bio-publisci 0.0.2 → 0.0.3

data/spec/generators/dataframe_spec.rb

@@ -11,7 +11,7 @@ describe R2RDF::Reader::Dataframe do
 		graph
 	end
 
-  context "with r/qtl dataframe" do
+  context "with r/qtl dataframe", no_travis: true do
 		before(:all) do 
 			@r = Rserve::Connection.new
 			@generator = R2RDF::Reader::Dataframe.new

data/spec/generators/r_matrix_spec.rb

@@ -22,7 +22,7 @@ describe R2RDF::Reader::RMatrix do
 		@connection = Rserve::Connection.new 
 	end
 
-	it "generators a simple output automatically" do
+	it "generators a simple output automatically", no_travis: true 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})

data/spec/r_builder_spec.rb

@@ -9,7 +9,7 @@ require_relative '../lib/bio-publisci.rb'
 
 describe R2RDF::Writer::Dataframe do
 
-	context "when using r/qtl dataframe" do
+	context "when using r/qtl dataframe", no_travis: true do
 
 		before(:all) do 
 			@r = Rserve::Connection.new
@@ -21,13 +21,13 @@ EOF
 			@builder = R2RDF::Writer::Builder.new
 		end
 
-		it "produces equivalent dataframe from rdf" do
+		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
+			# @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

@@ -0,0 +1,3 @@
+library(qtl)
+data(listeria)
+mr = scanone(listeria,method='mr')

data/spec/turtle/bacon

@@ -8,7 +8,6 @@
 @prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
 @prefix cs:    <http://www.rqtl.org/dc/dataset/bacon/cs/> .
 @prefix code:  <http://www.rqtl.org/dc/dataset/bacon/code/> .
-@prefix class: <http://www.rqtl.org/dc/dataset/bacon/class/> .
 @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/> .
@@ -16,32 +15,15 @@
 @prefix prov:     <http://www.w3.org/ns/prov#> .
 
 ns:dsd-bacon a qb:DataStructureDefinition;
-  qb:component
-    cs:chunkiness ,
-    cs:deliciousness ,
-    cs:producer ,
-    cs:pricerange .
+  qb:component [ qb:dimension prop:producer ] ;
+  qb:component [ qb:dimension prop:pricerange ] ;
+  qb:component [ qb:measure prop:chunkiness ] ;
+  qb:component [ qb:measure prop:deliciousness ] .
 
 ns:dataset-bacon a qb:DataSet ;
   rdfs:label "bacon"@en ;
   qb:structure ns:dsd-bacon .
 
-cs:producer a qb:ComponentSpecification ;
-  rdfs:label "producer Component" ;
-  qb:dimension prop:producer .
-
-cs:pricerange a qb:ComponentSpecification ;
-  rdfs:label "pricerange Component" ;
-  qb:dimension prop:pricerange .
-
-cs:chunkiness a qb:ComponentSpecification ;
-  rdfs:label "chunkiness Component" ;
-  qb:measure prop:chunkiness .
-
-cs:deliciousness a qb:ComponentSpecification ;
-  rdfs:label "deliciousness Component" ;
-  qb:measure prop:deliciousness .
-
 prop:producer a rdf:Property, qb:DimensionProperty ;
   rdfs:label "producer"@en ;
   qb:codeList code:producer ;

data/spec/turtle/reference

@@ -8,7 +8,6 @@
 @prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
 @prefix cs:    <http://www.rqtl.org/dc/dataset/mr/cs/> .
 @prefix code:  <http://www.rqtl.org/dc/dataset/mr/code/> .
-@prefix class: <http://www.rqtl.org/dc/dataset/mr/class/> .
 @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/> .
@@ -16,32 +15,15 @@
 @prefix prov:     <http://www.w3.org/ns/prov#> .
 
 ns:dsd-mr a qb:DataStructureDefinition;
-  qb:component
-    cs:chr ,
-    cs:pos ,
-    cs:lod ,
-    cs:refRow .
+  qb:component [ qb:dimension prop:refRow ] ;
+  qb:component [ qb:measure prop:chr ] ;
+  qb:component [ qb:measure prop:pos ] ;
+  qb:component [ qb:measure prop:lod ] .
 
 ns:dataset-mr a qb:DataSet ;
   rdfs:label "mr"@en ;
   qb:structure ns:dsd-mr .
 
-cs:refRow a qb:ComponentSpecification ;
-  rdfs:label "refRow Component" ;
-  qb:dimension prop:refRow .
-
-cs:chr a qb:ComponentSpecification ;
-  rdfs:label "chr Component" ;
-  qb:measure prop:chr .
-
-cs:pos a qb:ComponentSpecification ;
-  rdfs:label "pos Component" ;
-  qb:measure prop:pos .
-
-cs:lod a qb:ComponentSpecification ;
-  rdfs:label "lod Component" ;
-  qb:measure prop:lod .
-
 prop:refRow a rdf:Property, qb:DimensionProperty ;
   rdfs:label "refRow"@en ;
   qb:codeList code:refrow ;
@@ -58,15 +40,15 @@ prop:lod a rdf:Property, qb:MeasureProperty ;
 
 code:Refrow a rdfs:Class, owl:Class;
   rdfs:subClassOf skos:Concept ;
-  rdfs:label "Code list for refRow - codelist class"@en;
-  rdfs:comment "Specifies the refRow for each observation";
+  rdfs:label "Code list for refrow - codelist class"@en;
+  rdfs:comment "Specifies the refrow for each observation";
   rdfs:seeAlso code:refrow .
 
 code:refrow a skos:ConceptScheme;
-  skos:prefLabel "Code list for refRow - codelist scheme"@en;
-  rdfs:label "Code list for refRow - codelist scheme"@en;
+  skos:prefLabel "Code list for refrow - codelist scheme"@en;
+  rdfs:label "Code list for refrow - codelist scheme"@en;
   skos:notation "CL_REFROW";
-  skos:note "Specifies the refRow for each observation";
+  skos:note "Specifies the refrow for each observation";
   skos:hasTopConcept <code/refrow/D10M44> ;
   skos:hasTopConcept <code/refrow/D1M3> ;
   skos:hasTopConcept <code/refrow/D1M75> ;

metadata

@@ -1,100 +1,88 @@
 --- !ruby/object:Gem::Specification
 name: bio-publisci
 version: !ruby/object:Gem::Version
-  version: 0.0.2
-  prerelease: 
+  version: 0.0.3
 platform: ruby
 authors:
 - wstrinz
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-07-20 00:00:00.000000000 Z
+date: 2013-07-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdf
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rdf-4store
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rdf-turtle
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rserve-client
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: sparql
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -102,7 +90,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -110,7 +97,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -118,7 +104,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -126,23 +111,20 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: cucumber
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -150,7 +132,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -158,39 +139,34 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.0.21
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.0.21
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.2
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -198,13 +174,12 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: '3.12'
-description: ! 'A toolkit for publishing scientific results and datasets using RDF
-  and related technologies '
+description: 'A toolkit for publishing scientific results and datasets using RDF and
+  related technologies '
 email: wstrinz@gmail.com
 executables:
 - bio-publisci
@@ -226,6 +201,8 @@ files:
 - features/create_generator.feature
 - features/integration.feature
 - features/integration_steps.rb
+- features/metadata.feature
+- features/metadata_steps.rb
 - features/orm.feature
 - features/orm_steps.rb
 - features/reader.feature
@@ -241,8 +218,8 @@ files:
 - lib/bio-publisci/dataset/ORM/data_cube_orm.rb
 - lib/bio-publisci/dataset/ORM/observation.rb
 - lib/bio-publisci/dataset/data_cube.rb
+- lib/bio-publisci/dataset/dataset_for.rb
 - lib/bio-publisci/dataset/interactive.rb
-- lib/bio-publisci/loader.rb
 - lib/bio-publisci/metadata/metadata.rb
 - lib/bio-publisci/parser.rb
 - lib/bio-publisci/query/query_helper.rb
@@ -278,16 +255,22 @@ files:
 - lib/vocabs/wot.rb
 - lib/vocabs/xhtml.rb
 - lib/vocabs/xsd.rb
+- resources/queries/code_resources.rq
 - resources/queries/codes.rq
 - resources/queries/dataset.rq
 - resources/queries/dimension_ranges.rq
 - resources/queries/dimensions.rq
 - resources/queries/measures.rq
+- resources/queries/observation_labels.rq
 - resources/queries/observations.rq
+- resources/queries/properties.rq
 - resources/queries/test.rq
 - resources/weather.numeric.arff
+- scripts/islet_mlratio.rb
+- scripts/scan_islet.rb
+- scripts/update_reference.rb
+- spec/ORM/data_cube_orm_spec.rb
 - spec/analyzer_spec.rb
-- spec/bio-publisci_spec.rb
 - spec/csv/bacon.csv
 - spec/csv/moar_bacon.csv
 - spec/data_cube_spec.rb
@@ -305,35 +288,33 @@ files:
 - spec/queries/integrity/4.rq
 - spec/queries/integrity/5.rq
 - spec/r_builder_spec.rb
+- spec/resource/.RData
+- spec/resource/example.Rhistory
 - spec/spec_helper.rb
 - spec/turtle/bacon
 - spec/turtle/reference
 homepage: http://github.com/wstrinz/bioruby-publisci
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: -1178175655966297191
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.25
+rubygems_version: 2.0.3
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Publish science data using semantic web ontologies
 test_files: []

data/lib/bio-publisci/loader.rb

@@ -1,36 +0,0 @@
-# This is temporary, just to help w/ development so I don't have to rewrite r2rdf.rb to be
-# a standard gem base yet. Also load s the files instead of require for easy reloading
-require 'tempfile'
-require 'rdf'
-require 'csv'
-require 'rserve'
-require 'sparql'
-require 'sparql/client'
-require 'rdf/turtle'
-
-def load_folder(folder)
-	Dir.foreach(File.dirname(__FILE__) + "/#{folder}") do |file|
-		unless file == "." or file == ".."
-			load File.dirname(__FILE__) + "/#{folder}/" + file
-		end
-	end
-end
-
-load File.dirname(__FILE__) + '/dataset/interactive.rb'
-load File.dirname(__FILE__) + '/query/query_helper.rb'
-load File.dirname(__FILE__) + '/parser.rb'
-load File.dirname(__FILE__) + '/r_client.rb'
-load File.dirname(__FILE__) + '/analyzer.rb'
-load File.dirname(__FILE__) + '/store.rb'
-load File.dirname(__FILE__) + '/dataset/data_cube.rb'
-
-
-load_folder('metadata')
-load_folder('readers')
-load_folder('writers')
-load_folder('dataset/ORM')
-# Dir.foreach(File.dirname(__FILE__) + '/generators') do |file|
-# 	unless file == "." or file == ".."
-# 		load File.dirname(__FILE__) + '/generators/' + file
-# 	end
-# end

data/spec/bio-publisci_spec.rb

@@ -1,7 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
-
-describe "BioPublisci" do
-  it "fails" do
-    fail "hey buddy, you should probably rename this file and start specing for real"
-  end
-end