bio-publisci 0.0.7 → 0.0.8

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Files changed (43) hide show
  1. data/Gemfile +1 -1
  2. data/Rakefile +1 -1
  3. data/features/orm_steps.rb +4 -4
  4. data/features/reader.feature +3 -3
  5. data/features/reader_steps.rb +1 -0
  6. data/features/writer.feature +7 -2
  7. data/features/writer_steps.rb +8 -1
  8. data/lib/bio-publisci.rb +3 -1
  9. data/lib/bio-publisci/datacube_model.rb +46 -20
  10. data/lib/bio-publisci/dataset/ORM/data_cube_orm.rb +196 -194
  11. data/lib/bio-publisci/dataset/ORM/observation.rb +15 -13
  12. data/lib/bio-publisci/dataset/data_cube.rb +3 -3
  13. data/lib/bio-publisci/dataset/dataset_for.rb +25 -4
  14. data/lib/bio-publisci/dsl/dataset_dsl.rb +4 -2
  15. data/lib/bio-publisci/dsl/dsl.rb +3 -0
  16. data/lib/bio-publisci/metadata/generator.rb +1 -1
  17. data/lib/bio-publisci/metadata/metadata_model.rb +27 -0
  18. data/lib/bio-publisci/metadata/prov/activity.rb +1 -0
  19. data/lib/bio-publisci/metadata/prov/model/prov_models.rb +33 -2
  20. data/lib/bio-publisci/query/query_helper.rb +5 -1
  21. data/lib/bio-publisci/readers/arff.rb +2 -40
  22. data/lib/bio-publisci/readers/dataframe.rb +1 -1
  23. data/lib/bio-publisci/writers/arff.rb +42 -16
  24. data/lib/bio-publisci/writers/base.rb +77 -0
  25. data/lib/bio-publisci/writers/csv.rb +31 -0
  26. data/lib/bio-publisci/writers/dataframe.rb +2 -2
  27. data/resources/queries/codes.rq +10 -5
  28. data/resources/queries/dimensions.rq +9 -4
  29. data/resources/queries/measures.rq +7 -2
  30. data/resources/queries/observations.rq +5 -4
  31. data/resources/weather.numeric.arff +26 -21
  32. data/spec/ORM/data_cube_orm_spec.rb +23 -3
  33. data/spec/ORM/prov_model_spec.rb +53 -0
  34. data/spec/dataset_for_spec.rb +21 -0
  35. data/spec/dsl_spec.rb +5 -2
  36. data/spec/metadata/metadata_dsl_spec.rb +1 -1
  37. data/spec/r_builder_spec.rb +2 -2
  38. data/spec/turtle/bacon +1 -1
  39. data/spec/turtle/reference +1 -1
  40. data/spec/turtle/weather +275 -0
  41. data/spec/writer_spec.rb +61 -0
  42. metadata +66 -28
  43. checksums.yaml +0 -7
data/spec/writer_spec.rb ADDED
@@ -0,0 +1,61 @@
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+ require_relative '../lib/bio-publisci.rb'
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+
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+ describe PubliSci::Writers do
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+ before(:each) do
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+
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+ end
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+
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+ it "should create reference CSV from turtle" do
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+ writer = PubliSci::Writers::CSV.new
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+ out = writer.from_turtle('spec/turtle/bacon')
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+
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+ out.should == IO.read('spec/csv/bacon.csv')
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+ end
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+
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+ it "can use store as an input" do
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+ writer = PubliSci::Writers::CSV.new
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+ repo = RDF::Repository.load('spec/turtle/bacon')
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+ out = writer.from_store(repo)
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+
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+ out.should == IO.read('spec/csv/bacon.csv')
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+ end
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+
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+ it "can output Wekka ARFF from turtle string" do
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+ writer = PubliSci::Writers::ARFF.new
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+ out = writer.from_turtle('spec/turtle/weather')
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+ out.should == IO.read('resources/weather.numeric.arff')
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+ end
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+
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+ it "can output Wekka ARFF from a store" do
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+ writer = PubliSci::Writers::ARFF.new
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+ repo = RDF::Repository.load('spec/turtle/weather')
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+ out = writer.from_store(repo)
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+
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+ # minor hack since metadata isn't the same
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+ out = out.gsub(/%.*\n/,'')
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+
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+ out.should == IO.read('resources/weather.numeric.arff').gsub(/%.*\n/,'')
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+ end
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+
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+ context "can restrict to a particular dataset" do
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+ it "for arff" do
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+ writer = PubliSci::Writers::ARFF.new
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+ repo = RDF::Repository.load('spec/turtle/weather')
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+ repo.load('spec/turtle/bacon')
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+ out = writer.from_store(repo, 'http://www.rqtl.org/ns/dataset/weather/dataset-weather','weather')
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+
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+ out = out.gsub(/%.*\n/,'')
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+
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+ out.should == IO.read('resources/weather.numeric.arff').gsub(/%.*\n/,'')
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+ end
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+
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+ it "for csv" do
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+ writer = PubliSci::Writers::CSV.new
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+ repo = RDF::Repository.load('spec/turtle/reference')
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+ repo.load('spec/turtle/bacon')
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+ out = writer.from_store(repo,'http://www.rqtl.org/ns/dataset/bacon/dataset-bacon')
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+
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+ out.should == IO.read('spec/csv/bacon.csv')
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+ end
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+ end
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+ end
metadata CHANGED
@@ -1,88 +1,100 @@
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1
  --- !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: 0.0.7
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+ version: 0.0.8
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+ prerelease:
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  platform: ruby
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  authors:
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  - Will Strinz
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2013-08-09 00:00:00.000000000 Z
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+ date: 2013-08-21 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rdf
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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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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  type: :runtime
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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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+ - - ! '>='
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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: rdf-4store
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  requirement: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
31
- - - '>='
35
+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  type: :runtime
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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:
38
- - - '>='
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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: rdf-turtle
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  requirement: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
45
- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  type: :runtime
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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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+ - - ! '>='
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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: rserve-client
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  requirement: !ruby/object:Gem::Requirement
65
+ none: false
58
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  requirements:
59
- - - '>='
67
+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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+ none: false
65
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  requirements:
66
- - - '>='
75
+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
69
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  - !ruby/object:Gem::Dependency
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  name: sparql
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  requirement: !ruby/object:Gem::Requirement
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+ none: false
72
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  requirements:
73
- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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+ none: false
79
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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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  - !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
@@ -90,6 +102,7 @@ dependencies:
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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
93
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
@@ -97,6 +110,7 @@ dependencies:
97
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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:
101
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  - - ~>
102
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  - !ruby/object:Gem::Version
@@ -104,6 +118,7 @@ dependencies:
104
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  type: :development
105
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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:
108
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  - - ~>
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  - !ruby/object:Gem::Version
@@ -111,20 +126,23 @@ dependencies:
111
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  - !ruby/object:Gem::Dependency
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  name: cucumber
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  requirement: !ruby/object:Gem::Requirement
129
+ none: false
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  requirements:
115
- - - '>='
131
+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
118
134
  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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- - - '>='
139
+ - - ! '>='
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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
145
+ none: false
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  requirements:
129
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  - - ~>
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  - !ruby/object:Gem::Version
@@ -132,6 +150,7 @@ dependencies:
132
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  type: :development
133
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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+ none: false
135
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
@@ -139,34 +158,39 @@ dependencies:
139
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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
142
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  requirements:
143
- - - '>='
163
+ - - ! '>='
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  - !ruby/object:Gem::Version
145
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  version: 1.0.21
146
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  type: :development
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  prerelease: false
148
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  version_requirements: !ruby/object:Gem::Requirement
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+ none: false
149
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  requirements:
150
- - - '>='
171
+ - - ! '>='
151
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  - !ruby/object:Gem::Version
152
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  version: 1.0.21
153
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  - !ruby/object:Gem::Dependency
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  name: bio
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  requirement: !ruby/object:Gem::Requirement
177
+ none: false
156
178
  requirements:
157
- - - '>='
179
+ - - ! '>='
158
180
  - !ruby/object:Gem::Version
159
181
  version: 1.4.2
160
182
  type: :development
161
183
  prerelease: false
162
184
  version_requirements: !ruby/object:Gem::Requirement
185
+ none: false
163
186
  requirements:
164
- - - '>='
187
+ - - ! '>='
165
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  - !ruby/object:Gem::Version
166
189
  version: 1.4.2
167
190
  - !ruby/object:Gem::Dependency
168
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  name: rdoc
169
192
  requirement: !ruby/object:Gem::Requirement
193
+ none: false
170
194
  requirements:
171
195
  - - ~>
172
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  - !ruby/object:Gem::Version
@@ -174,6 +198,7 @@ dependencies:
174
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  type: :development
175
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
201
+ none: false
177
202
  requirements:
178
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  - - ~>
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  - !ruby/object:Gem::Version
@@ -181,32 +206,36 @@ dependencies:
181
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  - !ruby/object:Gem::Dependency
182
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  name: spoon
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  requirement: !ruby/object:Gem::Requirement
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+ none: false
184
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  requirements:
185
- - - '>='
211
+ - - ! '>='
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212
  - !ruby/object:Gem::Version
187
213
  version: '0'
188
214
  type: :development
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215
  prerelease: false
190
216
  version_requirements: !ruby/object:Gem::Requirement
217
+ none: false
191
218
  requirements:
192
- - - '>='
219
+ - - ! '>='
193
220
  - !ruby/object:Gem::Version
194
221
  version: '0'
195
222
  - !ruby/object:Gem::Dependency
196
223
  name: spira
197
224
  requirement: !ruby/object:Gem::Requirement
225
+ none: false
198
226
  requirements:
199
- - - '>='
227
+ - - ! '>='
200
228
  - !ruby/object:Gem::Version
201
229
  version: '0'
202
230
  type: :development
203
231
  prerelease: false
204
232
  version_requirements: !ruby/object:Gem::Requirement
233
+ none: false
205
234
  requirements:
206
- - - '>='
235
+ - - ! '>='
207
236
  - !ruby/object:Gem::Version
208
237
  version: '0'
209
- description: 'A toolkit for publishing scientific results and datasets using RDF,
238
+ description: ! 'A toolkit for publishing scientific results and datasets using RDF,
210
239
  OWL, and related technologies '
211
240
  email: wstrinz@gmail.com
212
241
  executables:
@@ -271,6 +300,7 @@ files:
271
300
  - lib/bio-publisci/dsl/prov_dsl.rb
272
301
  - lib/bio-publisci/metadata/generator.rb
273
302
  - lib/bio-publisci/metadata/metadata.rb
303
+ - lib/bio-publisci/metadata/metadata_model.rb
274
304
  - lib/bio-publisci/metadata/prov/activity.rb
275
305
  - lib/bio-publisci/metadata/prov/agent.rb
276
306
  - lib/bio-publisci/metadata/prov/association.rb
@@ -299,6 +329,8 @@ files:
299
329
  - lib/bio-publisci/readers/r_matrix.rb
300
330
  - lib/bio-publisci/store.rb
301
331
  - lib/bio-publisci/writers/arff.rb
332
+ - lib/bio-publisci/writers/base.rb
333
+ - lib/bio-publisci/writers/csv.rb
302
334
  - lib/bio-publisci/writers/dataframe.rb
303
335
  - lib/r2rdf.rb
304
336
  - lib/template_bak.rb
@@ -373,28 +405,34 @@ files:
373
405
  - spec/spec_helper.rb
374
406
  - spec/turtle/bacon
375
407
  - spec/turtle/reference
408
+ - spec/turtle/weather
409
+ - spec/writer_spec.rb
376
410
  homepage: http://github.com/wstrinz/bioruby-publisci
377
411
  licenses:
378
412
  - MIT
379
- metadata: {}
380
413
  post_install_message:
381
414
  rdoc_options: []
382
415
  require_paths:
383
416
  - lib
384
417
  required_ruby_version: !ruby/object:Gem::Requirement
418
+ none: false
385
419
  requirements:
386
- - - '>='
420
+ - - ! '>='
387
421
  - !ruby/object:Gem::Version
388
422
  version: '0'
423
+ segments:
424
+ - 0
425
+ hash: -2716100516942950987
389
426
  required_rubygems_version: !ruby/object:Gem::Requirement
427
+ none: false
390
428
  requirements:
391
- - - '>='
429
+ - - ! '>='
392
430
  - !ruby/object:Gem::Version
393
431
  version: '0'
394
432
  requirements: []
395
433
  rubyforge_project:
396
- rubygems_version: 2.0.3
434
+ rubygems_version: 1.8.25
397
435
  signing_key:
398
- specification_version: 4
436
+ specification_version: 3
399
437
  summary: Publish scientific results to the semantic web
400
438
  test_files: []
checksums.yaml DELETED
@@ -1,7 +0,0 @@
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2
- SHA1:
3
- metadata.gz: 84c3e7a1f4ffe93284a75856a424d4f86624032f
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