bio-publisci 0.0.1

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Files changed (95) hide show
  1. data/.document +5 -0
  2. data/.rspec +1 -0
  3. data/.travis.yml +13 -0
  4. data/Gemfile +24 -0
  5. data/LICENSE.txt +20 -0
  6. data/README.md +47 -0
  7. data/README.rdoc +48 -0
  8. data/Rakefile +70 -0
  9. data/bin/bio-publisci +83 -0
  10. data/features/create_generator.feature +25 -0
  11. data/features/integration.feature +12 -0
  12. data/features/integration_steps.rb +10 -0
  13. data/features/orm.feature +60 -0
  14. data/features/orm_steps.rb +74 -0
  15. data/features/reader.feature +25 -0
  16. data/features/reader_steps.rb +60 -0
  17. data/features/step_definitions/bio-publisci_steps.rb +0 -0
  18. data/features/store.feature +27 -0
  19. data/features/store_steps.rb +42 -0
  20. data/features/support/env.rb +13 -0
  21. data/features/writer.feature +9 -0
  22. data/features/writer_steps.rb +17 -0
  23. data/lib/bio-publisci/analyzer.rb +57 -0
  24. data/lib/bio-publisci/dataset/ORM/data_cube_orm.rb +219 -0
  25. data/lib/bio-publisci/dataset/ORM/observation.rb +20 -0
  26. data/lib/bio-publisci/dataset/data_cube.rb +308 -0
  27. data/lib/bio-publisci/dataset/interactive.rb +57 -0
  28. data/lib/bio-publisci/loader.rb +36 -0
  29. data/lib/bio-publisci/metadata/metadata.rb +105 -0
  30. data/lib/bio-publisci/parser.rb +64 -0
  31. data/lib/bio-publisci/query/query_helper.rb +114 -0
  32. data/lib/bio-publisci/r_client.rb +54 -0
  33. data/lib/bio-publisci/readers/arff.rb +87 -0
  34. data/lib/bio-publisci/readers/big_cross.rb +119 -0
  35. data/lib/bio-publisci/readers/cross.rb +72 -0
  36. data/lib/bio-publisci/readers/csv.rb +54 -0
  37. data/lib/bio-publisci/readers/dataframe.rb +66 -0
  38. data/lib/bio-publisci/readers/r_matrix.rb +152 -0
  39. data/lib/bio-publisci/store.rb +56 -0
  40. data/lib/bio-publisci/writers/arff.rb +66 -0
  41. data/lib/bio-publisci/writers/dataframe.rb +81 -0
  42. data/lib/bio-publisci.rb +36 -0
  43. data/lib/r2rdf.rb +226 -0
  44. data/lib/template_bak/publisci.rb +3 -0
  45. data/lib/template_bak.rb +12 -0
  46. data/lib/vocabs/cc.rb +18 -0
  47. data/lib/vocabs/cert.rb +13 -0
  48. data/lib/vocabs/dc.rb +63 -0
  49. data/lib/vocabs/dc11.rb +23 -0
  50. data/lib/vocabs/doap.rb +45 -0
  51. data/lib/vocabs/exif.rb +168 -0
  52. data/lib/vocabs/foaf.rb +69 -0
  53. data/lib/vocabs/geo.rb +13 -0
  54. data/lib/vocabs/http.rb +26 -0
  55. data/lib/vocabs/ma.rb +78 -0
  56. data/lib/vocabs/owl.rb +59 -0
  57. data/lib/vocabs/rdfs.rb +17 -0
  58. data/lib/vocabs/rsa.rb +12 -0
  59. data/lib/vocabs/rss.rb +14 -0
  60. data/lib/vocabs/sioc.rb +93 -0
  61. data/lib/vocabs/skos.rb +36 -0
  62. data/lib/vocabs/wot.rb +21 -0
  63. data/lib/vocabs/xhtml.rb +9 -0
  64. data/lib/vocabs/xsd.rb +58 -0
  65. data/resources/queries/codes.rq +13 -0
  66. data/resources/queries/dataset.rq +7 -0
  67. data/resources/queries/dimension_ranges.rq +8 -0
  68. data/resources/queries/dimensions.rq +7 -0
  69. data/resources/queries/measures.rq +7 -0
  70. data/resources/queries/observations.rq +12 -0
  71. data/resources/queries/test.rq +3 -0
  72. data/resources/weather.numeric.arff +23 -0
  73. data/spec/analyzer_spec.rb +36 -0
  74. data/spec/bio-publisci_spec.rb +7 -0
  75. data/spec/csv/bacon.csv +4 -0
  76. data/spec/csv/moar_bacon.csv +11 -0
  77. data/spec/data_cube_spec.rb +166 -0
  78. data/spec/generators/csv_spec.rb +44 -0
  79. data/spec/generators/dataframe_spec.rb +44 -0
  80. data/spec/generators/r_matrix_spec.rb +35 -0
  81. data/spec/queries/integrity/1.rq +21 -0
  82. data/spec/queries/integrity/11.rq +29 -0
  83. data/spec/queries/integrity/12.rq +37 -0
  84. data/spec/queries/integrity/14.rq +25 -0
  85. data/spec/queries/integrity/19_1.rq +21 -0
  86. data/spec/queries/integrity/19_2.rq +15 -0
  87. data/spec/queries/integrity/2.rq +22 -0
  88. data/spec/queries/integrity/3.rq +19 -0
  89. data/spec/queries/integrity/4.rq +13 -0
  90. data/spec/queries/integrity/5.rq +14 -0
  91. data/spec/r_builder_spec.rb +33 -0
  92. data/spec/spec_helper.rb +17 -0
  93. data/spec/turtle/bacon +149 -0
  94. data/spec/turtle/reference +2066 -0
  95. metadata +259 -0
metadata ADDED
@@ -0,0 +1,259 @@
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+ --- !ruby/object:Gem::Specification
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+ name: bio-publisci
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+ version: !ruby/object:Gem::Version
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+ version: 0.0.1
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+ prerelease:
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+ platform: ruby
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+ authors:
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+ - wstrinz
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+ date: 2013-07-20 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: rspec
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+ requirement: !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: 2.8.0
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+ type: :development
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+ prerelease: false
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+ version_requirements: !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: 2.8.0
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+ - !ruby/object:Gem::Dependency
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+ name: rdoc
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+ requirement: !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: '3.12'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !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: '3.12'
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+ - !ruby/object:Gem::Dependency
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+ name: cucumber
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+ requirement: !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: !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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+ - !ruby/object:Gem::Dependency
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+ name: jeweler
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+ requirement: !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: 1.8.4
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+ type: :development
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+ prerelease: false
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+ version_requirements: !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: 1.8.4
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+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ requirement: !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: 1.0.21
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+ type: :development
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+ prerelease: false
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+ version_requirements: !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: 1.0.21
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+ - !ruby/object:Gem::Dependency
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+ name: bio
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+ requirement: !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: 1.4.2
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+ type: :development
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+ prerelease: false
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+ version_requirements: !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: 1.4.2
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+ - !ruby/object:Gem::Dependency
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+ name: rdoc
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+ requirement: !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: '3.12'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !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: '3.12'
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+ description: ! 'A toolkit for publishing scientific results and datasets using RDF
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+ and related technologies '
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+ email: wstrinz@gmail.com
129
+ executables:
130
+ - bio-publisci
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+ extensions: []
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+ extra_rdoc_files:
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+ - LICENSE.txt
134
+ - README.md
135
+ - README.rdoc
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+ files:
137
+ - .document
138
+ - .rspec
139
+ - .travis.yml
140
+ - Gemfile
141
+ - LICENSE.txt
142
+ - README.md
143
+ - README.rdoc
144
+ - Rakefile
145
+ - bin/bio-publisci
146
+ - features/create_generator.feature
147
+ - features/integration.feature
148
+ - features/integration_steps.rb
149
+ - features/orm.feature
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+ - features/orm_steps.rb
151
+ - features/reader.feature
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+ - features/reader_steps.rb
153
+ - features/step_definitions/bio-publisci_steps.rb
154
+ - features/store.feature
155
+ - features/store_steps.rb
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+ - features/support/env.rb
157
+ - features/writer.feature
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+ - features/writer_steps.rb
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+ - lib/bio-publisci.rb
160
+ - lib/bio-publisci/analyzer.rb
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+ - lib/bio-publisci/dataset/ORM/data_cube_orm.rb
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+ - lib/bio-publisci/dataset/ORM/observation.rb
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+ - lib/bio-publisci/dataset/data_cube.rb
164
+ - lib/bio-publisci/dataset/interactive.rb
165
+ - lib/bio-publisci/loader.rb
166
+ - lib/bio-publisci/metadata/metadata.rb
167
+ - lib/bio-publisci/parser.rb
168
+ - lib/bio-publisci/query/query_helper.rb
169
+ - lib/bio-publisci/r_client.rb
170
+ - lib/bio-publisci/readers/arff.rb
171
+ - lib/bio-publisci/readers/big_cross.rb
172
+ - lib/bio-publisci/readers/cross.rb
173
+ - lib/bio-publisci/readers/csv.rb
174
+ - lib/bio-publisci/readers/dataframe.rb
175
+ - lib/bio-publisci/readers/r_matrix.rb
176
+ - lib/bio-publisci/store.rb
177
+ - lib/bio-publisci/writers/arff.rb
178
+ - lib/bio-publisci/writers/dataframe.rb
179
+ - lib/r2rdf.rb
180
+ - lib/template_bak.rb
181
+ - lib/template_bak/publisci.rb
182
+ - lib/vocabs/cc.rb
183
+ - lib/vocabs/cert.rb
184
+ - lib/vocabs/dc.rb
185
+ - lib/vocabs/dc11.rb
186
+ - lib/vocabs/doap.rb
187
+ - lib/vocabs/exif.rb
188
+ - lib/vocabs/foaf.rb
189
+ - lib/vocabs/geo.rb
190
+ - lib/vocabs/http.rb
191
+ - lib/vocabs/ma.rb
192
+ - lib/vocabs/owl.rb
193
+ - lib/vocabs/rdfs.rb
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+ - lib/vocabs/rsa.rb
195
+ - lib/vocabs/rss.rb
196
+ - lib/vocabs/sioc.rb
197
+ - lib/vocabs/skos.rb
198
+ - lib/vocabs/wot.rb
199
+ - lib/vocabs/xhtml.rb
200
+ - lib/vocabs/xsd.rb
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+ - resources/queries/codes.rq
202
+ - resources/queries/dataset.rq
203
+ - resources/queries/dimension_ranges.rq
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+ - resources/queries/dimensions.rq
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+ - resources/queries/measures.rq
206
+ - resources/queries/observations.rq
207
+ - resources/queries/test.rq
208
+ - resources/weather.numeric.arff
209
+ - spec/analyzer_spec.rb
210
+ - spec/bio-publisci_spec.rb
211
+ - spec/csv/bacon.csv
212
+ - spec/csv/moar_bacon.csv
213
+ - spec/data_cube_spec.rb
214
+ - spec/generators/csv_spec.rb
215
+ - spec/generators/dataframe_spec.rb
216
+ - spec/generators/r_matrix_spec.rb
217
+ - spec/queries/integrity/1.rq
218
+ - spec/queries/integrity/11.rq
219
+ - spec/queries/integrity/12.rq
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+ - spec/queries/integrity/14.rq
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+ - spec/queries/integrity/19_1.rq
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+ - spec/queries/integrity/19_2.rq
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+ - spec/queries/integrity/2.rq
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+ - spec/queries/integrity/3.rq
225
+ - spec/queries/integrity/4.rq
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+ - spec/queries/integrity/5.rq
227
+ - spec/r_builder_spec.rb
228
+ - spec/spec_helper.rb
229
+ - spec/turtle/bacon
230
+ - spec/turtle/reference
231
+ homepage: http://github.com/wstrinz/bioruby-publisci
232
+ licenses:
233
+ - MIT
234
+ post_install_message:
235
+ rdoc_options: []
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+ require_paths:
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+ - lib
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+ required_ruby_version: !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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+ segments:
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+ - 0
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+ hash: -2936459050988630907
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+ required_rubygems_version: !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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+ rubyforge_project:
255
+ rubygems_version: 1.8.25
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+ signing_key:
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+ specification_version: 3
258
+ summary: Publish science data using semantic web ontologies
259
+ test_files: []