workflow-to-galaxy 0.2.9 → 0.3.0
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- data/CHANGES +5 -0
- data/README +1 -1
- data/Rakefile +5 -10
- data/bin/workflow_to_galaxy.rb +58 -65
- data/doc/rdoc/CHANGES.html +10 -3
- data/doc/rdoc/Generator.html +49 -46
- data/doc/rdoc/LICENSE.html +3 -3
- data/doc/rdoc/README.html +4 -4
- data/doc/rdoc/WorkflowToGalaxy.html +33 -3
- data/doc/rdoc/WorkflowToGalaxy/GalaxyTool.html +338 -0
- data/doc/rdoc/WorkflowToGalaxy/Workflows.html +155 -0
- data/doc/rdoc/created.rid +6 -7
- data/doc/rdoc/index.html +6 -6
- data/doc/rdoc/lib/workflow-to-galaxy/constants_rb.html +52 -0
- data/doc/rdoc/lib/workflow-to-galaxy/generator_rb.html +7 -4
- data/doc/rdoc/lib/workflow-to-galaxy_rb.html +4 -2
- data/lib/workflow-to-galaxy.rb +4 -2
- data/lib/workflow-to-galaxy/constants.rb +8 -0
- data/lib/workflow-to-galaxy/galaxy.rb +628 -0
- metadata +22 -20
- data/lib/generator.rb +0 -265
- data/lib/workflow-to-galaxy/generator.rb +0 -511
- data/lib/workflow_to_galaxy.rb +0 -65
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<li><a href="../WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
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<h1 class="class">WorkflowToGalaxy::GalaxyTool</h1>
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<p>The <em><a href="GalaxyTool.html">GalaxyTool</a></em> class contains a
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<tt>generate</tt> public method that generates the required files (XML and
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script) for a Galaxy tool.</p>
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<p><tt>config</tt> contains data needed in relation to what the tool will do
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and <tt><a
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href="GalaxyTool.html#attribute-i-wkf_object">wkf_object</a></tt> contains
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the workflow object that will be used to generate the galaxy tool</p>
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<p><tt>config</tt> contains data needed in relation to what the tool will do
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and <tt><a
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href="GalaxyTool.html#attribute-i-wkf_object">wkf_object</a></tt> contains
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the workflow object that will be used to generate the galaxy tool</p>
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class="method-args">(config)</span>
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<p>-</p>
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<pre>TODO: does initialize appear in rdoc? -- these will go to README as well...</pre>
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<pre>
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<span class="ruby-comment"># File lib/workflow-to-galaxy/galaxy.rb, line 39</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">config</span>)
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<span class="method-callseq">generate() → nil</span>
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<div class="method-description">
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<p>Generates the two files needed for a Galaxy tool: a configuration file
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(XML) and a processing file (in our case a ruby script)</p>
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<pre>
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<span class="ruby-comment"># File lib/workflow-to-galaxy/galaxy.rb, line 575</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">generate</span>
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<span class="ruby-comment"># check the type of workflow source and acquire the appropriate data</span>
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<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>)
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<span class="ruby-comment"># TODO: check and add auth stuff -- even more unsafe with session cookies</span>
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<span class="ruby-comment"># since the myexp username/passwd will be saved in the galaxy ruby script</span>
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<span class="ruby-comment"># for all to see...</span>
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<span class="ruby-keyword">begin</span>
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<span class="ruby-comment"># Get workflow data from myexperiment -- a _MyExperimentWorkflow_ object is returned</span>
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<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>])
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<span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">e</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-string">"Problem acquiring workflow data from myExperiment!\n"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">e</span>
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<span class="ruby-keyword">end</span>
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<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>)
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<span class="ruby-keyword">begin</span>
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<span class="ruby-comment"># Get workflow data from t2flow file -- a _MyExperimentWorkflow_ object is returned</span>
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<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>])
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<span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">e</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-string">"Problem acquiring workflow data from t2flow file!\n"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">e</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-string">"No such workflow source supported!"</span>
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<span class="ruby-comment"># if an xml_out file handler was not given provide one with the title as the value</span>
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