oba-client 1.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.autotest +23 -0
- data/History.txt +6 -0
- data/Manifest.txt +8 -0
- data/README.txt +57 -0
- data/Rakefile +9 -0
- data/bin/oba_client +3 -0
- data/lib/oba_client.rb +137 -0
- data/test/test_oba_client.rb +68 -0
- metadata +109 -0
data/.autotest
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# -*- ruby -*-
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require 'autotest/restart'
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# Autotest.add_hook :initialize do |at|
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# at.extra_files << "../some/external/dependency.rb"
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#
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# at.libs << ":../some/external"
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#
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# at.add_exception 'vendor'
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#
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# at.add_mapping(/dependency.rb/) do |f, _|
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# at.files_matching(/test_.*rb$/)
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# end
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#
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# %w(TestA TestB).each do |klass|
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# at.extra_class_map[klass] = "test/test_misc.rb"
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# end
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# end
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# Autotest.add_hook :run_command do |at|
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# system "rake build"
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# end
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data/History.txt
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data/Manifest.txt
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data/README.txt
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= oba_client
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* http://rubyforge.org/oba-client
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== DESCRIPTION:
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FIX (describe your package)
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== FEATURES/PROBLEMS:
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* FIX (list of features or problems)
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== SYNOPSIS:
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FIX (code sample of usage)
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== REQUIREMENTS:
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* None
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== INSTALL:
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* FIX (sudo gem install, anything else)
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== DEVELOPERS:
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After checking out the source, run:
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$ rake newb
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This task will install any missing dependencies, run the tests/specs,
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and generate the RDoc.
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== LICENSE:
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(The MIT License)
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Copyright (c) 2010 FIX
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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'Software'), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
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CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
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TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/Rakefile
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data/bin/oba_client
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data/lib/oba_client.rb
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require "rubygems"
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require "nokogiri"
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require "cgi"
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require "net/http"
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require "uri"
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class OBAClient
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VERSION = "1.0.0"
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# A high HTTP read timeout, as the service sometimes takes awhile to respond.
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DEFAULT_TIMEOUT = 30
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# The endpoint URI for the production version of the Annotator service.
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DEFAULT_URI = "http://rest.bioontology.org/obs/annotator"
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# The header for every request. There's no need to specify this per-instance.
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HEADER = {"Content-Type" => "application/x-www-form-urlencoded"}
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# Parameters the annotator accepts. Any one not in this list (excluding
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# textToAnnotate) is not valid.
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ANNOTATOR_PARAMETERS = %w{
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wholeWordOnly
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scored
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ontologiesToExpand
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ontologiesToKeepInResult
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semanticTypes
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withDefaultStopWords
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format
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levelMax
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mappingTypes
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email
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}
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# Annotate a blob of text. Method options are:
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# - [String] uri: the URI of the annotator service (default: {DEFAULT_URI}).
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# - [Fixnum] timeout: the length of the read timeout (default: {DEFAULT_TIMEOUT}).
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# - [Boolean] parse_xml: whether to parse the received text (default: false).
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# @param [Hash<String, String>] options Parameters for the annotation.
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def initialize(options = {})
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@uri = URI.parse(options.delete(:uri) || DEFAULT_URI)
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@timeout = options.delete(:timeout) || DEFAULT_TIMEOUT
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@parse_xml = options.delete(:parse_xml)
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@options = {}
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options.each do |k, v|
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if !ANNOTATOR_PARAMETERS.include?(k)
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puts "WARNING: #{k} is not a valid annotator parameter."
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end
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if v.is_a? Array
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@options[k] = v.join(",")
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else
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@options[k] = v
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end
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end
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if !@options.include?(:email)
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puts "TIP: as a courtesy, consider including your email in the request."
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end
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end
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# Perform the annotation.
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# @param [String] text The text to annotate.
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# @return [Hash<Symbol, Array>, String, nil] A Hash representing the parsed
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# document, the raw XML if parsing is not requested, or nil if the
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# request times out.
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def execute(text)
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request = Net::HTTP::Post.new(@uri.path, initheader=HEADER)
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request.body = {:textToAnnotate => text}.merge(@options).map do |k, v|
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"#{CGI.escape(k.to_s)}=#{CGI.escape(v.to_s)}"
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end.join("&")
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begin
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response = Net::HTTP.new(@uri.host, @uri.port).start do |http|
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http.read_timeout = @timeout
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http.request(request)
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end
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@parse_xml ? self.class.parse(response.body) : response.body
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rescue Timeout::Error
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puts "Request for #{text[0..10]} timed-out at #{@timeout} seconds."
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end
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end
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# Parse the raw XML, returning a Hash with three elements: statistics,
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# annotations, and ontologies. Respectively, these represent the annotation
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# statistics (annotations by mapping type, etc., as a Hash), an Array of
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# each annotation (as a Hash), and an Array of ontologies used (also as
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# a Hash).
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# @param [String] xml The XMl we'll be parsing.
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# @return [Hash<Symbol, Object>] A Hash representation of the XML, as
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# described above.
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def self.parse(xml)
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statistics = []
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annotations = []
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ontologies = []
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doc = Nokogiri::XML.parse(xml)
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doc.xpath("//annotationBean").each do |ann|
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parsed = {}
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parsed[:score] = ann.xpath("score").text.to_i
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parsed[:id] = ann.xpath("concept/id").text.to_i
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parsed[:localConceptId] = ann.xpath("concept/localConceptId")
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parsed[:localOntologyId] = ann.xpath("concept/localOntologyId").text.to_i
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parsed[:isTopLevel] = ann.xpath("concept/isTopLevel").text.to_i
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parsed[:fullId] = ann.xpath("concept/fullId").text
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parsed[:preferredName] = ann.xpath("concept/preferredName").text
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synonyms = ann.xpath("concept/synonyms/synonym")
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parsed[:synonyms] = synonyms.map do |synonym|
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synonym.xpath("string").text
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end
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semanticTypeBeans = ann.xpath("concept/semanticTypes/semanticTypeBean")
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parsed[:semanticTypes] = semanticTypeBeans.map do |semanticType|
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{
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:id => semanticType.xpath("id").text.to_i,
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:semanticType => semanticType.xpath("semanticType").text,
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:description => semanticType.xpath("description").text
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}
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end
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annotations << parsed
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end
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doc.xpath("//ontologyUsedBean").each do |ontology|
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parsed = {}
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parsed[:localOntologyId] = ontology.xpath("localOntologyId").text
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parsed[:virtualOntologyId] = ontology.xpath("virtualOntologyId").text
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parsed[:name] = ontology.xpath("name").text
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ontologies << parsed
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end
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{
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:statistics => statistics,
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:annotations => annotations,
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:ontologies => ontologies
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}
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end
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end
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require "test/unit"
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require "oba_client"
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TEST_TEXTS = [
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"hello I am a monkeyfish with a benign neoplastic....\t\n\\n",
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"zebrafish echo delta tango TURN <?xml MY VOLUME UP cancer of the thorax.",
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"zebrafish DROP TABLE !!! TURN MY VOLUME UP cancer of the thorax.",
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%Q{LOROE aonuhaso unseu anoeuhs aeuhsaonuh asoneuhason uaosenuh aosenuhaose
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aoneuhasonuhaoenuh anoeuhasn euhasoneu haosneuhaosenuhaoesunahoeusnaoeuteeano
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aot tt t t t t t t tae \n!!@)$@(#)%@#!)@# asoeuaohsenutahoeusaheou
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}
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]
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class TestOBAClient < Test::Unit::TestCase
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def test_reuse_annotator_instance
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ann = OBAClient.new
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TEST_TEXTS.each do |text|
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xml = ann.execute(text)
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assert xml[0..4] == "<?xml"
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end
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end
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def test_annotation_no_parameters
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TEST_TEXTS.each do |text|
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ann = OBAClient.new
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xml = ann.execute(text)
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assert xml[0..4] == "<?xml"
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end
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end
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def test_annotation_parse
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TEST_TEXTS.each do |text|
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ann = OBAClient.new :parse_xml => true
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parsed = ann.execute(text)
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assert parsed[:statistics].is_a?(Array)
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assert parsed[:annotations].is_a?(Array)
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assert parsed[:ontologies].is_a?(Array)
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end
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end
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def test_annotation_keep_one_ontology
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TEST_TEXTS.each do |text|
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ann = OBAClient.new(
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:ontologiesToKeepInResult => [42812],
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:parse_xml => true
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)
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parsed = ann.execute(text)
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assert parsed[:statistics].is_a?(Array)
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assert parsed[:annotations].is_a?(Array)
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assert parsed[:ontologies].is_a?(Array)
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end
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end
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def test_annotation_invalid_parameters
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TEST_TEXTS.each do |text|
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ann = OBAClient.new(
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:ontologiesToKeepInResult => [42812],
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:parse_xml => true,
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:blah_blah => true,
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:hoho => ["merry", "christmas"]
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)
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parsed = ann.execute(text)
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assert parsed[:statistics].is_a?(Array)
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assert parsed[:annotations].is_a?(Array)
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assert parsed[:ontologies].is_a?(Array)
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end
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end
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end
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metadata
ADDED
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--- !ruby/object:Gem::Specification
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name: oba-client
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version: !ruby/object:Gem::Version
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hash: 23
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prerelease: false
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segments:
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- 1
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- 0
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- 0
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version: 1.0.0
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platform: ruby
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authors:
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- Rob Tirrell
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2010-07-08 00:00:00 -07:00
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default_executable:
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rubyforge
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prerelease: false
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requirement: &id001 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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hash: 7
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segments:
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- 2
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- 0
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- 4
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version: 2.0.4
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type: :development
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version_requirements: *id001
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- !ruby/object:Gem::Dependency
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name: hoe
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prerelease: false
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requirement: &id002 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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hash: 21
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segments:
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- 2
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- 6
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- 1
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version: 2.6.1
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type: :development
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version_requirements: *id002
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description: FIX (describe your package)
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email:
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- rpt@stanford.edu
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executables:
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- oba_client
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extensions: []
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extra_rdoc_files:
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- History.txt
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- Manifest.txt
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- README.txt
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files:
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- .autotest
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- History.txt
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- Manifest.txt
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- README.txt
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- Rakefile
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- bin/oba_client
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- lib/oba_client.rb
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- test/test_oba_client.rb
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has_rdoc: true
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homepage: http://rubyforge.org/oba-client
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licenses: []
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post_install_message:
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rdoc_options:
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- --main
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- README.txt
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require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
|
84
|
+
none: false
|
85
|
+
requirements:
|
86
|
+
- - ">="
|
87
|
+
- !ruby/object:Gem::Version
|
88
|
+
hash: 3
|
89
|
+
segments:
|
90
|
+
- 0
|
91
|
+
version: "0"
|
92
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
93
|
+
none: false
|
94
|
+
requirements:
|
95
|
+
- - ">="
|
96
|
+
- !ruby/object:Gem::Version
|
97
|
+
hash: 3
|
98
|
+
segments:
|
99
|
+
- 0
|
100
|
+
version: "0"
|
101
|
+
requirements: []
|
102
|
+
|
103
|
+
rubyforge_project: oba-client
|
104
|
+
rubygems_version: 1.3.7
|
105
|
+
signing_key:
|
106
|
+
specification_version: 3
|
107
|
+
summary: FIX (describe your package)
|
108
|
+
test_files:
|
109
|
+
- test/test_oba_client.rb
|