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/index.html CHANGED
@@ -2,63 +2,73 @@
2
2
 
3
3
  <html>
4
4
  <head>
5
- <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
5
+ <meta charset="UTF-8">
6
6
 
7
7
  <title>RDoc Documentation</title>
8
8
 
9
- <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
10
-
11
9
  <script type="text/javascript">
12
10
  var rdoc_rel_prefix = "./";
13
11
  </script>
14
12
 
15
- <script type="text/javascript" charset="utf-8" src="./js/jquery.js"></script>
16
- <script type="text/javascript" charset="utf-8" src="./js/navigation.js"></script>
17
- <script type="text/javascript" charset="utf-8" src="./js/search_index.js"></script>
18
- <script type="text/javascript" charset="utf-8" src="./js/search.js"></script>
19
- <script type="text/javascript" charset="utf-8" src="./js/searcher.js"></script>
20
- <script type="text/javascript" charset="utf-8" src="./js/darkfish.js"></script>
13
+ <script src="./js/jquery.js"></script>
14
+ <script src="./js/darkfish.js"></script>
15
+
16
+ <link href="./css/fonts.css" rel="stylesheet">
17
+ <link href="./css/rdoc.css" rel="stylesheet">
18
+
19
+
21
20
 
21
+ <body id="top" role="document" class="file">
22
+ <nav role="navigation">
23
+ <div id="project-navigation">
24
+ <div id="home-section" role="region" title="Quick navigation" class="nav-section">
25
+ <h2>
26
+ <a href="./index.html" rel="home">Home</a>
27
+ </h2>
22
28
 
23
- <body>
24
- <nav id="metadata">
25
- <nav id="home-section" class="section">
26
- <h3 class="section-header">
27
- <a href="./index.html">Home</a>
29
+ <div id="table-of-contents-navigation">
30
+ <a href="./table_of_contents.html#pages">Pages</a>
28
31
  <a href="./table_of_contents.html#classes">Classes</a>
29
32
  <a href="./table_of_contents.html#methods">Methods</a>
30
- </h3>
31
- </nav>
33
+ </div>
34
+ </div>
32
35
 
33
36
 
34
- <nav id="search-section" class="section project-section" class="initially-hidden">
37
+ <div id="search-section" role="search" class="project-section initially-hidden">
35
38
  <form action="#" method="get" accept-charset="utf-8">
36
- <h3 class="section-header">
37
- <input type="text" name="search" placeholder="Search" id="search-field"
39
+ <div id="search-field-wrapper">
40
+ <input id="search-field" role="combobox" aria-label="Search"
41
+ aria-autocomplete="list" aria-controls="search-results"
42
+ type="text" name="search" placeholder="Search" spellcheck="false"
38
43
  title="Type to search, Up and Down to navigate, Enter to load">
39
- </h3>
40
- </form>
44
+ </div>
41
45
 
42
- <ul id="search-results" class="initially-hidden"></ul>
43
- </nav>
46
+ <ul id="search-results" aria-label="Search Results"
47
+ aria-busy="false" aria-expanded="false"
48
+ aria-atomic="false" class="initially-hidden"></ul>
49
+ </form>
50
+ </div>
44
51
 
52
+ </div>
45
53
 
46
54
  <div id="project-metadata">
47
- <nav id="fileindex-section" class="section project-section">
48
- <h3 class="section-header">Pages</h3>
55
+ <div id="fileindex-section" class="nav-section">
56
+ <h3>Pages</h3>
49
57
 
50
- <ul>
58
+ <ul class="link-list">
51
59
 
52
- <li class="file"><a href="./README_md.html">README</a>
60
+ <li><a href="./README_md.html">README</a>
53
61
 
54
62
  </ul>
55
- </nav>
63
+ </div>
56
64
 
57
- <nav id="classindex-section" class="section project-section">
58
- <h3 class="section-header">Class and Module Index</h3>
65
+ <div id="classindex-section" class="nav-section">
66
+ <h3>Class and Module Index</h3>
59
67
 
60
68
  <ul class="link-list">
61
69
 
70
+ <li><a href="./BioCMerger.html">BioCMerger</a>
71
+
62
72
  <li><a href="./BioCReader.html">BioCReader</a>
63
73
 
64
74
  <li><a href="./BioCWriter.html">BioCWriter</a>
@@ -84,14 +94,15 @@
84
94
  <li><a href="./SimpleBioC/Sentence.html">SimpleBioC::Sentence</a>
85
95
 
86
96
  </ul>
87
- </nav>
97
+ </div>
88
98
 
89
99
  </div>
90
100
  </nav>
91
101
 
92
- <div id="documentation" class="description">
102
+ <main role="main">
93
103
 
94
- <h1 id="label-SimpleBioC"><a href="SimpleBioC.html">SimpleBioC</a><span><a href="#label-SimpleBioC">&para;</a> <a href="#documentation">&uarr;</a></span></h1>
104
+
105
+ <h1 id="label-SimpleBioC"><a href="SimpleBioC.html">SimpleBioC</a><span><a href="#label-SimpleBioC">&para;</a> <a href="#top">&uarr;</a></span></h1>
95
106
 
96
107
  <p><a href="SimpleBioC.html">SimpleBioC</a> is a simple parser / builder for
97
108
  BioC data format. BioC is a simple XML format to share text documents and
@@ -99,7 +110,7 @@ annotations. You can find more information about BioC from the official
99
110
  BioC web site (<a
100
111
  href="http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/">www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/</a>)</p>
101
112
 
102
- <h2 id="label-Feature%3A">Feature:<span><a href="#label-Feature%3A">&para;</a> <a href="#documentation">&uarr;</a></span></h2>
113
+ <h2 id="label-Feature-3A">Feature:<span><a href="#label-Feature-3A">&para;</a> <a href="#top">&uarr;</a></span></h2>
103
114
  <ul><li>
104
115
  <p>Parse &amp; convert a BioC document to an object instance compatible to
105
116
  BioC DTD</p>
@@ -109,11 +120,12 @@ BioC DTD</p>
109
120
  <p>Build a BioC document from an object instance</p>
110
121
  </li></ul>
111
122
 
112
- <h2 id="label-Installation">Installation<span><a href="#label-Installation">&para;</a> <a href="#documentation">&uarr;</a></span></h2>
123
+ <h2 id="label-Installation">Installation<span><a href="#label-Installation">&para;</a> <a href="#top">&uarr;</a></span></h2>
113
124
 
114
125
  <p>Add this line to your application&#39;s Gemfile:</p>
115
126
 
116
- <pre>gem &#39;simple_bioc&#39;</pre>
127
+ <pre class="ruby"><span class="ruby-identifier">gem</span> <span class="ruby-string">&#39;simple_bioc&#39;</span>
128
+ </pre>
117
129
 
118
130
  <p>And then execute:</p>
119
131
 
@@ -123,7 +135,7 @@ BioC DTD</p>
123
135
 
124
136
  <pre>$ gem install simple_bioc</pre>
125
137
 
126
- <h2 id="label-Simple+Usages">Simple Usages<span><a href="#label-Simple+Usages">&para;</a> <a href="#documentation">&uarr;</a></span></h2>
138
+ <h2 id="label-Simple+Usages">Simple Usages<span><a href="#label-Simple+Usages">&para;</a> <a href="#top">&uarr;</a></span></h2>
127
139
 
128
140
  <p>Include library</p>
129
141
 
@@ -132,7 +144,8 @@ BioC DTD</p>
132
144
 
133
145
  <p>Parse with a file name (path)</p>
134
146
 
135
- <pre>collection = SimpleBioC::from_xml(filename)</pre>
147
+ <pre class="ruby"><span class="ruby-identifier">collection</span> = <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-identifier">from_xml</span>(<span class="ruby-identifier">filename</span>)
148
+ </pre>
136
149
 
137
150
  <p>Traverse &amp; Manipulate Data. Data structure are almost the same as the
138
151
  DTD. Please refer <a
@@ -141,32 +154,36 @@ documents</a> and <a
141
154
  href="http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/BioCDTD.html">the
142
155
  BioC DTD</a>.</p>
143
156
 
144
- <pre>puts collection.documents[2].passages[0].text</pre>
157
+ <pre class="ruby"><span class="ruby-identifier">puts</span> <span class="ruby-identifier">collection</span>.<span class="ruby-identifier">documents</span>[<span class="ruby-value">2</span>].<span class="ruby-identifier">passages</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">text</span>
158
+ </pre>
145
159
 
146
160
  <p>Build XML text from data</p>
147
161
 
148
- <pre>puts SimpleBioC::to_xml(collection)</pre>
162
+ <pre class="ruby"><span class="ruby-identifier">puts</span> <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-identifier">to_xml</span>(<span class="ruby-identifier">collection</span>)
163
+ </pre>
149
164
 
150
- <h2 id="label-Options">Options<span><a href="#label-Options">&para;</a> <a href="#documentation">&uarr;</a></span></h2>
165
+ <h2 id="label-Options">Options<span><a href="#label-Options">&para;</a> <a href="#top">&uarr;</a></span></h2>
151
166
 
152
- <h3 id="label-Specify+set+of+%3Cdocument%3Es+to+parse">Specify set of &lt;document&gt;s to parse<span><a href="#label-Specify+set+of+%3Cdocument%3Es+to+parse">&para;</a> <a href="#documentation">&uarr;</a></span></h3>
167
+ <h3 id="label-Specify+set+of+-3Cdocument-3Es+to+parse">Specify set of &lt;document&gt;s to parse<span><a href="#label-Specify+set+of+-3Cdocument-3Es+to+parse">&para;</a> <a href="#top">&uarr;</a></span></h3>
153
168
 
154
169
  <p>You can parse only a set of document elements in a large xml document
155
170
  instead of parsing all the document elements. It may decrease the
156
171
  processing time. For example, the following code will return a collection
157
172
  with two documents (“1234”, “4567”).</p>
158
173
 
159
- <pre>collection = SimpleBioc::from_xml(filename, {documents: [&quot;1234&quot;, &quot;4567&quot;]})</pre>
174
+ <pre class="ruby"><span class="ruby-identifier">collection</span> = <span class="ruby-constant">SimpleBioc</span><span class="ruby-operator">::</span><span class="ruby-identifier">from_xml</span>(<span class="ruby-identifier">filename</span>, {<span class="ruby-identifier">documents</span><span class="ruby-operator">:</span> [<span class="ruby-string">&quot;1234&quot;</span>, <span class="ruby-string">&quot;4567&quot;</span>]})
175
+ </pre>
160
176
 
161
- <h3 id="label-No+whitespace+in+output">No whitespace in output<span><a href="#label-No+whitespace+in+output">&para;</a> <a href="#documentation">&uarr;</a></span></h3>
177
+ <h3 id="label-No+whitespace+in+output">No whitespace in output<span><a href="#label-No+whitespace+in+output">&para;</a> <a href="#top">&uarr;</a></span></h3>
162
178
 
163
179
  <p>By default, outputs of SimpleBioC::to_xml() will be formatted with
164
180
  whitespace. If you do not want this whitespace, you should pass
165
181
  &#39;save_with&#39; option with 0 to the to_xml() function.</p>
166
182
 
167
- <pre>puts SimpleBioC::to_xml(collection, {save_with:0})</pre>
183
+ <pre class="ruby"><span class="ruby-identifier">puts</span> <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-identifier">to_xml</span>(<span class="ruby-identifier">collection</span>, {<span class="ruby-identifier">save_with</span>:<span class="ruby-value">0</span>})
184
+ </pre>
168
185
 
169
- <h2 id="label-Sample">Sample<span><a href="#label-Sample">&para;</a> <a href="#documentation">&uarr;</a></span></h2>
186
+ <h2 id="label-Sample">Sample<span><a href="#label-Sample">&para;</a> <a href="#top">&uarr;</a></span></h2>
170
187
 
171
188
  <p>More samples can be found in Samples directory</p>
172
189
 
@@ -205,7 +222,7 @@ whitespace. If you do not want this whitespace, you should pass
205
222
  <span class="ruby-identifier">puts</span> <span class="ruby-identifier">xml</span>
206
223
  </pre>
207
224
 
208
- <h2 id="label-Contributing">Contributing<span><a href="#label-Contributing">&para;</a> <a href="#documentation">&uarr;</a></span></h2>
225
+ <h2 id="label-Contributing">Contributing<span><a href="#label-Contributing">&para;</a> <a href="#top">&uarr;</a></span></h2>
209
226
  <ol><li>
210
227
  <p>Fork it</p>
211
228
  </li><li>
@@ -219,17 +236,18 @@ feature&#39;</code>)</p>
219
236
  <p>Create new Pull Request</p>
220
237
  </li></ol>
221
238
 
222
- <h2 id="label-LICENSE">LICENSE<span><a href="#label-LICENSE">&para;</a> <a href="#documentation">&uarr;</a></span></h2>
239
+ <h2 id="label-LICENSE">LICENSE<span><a href="#label-LICENSE">&para;</a> <a href="#top">&uarr;</a></span></h2>
223
240
 
224
241
  <p>Copyright © 2013, Dongseop Kwon</p>
225
242
 
226
243
  <p>Released under the MIT License.</p>
227
- </div>
244
+ </main>
245
+
228
246
 
229
247
 
230
- <footer id="validator-badges">
231
- <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
232
- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.
233
- <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
248
+ <footer id="validator-badges" role="contentinfo">
249
+ <p><a href="http://validator.w3.org/check/referer">Validate</a>
250
+ <p>Generated by <a href="http://docs.seattlerb.org/rdoc/">RDoc</a> 4.2.0.
251
+ <p>Based on <a href="http://deveiate.org/projects/Darkfish-RDoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
234
252
  </footer>
235
253
 
data/html/js/darkfish.js CHANGED
@@ -44,28 +44,6 @@ function hookSourceViews() {
44
44
  $('.method-heading').click( showSource );
45
45
  };
46
46
 
47
- function toggleDebuggingSection() {
48
- $('.debugging-section').slideToggle();
49
- };
50
-
51
- function hookDebuggingToggle() {
52
- $('#debugging-toggle img').click( toggleDebuggingSection );
53
- };
54
-
55
- function hookTableOfContentsToggle() {
56
- $('.indexpage li .toc-toggle').each( function() {
57
- $(this).click( function() {
58
- $(this).toggleClass('open');
59
- });
60
-
61
- var section = $(this).next();
62
-
63
- $(this).click( function() {
64
- section.slideToggle();
65
- });
66
- });
67
- }
68
-
69
47
  function hookSearch() {
70
48
  var input = $('#search-field').eq(0);
71
49
  var result = $('#search-results').eq(0);
@@ -143,13 +121,41 @@ function highlightClickTarget( event ) {
143
121
  };
144
122
  };
145
123
 
124
+ function loadAsync(path, success) {
125
+ $.ajax({
126
+ url: rdoc_rel_prefix + path,
127
+ dataType: 'script',
128
+ success: success,
129
+ cache: true
130
+ });
131
+ };
146
132
 
147
133
  $(document).ready( function() {
148
134
  hookSourceViews();
149
- hookDebuggingToggle();
150
- hookSearch();
151
135
  highlightLocationTarget();
152
- hookTableOfContentsToggle();
153
-
154
136
  $('ul.link-list a').bind( "click", highlightClickTarget );
137
+
138
+ var search_scripts_loaded = {
139
+ navigation_loaded: false,
140
+ search_loaded: false,
141
+ search_index_loaded: false,
142
+ searcher_loaded: false,
143
+ }
144
+
145
+ var search_success_function = function(variable) {
146
+ return (function (data, status, xhr) {
147
+ search_scripts_loaded[variable] = true;
148
+
149
+ if (search_scripts_loaded['navigation_loaded'] == true &&
150
+ search_scripts_loaded['search_loaded'] == true &&
151
+ search_scripts_loaded['search_index_loaded'] == true &&
152
+ search_scripts_loaded['searcher_loaded'] == true)
153
+ hookSearch();
154
+ });
155
+ }
156
+
157
+ loadAsync('js/navigation.js', search_success_function('navigation_loaded'));
158
+ loadAsync('js/search.js', search_success_function('search_loaded'));
159
+ loadAsync('js/search_index.js', search_success_function('search_index_loaded'));
160
+ loadAsync('js/searcher.js', search_success_function('searcher_loaded'));
155
161
  });