bio-publisci 0.0.6 → 0.0.7

data/spec/metadata/metadata_dsl_spec.rb

@@ -0,0 +1,68 @@
+require_relative '../../lib/bio-publisci.rb'
+
+describe PubliSci::Metadata::DSL do
+  include PubliSci::Metadata::DSL
+
+  before(:each) do
+    PubliSci::Prov.registry.clear
+  end
+
+  it "can generate basic metadata as n3" do
+    dataset 'bacon'
+    title 'Bacon Data'
+    description 'a dataset about bacon'
+    creator 'Will'
+    topic 'Delicious Bacon'
+    str = generate_n3
+    str[/rdfs:label "(.+)";/,1].should == "Bacon Data"
+    str[/dct:creator "(.+)";/,1].should == "Will"
+    str[/dct:subject "(.+)";/,1].should == "Delicious Bacon"
+    str[/dct:description "(.+)";/,1].should == "a dataset about bacon"
+    str[/dct:issued "(.+)"\^\^xsd:date;/,1].should == Time.now.strftime("%Y-%m-%d")
+  end
+
+  it "can add additional information about publisher" do
+    dataset 'bacon'
+    p = publisher do
+      label "pub"
+      uri "http://some-organization.com"
+    end
+
+    p.label.should == "pub"
+    generate_n3[%r{dct:publisher <(.+)> .},1].should == "http://some-organization.com"
+  end
+
+  # it "can be created with a block" do
+  #   a = agent :ag do
+  #     subject "http://things.com/stuff"
+  #     name "Mr Person"
+  #   end
+  #   a.is_a?(Agent).should be true
+  #   a.subject.should == "http://things.com/stuff"
+  #   a.name.should == "Mr Person"
+  # end
+
+  # it "can be given a type corresponding to a subclass of prov:Agent" do
+  #   a = agent :name, type: "software"
+  #   a.type.should == :software
+  #   a.to_n3["prov:SoftwareAgent"].should_not be nil
+  # end
+
+  # it "can be created using the organization helper" do
+  #   a = organization :group
+  #   a.type.should == :organization
+  # end
+
+  # it "raises an exception when on_behalf_of does not refer to an agent" do
+  #   a = agent :name, on_behalf_of: :other
+  #   expect {a.on_behalf_of[0]}.to raise_error
+  # end
+
+  # it "lazy loads other objects, so declaration order doesn't usually matter" do
+  #   a = agent :name, on_behalf_of: :other
+  #   b = agent :other
+
+  #   a.on_behalf_of.should == b
+  # end
+
+end

data/spec/prov/activity_spec.rb

@@ -1,16 +1,16 @@
 require_relative '../../lib/bio-publisci.rb'
 include PubliSci::Prov::DSL
-include PubliSci::Prov
+# include PubliSci
 
 describe PubliSci::Prov::Activity do
 
   before(:each) do
-    @evaluator = PubliSci::Prov::DSL::Singleton.new
+    @evaluator = PubliSci::Prov::DSL::Instance.new
   end
 
   it "can generate activity fields from symbol" do
     a = activity :name
-    a.is_a?(Activity).should be true
+    a.is_a?(Prov::Activity).should be true
     a.subject.should == "http://rqtl.org/ns/activity/name"
   end
 
@@ -25,7 +25,7 @@ describe PubliSci::Prov::Activity do
       subject "http://things.com/stuff"
       generated :data
     end
-    a.is_a?(Activity).should be true
+    a.is_a?(Prov::Activity).should be true
     a.subject.should == "http://things.com/stuff"
   end
 

data/spec/prov/agent_spec.rb

@@ -1,16 +1,15 @@
 require_relative '../../lib/bio-publisci.rb'
 include PubliSci::Prov::DSL
-include PubliSci::Prov
 
 describe PubliSci::Prov::Agent do
 
   before(:each) do
-    @evaluator = PubliSci::Prov::DSL::Singleton.new
+    @evaluator = PubliSci::Prov::DSL::Instance.new
   end
 
   it "can generate agent fields from symbol" do
     a = agent :name
-    a.is_a?(Agent).should be true
+    a.is_a?(Prov::Agent).should be true
     a.subject.should == "http://rqtl.org/ns/agent/name"
   end
 
@@ -24,7 +23,7 @@ describe PubliSci::Prov::Agent do
       subject "http://things.com/stuff"
       name "Mr Person"
     end
-    a.is_a?(Agent).should be true
+    a.is_a?(Prov::Agent).should be true
     a.subject.should == "http://things.com/stuff"
     a.name.should == "Mr Person"
   end

data/spec/prov/association_spec.rb

@@ -1,10 +1,9 @@
 require_relative '../../lib/bio-publisci.rb'
-include PubliSci::Prov
 include PubliSci::Prov::DSL
 
 describe PubliSci::Prov::Association do
   before(:each) do
-    @ev = PubliSci::Prov::DSL::Singleton.new
+    @ev = PubliSci::Prov::DSL::Instance.new
   end
 
   it "can create simple associations" do

data/spec/prov/config_spec.rb

@@ -0,0 +1,28 @@
+require_relative '../../lib/bio-publisci.rb'
+include PubliSci::Prov::DSL
+include PubliSci
+
+describe PubliSci::Prov::Configuration do
+
+  before(:each) do
+    @evaluator = PubliSci::Prov::DSL::Instance.new
+  end
+
+  it "can set basic config methods" do
+    configure do |cfg|
+      cfg.output :to_repository
+    end
+    settings.output.should == :to_repository
+  end
+
+  it "can configure different repository types", no_travis: true do
+    configure do |cfg|
+      cfg.repository :fourstore
+    end
+    a = activity :name
+    a.is_a?(Prov::Activity).should be true
+    r=to_repository
+    a.subject.should == "http://rqtl.org/ns/activity/name"
+    r.is_a?(RDF::FourStore::Repository).should be true
+  end
+end

data/spec/prov/derivation_spec.rb

@@ -0,0 +1,30 @@
+require_relative '../../lib/bio-publisci.rb'
+include PubliSci::Prov::DSL
+
+describe PubliSci::Prov::Derivation do
+  before(:each) do
+    @ev = PubliSci::Prov::DSL::Instance.new
+  end
+
+  it "can create simple derivations" do
+    e = @ev.entity :name
+    f = @ev.entity :other, derived_from: :name
+    # g = @ev.activity :do_things, generated: :name, associated_with: :other
+    f.derived_from[0].should == e
+    @ev.generate_n3
+    @ev.generate_n3["prov:wasDerivedFrom"].size.should > 0
+  end
+
+  it "creates qualified derivations when a block is passed" do
+    e = @ev.entity :name
+    f = @ev.entity :other do
+      derived_from :name do
+        had_activity :do_things
+      end
+    end
+    g = @ev.activity :do_things do
+      generated :other
+    end
+    f.derived_from.first.had_activity.should == g
+  end
+end

data/spec/prov/entity_spec.rb

@@ -1,15 +1,14 @@
 require_relative '../../lib/bio-publisci.rb'
 include PubliSci::Prov::DSL
-include PubliSci::Prov
 
 describe PubliSci::Prov::Entity do
   before(:each) do
-    @evaluator = PubliSci::Prov::DSL::Singleton.new
+    @evaluator = PubliSci::Prov::DSL::Instance.new
   end
 
   it "can generate entity fields from symbol" do
     e = entity :name
-    e.is_a?(Entity).should be true
+    e.is_a?(Prov::Entity).should be true
     e.subject.should == "http://rqtl.org/ns/entity/name"
   end
 
@@ -23,7 +22,7 @@ describe PubliSci::Prov::Entity do
       subject "http://things.com/stuff"
       source "/somefile.txt"
     end
-    e.is_a?(Entity).should be true
+    e.is_a?(Prov::Entity).should be true
     e.subject.should == "http://things.com/stuff"
     e.source[0].should == "/somefile.txt"
   end

data/spec/prov/role_spec.rb

@@ -1,11 +1,10 @@
 require_relative '../../lib/bio-publisci.rb'
 include PubliSci::Prov::DSL
-include PubliSci::Prov
 
 describe PubliSci::Prov::Role do
 
   before(:each) do
-    @evaluator = PubliSci::Prov::DSL::Singleton.new
+    @evaluator = PubliSci::Prov::DSL::Instance.new
   end
 
   it "creates a role in a used block" do

data/spec/prov/usage_spec.rb

@@ -1,11 +1,10 @@
 require_relative '../../lib/bio-publisci.rb'
 include PubliSci::Prov::DSL
-include PubliSci::Prov
 
 describe PubliSci::Prov::Usage do
 
   before(:each) do
-    @evaluator = PubliSci::Prov::DSL::Singleton.new
+    @evaluator = PubliSci::Prov::DSL::Instance.new
   end
 
   it "can create simple associations" do

data/spec/r_builder_spec.rb

@@ -7,18 +7,18 @@
 require_relative '../lib/bio-publisci.rb'
 
 
-describe R2RDF::Writer::Dataframe do
+describe PubliSci::Writer::Dataframe do
 
 	context "when using r/qtl dataframe", no_travis: true do
 
-		before(:all) do 
+		before(:all) do
 			@r = Rserve::Connection.new
 			@r.eval <<-EOF
 				library(qtl)
 				data(listeria)
 				mr = scanone(listeria,method="mr")
 EOF
-			@builder = R2RDF::Writer::Builder.new
+			@builder = PubliSci::Writer::Builder.new
 		end
 
 		it "produces equivalent dataframe from rdf" #do

data/spec/turtle/bacon

@@ -15,15 +15,31 @@
 @prefix prov:     <http://www.w3.org/ns/prov#> .
 
 ns:dsd-bacon a qb:DataStructureDefinition;
-  qb:component [ qb:dimension prop:producer ] ;
-  qb:component [ qb:dimension prop:pricerange ] ;
-  qb:component [ qb:measure prop:chunkiness ] ;
-  qb:component [ qb:measure prop:deliciousness ] .
+  qb:component cs:producer ;
+  qb:component cs:pricerange ;
+  qb:component cs:chunkiness ;
+  qb:component cs:deliciousness .
 
 ns:dataset-bacon a qb:DataSet ;
   rdfs:label "bacon"@en ;
   qb:structure ns:dsd-bacon .
 
+cs:producer a qb:ComponentSpecification ;
+  rdfs:label "producer Component" ;
+  qb:dimension prop:producer .
+
+cs:pricerange a qb:ComponentSpecification ;
+  rdfs:label "pricerange Component" ;
+  qb:dimension prop:pricerange .
+
+cs:chunkiness a qb:ComponentSpecification ;
+  rdfs:label "chunkiness Component" ;
+  qb:measure prop:chunkiness .
+
+cs:deliciousness a qb:ComponentSpecification ;
+  rdfs:label "deliciousness Component" ;
+  qb:measure prop:deliciousness .
+
 prop:producer a rdf:Property, qb:DimensionProperty ;
   rdfs:label "producer"@en ;
   qb:codeList code:producer ;

data/spec/turtle/reference

@@ -15,15 +15,31 @@
 @prefix prov:     <http://www.w3.org/ns/prov#> .
 
 ns:dsd-mr a qb:DataStructureDefinition;
-  qb:component [ qb:dimension prop:refRow ] ;
-  qb:component [ qb:measure prop:chr ] ;
-  qb:component [ qb:measure prop:pos ] ;
-  qb:component [ qb:measure prop:lod ] .
+  qb:component cs:refRow ;
+  qb:component cs:chr ;
+  qb:component cs:pos ;
+  qb:component cs:lod .
 
 ns:dataset-mr a qb:DataSet ;
   rdfs:label "mr"@en ;
   qb:structure ns:dsd-mr .
 
+cs:refRow a qb:ComponentSpecification ;
+  rdfs:label "refRow Component" ;
+  qb:dimension prop:refRow .
+
+cs:chr a qb:ComponentSpecification ;
+  rdfs:label "chr Component" ;
+  qb:measure prop:chr .
+
+cs:pos a qb:ComponentSpecification ;
+  rdfs:label "pos Component" ;
+  qb:measure prop:pos .
+
+cs:lod a qb:ComponentSpecification ;
+  rdfs:label "lod Component" ;
+  qb:measure prop:lod .
+
 prop:refRow a rdf:Property, qb:DimensionProperty ;
   rdfs:label "refRow"@en ;
   qb:codeList code:refrow ;

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-publisci
 version: !ruby/object:Gem::Version
-  version: 0.0.6
+  version: 0.0.7
 platform: ruby
 authors:
 - Will Strinz
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-02 00:00:00.000000000 Z
+date: 2013-08-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdf
@@ -192,6 +192,20 @@ dependencies:
     - - '>='
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: spira
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: 'A toolkit for publishing scientific results and datasets using RDF,
   OWL, and related technologies '
 email: wstrinz@gmail.com
@@ -219,6 +233,10 @@ files:
 - examples/primer-full.prov
 - examples/primer.prov
 - examples/prov_dsl.prov
+- examples/safe_gen.rb
+- examples/visualization/primer.prov
+- examples/visualization/prov_viz.rb
+- examples/visualization/viz.rb
 - features/create_generator.feature
 - features/integration.feature
 - features/integration_steps.rb
@@ -238,17 +256,26 @@ files:
 - features/writer_steps.rb
 - lib/bio-publisci.rb
 - lib/bio-publisci/analyzer.rb
+- lib/bio-publisci/datacube_model.rb
 - lib/bio-publisci/dataset/ORM/data_cube_orm.rb
 - lib/bio-publisci/dataset/ORM/observation.rb
+- lib/bio-publisci/dataset/configuration.rb
 - lib/bio-publisci/dataset/data_cube.rb
+- lib/bio-publisci/dataset/dataset.rb
 - lib/bio-publisci/dataset/dataset_for.rb
 - lib/bio-publisci/dataset/interactive.rb
+- lib/bio-publisci/dsl/config.rb
+- lib/bio-publisci/dsl/dataset_dsl.rb
+- lib/bio-publisci/dsl/dsl.rb
+- lib/bio-publisci/dsl/metadata_dsl.rb
+- lib/bio-publisci/dsl/prov_dsl.rb
+- lib/bio-publisci/metadata/generator.rb
 - lib/bio-publisci/metadata/metadata.rb
 - lib/bio-publisci/metadata/prov/activity.rb
 - lib/bio-publisci/metadata/prov/agent.rb
 - lib/bio-publisci/metadata/prov/association.rb
+- lib/bio-publisci/metadata/prov/config.rb
 - lib/bio-publisci/metadata/prov/derivation.rb
-- lib/bio-publisci/metadata/prov/dsl.rb
 - lib/bio-publisci/metadata/prov/element.rb
 - lib/bio-publisci/metadata/prov/entity.rb
 - lib/bio-publisci/metadata/prov/model/prov_models.rb
@@ -256,8 +283,10 @@ files:
 - lib/bio-publisci/metadata/prov/prov.rb
 - lib/bio-publisci/metadata/prov/role.rb
 - lib/bio-publisci/metadata/prov/usage.rb
+- lib/bio-publisci/metadata/publisher.rb
 - lib/bio-publisci/mixins/custom_predicate.rb
 - lib/bio-publisci/mixins/dereferencable.rb
+- lib/bio-publisci/mixins/registry.rb
 - lib/bio-publisci/mixins/vocabulary.rb
 - lib/bio-publisci/output.rb
 - lib/bio-publisci/parser.rb
@@ -268,7 +297,6 @@ files:
 - lib/bio-publisci/readers/dataframe.rb
 - lib/bio-publisci/readers/r_cross.rb
 - lib/bio-publisci/readers/r_matrix.rb
-- lib/bio-publisci/spira.rb
 - lib/bio-publisci/store.rb
 - lib/bio-publisci/writers/arff.rb
 - lib/bio-publisci/writers/dataframe.rb
@@ -309,18 +337,23 @@ files:
 - scripts/scan_islet.rb
 - scripts/update_reference.rb
 - spec/ORM/data_cube_orm_spec.rb
+- spec/ORM/prov_model_spec.rb
 - spec/analyzer_spec.rb
 - spec/csv/bacon.csv
 - spec/csv/moar_bacon.csv
 - spec/data_cube_spec.rb
 - spec/dataset_for_spec.rb
+- spec/dsl_spec.rb
 - spec/generators/csv_spec.rb
 - spec/generators/dataframe_spec.rb
 - spec/generators/r_cross_spec.rb
 - spec/generators/r_matrix_spec.rb
+- spec/metadata/metadata_dsl_spec.rb
 - spec/prov/activity_spec.rb
 - spec/prov/agent_spec.rb
 - spec/prov/association_spec.rb
+- spec/prov/config_spec.rb
+- spec/prov/derivation_spec.rb
 - spec/prov/entity_spec.rb
 - spec/prov/role_spec.rb
 - spec/prov/usage_spec.rb