simple_bioc 0.0.1 → 0.0.2
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- checksums.yaml +4 -4
- data/README.md +73 -3
- data/Rakefile +5 -0
- data/html/BioCReader.html +657 -0
- data/html/BioCWriter.html +556 -0
- data/html/README_md.html +231 -0
- data/html/SimpleBioC.html +255 -0
- data/html/SimpleBioC/Annotation.html +279 -0
- data/html/SimpleBioC/Collection.html +316 -0
- data/html/SimpleBioC/Document.html +426 -0
- data/html/SimpleBioC/Location.html +288 -0
- data/html/SimpleBioC/Node.html +334 -0
- data/html/SimpleBioC/NodeBase.html +281 -0
- data/html/SimpleBioC/Passage.html +418 -0
- data/html/SimpleBioC/Relation.html +301 -0
- data/html/SimpleBioC/Sentence.html +399 -0
- data/html/created.rid +15 -0
- data/html/images/add.png +0 -0
- data/html/images/arrow_up.png +0 -0
- data/html/images/brick.png +0 -0
- data/html/images/brick_link.png +0 -0
- data/html/images/bug.png +0 -0
- data/html/images/bullet_black.png +0 -0
- data/html/images/bullet_toggle_minus.png +0 -0
- data/html/images/bullet_toggle_plus.png +0 -0
- data/html/images/date.png +0 -0
- data/html/images/delete.png +0 -0
- data/html/images/find.png +0 -0
- data/html/images/loadingAnimation.gif +0 -0
- data/html/images/macFFBgHack.png +0 -0
- data/html/images/package.png +0 -0
- data/html/images/page_green.png +0 -0
- data/html/images/page_white_text.png +0 -0
- data/html/images/page_white_width.png +0 -0
- data/html/images/plugin.png +0 -0
- data/html/images/ruby.png +0 -0
- data/html/images/tag_blue.png +0 -0
- data/html/images/tag_green.png +0 -0
- data/html/images/transparent.png +0 -0
- data/html/images/wrench.png +0 -0
- data/html/images/wrench_orange.png +0 -0
- data/html/images/zoom.png +0 -0
- data/html/index.html +212 -0
- data/html/js/darkfish.js +155 -0
- data/html/js/jquery.js +18 -0
- data/html/js/navigation.js +142 -0
- data/html/js/search.js +94 -0
- data/html/js/search_index.js +1 -0
- data/html/js/searcher.js +228 -0
- data/html/rdoc.css +595 -0
- data/html/table_of_contents.html +199 -0
- data/lib/simple_bioc.rb +4 -0
- data/lib/simple_bioc/annotation.rb +10 -6
- data/lib/simple_bioc/bioc_reader.rb +2 -2
- data/lib/simple_bioc/collection.rb +13 -11
- data/lib/simple_bioc/document.rb +31 -22
- data/lib/simple_bioc/location.rb +13 -7
- data/lib/simple_bioc/node.rb +14 -8
- data/lib/simple_bioc/node_base.rb +13 -10
- data/lib/simple_bioc/passage.rb +26 -23
- data/lib/simple_bioc/relation.rb +13 -8
- data/lib/simple_bioc/sentence.rb +21 -15
- data/lib/simple_bioc/version.rb +2 -2
- data/samples/print_annotation.rb +18 -0
- data/samples/sample1.rb +31 -0
- data/simple_bioc.gemspec +1 -1
- metadata +52 -2
checksums.yaml
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data.tar.gz: 9ecd0c5f1ab4fccd5313076f057bf979d192533f
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metadata.gz: 02c83c1d490001ccc56098e6370b74068d6b24e4ed167bad7b474f2d01cdaa605de44593a6c6090141cafefbe442e71203b4dcf0d994f1c8465d4fe97643363f
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data.tar.gz: 48a386b80cba3bd6fa754592b74d1b83d2e7c15f43b898fc72fda6c7d92f43d61a6576ec4375a928c6237e38495c9e31c3e65542a385c6db4ad6c172ea9302db
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data/README.md
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# SimpleBioc
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SimpleBioC is a simple parser / builder for BioC data format. BioC is a simple XML format to share text documents and annotations. You can find more information about BioC from the official BioC web site ([http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/](http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/))
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## Feature:
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* Parse & convert a BioC document to an object instance compatible to BioC DTD
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* Use plain ruby objects for simplicity
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* Build a BioC document from an object instance
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## Installation
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$ gem install simple_bioc
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## Usage
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## Usages
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Include library
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require 'simple_bioc'
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Parse with a file name (path)
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collection = SimpleBioC::from_xml(filename)
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Traverse & Manipulate Data. Data structure are almost the same as the DTD. Please refer [library documents](https://github.com/dongseop/simple_bioc/blob/master/html/index.html) and [the BioC DTD](http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/BioCDTD.html).
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puts collection.documents[2].passages[0].text
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Build XML text from data
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puts SimpleBioC::to_xml(collection)
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## Sample
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More samples can be found in Samples directory
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require 'simple_bioc'
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# Sample1: parse, traverse, manipulate, and build BioC data
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require 'simple_bioc'
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# parse BioC file
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collection = SimpleBioC.from_xml("../xml/everything.xml")
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# the returned object contains all the information in the BioC file
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# traverse & read information
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collection.documents.each do |document|
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puts document
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document.passages.each do |passage|
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puts passage
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end
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end
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# manipulate
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doc = SimpleBioC::Document.new(collection)
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doc.id = "23071747"
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doc.infons["journal"] = "PLoS One"
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collection.documents << doc
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p = SimpleBioC::Passage.new(doc)
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p.offset = 0
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p.text = "TRIP database 2.0: a manually curated information hub for accessing TRP channel interaction network."
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p.infons["type"] = "title"
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doc.passages << p
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# build BioC document from data
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xml = SimpleBioC.to_xml(collection)
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puts xml
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## Contributing
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3. Commit your changes (`git commit -am 'Add some feature'`)
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4. Push to the branch (`git push origin my-new-feature`)
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5. Create new Pull Request
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## LICENSE
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Copyright © 2013, Dongseop Kwon
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Released under the MIT License.
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data/Rakefile
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<!DOCTYPE html>
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<html>
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<head>
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<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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<title>module BioCReader - RDoc Documentation</title>
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<link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
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<script type="text/javascript">
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var rdoc_rel_prefix = "./";
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</script>
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<script type="text/javascript" charset="utf-8" src="./js/jquery.js"></script>
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<script type="text/javascript" charset="utf-8" src="./js/navigation.js"></script>
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<script type="text/javascript" charset="utf-8" src="./js/search_index.js"></script>
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<script type="text/javascript" charset="utf-8" src="./js/search.js"></script>
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<script type="text/javascript" charset="utf-8" src="./js/searcher.js"></script>
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<script type="text/javascript" charset="utf-8" src="./js/darkfish.js"></script>
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<body id="top" class="module">
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<nav id="metadata">
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<nav id="home-section" class="section">
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<h3 class="section-header">
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<a href="./index.html">Home</a>
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<a href="./table_of_contents.html#classes">Classes</a>
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<a href="./table_of_contents.html#methods">Methods</a>
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</h3>
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</nav>
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<nav id="search-section" class="section project-section" class="initially-hidden">
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<form action="#" method="get" accept-charset="utf-8">
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<h3 class="section-header">
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<input type="text" name="search" placeholder="Search" id="search-field"
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title="Type to search, Up and Down to navigate, Enter to load">
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</h3>
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</form>
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<ul id="search-results" class="initially-hidden"></ul>
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</nav>
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<div id="file-metadata">
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<nav id="file-list-section" class="section">
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<h3 class="section-header">Defined In</h3>
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<ul>
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<li>lib/simple_bioc/bioc_reader.rb
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</ul>
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</nav>
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</div>
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<div id="class-metadata">
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<!-- Method Quickref -->
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<nav id="method-list-section" class="section">
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<h3 class="section-header">Methods</h3>
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<ul class="link-list">
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<li ><a href="#method-i-read">#read</a>
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<li ><a href="#method-i-read_annotation">#read_annotation</a>
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<li ><a href="#method-i-read_collection">#read_collection</a>
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<li ><a href="#method-i-read_document">#read_document</a>
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<li ><a href="#method-i-read_infon">#read_infon</a>
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<li ><a href="#method-i-read_int">#read_int</a>
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<li ><a href="#method-i-read_location">#read_location</a>
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<li ><a href="#method-i-read_node">#read_node</a>
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<li ><a href="#method-i-read_passage">#read_passage</a>
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<li ><a href="#method-i-read_recursive">#read_recursive</a>
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<li ><a href="#method-i-read_relation">#read_relation</a>
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<li ><a href="#method-i-read_sentence">#read_sentence</a>
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<li ><a href="#method-i-read_text">#read_text</a>
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<div id="project-metadata">
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<nav id="fileindex-section" class="section project-section">
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<h3 class="section-header">Pages</h3>
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<ul>
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<li class="file"><a href="./README_md.html">README</a>
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<nav id="classindex-section" class="section project-section">
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<h3 class="section-header">Class and Module Index</h3>
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<ul class="link-list">
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<li><a href="./BioCReader.html">BioCReader</a>
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<li><a href="./BioCWriter.html">BioCWriter</a>
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<li><a href="./SimpleBioC.html">SimpleBioC</a>
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<li><a href="./SimpleBioC/Annotation.html">SimpleBioC::Annotation</a>
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<li><a href="./SimpleBioC/Collection.html">SimpleBioC::Collection</a>
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<li><a href="./SimpleBioC/Document.html">SimpleBioC::Document</a>
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<li><a href="./SimpleBioC/Location.html">SimpleBioC::Location</a>
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<li><a href="./SimpleBioC/Node.html">SimpleBioC::Node</a>
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<li><a href="./SimpleBioC/NodeBase.html">SimpleBioC::NodeBase</a>
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<li><a href="./SimpleBioC/Passage.html">SimpleBioC::Passage</a>
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<li><a href="./SimpleBioC/Relation.html">SimpleBioC::Relation</a>
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<li><a href="./SimpleBioC/Sentence.html">SimpleBioC::Sentence</a>
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<div id="documentation">
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<h1 class="module">module BioCReader</h1>
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<div id="description" class="description">
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</div><!-- description -->
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<section id="5Buntitled-5D" class="documentation-section">
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<!-- Methods -->
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<section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
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<h3 class="section-header">Public Instance Methods</h3>
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<div id="method-i-read" class="method-detail ">
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<div class="method-heading">
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<span class="method-name">read</span><span
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class="method-args">(path)</span>
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<span class="method-click-advice">click to toggle source</span>
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</div>
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 80</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">read_annotation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">annotation</span>)
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<span class="ruby-identifier">annotation</span>.<span class="ruby-identifier">text</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">"text"</span>)
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 47</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">read_collection</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">collection</span>)
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<span class="ruby-identifier">collection</span>.<span class="ruby-identifier">source</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">"source"</span>)
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<span class="ruby-identifier">collection</span>.<span class="ruby-identifier">date</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">"date"</span>)
|
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<span class="ruby-identifier">collection</span>.<span class="ruby-identifier">key</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">"key"</span>)
|
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<span class="ruby-identifier">read_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">collection</span>)
|
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<span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">collection</span>, <span class="ruby-string">"document"</span>)
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<span class="ruby-keyword">end</span></pre>
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 55</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">read_document</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">document</span>)
|
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|
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<span class="ruby-identifier">document</span>.<span class="ruby-identifier">id</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">"id"</span>)
|
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|
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|
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|
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<span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">document</span>, <span class="ruby-string">"relation"</span>)
|
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|
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<span class="ruby-identifier">document</span>.<span class="ruby-identifier">adjust_ref</span>
|
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|
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<span class="ruby-keyword">end</span></pre>
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|
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|
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 34</span>
|
|
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|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">read_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">obj</span>)
|
|
349
|
+
<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">xpath</span>(<span class="ruby-string">"infon"</span>).<span class="ruby-identifier">each</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span> <span class="ruby-identifier">obj</span>.<span class="ruby-identifier">infons</span>[<span class="ruby-identifier">i</span>[<span class="ruby-string">"key"</span>]] = <span class="ruby-identifier">i</span>.<span class="ruby-identifier">content</span>}
|
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|
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<span class="ruby-keyword">end</span></pre>
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<div id="method-i-read_int" class="method-detail ">
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<div class="method-heading">
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<span class="method-name">read_int</span><span
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class="method-args">(xml, name)</span>
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|
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|
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 29</span>
|
|
381
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">read_int</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">name</span>)
|
|
382
|
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<span class="ruby-identifier">val</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">name</span>)
|
|
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|
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<span class="ruby-identifier">val</span> <span class="ruby-operator">&&</span> <span class="ruby-identifier">val</span>.<span class="ruby-identifier">to_i</span>
|
|
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|
+
<span class="ruby-keyword">end</span></pre>
|
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|
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|
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</div><!-- read_int-method -->
|
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|
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<div id="method-i-read_location" class="method-detail ">
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|
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<div class="method-heading">
|
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|
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<span class="method-name">read_location</span><span
|
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399
|
+
class="method-args">(xml, location)</span>
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|
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401
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</div>
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|
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<div class="method-source-code" id="read_location-source">
|
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|
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 93</span>
|
|
415
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">read_location</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">location</span>)
|
|
416
|
+
<span class="ruby-identifier">location</span>.<span class="ruby-identifier">offset</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">"offset"</span>]
|
|
417
|
+
<span class="ruby-identifier">location</span>.<span class="ruby-identifier">length</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">"length"</span>]
|
|
418
|
+
<span class="ruby-keyword">end</span></pre>
|
|
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|
+
</div><!-- read_location-source -->
|
|
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|
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|
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|
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</div>
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|
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</div><!-- read_location-method -->
|
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|
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|
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|
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|
|
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|
+
<div id="method-i-read_node" class="method-detail ">
|
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|
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|
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|
+
<div class="method-heading">
|
|
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|
+
<span class="method-name">read_node</span><span
|
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|
+
class="method-args">(xml, node)</span>
|
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|
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|
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|
+
<span class="method-click-advice">click to toggle source</span>
|
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|
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|
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|
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</div>
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|
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|
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|
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|
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<div class="method-source-code" id="read_node-source">
|
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|
+
<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 98</span>
|
|
449
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">read_node</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">node</span>)
|
|
450
|
+
<span class="ruby-identifier">node</span>.<span class="ruby-identifier">refid</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">"refid"</span>]
|
|
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|
+
<span class="ruby-identifier">node</span>.<span class="ruby-identifier">role</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">"role"</span>]
|
|
452
|
+
<span class="ruby-keyword">end</span></pre>
|
|
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|
+
</div><!-- read_node-source -->
|
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|
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|
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|
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</div>
|
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|
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|
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</div><!-- read_node-method -->
|
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|
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<div id="method-i-read_passage" class="method-detail ">
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|
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|
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|
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<div class="method-heading">
|
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|
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<span class="method-name">read_passage</span><span
|
|
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|
+
class="method-args">(xml, passage)</span>
|
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|
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|
|
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|
+
<span class="method-click-advice">click to toggle source</span>
|
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</div>
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|
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|
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<div class="method-source-code" id="read_passage-source">
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 63</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">read_passage</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">passage</span>)
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<span class="ruby-identifier">passage</span>.<span class="ruby-identifier">text</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">"text"</span>)
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<span class="ruby-identifier">passage</span>.<span class="ruby-identifier">offset</span> = <span class="ruby-identifier">read_int</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">"offset"</span>)
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+
<span class="ruby-identifier">read_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">passage</span>)
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<span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">passage</span>, <span class="ruby-string">"sentence"</span>)
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488
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+
<span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">passage</span>, <span class="ruby-string">"annotation"</span>)
|
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<span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">passage</span>, <span class="ruby-string">"relation"</span>)
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<span class="ruby-keyword">end</span></pre>
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</div><!-- read_passage-source -->
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</div>
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</div><!-- read_passage-method -->
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<div id="method-i-read_recursive" class="method-detail ">
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<div class="method-heading">
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<span class="method-name">read_recursive</span><span
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class="method-args">(xml, obj, name)</span>
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<span class="method-click-advice">click to toggle source</span>
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</div>
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<div class="method-source-code" id="read_recursive-source">
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 38</span>
|
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">obj</span>, <span class="ruby-identifier">name</span>)
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522
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<span class="ruby-identifier">target_class</span> = <span class="ruby-constant">SimpleBioC</span>.<span class="ruby-identifier">const_get</span>(<span class="ruby-identifier">name</span>.<span class="ruby-identifier">capitalize</span>)
|
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+
<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">xpath</span>(<span class="ruby-identifier">name</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">node</span><span class="ruby-operator">|</span>
|
|
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|
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<span class="ruby-identifier">instance</span> = <span class="ruby-identifier">target_class</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">obj</span>)
|
|
525
|
+
<span class="ruby-identifier">send</span>(<span class="ruby-value">:"read_#{name}"</span>, <span class="ruby-identifier">node</span>, <span class="ruby-identifier">instance</span>)
|
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|
+
<span class="ruby-identifier">obj</span>.<span class="ruby-identifier">instance_variable_get</span>(<span class="ruby-value">:"@#{name}s"</span>) <span class="ruby-operator"><<</span> <span class="ruby-identifier">instance</span>
|
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527
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<span class="ruby-keyword">end</span>
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528
|
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<span class="ruby-keyword">end</span></pre>
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529
|
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</div><!-- read_recursive-source -->
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</div>
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</div><!-- read_recursive-method -->
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<div id="method-i-read_relation" class="method-detail ">
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541
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<div class="method-heading">
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542
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<span class="method-name">read_relation</span><span
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543
|
+
class="method-args">(xml, relation)</span>
|
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544
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|
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545
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<span class="method-click-advice">click to toggle source</span>
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</div>
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<div class="method-source-code" id="read_relation-source">
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 87</span>
|
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">read_relation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">relation</span>)
|
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560
|
+
<span class="ruby-identifier">relation</span>.<span class="ruby-identifier">id</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">"id"</span>]
|
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|
+
<span class="ruby-identifier">read_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">relation</span>)
|
|
562
|
+
<span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">relation</span>, <span class="ruby-string">"node"</span>)
|
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563
|
+
<span class="ruby-keyword">end</span></pre>
|
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564
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</div><!-- read_relation-source -->
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</div>
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</div><!-- read_relation-method -->
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<div id="method-i-read_sentence" class="method-detail ">
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+
|
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576
|
+
<div class="method-heading">
|
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577
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+
<span class="method-name">read_sentence</span><span
|
|
578
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+
class="method-args">(xml, sentence)</span>
|
|
579
|
+
|
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580
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+
<span class="method-click-advice">click to toggle source</span>
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581
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+
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582
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+
</div>
|
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583
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+
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<div class="method-description">
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+
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<div class="method-source-code" id="read_sentence-source">
|
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593
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+
<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 72</span>
|
|
594
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">read_sentence</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">sentence</span>)
|
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595
|
+
<span class="ruby-identifier">sentence</span>.<span class="ruby-identifier">text</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">"text"</span>)
|
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596
|
+
<span class="ruby-identifier">sentence</span>.<span class="ruby-identifier">offset</span> = <span class="ruby-identifier">read_int</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">"offset"</span>)
|
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597
|
+
<span class="ruby-identifier">read_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">sentence</span>)
|
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598
|
+
<span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">sentence</span>, <span class="ruby-string">"annotation"</span>)
|
|
599
|
+
<span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">sentence</span>, <span class="ruby-string">"relation"</span>)
|
|
600
|
+
<span class="ruby-keyword">end</span></pre>
|
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601
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+
</div><!-- read_sentence-source -->
|
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602
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+
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</div>
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607
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</div><!-- read_sentence-method -->
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<div id="method-i-read_text" class="method-detail ">
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<div class="method-heading">
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<span class="method-name">read_text</span><span
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615
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class="method-args">(xml, name)</span>
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616
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617
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<span class="method-click-advice">click to toggle source</span>
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618
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|
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619
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</div>
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621
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<div class="method-description">
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<div class="method-source-code" id="read_text-source">
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 24</span>
|
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631
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">name</span>)
|
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632
|
+
<span class="ruby-identifier">node</span> = <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">at_xpath</span>(<span class="ruby-identifier">name</span>)
|
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633
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+
<span class="ruby-identifier">node</span> <span class="ruby-operator">&&</span> <span class="ruby-identifier">node</span>.<span class="ruby-identifier">content</span>
|
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634
|
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<span class="ruby-keyword">end</span></pre>
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635
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</div><!-- read_text-source -->
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</div>
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</div><!-- read_text-method -->
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</section><!-- public-instance-method-details -->
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</section><!-- 5Buntitled-5D -->
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</div><!-- documentation -->
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<footer id="validator-badges">
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653
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<p><a href="http://validator.w3.org/check/referer">[Validate]</a>
|
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654
|
+
<p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.
|
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655
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<p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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</footer>
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