bio-publisci 0.0.7 → 0.0.8
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.
- data/Gemfile +1 -1
- data/Rakefile +1 -1
- data/features/orm_steps.rb +4 -4
- data/features/reader.feature +3 -3
- data/features/reader_steps.rb +1 -0
- data/features/writer.feature +7 -2
- data/features/writer_steps.rb +8 -1
- data/lib/bio-publisci.rb +3 -1
- data/lib/bio-publisci/datacube_model.rb +46 -20
- data/lib/bio-publisci/dataset/ORM/data_cube_orm.rb +196 -194
- data/lib/bio-publisci/dataset/ORM/observation.rb +15 -13
- data/lib/bio-publisci/dataset/data_cube.rb +3 -3
- data/lib/bio-publisci/dataset/dataset_for.rb +25 -4
- data/lib/bio-publisci/dsl/dataset_dsl.rb +4 -2
- data/lib/bio-publisci/dsl/dsl.rb +3 -0
- data/lib/bio-publisci/metadata/generator.rb +1 -1
- data/lib/bio-publisci/metadata/metadata_model.rb +27 -0
- data/lib/bio-publisci/metadata/prov/activity.rb +1 -0
- data/lib/bio-publisci/metadata/prov/model/prov_models.rb +33 -2
- data/lib/bio-publisci/query/query_helper.rb +5 -1
- data/lib/bio-publisci/readers/arff.rb +2 -40
- data/lib/bio-publisci/readers/dataframe.rb +1 -1
- data/lib/bio-publisci/writers/arff.rb +42 -16
- data/lib/bio-publisci/writers/base.rb +77 -0
- data/lib/bio-publisci/writers/csv.rb +31 -0
- data/lib/bio-publisci/writers/dataframe.rb +2 -2
- data/resources/queries/codes.rq +10 -5
- data/resources/queries/dimensions.rq +9 -4
- data/resources/queries/measures.rq +7 -2
- data/resources/queries/observations.rq +5 -4
- data/resources/weather.numeric.arff +26 -21
- data/spec/ORM/data_cube_orm_spec.rb +23 -3
- data/spec/ORM/prov_model_spec.rb +53 -0
- data/spec/dataset_for_spec.rb +21 -0
- data/spec/dsl_spec.rb +5 -2
- data/spec/metadata/metadata_dsl_spec.rb +1 -1
- data/spec/r_builder_spec.rb +2 -2
- data/spec/turtle/bacon +1 -1
- data/spec/turtle/reference +1 -1
- data/spec/turtle/weather +275 -0
- data/spec/writer_spec.rb +61 -0
- metadata +66 -28
- 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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end
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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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out.should == IO.read('spec/csv/bacon.csv')
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end
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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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out.should == IO.read('spec/csv/bacon.csv')
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end
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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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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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# minor hack since metadata isn't the same
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out = out.gsub(/%.*\n/,'')
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out.should == IO.read('resources/weather.numeric.arff').gsub(/%.*\n/,'')
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end
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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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out = out.gsub(/%.*\n/,'')
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out.should == IO.read('resources/weather.numeric.arff').gsub(/%.*\n/,'')
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end
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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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out.should == IO.read('spec/csv/bacon.csv')
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end
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end
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end
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metadata
CHANGED
@@ -1,88 +1,100 @@
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--- !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.
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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-
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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:
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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-turtle
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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: rserve-client
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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: sparql
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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: 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
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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
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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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:
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- - ~>
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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
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requirements:
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- - ~>
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- !ruby/object:Gem::Dependency
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name: cucumber
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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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version: '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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none: false
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requirements:
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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: jeweler
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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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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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- - ~>
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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
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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: 1.0.21
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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
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requirements:
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- - '>='
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- - ! '>='
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version: 1.0.21
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- !ruby/object:Gem::Dependency
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name: bio
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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: 1.4.2
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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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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: 1.4.2
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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:
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- - ~>
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@@ -174,6 +198,7 @@ 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
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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@@ -181,32 +206,36 @@ dependencies:
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- !ruby/object:Gem::Dependency
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name: spoon
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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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version: '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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none: false
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requirements:
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- - '>='
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- - ! '>='
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version: '0'
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- !ruby/object:Gem::Dependency
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name: spira
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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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version: '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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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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-
description: 'A toolkit for publishing scientific results and datasets using RDF,
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description: ! 'A toolkit for publishing scientific results and datasets using RDF,
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OWL, and related technologies '
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email: wstrinz@gmail.com
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executables:
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@@ -271,6 +300,7 @@ files:
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- lib/bio-publisci/dsl/prov_dsl.rb
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- lib/bio-publisci/metadata/generator.rb
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- lib/bio-publisci/metadata/metadata.rb
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+
- lib/bio-publisci/metadata/metadata_model.rb
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- lib/bio-publisci/metadata/prov/activity.rb
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- lib/bio-publisci/metadata/prov/agent.rb
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- lib/bio-publisci/metadata/prov/association.rb
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@@ -299,6 +329,8 @@ files:
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- lib/bio-publisci/readers/r_matrix.rb
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- lib/bio-publisci/store.rb
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- lib/bio-publisci/writers/arff.rb
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- lib/bio-publisci/writers/base.rb
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- lib/bio-publisci/writers/csv.rb
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- lib/bio-publisci/writers/dataframe.rb
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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:
|
434
|
+
rubygems_version: 1.8.25
|
397
435
|
signing_key:
|
398
|
-
specification_version:
|
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 @@
|
|
1
|
-
---
|
2
|
-
SHA1:
|
3
|
-
metadata.gz: 84c3e7a1f4ffe93284a75856a424d4f86624032f
|
4
|
-
data.tar.gz: 834eb95f1ef0e2353d3aab93bcf4d9c35f34a1d4
|
5
|
-
SHA512:
|
6
|
-
metadata.gz: b1c7a7e6f43f26f089a871fffafc10b0f6eb35b6367dde310e1e2df09c9ab40d725048d6291c5e67c12d32454d36a5539342f71130a90121bd4dd19946050f2b
|
7
|
-
data.tar.gz: 91a1bf68f52d3477d5fa5a89762619cdf7b038d3af49042cf34ce1b6f90e833324cea537bc60e9c6afc23c86163f44855f739e1838266cf0b905f5c20b2a9679
|