workflow-to-galaxy 0.3.0 → 0.3.1

data/CHANGES

@@ -1,5 +1,10 @@
 = Changes log for the Taverna-Galaxy Gem
 
+== Version 0.3.1
+* Use semver formally... (tag: v0.3.1 semver !!) ????
+* For safety default file names substiture ' ' with '_'
+
+
 == Version 0.3.0
 * Updated to newer myexperiment-rest lib (0.3.0).
 * Restructured, now more modular and extensible.

data/README

@@ -59,3 +59,7 @@ Galaxy::         http://galaxy.psu.edu
 Taverna2::       http://www.taverna.org.uk
 myExperiment::   http://www.myexperiment.org
 
+
+== Semantic Versioning
+
+This module uses semantic versioning concepts from http://semver.org/.

data/Rakefile

@@ -7,7 +7,7 @@ require 'rdoc/task'
 
 spec = Gem::Specification.new do |s|
   s.name = 'workflow-to-galaxy'
-  s.version = '0.3.0'
+  s.version = '0.3.1'
   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

@@ -82,6 +82,13 @@
     
 <h1>Changes log for the Taverna-Galaxy Gem</h1>
 
+<h2>Version 0.3.1</h2>
+<ul><li>
+<p>Use semver formally… (tag: v0.3.1 semver !!) ????</p>
+</li><li>
+<p>For safety default file names substiture ‘ ’ with ‘_’</p>
+</li></ul>
+
 <h2>Version 0.3.0</h2>
 <ul><li>
 <p>Updated to newer myexperiment-rest lib (0.3.0).</p>

data/doc/rdoc/README.html

@@ -157,6 +157,11 @@ href="https://trac.nbic.nl/elabfactory/wiki/eGalaxy">trac.nbic.nl/elabfactory/wi
 <p><a href="http://www.myexperiment.org">www.myexperiment.org</a></p>
 </td></tr></table>
 
+<h2>Semantic Versioning</h2>
+
+<p>This module uses semantic versioning concepts from <a
+href="http://semver.org/.">semver.org/.</a></p>
+
   </div>
 
   <div id="validator-badges">

data/doc/rdoc/WorkflowToGalaxy/GalaxyTool.html

@@ -294,7 +294,7 @@ 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">: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-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">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">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 +303,7 @@ 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-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">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">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/created.rid

@@ -1,7 +1,7 @@
-Thu, 13 Oct 2011 12:56:15 +0200
+Thu, 27 Oct 2011 11:03:06 +0200
 lib/workflow-to-galaxy.rb	Thu, 13 Oct 2011 12:51:40 +0200
 lib/workflow-to-galaxy/constants.rb	Mon, 10 Oct 2011 14:10:32 +0200
-lib/workflow-to-galaxy/galaxy.rb	Thu, 13 Oct 2011 12:47:28 +0200
+lib/workflow-to-galaxy/galaxy.rb	Thu, 27 Oct 2011 11:03:00 +0200
 LICENSE	Tue, 26 Jul 2011 16:35:55 +0200
-README	Tue, 04 Oct 2011 17:25:08 +0200
-CHANGES	Thu, 13 Oct 2011 12:55:19 +0200
+README	Thu, 13 Oct 2011 16:23:10 +0200
+CHANGES	Thu, 27 Oct 2011 10:48:55 +0200

data/doc/rdoc/index.html

@@ -100,6 +100,11 @@ href="https://trac.nbic.nl/elabfactory/wiki/eGalaxy">trac.nbic.nl/elabfactory/wi
 <p><a href="http://www.myexperiment.org">www.myexperiment.org</a></p>
 </td></tr></table>
 
+<h2>Semantic Versioning</h2>
+
+<p>This module uses semantic versioning concepts from <a
+href="http://semver.org/.">semver.org/.</a></p>
+
   </div>
   
 

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

@@ -0,0 +1,58 @@
+<?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: 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">Thu Oct 27 11:03:00 +0200 2011</dd>
+
+      
+      <dt class="requires">Requires</dt>
+      <dd class="requires">
+        <ul>
+        
+          <li>myexperiment-rest</li>
+        
+          <li>t2flow/model.rb</li>
+        
+          <li>t2flow/parser.rb</li>
+        
+        </ul>
+      </dd>
+      
+
+      
+    </dl>
+  </div>
+
+  <div id="documentation">
+    
+    <div class="description">
+      <h2>Description</h2>
+      
+    </div>
+    
+  </div>
+</body>
+</html>
+

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

@@ -54,7 +54,7 @@ module WorkflowToGalaxy
 
     # Galaxy's XML tool tag
     def tool_begin_tag(out, name)
-      out.write("<tool id=\"#{name}_id\" name=\"#{name}\">\n")
+      out.write("<tool id=\"#{name.gsub(/ /, '_')}_id\" name=\"#{name}\">\n")
     end
 
     # Galaxy's XML command tag
@@ -506,7 +506,7 @@ START_RUN
     # Generates the Galaxy tool's xml file responsible for the UI.
     # TODO: maybe clean arguments -- only xml_out is needed to be passed
     def generate_xml(t2_workflow, xml_out)
-      tool_begin_tag(xml_out, xml_out.path.match('([^\/]+)\..*$')[1])
+      tool_begin_tag(xml_out, t2_workflow.title)
       command_tag(xml_out, t2_workflow, xml_out.path.match('([^\/]+)\..*$')[1] + '.rb')
       inputs_tag(xml_out, t2_workflow.inputs)
       outputs_tag(xml_out, t2_workflow.outputs)
@@ -605,7 +605,7 @@ START_RUN
       if @config[:params][:xml_out]
         generate_xml(@wkf_object, @config[:params][:xml_out])
       else
-        xml_out = open(@wkf_object.title + ".xml", "w")
+        xml_out = open(@wkf_object.title.gsub(/ /, '_') + ".xml", "w")
         generate_xml(@wkf_object, xml_out)
         xml_out.close
       end
@@ -614,7 +614,7 @@ 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 + ".rb", "w")
+        rb_out = open(@wkf_object.title.gsub(/ /, '_') + ".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: 19
+  hash: 17
   prerelease: 
   segments: 
   - 0
   - 3
-  - 0
-  version: 0.3.0
+  - 1
+  version: 0.3.1
 platform: ruby
 authors: 
 - Kostas Karasavvas
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-10-13 00:00:00 Z
+date: 2011-10-27 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: myexperiment-rest
@@ -97,6 +97,7 @@ 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
@@ -116,6 +117,7 @@ files:
 - 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/galaxy_rb.html
 - doc/rdoc/lib/workflow-to-galaxy/generator_rb.html
 - doc/rdoc/lib/workflow-to-galaxy/constants_rb.html
 - doc/rdoc/created.rid