simple_bioc 0.0.1 → 0.0.2
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.
- 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: 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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<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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</ul>
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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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<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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<!-- 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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<span class="ruby-identifier">xml_doc</span> = <span class="ruby-constant">Nokogiri</span><span class="ruby-operator">::</span><span class="ruby-constant">XML</span>(<span class="ruby-identifier">file</span>) <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">config</span><span class="ruby-operator">|</span>
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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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|
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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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<span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">document</span>, <span class="ruby-string">"passage"</span>)
|
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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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|
+
<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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class="method-args">(xml, obj)</span>
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|
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<div class="method-source-code" id="read_infon-source">
|
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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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|
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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
|
+
<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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|
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<span class="ruby-keyword">end</span></pre>
|
|
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|
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|
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</div>
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</div><!-- read_int-method -->
|
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|
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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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|
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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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|
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401
|
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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_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>
|
|
419
|
+
</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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|
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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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|
|
429
|
+
<div id="method-i-read_node" class="method-detail ">
|
|
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|
+
|
|
431
|
+
<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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435
|
+
<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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|
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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>]
|
|
451
|
+
<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>
|
|
453
|
+
</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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|
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|
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|
+
</div><!-- read_node-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_passage" class="method-detail ">
|
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|
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|
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465
|
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<div class="method-heading">
|
|
466
|
+
<span class="method-name">read_passage</span><span
|
|
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|
+
class="method-args">(xml, passage)</span>
|
|
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|
+
|
|
469
|
+
<span class="method-click-advice">click to toggle source</span>
|
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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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|
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<div class="method-description">
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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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<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
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+
<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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</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
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+
<div class="method-heading">
|
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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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<div class="method-description">
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<div class="method-source-code" id="read_sentence-source">
|
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+
<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 72</span>
|
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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
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+
<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
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+
<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>)
|
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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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+
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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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