publisci 0.1.2

data/spec/prov/usage_spec.rb

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+require_relative '../../lib/bio-publisci.rb'
+include PubliSci::Prov::DSL
+
+describe PubliSci::Prov::Usage do
+
+  before(:each) do
+    @evaluator = PubliSci::Prov::DSL::Instance.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

data/spec/queries/integrity/1.rq

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+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX skos:    <http://www.w3.org/2004/02/skos/core#>
+PREFIX qb:      <http://purl.org/linked-data/cube#>
+PREFIX xsd:     <http://www.w3.org/2001/XMLSchema#>
+PREFIX owl:     <http://www.w3.org/2002/07/owl#>
+
+# IC-1. Unique DataSet
+
+SELECT ?obs {
+  {
+    # Check observation has a data set
+    ?obs a qb:Observation .
+    MINUS { ?obs qb:dataSet ?dataset1 . }
+  } UNION {
+    # Check has just one data set
+    ?obs a qb:Observation ;
+       qb:dataSet ?dataset1, ?dataset2 .
+    FILTER (?dataset1 != ?dataset2)
+  }
+}

data/spec/queries/integrity/11.rq

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+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX skos:    <http://www.w3.org/2004/02/skos/core#>
+PREFIX qb:      <http://purl.org/linked-data/cube#>
+PREFIX xsd:     <http://www.w3.org/2001/XMLSchema#>
+PREFIX owl:     <http://www.w3.org/2002/07/owl#>
+
+# IC-11. All dimensions required (modified)
+
+SELECT * WHERE {
+    #also include qb:dimension resources
+    {
+	    ?obs qb:dataSet ?ds .
+	    ?ds qb:structure ?dsd .
+	    ?dsd qb:component ?comp .
+	    ?comp qb:componentProperty ?dim .
+    }
+    UNION
+    {
+    	?obs qb:dataSet ?ds .
+    	?ds qb:structure ?dsd .
+    	?dsd qb:component ?comp .
+    	?comp qb:dimension ?dim .
+    }
+		
+
+    ?dim a qb:DimensionProperty;
+    FILTER NOT EXISTS { ?obs ?dim [] }
+}

data/spec/queries/integrity/12.rq

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+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX skos:    <http://www.w3.org/2004/02/skos/core#>
+PREFIX qb:      <http://purl.org/linked-data/cube#>
+PREFIX xsd:     <http://www.w3.org/2001/XMLSchema#>
+PREFIX owl:     <http://www.w3.org/2002/07/owl#>
+
+# IC-12. No duplicate observations (modified)
+# No two qb:Observations in the same qb:DataSet may have the same value for all dimensions.
+
+SELECT * WHERE {
+  FILTER( ?allEqual )
+  {
+    # For each pair of observations test if all the dimension values are the same
+    SELECT (MIN(?equal) AS ?allEqual) WHERE {
+        ?obs1 qb:dataSet ?dataset .
+        ?obs2 qb:dataSet ?dataset .
+        FILTER (?obs1 != ?obs2)
+        { 
+        	?dataset qb:structure ?dsd .
+        	?ds qb:component ?comp .
+        	?comp qb:componentProperty ?dim.
+        }
+        UNION
+        { 
+		      ?dataset qb:structure ?dsd .
+		      ?dsd qb:component ?comp .
+		      ?comp qb:dimension ?dim .
+        }
+
+        ?dim a qb:DimensionProperty .
+        ?obs1 ?dim ?value1 .
+        ?obs2 ?dim ?value2 .
+        BIND( ?value1 = ?value2 AS ?equal)
+    } GROUP BY ?obs1 ?obs2
+  }
+}

data/spec/queries/integrity/14.rq

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+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX skos:    <http://www.w3.org/2004/02/skos/core#>
+PREFIX qb:      <http://purl.org/linked-data/cube#>
+PREFIX xsd:     <http://www.w3.org/2001/XMLSchema#>
+PREFIX owl:     <http://www.w3.org/2002/07/owl#>
+
+# IC-14. All measures present
+
+SELECT * WHERE {
+    # Observation in a non-measureType cube
+    ?obs qb:dataSet ?dset .
+    ?dset qb:structure ?dsd .
+    FILTER NOT EXISTS { 
+    	?dsd qb:component ?comp .
+    	?comp qb:componentProperty ?prop .
+    	?prop qb:measureType [] .
+    }
+
+    # verify every measure is present
+    ?dsd qb:component ?comp .
+    ?comp qb:componentProperty ?measure .
+    ?measure a qb:MeasureProperty;
+    FILTER NOT EXISTS { ?obs ?measure [] }
+}

data/spec/queries/integrity/19_1.rq

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+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX skos:    <http://www.w3.org/2004/02/skos/core#>
+PREFIX qb:      <http://purl.org/linked-data/cube#>
+PREFIX xsd:     <http://www.w3.org/2001/XMLSchema#>
+PREFIX owl:     <http://www.w3.org/2002/07/owl#>
+
+#IC-19_1 Codes from code list
+
+SELECT * WHERE {
+    ?obs qb:dataSet ?ds .
+    ?ds qb:structure ?str .
+    ?str qb:component ?prop .
+    ?prop qb:componentProperty ?dim .
+    ?dim a qb:DimensionProperty ;
+        qb:codeList ?list .
+    ?list a skos:ConceptScheme .
+    ?obs ?dim ?v .
+    FILTER NOT EXISTS { ?v a skos:Concept ; skos:inScheme ?list }
+}
+

data/spec/queries/integrity/19_2.rq

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+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX skos:    <http://www.w3.org/2004/02/skos/core#>
+PREFIX qb:      <http://purl.org/linked-data/cube#>
+PREFIX xsd:     <http://www.w3.org/2001/XMLSchema#>
+PREFIX owl:     <http://www.w3.org/2002/07/owl#>
+
+SELECT * WHERE {
+    ?obs qb:dataSet/qb:structure/qb:component/qb:componentProperty ?dim .
+    ?dim a qb:DimensionProperty ;
+        qb:codeList ?list .
+    ?list a skos:Collection .
+    ?obs ?dim ?v .
+    FILTER NOT EXISTS { ?v a skos:Concept . ?list skos:member+ ?v }
+}

data/spec/queries/integrity/2.rq

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+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX skos:    <http://www.w3.org/2004/02/skos/core#>
+PREFIX qb:      <http://purl.org/linked-data/cube#>
+PREFIX xsd:     <http://www.w3.org/2001/XMLSchema#>
+PREFIX owl:     <http://www.w3.org/2002/07/owl#>
+
+# IC-2. Unique DSD
+
+SELECT * {
+  {
+    # Check dataset has a dsd
+    ?dataset a qb:DataSet .
+    FILTER NOT EXISTS { ?dataset qb:structure ?dsd . }
+  } UNION { 
+    # Check has just one dsd
+    ?dataset a qb:DataSet ;
+       qb:structure ?dsd1, ?dsd2 .
+    FILTER (?dsd1 != ?dsd2)
+  }
+}
+

data/spec/queries/integrity/3.rq

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+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX skos:    <http://www.w3.org/2004/02/skos/core#>
+PREFIX qb:      <http://purl.org/linked-data/cube#>
+PREFIX xsd:     <http://www.w3.org/2001/XMLSchema#>
+PREFIX owl:     <http://www.w3.org/2002/07/owl#>
+
+# IC-3. DSD includes measure (modified)
+
+SELECT * WHERE {
+  ?dsd a qb:DataStructureDefinition ;
+  
+  FILTER NOT EXISTS {
+  	#original spec missing this definition
+    { ?dsd qb:component [qb:measure []] }
+    UNION
+    { ?dsd qb:component [qb:componentProperty [a qb:MeasureProperty]] }
+  }
+}

data/spec/queries/integrity/4.rq

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+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX skos:    <http://www.w3.org/2004/02/skos/core#>
+PREFIX qb:      <http://purl.org/linked-data/cube#>
+PREFIX xsd:     <http://www.w3.org/2001/XMLSchema#>
+PREFIX owl:     <http://www.w3.org/2002/07/owl#>
+
+# IC-4. Dimensions have range
+
+SELECT * WHERE {
+  ?dim a qb:DimensionProperty .
+  FILTER NOT EXISTS { ?dim rdfs:range [] }
+}

data/spec/queries/integrity/5.rq

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+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX skos:    <http://www.w3.org/2004/02/skos/core#>
+PREFIX qb:      <http://purl.org/linked-data/cube#>
+PREFIX xsd:     <http://www.w3.org/2001/XMLSchema#>
+PREFIX owl:     <http://www.w3.org/2002/07/owl#>
+
+# IC-5. Concept dimensions have code lists
+
+SELECT * WHERE {
+  ?dim a qb:DimensionProperty ;
+       rdfs:range skos:Concept .
+  #FILTER NOT EXISTS { ?dim qb:codeList [] }
+}

data/spec/r_builder_spec.rb

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+# require_relative '../lib/r2rdf/data_cube.rb'
+# require_relative '../lib/r2rdf/generators/dataframe.rb'
+# require_relative '../lib/r2rdf/r_client.rb'
+# require_relative '../lib/r2rdf/r_builder.rb'
+# require_relative '../lib/r2rdf/query_helper.rb'
+# require_relative '../lib/r2rdf/generators/csv.rb'
+require_relative '../lib/bio-publisci.rb'
+
+
+describe PubliSci::Writers::Dataframe do
+
+	context "when using r/qtl dataframe", no_travis: true do
+
+		before(:all) do
+			@r = Rserve::Connection.new
+			@r.eval <<-EOF
+				library(qtl)
+				data(listeria)
+				mr = scanone(listeria,method="mr")
+EOF
+			@builder = PubliSci::Writers::Builder.new
+		end
+
+		it "produces equivalent dataframe from rdf" #do
+			#(a) problem is that builder and the @r connection are different b/c of
+			#how rserve works
+			# @builder.from_turtle(File.dirname(__FILE__) +'/turtle/reference', @r, 'mr', 'mo', false, false)
+			# puts @r.eval('ls()').payload.to_ruby
+			# @r.eval('identical(mr,mo)').to_ruby.should == true
+		#end
+
+	end
+end

data/spec/resource/example.Rhistory

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+library(qtl)
+data(listeria)
+mr = scanone(listeria,method='mr')

data/spec/spec_helper.rb

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+# This file was generated by the `rspec --init` command. Conventionally, all
+# specs live under a `spec` directory, which RSpec adds to the `$LOAD_PATH`.
+# Require this file using `require "spec_helper"` to ensure that it is only
+# loaded once.
+#
+# See http://rubydoc.info/gems/rspec-core/RSpec/Core/Configuration
+RSpec.configure do |config|
+  config.treat_symbols_as_metadata_keys_with_true_values = true
+  config.run_all_when_everything_filtered = true
+  config.filter_run :focus
+
+  # Run specs in random order to surface order dependencies. If you find an
+  # order dependency and want to debug it, you can fix the order by providing
+  # the seed, which is printed after each run.
+  #     --seed 1234
+  config.order = 'random'
+end

data/spec/turtle/bacon

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+@base <http://onto.strinz.me/dc/dataset/bacon/> .
+@prefix ns:    <http://onto.strinz.me/dc/dataset/bacon/> .
+@prefix qb:    <http://purl.org/linked-data/cube#> .
+@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix prop:  <http://onto.strinz.me/properties/> .
+@prefix dct:   <http://purl.org/dc/terms/> .
+@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
+@prefix cs:    <http://onto.strinz.me/dc/dataset/bacon/cs/> .
+@prefix code:  <http://onto.strinz.me/dc/dataset/bacon/code/> .
+@prefix owl:   <http://www.w3.org/2002/07/owl#> .
+@prefix skos:  <http://www.w3.org/2004/02/skos/core#> .
+@prefix foaf:     <http://xmlns.com/foaf/0.1/> .
+@prefix org:      <http://www.w3.org/ns/org#> .
+@prefix prov:     <http://www.w3.org/ns/prov#> .
+
+ns:dsd-bacon a qb:DataStructureDefinition;
+  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" ;
+  qb:dimension prop:producer .
+
+cs:pricerange a qb:ComponentSpecification ;
+  rdfs:label "pricerange" ;
+  qb:dimension prop:pricerange .
+
+cs:chunkiness a qb:ComponentSpecification ;
+  rdfs:label "chunkiness" ;
+  qb:measure prop:chunkiness .
+
+cs:deliciousness a qb:ComponentSpecification ;
+  rdfs:label "deliciousness" ;
+  qb:measure prop:deliciousness .
+
+prop:producer a rdf:Property, qb:DimensionProperty ;
+  rdfs:label "producer"@en ;
+  qb:codeList code:producer ;
+  rdfs:range code:Producer .
+
+prop:pricerange a rdf:Property, qb:DimensionProperty ;
+  rdfs:label "pricerange"@en ;
+  qb:codeList code:pricerange ;
+  rdfs:range code:Pricerange .
+
+prop:chunkiness a rdf:Property, qb:MeasureProperty ;
+  rdfs:label "chunkiness"@en .
+
+prop:deliciousness a rdf:Property, qb:MeasureProperty ;
+  rdfs:label "deliciousness"@en .
+
+code:Producer a rdfs:Class, owl:Class;
+  rdfs:subClassOf skos:Concept ;
+  rdfs:label "Code list for producer - codelist class"@en;
+  rdfs:comment "Specifies the producer for each observation";
+  rdfs:seeAlso code:producer .
+
+code:producer a skos:ConceptScheme;
+  skos:prefLabel "Code list for producer - codelist scheme"@en;
+  rdfs:label "Code list for producer - codelist scheme"@en;
+  skos:notation "CL_PRODUCER";
+  skos:note "Specifies the producer for each observation";
+  skos:hasTopConcept <code/producer/hormel> ;
+  skos:hasTopConcept <code/producer/newskies> ;
+  skos:hasTopConcept <code/producer/whys> ;
+  .
+
+code:Pricerange a rdfs:Class, owl:Class;
+  rdfs:subClassOf skos:Concept ;
+  rdfs:label "Code list for pricerange - codelist class"@en;
+  rdfs:comment "Specifies the pricerange for each observation";
+  rdfs:seeAlso code:pricerange .
+
+code:pricerange a skos:ConceptScheme;
+  skos:prefLabel "Code list for pricerange - codelist scheme"@en;
+  rdfs:label "Code list for pricerange - codelist scheme"@en;
+  skos:notation "CL_PRICERANGE";
+  skos:note "Specifies the pricerange for each observation";
+  skos:hasTopConcept <code/pricerange/low> ;
+  skos:hasTopConcept <code/pricerange/medium> ;
+  skos:hasTopConcept <code/pricerange/nonexistant> ;
+  .
+
+<code/producer/hormel> a skos:Concept, code:Producer;
+  skos:topConceptOf code:producer ;
+  skos:prefLabel "hormel" ;
+  skos:inScheme code:producer .
+
+<code/producer/newskies> a skos:Concept, code:Producer;
+  skos:topConceptOf code:producer ;
+  skos:prefLabel "newskies" ;
+  skos:inScheme code:producer .
+
+<code/producer/whys> a skos:Concept, code:Producer;
+  skos:topConceptOf code:producer ;
+  skos:prefLabel "whys" ;
+  skos:inScheme code:producer .
+
+<code/pricerange/low> a skos:Concept, code:Pricerange;
+  skos:topConceptOf code:pricerange ;
+  skos:prefLabel "low" ;
+  skos:inScheme code:pricerange .
+
+<code/pricerange/medium> a skos:Concept, code:Pricerange;
+  skos:topConceptOf code:pricerange ;
+  skos:prefLabel "medium" ;
+  skos:inScheme code:pricerange .
+
+<code/pricerange/nonexistant> a skos:Concept, code:Pricerange;
+  skos:topConceptOf code:pricerange ;
+  skos:prefLabel "nonexistant" ;
+  skos:inScheme code:pricerange .
+
+ns:obshormel a qb:Observation ;
+  qb:dataSet ns:dataset-bacon ;
+  rdfs:label "hormel" ;
+  prop:producer <code/producer/hormel> ;
+  prop:pricerange <code/pricerange/low> ;
+  prop:chunkiness 1 ;
+  prop:deliciousness 1 ;
+  .
+
+ns:obsnewskies a qb:Observation ;
+  qb:dataSet ns:dataset-bacon ;
+  rdfs:label "newskies" ;
+  prop:producer <code/producer/newskies> ;
+  prop:pricerange <code/pricerange/medium> ;
+  prop:chunkiness 6 ;
+  prop:deliciousness 9 ;
+  .
+
+ns:obswhys a qb:Observation ;
+  qb:dataSet ns:dataset-bacon ;
+  rdfs:label "whys" ;
+  prop:producer <code/producer/whys> ;
+  prop:pricerange <code/pricerange/nonexistant> ;
+  prop:chunkiness 9001 ;
+  prop:deliciousness 6 ;
+  .
+