bio-publisci 0.0.6 → 0.0.7

data/lib/bio-publisci/writers/dataframe.rb

@@ -1,4 +1,4 @@
-module R2RDF
+module PubliSci
   module Writer
     module Dataframe
 
@@ -39,7 +39,7 @@ module R2RDF
   end
 
   class Builder
-    include R2RDF::Writer::Dataframe
+    include PubliSci::Writer::Dataframe
 
 
     def from_turtle(turtle_file, connection, variable_in=nil, variable_out=nil, verbose=true, save=true)
@@ -51,7 +51,7 @@ module R2RDF
       repo = RDF::Repository.load(turtle_file)
       puts "loaded #{repo.size} statements into temporary repo" if verbose
       # connection = Rserve::Connection.new
-      query = R2RDF::QueryHelper.new
+      query = PubliSci::QueryHelper.new
       rows = get_rownames(variable_in, query, repo)
       puts "frame has #{rows.size} rows" if verbose
 
@@ -69,8 +69,8 @@ module R2RDF
       end
       puts "connecting to endpoint at #{endpoint_url}" if verbose
       sparql = SPARQL::Client.new(endpoint_url)
-      # client = R2RDF::Client.new
-      query = R2RDF::QueryHelper.new
+      # client = PubliSci::Client.new
+      query = PubliSci::QueryHelper.new
 
       rows = query.get_ary(sparql.query(query.row_names(variable_in))).flatten
 

data/scripts/islet_mlratio.rb

@@ -1,6 +1,6 @@
 load File.dirname(__FILE__) + '/../lib/bio-publisci.rb'
 
-gen = R2RDF::Reader::RMatrix.new
+gen = PubliSci::Reader::RMatrix.new
 con = Rserve::Connection.new
 con.eval("load('#{ARGV[0] || './.RData'}')")
 gen.generate_n3(con, "islet.mlratio", "pheno", {measures: ["probe","individual","pheno"], no_labels: true})

data/scripts/scan_islet.rb

@@ -1,6 +1,6 @@
 load File.dirname(__FILE__) + '/../lib/bio-publisci.rb'
 
-gen = R2RDF::Reader::RMatrix.new
+gen = PubliSci::Reader::RMatrix.new
 con = Rserve::Connection.new
 con.eval("load('#{ARGV[0] || './.RData'}')")
 gen.generate_n3(con, "scan.islet", "scan", {measures: ["probe","marker","lod"], no_labels: true})

data/scripts/update_reference.rb

@@ -4,12 +4,12 @@ exit unless gets.chomp == 'y'
 puts "overwriting #{File.absolute_path(File.dirname(__FILE__) + '/../spec/turtle/bacon')}"
 load File.dirname(__FILE__) + '/../lib/bio-publisci.rb'
 
-gen = R2RDF::Reader::CSV.new
+gen = PubliSci::Reader::CSV.new
 turtle_string = gen.generate_n3(File.dirname(__FILE__) + '/../spec/csv/bacon.csv','bacon',{dimensions:["producer","pricerange"], label_column:0})
 open(File.dirname(__FILE__) + '/../spec/turtle/bacon', 'w'){|f| f.write turtle_string}
 
 rcon = Rserve::Connection.new
-gen = R2RDF::Reader::Dataframe.new
+gen = PubliSci::Reader::Dataframe.new
 rcon.void_eval <<-EOF
 library(qtl)
 data(listeria)

data/spec/ORM/data_cube_orm_spec.rb

@@ -1,10 +1,10 @@
 require_relative '../../lib/bio-publisci.rb'
 
-describe R2RDF::ORM::DataCube do
+describe PubliSci::ORM::DataCube do
 
   it "should load and save a turtle file without loss of information" do
     ref = IO.read(File.dirname(__FILE__) + '/../turtle/bacon')
-    cube = R2RDF::ORM::DataCube.load(ref, {skip_metadata: true, generator_options: {label_column: 0}})
+    cube = PubliSci::ORM::DataCube.load(ref, {skip_metadata: true, generator_options: {label_column: 0}})
     cube.abbreviate_known(cube.to_n3).should == ref
     # cube.to_n3.should == ref
   end

data/spec/ORM/prov_model_spec.rb

@@ -0,0 +1,19 @@
+require_relative '../../lib/bio-publisci.rb'
+include PubliSci::Prov::DSL
+# include PubliSci::Prov
+
+describe PubliSci::Prov::Model do
+  it "can be loaded from" do
+    ev = PubliSci::Prov::DSL::Instance.new
+    r = ev.instance_eval do
+      entity :datathing
+
+      activity :process, generated: :datathing
+
+      to_repository
+    end
+
+    Spira.add_repository :default, r
+    PubliSci::Prov::Model::Entity.first.should_not be nil
+  end
+end

data/spec/analyzer_spec.rb

@@ -1,25 +1,25 @@
 require_relative '../lib/bio-publisci.rb'
 
-describe R2RDF::Analyzer do
-	class Ana 
-		include R2RDF::Analyzer
+describe PubliSci::Analyzer do
+	class Ana
+		include PubliSci::Analyzer
 	end
 
 	before(:all) do
 		@analyzer = Ana.new
-		
+
 		@measures = ['chunkiness','deliciousness']
 		@dimensions = ['producer', 'pricerange']
 		@labels = %w(hormel newskies whys)
-		@data = 
+		@data =
 		{
 			"producer" =>      ["hormel","newskies",  "whys"],
 			"pricerange" =>    ["low",   "medium",    "nonexistant"],
 			"chunkiness"=>     [1,         6,          9001],
-			"deliciousness"=>  [1,         9,          6]  
+			"deliciousness"=>  [1,         9,          6]
 		}
 	end
-	
+
 	it "should run a basic validation" do
 		newdata = []
 

data/spec/data_cube_spec.rb

@@ -7,13 +7,13 @@
 require_relative '../lib/bio-publisci.rb'
 
 
-describe R2RDF::Dataset::DataCube do
+describe PubliSci::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
+				include PubliSci::Dataset::DataCube
 			end
 
 			@generator = Gen.new
@@ -21,20 +21,20 @@ describe R2RDF::Dataset::DataCube do
 			@dimensions = ['producer', 'pricerange']
 			@codes = @dimensions #all dimensions coded for the tests
 			@labels = %w(hormel newskies whys)
-			@data = 
+			@data =
 			{
 				"producer" =>      ["hormel","newskies",  "whys"],
 				"pricerange" =>    ["low",   "medium",    "nonexistant"],
 				"chunkiness"=>     [1,         6,          9001],
-				"deliciousness"=>  [1,         9,          6]  
+				"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
+      turtle_string.should == ref
 		end
 
 		context "with missing values" do
@@ -45,12 +45,12 @@ describe R2RDF::Dataset::DataCube do
 					"producer" =>      "missingbacon",
 					"pricerange" =>    "unknown",
 					"chunkiness"=>     nil,
-					"deliciousness"=>  nil,  
+					"deliciousness"=>  nil,
 				}
 				missingobs.map{|k,v| @missing_data[k] << v}
 			end
 
-			it "skips observations with missing values by default" 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
@@ -78,7 +78,7 @@ describe R2RDF::Dataset::DataCube do
 			end
 
 			it 'generates component specifications' do
-				components = @generator.component_specifications(@measures , @dimensions, "bacon")
+				components = @generator.component_specifications(@measures , @dimensions, @codes, "bacon")
 				components.is_a?(Array).should == true
 				components.first.is_a?(String).should == true
 			end
@@ -97,16 +97,16 @@ describe R2RDF::Dataset::DataCube do
 
 			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)  		
+  		@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'
@@ -156,7 +156,7 @@ describe R2RDF::Dataset::DataCube do
   		# SPARQL.execute(@checks['19_2'], @graph).first.should be_nil
   	end
   end
-		
+
 
 		it "can set dimensions vs measures via hash" do
 

data/spec/dataset_for_spec.rb

@@ -1,18 +1,18 @@
 require_relative '../lib/bio-publisci.rb'
 
-describe R2RDF::Dataset do
+describe PubliSci::Dataset do
   context 'with a csv file' do
     before(:all) do
       @file = File.dirname(__FILE__) + '/csv/bacon.csv'
     end
 
     it "should load with no prompts if all details are specified" do
-      turtle_string = R2RDF::Dataset.for(@file,{dimensions:["producer"],measures:["pricerange"]},false)
+      turtle_string = PubliSci::Dataset.for(@file,{dimensions:["producer"],measures:["pricerange"]},false)
       (turtle_string =~ /qb:Observation/).should_not be nil
     end
 
     it "will request user input if not provided" do
-      gen = R2RDF::Reader::CSV.new
+      gen = PubliSci::Reader::CSV.new
       gen.stub(:gets).and_return('pricerange,producer')
       gen.stub(:puts)
       turtle_string = gen.automatic(@file,nil,{measures:["chunkiness"]})
@@ -21,7 +21,14 @@ describe R2RDF::Dataset do
     end
 
     it "will try to guess if told not to be interactive" do
-      turtle_string = R2RDF::Dataset.for(@file,false)
+      turtle_string = PubliSci::Dataset.for(@file,false)
+      (turtle_string =~ /prop:pricerange/).should_not be nil
+      (turtle_string =~ /prop:producer/).should_not be nil
+    end
+
+    it "will attempt to load remote file if given URI" do
+      loc = 'https://raw.github.com/wstrinz/bioruby-publisci/master/spec/csv/bacon.csv'
+      turtle_string = PubliSci::Dataset.for(loc,false)
       (turtle_string =~ /prop:pricerange/).should_not be nil
       (turtle_string =~ /prop:producer/).should_not be nil
     end

data/spec/dsl_spec.rb

@@ -0,0 +1,90 @@
+require_relative '../lib/bio-publisci.rb'
+
+describe PubliSci::DSL do
+  include PubliSci::DSL
+
+  before(:each) do
+    PubliSci::Prov.registry.clear
+    PubliSci::Metadata.registry.clear
+    PubliSci::Dataset.registry.clear
+  end
+
+  it "can generate dataset, metadata, and provenance when given a script" do
+
+    dat = data do
+      object 'spec/csv/bacon.csv'
+    end
+    met = metadata do
+      name "Will"
+    end
+    prv = provenance do
+      entity :a_thing
+    end
+
+    met.should_not be nil
+    prv.should_not be nil
+    dat.should_not be nil
+
+    generate_n3.size.should > 0
+  end
+
+  it "can generate dataset, metadata, and provenance when given a script" do
+    dat = data do
+      object 'https://raw.github.com/wstrinz/bioruby-publisci/master/spec/csv/bacon.csv'
+    end
+    dat.should_not be nil
+    generate_n3.size.should > 0
+  end
+
+  it "can set generator options" do
+    dat = data do
+      object 'spec/csv/bacon.csv'
+      option :no_labels, true
+    end
+
+    str = generate_n3
+    str[/rdfs:label "\d"/].should == nil
+  end
+
+  it "can output to in-memory repository" do
+    dat = data do
+      object 'spec/csv/bacon.csv'
+    end
+
+    repo = to_repository
+    repo.is_a?(RDF::Repository).should be true
+    repo.size.should > 0
+  end
+
+  it "can output to 4store repository", no_travis: true do
+    configure do |cfg|
+      cfg.repository = :fourstore
+    end
+
+    dat = data do
+      object 'spec/csv/bacon.csv'
+    end
+
+    repo = RDF::FourStore::Repository.new('http://localhost:8080/')
+    old_size = repo.size
+    repo = to_repository
+    repo.is_a?(RDF::FourStore::Repository).should be true
+    repo.size.should > old_size
+  end
+
+  it "can output provenance to 4store", no_travis: true do
+    ev = PubliSci::Prov::DSL::Instance.new
+    str = IO.read('examples/primer-full.prov')
+    ev.instance_eval(str,'examples/primer-full.prov')
+    ev.instance_eval <<-EOF
+      configure do |cfg|
+        cfg.repository = :fourstore
+      end
+    EOF
+    repo = RDF::FourStore::Repository.new('http://localhost:8080/')
+    old_size = repo.size
+    repo = ev.to_repository
+    repo.is_a?(RDF::FourStore::Repository).should be true
+    repo.size.should > old_size
+  end
+end

data/spec/generators/csv_spec.rb

@@ -5,8 +5,8 @@ require_relative '../../lib/bio-publisci.rb'
 # require 'rdf/turtle'
 require 'tempfile'
 
-describe R2RDF::Reader::CSV do
-	
+describe PubliSci::Reader::CSV do
+
 	def create_graph(turtle_string)
 		f = Tempfile.new('graph')
 		f.write(turtle_string)
@@ -16,8 +16,8 @@ describe R2RDF::Reader::CSV do
 		graph
 	end
 
-	before(:each) do 
-		@generator = R2RDF::Reader::CSV.new
+	before(:each) do
+		@generator = PubliSci::Reader::CSV.new
 	end
 
 	context 'with reference CSV' do

data/spec/generators/dataframe_spec.rb

@@ -1,7 +1,7 @@
 require_relative '../../lib/bio-publisci.rb'
 
-describe R2RDF::Reader::Dataframe do
-	
+describe PubliSci::Reader::Dataframe do
+
 	def create_graph(turtle_string)
 		f = Tempfile.new('graph')
 		f.write(turtle_string)
@@ -12,9 +12,9 @@ describe R2RDF::Reader::Dataframe do
 	end
 
   context "with r/qtl dataframe", no_travis: true do
-		before(:all) do 
+		before(:all) do
 			@r = Rserve::Connection.new
-			@generator = R2RDF::Reader::Dataframe.new
+			@generator = PubliSci::Reader::Dataframe.new
 			@r.eval <<-EOF
 				library(qtl)
 				data(listeria)
@@ -28,7 +28,7 @@ EOF
 			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
@@ -39,6 +39,6 @@ EOF
 		end
 	end
 
-		
+
 
 end

data/spec/generators/r_cross_spec.rb

@@ -2,7 +2,7 @@ require_relative '../../lib/bio-publisci.rb'
 
 require 'tempfile'
 
-describe R2RDF::Reader::RCross do
+describe PubliSci::Reader::RCross do
 
   def create_graph(turtle_string)
     f = Tempfile.new('graph')
@@ -16,7 +16,7 @@ describe R2RDF::Reader::RCross do
   context "with reduced listeria cross", no_travis: true do
     before(:all) do
       @r = Rserve::Connection.new
-      @generator = R2RDF::Reader::RCross.new
+      @generator = PubliSci::Reader::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 R2RDF::Reader::RMatrix do
+describe PubliSci::Reader::RMatrix do
 
 	def create_graph(turtle_string)
 		f = Tempfile.new('graph')
@@ -18,7 +18,7 @@ describe R2RDF::Reader::RMatrix do
 	end
 
 	before(:each) do
-		@generator = R2RDF::Reader::RMatrix.new
+		@generator = PubliSci::Reader::RMatrix.new
 		@connection = Rserve::Connection.new
 	end