxy.rb, line 40</span>
 <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">config</span>)
   <span class="ruby-ivar">@config</span> = <span class="ruby-identifier">config</span>
 <span class="ruby-keyword">end</span></pre>
@@ -260,41 +262,48 @@ the workflow object that will be used to generate the galaxy tool</p>
             
             <div class="method-source-code" id="generate-source">
 <pre>
-<span class="ruby-comment"># File lib/workflow-to-galaxy/galaxy.rb, line 575</span>
+<span class="ruby-comment"># File lib/workflow-to-galaxy/galaxy.rb, line 582</span>
 <span class="ruby-keyword">def</span> <span class="ruby-identifier">generate</span>
 
-  <span class="ruby-comment"># check the type of workflow source and acquire the appropriate data</span>
-  <span class="ruby-keyword">if</span>(<span class="ruby-identifier">config</span>[<span class="ruby-value">:wkf_source</span>] <span class="ruby-operator">==</span> <span class="ruby-constant">Workflows</span><span class="ruby-operator">::</span><span class="ruby-constant">MYEXPERIMENT_TAVERNA2</span>)
+  <span class="ruby-keyword">if</span>(<span class="ruby-identifier">config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:response</span>])
 
-    <span class="ruby-comment"># TODO: check and add auth stuff -- even more unsafe with session cookies</span>
-    <span class="ruby-comment"># since the myexp username/passwd will be saved in the galaxy ruby script</span>
-    <span class="ruby-comment"># for all to see...</span>
+    <span class="ruby-ivar">@wkf_object</span> = <span class="ruby-identifier">config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:response</span>]
 
-    <span class="ruby-keyword">begin</span>
-      <span class="ruby-comment"># Get workflow data from myexperiment -- a _MyExperimentWorkflow_ object is returned</span>
-      <span class="ruby-ivar">@wkf_object</span> = <span class="ruby-constant">MyExperimentREST</span><span class="ruby-operator">::</span><span class="ruby-constant">Workflow</span>.<span class="ruby-identifier">from_uri</span>(<span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:url</span>])
-    <span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">e</span>
-      <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;Problem acquiring workflow data from myExperiment!\n&quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">e</span>
-    <span class="ruby-keyword">end</span>
+  <span class="ruby-keyword">else</span>
 
-  <span class="ruby-keyword">elsif</span>(<span class="ruby-identifier">config</span>[<span class="ruby-value">:wkf_source</span>] <span class="ruby-operator">==</span> <span class="ruby-constant">Workflows</span><span class="ruby-operator">::</span><span class="ruby-constant">T2FLOW</span>)
+    <span class="ruby-comment"># check the type of workflow source and acquire the appropriate data</span>
+    <span class="ruby-keyword">if</span>(<span class="ruby-identifier">config</span>[<span class="ruby-value">:wkf_source</span>] <span class="ruby-operator">==</span> <span class="ruby-constant">Workflows</span><span class="ruby-operator">::</span><span class="ruby-constant">MYEXPERIMENT_TAVERNA2</span>)
 
-    <span class="ruby-keyword">begin</span>
-      <span class="ruby-comment"># Get workflow data from t2flow file -- a _MyExperimentWorkflow_ object is returned</span>
-      <span class="ruby-ivar">@wkf_object</span> = <span class="ruby-identifier">populate_taverna_workflow_from_t2flow</span>(<span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:t2flow</span>])
-    <span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">e</span>
-      <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;Problem acquiring workflow data from t2flow file!\n&quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">e</span>
-    <span class="ruby-keyword">end</span>
+      <span class="ruby-comment"># TODO: check and add auth stuff -- even more unsafe with session cookies</span>
+      <span class="ruby-comment"># since the myexp username/passwd will be saved in the galaxy ruby script</span>
+      <span class="ruby-comment"># for all to see...</span>
 
-  <span class="ruby-keyword">else</span>
-    <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;No such workflow source supported!&quot;</span>
+      <span class="ruby-keyword">begin</span>
+        <span class="ruby-comment"># Get workflow data from myexperiment -- a _MyExperimentWorkflow_ object is returned</span>
+        <span class="ruby-ivar">@wkf_object</span> = <span class="ruby-constant">MyExperimentREST</span><span class="ruby-operator">::</span><span class="ruby-constant">Workflow</span>.<span class="ruby-identifier">from_uri</span>(<span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:url</span>])
+      <span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">e</span>
+        <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;Problem acquiring workflow data from myExperiment!\n&quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">e</span>
+      <span class="ruby-keyword">end</span>
+
+    <span class="ruby-keyword">elsif</span>(<span class="ruby-identifier">config</span>[<span class="ruby-value">:wkf_source</span>] <span class="ruby-operator">==</span> <span class="ruby-constant">Workflows</span><span class="ruby-operator">::</span><span class="ruby-constant">T2FLOW</span>)
+
+      <span class="ruby-keyword">begin</span>
+        <span class="ruby-comment"># Get workflow data from t2flow file -- a _MyExperimentWorkflow_ object is returned</span>
+        <span class="ruby-ivar">@wkf_object</span> = <span class="ruby-identifier">populate_taverna_workflow_from_t2flow</span>(<span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:t2flow</span>])
+      <span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">e</span>
+        <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;Problem acquiring workflow data from t2flow file!\n&quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">e</span>
+      <span class="ruby-keyword">end</span>
+
+    <span class="ruby-keyword">else</span>
+      <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;No such workflow source supported!&quot;</span>
+    <span class="ruby-keyword">end</span>
   <span class="ruby-keyword">end</span>
 
   <span class="ruby-comment"># if an xml_out file handler was not given provide one with the title as the value</span>
   <span class="ruby-keyword">if</span> <span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:xml_out</span>]
     <span class="ruby-identifier">generate_xml</span>(<span class="ruby-ivar">@wkf_object</span>, <span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:xml_out</span>])
   <span class="ruby-keyword">else</span>
-    <span class="ruby-identifier">xml_out</span> = <span class="ruby-identifier">open</span>(<span class="ruby-ivar">@wkf_object</span>.<span class="ruby-identifier">title</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-regexp">/ /</span>, <span class="ruby-string">'_'</span>) <span class="ruby-operator">+</span> <span class="ruby-string">&quot;.xml&quot;</span>, <span class="ruby-string">&quot;w&quot;</span>)
+    <span class="ruby-identifier">xml_out</span> = <span class="ruby-identifier">open</span>(<span class="ruby-ivar">@wkf_object</span>.<span class="ruby-identifier">title</span>.<span class="ruby-identifier">to_filename</span> <span class="ruby-operator">+</span> <span class="ruby-string">&quot;.xml&quot;</span>, <span class="ruby-string">&quot;w&quot;</span>)
     <span class="ruby-identifier">generate_xml</span>(<span class="ruby-ivar">@wkf_object</span>, <span class="ruby-identifier">xml_out</span>)
     <span class="ruby-identifier">xml_out</span>.<span class="ruby-identifier">close</span>
   <span class="ruby-keyword">end</span>
@@ -303,7 +312,7 @@ the workflow object that will be used to generate the galaxy tool</p>
   <span class="ruby-keyword">if</span> <span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:rb_out</span>]
     <span class="ruby-identifier">generate_rb</span>(<span class="ruby-ivar">@wkf_object</span>, <span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:rb_out</span>], <span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:t2_server</span>])
   <span class="ruby-keyword">else</span>
-    <span class="ruby-identifier">rb_out</span> = <span class="ruby-identifier">open</span>(<span class="ruby-ivar">@wkf_object</span>.<span class="ruby-identifier">title</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-regexp">/ /</span>, <span class="ruby-string">'_'</span>) <span class="ruby-operator">+</span> <span class="ruby-string">&quot;.rb&quot;</span>, <span class="ruby-string">&quot;w&quot;</span>)
+    <span class="ruby-identifier">rb_out</span> = <span class="ruby-identifier">open</span>(<span class="ruby-ivar">@wkf_object</span>.<span class="ruby-identifier">title</span>.<span class="ruby-identifier">to_filename</span> <span class="ruby-operator">+</span> <span class="ruby-string">&quot;.rb&quot;</span>, <span class="ruby-string">&quot;w&quot;</span>)
     <span class="ruby-identifier">generate_rb</span>(<span class="ruby-ivar">@wkf_object</span>, <span class="ruby-identifier">rb_out</span>, <span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:t2_server</span>])
     <span class="ruby-identifier">rb_out</span>.<span class="ruby-identifier">close</span>
   <span class="ruby-keyword">end</span>

data/doc/rdoc/WorkflowToGalaxy/Workflows.html

@@ -94,6 +94,8 @@
         
           <li><a href="../WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
         
+          <li><a href="../String.html">String</a></li>
+        
         </ul>
         <div id="no-class-search-results" style="display: none;">No matching classes.</div>
       </div>

data/doc/rdoc/created.rid

@@ -1,7 +1,7 @@
-Thu, 27 Oct 2011 11:03:06 +0200
-lib/workflow-to-galaxy.rb	Thu, 13 Oct 2011 12:51:40 +0200
+Mon, 16 Jan 2012 16:21:48 +0100
+lib/workflow-to-galaxy.rb	Tue, 15 Nov 2011 15:48:17 +0100
 lib/workflow-to-galaxy/constants.rb	Mon, 10 Oct 2011 14:10:32 +0200
-lib/workflow-to-galaxy/galaxy.rb	Thu, 27 Oct 2011 11:03:00 +0200
+lib/workflow-to-galaxy/galaxy.rb	Mon, 16 Jan 2012 14:03:11 +0100
 LICENSE	Tue, 26 Jul 2011 16:35:55 +0200
-README	Thu, 13 Oct 2011 16:23:10 +0200
-CHANGES	Thu, 27 Oct 2011 10:48:55 +0200
+README	Thu, 12 Jan 2012 14:58:21 +0100
+CHANGES	Mon, 16 Jan 2012 16:21:32 +0100

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>0.3.0</p>
+<p>0.3.3</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>
@@ -131,6 +131,8 @@ href="http://semver.org/.">semver.org/.</a></p>
     
     <li class="module"><a href="WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
     
+    <li class="class"><a href="String.html">String</a></li>
+    
   </ul>
 
   <h2 id="methods">Methods</h2>
@@ -140,6 +142,8 @@ href="http://semver.org/.">semver.org/.</a></p>
     
       <li><a href="WorkflowToGalaxy/GalaxyTool.html#method-i-generate">#generate &mdash; WorkflowToGalaxy::GalaxyTool</a></li>
     
+      <li><a href="String.html#method-i-to_filename">#to_filename &mdash; String</a></li>
+    
   </ul>
 
   <div id="validator-badges">

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

@@ -24,7 +24,7 @@
   <div id="metadata">
     <dl>
       <dt class="modified-date">Last Modified</dt>
-      <dd class="modified-date">Thu Oct 27 11:03:00 +0200 2011</dd>
+      <dd class="modified-date">Mon Jan 16 14:03:11 +0100 2012</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">Thu Oct 13 12:51:40 +0200 2011</dd>
+      <dd class="modified-date">Tue Nov 15 15:48:17 +0100 2011</dd>
 
       
       <dt class="requires">Requires</dt>

data/lib/workflow-to-galaxy.rb

@@ -5,3 +5,17 @@ require 'workflow-to-galaxy/constants'
 module WorkflowToGalaxy  # TODO rename to WorkflowWrappers?
     
 end
+
+# Add methods to the String class to operate on file paths.
+class String
+
+  # :call-seq:
+  #   str.to_filename -> string
+  #
+  # Returns a new String with spaces substituted by underscores and
+  # removes all special characters.
+  def to_filename
+    self.gsub(/ /, '_').gsub(/[^A-Za-z0-9_]/, '')
+  end
+
+end

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

@@ -28,6 +28,7 @@ module WorkflowToGalaxy
     #   :url        (the myexperiment workflow URL)
     #   :xml_out    (the file handle for the generated xml -- optional)
     #   :rb_out    (the file handle for the generated rb -- optional)
+    #   :response  (the response from myExperiment if already obtained -- optional)
     #
     # :params     (a hash with the following parameters -- T2FLOW)
     #   :t2flow   (the file name and path)
@@ -54,6 +55,8 @@ module WorkflowToGalaxy
 
     # Galaxy's XML tool tag
     def tool_begin_tag(out, name)
+      # wkf title is used for id but spaces are changed to underscores
+      # TODO: delete other special characters!!
       out.write("<tool id=\"#{name.gsub(/ /, '_')}_id\" name=\"#{name}\">\n")
     end
 
@@ -217,7 +220,10 @@ module WorkflowToGalaxy
           if o.examples.size >= 1
             out.write "Examples include:\n\n"
             o.examples.each do |ex|
-              out.write "  - " + ex.to_s + "\n"
+              # We could substitute them with with &#xA; that works for HTML (e.g. wkf 1180)
+              # But if an example input is truly multiline then input descr. will
+              # display them all as separate inputs...
+              out.write "  - " + ex.to_s.gsub(/[\n]/, '&#xA;  - ') + "\n"
             end
           end
           out.write "\n"
@@ -278,6 +284,7 @@ module WorkflowToGalaxy
 
     # Galaxy's script utility methods
     # TODO: use ruby's flatten instead of our own !!!
+    # TODO: add_to_zip_file does not work for multiple files -- with new API??
     def script_util_methods(out)
 
       out.write <<'UTIL_METHODS'
@@ -574,38 +581,45 @@ START_RUN
     #
     def generate
 
-      # check the type of workflow source and acquire the appropriate data
-      if(config[:wkf_source] == Workflows::MYEXPERIMENT_TAVERNA2)
+      if(config[:params][:response])
 
-        # TODO: check and add auth stuff -- even more unsafe with session cookies
-        # since the myexp username/passwd will be saved in the galaxy ruby script
-        # for all to see...
+        @wkf_object = config[:params][:response]
 
-        begin
-          # Get workflow data from myexperiment -- a _MyExperimentWorkflow_ object is returned
-          @wkf_object = MyExperimentREST::Workflow.from_uri(@config[:params][:url])
-        rescue Exception => e
-          raise "Problem acquiring workflow data from myExperiment!\n" + e
-        end
+      else
 
-      elsif(config[:wkf_source] == Workflows::T2FLOW)
+        # check the type of workflow source and acquire the appropriate data
+        if(config[:wkf_source] == Workflows::MYEXPERIMENT_TAVERNA2)
 
-        begin
-          # Get workflow data from t2flow file -- a _MyExperimentWorkflow_ object is returned
-          @wkf_object = populate_taverna_workflow_from_t2flow(@config[:params][:t2flow])
-        rescue Exception => e
-          raise "Problem acquiring workflow data from t2flow file!\n" + e
-        end
+          # TODO: check and add auth stuff -- even more unsafe with session cookies
+          # since the myexp username/passwd will be saved in the galaxy ruby script
+          # for all to see...
 
-      else
-        raise "No such workflow source supported!"
+          begin
+            # Get workflow data from myexperiment -- a _MyExperimentWorkflow_ object is returned
+            @wkf_object = MyExperimentREST::Workflow.from_uri(@config[:params][:url])
+          rescue Exception => e
+            raise "Problem acquiring workflow data from myExperiment!\n" + e
+          end
+
+        elsif(config[:wkf_source] == Workflows::T2FLOW)
+
+          begin
+            # Get workflow data from t2flow file -- a _MyExperimentWorkflow_ object is returned
+            @wkf_object = populate_taverna_workflow_from_t2flow(@config[:params][:t2flow])
+          rescue Exception => e
+            raise "Problem acquiring workflow data from t2flow file!\n" + e
+          end
+
+        else
+          raise "No such workflow source supported!"
+        end
       end
 
       # if an xml_out file handler was not given provide one with the title as the value
       if @config[:params][:xml_out]
         generate_xml(@wkf_object, @config[:params][:xml_out])
       else
-        xml_out = open(@wkf_object.title.gsub(/ /, '_') + ".xml", "w")
+        xml_out = open(@wkf_object.title.to_filename + ".xml", "w")
         generate_xml(@wkf_object, xml_out)
         xml_out.close
       end
@@ -614,7 +628,7 @@ START_RUN
       if @config[:params][:rb_out]
         generate_rb(@wkf_object, @config[:params][:rb_out], @config[:params][:t2_server])
       else
-        rb_out = open(@wkf_object.title.gsub(/ /, '_') + ".rb", "w")
+        rb_out = open(@wkf_object.title.to_filename + ".rb", "w")
         generate_rb(@wkf_object, rb_out, @config[:params][:t2_server])
         rb_out.close
       end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: workflow-to-galaxy
 version: !ruby/object:Gem::Version 
-  hash: 17
+  hash: 21
   prerelease: 
   segments: 
   - 0
   - 3
-  - 1
-  version: 0.3.1
+  - 3
+  version: 0.3.3
 platform: ruby
 authors: 
 - Kostas Karasavvas
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-10-27 00:00:00 Z
+date: 2012-01-16 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: myexperiment-rest
@@ -97,7 +97,6 @@ files:
 - CHANGES
 - Rakefile
 - bin/workflow_to_galaxy.rb
-- bin/Fetch_PDB_flatfile_from_RCSB_server.xml
 - lib/workflow-to-galaxy/galaxy.rb
 - lib/workflow-to-galaxy/constants.rb
 - lib/workflow-to-galaxy.rb
@@ -122,6 +121,7 @@ files:
 - doc/rdoc/lib/workflow-to-galaxy/constants_rb.html
 - doc/rdoc/created.rid
 - doc/rdoc/CHANGES.html
+- doc/rdoc/String.html
 - doc/rdoc/images/find.png
 - doc/rdoc/images/bug.png
 - doc/rdoc/images/bullet_toggle_minus.png