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/README_md.html
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<ul class="link-list" role="directory">
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<li><a href="#label-SimpleBioC">SimpleBioC</a>
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<h1 id="label-SimpleBioC"><a href="SimpleBioC.html">SimpleBioC</a><span><a href="#label-SimpleBioC">¶</a> <a href="#
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<h1 id="label-SimpleBioC"><a href="SimpleBioC.html">SimpleBioC</a><span><a href="#label-SimpleBioC">¶</a> <a href="#top">↑</a></span></h1>
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<p><a href="SimpleBioC.html">SimpleBioC</a> is a simple parser / builder for
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BioC data format. BioC is a simple XML format to share text documents and
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BioC web site (<a
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href="http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/">www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/</a>)</p>
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<h2 id="label-Feature-3A">Feature:<span><a href="#label-Feature-3A">¶</a> <a href="#top">↑</a></span></h2>
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<ul><li>
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<p>Parse & convert a BioC document to an object instance compatible to
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<h2 id="label-Installation">Installation<span><a href="#label-Installation">¶</a> <a href="#top">↑</a></span></h2>
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<p>Add this line to your application's Gemfile:</p>
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<pre>gem
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<pre class="ruby"><span class="ruby-identifier">gem</span> <span class="ruby-string">'simple_bioc'</span>
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</pre>
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<p>And then execute:</p>
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<h2 id="label-Simple+Usages">Simple Usages<span><a href="#label-Simple+Usages">¶</a> <a href="#top">↑</a></span></h2>
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<p>Parse with a file name (path)</p>
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<pre class="ruby"><span class="ruby-identifier">collection</span> = <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-identifier">from_xml</span>(<span class="ruby-identifier">filename</span>)
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<p>Traverse & Manipulate Data. Data structure are almost the same as the
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DTD. Please refer <a
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href="http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/BioCDTD.html">the
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BioC DTD</a>.</p>
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<pre>puts collection
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<pre class="ruby"><span class="ruby-identifier">puts</span> <span class="ruby-identifier">collection</span>.<span class="ruby-identifier">documents</span>[<span class="ruby-value">2</span>].<span class="ruby-identifier">passages</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">text</span>
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<p>Build XML text from data</p>
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<pre class="ruby"><span class="ruby-identifier">puts</span> <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-identifier">to_xml</span>(<span class="ruby-identifier">collection</span>)
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<h2 id="label-Options">Options<span><a href="#label-Options">¶</a> <a href="#top">↑</a></span></h2>
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<h3 id="label-Specify+set+of+-3Cdocument-3Es+to+parse">Specify set of <document>s to parse<span><a href="#label-Specify+set+of+-3Cdocument-3Es+to+parse">¶</a> <a href="#top">↑</a></span></h3>
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<p>You can parse only a set of document elements in a large xml document
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instead of parsing all the document elements. It may decrease the
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processing time. For example, the following code will return a collection
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with two documents (“1234”, “4567”).</p>
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<pre class="ruby"><span class="ruby-identifier">collection</span> = <span class="ruby-constant">SimpleBioc</span><span class="ruby-operator">::</span><span class="ruby-identifier">from_xml</span>(<span class="ruby-identifier">filename</span>, {<span class="ruby-identifier">documents</span><span class="ruby-operator">:</span> [<span class="ruby-string">"1234"</span>, <span class="ruby-string">"4567"</span>]})
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<h3 id="label-No+whitespace+in+output">No whitespace in output<span><a href="#label-No+whitespace+in+output">¶</a> <a href="#top">↑</a></span></h3>
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'save_with' option with 0 to the to_xml() function.</p>
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<pre class="ruby"><span class="ruby-identifier">puts</span> <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-identifier">to_xml</span>(<span class="ruby-identifier">collection</span>, {<span class="ruby-identifier">save_with</span>:<span class="ruby-value">0</span>})
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<p>More samples can be found in Samples directory</p>
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<h2 id="label-Contributing">Contributing<span><a href="#label-Contributing">¶</a> <a href="#top">↑</a></span></h2>
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<p>Fork it</p>
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