simple_bioc 0.0.1

checksums.yaml

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+---
+SHA1:
+  metadata.gz: ac827766c1ee157f8eb3a836754da23968863299
+  data.tar.gz: 89bd14e8bba58e50e45d68221d6cf7b915512c96
+SHA512:
+  metadata.gz: bb1560756684d4f65393effcb32237304480718f24a14f871cce67f6cd302f5ee29911b5fcca26cd26f9b61873822cfdbb5405b8b095c0e5dcc0ab560f29cde9
+  data.tar.gz: 5e54ab65f41d74e85f48647f70d241edc2ede844cd2c32c21ebc3096a49cb8ed914304f8c7de004406476728d6d388d21bf6b44efbc454079a361c8deaab94fc

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+Gemfile.lock
+InstalledFiles
+coverage
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+# YARD artifacts
+.yardoc
+_yardoc
+doc/

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in simple_bioc.gemspec
+gemspec

data/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2013 Dongseop Kwon
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/LICENSE.txt

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+Copyright (c) 2013 Dongseop Kwon
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# SimpleBioc
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'simple_bioc'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install simple_bioc
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"
+require 'rspec/core/rake_task'
+require 'rdoc/task'
+
+task :default => [:spec]
+RSpec::Core::RakeTask.new do |t|
+    t.verbose = true
+end

data/lib/simple_bioc/annotation.rb

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+require 'simple_bioc/node_base'
+
+class Annotation < NodeBase
+  attr_accessor :locations, :text
+
+  def initialize(parent)
+    super(parent)
+
+    @locations = []
+  end
+end

data/lib/simple_bioc/bioc_reader.rb

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+require 'nokogiri'
+Dir[File.dirname(__FILE__) + '/*.rb'].each {|file| require file }
+
+module BioCReader
+  module_function
+
+  def read(path) 
+    collection = nil
+    File.open(path) do |file|
+      xml_doc  = Nokogiri::XML(file) do |config|
+        config.noent.strict.noblanks
+      end
+      xml = xml_doc.at_xpath("//collection")
+      if xml.nil?
+        fail 'Wrong format'
+      end
+      collection = Collection.new
+      read_collection(xml, collection)
+    end
+
+    collection
+  end
+
+  def read_text(xml, name)
+    node = xml.at_xpath(name)
+    node && node.content
+  end
+
+  def read_int(xml, name)
+    val = read_text(xml, name) 
+    val && val.to_i
+  end
+
+  def read_infon(xml, obj)
+    xml.xpath("infon").each{ |i| obj.infons[i["key"]] = i.content}
+  end
+
+  def read_recursive(xml, obj, name)
+    target_class = Module.const_get(name.capitalize)
+    xml.xpath(name).each do |node|
+      instance = target_class.new(obj)
+      send(:"read_#{name}", node, instance)
+      obj.instance_variable_get(:"@#{name}s")  << instance
+    end
+  end
+
+  def read_collection(xml, collection)
+    collection.source = read_text(xml, "source")
+    collection.date = read_text(xml, "date")
+    collection.key = read_text(xml, "key")
+    read_infon(xml, collection)
+    read_recursive(xml, collection, "document")
+  end  
+
+  def read_document(xml, document)
+    document.id = read_text(xml, "id")
+    read_infon(xml, document)
+    read_recursive(xml, document, "passage")
+    read_recursive(xml, document, "relation")
+    document.adjust_ref
+  end
+
+  def read_passage(xml, passage)
+    passage.text = read_text(xml, "text")
+    passage.offset = read_int(xml, "offset")
+    read_infon(xml, passage)
+    read_recursive(xml, passage, "sentence")
+    read_recursive(xml, passage, "annotation")
+    read_recursive(xml, passage, "relation")
+  end
+
+  def read_sentence(xml, sentence)
+    sentence.text = read_text(xml, "text")
+    sentence.offset = read_int(xml, "offset")
+    read_infon(xml, sentence)
+    read_recursive(xml, sentence, "annotation")
+    read_recursive(xml, sentence, "relation")
+  end
+
+  def read_annotation(xml, annotation) 
+    annotation.id = xml["id"]
+    annotation.text = read_text(xml, "text")
+    read_infon(xml, annotation)
+    read_recursive(xml, annotation, "location")
+  end
+
+  def read_relation(xml, relation) 
+    relation.id = xml["id"]
+    read_infon(xml, relation)
+    read_recursive(xml, relation, "node")
+  end
+
+  def read_location(xml, location) 
+    location.offset = xml["offset"]
+    location.length = xml["length"]
+  end
+
+  def read_node(xml, node)
+    node.refid = xml["refid"]
+    node.role = xml["role"]
+  end
+end

data/lib/simple_bioc/bioc_writer.rb

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+require 'nokogiri'
+Dir[File.dirname(__FILE__) + '/*.rb'].each {|file| require file }
+
+module BioCWriter
+  module_function
+  def write(collection) 
+    builder = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') do |xml|
+      write_collection(xml, collection)
+    end
+    builder.to_xml
+  end
+
+  def write_infon(xml, obj)
+    obj.infons.each do |k, v| 
+      xml.infon(:key => k) {
+        xml.text v
+      }
+    end
+  end
+
+  def write_collection(xml, collection)
+    xml.collection {
+      xml.source collection.source
+      xml.date collection.date
+      xml.key collection.key
+      write_infon(xml, collection)
+      collection.documents.each{|d| write_document(xml, d)}
+    }
+  end
+
+  def write_document(xml, document)
+    xml.document {
+      xml.id_ document.id
+      write_infon(xml, document)
+      document.passages.each{|p| write_passage(xml, p)}
+      document.relations.each{|r| write_relation(xml, r)}
+    }
+  end
+
+  def write_passage(xml, passage)
+    xml.passage {
+      write_infon(xml, passage)
+      xml.offset passage.offset
+      xml.text_ passage.text unless passage.text.nil?
+      passage.sentences.each{|s| write_sentence(xml, s)}
+      passage.annotations.each{|a| write_annotation(xml, a)}
+      passage.relations.each{|r| write_relation(xml, r)}
+    }
+  end
+
+  def write_sentence(xml, sentence)
+    xml.sentence {
+      write_infon(xml, sentence)
+      xml.offset sentence.offset
+      xml.text_ sentence.text unless sentence.text.nil?
+      sentence.annotations.each{|a| write_annotation(xml, a)}
+      sentence.relations.each{|r| write_relation(xml, r)}
+    }
+  end
+
+  def write_annotation(xml, annotation) 
+    if annotation.id.nil?
+      attribute = nil
+    else
+      attribute = {id: annotation.id}
+    end
+    xml.annotation(attribute) {
+      write_infon(xml, annotation)
+      xml.text_ annotation.text
+      annotation.locations.each{|l| write_location(xml, l)}
+    }
+  end
+
+  def write_relation(xml, relation) 
+    if relation.id.nil?
+      attribute = nil
+    else
+      attribute = {id: relation.id}
+    end
+    xml.relation(attribute) {
+      write_infon(xml, relation)
+      relation.nodes.each{|n| write_node(xml, n)}
+    }
+  end
+
+  def write_location(xml, location) 
+    xml.location(:offset => location.offset, :length => location.length)
+  end
+
+  def write_node(xml, node)
+    xml.node_(:refid => node.refid, :role => node.role)
+  end
+end

data/lib/simple_bioc/collection.rb

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+class Collection
+  attr_accessor :documents, :infons, :source, :date, :key
+
+  def initialize
+    @documents = []
+    @infons = {}
+    @source = ""
+    @date = ""
+    @key = ""
+  end
+
+  def to_xml
+    
+  end
+end

data/lib/simple_bioc/document.rb

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+class Document
+  attr_accessor :id, :infons, :passages, :relations
+  attr_reader :collection
+
+  def initialize(parent)
+    @infons = {}
+    @passages = []
+    @relations = []
+    @collection = parent
+  end
+
+  def find_node(id)
+    relations.each{|r| return r if r.id == id}
+    passages.each do |p|
+      ret = p.find_node(id)
+      return ret unless ret.nil?
+    end
+    nil
+  end
+
+  def adjust_ref
+    each_relation{|r| r.adjust_ref}
+  end
+
+  def each_relation
+    relations.each{|r| yield r}
+    passages.each{|p| p.each_relation{|r| yield r}}
+  end
+end

data/lib/simple_bioc/location.rb

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+class Location
+  attr_accessor :offset, :length
+  attr_reader :annotation
+
+  def initialize(parent)
+    @infons = {}
+    @locations = []
+    @annotation = parent
+  end
+end

data/lib/simple_bioc/node.rb

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+class Node
+  attr_accessor :refid, :role
+  attr_reader :ref, :relation
+
+  def initialize(parent)
+    @relation = parent
+  end
+
+  def adjust_ref
+    @ref = relation.document.find_node(refid)
+  end
+end

data/lib/simple_bioc/node_base.rb

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+class NodeBase
+  attr_accessor :id, :infons
+  attr_reader :document, :passage, :sentence
+
+  def initialize(parent)
+    @infons = {}
+    @document = parent if parent.is_a? Document
+    @passage  = parent if parent.is_a? Passage
+    @sentence = parent if parent.is_a? Sentence 
+
+    @passage  = @sentence.passage unless @sentence.nil?
+    @document = @passage.document unless @passage.nil?
+  end
+end

data/lib/simple_bioc/passage.rb

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+class Passage
+  attr_accessor :offset, :text, :infons, :sentences, :annotations, :relations
+  attr_reader :document
+
+  def initialize(parent)
+    @infons = {}
+    @sentences = []
+    @annotations = []
+    @relations = []
+    @document = parent
+  end
+
+  def to_s
+    "#{offset}:#{text}"  
+  end
+  def find_node(id)
+    (relations+annotations).each{|n| return n if n.id == id}
+    sentences.each do |s|
+      ret = s.find_node(id)
+      return ret unless ret.nil?
+    end
+    nil
+  end
+
+  def each_relation
+    relations.each{|r| yield r}
+    sentences.each{|s| s.each_relation{|r| yield r}}
+  end
+end

data/lib/simple_bioc/relation.rb

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+require 'simple_bioc/node_base'
+
+class Relation < NodeBase
+  attr_accessor :nodes
+
+  def initialize(parent)
+    super(parent)
+    @nodes = []
+  end
+
+  def adjust_ref
+    nodes.each{|n| n.adjust_ref}
+  end
+end

data/lib/simple_bioc/sentence.rb

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+class Sentence
+  attr_accessor :offset, :text, :infons, :annotations, :relations
+  attr_reader :passage
+
+  def initialize(parent)
+    @infons = {}
+    @annotations = []
+    @relations = []
+    @passage = parent
+  end
+
+  def find_node(id)
+    (relations+annotations).each{|n| return n if n.id == id}
+    nil
+  end
+
+  def each_relation
+    relations.each{|r| yield r}
+  end
+end

data/lib/simple_bioc/version.rb

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+module SimpleBioc
+  VERSION = "0.0.1"
+end

data/lib/simple_bioc.rb

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+require "simple_bioc/version"
+require "simple_bioc/bioc_reader"
+require "simple_bioc/bioc_writer"
+
+module SimpleBioC
+  module_function
+  def from_xml(file_path)
+    BioCReader.read(file_path)
+  end
+
+  def to_xml(collection)
+    BioCWriter.write(collection)
+  end
+end

data/simple_bioc.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'simple_bioc/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "simple_bioc"
+  spec.version       = SimpleBioc::VERSION
+  spec.authors       = ["Dongseop Kwon"]
+  spec.email         = ["dongseop@gmail.com"]
+  spec.description   = "Simple BioC parser/builder for ruby. BioC is a 'A Minimalist Approach to Interoperability for Biomedical Text Processing' (http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/BioCHome.html)"
+  spec.summary       = "Simple BioC parser/builder for ruby"
+  spec.homepage      = "https://github.com/dongseop/simple_bioc"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency("nokogiri",       [">= 1.3.2"])
+
+  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "rake"
+  spec.add_development_dependency("rspec-core", ["~> 2.2"])
+  spec.add_development_dependency("test-xml", ["~> 0.1.6"])
+end

data/spec/simple_bioc_spec.rb

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+# bowling_spec.rb
+require 'simple_bioc'
+require 'test_xml/spec'
+describe BioCReader do
+  it "should be load successfully" do
+    Dir["./xml/*.xml"].each do |file_path|
+      puts file_path
+      collection = SimpleBioC.from_xml(file_path)
+      output = SimpleBioC.to_xml(collection)
+      expected = File.read(file_path)
+      expect(output).to equal_xml(expected)
+    end
+  end
+end