bio-publisci 0.0.8 → 0.1.0

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Files changed (94) hide show
  1. checksums.yaml +7 -0
  2. data/Gemfile +10 -0
  3. data/Rakefile +1 -1
  4. data/bin/bio-publisci-server +50 -0
  5. data/features/reader_steps.rb +1 -1
  6. data/lib/bio-publisci.rb +11 -2
  7. data/lib/bio-publisci/datacube_model.rb +92 -88
  8. data/lib/bio-publisci/dataset/ORM/data_cube_orm.rb +0 -1
  9. data/lib/bio-publisci/dataset/data_cube.rb +78 -44
  10. data/lib/bio-publisci/dataset/dataset_for.rb +26 -27
  11. data/lib/bio-publisci/metadata/metadata_model.rb +21 -23
  12. data/lib/bio-publisci/metadata/prov/model/prov_models.rb +5 -5
  13. data/lib/bio-publisci/output.rb +1 -1
  14. data/lib/bio-publisci/parser.rb +130 -12
  15. data/lib/bio-publisci/post_processor.rb +95 -0
  16. data/lib/bio-publisci/query/query_helper.rb +13 -8
  17. data/lib/bio-publisci/readers/arff.rb +1 -1
  18. data/lib/bio-publisci/readers/base.rb +57 -0
  19. data/lib/bio-publisci/readers/csv.rb +2 -5
  20. data/lib/bio-publisci/readers/dataframe.rb +2 -2
  21. data/lib/bio-publisci/readers/maf.rb +199 -0
  22. data/lib/bio-publisci/readers/r_cross.rb +6 -10
  23. data/lib/bio-publisci/readers/r_matrix.rb +1 -1
  24. data/lib/bio-publisci/writers/base.rb +16 -0
  25. data/lib/bio-publisci/writers/json.rb +18 -0
  26. data/resources/maf_example.maf +10 -0
  27. data/resources/maf_rdf.ttl +1173 -0
  28. data/resources/primer.ttl +38 -0
  29. data/resources/queries/gene.rq +16 -0
  30. data/resources/queries/hugo_to_ensembl.rq +7 -0
  31. data/resources/queries/maf_column.rq +26 -0
  32. data/resources/queries/patient.rq +11 -0
  33. data/resources/queries/patient_list.rq +11 -0
  34. data/resources/queries/patients_with_mutation.rq +18 -0
  35. data/scripts/get_gene_lengths.rb +50 -0
  36. data/scripts/islet_mlratio.rb +1 -1
  37. data/scripts/scan_islet.rb +1 -1
  38. data/scripts/update_reference.rb +8 -3
  39. data/server/helpers.rb +215 -0
  40. data/server/public/src-min-noconflict/LICENSE +24 -0
  41. data/server/public/src-min-noconflict/ace.js +11 -0
  42. data/server/public/src-min-noconflict/ext-chromevox.js +1 -0
  43. data/server/public/src-min-noconflict/ext-elastic_tabstops_lite.js +1 -0
  44. data/server/public/src-min-noconflict/ext-emmet.js +1 -0
  45. data/server/public/src-min-noconflict/ext-keybinding_menu.js +1 -0
  46. data/server/public/src-min-noconflict/ext-language_tools.js +1 -0
  47. data/server/public/src-min-noconflict/ext-modelist.js +1 -0
  48. data/server/public/src-min-noconflict/ext-old_ie.js +1 -0
  49. data/server/public/src-min-noconflict/ext-searchbox.js +1 -0
  50. data/server/public/src-min-noconflict/ext-settings_menu.js +1 -0
  51. data/server/public/src-min-noconflict/ext-spellcheck.js +1 -0
  52. data/server/public/src-min-noconflict/ext-split.js +1 -0
  53. data/server/public/src-min-noconflict/ext-static_highlight.js +1 -0
  54. data/server/public/src-min-noconflict/ext-statusbar.js +1 -0
  55. data/server/public/src-min-noconflict/ext-textarea.js +1 -0
  56. data/server/public/src-min-noconflict/ext-themelist.js +1 -0
  57. data/server/public/src-min-noconflict/ext-whitespace.js +1 -0
  58. data/server/public/src-min-noconflict/keybinding-emacs.js +1 -0
  59. data/server/public/src-min-noconflict/keybinding-vim.js +1 -0
  60. data/server/public/src-min-noconflict/mode-ruby.js +1 -0
  61. data/server/public/src-min-noconflict/snippets/ruby.js +1 -0
  62. data/server/public/src-min-noconflict/theme-twilight.js +1 -0
  63. data/server/public/src-min-noconflict/worker-coffee.js +1 -0
  64. data/server/public/src-min-noconflict/worker-css.js +1 -0
  65. data/server/public/src-min-noconflict/worker-javascript.js +1 -0
  66. data/server/public/src-min-noconflict/worker-json.js +1 -0
  67. data/server/public/src-min-noconflict/worker-lua.js +1 -0
  68. data/server/public/src-min-noconflict/worker-php.js +1 -0
  69. data/server/public/src-min-noconflict/worker-xquery.js +1 -0
  70. data/server/routes.rb +123 -0
  71. data/server/views/dsl.haml +65 -0
  72. data/server/views/dump.haml +3 -0
  73. data/server/views/import.haml +35 -0
  74. data/server/views/new_repository.haml +25 -0
  75. data/server/views/query.haml +28 -0
  76. data/server/views/repository.haml +25 -0
  77. data/spec/ORM/data_cube_orm_spec.rb +1 -0
  78. data/spec/bnode_spec.rb +66 -0
  79. data/spec/data_cube_spec.rb +66 -63
  80. data/spec/dataset_for_spec.rb +36 -16
  81. data/spec/dsl_spec.rb +41 -0
  82. data/spec/generators/csv_spec.rb +3 -3
  83. data/spec/generators/dataframe_spec.rb +2 -2
  84. data/spec/generators/maf_spec.rb +40 -0
  85. data/spec/generators/r_cross_spec.rb +2 -2
  86. data/spec/generators/r_matrix_spec.rb +2 -2
  87. data/spec/length_lookup_spec.rb +0 -0
  88. data/spec/maf_query_spec.rb +343 -0
  89. data/spec/resource/example.Rhistory +1 -1
  90. data/spec/turtle/bacon +9 -9
  91. data/spec/turtle/reference +43 -43
  92. data/spec/turtle/weather +10 -10
  93. data/spec/writer_spec.rb +16 -2
  94. metadata +212 -61

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