simple_bioc 0.0.2 → 0.0.3
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- checksums.yaml +4 -4
- data/README.md +17 -3
- data/Rakefile +2 -1
- data/html/BioCReader.html +40 -30
- data/html/BioCWriter.html +14 -12
- data/html/README_md.html +31 -5
- data/html/SimpleBioC/NodeBase.html +3 -3
- data/html/SimpleBioC.html +48 -9
- data/html/created.rid +7 -7
- data/html/index.html +26 -3
- data/html/js/search_index.js +1 -1
- data/html/table_of_contents.html +5 -2
- data/lib/simple_bioc/bioc_reader.rb +24 -14
- data/lib/simple_bioc/bioc_writer.rb +4 -2
- data/lib/simple_bioc/version.rb +1 -1
- data/lib/simple_bioc.rb +29 -5
- data/simple_bioc.gemspec +1 -1
- data/spec/file_check_spec.rb +13 -0
- data/spec/simple_bioc_spec.rb +21 -10
- metadata +8 -4
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA1:
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-
metadata.gz:
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data.tar.gz:
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metadata.gz: ac0961af71c5744bc71ea16221f5325af35e4583
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data.tar.gz: 9f407b566a8dc6687d53f8145fc600f3d73039eb
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: ab77aa143472f5959a0ea97702ae68dba76bb6b75542086a065b625216234d8912a52d83a087f6acf3c553f0ee8adf5050ebafd94833171d9dd84d7a34124e0a
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7
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data.tar.gz: b02aa1b1d73ff1d0c6ed2650c0170ff88e22fd01a6e6df7d9508cf365e548bd6bf0413616a80a765b2fc35f9d3e1da2d20edf41cece737ceeb26577d39068251
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data/README.md
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-
#
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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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@@ -24,7 +24,7 @@ Or install it yourself as:
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$ gem install simple_bioc
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## Usages
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## Simple Usages
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Include library
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@@ -35,7 +35,7 @@ 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](
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Traverse & Manipulate Data. Data structure are almost the same as the DTD. Please refer [library documents](http://rubydoc.info/gems/simple_bioc/0.0.2/frames) 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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@@ -43,6 +43,20 @@ Build XML text from data
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puts SimpleBioC::to_xml(collection)
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## Options
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### Specify set of <document>s to parse
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You can parse only a set of document elements in a large xml document instead of parsing all the document elements. It may decrease the processing time. For example, the following code will return a collection with two documents ("1234", "4567").
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collection = SimpleBioc::from_xml(filename, {documents: ["1234", "4567"]})
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### No whitespace in output
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By default, outputs of SimpleBioC::to_xml() will be formatted with whitespace. If you do not want this whitespace, you should pass 'save_with' option with 0 to the to_xml() function.
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puts SimpleBioC::to_xml(collection, {save_with:0})
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## Sample
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data/Rakefile
CHANGED
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require "bundler/gem_tasks"
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require 'rspec/core/rake_task'
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require 'rdoc/task'
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require 'yard'
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task :default => [:spec]
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RSpec::Core::RakeTask.new do |t|
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@@ -10,4 +11,4 @@ end
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Rake::RDocTask.new do |rd|
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rd.main = "README.md"
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rd.rdoc_files.include("README.md", "lib/**/*.rb")
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end
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end
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data/html/BioCReader.html
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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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class="method-args">(path, options)</span>
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<div class="method-source-code" id="read-source">
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 7</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">read</span>(<span class="ruby-identifier">path</span>)
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">read</span>(<span class="ruby-identifier">path</span>, <span class="ruby-identifier">options</span>)
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<span class="ruby-identifier">collection</span> = <span class="ruby-keyword">nil</span>
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<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>) <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">file</span><span class="ruby-operator">|</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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@@ -200,7 +200,7 @@
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<span class="ruby-identifier">fail</span> <span class="ruby-string">'Wrong format'</span>
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<span class="ruby-keyword">end</span>
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<span class="ruby-identifier">collection</span> = <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-constant">Collection</span>.<span class="ruby-identifier">new</span>
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<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">read_collection</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">collection</span>, <span class="ruby-identifier">options</span>)
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<span class="ruby-keyword">end</span>
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<span class="ruby-identifier">collection</span>
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<div class="method-heading">
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<span class="method-name">read_annotation</span><span
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class="method-args">(xml, annotation)</span>
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class="method-args">(xml, annotation, options = {})</span>
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<div class="method-source-code" id="read_annotation-source">
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line
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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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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 86</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>, <span class="ruby-identifier">options</span> = {})
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<span class="ruby-identifier">annotation</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">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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<span class="ruby-identifier">read_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">annotation</span>)
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<span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">annotation</span>, <span class="ruby-string">"location"</span>)
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<span class="ruby-keyword">true</span>
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<span class="ruby-keyword">end</span></pre>
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</div><!-- read_annotation-source -->
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<div class="method-heading">
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<span class="method-name">read_collection</span><span
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class="method-args">(xml, collection)</span>
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class="method-args">(xml, collection, options = {})</span>
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<div class="method-source-code" id="read_collection-source">
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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-keyword">def</span> <span class="ruby-identifier">read_collection</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">collection</span>, <span class="ruby-identifier">options</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-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">collection</span>, <span class="ruby-string">"document"</span>, <span class="ruby-identifier">options</span>)
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<span class="ruby-keyword">end</span></pre>
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</div><!-- read_collection-source -->
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<div class="method-heading">
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<span class="method-name">read_document</span><span
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class="method-args">(xml, document)</span>
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class="method-args">(xml, document, options = {})</span>
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<div class="method-source-code" id="read_document-source">
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 55</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">read_document</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">document</span>)
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<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>, <span class="ruby-identifier">options</span> = {})
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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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<span class="ruby-keyword">if</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:documents</span>].<span class="ruby-identifier">kind_of?</span>(<span class="ruby-constant">Array</span>) <span class="ruby-operator">&&</span> <span class="ruby-operator">!</span><span class="ruby-identifier">options</span>[<span class="ruby-value">:documents</span>].<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">document</span>.<span class="ruby-identifier">id</span>)
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<span class="ruby-keyword">return</span> <span class="ruby-keyword">false</span>
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<span class="ruby-keyword">end</span>
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<span class="ruby-identifier">read_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">document</span>)
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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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<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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<span class="ruby-keyword">true</span>
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<span class="ruby-keyword">end</span></pre>
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</div><!-- read_document-source -->
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<div class="method-heading">
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<span class="method-name">read_location</span><span
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class="method-args">(xml, location)</span>
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class="method-args">(xml, location, options = {})</span>
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@@ -411,10 +416,11 @@
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<div class="method-source-code" id="read_location-source">
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line
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<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>)
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 101</span>
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<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>, <span class="ruby-identifier">options</span> = {})
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<span class="ruby-identifier">location</span>.<span class="ruby-identifier">offset</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">"offset"</span>]
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<span class="ruby-identifier">location</span>.<span class="ruby-identifier">length</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">"length"</span>]
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<span class="ruby-keyword">true</span>
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<span class="ruby-keyword">end</span></pre>
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</div><!-- read_location-source -->
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<div class="method-heading">
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<span class="method-name">read_node</span><span
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class="method-args">(xml, node)</span>
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class="method-args">(xml, node, options = {})</span>
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@@ -445,10 +451,11 @@
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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
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-
<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>)
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 107</span>
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<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>, <span class="ruby-identifier">options</span> = {})
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<span class="ruby-identifier">node</span>.<span class="ruby-identifier">refid</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">"refid"</span>]
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<span class="ruby-identifier">node</span>.<span class="ruby-identifier">role</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">"role"</span>]
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<span class="ruby-keyword">true</span>
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<span class="ruby-keyword">end</span></pre>
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</div><!-- read_node-source -->
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@@ -464,7 +471,7 @@
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<div class="method-heading">
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|
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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-identifier">xml</span>.<span class="ruby-identifier">infon</span>(<span class="ruby-value">:key</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">k</span>) {
|
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 88</span>
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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">></span> <span class="ruby-identifier">location</span>.<span class="ruby-identifier">offset</span>, <span class="ruby-value">:length</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">location</span>.<span class="ruby-identifier">length</span>)
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|
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|
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 92</span>
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|
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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">></span> <span class="ruby-identifier">node</span>.<span class="ruby-identifier">refid</span>, <span class="ruby-value">:role</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">node</span>.<span class="ruby-identifier">role</span>)
|
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|
|
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 42</span>
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|
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|
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|
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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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|
|
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|
|
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|
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|
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|
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line
|
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|
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 76</span>
|
|
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|
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|
|
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<h3 id="label-Specify+set+of+%3Cdocument%3Es+to+parse">Specify set of <document>s to parse<span><a href="#label-Specify+set+of+%3Cdocument%3Es+to+parse">¶</a> <a href="#documentation">↑</a></span></h3>
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processing time. For example, the following code will return a collection
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with two documents (“1234”, “4567”).</p>
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|
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<h4 id="method-i-from_xml-label-Arguments">Arguments<span><a href="#method-i-from_xml-label-Arguments">¶</a> <a href="#documentation">↑</a></span></h4>
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<h4 id="method-i-from_xml-label-Examples">Examples<span><a href="#method-i-from_xml-label-Examples">¶</a> <a href="#documentation">↑</a></span></h4>
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<pre>collection = SimpleBioC.from_xml("./xml/everything.xml")
|
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collection = SimpleBioC.from_xml("./xml/lemma.xml", {documents:[21785578, 21488974]})</pre>
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|
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|
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|
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<span class="ruby-identifier">options</span>[<span class="ruby-value">:documents</span>] = <span class="ruby-identifier">options</span>[<span class="ruby-value">:documents</span>].<span class="ruby-identifier">map</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">e</span><span class="ruby-operator">|</span> <span class="ruby-identifier">e</span>.<span class="ruby-identifier">to_s</span>} <span class="ruby-keyword">if</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:documents</span>].<span class="ruby-identifier">kind_of?</span>(<span class="ruby-constant">Array</span>)
|
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|
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<span class="ruby-constant">BioCReader</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">file_path</span>, <span class="ruby-identifier">options</span>)
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|
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|
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<h4 id="method-i-to_xml-label-Arguments">Arguments<span><a href="#method-i-to_xml-label-Arguments">¶</a> <a href="#documentation">↑</a></span></h4>
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<h4 id="method-i-to_xml-label-Options">Options<span><a href="#method-i-to_xml-label-Options">¶</a> <a href="#documentation">↑</a></span></h4>
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<pre>output = SimpleBioC.to_xml(collection)
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|
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|
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">to_xml</span>(<span class="ruby-identifier">collection</span>, <span class="ruby-identifier">options</span> = {})
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<span class="ruby-constant">BioCWriter</span>.<span class="ruby-identifier">write</span>(<span class="ruby-identifier">collection</span>, <span class="ruby-identifier">options</span>)
|
|
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|
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README.md
|
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|
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Sat, 21 Dec 2013 09:10:44 -0800
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README.md Sat, 21 Dec 2013 09:10:35 -0800
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lib/simple_bioc.rb Sat, 21 Dec 2013 08:58:11 -0800
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lib/simple_bioc/annotation.rb Fri, 06 Dec 2013 20:52:11 -0800
|
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lib/simple_bioc/bioc_reader.rb
|
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|
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lib/simple_bioc/bioc_writer.rb
|
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|
+
lib/simple_bioc/bioc_reader.rb Sat, 21 Dec 2013 08:39:36 -0800
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|
+
lib/simple_bioc/bioc_writer.rb Sat, 21 Dec 2013 08:09:06 -0800
|
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|
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|
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|
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lib/simple_bioc/node_base.rb Fri, 06 Dec 2013 22:
|
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|
+
lib/simple_bioc/node_base.rb Fri, 06 Dec 2013 22:06:00 -0800
|
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|
lib/simple_bioc/passage.rb Fri, 06 Dec 2013 20:52:11 -0800
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lib/simple_bioc/relation.rb Fri, 06 Dec 2013 20:52:11 -0800
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|
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CHANGED
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|
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|
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<h1 id="label-SimpleBioC"><a href="SimpleBioC.html">SimpleBioC</a><span><a href="#label-SimpleBioC">¶</a> <a href="#documentation">↑</a></span></h1>
|
|
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|
|
|
96
96
|
<p><a href="SimpleBioC.html">SimpleBioC</a> is a simple parser / builder for
|
|
97
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|
BioC data format. BioC is a simple XML format to share text documents and
|
|
@@ -123,7 +123,7 @@ BioC DTD</p>
|
|
|
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|
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|
124
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|
<pre>$ gem install simple_bioc</pre>
|
|
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|
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|
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<h2 id="label-Usages">Usages<span><a href="#label-Usages">¶</a> <a href="#documentation">↑</a></span></h2>
|
|
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|
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<h2 id="label-Simple+Usages">Simple Usages<span><a href="#label-Simple+Usages">¶</a> <a href="#documentation">↑</a></span></h2>
|
|
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127
|
|
|
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128
|
<p>Include library</p>
|
|
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|
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@@ -135,7 +135,11 @@ BioC DTD</p>
|
|
|
135
135
|
<pre>collection = SimpleBioC::from_xml(filename)</pre>
|
|
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|
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|
<p>Traverse & Manipulate Data. Data structure are almost the same as the
|
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|
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DTD. Please refer <a
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DTD. Please refer <a
|
|
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|
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href="http://rubydoc.info/gems/simple_bioc/0.0.2/frames">library
|
|
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|
+
documents</a> and <a
|
|
141
|
+
href="http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/BioCDTD.html">the
|
|
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|
+
BioC DTD</a>.</p>
|
|
139
143
|
|
|
140
144
|
<pre>puts collection.documents[2].passages[0].text</pre>
|
|
141
145
|
|
|
@@ -143,6 +147,25 @@ DTD. Please refer <a href="http://">library documents</a>.</p>
|
|
|
143
147
|
|
|
144
148
|
<pre>puts SimpleBioC::to_xml(collection)</pre>
|
|
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|
|
|
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|
+
<h2 id="label-Options">Options<span><a href="#label-Options">¶</a> <a href="#documentation">↑</a></span></h2>
|
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|
+
<h3 id="label-Specify+set+of+%3Cdocument%3Es+to+parse">Specify set of <document>s to parse<span><a href="#label-Specify+set+of+%3Cdocument%3Es+to+parse">¶</a> <a href="#documentation">↑</a></span></h3>
|
|
153
|
+
|
|
154
|
+
<p>You can parse only a set of document elements in a large xml document
|
|
155
|
+
instead of parsing all the document elements. It may decrease the
|
|
156
|
+
processing time. For example, the following code will return a collection
|
|
157
|
+
with two documents (“1234”, “4567”).</p>
|
|
158
|
+
|
|
159
|
+
<pre>collection = SimpleBioc::from_xml(filename, {documents: ["1234", "4567"]})</pre>
|
|
160
|
+
|
|
161
|
+
<h3 id="label-No+whitespace+in+output">No whitespace in output<span><a href="#label-No+whitespace+in+output">¶</a> <a href="#documentation">↑</a></span></h3>
|
|
162
|
+
|
|
163
|
+
<p>By default, outputs of SimpleBioC::to_xml() will be formatted with
|
|
164
|
+
whitespace. If you do not want this whitespace, you should pass
|
|
165
|
+
'save_with' option with 0 to the to_xml() function.</p>
|
|
166
|
+
|
|
167
|
+
<pre>puts SimpleBioC::to_xml(collection, {save_with:0})</pre>
|
|
168
|
+
|
|
146
169
|
<h2 id="label-Sample">Sample<span><a href="#label-Sample">¶</a> <a href="#documentation">↑</a></span></h2>
|
|
147
170
|
|
|
148
171
|
<p>More samples can be found in Samples directory</p>
|
data/html/js/search_index.js
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
var search_data = {"index":{"searchIndex":["biocreader","biocwriter","simplebioc","annotation","collection","document","location","node","nodebase","passage","relation","sentence","adjust_ref()","adjust_ref()","adjust_ref()","each_relation()","each_relation()","each_relation()","find_node()","find_node()","find_node()","from_xml()","new()","new()","new()","new()","new()","new()","new()","new()","new()","read()","read_annotation()","read_collection()","read_document()","read_infon()","read_int()","read_location()","read_node()","read_passage()","read_recursive()","read_relation()","read_sentence()","read_text()","to_c()","to_c()","to_c()","to_c()","to_s()","to_s()","to_s()","to_s()","to_xml()","write()","write_annotation()","write_collection()","write_document()","write_infon()","write_location()","write_node()","write_passage()","write_relation()","write_sentence()","readme"],"longSearchIndex":["biocreader","biocwriter","simplebioc","simplebioc::annotation","simplebioc::collection","simplebioc::document","simplebioc::location","simplebioc::node","simplebioc::nodebase","simplebioc::passage","simplebioc::relation","simplebioc::sentence","simplebioc::document#adjust_ref()","simplebioc::node#adjust_ref()","simplebioc::relation#adjust_ref()","simplebioc::document#each_relation()","simplebioc::passage#each_relation()","simplebioc::sentence#each_relation()","simplebioc::document#find_node()","simplebioc::passage#find_node()","simplebioc::sentence#find_node()","simplebioc#from_xml()","simplebioc::annotation::new()","simplebioc::collection::new()","simplebioc::document::new()","simplebioc::location::new()","simplebioc::node::new()","simplebioc::nodebase::new()","simplebioc::passage::new()","simplebioc::relation::new()","simplebioc::sentence::new()","biocreader#read()","biocreader#read_annotation()","biocreader#read_collection()","biocreader#read_document()","biocreader#read_infon()","biocreader#read_int()","biocreader#read_location()","biocreader#read_node()","biocreader#read_passage()","biocreader#read_recursive()","biocreader#read_relation()","biocreader#read_sentence()","biocreader#read_text()","simplebioc::collection#to_c()","simplebioc::node#to_c()","simplebioc::relation#to_c()","simplebioc::sentence#to_c()","simplebioc::annotation#to_s()","simplebioc::document#to_s()","simplebioc::location#to_s()","simplebioc::passage#to_s()","simplebioc#to_xml()","biocwriter#write()","biocwriter#write_annotation()","biocwriter#write_collection()","biocwriter#write_document()","biocwriter#write_infon()","biocwriter#write_location()","biocwriter#write_node()","biocwriter#write_passage()","biocwriter#write_relation()","biocwriter#write_sentence()",""],"info":[["BioCReader","","BioCReader.html","",""],["BioCWriter","","BioCWriter.html","",""],["SimpleBioC","","SimpleBioC.html","","<p>SimpleBioC main library\n"],["SimpleBioC::Annotation","","SimpleBioC/Annotation.html","",""],["SimpleBioC::Collection","","SimpleBioC/Collection.html","",""],["SimpleBioC::Document","","SimpleBioC/Document.html","",""],["SimpleBioC::Location","","SimpleBioC/Location.html","",""],["SimpleBioC::Node","","SimpleBioC/Node.html","",""],["SimpleBioC::NodeBase","","SimpleBioC/NodeBase.html","","<p>NodeBase is not
|
|
1
|
+
var search_data = {"index":{"searchIndex":["biocreader","biocwriter","simplebioc","annotation","collection","document","location","node","nodebase","passage","relation","sentence","adjust_ref()","adjust_ref()","adjust_ref()","each_relation()","each_relation()","each_relation()","find_node()","find_node()","find_node()","from_xml()","new()","new()","new()","new()","new()","new()","new()","new()","new()","read()","read_annotation()","read_collection()","read_document()","read_infon()","read_int()","read_location()","read_node()","read_passage()","read_recursive()","read_relation()","read_sentence()","read_text()","to_c()","to_c()","to_c()","to_c()","to_s()","to_s()","to_s()","to_s()","to_xml()","write()","write_annotation()","write_collection()","write_document()","write_infon()","write_location()","write_node()","write_passage()","write_relation()","write_sentence()","readme"],"longSearchIndex":["biocreader","biocwriter","simplebioc","simplebioc::annotation","simplebioc::collection","simplebioc::document","simplebioc::location","simplebioc::node","simplebioc::nodebase","simplebioc::passage","simplebioc::relation","simplebioc::sentence","simplebioc::document#adjust_ref()","simplebioc::node#adjust_ref()","simplebioc::relation#adjust_ref()","simplebioc::document#each_relation()","simplebioc::passage#each_relation()","simplebioc::sentence#each_relation()","simplebioc::document#find_node()","simplebioc::passage#find_node()","simplebioc::sentence#find_node()","simplebioc#from_xml()","simplebioc::annotation::new()","simplebioc::collection::new()","simplebioc::document::new()","simplebioc::location::new()","simplebioc::node::new()","simplebioc::nodebase::new()","simplebioc::passage::new()","simplebioc::relation::new()","simplebioc::sentence::new()","biocreader#read()","biocreader#read_annotation()","biocreader#read_collection()","biocreader#read_document()","biocreader#read_infon()","biocreader#read_int()","biocreader#read_location()","biocreader#read_node()","biocreader#read_passage()","biocreader#read_recursive()","biocreader#read_relation()","biocreader#read_sentence()","biocreader#read_text()","simplebioc::collection#to_c()","simplebioc::node#to_c()","simplebioc::relation#to_c()","simplebioc::sentence#to_c()","simplebioc::annotation#to_s()","simplebioc::document#to_s()","simplebioc::location#to_s()","simplebioc::passage#to_s()","simplebioc#to_xml()","biocwriter#write()","biocwriter#write_annotation()","biocwriter#write_collection()","biocwriter#write_document()","biocwriter#write_infon()","biocwriter#write_location()","biocwriter#write_node()","biocwriter#write_passage()","biocwriter#write_relation()","biocwriter#write_sentence()",""],"info":[["BioCReader","","BioCReader.html","",""],["BioCWriter","","BioCWriter.html","",""],["SimpleBioC","","SimpleBioC.html","","<p>SimpleBioC main library\n"],["SimpleBioC::Annotation","","SimpleBioC/Annotation.html","",""],["SimpleBioC::Collection","","SimpleBioC/Collection.html","",""],["SimpleBioC::Document","","SimpleBioC/Document.html","",""],["SimpleBioC::Location","","SimpleBioC/Location.html","",""],["SimpleBioC::Node","","SimpleBioC/Node.html","",""],["SimpleBioC::NodeBase","","SimpleBioC/NodeBase.html","","<p>NodeBase is not a BioC DTD entity. This is a super class of Annotation\n& Relation.\n"],["SimpleBioC::Passage","","SimpleBioC/Passage.html","",""],["SimpleBioC::Relation","","SimpleBioC/Relation.html","",""],["SimpleBioC::Sentence","","SimpleBioC/Sentence.html","",""],["adjust_ref","SimpleBioC::Document","SimpleBioC/Document.html#method-i-adjust_ref","()",""],["adjust_ref","SimpleBioC::Node","SimpleBioC/Node.html#method-i-adjust_ref","()",""],["adjust_ref","SimpleBioC::Relation","SimpleBioC/Relation.html#method-i-adjust_ref","()",""],["each_relation","SimpleBioC::Document","SimpleBioC/Document.html#method-i-each_relation","()",""],["each_relation","SimpleBioC::Passage","SimpleBioC/Passage.html#method-i-each_relation","()",""],["each_relation","SimpleBioC::Sentence","SimpleBioC/Sentence.html#method-i-each_relation","()",""],["find_node","SimpleBioC::Document","SimpleBioC/Document.html#method-i-find_node","(id)",""],["find_node","SimpleBioC::Passage","SimpleBioC/Passage.html#method-i-find_node","(id)",""],["find_node","SimpleBioC::Sentence","SimpleBioC/Sentence.html#method-i-find_node","(id)",""],["from_xml","SimpleBioC","SimpleBioC.html#method-i-from_xml","(file_path, options = {})","<p>parse a BioC XML file in the given path and convert it into a collection\ninstance\n<p>Arguments\n<p><code>file_path</code> - …\n"],["new","SimpleBioC::Annotation","SimpleBioC/Annotation.html#method-c-new","(parent)",""],["new","SimpleBioC::Collection","SimpleBioC/Collection.html#method-c-new","()",""],["new","SimpleBioC::Document","SimpleBioC/Document.html#method-c-new","(parent)",""],["new","SimpleBioC::Location","SimpleBioC/Location.html#method-c-new","(parent)",""],["new","SimpleBioC::Node","SimpleBioC/Node.html#method-c-new","(parent)",""],["new","SimpleBioC::NodeBase","SimpleBioC/NodeBase.html#method-c-new","(parent)",""],["new","SimpleBioC::Passage","SimpleBioC/Passage.html#method-c-new","(parent)",""],["new","SimpleBioC::Relation","SimpleBioC/Relation.html#method-c-new","(parent)",""],["new","SimpleBioC::Sentence","SimpleBioC/Sentence.html#method-c-new","(parent)",""],["read","BioCReader","BioCReader.html#method-i-read","(path, options)",""],["read_annotation","BioCReader","BioCReader.html#method-i-read_annotation","(xml, annotation, options = {})",""],["read_collection","BioCReader","BioCReader.html#method-i-read_collection","(xml, collection, options = {})",""],["read_document","BioCReader","BioCReader.html#method-i-read_document","(xml, document, options = {})",""],["read_infon","BioCReader","BioCReader.html#method-i-read_infon","(xml, obj)",""],["read_int","BioCReader","BioCReader.html#method-i-read_int","(xml, name)",""],["read_location","BioCReader","BioCReader.html#method-i-read_location","(xml, location, options = {})",""],["read_node","BioCReader","BioCReader.html#method-i-read_node","(xml, node, options = {})",""],["read_passage","BioCReader","BioCReader.html#method-i-read_passage","(xml, passage, options = {})",""],["read_recursive","BioCReader","BioCReader.html#method-i-read_recursive","(xml, obj, name, options = {})",""],["read_relation","BioCReader","BioCReader.html#method-i-read_relation","(xml, relation, options = {})",""],["read_sentence","BioCReader","BioCReader.html#method-i-read_sentence","(xml, sentence, options = {})",""],["read_text","BioCReader","BioCReader.html#method-i-read_text","(xml, name)",""],["to_c","SimpleBioC::Collection","SimpleBioC/Collection.html#method-i-to_c","()",""],["to_c","SimpleBioC::Node","SimpleBioC/Node.html#method-i-to_c","()",""],["to_c","SimpleBioC::Relation","SimpleBioC/Relation.html#method-i-to_c","()",""],["to_c","SimpleBioC::Sentence","SimpleBioC/Sentence.html#method-i-to_c","()",""],["to_s","SimpleBioC::Annotation","SimpleBioC/Annotation.html#method-i-to_s","()",""],["to_s","SimpleBioC::Document","SimpleBioC/Document.html#method-i-to_s","()",""],["to_s","SimpleBioC::Location","SimpleBioC/Location.html#method-i-to_s","()",""],["to_s","SimpleBioC::Passage","SimpleBioC/Passage.html#method-i-to_s","()",""],["to_xml","SimpleBioC","SimpleBioC.html#method-i-to_xml","(collection, options = {})","<p>convert a collection instance to a BioC XML text. Output will return as\nstring\n<p>Arguments\n<p><code>collection</code> - …\n"],["write","BioCWriter","BioCWriter.html#method-i-write","(collection, options = {})",""],["write_annotation","BioCWriter","BioCWriter.html#method-i-write_annotation","(xml, annotation)",""],["write_collection","BioCWriter","BioCWriter.html#method-i-write_collection","(xml, collection)",""],["write_document","BioCWriter","BioCWriter.html#method-i-write_document","(xml, document)",""],["write_infon","BioCWriter","BioCWriter.html#method-i-write_infon","(xml, obj)",""],["write_location","BioCWriter","BioCWriter.html#method-i-write_location","(xml, location)",""],["write_node","BioCWriter","BioCWriter.html#method-i-write_node","(xml, node)",""],["write_passage","BioCWriter","BioCWriter.html#method-i-write_passage","(xml, passage)",""],["write_relation","BioCWriter","BioCWriter.html#method-i-write_relation","(xml, relation)",""],["write_sentence","BioCWriter","BioCWriter.html#method-i-write_sentence","(xml, sentence)",""],["README","","README_md.html","","<p>SimpleBioC\n<p>SimpleBioC is a simple parser / builder for BioC data format. BioC is a\nsimple XML format to …\n"]]}}
|
data/html/table_of_contents.html
CHANGED
|
@@ -30,10 +30,13 @@
|
|
|
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30
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|
31
31
|
<img class="toc-toggle" src="images/transparent.png" alt="" title="toggle headings">
|
|
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32
|
<ul class="initially-hidden">
|
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33
|
-
<li><a href="README_md.html#label-
|
|
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+
<li><a href="README_md.html#label-SimpleBioC">SimpleBioC</a>
|
|
34
34
|
<li><a href="README_md.html#label-Feature%3A">Feature:</a>
|
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35
35
|
<li><a href="README_md.html#label-Installation">Installation</a>
|
|
36
|
-
<li><a href="README_md.html#label-Usages">Usages</a>
|
|
36
|
+
<li><a href="README_md.html#label-Simple+Usages">Simple Usages</a>
|
|
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|
+
<li><a href="README_md.html#label-Options">Options</a>
|
|
38
|
+
<li><a href="README_md.html#label-Specify+set+of+%3Cdocument%3Es+to+parse">Specify set of <document>s to parse</a>
|
|
39
|
+
<li><a href="README_md.html#label-No+whitespace+in+output">No whitespace in output</a>
|
|
37
40
|
<li><a href="README_md.html#label-Sample">Sample</a>
|
|
38
41
|
<li><a href="README_md.html#label-Contributing">Contributing</a>
|
|
39
42
|
<li><a href="README_md.html#label-LICENSE">LICENSE</a>
|
|
@@ -4,7 +4,7 @@ Dir[File.dirname(__FILE__) + '/*.rb'].each {|file| require file }
|
|
|
4
4
|
module BioCReader
|
|
5
5
|
module_function
|
|
6
6
|
|
|
7
|
-
def read(path)
|
|
7
|
+
def read(path, options)
|
|
8
8
|
collection = nil
|
|
9
9
|
File.open(path) do |file|
|
|
10
10
|
xml_doc = Nokogiri::XML(file) do |config|
|
|
@@ -15,7 +15,7 @@ module BioCReader
|
|
|
15
15
|
fail 'Wrong format'
|
|
16
16
|
end
|
|
17
17
|
collection = SimpleBioC::Collection.new
|
|
18
|
-
read_collection(xml, collection)
|
|
18
|
+
read_collection(xml, collection, options)
|
|
19
19
|
end
|
|
20
20
|
|
|
21
21
|
collection
|
|
@@ -35,68 +35,78 @@ module BioCReader
|
|
|
35
35
|
xml.xpath("infon").each{ |i| obj.infons[i["key"]] = i.content}
|
|
36
36
|
end
|
|
37
37
|
|
|
38
|
-
def read_recursive(xml, obj, name)
|
|
38
|
+
def read_recursive(xml, obj, name, options = {})
|
|
39
39
|
target_class = SimpleBioC.const_get(name.capitalize)
|
|
40
40
|
xml.xpath(name).each do |node|
|
|
41
41
|
instance = target_class.new(obj)
|
|
42
|
-
send(:"read_#{name}", node, instance)
|
|
43
|
-
obj.instance_variable_get(:"@#{name}s") << instance
|
|
42
|
+
ret = send(:"read_#{name}", node, instance, options)
|
|
43
|
+
obj.instance_variable_get(:"@#{name}s") << instance if ret
|
|
44
44
|
end
|
|
45
45
|
end
|
|
46
46
|
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|
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|
-
def read_collection(xml, collection)
|
|
47
|
+
def read_collection(xml, collection, options = {})
|
|
48
48
|
collection.source = read_text(xml, "source")
|
|
49
49
|
collection.date = read_text(xml, "date")
|
|
50
50
|
collection.key = read_text(xml, "key")
|
|
51
51
|
read_infon(xml, collection)
|
|
52
|
-
read_recursive(xml, collection, "document")
|
|
52
|
+
read_recursive(xml, collection, "document", options)
|
|
53
53
|
end
|
|
54
54
|
|
|
55
|
-
def read_document(xml, document)
|
|
55
|
+
def read_document(xml, document, options = {})
|
|
56
56
|
document.id = read_text(xml, "id")
|
|
57
|
+
if options[:documents].kind_of?(Array) && !options[:documents].include?(document.id)
|
|
58
|
+
return false
|
|
59
|
+
end
|
|
57
60
|
read_infon(xml, document)
|
|
58
61
|
read_recursive(xml, document, "passage")
|
|
59
62
|
read_recursive(xml, document, "relation")
|
|
60
63
|
document.adjust_ref
|
|
64
|
+
true
|
|
61
65
|
end
|
|
62
66
|
|
|
63
|
-
def read_passage(xml, passage)
|
|
67
|
+
def read_passage(xml, passage, options = {})
|
|
64
68
|
passage.text = read_text(xml, "text")
|
|
65
69
|
passage.offset = read_int(xml, "offset")
|
|
66
70
|
read_infon(xml, passage)
|
|
67
71
|
read_recursive(xml, passage, "sentence")
|
|
68
72
|
read_recursive(xml, passage, "annotation")
|
|
69
73
|
read_recursive(xml, passage, "relation")
|
|
74
|
+
true
|
|
70
75
|
end
|
|
71
76
|
|
|
72
|
-
def read_sentence(xml, sentence)
|
|
77
|
+
def read_sentence(xml, sentence, options = {})
|
|
73
78
|
sentence.text = read_text(xml, "text")
|
|
74
79
|
sentence.offset = read_int(xml, "offset")
|
|
75
80
|
read_infon(xml, sentence)
|
|
76
81
|
read_recursive(xml, sentence, "annotation")
|
|
77
82
|
read_recursive(xml, sentence, "relation")
|
|
83
|
+
true
|
|
78
84
|
end
|
|
79
85
|
|
|
80
|
-
def read_annotation(xml, annotation)
|
|
86
|
+
def read_annotation(xml, annotation, options = {})
|
|
81
87
|
annotation.id = xml["id"]
|
|
82
88
|
annotation.text = read_text(xml, "text")
|
|
83
89
|
read_infon(xml, annotation)
|
|
84
90
|
read_recursive(xml, annotation, "location")
|
|
91
|
+
true
|
|
85
92
|
end
|
|
86
93
|
|
|
87
|
-
def read_relation(xml, relation)
|
|
94
|
+
def read_relation(xml, relation, options = {})
|
|
88
95
|
relation.id = xml["id"]
|
|
89
96
|
read_infon(xml, relation)
|
|
90
97
|
read_recursive(xml, relation, "node")
|
|
98
|
+
true
|
|
91
99
|
end
|
|
92
100
|
|
|
93
|
-
def read_location(xml, location)
|
|
101
|
+
def read_location(xml, location, options = {})
|
|
94
102
|
location.offset = xml["offset"]
|
|
95
103
|
location.length = xml["length"]
|
|
104
|
+
true
|
|
96
105
|
end
|
|
97
106
|
|
|
98
|
-
def read_node(xml, node)
|
|
107
|
+
def read_node(xml, node, options = {})
|
|
99
108
|
node.refid = xml["refid"]
|
|
100
109
|
node.role = xml["role"]
|
|
110
|
+
true
|
|
101
111
|
end
|
|
102
112
|
end
|
|
@@ -3,11 +3,13 @@ Dir[File.dirname(__FILE__) + '/*.rb'].each {|file| require file }
|
|
|
3
3
|
|
|
4
4
|
module BioCWriter
|
|
5
5
|
module_function
|
|
6
|
-
def write(collection)
|
|
6
|
+
def write(collection, options = {})
|
|
7
|
+
options[:save_with] = 1 if options[:save_with].nil?
|
|
7
8
|
builder = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') do |xml|
|
|
9
|
+
xml.doc.create_internal_subset( 'collection', nil, 'BioC.dtd' )
|
|
8
10
|
write_collection(xml, collection)
|
|
9
11
|
end
|
|
10
|
-
builder.to_xml
|
|
12
|
+
builder.to_xml(options)
|
|
11
13
|
end
|
|
12
14
|
|
|
13
15
|
def write_infon(xml, obj)
|
data/lib/simple_bioc/version.rb
CHANGED
data/lib/simple_bioc.rb
CHANGED
|
@@ -1,3 +1,4 @@
|
|
|
1
|
+
# @author Dongseop Kwon
|
|
1
2
|
require "simple_bioc/version"
|
|
2
3
|
require "simple_bioc/bioc_reader"
|
|
3
4
|
require "simple_bioc/bioc_writer"
|
|
@@ -7,12 +8,35 @@ module SimpleBioC
|
|
|
7
8
|
module_function
|
|
8
9
|
|
|
9
10
|
# parse a BioC XML file in the given path and convert it into a collection instance
|
|
10
|
-
|
|
11
|
-
|
|
11
|
+
#
|
|
12
|
+
# ==== Arguments
|
|
13
|
+
# * +file_path+ - file path for parse
|
|
14
|
+
# * +options+ - (optional) additional options
|
|
15
|
+
#
|
|
16
|
+
# ==== Options
|
|
17
|
+
# * +documents+ - specify IDs of documents to parse. The result will include only the specified documents
|
|
18
|
+
#
|
|
19
|
+
# ==== Examples
|
|
20
|
+
# collection = SimpleBioC.from_xml("./xml/everything.xml")
|
|
21
|
+
# collection = SimpleBioC.from_xml("./xml/lemma.xml", {documents:[21785578, 21488974]})
|
|
22
|
+
def from_xml(file_path, options = {})
|
|
23
|
+
options[:documents] = options[:documents].map{|e| e.to_s} if options[:documents].kind_of?(Array)
|
|
24
|
+
BioCReader.read(file_path, options)
|
|
12
25
|
end
|
|
13
26
|
|
|
14
|
-
# convert a collection instance to a BioC XML text
|
|
15
|
-
|
|
16
|
-
|
|
27
|
+
# convert a collection instance to a BioC XML text. Output will return as string
|
|
28
|
+
#
|
|
29
|
+
# ==== Arguments
|
|
30
|
+
# * +collection+ - Collection instance to process
|
|
31
|
+
# * +options+ - (optional) additional options
|
|
32
|
+
#
|
|
33
|
+
# ==== Options
|
|
34
|
+
# * +save_with+ - SaveOption for Nokorigi. If you set this 0, output has no format (no indentation, no whitespace)
|
|
35
|
+
#
|
|
36
|
+
# ==== Examples
|
|
37
|
+
# output = SimpleBioC.to_xml(collection)
|
|
38
|
+
# output = SimpleBioC.to_xml(collection, {save_with: 0})
|
|
39
|
+
def to_xml(collection, options = {})
|
|
40
|
+
BioCWriter.write(collection, options)
|
|
17
41
|
end
|
|
18
42
|
end
|
data/simple_bioc.gemspec
CHANGED
|
@@ -8,7 +8,7 @@ Gem::Specification.new do |spec|
|
|
|
8
8
|
spec.version = SimpleBioC::VERSION
|
|
9
9
|
spec.authors = ["Dongseop Kwon"]
|
|
10
10
|
spec.email = ["dongseop@gmail.com"]
|
|
11
|
-
spec.description = "
|
|
11
|
+
spec.description = "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/)"
|
|
12
12
|
spec.summary = "Simple BioC parser/builder for ruby"
|
|
13
13
|
spec.homepage = "https://github.com/dongseop/simple_bioc"
|
|
14
14
|
spec.license = "MIT"
|
|
@@ -0,0 +1,13 @@
|
|
|
1
|
+
require 'simple_bioc'
|
|
2
|
+
require 'test_xml/spec'
|
|
3
|
+
describe "File Check" do
|
|
4
|
+
it "should be load successfully" do
|
|
5
|
+
Dir["./xml/*.xml"].each do |file_path|
|
|
6
|
+
puts file_path
|
|
7
|
+
collection = SimpleBioC.from_xml(file_path)
|
|
8
|
+
output = SimpleBioC.to_xml(collection)
|
|
9
|
+
expected = File.read(file_path)
|
|
10
|
+
expect(output).to equal_xml(expected)
|
|
11
|
+
end
|
|
12
|
+
end
|
|
13
|
+
end
|
data/spec/simple_bioc_spec.rb
CHANGED
|
@@ -1,14 +1,25 @@
|
|
|
1
|
-
# bowling_spec.rb
|
|
2
1
|
require 'simple_bioc'
|
|
3
2
|
require 'test_xml/spec'
|
|
4
|
-
describe
|
|
5
|
-
it "should
|
|
6
|
-
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
3
|
+
describe "Simple function" do
|
|
4
|
+
it "should have a DTD declaration" do
|
|
5
|
+
collection = SimpleBioC.from_xml("./xml/everything.xml")
|
|
6
|
+
output = SimpleBioC.to_xml(collection)
|
|
7
|
+
output.should include('<!DOCTYPE collection SYSTEM "BioC.dtd">')
|
|
8
|
+
end
|
|
9
|
+
|
|
10
|
+
it "should no space when save_with = 0" do
|
|
11
|
+
collection = SimpleBioC.from_xml("./xml/everything.xml")
|
|
12
|
+
output = SimpleBioC.to_xml(collection, {save_with: 0})
|
|
13
|
+
output.should include('<collection><source>Made up file to test that everything is allowed and processed. Has text in the passage.</source><date>20130426</date><key>everything.key</key><infon key="collection-infon-key">collection-infon-value</infon><document><id>1</id><infon key="document-infon-key">document-infon-value</infon><passage><infon key="passage-infon-key">passage-infon-value</infon><offset>0</offset><text>text of passage</text><annotation id="P1"><infon key="annotation-infon-key">annotation-infon-value</infon><text>annotation text</text><location offset="1" length="2"/></annotation><relation id="RP1"><infon key="passage-relation-infon-key">passage-relation-infon-value</infon><node refid="RP1" role="passage-relation"/></relation></passage><relation id="D1"><infon key="document-relation-infon-key">document-relation-infon-value</infon><node refid="RD1" role="document-relation"/></relation></document></collection>')
|
|
14
|
+
end
|
|
15
|
+
|
|
16
|
+
it "should process only one document by options" do
|
|
17
|
+
collection = SimpleBioC.from_xml("./xml/lemma.xml", {documents:[21785578, 21488974]})
|
|
18
|
+
output = SimpleBioC.to_xml(collection, {save_with: 0})
|
|
19
|
+
output.scan("<document>").size.should equal 2
|
|
20
|
+
output.should include("<document><id>21785578</id>")
|
|
21
|
+
output.should include("<document><id>21488974</id>")
|
|
22
|
+
output.should_not include("<document><id>21660417</id>")
|
|
23
|
+
output.should_not include("<document><id>21951408</id>")
|
|
13
24
|
end
|
|
14
25
|
end
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: simple_bioc
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.0.
|
|
4
|
+
version: 0.0.3
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Dongseop Kwon
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2013-12-
|
|
11
|
+
date: 2013-12-21 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: nokogiri
|
|
@@ -80,8 +80,9 @@ dependencies:
|
|
|
80
80
|
- - ~>
|
|
81
81
|
- !ruby/object:Gem::Version
|
|
82
82
|
version: 0.1.6
|
|
83
|
-
description:
|
|
84
|
-
to
|
|
83
|
+
description: SimpleBioC is a simple parser / builder for BioC data format. BioC is
|
|
84
|
+
a simple XML format to share text documents and annotations. You can find more information
|
|
85
|
+
about BioC from the official BioC web site (http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/)
|
|
85
86
|
email:
|
|
86
87
|
- dongseop@gmail.com
|
|
87
88
|
executables: []
|
|
@@ -158,6 +159,7 @@ files:
|
|
|
158
159
|
- samples/print_annotation.rb
|
|
159
160
|
- samples/sample1.rb
|
|
160
161
|
- simple_bioc.gemspec
|
|
162
|
+
- spec/file_check_spec.rb
|
|
161
163
|
- spec/simple_bioc_spec.rb
|
|
162
164
|
- xml/BioC.dtd
|
|
163
165
|
- xml/PMID-8557975-simplified-sentences-tokens.xml
|
|
@@ -200,4 +202,6 @@ signing_key:
|
|
|
200
202
|
specification_version: 4
|
|
201
203
|
summary: Simple BioC parser/builder for ruby
|
|
202
204
|
test_files:
|
|
205
|
+
- spec/file_check_spec.rb
|
|
203
206
|
- spec/simple_bioc_spec.rb
|
|
207
|
+
has_rdoc:
|