workflow-to-galaxy 0.2.9 → 0.3.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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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<div id="description" class="description">
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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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class="attribute-access-type">[RW]</span>
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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="attribute-access-type">[RW]</span>
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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="ruby-ivar">@config</span> = <span class="ruby-identifier">config</span>
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<span class="ruby-keyword">end</span></pre>
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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-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-keyword">end</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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