simple_bioc 0.0.5 → 0.0.6

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (46) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +13 -0
  3. data/html/BioCMerger.html +748 -0
  4. data/html/BioCReader.html +138 -146
  5. data/html/BioCWriter.html +84 -131
  6. data/html/README_md.html +79 -100
  7. data/html/SimpleBioC/Annotation.html +70 -113
  8. data/html/SimpleBioC/Collection.html +70 -113
  9. data/html/SimpleBioC/Document.html +76 -119
  10. data/html/SimpleBioC/Location.html +70 -113
  11. data/html/SimpleBioC/Node.html +72 -115
  12. data/html/SimpleBioC/NodeBase.html +63 -108
  13. data/html/SimpleBioC/Passage.html +74 -117
  14. data/html/SimpleBioC/Relation.html +85 -115
  15. data/html/SimpleBioC/Sentence.html +74 -117
  16. data/html/SimpleBioC.html +221 -129
  17. data/html/created.rid +16 -15
  18. data/html/css/fonts.css +167 -0
  19. data/html/css/rdoc.css +590 -0
  20. data/html/fonts/Lato-Light.ttf +0 -0
  21. data/html/fonts/Lato-LightItalic.ttf +0 -0
  22. data/html/fonts/Lato-Regular.ttf +0 -0
  23. data/html/fonts/Lato-RegularItalic.ttf +0 -0
  24. data/html/fonts/SourceCodePro-Bold.ttf +0 -0
  25. data/html/fonts/SourceCodePro-Regular.ttf +0 -0
  26. data/html/index.html +71 -53
  27. data/html/js/darkfish.js +32 -26
  28. data/html/js/jquery.js +4 -18
  29. data/html/js/navigation.js.gz +0 -0
  30. data/html/js/search.js +20 -5
  31. data/html/js/search_index.js +1 -1
  32. data/html/js/search_index.js.gz +0 -0
  33. data/html/js/searcher.js.gz +0 -0
  34. data/html/table_of_contents.html +379 -136
  35. data/lib/simple_bioc/bioc_merger.rb +209 -0
  36. data/lib/simple_bioc/relation.rb +1 -1
  37. data/lib/simple_bioc/version.rb +1 -1
  38. data/lib/simple_bioc.rb +8 -4
  39. data/spec/file_check_spec.rb +14 -1
  40. data/xml/PMC2133144.xml +3 -0
  41. data/xml/merge/9864355.xml +1 -0
  42. data/xml/merge/9864355_1.xml +1 -0
  43. data/xml/merge/9864355_2.xml +1974 -0
  44. data/xml/merge/9864355_3.xml +1 -0
  45. data/xml/merge/output.xml +6742 -0
  46. metadata +21 -2
data/html/BioCWriter.html CHANGED
@@ -2,70 +2,66 @@
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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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+ <meta charset="UTF-8">
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  <title>module BioCWriter - RDoc Documentation</title>
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- <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
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-
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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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+ <script src="./js/jquery.js"></script>
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+ <script src="./js/darkfish.js"></script>
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+
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+ <link href="./css/fonts.css" rel="stylesheet">
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+ <link href="./css/rdoc.css" rel="stylesheet">
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+
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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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+ <body id="top" role="document" class="module">
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+ <nav role="navigation">
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+ <div id="project-navigation">
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+ <div id="home-section" role="region" title="Quick navigation" class="nav-section">
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+ <h2>
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+ <a href="./index.html" rel="home">Home</a>
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+ </h2>
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+
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+ <div id="table-of-contents-navigation">
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+ <a href="./table_of_contents.html#pages">Pages</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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-
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+ </div>
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+ </div>
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- <nav id="search-section" class="section project-section" class="initially-hidden">
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+ <div id="search-section" role="search" class="project-section 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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+ <div id="search-field-wrapper">
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+ <input id="search-field" role="combobox" aria-label="Search"
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+ aria-autocomplete="list" aria-controls="search-results"
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+ type="text" name="search" placeholder="Search" spellcheck="false"
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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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+ </div>
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- <ul id="search-results" class="initially-hidden"></ul>
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- </nav>
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+ <ul id="search-results" aria-label="Search Results"
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+ aria-busy="false" aria-expanded="false"
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+ aria-atomic="false" class="initially-hidden"></ul>
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+ </form>
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+ </div>
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+ </div>
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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_writer.rb
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- </ul>
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- </nav>
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-
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-
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- </div>
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-
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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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+ <div id="method-list-section" class="nav-section">
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+ <h3>Methods</h3>
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- <ul class="link-list">
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+ <ul class="link-list" role="directory">
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  <li ><a href="#method-i-write">#write</a>
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@@ -88,62 +84,19 @@
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  <li ><a href="#method-i-write_sentence">#write_sentence</a>
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  </ul>
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- </nav>
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-
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- </div>
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-
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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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-
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- <ul>
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-
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- <li class="file"><a href="./README_md.html">README</a>
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-
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- </ul>
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- </nav>
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-
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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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-
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- <ul class="link-list">
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-
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- <li><a href="./BioCReader.html">BioCReader</a>
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-
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- <li><a href="./BioCWriter.html">BioCWriter</a>
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-
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- <li><a href="./SimpleBioC.html">SimpleBioC</a>
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-
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- <li><a href="./SimpleBioC/Annotation.html">SimpleBioC::Annotation</a>
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-
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- <li><a href="./SimpleBioC/Collection.html">SimpleBioC::Collection</a>
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-
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- <li><a href="./SimpleBioC/Document.html">SimpleBioC::Document</a>
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-
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- <li><a href="./SimpleBioC/Location.html">SimpleBioC::Location</a>
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-
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- <li><a href="./SimpleBioC/Node.html">SimpleBioC::Node</a>
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-
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- <li><a href="./SimpleBioC/NodeBase.html">SimpleBioC::NodeBase</a>
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-
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- <li><a href="./SimpleBioC/Passage.html">SimpleBioC::Passage</a>
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-
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- <li><a href="./SimpleBioC/Relation.html">SimpleBioC::Relation</a>
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-
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- <li><a href="./SimpleBioC/Sentence.html">SimpleBioC::Sentence</a>
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-
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- </ul>
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- </nav>
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+ </div>
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  </div>
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  </nav>
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- <div id="documentation">
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- <h1 class="module">module BioCWriter</h1>
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+ <main role="main" aria-labelledby="module-BioCWriter">
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+ <h1 id="module-BioCWriter" class="module">
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+ module BioCWriter
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+ </h1>
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- <div id="description" class="description">
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+ <section class="description">
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- </div><!-- description -->
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+ </section>
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@@ -157,10 +110,11 @@
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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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+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section">
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+ <header>
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+ <h3>Public Instance Methods</h3>
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+ </header>
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  <div id="method-i-write" class="method-detail ">
@@ -182,7 +136,7 @@
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  <div class="method-source-code" id="write-source">
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- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 6</span>
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+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 8</span>
186
140
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">write</span>(<span class="ruby-identifier">collection</span>, <span class="ruby-identifier">options</span> = {})
187
141
  <span class="ruby-identifier">options</span>[<span class="ruby-value">:save_with</span>] = <span class="ruby-value">1</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:save_with</span>].<span class="ruby-identifier">nil?</span>
188
142
  <span class="ruby-identifier">builder</span> = <span class="ruby-constant">Nokogiri</span><span class="ruby-operator">::</span><span class="ruby-constant">XML</span><span class="ruby-operator">::</span><span class="ruby-constant">Builder</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:encoding</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&#39;UTF-8&#39;</span>) <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">xml</span><span class="ruby-operator">|</span>
@@ -191,14 +145,14 @@
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  <span class="ruby-keyword">end</span>
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146
  <span class="ruby-identifier">builder</span>.<span class="ruby-identifier">to_xml</span>(<span class="ruby-identifier">options</span>)
193
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  <span class="ruby-keyword">end</span></pre>
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- </div><!-- write-source -->
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+ </div>
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  </div>
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@@ -220,7 +174,7 @@
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  <div class="method-source-code" id="write_annotation-source">
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- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 63</span>
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+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 65</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">write_annotation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">annotation</span>)
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  <span class="ruby-keyword">if</span> <span class="ruby-identifier">annotation</span>.<span class="ruby-identifier">id</span>.<span class="ruby-identifier">nil?</span>
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  <span class="ruby-identifier">attribute</span> = <span class="ruby-keyword">nil</span>
@@ -229,18 +183,18 @@
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183
  <span class="ruby-keyword">end</span>
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184
  <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">annotation</span>(<span class="ruby-identifier">attribute</span>) {
231
185
  <span class="ruby-identifier">write_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">annotation</span>)
232
- <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">text_</span> <span class="ruby-identifier">annotation</span>.<span class="ruby-identifier">text</span>
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186
  <span class="ruby-identifier">annotation</span>.<span class="ruby-identifier">locations</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">write_location</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">l</span>)}
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+ <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">text_</span> <span class="ruby-identifier">annotation</span>.<span class="ruby-identifier">text</span>
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188
  }
235
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  <span class="ruby-keyword">end</span></pre>
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  <div id="method-i-write_collection" class="method-detail ">
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- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 23</span>
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+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 25</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">write_collection</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">collection</span>)
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@@ -272,14 +226,14 @@
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  <span class="ruby-identifier">collection</span>.<span class="ruby-identifier">documents</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">d</span><span class="ruby-operator">|</span> <span class="ruby-identifier">write_document</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">d</span>)}
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  }
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  <div id="method-i-write_document" class="method-detail ">
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- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 33</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">write_document</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">document</span>)
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  <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">document</span> {
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  <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">id_</span> <span class="ruby-identifier">document</span>.<span class="ruby-identifier">id</span>
@@ -310,14 +264,14 @@
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  <span class="ruby-identifier">document</span>.<span class="ruby-identifier">relations</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">r</span><span class="ruby-operator">|</span> <span class="ruby-identifier">write_relation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">r</span>)}
311
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  }
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  <div id="method-i-write_infon" class="method-detail ">
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">write_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">obj</span>)
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  <span class="ruby-identifier">obj</span>.<span class="ruby-identifier">infons</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span>, <span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
345
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  <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">infon</span>(<span class="ruby-value">:key</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">k</span>) {
@@ -347,14 +301,14 @@
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  }
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  <div id="method-i-write_location" class="method-detail ">
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">write_location</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">location</span>)
381
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  <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">location</span>(<span class="ruby-value">:offset</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">location</span>.<span class="ruby-identifier">offset</span>, <span class="ruby-value">:length</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">location</span>.<span class="ruby-identifier">length</span>)
382
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  <span class="ruby-keyword">end</span></pre>
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  <div id="method-i-write_node" class="method-detail ">
@@ -409,18 +363,18 @@
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- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 92</span>
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+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 94</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">write_node</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">node</span>)
414
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  <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">node_</span>(<span class="ruby-value">:refid</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">node</span>.<span class="ruby-identifier">refid</span>, <span class="ruby-value">:role</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">node</span>.<span class="ruby-identifier">role</span>)
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  <span class="ruby-keyword">end</span></pre>
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  <div id="method-i-write_passage" class="method-detail ">
@@ -442,25 +396,25 @@
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- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 42</span>
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+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 44</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">write_passage</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">passage</span>)
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  <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">passage</span> {
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  <span class="ruby-identifier">write_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">passage</span>)
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  <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">offset</span> <span class="ruby-identifier">passage</span>.<span class="ruby-identifier">offset</span>
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  <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">text_</span> <span class="ruby-identifier">passage</span>.<span class="ruby-identifier">text</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">passage</span>.<span class="ruby-identifier">text</span>.<span class="ruby-identifier">nil?</span>
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- <span class="ruby-identifier">passage</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span> <span class="ruby-identifier">write_sentence</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">s</span>)}
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  <span class="ruby-identifier">passage</span>.<span class="ruby-identifier">annotations</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span> <span class="ruby-identifier">write_annotation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">a</span>)}
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+ <span class="ruby-identifier">passage</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span> <span class="ruby-identifier">write_sentence</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">s</span>)}
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  <span class="ruby-identifier">passage</span>.<span class="ruby-identifier">relations</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">r</span><span class="ruby-operator">|</span> <span class="ruby-identifier">write_relation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">r</span>)}
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  }
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  <span class="ruby-keyword">end</span></pre>
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- </div><!-- write_passage-source -->
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+ </div>
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  </div>
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- </div><!-- write_passage-method -->
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+ </div>
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  <div id="method-i-write_relation" class="method-detail ">
@@ -482,7 +436,7 @@
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  <div class="method-source-code" id="write_relation-source">
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- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 76</span>
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+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 78</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">write_relation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">relation</span>)
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  <span class="ruby-keyword">if</span> <span class="ruby-identifier">relation</span>.<span class="ruby-identifier">id</span>.<span class="ruby-identifier">nil?</span>
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  <span class="ruby-identifier">attribute</span> = <span class="ruby-keyword">nil</span>
@@ -494,14 +448,14 @@
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  <span class="ruby-identifier">relation</span>.<span class="ruby-identifier">nodes</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">n</span><span class="ruby-operator">|</span> <span class="ruby-identifier">write_node</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">n</span>)}
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  }
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  <span class="ruby-keyword">end</span></pre>
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- </div><!-- write_relation-source -->
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+ </div>
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  </div>
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- </div><!-- write_relation-method -->
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+ </div>
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  <div id="method-i-write_sentence" class="method-detail ">
@@ -523,7 +477,7 @@
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  <div class="method-source-code" id="write_sentence-source">
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- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 53</span>
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+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 55</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">write_sentence</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">sentence</span>)
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  <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">sentence</span> {
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  <span class="ruby-identifier">write_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">sentence</span>)
@@ -533,26 +487,25 @@
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  <span class="ruby-identifier">sentence</span>.<span class="ruby-identifier">relations</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">r</span><span class="ruby-operator">|</span> <span class="ruby-identifier">write_relation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">r</span>)}
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  }
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  <span class="ruby-keyword">end</span></pre>
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- </div><!-- write_sentence-source -->
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+ </div>
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  </div>
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- </div><!-- write_sentence-method -->
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+ </div>
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- </section><!-- public-instance-method-details -->
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+ </section>
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- </section><!-- 5Buntitled-5D -->
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-
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- </div><!-- documentation -->
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+ </section>
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+ </main>
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- <footer id="validator-badges">
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- <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.
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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 id="validator-badges" role="contentinfo">
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+ <p><a href="http://validator.w3.org/check/referer">Validate</a>
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+ <p>Generated by <a href="http://docs.seattlerb.org/rdoc/">RDoc</a> 4.2.0.
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+ <p>Based on <a href="http://deveiate.org/projects/Darkfish-RDoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
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  </footer>
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