publisci 0.1.2

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Files changed (220) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.rspec +1 -0
  4. data/.travis.yml +13 -0
  5. data/Gemfile +36 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +51 -0
  8. data/README.rdoc +48 -0
  9. data/Rakefile +68 -0
  10. data/bin/bio-publisci +106 -0
  11. data/bin/bio-publisci-server +50 -0
  12. data/examples/bio-band_integration.rb +9 -0
  13. data/examples/no_magic.prov +58 -0
  14. data/examples/no_magic.rb +58 -0
  15. data/examples/orm.prov +48 -0
  16. data/examples/primer-full.prov +120 -0
  17. data/examples/primer.prov +66 -0
  18. data/examples/prov_dsl.prov +85 -0
  19. data/examples/safe_gen.rb +7 -0
  20. data/examples/visualization/primer.prov +66 -0
  21. data/examples/visualization/prov_viz.rb +140 -0
  22. data/examples/visualization/viz.rb +35 -0
  23. data/features/create_generator.feature +21 -0
  24. data/features/integration.feature +12 -0
  25. data/features/integration_steps.rb +10 -0
  26. data/features/metadata.feature +37 -0
  27. data/features/metadata_steps.rb +40 -0
  28. data/features/orm.feature +60 -0
  29. data/features/orm_steps.rb +74 -0
  30. data/features/prov_dsl.feature +14 -0
  31. data/features/prov_dsl_steps.rb +11 -0
  32. data/features/reader.feature +25 -0
  33. data/features/reader_steps.rb +61 -0
  34. data/features/step_definitions/bio-publisci_steps.rb +0 -0
  35. data/features/store.feature +27 -0
  36. data/features/store_steps.rb +42 -0
  37. data/features/support/env.rb +13 -0
  38. data/features/writer.feature +14 -0
  39. data/features/writer_steps.rb +24 -0
  40. data/lib/bio-publisci.rb +64 -0
  41. data/lib/bio-publisci/analyzer.rb +57 -0
  42. data/lib/bio-publisci/datacube_model.rb +111 -0
  43. data/lib/bio-publisci/dataset/ORM/data_cube_orm.rb +240 -0
  44. data/lib/bio-publisci/dataset/ORM/observation.rb +20 -0
  45. data/lib/bio-publisci/dataset/configuration.rb +31 -0
  46. data/lib/bio-publisci/dataset/data_cube.rb +418 -0
  47. data/lib/bio-publisci/dataset/dataset.rb +11 -0
  48. data/lib/bio-publisci/dataset/dataset_for.rb +186 -0
  49. data/lib/bio-publisci/dataset/interactive.rb +72 -0
  50. data/lib/bio-publisci/dsl/config.rb +34 -0
  51. data/lib/bio-publisci/dsl/dataset_dsl.rb +93 -0
  52. data/lib/bio-publisci/dsl/dsl.rb +72 -0
  53. data/lib/bio-publisci/dsl/metadata_dsl.rb +85 -0
  54. data/lib/bio-publisci/dsl/prov_dsl.rb +143 -0
  55. data/lib/bio-publisci/metadata/generator.rb +323 -0
  56. data/lib/bio-publisci/metadata/metadata.rb +5 -0
  57. data/lib/bio-publisci/metadata/metadata_model.rb +25 -0
  58. data/lib/bio-publisci/metadata/prov/activity.rb +88 -0
  59. data/lib/bio-publisci/metadata/prov/agent.rb +100 -0
  60. data/lib/bio-publisci/metadata/prov/association.rb +107 -0
  61. data/lib/bio-publisci/metadata/prov/config.rb +34 -0
  62. data/lib/bio-publisci/metadata/prov/derivation.rb +60 -0
  63. data/lib/bio-publisci/metadata/prov/element.rb +120 -0
  64. data/lib/bio-publisci/metadata/prov/entity.rb +64 -0
  65. data/lib/bio-publisci/metadata/prov/model/prov_models.rb +109 -0
  66. data/lib/bio-publisci/metadata/prov/plan.rb +32 -0
  67. data/lib/bio-publisci/metadata/prov/prov.rb +78 -0
  68. data/lib/bio-publisci/metadata/prov/role.rb +40 -0
  69. data/lib/bio-publisci/metadata/prov/usage.rb +64 -0
  70. data/lib/bio-publisci/metadata/publisher.rb +25 -0
  71. data/lib/bio-publisci/mixins/custom_predicate.rb +38 -0
  72. data/lib/bio-publisci/mixins/dereferencable.rb +34 -0
  73. data/lib/bio-publisci/mixins/registry.rb +27 -0
  74. data/lib/bio-publisci/mixins/vocabulary.rb +8 -0
  75. data/lib/bio-publisci/output.rb +27 -0
  76. data/lib/bio-publisci/parser.rb +266 -0
  77. data/lib/bio-publisci/post_processor.rb +95 -0
  78. data/lib/bio-publisci/query/query_helper.rb +123 -0
  79. data/lib/bio-publisci/r_client.rb +54 -0
  80. data/lib/bio-publisci/readers/arff.rb +49 -0
  81. data/lib/bio-publisci/readers/base.rb +57 -0
  82. data/lib/bio-publisci/readers/csv.rb +88 -0
  83. data/lib/bio-publisci/readers/dataframe.rb +67 -0
  84. data/lib/bio-publisci/readers/maf.rb +199 -0
  85. data/lib/bio-publisci/readers/r_cross.rb +112 -0
  86. data/lib/bio-publisci/readers/r_matrix.rb +176 -0
  87. data/lib/bio-publisci/store.rb +56 -0
  88. data/lib/bio-publisci/writers/arff.rb +91 -0
  89. data/lib/bio-publisci/writers/base.rb +93 -0
  90. data/lib/bio-publisci/writers/csv.rb +31 -0
  91. data/lib/bio-publisci/writers/dataframe.rb +81 -0
  92. data/lib/bio-publisci/writers/json.rb +18 -0
  93. data/lib/r2rdf.rb +226 -0
  94. data/lib/template_bak.rb +12 -0
  95. data/lib/template_bak/publisci.rb +3 -0
  96. data/lib/vocabs/cc.rb +18 -0
  97. data/lib/vocabs/cert.rb +13 -0
  98. data/lib/vocabs/dc.rb +63 -0
  99. data/lib/vocabs/dc11.rb +23 -0
  100. data/lib/vocabs/doap.rb +45 -0
  101. data/lib/vocabs/exif.rb +168 -0
  102. data/lib/vocabs/foaf.rb +69 -0
  103. data/lib/vocabs/geo.rb +13 -0
  104. data/lib/vocabs/http.rb +26 -0
  105. data/lib/vocabs/ma.rb +78 -0
  106. data/lib/vocabs/owl.rb +59 -0
  107. data/lib/vocabs/rdfs.rb +17 -0
  108. data/lib/vocabs/rsa.rb +12 -0
  109. data/lib/vocabs/rss.rb +14 -0
  110. data/lib/vocabs/sioc.rb +93 -0
  111. data/lib/vocabs/skos.rb +36 -0
  112. data/lib/vocabs/wot.rb +21 -0
  113. data/lib/vocabs/xhtml.rb +9 -0
  114. data/lib/vocabs/xsd.rb +58 -0
  115. data/resources/maf_example.maf +10 -0
  116. data/resources/maf_rdf.ttl +1173 -0
  117. data/resources/primer.ttl +38 -0
  118. data/resources/queries/code_resources.rq +10 -0
  119. data/resources/queries/codes.rq +18 -0
  120. data/resources/queries/dataset.rq +7 -0
  121. data/resources/queries/dimension_ranges.rq +8 -0
  122. data/resources/queries/dimensions.rq +12 -0
  123. data/resources/queries/gene.rq +16 -0
  124. data/resources/queries/hugo_to_ensembl.rq +7 -0
  125. data/resources/queries/maf_column.rq +26 -0
  126. data/resources/queries/measures.rq +12 -0
  127. data/resources/queries/observation_labels.rq +8 -0
  128. data/resources/queries/observations.rq +13 -0
  129. data/resources/queries/patient.rq +11 -0
  130. data/resources/queries/patient_list.rq +11 -0
  131. data/resources/queries/patients_with_mutation.rq +18 -0
  132. data/resources/queries/properties.rq +8 -0
  133. data/resources/queries/test.rq +3 -0
  134. data/resources/weather.numeric.arff +28 -0
  135. data/scripts/get_gene_lengths.rb +50 -0
  136. data/scripts/islet_mlratio.rb +6 -0
  137. data/scripts/scan_islet.rb +6 -0
  138. data/scripts/update_reference.rb +25 -0
  139. data/server/helpers.rb +215 -0
  140. data/server/public/src-min-noconflict/LICENSE +24 -0
  141. data/server/public/src-min-noconflict/ace.js +11 -0
  142. data/server/public/src-min-noconflict/ext-chromevox.js +1 -0
  143. data/server/public/src-min-noconflict/ext-elastic_tabstops_lite.js +1 -0
  144. data/server/public/src-min-noconflict/ext-emmet.js +1 -0
  145. data/server/public/src-min-noconflict/ext-keybinding_menu.js +1 -0
  146. data/server/public/src-min-noconflict/ext-language_tools.js +1 -0
  147. data/server/public/src-min-noconflict/ext-modelist.js +1 -0
  148. data/server/public/src-min-noconflict/ext-old_ie.js +1 -0
  149. data/server/public/src-min-noconflict/ext-searchbox.js +1 -0
  150. data/server/public/src-min-noconflict/ext-settings_menu.js +1 -0
  151. data/server/public/src-min-noconflict/ext-spellcheck.js +1 -0
  152. data/server/public/src-min-noconflict/ext-split.js +1 -0
  153. data/server/public/src-min-noconflict/ext-static_highlight.js +1 -0
  154. data/server/public/src-min-noconflict/ext-statusbar.js +1 -0
  155. data/server/public/src-min-noconflict/ext-textarea.js +1 -0
  156. data/server/public/src-min-noconflict/ext-themelist.js +1 -0
  157. data/server/public/src-min-noconflict/ext-whitespace.js +1 -0
  158. data/server/public/src-min-noconflict/keybinding-emacs.js +1 -0
  159. data/server/public/src-min-noconflict/keybinding-vim.js +1 -0
  160. data/server/public/src-min-noconflict/mode-ruby.js +1 -0
  161. data/server/public/src-min-noconflict/snippets/ruby.js +1 -0
  162. data/server/public/src-min-noconflict/theme-twilight.js +1 -0
  163. data/server/public/src-min-noconflict/worker-coffee.js +1 -0
  164. data/server/public/src-min-noconflict/worker-css.js +1 -0
  165. data/server/public/src-min-noconflict/worker-javascript.js +1 -0
  166. data/server/public/src-min-noconflict/worker-json.js +1 -0
  167. data/server/public/src-min-noconflict/worker-lua.js +1 -0
  168. data/server/public/src-min-noconflict/worker-php.js +1 -0
  169. data/server/public/src-min-noconflict/worker-xquery.js +1 -0
  170. data/server/routes.rb +123 -0
  171. data/server/views/dsl.haml +65 -0
  172. data/server/views/dump.haml +3 -0
  173. data/server/views/import.haml +35 -0
  174. data/server/views/new_repository.haml +25 -0
  175. data/server/views/query.haml +28 -0
  176. data/server/views/repository.haml +25 -0
  177. data/spec/ORM/data_cube_orm_spec.rb +33 -0
  178. data/spec/ORM/prov_model_spec.rb +72 -0
  179. data/spec/analyzer_spec.rb +36 -0
  180. data/spec/bnode_spec.rb +66 -0
  181. data/spec/csv/bacon.csv +4 -0
  182. data/spec/csv/moar_bacon.csv +11 -0
  183. data/spec/data_cube_spec.rb +169 -0
  184. data/spec/dataset_for_spec.rb +77 -0
  185. data/spec/dsl_spec.rb +134 -0
  186. data/spec/generators/csv_spec.rb +44 -0
  187. data/spec/generators/dataframe_spec.rb +44 -0
  188. data/spec/generators/maf_spec.rb +40 -0
  189. data/spec/generators/r_cross_spec.rb +51 -0
  190. data/spec/generators/r_matrix_spec.rb +44 -0
  191. data/spec/length_lookup_spec.rb +0 -0
  192. data/spec/maf_query_spec.rb +343 -0
  193. data/spec/metadata/metadata_dsl_spec.rb +68 -0
  194. data/spec/prov/activity_spec.rb +74 -0
  195. data/spec/prov/agent_spec.rb +54 -0
  196. data/spec/prov/association_spec.rb +55 -0
  197. data/spec/prov/config_spec.rb +28 -0
  198. data/spec/prov/derivation_spec.rb +30 -0
  199. data/spec/prov/entity_spec.rb +52 -0
  200. data/spec/prov/role_spec.rb +94 -0
  201. data/spec/prov/usage_spec.rb +98 -0
  202. data/spec/queries/integrity/1.rq +21 -0
  203. data/spec/queries/integrity/11.rq +29 -0
  204. data/spec/queries/integrity/12.rq +37 -0
  205. data/spec/queries/integrity/14.rq +25 -0
  206. data/spec/queries/integrity/19_1.rq +21 -0
  207. data/spec/queries/integrity/19_2.rq +15 -0
  208. data/spec/queries/integrity/2.rq +22 -0
  209. data/spec/queries/integrity/3.rq +19 -0
  210. data/spec/queries/integrity/4.rq +13 -0
  211. data/spec/queries/integrity/5.rq +14 -0
  212. data/spec/r_builder_spec.rb +33 -0
  213. data/spec/resource/.RData +0 -0
  214. data/spec/resource/example.Rhistory +3 -0
  215. data/spec/spec_helper.rb +17 -0
  216. data/spec/turtle/bacon +147 -0
  217. data/spec/turtle/reference +2064 -0
  218. data/spec/turtle/weather +275 -0
  219. data/spec/writer_spec.rb +75 -0
  220. metadata +589 -0

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