bel 0.3.1-x86-mingw32 → 0.3.2-x86-mingw32

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 (22) hide show
  1. checksums.yaml +5 -13
  2. data/README.md +13 -1
  3. data/bel.gemspec +4 -1
  4. data/bin/bel +1 -0
  5. data/bin/bel2rdf.rb +2 -2
  6. data/bin/bel_compare.rb +2 -2
  7. data/bin/bel_parse.rb +1 -1
  8. data/bin/bel_summarize.rb +1 -1
  9. data/bin/bel_upgrade.rb +2 -2
  10. data/lib/bel/2.0/libbel.so +0 -0
  11. data/lib/bel/2.1/libbel.so +0 -0
  12. data/lib/bel/2.2/libbel.so +0 -0
  13. data/lib/bel/evidence_model/bel_parameter.rb +1 -1
  14. data/lib/bel/evidence_model/bel_term.rb +48 -1
  15. data/lib/bel/extensions/jgf.rb +5 -3
  16. data/lib/bel/extensions/rdf/bel_rdf.rb +93 -77
  17. data/lib/bel/extensions/rdf/rdf.rb +247 -11
  18. data/lib/bel/namespace.rb +16 -4
  19. data/lib/bel/nonblocking_io_wrapper.rb +52 -0
  20. data/lib/bel/script.rb +138159 -138382
  21. data/lib/bel/version.rb +1 -1
  22. metadata +112 -69
data/lib/bel/version.rb CHANGED
@@ -1,3 +1,3 @@
1
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  module BEL
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- VERSION = '0.3.1'
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+ VERSION = '0.3.2'
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  end
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: bel
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  version: !ruby/object:Gem::Version
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- version: 0.3.1
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+ version: 0.3.2
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  platform: x86-mingw32
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  authors:
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  - Anthony Bargnesi
@@ -11,7 +11,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2015-06-19 00:00:00.000000000 Z
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+ date: 2015-07-31 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: ffi
@@ -28,7 +28,7 @@ dependencies:
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  - !ruby/object:Gem::Version
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  version: 1.9.8
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  - !ruby/object:Gem::Dependency
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- name: uuid
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+ name: addressable
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - ~>
@@ -42,21 +42,21 @@ dependencies:
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  - !ruby/object:Gem::Version
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  version: '2.3'
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  - !ruby/object:Gem::Dependency
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- name: addressable
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+ name: rdf
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: '2.3'
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+ version: '1.1'
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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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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: '2.3'
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+ version: '1.1'
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  - !ruby/object:Gem::Dependency
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- name: rdf
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+ name: rdf-turtle
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - ~>
@@ -70,19 +70,61 @@ dependencies:
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  - !ruby/object:Gem::Version
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  version: '1.1'
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  - !ruby/object:Gem::Dependency
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- name: rdf-turtle
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+ name: uuid
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: '1.1'
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+ version: '2.3'
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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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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: '1.1'
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+ version: '2.3'
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+ - !ruby/object:Gem::Dependency
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+ name: byebug
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '5.0'
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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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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '5.0'
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+ - !ruby/object:Gem::Dependency
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+ name: minitest
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '5.7'
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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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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '5.7'
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+ - !ruby/object:Gem::Dependency
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+ name: pry-byebug
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '3.2'
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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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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '3.2'
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  - !ruby/object:Gem::Dependency
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  name: rake
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  requirement: !ruby/object:Gem::Requirement
@@ -153,7 +195,7 @@ dependencies:
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  - - ~>
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  - !ruby/object:Gem::Version
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  version: '0.8'
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- description: ! ' The BEL gem allows the reading, writing, and processing of BEL (Biological
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+ description: ' The BEL gem allows the reading, writing, and processing of BEL (Biological
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  Expression Language) with a natural DSL. '
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  email:
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  - abargnesi@selventa.com
@@ -171,77 +213,78 @@ executables:
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  extensions: []
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  extra_rdoc_files: []
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  files:
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- - INSTALL.md
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- - INSTALL_RUBY.md
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- - LICENSE
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- - README.md
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- - bel.gemspec
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- - bin/bel
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- - bin/bel2rdf.rb
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- - bin/bel_compare.rb
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- - bin/bel_parse.rb
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- - bin/bel_rdfschema.rb
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- - bin/bel_summarize.rb
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- - bin/bel_upgrade.rb
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- - ext/mri/bel-ast.c
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- - ext/mri/bel-ast.h
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- - ext/mri/bel-node-stack.c
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- - ext/mri/bel-node-stack.h
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- - ext/mri/bel-parse-statement.c
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- - ext/mri/bel-parse-term.c
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- - ext/mri/bel-parser.c
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- - ext/mri/bel-parser.h
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- - ext/mri/bel-token.c
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- - ext/mri/bel-token.h
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- - ext/mri/bel-tokenize-term.c
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- - ext/mri/extconf.rb
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- - ext/mri/libbel.c
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- - ext/mri/libbel.def
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216
  - lib/bel.rb
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- - lib/bel/2.0/libbel.so
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- - lib/bel/2.1/libbel.so
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- - lib/bel/2.2/libbel.so
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- - lib/bel/completion.rb
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- - lib/bel/completion_rule.rb
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- - lib/bel/evidence_model.rb
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- - lib/bel/evidence_model/bel_parameter.rb
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+ - lib/bel/util.rb
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  - lib/bel/evidence_model/bel_statement.rb
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- - lib/bel/evidence_model/bel_term.rb
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  - lib/bel/evidence_model/citation.rb
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- - lib/bel/evidence_model/evidence.rb
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- - lib/bel/evidence_model/experiment_context.rb
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+ - lib/bel/evidence_model/bel_parameter.rb
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  - lib/bel/evidence_model/metadata.rb
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- - lib/bel/evidence_model/references.rb
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+ - lib/bel/evidence_model/bel_term.rb
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  - lib/bel/evidence_model/summary_text.rb
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- - lib/bel/extension.rb
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+ - lib/bel/evidence_model/evidence.rb
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+ - lib/bel/evidence_model/references.rb
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+ - lib/bel/evidence_model/experiment_context.rb
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+ - lib/bel/evidence_model.rb
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+ - lib/bel/nonblocking_io_wrapper.rb
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  - lib/bel/extension_format.rb
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+ - lib/bel/script.rb
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+ - lib/bel/extensions/rdf/bel_rdf.rb
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+ - lib/bel/extensions/rdf/rdf.rb
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  - lib/bel/extensions/bel.rb
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  - lib/bel/extensions/jgf.rb
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- - lib/bel/extensions/json/jrjackson.rb
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  - lib/bel/extensions/json/json.rb
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  - lib/bel/extensions/json/multi_json.rb
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- - lib/bel/extensions/json/oj.rb
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  - lib/bel/extensions/json/ruby_json.rb
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- - lib/bel/extensions/rdf/bel_rdf.rb
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- - lib/bel/extensions/rdf/rdf.rb
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+ - lib/bel/extensions/json/jrjackson.rb
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+ - lib/bel/extensions/json/oj.rb
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  - lib/bel/extensions/xbel.rb
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- - lib/bel/format.rb
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- - lib/bel/language.rb
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- - lib/bel/libbel.rb
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- - lib/bel/libbel/bel_ast_structs.rb
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- - lib/bel/libbel/bel_token.rb
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- - lib/bel/libbel/bel_token_iterator.rb
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+ - lib/bel/extension.rb
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+ - lib/bel/libbel/node_traversal.rb
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+ - lib/bel/libbel/node_transformation.rb
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  - lib/bel/libbel/bel_token_list.rb
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+ - lib/bel/libbel/bel_token.rb
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  - lib/bel/libbel/node_test.rb
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- - lib/bel/libbel/node_transformation.rb
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- - lib/bel/libbel/node_traversal.rb
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- - lib/bel/namespace.rb
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+ - lib/bel/libbel/bel_ast_structs.rb
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+ - lib/bel/libbel/bel_token_iterator.rb
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+ - lib/bel/completion_rule.rb
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  - lib/bel/parser.rb
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- - lib/bel/quoting.rb
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- - lib/bel/script.rb
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- - lib/bel/util.rb
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- - lib/bel/vendor/trollop.rb
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  - lib/bel/version.rb
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+ - lib/bel/format.rb
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+ - lib/bel/namespace.rb
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+ - lib/bel/vendor/trollop.rb
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+ - lib/bel/libbel.rb
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+ - lib/bel/language.rb
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+ - lib/bel/quoting.rb
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+ - lib/bel/completion.rb
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+ - ext/mri/bel-token.c
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+ - ext/mri/libbel.c
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+ - ext/mri/bel-parse-term.c
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+ - ext/mri/bel-node-stack.c
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+ - ext/mri/bel-parser.c
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+ - ext/mri/bel-parse-statement.c
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+ - ext/mri/bel-tokenize-term.c
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+ - ext/mri/bel-ast.c
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+ - ext/mri/bel-parser.h
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+ - ext/mri/bel-node-stack.h
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+ - ext/mri/bel-token.h
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+ - ext/mri/bel-ast.h
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+ - ext/mri/libbel.def
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+ - bel.gemspec
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+ - LICENSE
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+ - INSTALL.md
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+ - INSTALL_RUBY.md
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+ - README.md
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+ - bin/bel_summarize.rb
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+ - bin/bel_upgrade.rb
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+ - bin/bel_parse.rb
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+ - bin/bel
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+ - bin/bel2rdf.rb
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+ - bin/bel_compare.rb
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+ - bin/bel_rdfschema.rb
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+ - ext/mri/extconf.rb
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+ - lib/bel/2.0/libbel.so
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+ - lib/bel/2.1/libbel.so
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+ - lib/bel/2.2/libbel.so
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  homepage: https://github.com/OpenBEL/bel.rb
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  licenses:
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  - Apache-2.0
@@ -271,17 +314,17 @@ require_paths:
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  - lib
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  required_ruby_version: !ruby/object:Gem::Requirement
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  requirements:
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- - - ! '>='
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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: 2.0.0
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  requirements:
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- - - ! '>='
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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:
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- rubygems_version: 2.4.3
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+ rubygems_version: 2.0.14
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  signing_key:
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  specification_version: 4
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  summary: Process BEL with ruby.