bio-publisci 0.0.8 → 0.1.0

data/spec/data_cube_spec.rb

@@ -52,12 +52,14 @@ describe PubliSci::Dataset::DataCube do
 
 			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
+        turtle_string[/.*obsmissingbacon.*\n/].should_not be nil
+        turtle_string[/\S+obsmissingbacon.*prop:chunkiness.*\n\n/m].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
+  			turtle_string[/\S+obsmissingbacon.*prop:chunkiness.*\n\n/m].should_not be nil
 			end
 
 		end
@@ -102,65 +104,66 @@ describe PubliSci::Dataset::DataCube do
 				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
+      it "coerces single values into arrays" do
+        newdata = Hash[@data.map{|k,v| [k,v.first] }]
+        observations = @generator.observations(@measures, @dimensions, @codes, newdata, @labels[0], "bacon")
+        observations.is_a?(Array).should == true
+        observations.first.is_a?(String).should == true
+      end
   end
 
 
-		it "can set dimensions vs measures via hash" do
-
-		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
 end

data/spec/dataset_for_spec.rb

@@ -1,6 +1,40 @@
 require_relative '../lib/bio-publisci.rb'
 
 describe PubliSci::Dataset do
+  it "should use sio:has_value for unknown string types" do
+    pending("pending refactor dataset_for to handle raw remote files better")
+    turtle_string = PubliSci::Dataset.for('http://www.biostat.wisc.edu/~kbroman/D3/cistrans/data/probe_data/probe497638.json',false)
+    (turtle_string =~ /hasValue/).should_not be nil
+    # open('ttl.ttl','w'){|f| f.write turtle_string}
+    repo = RDF::Repository.new
+
+    f = Tempfile.new(['repo','.ttl'])
+    f.write(turtle_string)
+    f.close
+    repo.load(f.path, :format => :ttl)
+    f.unlink
+
+    repo.size.should > 0
+  end
+
+  it "can convert arff files" do
+    turtle_string = PubliSci::Dataset.for('resources/weather.numeric.arff',false)
+    turtle_string.should == IO.read('spec/turtle/weather')
+  end
+
+  describe ".register_reader" do
+    it "can register readers to be used by Dataset.for" do
+      PubliSci::Dataset.reader_registry.clear
+      expect { PubliSci::Dataset.for('resources/maf_example.maf') }.to raise_error
+      PubliSci::Dataset.register_reader('.maf',PubliSci::Readers::MAF)
+      file = PubliSci::Dataset.for('resources/maf_example.maf')
+      str = IO.read(file)
+      File.delete(file.path)
+      str.size.should > 0
+      (str =~ /qb:Observation/).should_not be nil
+    end
+  end
+
   context 'with a csv file' do
     before(:all) do
       @file = File.dirname(__FILE__) + '/csv/bacon.csv'
@@ -11,21 +45,6 @@ describe PubliSci::Dataset do
       (turtle_string =~ /qb:Observation/).should_not be nil
     end
 
-    it "should use sio:has_value for unknown string types" do
-      turtle_string = PubliSci::Dataset.for('http://www.biostat.wisc.edu/~kbroman/D3/cistrans/data/probe_data/probe497638.json',false)
-      (turtle_string =~ /hasValue/).should_not be nil
-      # open('ttl.ttl','w'){|f| f.write turtle_string}
-      repo = RDF::Repository.new
-
-      f = Tempfile.new(['repo','.ttl'])
-      f.write(turtle_string)
-      f.close
-      repo.load(f.path, :format => :ttl)
-      f.unlink
-
-      repo.size.should > 0
-    end
-
     it "will download remote files" do
       turtle_string = PubliSci::Dataset.for('https://raw.github.com/wstrinz/bioruby-publisci/master/spec/csv/bacon.csv',false)
       (turtle_string =~ /prop:pricerange/).should_not be nil
@@ -33,7 +52,7 @@ describe PubliSci::Dataset do
     end
 
     it "will request user input if not provided" do
-      gen = PubliSci::Reader::CSV.new
+      gen = PubliSci::Readers::CSV.new
       gen.stub(:gets).and_return('pricerange,producer')
       gen.stub(:puts)
       turtle_string = gen.automatic(@file,nil,{measures:["chunkiness"]})
@@ -54,4 +73,5 @@ describe PubliSci::Dataset do
       (turtle_string =~ /prop:producer/).should_not be nil
     end
   end
+
 end

data/spec/dsl_spec.rb

@@ -9,6 +9,45 @@ describe PubliSci::DSL do
     PubliSci::Dataset.registry.clear
   end
 
+  context "maf files" do
+    describe "set options" do
+      before { PubliSci::Dataset.register_reader('.maf',PubliSci::Readers::MAF) }
+      it "can change output type" do
+
+        dat = data do
+          object 'resources/maf_example.maf'
+          option :output, :print
+        end
+
+        str = generate_n3
+        str[/a qb:Observation/].should_not == nil
+      end
+
+      it "can output to repository" do
+        dat = data do
+          object 'resources/maf_example.maf'
+          option :output, :print
+        end
+
+        repo = to_repository
+        repo.is_a?(RDF::Repository).should be true
+        repo.size.should > 0
+
+        qry = <<-EOF
+        SELECT ?observation where {
+          ?observation a <http://purl.org/linked-data/cube#Observation>;
+            <http://onto.strinz.me/properties/Hugo_Symbol> ?node.
+
+        }
+
+        EOF
+
+        sparql = SPARQL::Client.new(repo)
+        sparql.query(qry).size.should > 0
+      end
+    end
+  end
+
   it "can generate dataset, metadata, and provenance when given a script" do
 
     dat = data do
@@ -49,6 +88,8 @@ describe PubliSci::DSL do
     str[/rdfs:label "\d"/].should == nil
   end
 
+
+
   it "can output to in-memory repository" do
     dat = data do
       object 'spec/csv/bacon.csv'

data/spec/generators/csv_spec.rb

@@ -5,7 +5,7 @@ require_relative '../../lib/bio-publisci.rb'
 # require 'rdf/turtle'
 require 'tempfile'
 
-describe PubliSci::Reader::CSV do
+describe PubliSci::Readers::CSV do
 
 	def create_graph(turtle_string)
 		f = Tempfile.new('graph')
@@ -17,7 +17,7 @@ describe PubliSci::Reader::CSV do
 	end
 
 	before(:each) do
-		@generator = PubliSci::Reader::CSV.new
+		@generator = PubliSci::Readers::CSV.new
 	end
 
 	context 'with reference CSV' do
@@ -35,7 +35,7 @@ describe PubliSci::Reader::CSV do
 
 		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"
+		dims.first[:dimension].to_s.should == "http://onto.strinz.me/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"]

data/spec/generators/dataframe_spec.rb

@@ -1,6 +1,6 @@
 require_relative '../../lib/bio-publisci.rb'
 
-describe PubliSci::Reader::Dataframe do
+describe PubliSci::Readers::Dataframe do
 
 	def create_graph(turtle_string)
 		f = Tempfile.new('graph')
@@ -14,7 +14,7 @@ describe PubliSci::Reader::Dataframe do
   context "with r/qtl dataframe", no_travis: true do
 		before(:all) do
 			@r = Rserve::Connection.new
-			@generator = PubliSci::Reader::Dataframe.new
+			@generator = PubliSci::Readers::Dataframe.new
 			@r.eval <<-EOF
 				library(qtl)
 				data(listeria)

data/spec/generators/maf_spec.rb

@@ -0,0 +1,40 @@
+# 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 PubliSci::Readers::MAF do
+  before(:each) do
+    @generator = PubliSci::Readers::MAF.new
+    @in_file = 'resources/maf_example.maf'
+  end
+
+  describe ".generate_n3" do
+    def is_cube(str)
+      str[/a qb:Observation/].should_not be nil
+      str[/a rdf:Property, qb:DimensionProperty/].should_not be nil
+      str[/a rdf:Property, qb:MeasureProperty/].should_not be nil
+      str[/a qb:ComponentSpecification/].should_not be nil
+    end
+
+    context "print output" do
+      before { @str = @generator.generate_n3(@in_file, {output: :print})}
+      it { is_cube(@str) }
+    end
+
+    context "file output" do
+      before {
+        f = Tempfile.new('graph')
+        f.close
+        @generator.generate_n3(@in_file,{output: :file, output_base: f.path})
+        @str = IO.read(f.path+'.ttl')
+        open('resources/maf_rdf.ttl','w'){|f| f.write @str}
+        f.unlink
+      }
+
+      it { is_cube(@str) }
+    end
+  end
+end

data/spec/generators/r_cross_spec.rb

@@ -2,7 +2,7 @@ require_relative '../../lib/bio-publisci.rb'
 
 require 'tempfile'
 
-describe PubliSci::Reader::RCross do
+describe PubliSci::Readers::RCross do
 
   def create_graph(turtle_string)
     f = Tempfile.new('graph')
@@ -16,7 +16,7 @@ describe PubliSci::Reader::RCross do
   context "with reduced listeria cross", no_travis: true do
     before(:all) do
       @r = Rserve::Connection.new
-      @generator = PubliSci::Reader::RCross.new
+      @generator = PubliSci::Readers::RCross.new
       @r.eval <<-EOF
         library(qtl)
         data(listeria)

data/spec/generators/r_matrix_spec.rb

@@ -6,7 +6,7 @@ require_relative '../../lib/bio-publisci.rb'
 
 require 'tempfile'
 
-describe PubliSci::Reader::RMatrix do
+describe PubliSci::Readers::RMatrix do
 
 	def create_graph(turtle_string)
 		f = Tempfile.new('graph')
@@ -18,7 +18,7 @@ describe PubliSci::Reader::RMatrix do
 	end
 
 	before(:each) do
-		@generator = PubliSci::Reader::RMatrix.new
+		@generator = PubliSci::Readers::RMatrix.new
 		@connection = Rserve::Connection.new
 	end
 

data/spec/maf_query_spec.rb

@@ -0,0 +1,343 @@
+require_relative '../lib/bio-publisci.rb'
+
+#sparql = SPARQL::Client.new("#{repo.uri}/sparql/").query(qry)
+
+class MafQuery
+  RESTRICTIONS = {
+    patient: '<http://onto.strinz.me/properties/patient_id>',
+    sample: '<http://onto.strinz.me/properties/sample_id>',
+    gene: '<http://onto.strinz.me/properties/Hugo_Symbol>',
+  }
+
+    def to_por(solution)
+      if solution.is_a?(Fixnum) or solution.is_a?(String) or solution.is_a?(Symbol)
+        solution
+      elsif solution.is_a? RDF::Query::Solutions
+        solution.map{|sol|
+          if sol.bindings.size == 1
+            to_por(sol.bindings.first.last)
+          else
+            Hash(solution.bindings.map{|bind,result| [bind,to_por(result)]})
+          end
+        }
+      elsif solution.is_a? RDF::Query::Solution
+        if solution.bindings.size == 1
+          to_por(solution.bindings.first.last)
+        else
+          solution.bindings.map{|bind,result| [bind,to_por(result)] }
+        end
+      elsif solution.is_a? Array
+        if solution.size == 1
+          to_por(solution.first)
+        else
+          solution.map{|sol| to_por(sol)}
+        end
+      else
+        if solution.is_a? RDF::Literal
+          solution.object
+        elsif solution.is_a? RDF::URI
+          solution.to_s
+        else
+          puts "don't recognzize #{solution.class}"
+          solution.to_s
+        end
+      end
+    end
+
+    def generate_data
+    	generator = PubliSci::Readers::MAF.new
+    	in_file = 'resources/maf_example.maf'
+    	f = Tempfile.new('graph')
+    	f.close
+    	generator.generate_n3(in_file, {output: :file, output_base: f.path})
+    	repo = RDF::Repository.load(f.path+'.ttl')
+      File.delete(f.path+'.ttl')
+    	f.unlink
+      repo
+    end
+
+    def select_patient_count(repo,patient_id="A8-A08G")
+      qry = IO.read('resources/queries/patient.rq')
+      qry = qry.gsub('%{patient}',patient_id)
+      SPARQL.execute(qry,repo).first[:barcodes]
+    end
+
+    def patients(repo)
+      qry = IO.read('resources/queries/patient_list.rq')
+      SPARQL.execute(qry,repo) #.map(&:id).map(&:to_s)
+    end
+
+    def select_patient_genes(repo,patient_id="A8-A08G")
+      qry = IO.read('resources/queries/gene.rq')
+      qry = qry.gsub('%{patient}',patient_id)
+      SPARQL.execute(qry,repo)
+    end
+
+    def select_property(repo,property=["Hugo_Symbol"],restrictions={})
+    	# qry = IO.read('resources/queries/maf_column.rq').gsub('%{patient}',patient_id).gsub('%{column}',property)
+      property = Array(property)
+      selects = property
+      property = property.map{|prop|
+        RESTRICTIONS[prop.to_sym] || "<http://onto.strinz.me/properties/#{prop}>"
+      }
+
+      targets = ""
+      property.each_with_index{|p,i|
+        targets << "\n  #{p} ?#{selects[i]} ;"
+      }
+
+      str = ""
+      restrictions.each{|restrict,value|
+        prop = RESTRICTIONS[restrict.to_sym] || "<http://onto.strinz.me/properties/#{restrict}>"
+        if value.is_a? String
+          if RDF::Resource(value).valid?
+            if(value[/http:\/\//])
+              value = RDF::Resource(value).to_base
+            end
+          else
+            value = '"' + value + '"'
+          end
+        end
+        str << "\n  #{prop} #{value} ;"
+      }
+
+
+      qry = <<-EOF
+      PREFIX qb:   <http://purl.org/linked-data/cube#>
+      PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+      PREFIX sio: <http://semanticscience.org/resource/>
+
+      SELECT DISTINCT ?#{selects.join(" ?")} WHERE {
+        ?obs a qb:Observation;
+        #{str}
+        #{targets}
+        .
+      }
+      EOF
+
+      results = SPARQL.execute(qry,repo)
+      # results = results.map{ |solution|
+      #   solution.bindings.map{ |bind,result| [bind, result]}
+
+      #         # .map(&:column).map{|val|
+      #   # if val.is_a?(RDF::URI) and val.to_s["node"]
+      #   #   node_value(repo,val)
+      #   # else
+      #   #   val
+      #   # end
+
+      # }.flatten
+
+      if results.size == 1
+        results.first
+      else
+        results
+      end
+    end
+
+    def node_value(repo,uri)
+      qry = "SELECT DISTINCT ?p ?o where { <#{uri.to_s}> ?p ?o}"
+      SPARQL.execute(qry,repo).map{|sol|
+        if sol[:p].to_s == "http://semanticscience.org/resource/SIO_000300"
+          sol[:o]
+        elsif sol[:p].to_s == "http://semanticscience.org/resource/SIO_000008"
+          qry = "SELECT DISTINCT ?p ?o where { <#{sol[:o].to_s}> ?p ?o}"
+          SPARQL.execute(qry,repo).select{|sol| sol[:p].to_s == "http://semanticscience.org/resource/SIO_000300"}.first[:o]
+        elsif sol[:p].to_s != "http://www.w3.org/1999/02/22-rdf-syntax-ns#type"
+          sol[:o]
+        end
+      }.reject{|sol| sol == nil}
+    end
+
+    def official_symbol(hugo_symbol)
+      qry = <<-EOF
+
+      SELECT distinct ?official where {
+       {?hgnc <http://bio2rdf.org/hgnc_vocabulary:approved_symbol> "#{hugo_symbol}"}
+       UNION
+       {?hgnc <http://bio2rdf.org/hgnc_vocabulary:synonym> "#{hugo_symbol}"}
+
+       ?hgnc <http://bio2rdf.org/hgnc_vocabulary:approved_symbol> ?official
+      }
+
+      EOF
+
+      sparql = SPARQL::Client.new("http://cu.hgnc.bio2rdf.org/sparql")
+      sparql.query(qry).map(&:official).first.to_s
+    end
+
+    def gene_length(hugo_symbol)
+      hugo_symbol = official_symbol(hugo_symbol.split('/').last)
+      qry = IO.read('resources/queries/hugo_to_ensembl.rq').gsub('%{hugo_symbol}',hugo_symbol)
+      sparql = SPARQL::Client.new("http://cu.hgnc.bio2rdf.org/sparql")
+      sol = sparql.query(qry)
+
+      if sol.size == 0
+        raise "No Ensembl entry found for #{hugo_symbol}"
+      else
+        ensemble_id = sol.map(&:ensembl).first.to_s.split(':').last
+      end
+
+      url = URI.parse('http://beta.rest.ensembl.org/')
+      http = Net::HTTP.new(url.host, url.port)
+      request = Net::HTTP::Get.new('/lookup/id/' + ensemble_id + '?format=full', {'Content-Type' => 'application/json'})
+      response = http.request(request)
+
+      if response.code != "200"
+        raise "Invalid response: #{response.code}"
+      else
+        js = JSON.parse(response.body)
+        js['end'] - js['start']
+      end
+    end
+
+    def derive_gene_lengths
+
+    end
+
+    def patient_info(id,repo)
+      symbols = Array(to_por(select_property(repo,"Hugo_Symbol",patient: id)))
+      # patient_id = select_property(repo,"patient_id",patient: id).to_s
+      patient = {patient_id: id, mutation_count: symbols.size, mutations:[]}
+
+      symbols.each{|sym| patient[:mutations] << {symbol: sym, length: gene_length(sym)}}
+      patient
+    end
+
+    def gene_info(hugo_symbol,repo)
+      qry = IO.read('resources/queries/patients_with_mutation.rq').gsub('%{hugo_symbol}',hugo_symbol)
+      sols = SPARQL.execute(qry,repo)
+      patient_count = sols.size
+      {mutations: patient_count, gene_length: gene_length(hugo_symbol), patients: sols.map(&:patient_id).map(&:to_s)}
+
+      # symbols = select_property(repo,"Hugo_Symbol",id).map(&:to_s)
+      # patient_id = select_property(repo,"patient_id",id).first.to_s
+      # patient = {patient_id: patient_id, mutation_count: symbols.size, mutations:[]}
+
+      # symbols.each{|sym| patient[:mutations] << {symbol: sym, length: gene_length(sym)}}
+      # patient
+    end
+end
+
+
+
+describe MafQuery do
+	before(:all) do
+    @maf = MafQuery.new
+		@repo = @maf.generate_data
+	end
+
+  describe "query genes" do
+    it { @maf.select_patient_genes(@repo,"BH-A0HP").size.should > 0 }
+  end
+
+  describe "query number of entries" do
+    it { @maf.select_patient_count(@repo,"BH-A0HP").should > 0 }
+  end
+
+
+  describe ".patients" do
+    it "retrieves a list of patients" do
+      @maf.to_por(@maf.patients(@repo)).first.should == "E9-A22B"
+    end
+  end
+
+  describe ".select_property" do
+  	it { @maf.to_por(@maf.select_property(@repo,"Hugo_Symbol", patient: "BH-A0HP")).should == "http://identifiers.org/hgnc.symbol/A1CF" }
+    it { @maf.select_property(@repo,"Entrez_Gene_Id",patient: "BH-A0HP")[:Entrez_Gene_Id].to_s.should == 'http://identifiers.org/ncbigene/29974' }
+    it { @maf.select_property(@repo,"Center",patient: "BH-A0HP")[:Center].to_s.should == "genome.wustl.edu" }
+    it { @maf.select_property(@repo,"NCBI_Build",patient: "BH-A0HP")[:NCBI_Build].to_i.should == 37 }
+
+    context "extra parsed properties" do
+      it { @maf.select_property(@repo,"sample_id",patient: "BH-A0HP")[:sample_id].should == "01A-12D-A099-09" }
+      it { @maf.select_property(@repo,"patient_id",patient: "BH-A0HP")[:patient_id].should ==  "BH-A0HP" }
+    end
+
+    context "multiple restrictions" do
+      it { @maf.select_property(@repo,"Entrez_Gene_Id",patient: "BH-A0HP", :Chromosome => 10)[:Entrez_Gene_Id].to_s.should == 'http://identifiers.org/ncbigene/29974' }
+      it { @maf.select_property(@repo,"Entrez_Gene_Id",patient: "BH-A0HP", :Chromosome => 2).should == [] }
+    end
+
+    context "multiple selections" do
+      it { @maf.select_property(@repo,['Hugo_Symbol', 'Entrez_Gene_Id'],patient: "BH-A0HP")[:Entrez_Gene_Id].to_s.should == 'http://identifiers.org/ncbigene/29974' }
+      it { @maf.select_property(@repo,['Hugo_Symbol', 'Entrez_Gene_Id'],patient: "BH-A0HP")[:Hugo_Symbol].to_s.should == 'http://identifiers.org/hgnc.symbol/A1CF' }
+
+    end
+
+  	context "non-existant properties" do
+  		it { @maf.select_property(@repo,"Chunkiness",patient: "BH-A0HP").should == [] }
+  	end
+  end
+
+  context "remote service calls", no_travis: true do
+    describe ".gene_length" do
+      it { @maf.gene_length('A2BP1').should == 1694245 }
+    end
+
+    # describe ".official_symbol" do
+    #   it { @maf.official_symbol('A2BP1').should == 'RBFOX1' }
+    # end
+
+    describe ".gene_info" do
+      it 'collects the number of mutations and gene lengths for each mutation' do
+        gene = @maf.gene_info('A1BG',@repo)
+        gene[:mutations].should == 2
+        gene[:gene_length].should == 8321
+        gene[:patients].first.should == "E9-A22B"
+      end
+    end
+
+    describe ".patient_info" do
+      it 'collects the number of patients with a mutation in a gene and its length' do
+        patient = @maf.patient_info('BH-A0HP',@repo)
+        patient[:mutation_count].should == 1
+        patient[:mutations].first[:length].should == 79113
+        patient[:mutations].first[:symbol].should == 'http://identifiers.org/hgnc.symbol/A1CF'
+      end
+    end
+  end
+end
+
+class QueryScript
+  def initialize(repo=nil)
+    @__maf = MafQuery.new
+    unless repo
+      @__repo = @__maf.generate_data
+    else
+      @__repo = repo
+    end
+  end
+
+  def select(operation,*args)
+    if @__maf.methods.include?(:"select_#{operation}")
+      @__maf.to_por(@__maf.send(:"select_#{operation}",@__repo,*args))
+    else
+      @__maf.to_por(@__maf.select_property(@__repo,operation,*args))
+    end
+  end
+
+  def gene_length(gene)
+    @__maf.to_por(@__maf.gene_length(gene))
+  end
+
+  def report_for(type, id)
+    @__maf.send(:"#{type}_info",id, @__repo)
+  end
+end
+
+describe QueryScript do
+  describe ".select" do
+    before(:all){
+      @ev = QueryScript.new
+    }
+
+    it { @ev.select('patient_count', "BH-A0HP").should > 0 }
+
+    context "with instance_eval" do
+      it { @ev.instance_eval("select 'patient_count', patient: 'BH-A0HP'").should > 0 }
+      it { @ev.instance_eval("select 'Hugo_Symbol', patient: 'BH-A0HP'").should == 'http://identifiers.org/hgnc.symbol/A1CF' }
+      it { @ev.instance_eval("select 'Chromosome', patient: 'BH-A0HP'").is_a?(Fixnum).should be true }
+      it { @ev.instance_eval("report_for 'patient', 'BH-A0HP'").is_a?(Hash).should be true }
+    end
+  end
+end