simple_bioc 0.0.1 → 0.0.2
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- checksums.yaml +4 -4
- data/README.md +73 -3
- data/Rakefile +5 -0
- data/html/BioCReader.html +657 -0
- data/html/BioCWriter.html +556 -0
- data/html/README_md.html +231 -0
- data/html/SimpleBioC.html +255 -0
- data/html/SimpleBioC/Annotation.html +279 -0
- data/html/SimpleBioC/Collection.html +316 -0
- data/html/SimpleBioC/Document.html +426 -0
- data/html/SimpleBioC/Location.html +288 -0
- data/html/SimpleBioC/Node.html +334 -0
- data/html/SimpleBioC/NodeBase.html +281 -0
- data/html/SimpleBioC/Passage.html +418 -0
- data/html/SimpleBioC/Relation.html +301 -0
- data/html/SimpleBioC/Sentence.html +399 -0
- data/html/created.rid +15 -0
- data/html/images/add.png +0 -0
- data/html/images/arrow_up.png +0 -0
- data/html/images/brick.png +0 -0
- data/html/images/brick_link.png +0 -0
- data/html/images/bug.png +0 -0
- data/html/images/bullet_black.png +0 -0
- data/html/images/bullet_toggle_minus.png +0 -0
- data/html/images/bullet_toggle_plus.png +0 -0
- data/html/images/date.png +0 -0
- data/html/images/delete.png +0 -0
- data/html/images/find.png +0 -0
- data/html/images/loadingAnimation.gif +0 -0
- data/html/images/macFFBgHack.png +0 -0
- data/html/images/package.png +0 -0
- data/html/images/page_green.png +0 -0
- data/html/images/page_white_text.png +0 -0
- data/html/images/page_white_width.png +0 -0
- data/html/images/plugin.png +0 -0
- data/html/images/ruby.png +0 -0
- data/html/images/tag_blue.png +0 -0
- data/html/images/tag_green.png +0 -0
- data/html/images/transparent.png +0 -0
- data/html/images/wrench.png +0 -0
- data/html/images/wrench_orange.png +0 -0
- data/html/images/zoom.png +0 -0
- data/html/index.html +212 -0
- data/html/js/darkfish.js +155 -0
- data/html/js/jquery.js +18 -0
- data/html/js/navigation.js +142 -0
- data/html/js/search.js +94 -0
- data/html/js/search_index.js +1 -0
- data/html/js/searcher.js +228 -0
- data/html/rdoc.css +595 -0
- data/html/table_of_contents.html +199 -0
- data/lib/simple_bioc.rb +4 -0
- data/lib/simple_bioc/annotation.rb +10 -6
- data/lib/simple_bioc/bioc_reader.rb +2 -2
- data/lib/simple_bioc/collection.rb +13 -11
- data/lib/simple_bioc/document.rb +31 -22
- data/lib/simple_bioc/location.rb +13 -7
- data/lib/simple_bioc/node.rb +14 -8
- data/lib/simple_bioc/node_base.rb +13 -10
- data/lib/simple_bioc/passage.rb +26 -23
- data/lib/simple_bioc/relation.rb +13 -8
- data/lib/simple_bioc/sentence.rb +21 -15
- data/lib/simple_bioc/version.rb +2 -2
- data/samples/print_annotation.rb +18 -0
- data/samples/sample1.rb +31 -0
- data/simple_bioc.gemspec +1 -1
- metadata +52 -2
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<body class="indexpage">
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<h1>Table of Contents - RDoc Documentation</h1>
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<h2>Pages</h2>
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<a href="README_md.html">README</a>
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<img class="toc-toggle" src="images/transparent.png" alt="" title="toggle headings">
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<ul class="initially-hidden">
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<li><a href="README_md.html#label-SimpleBioc">SimpleBioc</a>
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<li><a href="README_md.html#label-Feature%3A">Feature:</a>
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<li><a href="README_md.html#label-Installation">Installation</a>
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<li><a href="README_md.html#label-Usages">Usages</a>
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<li><a href="README_md.html#label-Sample">Sample</a>
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<li><a href="README_md.html#label-Contributing">Contributing</a>
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<h2 id="classes">Classes/Modules</h2>
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<li class="module">
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<a href="BioCReader.html">BioCReader</a>
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<li class="module">
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<a href="BioCWriter.html">BioCWriter</a>
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<a href="SimpleBioC.html">SimpleBioC</a>
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</li>
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<li class="class">
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<a href="SimpleBioC/Annotation.html">SimpleBioC::Annotation</a>
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<li class="class">
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<a href="SimpleBioC/Collection.html">SimpleBioC::Collection</a>
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<a href="SimpleBioC/Document.html">SimpleBioC::Document</a>
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<a href="SimpleBioC/Location.html">SimpleBioC::Location</a>
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<a href="SimpleBioC/Node.html">SimpleBioC::Node</a>
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<a href="SimpleBioC/NodeBase.html">SimpleBioC::NodeBase</a>
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<h2 id="methods">Methods</h2>
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<li class="method"><a href="SimpleBioC/Annotation.html#method-c-new">::new — SimpleBioC::Annotation</a>
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<li class="method"><a href="SimpleBioC/Passage.html#method-c-new">::new — SimpleBioC::Passage</a>
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<li class="method"><a href="SimpleBioC/NodeBase.html#method-c-new">::new — SimpleBioC::NodeBase</a>
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<li class="method"><a href="SimpleBioC/Node.html#method-c-new">::new — SimpleBioC::Node</a>
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<li class="method"><a href="SimpleBioC/Location.html#method-c-new">::new — SimpleBioC::Location</a>
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<li class="method"><a href="SimpleBioC/Sentence.html#method-c-new">::new — SimpleBioC::Sentence</a>
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<li class="method"><a href="SimpleBioC/Node.html#method-i-adjust_ref">#adjust_ref — SimpleBioC::Node</a>
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<li class="method"><a href="SimpleBioC/Document.html#method-i-each_relation">#each_relation — SimpleBioC::Document</a>
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<li class="method"><a href="SimpleBioC/Document.html#method-i-find_node">#find_node — SimpleBioC::Document</a>
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<li class="method"><a href="SimpleBioC.html#method-i-from_xml">#from_xml — SimpleBioC</a>
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<li class="method"><a href="BioCReader.html#method-i-read">#read — BioCReader</a>
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data/lib/simple_bioc.rb
CHANGED
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@@ -2,12 +2,16 @@ require "simple_bioc/version"
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require "simple_bioc/bioc_reader"
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require "simple_bioc/bioc_writer"
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# SimpleBioC main library
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module SimpleBioC
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module_function
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# parse a BioC XML file in the given path and convert it into a collection instance
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def from_xml(file_path)
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BioCReader.read(file_path)
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end
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# convert a collection instance to a BioC XML text
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def to_xml(collection)
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BioCWriter.write(collection)
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end
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require 'simple_bioc/node_base'
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module SimpleBioC
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class Annotation < NodeBase
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attr_accessor :locations, :text
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def initialize(parent)
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super(parent)
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@locations = []
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end
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@locations = []
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def to_s
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"Annotation:#{id} #{text}"
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end
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end
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end
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@@ -14,7 +14,7 @@ module BioCReader
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14
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if xml.nil?
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fail 'Wrong format'
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end
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collection = Collection.new
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collection = SimpleBioC::Collection.new
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read_collection(xml, collection)
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end
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@@ -36,7 +36,7 @@ module BioCReader
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end
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def read_recursive(xml, obj, name)
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target_class =
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target_class = SimpleBioC.const_get(name.capitalize)
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xml.xpath(name).each do |node|
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instance = target_class.new(obj)
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send(:"read_#{name}", node, instance)
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@@ -1,15 +1,17 @@
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module SimpleBioC
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class Collection
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attr_accessor :documents, :infons, :source, :date, :key
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def initialize
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@documents = []
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@infons = {}
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@source = ""
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@date = ""
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@key = ""
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end
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def to_c
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"Collection(source: #{source}, date: #{date}, key: #{key})"
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end
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end
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end
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data/lib/simple_bioc/document.rb
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@@ -1,29 +1,38 @@
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module SimpleBioC
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class Document
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# attribute
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attr_accessor :id, :infons, :passages, :relations
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@passages = []
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@relations = []
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@collection = parent
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end
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# parent
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attr_reader :collection
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def initialize(parent)
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@infons = {}
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@passages = []
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@relations = []
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@collection = parent
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end
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nil
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end
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def find_node(id)
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relations.each{|r| return r if r.id == id}
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passages.each do |p|
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ret = p.find_node(id)
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return ret unless ret.nil?
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end
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nil
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end
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def adjust_ref
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each_relation{|r| r.adjust_ref}
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end
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def each_relation
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relations.each{|r| yield r}
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passages.each{|p| p.each_relation{|r| yield r}}
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end
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def to_s
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"Document:#{id}"
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end
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end
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end
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data/lib/simple_bioc/location.rb
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@@ -1,10 +1,16 @@
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module SimpleBioC
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class Location
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attr_accessor :offset, :length
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attr_reader :annotation
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def initialize(parent)
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@infons = {}
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@locations = []
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@annotation = parent
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end
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def to_s
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"Location @#{offset}:#{length}"
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end
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end
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end
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data/lib/simple_bioc/node.rb
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@@ -1,12 +1,18 @@
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module SimpleBioC
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class Node
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attr_accessor :refid, :role
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attr_reader :ref, :relation
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def initialize(parent)
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@relation = parent
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end
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def adjust_ref
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@ref = relation.document.find_node(refid)
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end
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def to_c
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"Node @#{refid}: #{role})"
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end
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end
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end
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@@ -1,14 +1,17 @@
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module SimpleBioC
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# NodeBase is not a BioC DTD entity. This is a super class of Annotation & Relation.
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class NodeBase
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attr_accessor :id, :infons
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attr_reader :document, :passage, :sentence
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def initialize(parent)
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@infons = {}
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@document = parent if parent.is_a? Document
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@passage = parent if parent.is_a? Passage
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@sentence = parent if parent.is_a? Sentence
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@passage = @sentence.passage unless @sentence.nil?
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@document = @passage.document unless @passage.nil?
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end
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end
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end
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data/lib/simple_bioc/passage.rb
CHANGED
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@@ -1,29 +1,32 @@
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module SimpleBioC
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class Passage
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attr_accessor :offset, :text, :infons, :sentences, :annotations, :relations
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attr_reader :document
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def initialize(parent)
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@infons = {}
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@sentences = []
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@annotations = []
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@relations = []
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@document = parent
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end
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end
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def find_node(id)
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(relations+annotations).each{|n| return n if n.id == id}
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sentences.each do |s|
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ret = s.find_node(id)
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return ret unless ret.nil?
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def to_s
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"Passage @#{offset}: #{text}"
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end
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nil
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end
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def find_node(id)
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(relations+annotations).each{|n| return n if n.id == id}
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sentences.each do |s|
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ret = s.find_node(id)
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return ret unless ret.nil?
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end
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nil
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end
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def each_relation
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relations.each{|r| yield r}
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sentences.each{|s| s.each_relation{|r| yield r}}
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end
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end
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end
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