bio-publisci 0.0.5 → 0.0.6

data/spec/prov/entity_spec.rb

@@ -0,0 +1,53 @@
+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
+  end
+
+  it "can generate entity fields from symbol" do
+    e = entity :name
+    e.is_a?(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?(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

@@ -0,0 +1,95 @@
+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
+  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

data/spec/prov/usage_spec.rb

@@ -0,0 +1,99 @@
+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
+  end
+
+  it "can create simple associations" 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].entity.should == ent2
+  end
+
+  it "can generate n3" 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.to_n3["prov:qualifiedUsage"].size.should > 0
+    act.used[0].to_n3["a prov:Usage"].size.should > 0
+  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?(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

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-publisci
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 0.0.6
 platform: ruby
 authors:
 - Will Strinz
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-07-31 00:00:00.000000000 Z
+date: 2013-08-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdf
@@ -214,6 +214,9 @@ files:
 - bin/bio-publisci
 - examples/bio-band_integration.rb
 - examples/no_magic.prov
+- examples/no_magic.rb
+- examples/orm.prov
+- examples/primer-full.prov
 - examples/primer.prov
 - examples/prov_dsl.prov
 - features/create_generator.feature
@@ -248,9 +251,13 @@ files:
 - 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
 - lib/bio-publisci/metadata/prov/plan.rb
 - lib/bio-publisci/metadata/prov/prov.rb
+- lib/bio-publisci/metadata/prov/role.rb
+- lib/bio-publisci/metadata/prov/usage.rb
 - lib/bio-publisci/mixins/custom_predicate.rb
+- lib/bio-publisci/mixins/dereferencable.rb
 - lib/bio-publisci/mixins/vocabulary.rb
 - lib/bio-publisci/output.rb
 - lib/bio-publisci/parser.rb
@@ -311,6 +318,12 @@ files:
 - spec/generators/dataframe_spec.rb
 - spec/generators/r_cross_spec.rb
 - spec/generators/r_matrix_spec.rb
+- spec/prov/activity_spec.rb
+- spec/prov/agent_spec.rb
+- spec/prov/association_spec.rb
+- spec/prov/entity_spec.rb
+- spec/prov/role_spec.rb
+- spec/prov/usage_spec.rb
 - spec/queries/integrity/1.rq
 - spec/queries/integrity/11.rq
 - spec/queries/integrity/12.rq