mspire-obo 0.0.3

data/spec/mspire/obo/group_spec.rb

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+require 'spec_helper'
+
+require 'mspire/obo/group'
+
+describe Mspire::Obo::Group do 
+
+  let(:obos) { %i(ims uo).map {|key| Mspire::Obo[key] } }
+  subject { Mspire::Obo::Group.new(obos) }
+
+  it 'is built with Mspire::Obo objects' do
+    expect(subject.obos).to eq(obos)
+  end
+
+  describe 'making individual hashes' do
+
+    specify '#id_to_name! builds id_to_name meta hash' do
+      expect(subject.id_to_name!.id_to_name["UO:0000012"]).to eq "kelvin"
+      expect(subject.id_to_name!.id_to_name["IMS:1000013"]).to eq "unit"
+    end
+
+    specify '#id_to_cast! builds id_to_name meta hash' do
+      expect(subject.id_to_cast!.id_to_cast["UO:0000012"]).to eq false
+      expect(subject.id_to_cast!.id_to_cast["IMS:1001207"]).to eq :to_f
+    end
+
+    specify '#id_to_stanza! builds id_to_name meta hash' do
+      expect(subject.id_to_stanza!.id_to_stanza["UO:0000012"].class).to eq Obo::Stanza
+      expect(subject.id_to_stanza!.id_to_stanza["IMS:1001207"].class).to eq Obo::Stanza
+    end
+
+    specify '' do
+      expect(subject.name_to_id!.name_to_id['kelvin']).to eq "UO:0000012"
+      expect(subject.name_to_id!.name_to_id['unit']).to eq "UO:0000000"  # <- clobbered "IMS:1000013"
+    end
+
+    describe 'resolving collisions with name_to_id' do
+      specify '#name_to_id allows lookup with namespace' do
+        subject.name_to_id!
+        expect(subject.name_to_id.class).to eq Hash
+        expect(subject.name_to_id['unit']).to eq "UO:0000000"
+        expect(subject.name_to_id('unit')).to eq "UO:0000000"
+        expect(subject.name_to_id("unit", 'IMS')).to eq "IMS:1000013"
+      end
+    end
+  end
+
+  describe '#make_all! building all hashes' do
+    let(:made) { subject.make_all! }
+
+    it 'builds id_to_name' do
+      expect(made.id_to_name["UO:0000012"]).to eq "kelvin"
+      expect(made.id_to_name["IMS:1000013"]).to eq "unit"
+    end
+
+    it 'builds id_to_cast' do
+      expect(made.id_to_cast["UO:0000012"]).to eq false
+      expect(made.id_to_cast["IMS:1001207"]).to eq :to_f
+    end
+
+    it 'builds id_to_stanza' do
+      expect(made.id_to_stanza["UO:0000012"].class).to eq Obo::Stanza
+      expect(made.id_to_stanza["IMS:1001207"].class).to eq Obo::Stanza
+    end
+
+    it "builds name_to_id, clobbering early ids when names collide (later takes precedence)" do
+      expect(made.name_to_id['kelvin']).to eq "UO:0000012"
+      expect(made.name_to_id['unit']).to eq "UO:0000000"  # <- clobbered "IMS:1000013"
+    end
+  end
+
+  
+end

data/spec/mspire/obo/header_parser_spec.rb

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+require 'spec_helper'
+require 'mspire/obo'
+require 'mspire/obo/header_parser'
+
+
+describe Mspire::Obo::HeaderParser do
+  let(:obo_file) { Mspire::Obo::DIR + "/unit.obo" }
+
+  it 'reads headers from obo files' do
+    header = described_class.new.header(obo_file)
+    {"format-version"=>["1.2"], "date"=>["12:10:2011 11:21"], "saved-by"=>["George Gkoutos"], "auto-generated-by"=>["OBO-Edit 2.1-beta13"], "subsetdef"=>["unit_group_slim \"unit group slim\"", "unit_slim \"unit slim\""], "default-namespace"=>["unit.ontology"], "namespace-id-rule"=>["* UO:$sequence(7,0,9999999)$"], "import"=>["http://purl.obolibrary.org/obo/pato.obo"]}.each do |key, expect|
+      expect(header.tagvalues[key]).to eq expect
+    end
+  end
+
+end

data/spec/mspire/obo_spec.rb

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+require 'spec_helper'
+
+require 'mspire/obo'
+
+
+describe Mspire::Obo do 
+
+  let(:bases) { %w(psi-ms unit imagingMS PSI-MOD quality) }
+  let(:filename) { Hash[bases.map {|base| [base, Mspire::Obo::DIR + "/#{base}.obo"] }] }
+
+  let(:normal) { /\A[\d\.]{5,10}\Z/ }# "0.9.1" or "0.91.132"
+  let(:date) { /\A[\d:]{8,15}\Z/ } # "09:04:2014"
+
+  describe 'the Mspire::Obo class' do
+    specify '#version(filename) returns the version' do
+      expect(Mspire::Obo.version(filename['psi-ms'])).to match(normal)
+    end
+
+    specify '#available returns an informative hash for each obo' do
+      hashes = Mspire::Obo.available
+      hashes.each {|hash| expect(hash.keys.sort).to eq [:full_name, :uri, :namespace, :path, :version, :key].sort }
+      ms_hash = hashes.find {|hash| hash[:namespace] == 'MS' }
+      expect(ms_hash[:full_name].split(' ').first).to eq('Proteomics')
+      expect(ms_hash[:uri]).to match(/psidev.*psi-ms.obo/)
+      expect(ms_hash[:namespace]).to eq "MS"
+      expect(ms_hash[:path]).to match(/.+obo\/psi-ms.obo/)
+      expect(ms_hash[:version]).to match normal
+      expect(ms_hash[:key]).to eq :ms
+    end
+
+    specify '#[symbol] loads an obo with a simple key symbol' do
+      obo = Mspire::Obo[:ms]
+      expect(obo.class).to eq Mspire::Obo
+      expect(obo.full_name.split(' ').first).to eq('Proteomics')
+      expect(obo.version).to match normal
+      expect(obo.uri).to match(/psidev.*psi-ms.obo/)
+      expect(obo.stanzas.size).to be > 2000
+    end
+    specify '#[symbol, false] loads an obo (no file loaded) with a simple key symbol' do
+      obo = Mspire::Obo[:ms, false]
+      expect(obo.class).to eq Mspire::Obo
+      expect(obo.version).to match normal
+      expect(obo.stanzas).to be nil
+    end
+  end
+
+  it 'can set the version from a file (only reads the header)' do
+    versions = bases.map do |base|
+      Mspire::Obo.new.set_version!(filename[base]).version
+    end
+    [normal, date, normal, normal, date].zip(versions) do |exp_re, act|
+      expect(act).to match(exp_re)
+    end
+  end
+
+  context 'accessing ontology information from a file' do
+    let(:obo) { Mspire::Obo.new(filename['psi-ms']) }
+
+    describe 'Obo::Stanza' do
+      it 'can properly cast values' do
+        hash = obo.make_id_to_stanza
+        expect(hash.size > 10).to eq true # check for the hash
+        {
+          'MS:1000511' => ['1', 1],
+          'MS:1000004' => ['2.2', 2.2],
+          'MS:1000011' => ['2.2', '2.2'],
+          'MS:1000018' => ['low to high', 'low to high'],
+        }.each do |id, vals|
+          expect( hash[id].cast(vals.first) ).to eq(vals.last)
+        end
+      end
+    end
+
+    it 'has no uri or full_name unless provided' do
+      expect([:uri, :full_name].map {|attr| obo.send(attr) }).to eq [nil,nil]
+    end
+
+    it 'automatically sets a version from the header information' do
+      normal = /\A[\d\.]{5,10}\Z/
+      expect(obo.version).to match(normal)
+    end
+
+    describe 'attr_accessor methods require hashes be built first' do
+      describe 'attr_accessor methods for hashes before building' do
+        specify 'they all yield nil' do
+          expect([obo.id_to_name, obo.id_to_cast, obo.id_to_stanza, obo.name_to_id]).to eq [nil].*(4)
+        end
+      end
+
+      it 'yields a hash if properly initialized' do
+        [obo.id_to_stanza!.id_to_stanza, 
+         obo.id_to_name!.id_to_name,
+         obo.id_to_cast!.id_to_cast,
+         obo.name_to_id!.name_to_id].each do |hash|
+           expect(hash.class).to eq Hash
+         end
+      end
+    end
+
+    describe 'methods returning hashes' do
+      specify '#make_id_to_name' do
+        hash = obo.make_id_to_name
+        expect(hash.class).to eq Hash
+        expect(hash['MS:1000005']).to eq 'sample volume'
+      end
+      specify '#make_id_to_cast' do
+        hash = obo.make_id_to_cast
+        expect(hash.class).to eq Hash
+        expect(hash['MS:1000511']).to eq :to_i
+        expect(hash['MS:1000004']).to eq :to_f
+        expect(hash['MS:1000018']).to eq false
+        expect(hash['MS:1000032']).to eq :to_s
+      end
+      specify '#make_name_to_id' do
+        hash = obo.make_name_to_id
+        expect(hash.class).to eq Hash
+        expect(hash['ProteinProspector']).to eq 'MS:1002043'
+      end
+      specify '#make_id_to_stanza' do
+        hash = obo.make_id_to_stanza
+        expect(hash.class).to eq Hash
+        stanza = hash['MS:1001994']
+        expect(stanza.class).to eq Obo::Stanza
+        expect(stanza['name']).to eq('top hat baseline reduction')
+      end
+    end
+  end
+end

data/spec/spec_helper.rb

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+require 'simplecov'
+SimpleCov.start
+
+require 'rspec'
+
+#TESTFILES = File.dirname(__FILE__) + '/testfiles'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+#Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  config.treat_symbols_as_metadata_keys_with_true_values = true
+  config.color_enabled = true
+  config.tty = true
+  config.formatter = :documentation  # :progress, :html, :textmate
+  #config.formatter = :progress # :progress, :html, :textmate
+end
+
+

metadata

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+--- !ruby/object:Gem::Specification
+name: mspire-obo
+version: !ruby/object:Gem::Version
+  version: 0.0.3
+platform: ruby
+authors:
+- John T. Prince
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-05-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: obo
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.5
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.5
+- !ruby/object:Gem::Dependency
+  name: andand
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.3.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.3.3
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.6.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.6.2
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.14.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.14.1
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 4.1.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 4.1.1
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.8.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.8.2
+description: simplified access for obo ontology files.  Builds hashes for quick lookup
+  of terms and finds version, etc.
+email:
+- jtprince@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/ext/obo.rb
+- lib/mspire/obo.rb
+- lib/mspire/obo/group.rb
+- lib/mspire/obo/hash_provider.rb
+- lib/mspire/obo/header_parser.rb
+- lib/mspire/obo/version.rb
+- mspire-obo.gemspec
+- obo/PSI-MOD.meta
+- obo/PSI-MOD.obo
+- obo/imagingMS.meta
+- obo/imagingMS.obo
+- obo/psi-ms.meta
+- obo/psi-ms.obo
+- obo/quality.meta
+- obo/quality.obo
+- obo/unit.meta
+- obo/unit.obo
+- spec/mspire/obo/group_spec.rb
+- spec/mspire/obo/header_parser_spec.rb
+- spec/mspire/obo_spec.rb
+- spec/spec_helper.rb
+homepage: ''
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: simplified access for obo ontology files
+test_files:
+- spec/mspire/obo/group_spec.rb
+- spec/mspire/obo/header_parser_spec.rb
+- spec/mspire/obo_spec.rb
+- spec/spec_helper.rb