bel 0.3.3 → 0.4.0.beta1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (73) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +53 -8
  3. data/bel.gemspec +10 -15
  4. data/bin/bel +63 -4
  5. data/bin/bel2rdf.rb +1 -1
  6. data/bin/bel_compare.rb +1 -1
  7. data/bin/bel_parse.rb +1 -1
  8. data/bin/bel_rdfschema.rb +1 -1
  9. data/bin/bel_summarize.rb +1 -1
  10. data/bin/bel_upgrade.rb +1 -1
  11. data/lib/bel.rb +8 -10
  12. data/lib/bel/completion.rb +3 -2
  13. data/lib/bel/completion/value_match_rule.rb +10 -0
  14. data/lib/bel/evidence_model/citation.rb +101 -43
  15. data/lib/bel/evidence_model/evidence.rb +2 -2
  16. data/lib/bel/evidence_model/experiment_context.rb +1 -0
  17. data/lib/bel/evidence_model/metadata.rb +15 -2
  18. data/lib/bel/evidence_model/references.rb +10 -10
  19. data/lib/bel/json.rb +63 -0
  20. data/lib/bel/json/adapter/multi_json.rb +36 -0
  21. data/lib/bel/json/adapter/oj.rb +65 -0
  22. data/lib/bel/json/adapter/ruby_json.rb +28 -0
  23. data/lib/bel/json/reader.rb +9 -0
  24. data/lib/bel/json/writer.rb +9 -0
  25. data/lib/bel/libbel.rb +1 -4
  26. data/lib/bel/parser.rb +2 -2
  27. data/lib/bel/rdf_repository.rb +18 -0
  28. data/lib/bel/rdf_repository/plugins/memory.rb +28 -0
  29. data/lib/bel/rdf_repository/plugins/mongo.rb +28 -0
  30. data/lib/bel/resource.rb +24 -0
  31. data/lib/bel/resource/namespace.rb +122 -0
  32. data/lib/bel/resource/namespace_value.rb +69 -0
  33. data/lib/bel/resource/namespaces.rb +83 -0
  34. data/lib/bel/resource/search.rb +26 -0
  35. data/lib/bel/resource/search/api.rb +36 -0
  36. data/lib/bel/resource/search/search_result.rb +32 -0
  37. data/lib/bel/translate.rb +108 -0
  38. data/lib/bel/translator.rb +69 -0
  39. data/lib/bel/translator/plugins/bel_script.rb +36 -0
  40. data/lib/bel/translator/plugins/bel_script/bel_yielder.rb +144 -0
  41. data/lib/bel/translator/plugins/bel_script/evidence_yielder.rb +95 -0
  42. data/lib/bel/translator/plugins/bel_script/translator.rb +24 -0
  43. data/lib/bel/translator/plugins/jgf.rb +37 -0
  44. data/lib/bel/translator/plugins/jgf/translator.rb +160 -0
  45. data/lib/bel/translator/plugins/json_evidence.rb +38 -0
  46. data/lib/bel/translator/plugins/json_evidence/translator.rb +90 -0
  47. data/lib/bel/translator/plugins/rdf.rb +48 -0
  48. data/lib/bel/translator/plugins/rdf/bel_schema.rb +339 -0
  49. data/lib/bel/translator/plugins/rdf/monkey_patch.rb +310 -0
  50. data/lib/bel/translator/plugins/rdf/reader.rb +173 -0
  51. data/lib/bel/translator/plugins/rdf/translator.rb +40 -0
  52. data/lib/bel/translator/plugins/rdf/writer.rb +45 -0
  53. data/lib/bel/translator/plugins/xbel.rb +36 -0
  54. data/lib/bel/translator/plugins/xbel/evidence_handler.rb +468 -0
  55. data/lib/bel/translator/plugins/xbel/evidence_yielder.rb +24 -0
  56. data/lib/bel/translator/plugins/xbel/translator.rb +24 -0
  57. data/lib/bel/translator/plugins/xbel/xbel_yielder.rb +414 -0
  58. data/lib/bel/vendor/little-plugger.rb +323 -0
  59. data/lib/bel/version.rb +1 -1
  60. metadata +44 -158
  61. data/lib/bel/extension.rb +0 -37
  62. data/lib/bel/extension_format.rb +0 -207
  63. data/lib/bel/extensions/bel.rb +0 -258
  64. data/lib/bel/extensions/jgf.rb +0 -219
  65. data/lib/bel/extensions/json/jrjackson.rb +0 -31
  66. data/lib/bel/extensions/json/json.rb +0 -133
  67. data/lib/bel/extensions/json/multi_json.rb +0 -29
  68. data/lib/bel/extensions/json/oj.rb +0 -68
  69. data/lib/bel/extensions/json/ruby_json.rb +0 -29
  70. data/lib/bel/extensions/rdf/bel_rdf.rb +0 -338
  71. data/lib/bel/extensions/rdf/rdf.rb +0 -584
  72. data/lib/bel/extensions/xbel.rb +0 -923
  73. data/lib/bel/format.rb +0 -58
data/lib/bel/format.rb DELETED
@@ -1,58 +0,0 @@
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- module BEL
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- module Format
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- Format = BEL::Extension::Format
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- FormatError = BEL::Extension::Format::FormatError
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-
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- def self.evidence(input, input_format)
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- prepared_input = process_input(input)
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-
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- in_formatter = BEL::Extension::Format.formatters(input_format) or
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- raise FormatError.new(input_format)
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-
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- EvidenceIterable.new(prepared_input, in_formatter)
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- end
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-
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- def self.translate(input, input_format, output_format, writer = nil)
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- prepared_input = process_input(input)
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-
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- in_formatter = BEL::Extension::Format.formatters(input_format) or
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- raise FormatError.new(input_format)
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-
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- out_formatter = BEL::Extension::Format.formatters(output_format) or
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- raise FormatError.new(output_format)
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-
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- objects = in_formatter.deserialize(prepared_input)
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- output = out_formatter.serialize(objects, writer)
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- end
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-
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- def self.process_input(input)
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- if input.respond_to? :read
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- input
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- elsif File.exist?(input)
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- File.open(input, :ext_enc => Encoding::UTF_8)
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- elsif input.respond_to? :to_s
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- input.to_s
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- end
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- end
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- private_class_method :process_input
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-
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- class EvidenceIterable
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- include Enumerable
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-
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- def initialize(input, format)
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- @input = input
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- @format = format
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- end
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-
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- def each
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- if block_given?
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- @format.deserialize(@input).each do |evidence|
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- yield evidence
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- end
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- else
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- to_enum(:each)
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- end
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- end
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- end
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- end
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- end