oba-client 1.0.0

data/.autotest

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+# -*- ruby -*-
+
+require 'autotest/restart'
+
+# Autotest.add_hook :initialize do |at|
+#   at.extra_files << "../some/external/dependency.rb"
+#
+#   at.libs << ":../some/external"
+#
+#   at.add_exception 'vendor'
+#
+#   at.add_mapping(/dependency.rb/) do |f, _|
+#     at.files_matching(/test_.*rb$/)
+#   end
+#
+#   %w(TestA TestB).each do |klass|
+#     at.extra_class_map[klass] = "test/test_misc.rb"
+#   end
+# end
+
+# Autotest.add_hook :run_command do |at|
+#   system "rake build"
+# end

data/History.txt

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+=== 1.0.0 / 2010-07-07
+
+* 1 Initial release
+
+  * Does not yet parse statistics.
+

data/Manifest.txt

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+.autotest
+History.txt
+Manifest.txt
+README.txt
+Rakefile
+bin/oba_client
+lib/oba_client.rb
+test/test_oba_client.rb

data/README.txt

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+= oba_client
+
+* http://rubyforge.org/oba-client
+
+== DESCRIPTION:
+
+FIX (describe your package)
+
+== FEATURES/PROBLEMS:
+
+* FIX (list of features or problems)
+
+== SYNOPSIS:
+
+  FIX (code sample of usage)
+
+== REQUIREMENTS:
+
+* None
+
+== INSTALL:
+
+* FIX (sudo gem install, anything else)
+
+== DEVELOPERS:
+
+After checking out the source, run:
+
+  $ rake newb
+
+This task will install any missing dependencies, run the tests/specs,
+and generate the RDoc.
+
+== LICENSE:
+
+(The MIT License)
+
+Copyright (c) 2010 FIX
+
+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/Rakefile

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+require "rubygems"
+require "hoe"
+
+Hoe.spec "oba-client" do
+  developer("Rob Tirrell", "rpt@stanford.edu")
+
+  self.rubyforge_name = "oba-client"
+end
+

data/bin/oba_client

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+#!/usr/bin/env ruby
+
+abort "you need to write me"

data/lib/oba_client.rb

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+require "rubygems"
+require "nokogiri"
+require "cgi"
+require "net/http"
+require "uri"
+
+class OBAClient
+  VERSION = "1.0.0"
+
+  # A high HTTP read timeout, as the service sometimes takes awhile to respond.
+  DEFAULT_TIMEOUT = 30
+
+  # The endpoint URI for the production version of the Annotator service.
+  DEFAULT_URI = "http://rest.bioontology.org/obs/annotator"
+
+  # The header for every request. There's no need to specify this per-instance.
+  HEADER = {"Content-Type" => "application/x-www-form-urlencoded"}
+    
+  # Parameters the annotator accepts. Any one not in this list (excluding
+  # textToAnnotate) is not valid.
+  ANNOTATOR_PARAMETERS = %w{
+    wholeWordOnly
+    scored
+    ontologiesToExpand
+    ontologiesToKeepInResult
+    semanticTypes
+    withDefaultStopWords
+    format
+    levelMax
+    mappingTypes
+    email
+  }
+
+  # Annotate a blob of text. Method options are:
+  # - [String] uri: the URI of the annotator service (default: {DEFAULT_URI}).
+  # - [Fixnum] timeout: the length of the read timeout (default: {DEFAULT_TIMEOUT}).
+  # - [Boolean] parse_xml: whether to parse the received text (default: false).
+  # @param [Hash<String, String>] options Parameters for the annotation.
+  def initialize(options = {})
+    @uri         = URI.parse(options.delete(:uri) || DEFAULT_URI)
+    @timeout     = options.delete(:timeout) || DEFAULT_TIMEOUT
+    @parse_xml   = options.delete(:parse_xml)
+    
+    @options     = {}
+    options.each do |k, v|
+      if !ANNOTATOR_PARAMETERS.include?(k)
+        puts "WARNING: #{k} is not a valid annotator parameter."
+      end
+      if v.is_a? Array
+        @options[k] = v.join(",")
+      else
+        @options[k] = v
+      end
+    end
+    
+    if !@options.include?(:email)
+      puts "TIP: as a courtesy, consider including your email in the request."
+    end
+  end
+
+  # Perform the annotation.
+  # @param [String] text The text to annotate.
+  # @return [Hash<Symbol, Array>, String, nil] A Hash representing the parsed
+  #   document, the raw XML if parsing is not requested, or nil if the
+  #   request times out.
+  def execute(text)
+    request = Net::HTTP::Post.new(@uri.path, initheader=HEADER)
+    request.body = {:textToAnnotate => text}.merge(@options).map do |k, v|
+      "#{CGI.escape(k.to_s)}=#{CGI.escape(v.to_s)}"
+    end.join("&")
+
+    begin
+      response = Net::HTTP.new(@uri.host, @uri.port).start do |http|
+        http.read_timeout = @timeout
+        http.request(request)
+      end
+      @parse_xml ? self.class.parse(response.body) : response.body
+    rescue Timeout::Error
+      puts "Request for #{text[0..10]} timed-out at #{@timeout} seconds."
+    end
+  end
+
+  # Parse the raw XML, returning a Hash with three elements: statistics,
+  #   annotations, and ontologies. Respectively, these represent the annotation
+  #   statistics (annotations by mapping type, etc., as a Hash), an Array of
+  #   each annotation (as a Hash), and an Array of ontologies used (also as
+  #   a Hash).
+  # @param [String] xml The XMl we'll be parsing.
+  # @return [Hash<Symbol, Object>] A Hash representation of the XML, as
+  #   described above.
+  def self.parse(xml)
+    statistics  = []
+    annotations = []
+    ontologies  = []
+    doc = Nokogiri::XML.parse(xml)
+
+    doc.xpath("//annotationBean").each do |ann|
+      parsed = {}
+      parsed[:score]           = ann.xpath("score").text.to_i
+      parsed[:id]              = ann.xpath("concept/id").text.to_i
+      parsed[:localConceptId]  = ann.xpath("concept/localConceptId")
+      parsed[:localOntologyId] = ann.xpath("concept/localOntologyId").text.to_i
+      parsed[:isTopLevel]      = ann.xpath("concept/isTopLevel").text.to_i
+      parsed[:fullId]          = ann.xpath("concept/fullId").text
+      parsed[:preferredName]   = ann.xpath("concept/preferredName").text
+
+      synonyms = ann.xpath("concept/synonyms/synonym")
+      parsed[:synonyms] = synonyms.map do |synonym|
+        synonym.xpath("string").text
+      end
+
+      semanticTypeBeans = ann.xpath("concept/semanticTypes/semanticTypeBean")
+      parsed[:semanticTypes] = semanticTypeBeans.map do |semanticType|
+        {
+          :id           => semanticType.xpath("id").text.to_i,
+          :semanticType => semanticType.xpath("semanticType").text,
+          :description  => semanticType.xpath("description").text
+        }
+      end
+      annotations << parsed
+    end
+
+    doc.xpath("//ontologyUsedBean").each do |ontology|
+      parsed = {}
+      parsed[:localOntologyId]   = ontology.xpath("localOntologyId").text
+      parsed[:virtualOntologyId] = ontology.xpath("virtualOntologyId").text
+      parsed[:name]              = ontology.xpath("name").text
+      ontologies << parsed
+    end
+
+    {
+      :statistics  => statistics,
+      :annotations => annotations,
+      :ontologies  => ontologies
+    }
+  end
+end

data/test/test_oba_client.rb

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+require "test/unit"
+require "oba_client"
+
+TEST_TEXTS = [
+   "hello I am a monkeyfish with a benign neoplastic....\t\n\\n",
+  "zebrafish echo delta tango TURN <?xml MY VOLUME UP cancer of the thorax.",
+  "zebrafish DROP TABLE !!! TURN MY VOLUME UP cancer of the thorax.",
+  %Q{LOROE aonuhaso unseu anoeuhs aeuhsaonuh asoneuhason uaosenuh aosenuhaose
+  aoneuhasonuhaoenuh anoeuhasn euhasoneu haosneuhaosenuhaoesunahoeusnaoeuteeano
+  aot tt t t t t t t tae \n!!@)$@(#)%@#!)@# asoeuaohsenutahoeusaheou
+  }
+]
+
+class TestOBAClient < Test::Unit::TestCase
+  def test_reuse_annotator_instance
+    ann = OBAClient.new
+    TEST_TEXTS.each do |text|
+      xml = ann.execute(text)
+      assert xml[0..4] == "<?xml"
+    end
+  end
+  
+  def test_annotation_no_parameters
+    TEST_TEXTS.each do |text|
+      ann = OBAClient.new 
+      xml = ann.execute(text)
+      assert xml[0..4] == "<?xml"
+    end
+  end
+  
+  def test_annotation_parse
+    TEST_TEXTS.each do |text|
+      ann = OBAClient.new :parse_xml => true
+      parsed = ann.execute(text)
+      assert parsed[:statistics].is_a?(Array)
+      assert parsed[:annotations].is_a?(Array)
+      assert parsed[:ontologies].is_a?(Array)
+    end
+  end
+  
+  def test_annotation_keep_one_ontology
+    TEST_TEXTS.each do |text|
+      ann = OBAClient.new(
+        :ontologiesToKeepInResult => [42812],
+        :parse_xml => true
+      )
+      parsed = ann.execute(text)
+      assert parsed[:statistics].is_a?(Array)
+      assert parsed[:annotations].is_a?(Array)
+      assert parsed[:ontologies].is_a?(Array)
+    end
+  end
+  
+  def test_annotation_invalid_parameters
+    TEST_TEXTS.each do |text|
+      ann = OBAClient.new(
+        :ontologiesToKeepInResult => [42812],
+        :parse_xml                => true,
+        :blah_blah                => true,
+        :hoho                     => ["merry", "christmas"]
+      )
+      parsed = ann.execute(text)
+      assert parsed[:statistics].is_a?(Array)
+      assert parsed[:annotations].is_a?(Array)
+      assert parsed[:ontologies].is_a?(Array)
+    end
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: oba-client
+version: !ruby/object:Gem::Version 
+  hash: 23
+  prerelease: false
+  segments: 
+  - 1
+  - 0
+  - 0
+  version: 1.0.0
+platform: ruby
+authors: 
+- Rob Tirrell
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-07-08 00:00:00 -07:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: rubyforge
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 2
+        - 0
+        - 4
+        version: 2.0.4
+  type: :development
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: hoe
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 21
+        segments: 
+        - 2
+        - 6
+        - 1
+        version: 2.6.1
+  type: :development
+  version_requirements: *id002
+description: FIX (describe your package)
+email: 
+- rpt@stanford.edu
+executables: 
+- oba_client
+extensions: []
+
+extra_rdoc_files: 
+- History.txt
+- Manifest.txt
+- README.txt
+files: 
+- .autotest
+- History.txt
+- Manifest.txt
+- README.txt
+- Rakefile
+- bin/oba_client
+- lib/oba_client.rb
+- test/test_oba_client.rb
+has_rdoc: true
+homepage: http://rubyforge.org/oba-client
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --main
+- README.txt
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: oba-client
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 3
+summary: FIX (describe your package)
+test_files: 
+- test/test_oba_client.rb