publisci 0.1.2

data/spec/metadata/metadata_dsl_spec.rb

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+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

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+require_relative '../../lib/bio-publisci.rb'
+include PubliSci::Prov::DSL
+# include PubliSci
+
+describe PubliSci::Prov::Activity do
+
+  before(:each) do
+    @evaluator = PubliSci::Prov::DSL::Instance.new
+  end
+
+  it "can generate activity fields from symbol" do
+    a = activity :name
+    a.is_a?(Prov::Activity).should be true
+    a.subject.should == "http://rqtl.org/ns/activity/name"
+  end
+
+  it "can specify fields manually" do
+    a = activity :name, subject: "http://example.org/name"
+    a.subject.should == "http://example.org/name"
+  end
+
+  it "can be created with a block" do
+    e = entity :data
+    a = activity :ag do
+      subject "http://things.com/stuff"
+      generated :data
+    end
+    a.is_a?(Prov::Activity).should be true
+    a.subject.should == "http://things.com/stuff"
+  end
+
+  it "lazy loads other objects" do
+    a = activity :ag do
+      subject "http://things.com/stuff"
+      generated :data
+    end
+    e = entity :data
+
+    a.generated[0].should == e
+  end
+
+  it "raises an exception when used does not refer to an entity" do
+    a = activity :name, used: :some_data
+    expect {a.used[0]}.to raise_error
+  end
+
+  it "raises an exception when generated does not refer to an entity" do
+    a = activity :name, generated: :other_data
+    expect {a.generated[0]}.to raise_error
+  end
+
+  it "lazy loads generated relationships" do
+    a = activity :act, generated: :data
+    e = entity :data
+
+    a.generated[0].should == e
+  end
+
+  it "lazy loads used relationships" do
+    a = activity :act, generated: :data, used: :other_data
+    e = entity :data
+    f = entity :other_data
+
+    a.used[0].should == f
+  end
+
+  # it "lazy loads other objects, so declaration order doesn't usually matter" do
+  #   a = activity :name, on_behalf_of: :other
+  #   b = activity :other
+
+  #   a.on_behalf_of.should == b
+  # end
+
+end

data/spec/prov/agent_spec.rb

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+require_relative '../../lib/bio-publisci.rb'
+include PubliSci::Prov::DSL
+
+describe PubliSci::Prov::Agent do
+
+  before(:each) do
+    @evaluator = PubliSci::Prov::DSL::Instance.new
+  end
+
+  it "can generate agent fields from symbol" do
+    a = agent :name
+    a.is_a?(Prov::Agent).should be true
+    a.subject.should == "http://rqtl.org/ns/agent/name"
+  end
+
+  it "can specify fields manually" do
+    a = agent :name, subject: "http://example.org/name"
+    a.subject.should == "http://example.org/name"
+  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?(Prov::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/association_spec.rb

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+require_relative '../../lib/bio-publisci.rb'
+include PubliSci::Prov::DSL
+
+describe PubliSci::Prov::Association do
+  before(:each) do
+    @ev = PubliSci::Prov::DSL::Instance.new
+  end
+
+  it "can create simple associations" do
+    e = @ev.entity :name
+    f = @ev.agent :other
+    g = @ev.activity :do_things, generated: :name, associated_with: :other
+    g.associated_with[0].should == f
+    @ev.generate_n3["prov:wasAssociatedWith"].size.should > 0
+  end
+
+  it "creates qualified associations when a block is passed" do
+    e = @ev.entity :name
+    f = @ev.agent :other
+    p = @ev.plan :the_plan
+    g = @ev.activity :do_things do
+      generated :name
+      associated_with do
+        agent :other
+        plan :the_plan
+      end
+    end
+    g.associated_with.first.agent.should == f
+    @ev.generate_n3["prov:wasAssociatedWith"].size.should > 0
+    @ev.generate_n3["prov:qualifiedAssociation"].size.should > 0
+  end
+
+  # it "raises an exception when derivation does not refer to an entity" do
+  #   e = entity :name, derived_from: :dataset
+  #   expect {e.derived_from[0]}.to raise_error
+  # end
+
+  # it "raises an exception when attribution does not refer to an agent" do
+  #   e = entity :name, attributed_to: :person
+  #   expect {e.attributed_to[0]}.to raise_error
+  # end
+
+  # it "raises an exception when generated_by does not refer to an activity" do
+  #   e = entity :name, generated_by: :act
+  #   expect {e.generated_by[0]}.to raise_error
+  # end
+
+  # it "lazy loads other objects, so declaration order doesn't usually matter" do
+  #   e = entity :name, derived_from: :other
+  #   f = entity :other
+
+
+  #   e.derived_from[0].should == f
+  # end
+end

data/spec/prov/config_spec.rb

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+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

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+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

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+require_relative '../../lib/bio-publisci.rb'
+include PubliSci::Prov::DSL
+
+describe PubliSci::Prov::Entity do
+  before(:each) do
+    @evaluator = PubliSci::Prov::DSL::Instance.new
+  end
+
+  it "can generate entity fields from symbol" do
+    e = entity :name
+    e.is_a?(Prov::Entity).should be true
+    e.subject.should == "http://rqtl.org/ns/entity/name"
+  end
+
+  it "can specify fields manually" do
+    e = entity :name, subject: "http://example.org/name"
+    e.subject.should == "http://example.org/name"
+  end
+
+  it "can be created with a block" do
+    e = entity :ent do
+      subject "http://things.com/stuff"
+      source "/somefile.txt"
+    end
+    e.is_a?(Prov::Entity).should be true
+    e.subject.should == "http://things.com/stuff"
+    e.source[0].should == "/somefile.txt"
+  end
+
+  it "raises an exception when derivation does not refer to an entity" do
+    e = entity :name, derived_from: :dataset
+    expect {e.derived_from[0]}.to raise_error
+  end
+
+  it "raises an exception when attribution does not refer to an agent" do
+    e = entity :name, attributed_to: :person
+    expect {e.attributed_to[0]}.to raise_error
+  end
+
+  it "raises an exception when generated_by does not refer to an activity" do
+    e = entity :name, generated_by: :act
+    expect {e.generated_by[0]}.to raise_error
+  end
+
+  it "lazy loads other objects, so declaration order doesn't usually matter" do
+    e = entity :name, derived_from: :other
+    f = entity :other
+
+
+    e.derived_from[0].should == f
+  end
+end

data/spec/prov/role_spec.rb

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+require_relative '../../lib/bio-publisci.rb'
+include PubliSci::Prov::DSL
+
+describe PubliSci::Prov::Role do
+
+  before(:each) do
+    @evaluator = PubliSci::Prov::DSL::Instance.new
+  end
+
+  it "creates a role in a used block" do
+    ent1 = @ev.entity :some_data
+    ent2 = @ev.entity :other_data
+    ag = @ev.agent :some_guy
+    act = @ev.activity :do_things do
+      generated :some_data
+      associated_with :some_guy
+      used do
+        entity :other_data
+        role :plagirized
+      end
+    end
+    act.used[0].role.to_n3["a prov:Role"].size.should > 0
+  end
+
+  it "can have a comment attached" do
+    ent1 = @ev.entity :some_data
+    ent2 = @ev.entity :other_data
+    ag = @ev.agent :some_guy
+    act = @ev.activity :do_things do
+      generated :some_data
+      associated_with :some_guy
+      used do
+        entity :other_data
+        role :plagirized do
+          comment "I stole all of this data"
+        end
+      end
+    end
+    act.used[0].role.to_n3["rdfs:comment"].size.should > 0
+  end
+
+  # it "can be created with a block" do
+  #   e = entity :data
+  #   a = activity :ag do
+  #     subject "http://things.com/stuff"
+  #     generated :data
+  #   end
+  #   a.is_a?(Activity).should be true
+  #   a.subject.should == "http://things.com/stuff"
+  # end
+
+  # it "lazy loads other objects" do
+  #   a = activity :ag do
+  #     subject "http://things.com/stuff"
+  #     generated :data
+  #   end
+  #   e = entity :data
+
+  #   a.generated[0].should == e
+  # end
+
+  # it "raises an exception when used does not refer to an entity" do
+  #   a = activity :name, used: :some_data
+  #   expect {a.used[0]}.to raise_error
+  # end
+
+  # it "raises an exception when generated does not refer to an entity" do
+  #   a = activity :name, generated: :other_data
+  #   expect {a.generated[0]}.to raise_error
+  # end
+
+  # it "lazy loads generated relationships" do
+  #   a = activity :act, generated: :data
+  #   e = entity :data
+
+  #   a.generated[0].should == e
+  # end
+
+  # it "lazy loads used relationships" do
+  #   a = activity :act, generated: :data, used: :other_data
+  #   e = entity :data
+  #   f = entity :other_data
+
+  #   a.used[0].should == f
+  # end
+
+  # it "lazy loads other objects, so declaration order doesn't usually matter" do
+  #   a = activity :name, on_behalf_of: :other
+  #   b = activity :other
+
+  #   a.on_behalf_of.should == b
+  # end
+
+end