simple_bioc 0.0.5 → 0.0.6
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- checksums.yaml +4 -4
- data/.gitignore +13 -0
- data/html/BioCMerger.html +748 -0
- data/html/BioCReader.html +138 -146
- data/html/BioCWriter.html +84 -131
- data/html/README_md.html +79 -100
- data/html/SimpleBioC/Annotation.html +70 -113
- data/html/SimpleBioC/Collection.html +70 -113
- data/html/SimpleBioC/Document.html +76 -119
- data/html/SimpleBioC/Location.html +70 -113
- data/html/SimpleBioC/Node.html +72 -115
- data/html/SimpleBioC/NodeBase.html +63 -108
- data/html/SimpleBioC/Passage.html +74 -117
- data/html/SimpleBioC/Relation.html +85 -115
- data/html/SimpleBioC/Sentence.html +74 -117
- data/html/SimpleBioC.html +221 -129
- data/html/created.rid +16 -15
- data/html/css/fonts.css +167 -0
- data/html/css/rdoc.css +590 -0
- data/html/fonts/Lato-Light.ttf +0 -0
- data/html/fonts/Lato-LightItalic.ttf +0 -0
- data/html/fonts/Lato-Regular.ttf +0 -0
- data/html/fonts/Lato-RegularItalic.ttf +0 -0
- data/html/fonts/SourceCodePro-Bold.ttf +0 -0
- data/html/fonts/SourceCodePro-Regular.ttf +0 -0
- data/html/index.html +71 -53
- data/html/js/darkfish.js +32 -26
- data/html/js/jquery.js +4 -18
- data/html/js/navigation.js.gz +0 -0
- data/html/js/search.js +20 -5
- data/html/js/search_index.js +1 -1
- data/html/js/search_index.js.gz +0 -0
- data/html/js/searcher.js.gz +0 -0
- data/html/table_of_contents.html +379 -136
- data/lib/simple_bioc/bioc_merger.rb +209 -0
- data/lib/simple_bioc/relation.rb +1 -1
- data/lib/simple_bioc/version.rb +1 -1
- data/lib/simple_bioc.rb +8 -4
- data/spec/file_check_spec.rb +14 -1
- data/xml/PMC2133144.xml +3 -0
- data/xml/merge/9864355.xml +1 -0
- data/xml/merge/9864355_1.xml +1 -0
- data/xml/merge/9864355_2.xml +1974 -0
- data/xml/merge/9864355_3.xml +1 -0
- data/xml/merge/output.xml +6742 -0
- metadata +21 -2
data/html/SimpleBioC.html
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module SimpleBioC
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<p><a href="SimpleBioC.html">SimpleBioC</a> main library</p>
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<p>parse a BioC XML file in the given path and convert it into a collection
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instance</p>
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<p><code>file_path</code> - file path for parse</p>
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<p><code>options</code> - (optional) additional options</p>
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<h4 id="method-i-from_xml-label-Options">Options<span><a href="#method-i-from_xml-label-Options">¶</a> <a href="#top">↑</a></span></h4>
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<h4 id="method-i-from_xml-label-Examples">Examples<span><a href="#method-i-from_xml-label-Examples">¶</a> <a href="#top">↑</a></span></h4>
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<pre class="ruby"><span class="ruby-identifier">collection</span> = <span class="ruby-constant">SimpleBioC</span>.<span class="ruby-identifier">from_xml</span>(<span class="ruby-string">"./xml/everything.xml"</span>)
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<span class="ruby-identifier">collection</span> = <span class="ruby-constant">SimpleBioC</span>.<span class="ruby-identifier">from_xml</span>(<span class="ruby-string">"./xml/lemma.xml"</span>, {<span class="ruby-identifier">documents</span>:[<span class="ruby-value">21785578</span>, <span class="ruby-value">21488974</span>]})
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<span class="ruby-identifier">options</span>[<span class="ruby-value">:documents</span>] = <span class="ruby-identifier">options</span>[<span class="ruby-value">:documents</span>].<span class="ruby-identifier">map</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">e</span><span class="ruby-operator">|</span> <span class="ruby-identifier">e</span>.<span class="ruby-identifier">to_s</span>} <span class="ruby-keyword">if</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:documents</span>].<span class="ruby-identifier">kind_of?</span>(<span class="ruby-constant">Array</span>)
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<span class="ruby-constant">BioCReader</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">file_path</span>, <span class="ruby-identifier">options</span>)
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<span class="ruby-keyword">end</span></pre>
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class="method-args">(file, options = {})</span>
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<p>parse a BioC XML file and convert it into a collection instance</p>
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<h4 id="method-i-from_xml_file-label-Arguments">Arguments<span><a href="#method-i-from_xml_file-label-Arguments">¶</a> <a href="#top">↑</a></span></h4>
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<span class="ruby-identifier">collection</span> = <span class="ruby-constant">SimpleBioC</span>.<span class="ruby-identifier">from_xml</span>(<span class="ruby-identifier">content</span>, {<span class="ruby-identifier">documents</span>:[<span class="ruby-value">21785578</span>, <span class="ruby-value">21488974</span>]})
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<span class="ruby-identifier">options</span>[<span class="ruby-value">:documents</span>] = <span class="ruby-identifier">options</span>[<span class="ruby-value">:documents</span>].<span class="ruby-identifier">map</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">e</span><span class="ruby-operator">|</span> <span class="ruby-identifier">e</span>.<span class="ruby-identifier">to_s</span>} <span class="ruby-keyword">if</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:documents</span>].<span class="ruby-identifier">kind_of?</span>(<span class="ruby-constant">Array</span>)
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<span class="ruby-keyword">return</span> <span class="ruby-constant">BioCMerger</span>.<span class="ruby-identifier">merge</span>(<span class="ruby-identifier">dest_bioc</span>, <span class="ruby-identifier">src_bioc</span>)
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|
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<span class="ruby-identifier">output</span> = <span class="ruby-constant">SimpleBioC</span>.<span class="ruby-identifier">to_xml</span>(<span class="ruby-identifier">collection</span>, {<span class="ruby-identifier">save_with</span><span class="ruby-operator">:</span> <span class="ruby-value">0</span>})
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lib/simple_bioc/bioc_merger.rb Mon, 07 Dec 2015 15:53:30 +0900
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lib/simple_bioc/bioc_reader.rb Sun, 06 Dec 2015 21:47:53 +0900
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lib/simple_bioc/bioc_writer.rb Tue, 23 Jun 2015 05:02:37 +0900
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lib/simple_bioc/document.rb Mon, 07 Dec 2015 07:32:29 +0900
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lib/simple_bioc/location.rb Thu, 11 Jun 2015 16:42:00 +0900
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lib/simple_bioc/relation.rb Mon, 07 Dec 2015 13:54:45 +0900
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lib/simple_bioc/version.rb Tue, 23 Jun 2015 03:50:17 +0900
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