bio-publisci 0.0.6 → 0.0.7
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.
- checksums.yaml +4 -4
- data/Gemfile +1 -0
- data/Rakefile +1 -1
- data/examples/prov_dsl.prov +2 -1
- data/examples/safe_gen.rb +7 -0
- data/examples/visualization/primer.prov +66 -0
- data/examples/visualization/prov_viz.rb +140 -0
- data/examples/visualization/viz.rb +35 -0
- data/features/metadata_steps.rb +2 -4
- data/features/orm_steps.rb +4 -4
- data/features/reader_steps.rb +1 -1
- data/features/store_steps.rb +1 -1
- data/features/writer.feature +1 -1
- data/features/writer_steps.rb +1 -1
- data/lib/bio-publisci.rb +10 -2
- data/lib/bio-publisci/analyzer.rb +4 -4
- data/lib/bio-publisci/{spira.rb → datacube_model.rb} +4 -5
- data/lib/bio-publisci/dataset/ORM/data_cube_orm.rb +12 -12
- data/lib/bio-publisci/dataset/ORM/observation.rb +1 -1
- data/lib/bio-publisci/dataset/configuration.rb +31 -0
- data/lib/bio-publisci/dataset/data_cube.rb +28 -17
- data/lib/bio-publisci/dataset/dataset.rb +11 -0
- data/lib/bio-publisci/dataset/dataset_for.rb +19 -9
- data/lib/bio-publisci/dataset/interactive.rb +1 -1
- data/lib/bio-publisci/dsl/config.rb +34 -0
- data/lib/bio-publisci/dsl/dataset_dsl.rb +91 -0
- data/lib/bio-publisci/dsl/dsl.rb +69 -0
- data/lib/bio-publisci/dsl/metadata_dsl.rb +85 -0
- data/lib/bio-publisci/{metadata/prov/dsl.rb → dsl/prov_dsl.rb} +30 -6
- data/lib/bio-publisci/metadata/generator.rb +323 -0
- data/lib/bio-publisci/metadata/metadata.rb +3 -314
- data/lib/bio-publisci/metadata/prov/activity.rb +3 -1
- data/lib/bio-publisci/metadata/prov/agent.rb +1 -1
- data/lib/bio-publisci/metadata/prov/association.rb +2 -2
- data/lib/bio-publisci/metadata/prov/config.rb +34 -0
- data/lib/bio-publisci/metadata/prov/derivation.rb +7 -2
- data/lib/bio-publisci/metadata/prov/element.rb +2 -2
- data/lib/bio-publisci/metadata/prov/entity.rb +1 -22
- data/lib/bio-publisci/metadata/prov/model/prov_models.rb +8 -9
- data/lib/bio-publisci/metadata/prov/plan.rb +1 -1
- data/lib/bio-publisci/metadata/prov/prov.rb +23 -21
- data/lib/bio-publisci/metadata/prov/role.rb +1 -1
- data/lib/bio-publisci/metadata/prov/usage.rb +1 -1
- data/lib/bio-publisci/metadata/publisher.rb +25 -0
- data/lib/bio-publisci/mixins/dereferencable.rb +1 -1
- data/lib/bio-publisci/mixins/registry.rb +27 -0
- data/lib/bio-publisci/output.rb +1 -1
- data/lib/bio-publisci/parser.rb +1 -1
- data/lib/bio-publisci/query/query_helper.rb +14 -14
- data/lib/bio-publisci/r_client.rb +5 -5
- data/lib/bio-publisci/readers/arff.rb +5 -5
- data/lib/bio-publisci/readers/csv.rb +3 -3
- data/lib/bio-publisci/readers/dataframe.rb +3 -3
- data/lib/bio-publisci/readers/r_cross.rb +4 -4
- data/lib/bio-publisci/readers/r_matrix.rb +3 -3
- data/lib/bio-publisci/store.rb +3 -3
- data/lib/bio-publisci/writers/arff.rb +6 -6
- data/lib/bio-publisci/writers/dataframe.rb +5 -5
- data/scripts/islet_mlratio.rb +1 -1
- data/scripts/scan_islet.rb +1 -1
- data/scripts/update_reference.rb +2 -2
- data/spec/ORM/data_cube_orm_spec.rb +2 -2
- data/spec/ORM/prov_model_spec.rb +19 -0
- data/spec/analyzer_spec.rb +7 -7
- data/spec/data_cube_spec.rb +13 -13
- data/spec/dataset_for_spec.rb +11 -4
- data/spec/dsl_spec.rb +90 -0
- data/spec/generators/csv_spec.rb +4 -4
- data/spec/generators/dataframe_spec.rb +6 -6
- data/spec/generators/r_cross_spec.rb +2 -2
- data/spec/generators/r_matrix_spec.rb +2 -2
- data/spec/metadata/metadata_dsl_spec.rb +68 -0
- data/spec/prov/activity_spec.rb +4 -4
- data/spec/prov/agent_spec.rb +3 -4
- data/spec/prov/association_spec.rb +1 -2
- data/spec/prov/config_spec.rb +28 -0
- data/spec/prov/derivation_spec.rb +30 -0
- data/spec/prov/entity_spec.rb +3 -4
- data/spec/prov/role_spec.rb +1 -2
- data/spec/prov/usage_spec.rb +1 -2
- data/spec/r_builder_spec.rb +3 -3
- data/spec/turtle/bacon +20 -4
- data/spec/turtle/reference +20 -4
- metadata +37 -4
@@ -0,0 +1,68 @@
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require_relative '../../lib/bio-publisci.rb'
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describe PubliSci::Metadata::DSL do
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include PubliSci::Metadata::DSL
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before(:each) do
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PubliSci::Prov.registry.clear
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end
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it "can generate basic metadata as n3" do
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dataset 'bacon'
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title 'Bacon Data'
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description 'a dataset about bacon'
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creator 'Will'
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topic 'Delicious Bacon'
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str = generate_n3
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str[/rdfs:label "(.+)";/,1].should == "Bacon Data"
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str[/dct:creator "(.+)";/,1].should == "Will"
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str[/dct:subject "(.+)";/,1].should == "Delicious Bacon"
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str[/dct:description "(.+)";/,1].should == "a dataset about bacon"
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str[/dct:issued "(.+)"\^\^xsd:date;/,1].should == Time.now.strftime("%Y-%m-%d")
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end
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it "can add additional information about publisher" do
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dataset 'bacon'
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p = publisher do
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label "pub"
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uri "http://some-organization.com"
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end
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p.label.should == "pub"
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generate_n3[%r{dct:publisher <(.+)> .},1].should == "http://some-organization.com"
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end
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# it "can be created with a block" do
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# a = agent :ag do
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# subject "http://things.com/stuff"
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# name "Mr Person"
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# end
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# a.is_a?(Agent).should be true
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# a.subject.should == "http://things.com/stuff"
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# a.name.should == "Mr Person"
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# end
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# it "can be given a type corresponding to a subclass of prov:Agent" do
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# a = agent :name, type: "software"
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# a.type.should == :software
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# a.to_n3["prov:SoftwareAgent"].should_not be nil
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# end
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# it "can be created using the organization helper" do
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# a = organization :group
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# a.type.should == :organization
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# end
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# it "raises an exception when on_behalf_of does not refer to an agent" do
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# a = agent :name, on_behalf_of: :other
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# expect {a.on_behalf_of[0]}.to raise_error
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# end
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# it "lazy loads other objects, so declaration order doesn't usually matter" do
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# a = agent :name, on_behalf_of: :other
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# b = agent :other
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# a.on_behalf_of.should == b
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# end
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end
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data/spec/prov/activity_spec.rb
CHANGED
@@ -1,16 +1,16 @@
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require_relative '../../lib/bio-publisci.rb'
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include PubliSci::Prov::DSL
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include PubliSci
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# include PubliSci
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describe PubliSci::Prov::Activity do
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before(:each) do
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@evaluator = PubliSci::Prov::DSL::
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@evaluator = PubliSci::Prov::DSL::Instance.new
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end
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it "can generate activity fields from symbol" do
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a = activity :name
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a.is_a?(Activity).should be true
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a.is_a?(Prov::Activity).should be true
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a.subject.should == "http://rqtl.org/ns/activity/name"
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end
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@@ -25,7 +25,7 @@ describe PubliSci::Prov::Activity do
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subject "http://things.com/stuff"
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generated :data
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end
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a.is_a?(Activity).should be true
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a.is_a?(Prov::Activity).should be true
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a.subject.should == "http://things.com/stuff"
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end
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data/spec/prov/agent_spec.rb
CHANGED
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require_relative '../../lib/bio-publisci.rb'
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include PubliSci::Prov::DSL
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include PubliSci::Prov
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describe PubliSci::Prov::Agent do
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before(:each) do
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@evaluator = PubliSci::Prov::DSL::
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@evaluator = PubliSci::Prov::DSL::Instance.new
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end
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it "can generate agent fields from symbol" do
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a = agent :name
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a.is_a?(Agent).should be true
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a.is_a?(Prov::Agent).should be true
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a.subject.should == "http://rqtl.org/ns/agent/name"
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end
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subject "http://things.com/stuff"
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name "Mr Person"
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end
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a.is_a?(Agent).should be true
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a.is_a?(Prov::Agent).should be true
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a.subject.should == "http://things.com/stuff"
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a.name.should == "Mr Person"
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end
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require_relative '../../lib/bio-publisci.rb'
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include PubliSci::Prov
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include PubliSci::Prov::DSL
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describe PubliSci::Prov::Association do
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before(:each) do
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@ev = PubliSci::Prov::DSL::
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@ev = PubliSci::Prov::DSL::Instance.new
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end
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it "can create simple associations" do
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require_relative '../../lib/bio-publisci.rb'
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include PubliSci::Prov::DSL
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include PubliSci
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describe PubliSci::Prov::Configuration do
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before(:each) do
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@evaluator = PubliSci::Prov::DSL::Instance.new
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end
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it "can set basic config methods" do
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configure do |cfg|
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cfg.output :to_repository
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end
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settings.output.should == :to_repository
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end
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it "can configure different repository types", no_travis: true do
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configure do |cfg|
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cfg.repository :fourstore
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end
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a = activity :name
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a.is_a?(Prov::Activity).should be true
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r=to_repository
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a.subject.should == "http://rqtl.org/ns/activity/name"
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r.is_a?(RDF::FourStore::Repository).should be true
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end
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end
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require_relative '../../lib/bio-publisci.rb'
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include PubliSci::Prov::DSL
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describe PubliSci::Prov::Derivation do
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before(:each) do
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@ev = PubliSci::Prov::DSL::Instance.new
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end
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it "can create simple derivations" do
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e = @ev.entity :name
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f = @ev.entity :other, derived_from: :name
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# g = @ev.activity :do_things, generated: :name, associated_with: :other
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f.derived_from[0].should == e
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@ev.generate_n3
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@ev.generate_n3["prov:wasDerivedFrom"].size.should > 0
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end
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it "creates qualified derivations when a block is passed" do
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e = @ev.entity :name
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f = @ev.entity :other do
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derived_from :name do
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had_activity :do_things
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end
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end
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g = @ev.activity :do_things do
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generated :other
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end
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f.derived_from.first.had_activity.should == g
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end
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end
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data/spec/prov/entity_spec.rb
CHANGED
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require_relative '../../lib/bio-publisci.rb'
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include PubliSci::Prov::DSL
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include PubliSci::Prov
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describe PubliSci::Prov::Entity do
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before(:each) do
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@evaluator = PubliSci::Prov::DSL::
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@evaluator = PubliSci::Prov::DSL::Instance.new
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end
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it "can generate entity fields from symbol" do
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e = entity :name
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e.is_a?(Entity).should be true
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e.is_a?(Prov::Entity).should be true
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e.subject.should == "http://rqtl.org/ns/entity/name"
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end
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subject "http://things.com/stuff"
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source "/somefile.txt"
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end
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e.is_a?(Entity).should be true
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e.is_a?(Prov::Entity).should be true
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e.subject.should == "http://things.com/stuff"
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e.source[0].should == "/somefile.txt"
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end
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data/spec/prov/role_spec.rb
CHANGED
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require_relative '../../lib/bio-publisci.rb'
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include PubliSci::Prov::DSL
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include PubliSci::Prov
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describe PubliSci::Prov::Role do
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before(:each) do
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@evaluator = PubliSci::Prov::DSL::
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@evaluator = PubliSci::Prov::DSL::Instance.new
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end
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it "creates a role in a used block" do
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data/spec/prov/usage_spec.rb
CHANGED
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require_relative '../../lib/bio-publisci.rb'
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include PubliSci::Prov::DSL
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include PubliSci::Prov
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describe PubliSci::Prov::Usage do
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before(:each) do
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@evaluator = PubliSci::Prov::DSL::
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@evaluator = PubliSci::Prov::DSL::Instance.new
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end
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it "can create simple associations" do
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data/spec/r_builder_spec.rb
CHANGED
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require_relative '../lib/bio-publisci.rb'
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describe
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describe PubliSci::Writer::Dataframe do
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context "when using r/qtl dataframe", no_travis: true do
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before(:all) do
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before(:all) do
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@r = Rserve::Connection.new
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@r.eval <<-EOF
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library(qtl)
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data(listeria)
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mr = scanone(listeria,method="mr")
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EOF
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@builder =
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@builder = PubliSci::Writer::Builder.new
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end
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it "produces equivalent dataframe from rdf" #do
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data/spec/turtle/bacon
CHANGED
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@prefix prov: <http://www.w3.org/ns/prov#> .
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ns:dsd-bacon a qb:DataStructureDefinition;
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qb:component
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qb:component
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qb:component
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qb:component
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qb:component cs:producer ;
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qb:component cs:pricerange ;
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qb:component cs:chunkiness ;
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qb:component cs:deliciousness .
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ns:dataset-bacon a qb:DataSet ;
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rdfs:label "bacon"@en ;
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qb:structure ns:dsd-bacon .
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cs:producer a qb:ComponentSpecification ;
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rdfs:label "producer Component" ;
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|
+
qb:dimension prop:producer .
|
30
|
+
|
31
|
+
cs:pricerange a qb:ComponentSpecification ;
|
32
|
+
rdfs:label "pricerange Component" ;
|
33
|
+
qb:dimension prop:pricerange .
|
34
|
+
|
35
|
+
cs:chunkiness a qb:ComponentSpecification ;
|
36
|
+
rdfs:label "chunkiness Component" ;
|
37
|
+
qb:measure prop:chunkiness .
|
38
|
+
|
39
|
+
cs:deliciousness a qb:ComponentSpecification ;
|
40
|
+
rdfs:label "deliciousness Component" ;
|
41
|
+
qb:measure prop:deliciousness .
|
42
|
+
|
27
43
|
prop:producer a rdf:Property, qb:DimensionProperty ;
|
28
44
|
rdfs:label "producer"@en ;
|
29
45
|
qb:codeList code:producer ;
|
data/spec/turtle/reference
CHANGED
@@ -15,15 +15,31 @@
|
|
15
15
|
@prefix prov: <http://www.w3.org/ns/prov#> .
|
16
16
|
|
17
17
|
ns:dsd-mr a qb:DataStructureDefinition;
|
18
|
-
qb:component
|
19
|
-
qb:component
|
20
|
-
qb:component
|
21
|
-
qb:component
|
18
|
+
qb:component cs:refRow ;
|
19
|
+
qb:component cs:chr ;
|
20
|
+
qb:component cs:pos ;
|
21
|
+
qb:component cs:lod .
|
22
22
|
|
23
23
|
ns:dataset-mr a qb:DataSet ;
|
24
24
|
rdfs:label "mr"@en ;
|
25
25
|
qb:structure ns:dsd-mr .
|
26
26
|
|
27
|
+
cs:refRow a qb:ComponentSpecification ;
|
28
|
+
rdfs:label "refRow Component" ;
|
29
|
+
qb:dimension prop:refRow .
|
30
|
+
|
31
|
+
cs:chr a qb:ComponentSpecification ;
|
32
|
+
rdfs:label "chr Component" ;
|
33
|
+
qb:measure prop:chr .
|
34
|
+
|
35
|
+
cs:pos a qb:ComponentSpecification ;
|
36
|
+
rdfs:label "pos Component" ;
|
37
|
+
qb:measure prop:pos .
|
38
|
+
|
39
|
+
cs:lod a qb:ComponentSpecification ;
|
40
|
+
rdfs:label "lod Component" ;
|
41
|
+
qb:measure prop:lod .
|
42
|
+
|
27
43
|
prop:refRow a rdf:Property, qb:DimensionProperty ;
|
28
44
|
rdfs:label "refRow"@en ;
|
29
45
|
qb:codeList code:refrow ;
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: bio-publisci
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
4
|
+
version: 0.0.7
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Will Strinz
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2013-08-
|
11
|
+
date: 2013-08-09 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rdf
|
@@ -192,6 +192,20 @@ dependencies:
|
|
192
192
|
- - '>='
|
193
193
|
- !ruby/object:Gem::Version
|
194
194
|
version: '0'
|
195
|
+
- !ruby/object:Gem::Dependency
|
196
|
+
name: spira
|
197
|
+
requirement: !ruby/object:Gem::Requirement
|
198
|
+
requirements:
|
199
|
+
- - '>='
|
200
|
+
- !ruby/object:Gem::Version
|
201
|
+
version: '0'
|
202
|
+
type: :development
|
203
|
+
prerelease: false
|
204
|
+
version_requirements: !ruby/object:Gem::Requirement
|
205
|
+
requirements:
|
206
|
+
- - '>='
|
207
|
+
- !ruby/object:Gem::Version
|
208
|
+
version: '0'
|
195
209
|
description: 'A toolkit for publishing scientific results and datasets using RDF,
|
196
210
|
OWL, and related technologies '
|
197
211
|
email: wstrinz@gmail.com
|
@@ -219,6 +233,10 @@ files:
|
|
219
233
|
- examples/primer-full.prov
|
220
234
|
- examples/primer.prov
|
221
235
|
- examples/prov_dsl.prov
|
236
|
+
- examples/safe_gen.rb
|
237
|
+
- examples/visualization/primer.prov
|
238
|
+
- examples/visualization/prov_viz.rb
|
239
|
+
- examples/visualization/viz.rb
|
222
240
|
- features/create_generator.feature
|
223
241
|
- features/integration.feature
|
224
242
|
- features/integration_steps.rb
|
@@ -238,17 +256,26 @@ files:
|
|
238
256
|
- features/writer_steps.rb
|
239
257
|
- lib/bio-publisci.rb
|
240
258
|
- lib/bio-publisci/analyzer.rb
|
259
|
+
- lib/bio-publisci/datacube_model.rb
|
241
260
|
- lib/bio-publisci/dataset/ORM/data_cube_orm.rb
|
242
261
|
- lib/bio-publisci/dataset/ORM/observation.rb
|
262
|
+
- lib/bio-publisci/dataset/configuration.rb
|
243
263
|
- lib/bio-publisci/dataset/data_cube.rb
|
264
|
+
- lib/bio-publisci/dataset/dataset.rb
|
244
265
|
- lib/bio-publisci/dataset/dataset_for.rb
|
245
266
|
- lib/bio-publisci/dataset/interactive.rb
|
267
|
+
- lib/bio-publisci/dsl/config.rb
|
268
|
+
- lib/bio-publisci/dsl/dataset_dsl.rb
|
269
|
+
- lib/bio-publisci/dsl/dsl.rb
|
270
|
+
- lib/bio-publisci/dsl/metadata_dsl.rb
|
271
|
+
- lib/bio-publisci/dsl/prov_dsl.rb
|
272
|
+
- lib/bio-publisci/metadata/generator.rb
|
246
273
|
- lib/bio-publisci/metadata/metadata.rb
|
247
274
|
- lib/bio-publisci/metadata/prov/activity.rb
|
248
275
|
- lib/bio-publisci/metadata/prov/agent.rb
|
249
276
|
- lib/bio-publisci/metadata/prov/association.rb
|
277
|
+
- lib/bio-publisci/metadata/prov/config.rb
|
250
278
|
- lib/bio-publisci/metadata/prov/derivation.rb
|
251
|
-
- lib/bio-publisci/metadata/prov/dsl.rb
|
252
279
|
- lib/bio-publisci/metadata/prov/element.rb
|
253
280
|
- lib/bio-publisci/metadata/prov/entity.rb
|
254
281
|
- lib/bio-publisci/metadata/prov/model/prov_models.rb
|
@@ -256,8 +283,10 @@ files:
|
|
256
283
|
- lib/bio-publisci/metadata/prov/prov.rb
|
257
284
|
- lib/bio-publisci/metadata/prov/role.rb
|
258
285
|
- lib/bio-publisci/metadata/prov/usage.rb
|
286
|
+
- lib/bio-publisci/metadata/publisher.rb
|
259
287
|
- lib/bio-publisci/mixins/custom_predicate.rb
|
260
288
|
- lib/bio-publisci/mixins/dereferencable.rb
|
289
|
+
- lib/bio-publisci/mixins/registry.rb
|
261
290
|
- lib/bio-publisci/mixins/vocabulary.rb
|
262
291
|
- lib/bio-publisci/output.rb
|
263
292
|
- lib/bio-publisci/parser.rb
|
@@ -268,7 +297,6 @@ files:
|
|
268
297
|
- lib/bio-publisci/readers/dataframe.rb
|
269
298
|
- lib/bio-publisci/readers/r_cross.rb
|
270
299
|
- lib/bio-publisci/readers/r_matrix.rb
|
271
|
-
- lib/bio-publisci/spira.rb
|
272
300
|
- lib/bio-publisci/store.rb
|
273
301
|
- lib/bio-publisci/writers/arff.rb
|
274
302
|
- lib/bio-publisci/writers/dataframe.rb
|
@@ -309,18 +337,23 @@ files:
|
|
309
337
|
- scripts/scan_islet.rb
|
310
338
|
- scripts/update_reference.rb
|
311
339
|
- spec/ORM/data_cube_orm_spec.rb
|
340
|
+
- spec/ORM/prov_model_spec.rb
|
312
341
|
- spec/analyzer_spec.rb
|
313
342
|
- spec/csv/bacon.csv
|
314
343
|
- spec/csv/moar_bacon.csv
|
315
344
|
- spec/data_cube_spec.rb
|
316
345
|
- spec/dataset_for_spec.rb
|
346
|
+
- spec/dsl_spec.rb
|
317
347
|
- spec/generators/csv_spec.rb
|
318
348
|
- spec/generators/dataframe_spec.rb
|
319
349
|
- spec/generators/r_cross_spec.rb
|
320
350
|
- spec/generators/r_matrix_spec.rb
|
351
|
+
- spec/metadata/metadata_dsl_spec.rb
|
321
352
|
- spec/prov/activity_spec.rb
|
322
353
|
- spec/prov/agent_spec.rb
|
323
354
|
- spec/prov/association_spec.rb
|
355
|
+
- spec/prov/config_spec.rb
|
356
|
+
- spec/prov/derivation_spec.rb
|
324
357
|
- spec/prov/entity_spec.rb
|
325
358
|
- spec/prov/role_spec.rb
|
326
359
|
- spec/prov/usage_spec.rb
|