bio-publisci 0.0.1

data/spec/data_cube_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/generators/csv.rb'
+
+require_relative '../lib/bio-publisci.rb'
+
+
+describe R2RDF::Dataset::DataCube do
+
+	context "with Plain Old Ruby objects" do
+		#define a temporary class to use module methods
+		before(:all) do
+			class Gen
+				include R2RDF::Dataset::DataCube
+			end
+
+			@generator = Gen.new
+			@measures = ['chunkiness','deliciousness']
+			@dimensions = ['producer', 'pricerange']
+			@codes = @dimensions #all dimensions coded for the tests
+			@labels = %w(hormel newskies whys)
+			@data = 
+			{
+				"producer" =>      ["hormel","newskies",  "whys"],
+				"pricerange" =>    ["low",   "medium",    "nonexistant"],
+				"chunkiness"=>     [1,         6,          9001],
+				"deliciousness"=>  [1,         9,          6]  
+			}
+		end
+
+		it "should have correct output according to the reference file" do
+			
+			turtle_string = @generator.generate(@measures, @dimensions, @codes,	@data, @labels, 'bacon')
+			ref = IO.read(File.dirname(__FILE__) + '/turtle/bacon')
+			turtle_string.should == ref
+		end
+
+		context "with missing values" do
+
+			before(:all) do
+				@missing_data = Marshal.load(Marshal.dump(@data))
+				missingobs = {
+					"producer" =>      "missingbacon",
+					"pricerange" =>    "unknown",
+					"chunkiness"=>     nil,
+					"deliciousness"=>  nil,  
+				}
+				missingobs.map{|k,v| @missing_data[k] << v}
+			end
+
+			it "skips observations with missing values by default" do				
+				turtle_string = @generator.generate(@measures, @dimensions, @codes,	@missing_data, @labels + ["missingbacon"], 'bacon')
+				turtle_string[/.*obsmissingbacon.*\n/].should be nil
+			end
+
+			it "includes observations with missing values if flag is set" do
+				turtle_string = @generator.generate(@measures, @dimensions, @codes,	@missing_data, @labels + ["missingbacon"], 'bacon',{encode_nulls: true})
+				turtle_string[/.*obsmissingbacon.*\n/].should_not be nil
+			end
+
+		end
+
+		it 'generates prefixes' do
+				prefixes = @generator.prefixes('bacon')
+				prefixes.is_a?(String).should == true
+			end
+
+			it 'generates data structure definition' do
+				dsd = @generator.data_structure_definition(@measures | @dimensions, "bacon")
+				dsd.is_a?(String).should == true
+			end
+
+			it 'generates dataset' do
+				dsd = @generator.dataset("bacon")
+				dsd.is_a?(String).should == true
+			end
+
+			it 'generates component specifications' do
+				components = @generator.component_specifications(@measures , @dimensions, "bacon")
+				components.is_a?(Array).should == true
+				components.first.is_a?(String).should == true
+			end
+
+			it 'generates dimension properties' do
+				dimensions = @generator.dimension_properties(@dimensions,@codes,"bacon")
+				dimensions.is_a?(Array).should == true
+				dimensions.first.is_a?(String).should == true
+			end
+
+			it 'generates measure properties' do
+				measures = @generator.measure_properties(@measures, "bacon")
+				measures.is_a?(Array).should == true
+				measures.first.is_a?(String).should == true
+			end
+
+			it 'generates observations' do
+				#measures, dimensions, codes, var, observation_labels, data, options={}
+				
+				observations = @generator.observations(@measures, @dimensions, @codes, @data, @labels, "bacon")
+				observations.is_a?(Array).should == true
+				observations.first.is_a?(String).should == true
+			end
+	end
+	
+  context "under official integrity constraints" do
+  	before(:all) do
+  		@graph = RDF::Graph.load(File.dirname(__FILE__) + '/turtle/reference', :format => :ttl)  		
+			@checks = {}
+			Dir.foreach(File.dirname(__FILE__) + '/queries/integrity') do |file|
+				if file.split('.').last == 'rq'
+					@checks[file.split('.').first] = IO.read(File.dirname(__FILE__) + '/queries/integrity/' + file)
+				end
+			end
+  	end
+
+  	it 'obeys IC-1, has a unique dataset for each observation' do
+  		SPARQL.execute(@checks['1'], @graph).first.should be_nil
+  	end
+
+  	it 'obeys IC-2, has a unique data structure definition of each dataset' do
+  		SPARQL.execute(@checks['2'], @graph).first.should be_nil
+  	end
+
+  	it 'obeys IC-3, has a measure property specified for each dataset' do
+  		SPARQL.execute(@checks['3'], @graph).first.should be_nil
+  	end
+
+  	it 'obeys IC-4, specifies a range for all dimensions' do
+  		SPARQL.execute(@checks['4'], @graph).first.should be_nil
+  	end
+
+  	it 'obeys IC-5, every dimension with range skos:Concept must have a qb:codeList' do
+  		SPARQL.execute(@checks['5'], @graph).first.should be_nil
+  	end
+
+  	it 'obeys IC-11, has a value for each dimension in every observation' do
+  		SPARQL.execute(@checks['11'], @graph).first.should be_nil
+  	end
+
+  	## currently locks up. possible bug in SPARQL gem parsing?
+  	## works fine as a raw query
+  	# it 'obeys IC-12, has do duplicate observations' do
+  	# 	SPARQL.execute(@checks['12'], @graph).first.should be_nil
+  	# end
+
+  	it 'obeys IC-14, has a value for each measure in every observation' do
+  		SPARQL.execute(@checks['14'], @graph).first.should be_nil
+  	end
+
+  	it 'obeys IC-19, all codes for each codeList are included' do
+  		SPARQL.execute(@checks['19_1'], @graph).first.should be_nil
+  		## second query for IC-19 uses property paths that aren't as easy to
+  		## convert to sparql 1.0, so for now I've left it out
+  		# SPARQL.execute(@checks['19_2'], @graph).first.should be_nil
+  	end
+  end
+		
+
+		it "can set dimensions vs measures via hash" do
+
+		end
+
+
+end

data/spec/generators/csv_spec.rb

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+# require_relative '../../lib/r2rdf/data_cube.rb'
+# require_relative '../../lib/r2rdf/generators/csv.rb'
+require_relative '../../lib/bio-publisci.rb'
+
+# require 'rdf/turtle'
+require 'tempfile'
+
+describe R2RDF::Reader::CSV do
+	
+	def create_graph(turtle_string)
+		f = Tempfile.new('graph')
+		f.write(turtle_string)
+		f.close
+		graph = RDF::Graph.load(f.path, :format => :ttl)
+		f.unlink
+		graph
+	end
+
+	before(:each) do 
+		@generator = R2RDF::Reader::CSV.new
+	end
+
+	context 'with reference CSV' do
+		it "should generate correct output for reference file" do
+			turtle_string = @generator.generate_n3(File.dirname(__FILE__) + '/../csv/bacon.csv','bacon',{dimensions:["producer","pricerange"], label_column:0})
+			ref = IO.read(File.dirname(__FILE__) + '/../turtle/bacon')
+			turtle_string.should == ref
+		end
+	end
+
+	it "selects first column as a coded dimension and creates measures from the rest by default" do
+		turtle_string = @generator.generate_n3(File.dirname(__FILE__) + '/../csv/bacon.csv','bacon')
+		graph = create_graph(turtle_string)
+		qb = RDF::Vocabulary.new("http://purl.org/linked-data/cube#")
+
+		dims = RDF::Query.execute(graph){ pattern [:dataset, qb.dimension, :dimension] }
+		dims.size.should == 1
+		dims.first[:dimension].to_s.should == "http://www.rqtl.org/dc/properties/producer"
+
+		measures = RDF::Query.execute(graph){ pattern [:dataset, qb.measure, :measure] }
+		measures.map{|s| s[:measure].to_s.split('/').last}.should == ["pricerange", "chunkiness", "deliciousness"]
+	end
+
+end

data/spec/generators/dataframe_spec.rb

@@ -0,0 +1,44 @@
+require_relative '../../lib/bio-publisci.rb'
+
+describe R2RDF::Reader::Dataframe do
+	
+	def create_graph(turtle_string)
+		f = Tempfile.new('graph')
+		f.write(turtle_string)
+		f.close
+		graph = RDF::Graph.load(f.path, :format => :ttl)
+		f.unlink
+		graph
+	end
+
+  context "with r/qtl dataframe" do
+		before(:all) do 
+			@r = Rserve::Connection.new
+			@generator = R2RDF::Reader::Dataframe.new
+			@r.eval <<-EOF
+				library(qtl)
+				data(listeria)
+				mr = scanone(listeria,method="mr")
+EOF
+			@rexp = @r.eval 'mr'
+			@turtle = @generator.generate_n3(@rexp,'mr')
+		end
+
+		it "generates rdf from R dataframe" do
+			turtle = @generator.generate_n3(@rexp,'mr')
+			turtle.is_a?(String).should be true
+		end
+		
+		it "creates correct graph according to refrence file" do
+			reference = IO.read(File.dirname(__FILE__) + '/../turtle/reference')
+			@turtle.should eq reference
+		end
+
+		it "can optionally specify a row label" do
+			@turtle = @generator.generate_n3(@rexp,'mr',{row_label:"markers"})
+		end
+	end
+
+		
+
+end

data/spec/generators/r_matrix_spec.rb

@@ -0,0 +1,35 @@
+# require_relative '../../lib/r2rdf/data_cube.rb'
+# require_relative '../../lib/r2rdf/generators/r_matrix.rb'
+# require 'rdf/turtle'
+# require 'rserve'
+require_relative '../../lib/bio-publisci.rb'
+
+require 'tempfile'
+
+describe R2RDF::Reader::RMatrix do
+	
+	def create_graph(turtle_string)
+		f = Tempfile.new('graph')
+		f.write(turtle_string)
+		f.close
+		graph = RDF::Graph.load(f.path, :format => :ttl)
+		f.unlink
+		graph
+	end
+
+	before(:each) do 
+		@generator = R2RDF::Reader::RMatrix.new
+		@connection = Rserve::Connection.new 
+	end
+
+	it "generators a simple output automatically" do
+		f=Tempfile.new('matrix')
+		@connection.eval "mat = matrix(c(2, 4, 3, 1, 5, 7), nrow=3, ncol=2)" 
+		@generator.generate_n3(@connection,'mat',f.path,{quiet: true})
+
+		turtle_string = IO.read("#{f.path}_structure.ttl") + IO.read("#{f.path}_0.ttl")
+		graph = create_graph(turtle_string) 
+		graph.size.should > 0
+	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

@@ -0,0 +1,37 @@
+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

@@ -0,0 +1,25 @@
+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

@@ -0,0 +1,21 @@
+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

@@ -0,0 +1,15 @@
+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

@@ -0,0 +1,22 @@
+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

@@ -0,0 +1,19 @@
+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

@@ -0,0 +1,13 @@
+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

@@ -0,0 +1,14 @@
+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

@@ -0,0 +1,33 @@
+# 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 R2RDF::Writer::Dataframe do
+
+	context "when using r/qtl dataframe" 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
+		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/spec_helper.rb

@@ -0,0 +1,17 @@
+# 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