workflow-to-galaxy 0.2.8 → 0.2.9
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- data/CHANGES +5 -0
- data/README +1 -1
- data/Rakefile +1 -1
- data/doc/rdoc/CHANGES.html +9 -0
- data/doc/rdoc/Generator.html +46 -49
- data/doc/rdoc/LICENSE.html +2 -0
- data/doc/rdoc/Object.html +161 -0
- data/doc/rdoc/README.html +3 -1
- data/doc/rdoc/WorkflowToGalaxy.html +2 -0
- data/doc/rdoc/created.rid +8 -6
- data/doc/rdoc/index.html +3 -1
- data/doc/rdoc/lib/generator_rb.html +54 -0
- data/doc/rdoc/lib/workflow-to-galaxy/generator_rb.html +1 -1
- data/doc/rdoc/lib/workflow-to-galaxy_rb.html +1 -1
- data/doc/rdoc/lib/workflow_to_galaxy_rb.html +60 -0
- data/lib/generator.rb +265 -0
- data/lib/workflow-to-galaxy/generator.rb +31 -17
- data/lib/workflow_to_galaxy.rb +65 -0
- metadata +9 -4
data/CHANGES
CHANGED
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= Changes log for the Taverna-Galaxy Gem
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== Version 0.2.9
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* Fixed minor bug when workflow had empty description
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* Added instructions to generated scripts on how to run them without Galaxy.
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== Version 0.2.8
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* Clean up of documentation
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* Added rubyzip dependency to gemspec
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data/README
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Authors:: Konstantinos Karasavvas
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Gem Version:: 0.2.
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Gem Version:: 0.2.9
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Contact:: mailto:kostas.karasavvas@nbic.nl
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Licence:: MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
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Copyright:: (c) 2010 Netherlands Bioinformatics Centre, The Netherlands
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data/Rakefile
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spec = Gem::Specification.new do |s|
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s.name = 'workflow-to-galaxy'
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s.version = '0.2.
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s.version = '0.2.9'
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s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
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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).'
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s.description = s.summary
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data/doc/rdoc/CHANGES.html
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<li><a href="./Generator.html">Generator</a></li>
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<li><a href="./Object.html">Object</a></li>
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<li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
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</ul>
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<h1>Changes log for the Taverna-Galaxy Gem</h1>
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<h2>Version 0.2.9</h2>
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<ul><li>
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<p>Fixed minor bug when workflow had empty description</p>
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</li><li>
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<p>Added instructions to generated scripts on how to run them without Galaxy.</p>
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</li></ul>
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+
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<h2>Version 0.2.8</h2>
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<ul><li>
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<p>Clean up of documentation</p>
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data/doc/rdoc/Generator.html
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<div class="section-body">
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<ul>
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<li><a href="./lib/generator_rb.html?TB_iframe=true&height=550&width=785"
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class="thickbox" title="lib/generator.rb">lib/generator.rb</a></li>
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<li><a href="./lib/workflow-to-galaxy/generator_rb.html?TB_iframe=true&height=550&width=785"
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class="thickbox" title="lib/workflow-to-galaxy/generator.rb">lib/workflow-to-galaxy/generator.rb</a></li>
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<li><a href="./Generator.html">Generator</a></li>
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<li><a href="./Object.html">Object</a></li>
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<li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
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</ul>
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<div id="description" class="description">
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<p>Contains code to generate the Galaxy’s tool xml and script files</p>
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<hr style="height: 1px">
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<p>The <a href="Generator.html">Generator</a> module contains two public
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methods that generate a Galaxy’s tool XML and script files</p>
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<!-- Constants -->
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<div id="constants-list" class="section">
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<h3 class="section-header">Constants</h3>
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<dl>
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<dt><a name="INDENT">INDENT</a></dt>
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<dd class="description"></dd>
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</dl>
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</div>
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@@ -142,45 +163,33 @@ methods that generate a Galaxy’s tool XML and script files</p>
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<a name="method-i-generate_script"></a>
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-
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<div class="method-heading">
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<span class="method-
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<span class="method-name">generate_script</span><span
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class="method-args">(me_rest, t2_server, script_file)</span>
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<span class="method-click-advice">click to toggle source</span>
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</div>
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<div class="method-description">
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<p>Generates the Galaxy tool’s script file responsible for talking to the
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taverna server</p>
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<dl class="rdoc-list"><dt><tt>my_exp_rest</tt></dt>
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<dd>
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<p>a <em>Workflow</em> object as returned from
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<em>MyExperimentREST.ReadWorkflow.new(url)</em></p>
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</dd><dt><tt>t2_server</tt></dt>
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<dd>
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<p>a string containing the URL of the taverna 2 server</p>
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</dd><dt><tt>script_out</tt></dt>
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<dd>
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<p>the file handler to write the generated script code</p>
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</dd></dl>
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<div class="method-source-code" id="generate_script-source">
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<pre>
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<span class="ruby-comment"># File lib/
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">generate_script</span>(<span class="ruby-identifier">
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<span class="ruby-identifier">
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<span class="ruby-identifier">
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<span class="ruby-identifier">
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<span class="ruby-identifier">
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<span class="ruby-identifier">
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<span class="ruby-identifier">
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<span class="ruby-identifier">
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<span class="ruby-comment"># File lib/generator.rb, line 253</span>
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<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>)
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<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">"w"</span>)
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<span class="ruby-identifier">script_preample</span>(<span class="ruby-identifier">out</span>)
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<span class="ruby-identifier">script_util_methods</span>(<span class="ruby-identifier">out</span>)
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<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>)
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<span class="ruby-identifier">script_init_inputs</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>)
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<span class="ruby-identifier">script_start_run</span>(<span class="ruby-identifier">out</span>)
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<span class="ruby-identifier">script_get_outputs</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>)
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<span class="ruby-identifier">script_finish_run</span>(<span class="ruby-identifier">out</span>)
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<span class="ruby-identifier">out</span>.<span class="ruby-identifier">close</span>
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<span class="ruby-keyword">end</span></pre>
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</div><!-- generate_script-source -->
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<a name="method-i-generate_xml"></a>
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<div class="method-heading">
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<span class="method-
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<span class="method-name">generate_xml</span><span
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class="method-args">(me_rest, xml_file)</span>
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<span class="method-click-advice">click to toggle source</span>
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</div>
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<div class="method-description">
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<p>Generates the Galaxy tool’s xml file responsible for the UI.</p>
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<dl class="rdoc-list"><dt><tt>t2_workflow</tt></dt>
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<dd>
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<p>a <em>Workflow</em> object as returned from
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<em>MyExperimentREST::Workflows.new.read(url)</em></p>
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</dd><dt><tt>xml_file</tt></dt>
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<dd>
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<p>a string containing the name of the generated XML file</p>
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</dd><dt><tt>xml_out</tt></dt>
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<dd>
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<p>the file handler to write the generated XML tags</p>
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</dd></dl>
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<div class="method-source-code" id="generate_xml-source">
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<pre>
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<span class="ruby-comment"># File lib/
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">generate_xml</span>(<span class="ruby-identifier">
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<span class="ruby-identifier">
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<span class="ruby-comment"># File lib/generator.rb, line 238</span>
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<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>)
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<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">"w"</span>)
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<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>)
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<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>))
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<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>)
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<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>)
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<span class="ruby-identifier">help_be</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>)
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<span class="ruby-identifier">tool_e</span>(<span class="ruby-identifier">out</span>)
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<span class="ruby-identifier">out</span>.<span class="ruby-identifier">close</span>
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<span class="ruby-keyword">end</span></pre>
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</div><!-- generate_xml-source -->
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data/doc/rdoc/LICENSE.html
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<head>
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<meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
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<title>Class: Object</title>
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<link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
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<script src="./js/jquery.js" type="text/javascript" charset="utf-8"></script>
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<script src="./js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
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<script src="./js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
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<script src="./js/darkfish.js" type="text/javascript" charset="utf-8"></script>
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</head>
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<body id="top" class="class">
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<div id="metadata">
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<div id="home-metadata">
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<div id="home-section" class="section">
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<h3 class="section-header">
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<a href="./index.html">Home</a>
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<a href="./index.html#classes">Classes</a>
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<a href="./index.html#methods">Methods</a>
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</h3>
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</div>
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</div>
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<div id="file-metadata">
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<div id="file-list-section" class="section">
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<h3 class="section-header">In Files</h3>
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<div class="section-body">
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<ul>
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<li><a href="./lib/workflow_to_galaxy_rb.html?TB_iframe=true&height=550&width=785"
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class="thickbox" title="lib/workflow_to_galaxy.rb">lib/workflow_to_galaxy.rb</a></li>
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</ul>
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</div>
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</div>
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</div>
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<div id="class-metadata">
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<!-- Parent Class -->
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<div id="parent-class-section" class="section">
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<h3 class="section-header">Parent</h3>
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<p class="link"></p>
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</div>
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<!-- Included Modules -->
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<div id="includes-section" class="section">
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<h3 class="section-header">Included Modules</h3>
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<ul class="link-list">
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<li><span class="include">MyExperimentREST</span></li>
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<li><a class="include" href="Generator.html">Generator</a></li>
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</ul>
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</div>
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</div>
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<div id="project-metadata">
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<div id="fileindex-section" class="section project-section">
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<h3 class="section-header">Files</h3>
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<ul>
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<li class="file"><a href="./CHANGES.html">CHANGES</a></li>
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<li class="file"><a href="./LICENSE.html">LICENSE</a></li>
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<li class="file"><a href="./README.html">README</a></li>
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</ul>
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</div>
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<div id="classindex-section" class="section project-section">
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<h3 class="section-header">Class/Module Index
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<span class="search-toggle"><img src="./images/find.png"
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height="16" width="16" alt="[+]"
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title="show/hide quicksearch" /></span></h3>
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<p>Contains code to generate the Galaxy’s tool xml and script files</p>
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<ul>
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<li>rubygems</li>
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<li>optparse</li>
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<li>myexperiment-rest</li>
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<li>generator</li>
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</ul>
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data/lib/generator.rb
ADDED
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|
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|
+
|
2
|
+
# Contains code to generate the Galaxy's tool xml and script files
|
3
|
+
module Generator
|
4
|
+
|
5
|
+
INDENT = " "
|
6
|
+
|
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|
+
|
8
|
+
# private methods
|
9
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private
|
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def tool_b(out, name)
|
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+
out.write("<tool id=\"#{name}_id\" name=\"#{name}\">\n")
|
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+
end
|
14
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|
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def command_be(out, me_rest, script)
|
16
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out.write "#{INDENT}<command interpreter=\"ruby\">"
|
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out.write script + " "
|
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+
me_rest.workflow.inputs.each do |i|
|
19
|
+
out.write "\"$#{i.name}\" "
|
20
|
+
end
|
21
|
+
me_rest.workflow.outputs.each do |o|
|
22
|
+
out.write "$#{o.name} "
|
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|
+
end
|
24
|
+
out.write "</command>\n"
|
25
|
+
end
|
26
|
+
|
27
|
+
def inputs_be(out, inputs)
|
28
|
+
out.write "#{INDENT}<inputs>\n"
|
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|
+
if inputs.size >= 1
|
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|
+
inputs.each do |i|
|
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|
+
2.times { out.write "#{INDENT}" }
|
32
|
+
out.write "<param name=\"#{i.name}\" type=\"text\" size=\"30\" "
|
33
|
+
if i.examples.size >= 1
|
34
|
+
# escape double quotes characters for galaxy's xml file
|
35
|
+
ex = i.examples[0].to_s.gsub('"', '"')
|
36
|
+
out.write "value=\"#{ex}\" "
|
37
|
+
end
|
38
|
+
out.write "label=\"Enter #{i.name}\"/>\n"
|
39
|
+
end
|
40
|
+
else
|
41
|
+
2.times { out.write "#{INDENT}" }
|
42
|
+
out.write "<param name=\"input\" type=\"select\" display=\"radio\" size=\"250\" label=\"This workflow has no inputs\" />\n"
|
43
|
+
end
|
44
|
+
out.write "#{INDENT}</inputs>\n"
|
45
|
+
end
|
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|
+
|
47
|
+
def outputs_be(out, outputs)
|
48
|
+
out.write "#{INDENT}<outputs>\n"
|
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|
+
outputs.each do |o|
|
50
|
+
2.times { out.write "#{INDENT}" }
|
51
|
+
out.write "<data format=\"tabular\" name=\"#{o.name}\" label=\"#{o.name}\"/>\n"
|
52
|
+
end
|
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|
+
out.write "#{INDENT}</outputs>\n"
|
54
|
+
end
|
55
|
+
|
56
|
+
def help_be(out, me_rest)
|
57
|
+
out.write "#{INDENT}<help>\n"
|
58
|
+
out.write "**What it does**\n\n"
|
59
|
+
|
60
|
+
# Sometimes the workflow description contains HTML tags that are not allowed
|
61
|
+
# in Galaxy's xml interface specification and thus are removed! Same for
|
62
|
+
# HTML entities!
|
63
|
+
out.write me_rest.workflow.description.gsub(/<.*?>|&.*?;/, '') + "\n\n"
|
64
|
+
|
65
|
+
if me_rest.workflow.inputs.size >= 1
|
66
|
+
out.write "-----\n\n"
|
67
|
+
out.write "**Inputs**\n\n"
|
68
|
+
me_rest.workflow.inputs.each do |i|
|
69
|
+
out.write "- **#{i.name}** "
|
70
|
+
if i.descriptions.size >= 1
|
71
|
+
i.descriptions.each do |desc|
|
72
|
+
out.write desc.to_s + " "
|
73
|
+
end
|
74
|
+
end
|
75
|
+
if i.examples.size >= 1
|
76
|
+
out.write "Examples include:\n\n"
|
77
|
+
i.examples.each do |ex|
|
78
|
+
out.write " - " + ex.to_s + "\n"
|
79
|
+
end
|
80
|
+
end
|
81
|
+
out.write "\n"
|
82
|
+
end
|
83
|
+
out.write "\n"
|
84
|
+
end
|
85
|
+
|
86
|
+
# TODO this code is identical to the inputs code above -- method?
|
87
|
+
if me_rest.workflow.outputs.size >= 1
|
88
|
+
out.write "-----\n\n"
|
89
|
+
out.write "**Outputs**\n\n"
|
90
|
+
me_rest.workflow.outputs.each do |o|
|
91
|
+
out.write "- **#{o.name}** "
|
92
|
+
if o.descriptions.size >= 1
|
93
|
+
o.descriptions.each do |desc|
|
94
|
+
out.write desc.to_s + " "
|
95
|
+
end
|
96
|
+
end
|
97
|
+
if o.examples.size >= 1
|
98
|
+
out.write "Examples include:\n\n"
|
99
|
+
o.examples.each do |ex|
|
100
|
+
out.write " - " + ex.to_s + "\n"
|
101
|
+
end
|
102
|
+
end
|
103
|
+
out.write "\n"
|
104
|
+
end
|
105
|
+
out.write "\n"
|
106
|
+
end
|
107
|
+
|
108
|
+
|
109
|
+
out.write "-----\n\n"
|
110
|
+
out.write "For more information on that workflow please visit #{me_rest.uri.gsub(/(.*workflows\/\d+)[\/.].*/, '\1')}.\n"
|
111
|
+
|
112
|
+
out.write "#{INDENT}</help>\n"
|
113
|
+
end
|
114
|
+
|
115
|
+
def tool_e(out)
|
116
|
+
out.write("</tool>\n")
|
117
|
+
end
|
118
|
+
|
119
|
+
|
120
|
+
|
121
|
+
|
122
|
+
def script_preample(out)
|
123
|
+
out.write("#!/usr/bin/env ruby\n\n")
|
124
|
+
out.write("require 'rubygems'\n")
|
125
|
+
out.write("require 't2-server'\n")
|
126
|
+
out.write("require 'open-uri'\n\n")
|
127
|
+
end
|
128
|
+
|
129
|
+
def script_util_methods(out)
|
130
|
+
|
131
|
+
out.write <<UTIL_METHODS
|
132
|
+
|
133
|
+
# method that flattens the list of list of list ... result of get_output
|
134
|
+
def print_flattened_result(out, data_lists)
|
135
|
+
data_lists.each do |l|
|
136
|
+
if l.instance_of? Array
|
137
|
+
print_flattened_result(out, l)
|
138
|
+
else
|
139
|
+
out.puts l
|
140
|
+
end
|
141
|
+
end
|
142
|
+
end
|
143
|
+
|
144
|
+
|
145
|
+
# method that acquires all the results of the specified output
|
146
|
+
def get_outputs(run, refs, outfile, dir)
|
147
|
+
data_lists = run.get_output(dir, refs)
|
148
|
+
print_flattened_result(outfile, data_lists)
|
149
|
+
end
|
150
|
+
|
151
|
+
|
152
|
+
#
|
153
|
+
# Sanitize single and double quotes in str. E.g. galaxy substitures them to
|
154
|
+
# __sq__ and __dq__ respectively. This methods turns them back to their
|
155
|
+
# original values before using them
|
156
|
+
#
|
157
|
+
def sanitize(string)
|
158
|
+
string.gsub(/(__sq__|__dq__|__at__)/) do
|
159
|
+
if $1 == '__sq__'
|
160
|
+
"'"
|
161
|
+
elsif $1 == '__dq__'
|
162
|
+
'\\\"'
|
163
|
+
else
|
164
|
+
'@'
|
165
|
+
end
|
166
|
+
end
|
167
|
+
end
|
168
|
+
|
169
|
+
UTIL_METHODS
|
170
|
+
|
171
|
+
end
|
172
|
+
|
173
|
+
|
174
|
+
def script_create_t2_run(out, wkf_uri, t2_uri)
|
175
|
+
out.write <<CREATE_T2_RUN
|
176
|
+
|
177
|
+
# use the uri reference to download the workflow locally
|
178
|
+
wkf_file = URI.parse('#{wkf_uri}')
|
179
|
+
in_wkf = open(wkf_file)
|
180
|
+
wkf = in_wkf.read()
|
181
|
+
|
182
|
+
# create run
|
183
|
+
begin
|
184
|
+
run = T2Server::Run.create('#{t2_uri}', wkf)
|
185
|
+
rescue T2Server::T2ServerError => e
|
186
|
+
exit 1
|
187
|
+
end
|
188
|
+
|
189
|
+
CREATE_T2_RUN
|
190
|
+
|
191
|
+
end
|
192
|
+
|
193
|
+
|
194
|
+
def script_init_inputs(out, me_rest)
|
195
|
+
out.write "# get input arguments\n"
|
196
|
+
0.upto(me_rest.workflow.inputs.size-1) do |i|
|
197
|
+
out.write "input#{i}_arg = ARGV[#{i}].chomp\n"
|
198
|
+
out.write "run.set_input('" + me_rest.workflow.inputs[i].name.to_s + "', sanitize(input#{i}_arg))\n"
|
199
|
+
end
|
200
|
+
|
201
|
+
end
|
202
|
+
|
203
|
+
|
204
|
+
def script_start_run(out)
|
205
|
+
out.write <<START_RUN
|
206
|
+
|
207
|
+
# start run and wait until it is finished
|
208
|
+
run.start
|
209
|
+
run.wait(:progress => true)
|
210
|
+
|
211
|
+
START_RUN
|
212
|
+
end
|
213
|
+
|
214
|
+
|
215
|
+
def script_get_outputs(out, me_rest)
|
216
|
+
outputs_start_index = me_rest.workflow.inputs.size
|
217
|
+
outputs_end_index = outputs_start_index + me_rest.workflow.outputs.size - 1
|
218
|
+
out.write "# get output arguments and associated them with a file\n"
|
219
|
+
outputs_start_index.upto(outputs_end_index) do |o|
|
220
|
+
out.write "output#{o} = File.open(ARGV[#{o}], \"w\")\n"
|
221
|
+
out.write "get_outputs(run, false, output#{o}, '" + me_rest.workflow.outputs[o - outputs_start_index].name.to_s + "')\n"
|
222
|
+
end
|
223
|
+
|
224
|
+
end
|
225
|
+
|
226
|
+
|
227
|
+
def script_finish_run(out)
|
228
|
+
out.write "\n# delete run\n"
|
229
|
+
out.write "run.delete\n"
|
230
|
+
end
|
231
|
+
|
232
|
+
|
233
|
+
|
234
|
+
# public methods from here onwards
|
235
|
+
public
|
236
|
+
|
237
|
+
# Generates the Galaxy tool's xml file responsible for the UI.
|
238
|
+
def generate_xml(me_rest, xml_file)
|
239
|
+
out = File.open(xml_file, "w")
|
240
|
+
tool_b(out, me_rest.workflow.title)
|
241
|
+
command_be(out, me_rest, xml_file.gsub('.xml', '.rb'))
|
242
|
+
inputs_be(out, me_rest.workflow.inputs)
|
243
|
+
outputs_be(out, me_rest.workflow.outputs)
|
244
|
+
help_be(out, me_rest)
|
245
|
+
tool_e(out)
|
246
|
+
out.close
|
247
|
+
end
|
248
|
+
|
249
|
+
#
|
250
|
+
# Generates the Galaxy tool's script file responsible for talking to the
|
251
|
+
# taverna server
|
252
|
+
#
|
253
|
+
def generate_script(me_rest, t2_server, script_file)
|
254
|
+
out = File.open(script_file, "w")
|
255
|
+
script_preample(out)
|
256
|
+
script_util_methods(out)
|
257
|
+
script_create_t2_run(out, me_rest.uri, t2_server)
|
258
|
+
script_init_inputs(out, me_rest)
|
259
|
+
script_start_run(out)
|
260
|
+
script_get_outputs(out, me_rest)
|
261
|
+
script_finish_run(out)
|
262
|
+
out.close
|
263
|
+
end
|
264
|
+
|
265
|
+
end
|
@@ -1,7 +1,8 @@
|
|
1
1
|
#
|
2
2
|
# The Generator module contains two public methods that generate a Galaxy's tool
|
3
3
|
# XML and script files
|
4
|
-
|
4
|
+
#--
|
5
|
+
# Add appropriate requires here. Currently they are all in the executable!
|
5
6
|
module Generator
|
6
7
|
|
7
8
|
# private methods
|
@@ -106,27 +107,30 @@ module Generator
|
|
106
107
|
# Galaxy's XML help tag
|
107
108
|
def help_tag(out, t2_workflow)
|
108
109
|
out.write indent(1) + "<help>\n"
|
109
|
-
out.write "**What it does**\n\n"
|
110
110
|
|
111
|
-
|
111
|
+
if t2_workflow.description
|
112
|
+
out.write "**What it does**\n\n"
|
112
113
|
|
113
|
-
|
114
|
-
# in Galaxy's xml interface specification and thus are removed! Same for
|
115
|
-
# HTML entities!
|
116
|
-
# TODO go through tags and find Galaxy's equivalent to include
|
117
|
-
description.gsub!(/<.*?>|&.*?;/, '')
|
114
|
+
description = t2_workflow.description + "\n\n"
|
118
115
|
|
119
|
-
|
120
|
-
|
121
|
-
|
122
|
-
|
123
|
-
|
116
|
+
# Sometimes the workflow description contains HTML tags that are not allowed
|
117
|
+
# in Galaxy's xml interface specification and thus are removed! Same for
|
118
|
+
# HTML entities!
|
119
|
+
# TODO go through tags and find Galaxy's equivalent to include
|
120
|
+
description.gsub!(/<.*?>|&.*?;/, '')
|
121
|
+
|
122
|
+
# To remove ^M (cntl-v + cntl-m) characters that DOS files might have
|
123
|
+
description.gsub!(/\r/, '')
|
124
|
+
|
125
|
+
# TODO that works as a literal too but font changes to courier!
|
126
|
+
#out.write "::\n\n" # Start Galaxy's literal block to ignore indendation
|
124
127
|
|
125
|
-
|
126
|
-
|
128
|
+
# remove indendation from all description lines since Galaxy is confused by it
|
129
|
+
description.split(/[\n]/).each { |l| out.write "#{l.gsub(/^\s+/, '')}\n" }
|
127
130
|
|
128
|
-
|
129
|
-
|
131
|
+
# endline makes the following be parsed as a Galaxy GUI construct
|
132
|
+
out.write "\n"
|
133
|
+
end
|
130
134
|
|
131
135
|
# if at least one input add it to tool's UI help description
|
132
136
|
if t2_workflow.inputs.size >= 1
|
@@ -218,6 +222,16 @@ module Generator
|
|
218
222
|
# Galaxy's script preample
|
219
223
|
def script_preample(out)
|
220
224
|
out.write("#!/usr/bin/env ruby\n\n")
|
225
|
+
|
226
|
+
out.write("# This script can be tested without Galaxy. You can run from the shell as follows:\n#\n")
|
227
|
+
out.write("# $ script_name.rb <input1> true|false <input2> true|false yes|no <output1> <output2>\n#\n")
|
228
|
+
out.write("# After each input value a boolean specifies if the value is literal (false) or if\n")
|
229
|
+
out.write("# it specifies a file name to read as input.\n#\n")
|
230
|
+
out.write("# After all workflow inputs a yes or no input specifies if we also want our results zipped.\n#\n")
|
231
|
+
out.write("# Finally, all the output files follow. Note that if you selected to also get a zip\n")
|
232
|
+
out.write("# then you need to specify an additional output in the end after the normal workflow\n")
|
233
|
+
out.write("# outputs.\n\n")
|
234
|
+
|
221
235
|
out.write("require 'rubygems'\n")
|
222
236
|
out.write("require 't2-server'\n")
|
223
237
|
out.write("require 'open-uri'\n")
|
@@ -0,0 +1,65 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
|
3
|
+
require 'rubygems'
|
4
|
+
require 'optparse'
|
5
|
+
require 'myexperiment-rest'
|
6
|
+
require 'generator'
|
7
|
+
|
8
|
+
include MyExperimentREST
|
9
|
+
include Generator
|
10
|
+
|
11
|
+
|
12
|
+
# Set up and parse arguments
|
13
|
+
out_file = ""
|
14
|
+
t2_server = ""
|
15
|
+
opts = OptionParser.new do |opt|
|
16
|
+
opt.banner = "Usage: workflow_to_galaxy [options] <myExperiement-workflow>"
|
17
|
+
opt.separator ""
|
18
|
+
opt.separator "Generates a Galaxy tool (a UI xml definition plus a script) for the "
|
19
|
+
opt.separator "specified Taverna2 workflow, where <myExperiment-workflow> is "
|
20
|
+
opt.separator "the full URL of the workflow in the myExperiment website. Available "
|
21
|
+
opt.separator "options are:"
|
22
|
+
|
23
|
+
opt.on("-o OUTPUT", "--output=OUTPUT", "The file name(s) of the generated tool. " +
|
24
|
+
"If it is not specified then the workflow's name will be used.") do |val|
|
25
|
+
out_file = val if val != nil
|
26
|
+
end
|
27
|
+
|
28
|
+
opt.on("-s SERVER", "--server=SERVER", "The taverna server that the script will request execution from. " +
|
29
|
+
"If it is not specified then 'http://localhost:8980/taverna-server' will be used.") do |val|
|
30
|
+
t2_server = val if val != nil
|
31
|
+
end
|
32
|
+
end
|
33
|
+
|
34
|
+
opts.parse!
|
35
|
+
|
36
|
+
# Read and check workflow URL
|
37
|
+
url = ARGV.shift
|
38
|
+
if url == nil
|
39
|
+
puts opts
|
40
|
+
exit 1
|
41
|
+
end
|
42
|
+
|
43
|
+
# Get workflow data from myexperiment
|
44
|
+
me_rest = ReadWorkflow.new(url)
|
45
|
+
|
46
|
+
# Set output files
|
47
|
+
if out_file != ""
|
48
|
+
xml_file = "#{out_file}.xml"
|
49
|
+
script_file = "#{out_file}.rb"
|
50
|
+
else
|
51
|
+
xml_file = "#{me_rest.workflow.title}".gsub(/\W/, '') + ".xml"
|
52
|
+
script_file = "#{me_rest.workflow.title}".gsub(/\W/, '') + ".rb"
|
53
|
+
end
|
54
|
+
|
55
|
+
# Set taverna server
|
56
|
+
if t2_server == ""
|
57
|
+
t2_server = "http://localhost:8980/taverna-server"
|
58
|
+
end
|
59
|
+
|
60
|
+
|
61
|
+
|
62
|
+
generate_xml(me_rest, xml_file)
|
63
|
+
generate_script(me_rest, t2_server, script_file)
|
64
|
+
|
65
|
+
|
metadata
CHANGED
@@ -1,13 +1,13 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: workflow-to-galaxy
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
hash:
|
4
|
+
hash: 5
|
5
5
|
prerelease:
|
6
6
|
segments:
|
7
7
|
- 0
|
8
8
|
- 2
|
9
|
-
-
|
10
|
-
version: 0.2.
|
9
|
+
- 9
|
10
|
+
version: 0.2.9
|
11
11
|
platform: ruby
|
12
12
|
authors:
|
13
13
|
- Kostas Karasavvas
|
@@ -15,7 +15,7 @@ autorequire:
|
|
15
15
|
bindir: bin
|
16
16
|
cert_chain: []
|
17
17
|
|
18
|
-
date: 2011-07-
|
18
|
+
date: 2011-07-26 00:00:00 Z
|
19
19
|
dependencies:
|
20
20
|
- !ruby/object:Gem::Dependency
|
21
21
|
name: myexperiment-rest
|
@@ -97,6 +97,8 @@ files:
|
|
97
97
|
- CHANGES
|
98
98
|
- Rakefile
|
99
99
|
- bin/workflow_to_galaxy.rb
|
100
|
+
- lib/workflow_to_galaxy.rb
|
101
|
+
- lib/generator.rb
|
100
102
|
- lib/workflow-to-galaxy/generator.rb
|
101
103
|
- lib/workflow-to-galaxy.rb
|
102
104
|
- doc/rdoc/WorkflowToGalaxy.html
|
@@ -109,7 +111,10 @@ files:
|
|
109
111
|
- doc/rdoc/js/darkfish.js
|
110
112
|
- doc/rdoc/js/quicksearch.js
|
111
113
|
- doc/rdoc/README.html
|
114
|
+
- doc/rdoc/Object.html
|
115
|
+
- doc/rdoc/lib/workflow_to_galaxy_rb.html
|
112
116
|
- doc/rdoc/lib/workflow-to-galaxy_rb.html
|
117
|
+
- doc/rdoc/lib/generator_rb.html
|
113
118
|
- doc/rdoc/lib/workflow-to-galaxy/generator_rb.html
|
114
119
|
- doc/rdoc/created.rid
|
115
120
|
- doc/rdoc/CHANGES.html
|