ols 0.0.1 → 0.1.0

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Files changed (15) hide show
  1. data/.gitignore +8 -1
  2. data/Gemfile +4 -0
  3. data/History.txt +6 -0
  4. data/README.rdoc +48 -57
  5. data/lib/ols.rb +115 -387
  6. data/lib/ols/graph.rb +91 -0
  7. data/lib/ols/term.rb +647 -0
  8. data/lib/ols/version.rb +4 -1
  9. data/ols.gemspec +7 -12
  10. data/script/console +9 -0
  11. data/test/test_helper.rb +24 -9
  12. data/test/test_ols.rb +44 -112
  13. data/test/test_ols_graph.rb +36 -0
  14. data/test/test_ols_term.rb +484 -0
  15. metadata +100 -105
metadata CHANGED
@@ -1,160 +1,155 @@
1
- --- !ruby/object:Gem::Specification
1
+ --- !ruby/object:Gem::Specification
2
2
  name: ols
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- version: !ruby/object:Gem::Version
3
+ version: !ruby/object:Gem::Version
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+ version: 0.1.0
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  prerelease:
5
- version: 0.0.1
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  platform: ruby
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- authors:
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+ authors:
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  - Darren Oakley
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  autorequire:
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  bindir: bin
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  cert_chain: []
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-
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- date: 2011-04-15 00:00:00 +01:00
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- default_executable:
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- dependencies:
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- - !ruby/object:Gem::Dependency
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- name: rubytree
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- requirement: &id001 !ruby/object:Gem::Requirement
12
+ date: 2011-11-04 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: savon
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+ requirement: &2152733760 !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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- version: "0"
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  type: :runtime
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  prerelease: false
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- version_requirements: *id001
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- - !ruby/object:Gem::Dependency
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- name: sequel
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- requirement: &id002 !ruby/object:Gem::Requirement
30
- none: false
31
- requirements:
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- - - ">="
33
- - !ruby/object:Gem::Version
34
- version: "0"
35
- type: :runtime
36
- prerelease: false
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- version_requirements: *id002
38
- - !ruby/object:Gem::Dependency
39
- name: mysql2
40
- requirement: &id003 !ruby/object:Gem::Requirement
24
+ version_requirements: *2152733760
25
+ - !ruby/object:Gem::Dependency
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+ name: rake
27
+ requirement: &2152733260 !ruby/object:Gem::Requirement
41
28
  none: false
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- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
45
- version: "0"
46
- type: :runtime
29
+ requirements:
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+ - - ! '>='
31
+ - !ruby/object:Gem::Version
32
+ version: '0'
33
+ type: :development
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  prerelease: false
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- version_requirements: *id003
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- - !ruby/object:Gem::Dependency
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- name: json
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- requirement: &id004 !ruby/object:Gem::Requirement
35
+ version_requirements: *2152733260
36
+ - !ruby/object:Gem::Dependency
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+ name: shoulda
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+ requirement: &2152732720 !ruby/object:Gem::Requirement
52
39
  none: false
53
- requirements:
54
- - - ">="
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- - !ruby/object:Gem::Version
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- version: "0"
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- type: :runtime
40
+ requirements:
41
+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :development
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  prerelease: false
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- version_requirements: *id004
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- - !ruby/object:Gem::Dependency
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- name: rake
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- requirement: &id005 !ruby/object:Gem::Requirement
46
+ version_requirements: *2152732720
47
+ - !ruby/object:Gem::Dependency
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+ name: vcr
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+ requirement: &2152731500 !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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- version: "0"
51
+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  type: :development
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56
  prerelease: false
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- version_requirements: *id005
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- - !ruby/object:Gem::Dependency
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- name: shoulda
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- requirement: &id006 !ruby/object:Gem::Requirement
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+ version_requirements: *2152731500
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+ - !ruby/object:Gem::Dependency
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+ name: webmock
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+ requirement: &2152730520 !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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- version: "0"
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *id006
82
- - !ruby/object:Gem::Dependency
68
+ version_requirements: *2152730520
69
+ - !ruby/object:Gem::Dependency
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70
  name: simplecov
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- requirement: &id007 !ruby/object:Gem::Requirement
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+ requirement: &2152728460 !ruby/object:Gem::Requirement
85
72
  none: false
86
- requirements:
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- - - ">="
88
- - !ruby/object:Gem::Version
89
- version: "0"
73
+ requirements:
74
+ - - ! '>='
75
+ - !ruby/object:Gem::Version
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+ version: '0'
90
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  type: :development
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  prerelease: false
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- version_requirements: *id007
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- - !ruby/object:Gem::Dependency
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+ version_requirements: *2152728460
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+ - !ruby/object:Gem::Dependency
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  name: simplecov-rcov
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- requirement: &id008 !ruby/object:Gem::Requirement
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+ requirement: &2152727120 !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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+ version: '0'
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+ type: :development
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+ prerelease: false
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+ version_requirements: *2152727120
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+ - !ruby/object:Gem::Dependency
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+ name: mocha
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+ requirement: &2152725360 !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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- version: "0"
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *id008
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- description: "\n OLS provides a simple interface to the EBI's Ontology Lookup Service (http://www.ebi.ac.uk/ontology-lookup/). \n It provides an easy lookup of ontology terms and automagically builds up ontology trees using RubyTree \n (http://rubytree.rubyforge.org/) as a base library.\n\n PLEASE NOTE: The current version of this gem requires a local install of the OLS database running on MySQL. \n Please see http://www.ebi.ac.uk/ontology-lookup/databaseExport.do I will update the code in the future \n to run off the soap service.\n "
105
- email:
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+ version_requirements: *2152725360
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+ description: ! "\n OLS provides a simple interface to the EBI's Ontology Lookup
103
+ Service (http://www.ebi.ac.uk/ontology-lookup/).\n It provides an easy lookup
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+ of ontology terms and automagically builds up ontology trees for you.\n "
105
+ email:
106
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  - daz.oakley@gmail.com
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  executables: []
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-
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  extensions: []
110
-
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  extra_rdoc_files: []
112
-
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- files:
110
+ files:
114
111
  - .gitignore
115
112
  - Gemfile
116
113
  - History.txt
117
114
  - README.rdoc
118
115
  - Rakefile
119
116
  - lib/ols.rb
117
+ - lib/ols/graph.rb
118
+ - lib/ols/term.rb
120
119
  - lib/ols/version.rb
121
120
  - ols.gemspec
121
+ - script/console
122
122
  - test/test_helper.rb
123
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  - test/test_ols.rb
124
- has_rdoc: true
124
+ - test/test_ols_graph.rb
125
+ - test/test_ols_term.rb
125
126
  homepage: https://github.com/dazoakley/ols
126
127
  licenses: []
127
-
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  post_install_message:
129
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  rdoc_options: []
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-
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- require_paths:
130
+ require_paths:
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131
  - lib
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- required_ruby_version: !ruby/object:Gem::Requirement
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+ required_ruby_version: !ruby/object:Gem::Requirement
134
133
  none: false
135
- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- hash: -2283321119041692548
139
- segments:
140
- - 0
141
- version: "0"
142
- required_rubygems_version: !ruby/object:Gem::Requirement
134
+ requirements:
135
+ - - ! '>='
136
+ - !ruby/object:Gem::Version
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+ version: '0'
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+ required_rubygems_version: !ruby/object:Gem::Requirement
143
139
  none: false
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- requirements:
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- - - ">="
146
- - !ruby/object:Gem::Version
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- hash: -2283321119041692548
148
- segments:
149
- - 0
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- version: "0"
140
+ requirements:
141
+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  requirements: []
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-
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  rubyforge_project: ols
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- rubygems_version: 1.6.2
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+ rubygems_version: 1.8.10
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  signing_key:
156
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  specification_version: 3
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- summary: A simple wrapper around a local copy of the OLS database
158
- test_files:
149
+ summary: A simple wrapper around the EBI's Ontology Lookup Service (OLS)
150
+ test_files:
159
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  - test/test_helper.rb
160
152
  - test/test_ols.rb
153
+ - test/test_ols_graph.rb
154
+ - test/test_ols_term.rb
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+ has_rdoc: