myexperiment-rest 0.2.6
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 +9 -0
- data/LICENSE +23 -0
- data/README +33 -0
- data/Rakefile +45 -0
- data/bin/get_workflow_data.rb +31 -0
- data/doc/classes/MyExperimentREST.html +113 -0
- data/doc/classes/MyExperimentREST/IOData.html +169 -0
- data/doc/classes/MyExperimentREST/IOData.src/M000003.html +20 -0
- data/doc/classes/MyExperimentREST/ReadWorkflow.html +184 -0
- data/doc/classes/MyExperimentREST/ReadWorkflow.src/M000002.html +39 -0
- data/doc/classes/MyExperimentREST/ReadWorkflow.src/M000005.html +41 -0
- data/doc/classes/MyExperimentREST/TavernaIOData.html +167 -0
- data/doc/classes/MyExperimentREST/TavernaIOData.src/M000006.html +20 -0
- data/doc/classes/MyExperimentREST/TavernaIOData.src/M000007.html +20 -0
- data/doc/classes/MyExperimentREST/TavernaWorkflow.html +209 -0
- data/doc/classes/MyExperimentREST/TavernaWorkflow.src/M000005.html +23 -0
- data/doc/classes/MyExperimentREST/TavernaWorkflow.src/M000006.html +22 -0
- data/doc/classes/MyExperimentREST/Workflow.html +172 -0
- data/doc/classes/MyExperimentREST/Workflow.src/M000001.html +21 -0
- data/doc/classes/MyExperimentREST/Workflows.html +167 -0
- data/doc/classes/MyExperimentREST/Workflows.src/M000004.html +41 -0
- data/doc/classes/TestReadWorkflow.html +167 -0
- data/doc/classes/TestReadWorkflow.src/M000001.html +18 -0
- data/doc/classes/TestReadWorkflow.src/M000002.html +24 -0
- data/doc/classes/TestReadWorkflow.src/M000003.html +20 -0
- data/doc/classes/TestReadWorkflow.src/M000004.html +20 -0
- data/doc/created.rid +1 -0
- data/doc/files/bin/get_workflow_data_rb.html +116 -0
- data/doc/files/lib/myexperiment-rest/my_experiment_rest_rb.html +110 -0
- data/doc/files/lib/myexperiment-rest/myexperiment_rest_rb.html +110 -0
- data/doc/files/lib/myexperiment-rest_rb.html +108 -0
- data/doc/files/test/test_read_workflow_rb.html +122 -0
- data/doc/fr_class_index.html +31 -0
- data/doc/fr_file_index.html +29 -0
- data/doc/fr_method_index.html +32 -0
- data/doc/index.html +24 -0
- data/doc/rdoc-style.css +208 -0
- data/doc/rdoc/classes/MyExperimentREST.html +117 -0
- data/doc/rdoc/classes/MyExperimentREST/TavernaIOData.html +178 -0
- data/doc/rdoc/classes/MyExperimentREST/TavernaWorkflow.html +223 -0
- data/doc/rdoc/classes/MyExperimentREST/Workflows.html +199 -0
- data/doc/rdoc/created.rid +1 -0
- data/doc/rdoc/files/CHANGES.html +121 -0
- data/doc/rdoc/files/LICENSE.html +133 -0
- data/doc/rdoc/files/README.html +148 -0
- data/doc/rdoc/files/lib/myexperiment-rest/myexperiment_rest_rb.html +110 -0
- data/doc/rdoc/files/lib/myexperiment-rest_rb.html +108 -0
- data/doc/rdoc/fr_class_index.html +30 -0
- data/doc/rdoc/fr_file_index.html +31 -0
- data/doc/rdoc/fr_method_index.html +29 -0
- data/doc/rdoc/index.html +24 -0
- data/doc/rdoc/rdoc-style.css +208 -0
- data/lib/myexperiment-rest.rb +5 -0
- data/lib/myexperiment-rest/myexperiment_rest.rb +146 -0
- metadata +133 -0
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<title>new (MyExperimentREST::Workflow)</title>
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<pre><span class="ruby-comment cmt"># File lib/myexperiment-rest/my_experiment_rest.rb, line 97</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">title</span>, <span class="ruby-identifier">description</span>, <span class="ruby-identifier">inputs</span>, <span class="ruby-identifier">outputs</span>)
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<span class="ruby-ivar">@outputs</span> = <span class="ruby-identifier">outputs</span>
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<title>Class: MyExperimentREST::Workflows</title>
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<td><strong>Class</strong></td>
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<td class="class-name-in-header">MyExperimentREST::Workflows</td>
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</tr>
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<td><strong>In:</strong></td>
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<td>
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<a href="../../files/lib/myexperiment-rest/myexperiment_rest_rb.html">
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lib/myexperiment-rest/myexperiment_rest.rb
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Object
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Connects to myExperiment REST API and creates a <em><a
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href="TavernaWorkflow.html">TavernaWorkflow</a></em> object.
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</p>
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<h3 class="section-bar">Methods</h3>
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<a href="#M000004">read</a>
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<h3 class="section-bar">Attributes</h3>
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<td class="context-item-name">uri</td>
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<td class="context-item-value"> [R] </td>
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<a name="M000004"></a>
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<a href="Workflows.src/M000004.html" target="Code" class="method-signature"
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onclick="popupCode('Workflows.src/M000004.html');return false;">
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<span class="method-name">read</span><span class="method-args">(uri)</span>
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</a>
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Requires the URI of the workflow in the repository as a String.
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<title>read (MyExperimentREST::Workflows)</title>
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<pre><span class="ruby-comment cmt"># File lib/myexperiment-rest/myexperiment_rest.rb, line 19</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">read</span>(<span class="ruby-identifier">uri</span>)
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<span class="ruby-identifier">workflow_id</span> = <span class="ruby-value str">''</span>
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<span class="ruby-identifier">workflow_version</span> = <span class="ruby-value str">''</span>
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<span class="ruby-comment cmt"># Get workflow id</span>
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<span class="ruby-identifier">uri_id</span> = <span class="ruby-identifier">uri</span>.<span class="ruby-identifier">match</span>(<span class="ruby-regexp re">/workflows\/(\d+)/</span>)
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<span class="ruby-identifier">workflow_id</span> = <span class="ruby-identifier">uri_id</span>[<span class="ruby-value">1</span>]
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<span class="ruby-keyword kw">else</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-value str">"Could not match workflow id."</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-comment cmt"># Get workflow version if it exists</span>
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<span class="ruby-identifier">uri_version</span> = <span class="ruby-identifier">uri</span>.<span class="ruby-identifier">match</span>(<span class="ruby-regexp re">/version=(\d+)/</span>)
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<span class="ruby-identifier">workflow_version</span> = <span class="ruby-identifier">uri_version</span>[<span class="ruby-value">1</span>]
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-comment cmt"># Get workflow resource information -- if version is empty it returns the current version</span>
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<span class="ruby-identifier">response</span> = <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span>(<span class="ruby-value str">'http://www.myexperiment.org/workflow.xml'</span>, {<span class="ruby-identifier">:params</span> =<span class="ruby-operator">></span> {<span class="ruby-value str">'id'</span> =<span class="ruby-operator">></span> <span class="ruby-node">"#{workflow_id}"</span>,
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<span class="ruby-value str">'version'</span> =<span class="ruby-operator">></span> <span class="ruby-node">"#{workflow_version}"</span>,
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<span class="ruby-value str">'elements'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'title,description,content-uri,components'</span>} } )
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<span class="ruby-identifier">populate_workflow</span>(<span class="ruby-identifier">response</span>)
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<span class="ruby-keyword kw">end</span></pre>
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<title>Class: TestReadWorkflow</title>
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<td><strong>Class</strong></td>
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<td class="class-name-in-header">TestReadWorkflow</td>
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<td><strong>In:</strong></td>
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<td>
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<a href="../files/test/test_read_workflow_rb.html">
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<pre><span class="ruby-comment cmt"># File test/test_read_workflow.rb, line 11</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">setup</span>
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<span class="ruby-ivar">@wkf</span> = <span class="ruby-constant">Workflows</span>.<span class="ruby-identifier">new</span>.<span class="ruby-identifier">read</span>(<span class="ruby-value str">'http://www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_221429.xml?version=3'</span>)
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<pre><span class="ruby-comment cmt"># File test/test_read_workflow.rb, line 15</span>
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<span class="ruby-identifier">assert_equal</span> <span class="ruby-value str">'http://www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_221429.xml'</span>, <span class="ruby-ivar">@wkf</span>.<span class="ruby-identifier">xml_uri</span>, <span class="ruby-value str">"Workflow's XML URI not properly initialized!"</span>
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<span class="ruby-identifier">assert_equal</span> <span class="ruby-value str">'<p>The workflow extracts protein names from documents retrieved from MedLine based on a user Query (cf Apache Lucene syntax). The protein names are filtered by checking if there exists a valid UniProt ID for the given protein name.</p>'</span>,
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<pre><span class="ruby-comment cmt"># File test/test_read_workflow.rb, line 25</span>
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|
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<span class="ruby-identifier">assert_equal</span> <span class="ruby-value str">'Query'</span>, <span class="ruby-ivar">@wkf</span>.<span class="ruby-identifier">inputs</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">name</span>, <span class="ruby-value str">"Workflow's first input name not properly initialized!"</span>
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<span class="ruby-identifier">assert_equal</span> <span class="ruby-value str">'Maximum number of documents to extract proteins from.'</span>, <span class="ruby-ivar">@wkf</span>.<span class="ruby-identifier">inputs</span>[<span class="ruby-value">1</span>].<span class="ruby-identifier">descriptions</span>[<span class="ruby-value">1</span>], <span class="ruby-value str">"Workflow's second input's description not properly initialized!"</span>
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<span class="ruby-identifier">assert_equal</span> <span class="ruby-value str">'"transmembrane proteins" AND amyloid'</span>, <span class="ruby-ivar">@wkf</span>.<span class="ruby-identifier">inputs</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">examples</span>[<span class="ruby-value">0</span>], <span class="ruby-value str">"Workflow's first input's example not properly initialized!"</span>
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