bio-publisci 0.0.6 → 0.0.7
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/Gemfile +1 -0
- data/Rakefile +1 -1
- data/examples/prov_dsl.prov +2 -1
- data/examples/safe_gen.rb +7 -0
- data/examples/visualization/primer.prov +66 -0
- data/examples/visualization/prov_viz.rb +140 -0
- data/examples/visualization/viz.rb +35 -0
- data/features/metadata_steps.rb +2 -4
- data/features/orm_steps.rb +4 -4
- data/features/reader_steps.rb +1 -1
- data/features/store_steps.rb +1 -1
- data/features/writer.feature +1 -1
- data/features/writer_steps.rb +1 -1
- data/lib/bio-publisci.rb +10 -2
- data/lib/bio-publisci/analyzer.rb +4 -4
- data/lib/bio-publisci/{spira.rb → datacube_model.rb} +4 -5
- data/lib/bio-publisci/dataset/ORM/data_cube_orm.rb +12 -12
- data/lib/bio-publisci/dataset/ORM/observation.rb +1 -1
- data/lib/bio-publisci/dataset/configuration.rb +31 -0
- data/lib/bio-publisci/dataset/data_cube.rb +28 -17
- data/lib/bio-publisci/dataset/dataset.rb +11 -0
- data/lib/bio-publisci/dataset/dataset_for.rb +19 -9
- data/lib/bio-publisci/dataset/interactive.rb +1 -1
- data/lib/bio-publisci/dsl/config.rb +34 -0
- data/lib/bio-publisci/dsl/dataset_dsl.rb +91 -0
- data/lib/bio-publisci/dsl/dsl.rb +69 -0
- data/lib/bio-publisci/dsl/metadata_dsl.rb +85 -0
- data/lib/bio-publisci/{metadata/prov/dsl.rb → dsl/prov_dsl.rb} +30 -6
- data/lib/bio-publisci/metadata/generator.rb +323 -0
- data/lib/bio-publisci/metadata/metadata.rb +3 -314
- data/lib/bio-publisci/metadata/prov/activity.rb +3 -1
- data/lib/bio-publisci/metadata/prov/agent.rb +1 -1
- data/lib/bio-publisci/metadata/prov/association.rb +2 -2
- data/lib/bio-publisci/metadata/prov/config.rb +34 -0
- data/lib/bio-publisci/metadata/prov/derivation.rb +7 -2
- data/lib/bio-publisci/metadata/prov/element.rb +2 -2
- data/lib/bio-publisci/metadata/prov/entity.rb +1 -22
- data/lib/bio-publisci/metadata/prov/model/prov_models.rb +8 -9
- data/lib/bio-publisci/metadata/prov/plan.rb +1 -1
- data/lib/bio-publisci/metadata/prov/prov.rb +23 -21
- data/lib/bio-publisci/metadata/prov/role.rb +1 -1
- data/lib/bio-publisci/metadata/prov/usage.rb +1 -1
- data/lib/bio-publisci/metadata/publisher.rb +25 -0
- data/lib/bio-publisci/mixins/dereferencable.rb +1 -1
- data/lib/bio-publisci/mixins/registry.rb +27 -0
- data/lib/bio-publisci/output.rb +1 -1
- data/lib/bio-publisci/parser.rb +1 -1
- data/lib/bio-publisci/query/query_helper.rb +14 -14
- data/lib/bio-publisci/r_client.rb +5 -5
- data/lib/bio-publisci/readers/arff.rb +5 -5
- data/lib/bio-publisci/readers/csv.rb +3 -3
- data/lib/bio-publisci/readers/dataframe.rb +3 -3
- data/lib/bio-publisci/readers/r_cross.rb +4 -4
- data/lib/bio-publisci/readers/r_matrix.rb +3 -3
- data/lib/bio-publisci/store.rb +3 -3
- data/lib/bio-publisci/writers/arff.rb +6 -6
- data/lib/bio-publisci/writers/dataframe.rb +5 -5
- data/scripts/islet_mlratio.rb +1 -1
- data/scripts/scan_islet.rb +1 -1
- data/scripts/update_reference.rb +2 -2
- data/spec/ORM/data_cube_orm_spec.rb +2 -2
- data/spec/ORM/prov_model_spec.rb +19 -0
- data/spec/analyzer_spec.rb +7 -7
- data/spec/data_cube_spec.rb +13 -13
- data/spec/dataset_for_spec.rb +11 -4
- data/spec/dsl_spec.rb +90 -0
- data/spec/generators/csv_spec.rb +4 -4
- data/spec/generators/dataframe_spec.rb +6 -6
- data/spec/generators/r_cross_spec.rb +2 -2
- data/spec/generators/r_matrix_spec.rb +2 -2
- data/spec/metadata/metadata_dsl_spec.rb +68 -0
- data/spec/prov/activity_spec.rb +4 -4
- data/spec/prov/agent_spec.rb +3 -4
- data/spec/prov/association_spec.rb +1 -2
- data/spec/prov/config_spec.rb +28 -0
- data/spec/prov/derivation_spec.rb +30 -0
- data/spec/prov/entity_spec.rb +3 -4
- data/spec/prov/role_spec.rb +1 -2
- data/spec/prov/usage_spec.rb +1 -2
- data/spec/r_builder_spec.rb +3 -3
- data/spec/turtle/bacon +20 -4
- data/spec/turtle/reference +20 -4
- metadata +37 -4
@@ -1,4 +1,4 @@
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module
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module PubliSci
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module Writer
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module Dataframe
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@@ -39,7 +39,7 @@ module R2RDF
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end
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class Builder
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include
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include PubliSci::Writer::Dataframe
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def from_turtle(turtle_file, connection, variable_in=nil, variable_out=nil, verbose=true, save=true)
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@@ -51,7 +51,7 @@ module R2RDF
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repo = RDF::Repository.load(turtle_file)
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puts "loaded #{repo.size} statements into temporary repo" if verbose
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# connection = Rserve::Connection.new
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query =
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query = PubliSci::QueryHelper.new
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rows = get_rownames(variable_in, query, repo)
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puts "frame has #{rows.size} rows" if verbose
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@@ -69,8 +69,8 @@ module R2RDF
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end
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puts "connecting to endpoint at #{endpoint_url}" if verbose
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sparql = SPARQL::Client.new(endpoint_url)
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# client =
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query =
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# client = PubliSci::Client.new
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query = PubliSci::QueryHelper.new
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rows = query.get_ary(sparql.query(query.row_names(variable_in))).flatten
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data/scripts/islet_mlratio.rb
CHANGED
@@ -1,6 +1,6 @@
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load File.dirname(__FILE__) + '/../lib/bio-publisci.rb'
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gen =
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gen = PubliSci::Reader::RMatrix.new
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con = Rserve::Connection.new
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con.eval("load('#{ARGV[0] || './.RData'}')")
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gen.generate_n3(con, "islet.mlratio", "pheno", {measures: ["probe","individual","pheno"], no_labels: true})
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data/scripts/scan_islet.rb
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@@ -1,6 +1,6 @@
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load File.dirname(__FILE__) + '/../lib/bio-publisci.rb'
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gen =
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gen = PubliSci::Reader::RMatrix.new
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con = Rserve::Connection.new
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con.eval("load('#{ARGV[0] || './.RData'}')")
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gen.generate_n3(con, "scan.islet", "scan", {measures: ["probe","marker","lod"], no_labels: true})
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data/scripts/update_reference.rb
CHANGED
@@ -4,12 +4,12 @@ exit unless gets.chomp == 'y'
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puts "overwriting #{File.absolute_path(File.dirname(__FILE__) + '/../spec/turtle/bacon')}"
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load File.dirname(__FILE__) + '/../lib/bio-publisci.rb'
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gen =
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gen = PubliSci::Reader::CSV.new
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turtle_string = gen.generate_n3(File.dirname(__FILE__) + '/../spec/csv/bacon.csv','bacon',{dimensions:["producer","pricerange"], label_column:0})
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open(File.dirname(__FILE__) + '/../spec/turtle/bacon', 'w'){|f| f.write turtle_string}
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rcon = Rserve::Connection.new
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gen =
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gen = PubliSci::Reader::Dataframe.new
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rcon.void_eval <<-EOF
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library(qtl)
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data(listeria)
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require_relative '../../lib/bio-publisci.rb'
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describe
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describe PubliSci::ORM::DataCube do
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it "should load and save a turtle file without loss of information" do
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ref = IO.read(File.dirname(__FILE__) + '/../turtle/bacon')
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cube =
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cube = PubliSci::ORM::DataCube.load(ref, {skip_metadata: true, generator_options: {label_column: 0}})
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cube.abbreviate_known(cube.to_n3).should == ref
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# cube.to_n3.should == ref
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end
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@@ -0,0 +1,19 @@
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require_relative '../../lib/bio-publisci.rb'
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include PubliSci::Prov::DSL
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# include PubliSci::Prov
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describe PubliSci::Prov::Model do
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it "can be loaded from" do
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ev = PubliSci::Prov::DSL::Instance.new
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r = ev.instance_eval do
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entity :datathing
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activity :process, generated: :datathing
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to_repository
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end
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Spira.add_repository :default, r
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PubliSci::Prov::Model::Entity.first.should_not be nil
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end
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end
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data/spec/analyzer_spec.rb
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require_relative '../lib/bio-publisci.rb'
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describe
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class Ana
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include
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describe PubliSci::Analyzer do
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class Ana
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include PubliSci::Analyzer
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end
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before(:all) do
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@analyzer = Ana.new
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@measures = ['chunkiness','deliciousness']
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@dimensions = ['producer', 'pricerange']
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@labels = %w(hormel newskies whys)
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@data =
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@data =
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{
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"producer" => ["hormel","newskies", "whys"],
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"pricerange" => ["low", "medium", "nonexistant"],
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"chunkiness"=> [1, 6, 9001],
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"deliciousness"=> [1, 9, 6]
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"deliciousness"=> [1, 9, 6]
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}
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end
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it "should run a basic validation" do
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newdata = []
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data/spec/data_cube_spec.rb
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require_relative '../lib/bio-publisci.rb'
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describe
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describe PubliSci::Dataset::DataCube do
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context "with Plain Old Ruby objects" do
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#define a temporary class to use module methods
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before(:all) do
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class Gen
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include
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include PubliSci::Dataset::DataCube
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end
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@generator = Gen.new
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@dimensions = ['producer', 'pricerange']
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@codes = @dimensions #all dimensions coded for the tests
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@labels = %w(hormel newskies whys)
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@data =
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@data =
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{
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"producer" => ["hormel","newskies", "whys"],
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"pricerange" => ["low", "medium", "nonexistant"],
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"chunkiness"=> [1, 6, 9001],
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"deliciousness"=> [1, 9, 6]
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"deliciousness"=> [1, 9, 6]
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}
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end
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it "should have correct output according to the reference file" do
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turtle_string = @generator.generate(@measures, @dimensions, @codes, @data, @labels, 'bacon')
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ref = IO.read(File.dirname(__FILE__) + '/turtle/bacon')
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turtle_string.should == ref
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end
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context "with missing values" do
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"producer" => "missingbacon",
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"pricerange" => "unknown",
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"chunkiness"=> nil,
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"deliciousness"=> nil,
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"deliciousness"=> nil,
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}
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missingobs.map{|k,v| @missing_data[k] << v}
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end
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it "skips observations with missing values by default" do
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it "skips observations with missing values by default" do
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turtle_string = @generator.generate(@measures, @dimensions, @codes, @missing_data, @labels + ["missingbacon"], 'bacon')
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turtle_string[/.*obsmissingbacon.*\n/].should be nil
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end
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end
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it 'generates component specifications' do
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components = @generator.component_specifications(@measures , @dimensions, "bacon")
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components = @generator.component_specifications(@measures , @dimensions, @codes, "bacon")
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components.is_a?(Array).should == true
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components.first.is_a?(String).should == true
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end
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it 'generates observations' do
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#measures, dimensions, codes, var, observation_labels, data, options={}
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observations = @generator.observations(@measures, @dimensions, @codes, @data, @labels, "bacon")
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observations.is_a?(Array).should == true
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observations.first.is_a?(String).should == true
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end
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end
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context "under official integrity constraints" do
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before(:all) do
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@graph = RDF::Graph.load(File.dirname(__FILE__) + '/turtle/reference', :format => :ttl)
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@graph = RDF::Graph.load(File.dirname(__FILE__) + '/turtle/reference', :format => :ttl)
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@checks = {}
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Dir.foreach(File.dirname(__FILE__) + '/queries/integrity') do |file|
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if file.split('.').last == 'rq'
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# SPARQL.execute(@checks['19_2'], @graph).first.should be_nil
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end
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end
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it "can set dimensions vs measures via hash" do
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data/spec/dataset_for_spec.rb
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require_relative '../lib/bio-publisci.rb'
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describe
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describe PubliSci::Dataset do
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context 'with a csv file' do
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before(:all) do
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@file = File.dirname(__FILE__) + '/csv/bacon.csv'
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end
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it "should load with no prompts if all details are specified" do
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turtle_string =
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turtle_string = PubliSci::Dataset.for(@file,{dimensions:["producer"],measures:["pricerange"]},false)
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(turtle_string =~ /qb:Observation/).should_not be nil
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end
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it "will request user input if not provided" do
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gen =
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gen = PubliSci::Reader::CSV.new
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gen.stub(:gets).and_return('pricerange,producer')
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gen.stub(:puts)
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turtle_string = gen.automatic(@file,nil,{measures:["chunkiness"]})
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end
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it "will try to guess if told not to be interactive" do
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turtle_string =
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turtle_string = PubliSci::Dataset.for(@file,false)
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(turtle_string =~ /prop:pricerange/).should_not be nil
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(turtle_string =~ /prop:producer/).should_not be nil
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end
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it "will attempt to load remote file if given URI" do
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loc = 'https://raw.github.com/wstrinz/bioruby-publisci/master/spec/csv/bacon.csv'
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turtle_string = PubliSci::Dataset.for(loc,false)
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(turtle_string =~ /prop:pricerange/).should_not be nil
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(turtle_string =~ /prop:producer/).should_not be nil
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end
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data/spec/dsl_spec.rb
ADDED
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require_relative '../lib/bio-publisci.rb'
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describe PubliSci::DSL do
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include PubliSci::DSL
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before(:each) do
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PubliSci::Prov.registry.clear
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PubliSci::Metadata.registry.clear
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PubliSci::Dataset.registry.clear
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end
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it "can generate dataset, metadata, and provenance when given a script" do
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dat = data do
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|
+
object 'spec/csv/bacon.csv'
|
16
|
+
end
|
17
|
+
met = metadata do
|
18
|
+
name "Will"
|
19
|
+
end
|
20
|
+
prv = provenance do
|
21
|
+
entity :a_thing
|
22
|
+
end
|
23
|
+
|
24
|
+
met.should_not be nil
|
25
|
+
prv.should_not be nil
|
26
|
+
dat.should_not be nil
|
27
|
+
|
28
|
+
generate_n3.size.should > 0
|
29
|
+
end
|
30
|
+
|
31
|
+
it "can generate dataset, metadata, and provenance when given a script" do
|
32
|
+
dat = data do
|
33
|
+
object 'https://raw.github.com/wstrinz/bioruby-publisci/master/spec/csv/bacon.csv'
|
34
|
+
end
|
35
|
+
dat.should_not be nil
|
36
|
+
generate_n3.size.should > 0
|
37
|
+
end
|
38
|
+
|
39
|
+
it "can set generator options" do
|
40
|
+
dat = data do
|
41
|
+
object 'spec/csv/bacon.csv'
|
42
|
+
option :no_labels, true
|
43
|
+
end
|
44
|
+
|
45
|
+
str = generate_n3
|
46
|
+
str[/rdfs:label "\d"/].should == nil
|
47
|
+
end
|
48
|
+
|
49
|
+
it "can output to in-memory repository" do
|
50
|
+
dat = data do
|
51
|
+
object 'spec/csv/bacon.csv'
|
52
|
+
end
|
53
|
+
|
54
|
+
repo = to_repository
|
55
|
+
repo.is_a?(RDF::Repository).should be true
|
56
|
+
repo.size.should > 0
|
57
|
+
end
|
58
|
+
|
59
|
+
it "can output to 4store repository", no_travis: true do
|
60
|
+
configure do |cfg|
|
61
|
+
cfg.repository = :fourstore
|
62
|
+
end
|
63
|
+
|
64
|
+
dat = data do
|
65
|
+
object 'spec/csv/bacon.csv'
|
66
|
+
end
|
67
|
+
|
68
|
+
repo = RDF::FourStore::Repository.new('http://localhost:8080/')
|
69
|
+
old_size = repo.size
|
70
|
+
repo = to_repository
|
71
|
+
repo.is_a?(RDF::FourStore::Repository).should be true
|
72
|
+
repo.size.should > old_size
|
73
|
+
end
|
74
|
+
|
75
|
+
it "can output provenance to 4store", no_travis: true do
|
76
|
+
ev = PubliSci::Prov::DSL::Instance.new
|
77
|
+
str = IO.read('examples/primer-full.prov')
|
78
|
+
ev.instance_eval(str,'examples/primer-full.prov')
|
79
|
+
ev.instance_eval <<-EOF
|
80
|
+
configure do |cfg|
|
81
|
+
cfg.repository = :fourstore
|
82
|
+
end
|
83
|
+
EOF
|
84
|
+
repo = RDF::FourStore::Repository.new('http://localhost:8080/')
|
85
|
+
old_size = repo.size
|
86
|
+
repo = ev.to_repository
|
87
|
+
repo.is_a?(RDF::FourStore::Repository).should be true
|
88
|
+
repo.size.should > old_size
|
89
|
+
end
|
90
|
+
end
|
data/spec/generators/csv_spec.rb
CHANGED
@@ -5,8 +5,8 @@ require_relative '../../lib/bio-publisci.rb'
|
|
5
5
|
# require 'rdf/turtle'
|
6
6
|
require 'tempfile'
|
7
7
|
|
8
|
-
describe
|
9
|
-
|
8
|
+
describe PubliSci::Reader::CSV do
|
9
|
+
|
10
10
|
def create_graph(turtle_string)
|
11
11
|
f = Tempfile.new('graph')
|
12
12
|
f.write(turtle_string)
|
@@ -16,8 +16,8 @@ describe R2RDF::Reader::CSV do
|
|
16
16
|
graph
|
17
17
|
end
|
18
18
|
|
19
|
-
before(:each) do
|
20
|
-
@generator =
|
19
|
+
before(:each) do
|
20
|
+
@generator = PubliSci::Reader::CSV.new
|
21
21
|
end
|
22
22
|
|
23
23
|
context 'with reference CSV' do
|
@@ -1,7 +1,7 @@
|
|
1
1
|
require_relative '../../lib/bio-publisci.rb'
|
2
2
|
|
3
|
-
describe
|
4
|
-
|
3
|
+
describe PubliSci::Reader::Dataframe do
|
4
|
+
|
5
5
|
def create_graph(turtle_string)
|
6
6
|
f = Tempfile.new('graph')
|
7
7
|
f.write(turtle_string)
|
@@ -12,9 +12,9 @@ describe R2RDF::Reader::Dataframe do
|
|
12
12
|
end
|
13
13
|
|
14
14
|
context "with r/qtl dataframe", no_travis: true do
|
15
|
-
before(:all) do
|
15
|
+
before(:all) do
|
16
16
|
@r = Rserve::Connection.new
|
17
|
-
@generator =
|
17
|
+
@generator = PubliSci::Reader::Dataframe.new
|
18
18
|
@r.eval <<-EOF
|
19
19
|
library(qtl)
|
20
20
|
data(listeria)
|
@@ -28,7 +28,7 @@ EOF
|
|
28
28
|
turtle = @generator.generate_n3(@rexp,'mr')
|
29
29
|
turtle.is_a?(String).should be true
|
30
30
|
end
|
31
|
-
|
31
|
+
|
32
32
|
it "creates correct graph according to refrence file" do
|
33
33
|
reference = IO.read(File.dirname(__FILE__) + '/../turtle/reference')
|
34
34
|
@turtle.should eq reference
|
@@ -39,6 +39,6 @@ EOF
|
|
39
39
|
end
|
40
40
|
end
|
41
41
|
|
42
|
-
|
42
|
+
|
43
43
|
|
44
44
|
end
|
@@ -2,7 +2,7 @@ require_relative '../../lib/bio-publisci.rb'
|
|
2
2
|
|
3
3
|
require 'tempfile'
|
4
4
|
|
5
|
-
describe
|
5
|
+
describe PubliSci::Reader::RCross do
|
6
6
|
|
7
7
|
def create_graph(turtle_string)
|
8
8
|
f = Tempfile.new('graph')
|
@@ -16,7 +16,7 @@ describe R2RDF::Reader::RCross do
|
|
16
16
|
context "with reduced listeria cross", no_travis: true do
|
17
17
|
before(:all) do
|
18
18
|
@r = Rserve::Connection.new
|
19
|
-
@generator =
|
19
|
+
@generator = PubliSci::Reader::RCross.new
|
20
20
|
@r.eval <<-EOF
|
21
21
|
library(qtl)
|
22
22
|
data(listeria)
|
@@ -6,7 +6,7 @@ require_relative '../../lib/bio-publisci.rb'
|
|
6
6
|
|
7
7
|
require 'tempfile'
|
8
8
|
|
9
|
-
describe
|
9
|
+
describe PubliSci::Reader::RMatrix do
|
10
10
|
|
11
11
|
def create_graph(turtle_string)
|
12
12
|
f = Tempfile.new('graph')
|
@@ -18,7 +18,7 @@ describe R2RDF::Reader::RMatrix do
|
|
18
18
|
end
|
19
19
|
|
20
20
|
before(:each) do
|
21
|
-
@generator =
|
21
|
+
@generator = PubliSci::Reader::RMatrix.new
|
22
22
|
@connection = Rserve::Connection.new
|
23
23
|
end
|
24
24
|
|