publisci 0.1.2

data/spec/turtle/weather

@@ -0,0 +1,275 @@
+@base <http://onto.strinz.me/dc/dataset/weather/> .
+@prefix ns:    <http://onto.strinz.me/dc/dataset/weather/> .
+@prefix qb:    <http://purl.org/linked-data/cube#> .
+@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix prop:  <http://onto.strinz.me/properties/> .
+@prefix dct:   <http://purl.org/dc/terms/> .
+@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
+@prefix cs:    <http://onto.strinz.me/dc/dataset/weather/cs/> .
+@prefix code:  <http://onto.strinz.me/dc/dataset/weather/code/> .
+@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/> .
+@prefix org:      <http://www.w3.org/ns/org#> .
+@prefix prov:     <http://www.w3.org/ns/prov#> .
+
+ns:dsd-weather a qb:DataStructureDefinition;
+  qb:component cs:outlook ;
+  qb:component cs:play ;
+  qb:component cs:windy ;
+  qb:component cs:humidity ;
+  qb:component cs:temperature .
+
+ns:dataset-weather a qb:DataSet ;
+  rdfs:label "weather"@en ;
+  qb:structure ns:dsd-weather .
+
+cs:outlook a qb:ComponentSpecification ;
+  rdfs:label "outlook" ;
+  qb:dimension prop:outlook .
+
+cs:play a qb:ComponentSpecification ;
+  rdfs:label "play" ;
+  qb:dimension prop:play .
+
+cs:windy a qb:ComponentSpecification ;
+  rdfs:label "windy" ;
+  qb:dimension prop:windy .
+
+cs:humidity a qb:ComponentSpecification ;
+  rdfs:label "humidity" ;
+  qb:measure prop:humidity .
+
+cs:temperature a qb:ComponentSpecification ;
+  rdfs:label "temperature" ;
+  qb:measure prop:temperature .
+
+prop:outlook a rdf:Property, qb:DimensionProperty ;
+  rdfs:label "outlook"@en ;
+  qb:codeList code:outlook ;
+  rdfs:range code:Outlook .
+
+prop:play a rdf:Property, qb:DimensionProperty ;
+  rdfs:label "play"@en ;
+  qb:codeList code:play ;
+  rdfs:range code:Play .
+
+prop:windy a rdf:Property, qb:DimensionProperty ;
+  rdfs:label "windy"@en ;
+  qb:codeList code:windy ;
+  rdfs:range code:Windy .
+
+prop:humidity a rdf:Property, qb:MeasureProperty ;
+  rdfs:label "humidity"@en .
+
+prop:temperature a rdf:Property, qb:MeasureProperty ;
+  rdfs:label "temperature"@en .
+
+code:Outlook a rdfs:Class, owl:Class;
+  rdfs:subClassOf skos:Concept ;
+  rdfs:label "Code list for outlook - codelist class"@en;
+  rdfs:comment "Specifies the outlook for each observation";
+  rdfs:seeAlso code:outlook .
+
+code:outlook a skos:ConceptScheme;
+  skos:prefLabel "Code list for outlook - codelist scheme"@en;
+  rdfs:label "Code list for outlook - codelist scheme"@en;
+  skos:notation "CL_OUTLOOK";
+  skos:note "Specifies the outlook for each observation";
+  skos:hasTopConcept <code/outlook/sunny> ;
+  skos:hasTopConcept <code/outlook/overcast> ;
+  skos:hasTopConcept <code/outlook/rainy> ;
+  .
+
+code:Play a rdfs:Class, owl:Class;
+  rdfs:subClassOf skos:Concept ;
+  rdfs:label "Code list for play - codelist class"@en;
+  rdfs:comment "Specifies the play for each observation";
+  rdfs:seeAlso code:play .
+
+code:play a skos:ConceptScheme;
+  skos:prefLabel "Code list for play - codelist scheme"@en;
+  rdfs:label "Code list for play - codelist scheme"@en;
+  skos:notation "CL_PLAY";
+  skos:note "Specifies the play for each observation";
+  skos:hasTopConcept <code/play/no> ;
+  skos:hasTopConcept <code/play/yes> ;
+  .
+
+code:Windy a rdfs:Class, owl:Class;
+  rdfs:subClassOf skos:Concept ;
+  rdfs:label "Code list for windy - codelist class"@en;
+  rdfs:comment "Specifies the windy for each observation";
+  rdfs:seeAlso code:windy .
+
+code:windy a skos:ConceptScheme;
+  skos:prefLabel "Code list for windy - codelist scheme"@en;
+  rdfs:label "Code list for windy - codelist scheme"@en;
+  skos:notation "CL_WINDY";
+  skos:note "Specifies the windy for each observation";
+  skos:hasTopConcept <code/windy/FALSE> ;
+  skos:hasTopConcept <code/windy/TRUE> ;
+  .
+
+<code/outlook/sunny> a skos:Concept, code:Outlook;
+  skos:topConceptOf code:outlook ;
+  skos:prefLabel "sunny" ;
+  skos:inScheme code:outlook .
+
+<code/outlook/overcast> a skos:Concept, code:Outlook;
+  skos:topConceptOf code:outlook ;
+  skos:prefLabel "overcast" ;
+  skos:inScheme code:outlook .
+
+<code/outlook/rainy> a skos:Concept, code:Outlook;
+  skos:topConceptOf code:outlook ;
+  skos:prefLabel "rainy" ;
+  skos:inScheme code:outlook .
+
+<code/play/no> a skos:Concept, code:Play;
+  skos:topConceptOf code:play ;
+  skos:prefLabel "no" ;
+  skos:inScheme code:play .
+
+<code/play/yes> a skos:Concept, code:Play;
+  skos:topConceptOf code:play ;
+  skos:prefLabel "yes" ;
+  skos:inScheme code:play .
+
+<code/windy/FALSE> a skos:Concept, code:Windy;
+  skos:topConceptOf code:windy ;
+  skos:prefLabel "FALSE" ;
+  skos:inScheme code:windy .
+
+<code/windy/TRUE> a skos:Concept, code:Windy;
+  skos:topConceptOf code:windy ;
+  skos:prefLabel "TRUE" ;
+  skos:inScheme code:windy .
+
+ns:obs1 a qb:Observation ;
+  qb:dataSet ns:dataset-weather ;
+  prop:outlook <code/outlook/sunny> ;
+  prop:play <code/play/no> ;
+  prop:windy <code/windy/FALSE> ;
+  prop:humidity 85 ;
+  prop:temperature 85 ;
+  .
+
+ns:obs2 a qb:Observation ;
+  qb:dataSet ns:dataset-weather ;
+  prop:outlook <code/outlook/sunny> ;
+  prop:play <code/play/no> ;
+  prop:windy <code/windy/TRUE> ;
+  prop:humidity 90 ;
+  prop:temperature 80 ;
+  .
+
+ns:obs3 a qb:Observation ;
+  qb:dataSet ns:dataset-weather ;
+  prop:outlook <code/outlook/overcast> ;
+  prop:play <code/play/yes> ;
+  prop:windy <code/windy/FALSE> ;
+  prop:humidity 86 ;
+  prop:temperature 83 ;
+  .
+
+ns:obs4 a qb:Observation ;
+  qb:dataSet ns:dataset-weather ;
+  prop:outlook <code/outlook/rainy> ;
+  prop:play <code/play/yes> ;
+  prop:windy <code/windy/FALSE> ;
+  prop:humidity 96 ;
+  prop:temperature 70 ;
+  .
+
+ns:obs5 a qb:Observation ;
+  qb:dataSet ns:dataset-weather ;
+  prop:outlook <code/outlook/rainy> ;
+  prop:play <code/play/yes> ;
+  prop:windy <code/windy/FALSE> ;
+  prop:humidity 80 ;
+  prop:temperature 68 ;
+  .
+
+ns:obs6 a qb:Observation ;
+  qb:dataSet ns:dataset-weather ;
+  prop:outlook <code/outlook/rainy> ;
+  prop:play <code/play/no> ;
+  prop:windy <code/windy/TRUE> ;
+  prop:humidity 70 ;
+  prop:temperature 65 ;
+  .
+
+ns:obs7 a qb:Observation ;
+  qb:dataSet ns:dataset-weather ;
+  prop:outlook <code/outlook/overcast> ;
+  prop:play <code/play/yes> ;
+  prop:windy <code/windy/TRUE> ;
+  prop:humidity 65 ;
+  prop:temperature 64 ;
+  .
+
+ns:obs8 a qb:Observation ;
+  qb:dataSet ns:dataset-weather ;
+  prop:outlook <code/outlook/sunny> ;
+  prop:play <code/play/no> ;
+  prop:windy <code/windy/FALSE> ;
+  prop:humidity 95 ;
+  prop:temperature 72 ;
+  .
+
+ns:obs9 a qb:Observation ;
+  qb:dataSet ns:dataset-weather ;
+  prop:outlook <code/outlook/sunny> ;
+  prop:play <code/play/yes> ;
+  prop:windy <code/windy/FALSE> ;
+  prop:humidity 70 ;
+  prop:temperature 69 ;
+  .
+
+ns:obs10 a qb:Observation ;
+  qb:dataSet ns:dataset-weather ;
+  prop:outlook <code/outlook/rainy> ;
+  prop:play <code/play/yes> ;
+  prop:windy <code/windy/FALSE> ;
+  prop:humidity 80 ;
+  prop:temperature 75 ;
+  .
+
+ns:obs11 a qb:Observation ;
+  qb:dataSet ns:dataset-weather ;
+  prop:outlook <code/outlook/sunny> ;
+  prop:play <code/play/yes> ;
+  prop:windy <code/windy/TRUE> ;
+  prop:humidity 70 ;
+  prop:temperature 75 ;
+  .
+
+ns:obs12 a qb:Observation ;
+  qb:dataSet ns:dataset-weather ;
+  prop:outlook <code/outlook/overcast> ;
+  prop:play <code/play/yes> ;
+  prop:windy <code/windy/TRUE> ;
+  prop:humidity 90 ;
+  prop:temperature 72 ;
+  .
+
+ns:obs13 a qb:Observation ;
+  qb:dataSet ns:dataset-weather ;
+  prop:outlook <code/outlook/overcast> ;
+  prop:play <code/play/yes> ;
+  prop:windy <code/windy/FALSE> ;
+  prop:humidity 75 ;
+  prop:temperature 81 ;
+  .
+
+ns:obs14 a qb:Observation ;
+  qb:dataSet ns:dataset-weather ;
+  prop:outlook <code/outlook/rainy> ;
+  prop:play <code/play/no> ;
+  prop:windy <code/windy/TRUE> ;
+  prop:humidity 91 ;
+  prop:temperature 71 ;
+  .
+

data/spec/writer_spec.rb

@@ -0,0 +1,75 @@
+require_relative '../lib/bio-publisci.rb'
+
+describe PubliSci::Writers do
+  before(:each) do
+
+  end
+
+  it "should create reference CSV from turtle" do
+    writer = PubliSci::Writers::CSV.new
+    out = writer.from_turtle('spec/turtle/bacon')
+
+    out.should == IO.read('spec/csv/bacon.csv')
+  end
+
+  it "can use store as an input" do
+    writer = PubliSci::Writers::CSV.new
+    repo = RDF::Repository.load('spec/turtle/bacon')
+    out = writer.from_store(repo)
+
+    out.should == IO.read('spec/csv/bacon.csv')
+  end
+
+  it "can output Wekka ARFF from turtle string" do
+    writer = PubliSci::Writers::ARFF.new
+    out = writer.from_turtle('spec/turtle/weather')
+    out.should == IO.read('resources/weather.numeric.arff')
+  end
+
+  it "can output Wekka ARFF from a store" do
+    writer = PubliSci::Writers::ARFF.new
+    repo = RDF::Repository.load('spec/turtle/weather')
+    out = writer.from_store(repo)
+
+    # minor hack since metadata isn't the same
+    out = out.gsub(/%.*\n/,'')
+
+    out.should == IO.read('resources/weather.numeric.arff').gsub(/%.*\n/,'')
+  end
+
+  it "can output JSON from turtle string" do
+    writer = PubliSci::Writers::JSON.new
+    out = writer.from_turtle('spec/turtle/weather')
+    JSON.parse(out).size.should > 0
+  end
+
+  it "can output JSON from a store" do
+    writer = PubliSci::Writers::JSON.new
+    repo = RDF::Repository.load('spec/turtle/weather')
+    out = writer.from_store(repo)
+    # minor hack since metadata isn't the same
+    JSON.parse(out).size.should > 0
+  end
+
+  context "can restrict to a particular dataset" do
+    it "for arff" do
+      writer = PubliSci::Writers::ARFF.new
+      repo = RDF::Repository.load('spec/turtle/weather')
+      repo.load('spec/turtle/bacon')
+      out = writer.from_store(repo, 'http://onto.strinz.me/dc/dataset/weather/dataset-weather','weather')
+
+      out = out.gsub(/%.*\n/,'')
+
+      out.should == IO.read('resources/weather.numeric.arff').gsub(/%.*\n/,'')
+    end
+
+    it "for csv" do
+      writer = PubliSci::Writers::CSV.new
+      repo = RDF::Repository.load('spec/turtle/reference')
+      repo.load('spec/turtle/bacon')
+      out = writer.from_store(repo,'http://onto.strinz.me/dc/dataset/bacon/dataset-bacon')
+
+      out.should == IO.read('spec/csv/bacon.csv')
+    end
+  end
+end

metadata

@@ -0,0 +1,589 @@
+--- !ruby/object:Gem::Specification
+name: publisci
+version: !ruby/object:Gem::Version
+  version: 0.1.2
+platform: ruby
+authors:
+- Will Strinz
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-09-26 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rdf
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdf-4store
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdf-turtle
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdf-rdfxml
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: json-ld
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rserve-client
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: sparql
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: slop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: sinatra
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: sinatra-contrib
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: sinatra-linkeddata
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: sinatra-cross_origin
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rack-flash3
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rest-client
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: spoon
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: spira
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: 'A toolkit for publishing scientific results and datasets using RDF,
+  OWL, and related technologies '
+email: wstrinz@gmail.com
+executables:
+- bio-publisci
+- bio-publisci-server
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- .document
+- .rspec
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- bin/bio-publisci
+- bin/bio-publisci-server
+- examples/bio-band_integration.rb
+- examples/no_magic.prov
+- examples/no_magic.rb
+- examples/orm.prov
+- examples/primer-full.prov
+- examples/primer.prov
+- examples/prov_dsl.prov
+- examples/safe_gen.rb
+- examples/visualization/primer.prov
+- examples/visualization/prov_viz.rb
+- examples/visualization/viz.rb
+- 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/prov_dsl.feature
+- features/prov_dsl_steps.rb
+- features/reader.feature
+- features/reader_steps.rb
+- features/step_definitions/bio-publisci_steps.rb
+- features/store.feature
+- features/store_steps.rb
+- features/support/env.rb
+- features/writer.feature
+- features/writer_steps.rb
+- lib/bio-publisci.rb
+- lib/bio-publisci/analyzer.rb
+- lib/bio-publisci/datacube_model.rb
+- lib/bio-publisci/dataset/ORM/data_cube_orm.rb
+- lib/bio-publisci/dataset/ORM/observation.rb
+- lib/bio-publisci/dataset/configuration.rb
+- lib/bio-publisci/dataset/data_cube.rb
+- lib/bio-publisci/dataset/dataset.rb
+- lib/bio-publisci/dataset/dataset_for.rb
+- lib/bio-publisci/dataset/interactive.rb
+- lib/bio-publisci/dsl/config.rb
+- lib/bio-publisci/dsl/dataset_dsl.rb
+- lib/bio-publisci/dsl/dsl.rb
+- lib/bio-publisci/dsl/metadata_dsl.rb
+- lib/bio-publisci/dsl/prov_dsl.rb
+- lib/bio-publisci/metadata/generator.rb
+- lib/bio-publisci/metadata/metadata.rb
+- lib/bio-publisci/metadata/metadata_model.rb
+- lib/bio-publisci/metadata/prov/activity.rb
+- lib/bio-publisci/metadata/prov/agent.rb
+- lib/bio-publisci/metadata/prov/association.rb
+- lib/bio-publisci/metadata/prov/config.rb
+- lib/bio-publisci/metadata/prov/derivation.rb
+- lib/bio-publisci/metadata/prov/element.rb
+- lib/bio-publisci/metadata/prov/entity.rb
+- lib/bio-publisci/metadata/prov/model/prov_models.rb
+- lib/bio-publisci/metadata/prov/plan.rb
+- lib/bio-publisci/metadata/prov/prov.rb
+- lib/bio-publisci/metadata/prov/role.rb
+- lib/bio-publisci/metadata/prov/usage.rb
+- lib/bio-publisci/metadata/publisher.rb
+- lib/bio-publisci/mixins/custom_predicate.rb
+- lib/bio-publisci/mixins/dereferencable.rb
+- lib/bio-publisci/mixins/registry.rb
+- lib/bio-publisci/mixins/vocabulary.rb
+- lib/bio-publisci/output.rb
+- lib/bio-publisci/parser.rb
+- lib/bio-publisci/post_processor.rb
+- lib/bio-publisci/query/query_helper.rb
+- lib/bio-publisci/r_client.rb
+- lib/bio-publisci/readers/arff.rb
+- lib/bio-publisci/readers/base.rb
+- lib/bio-publisci/readers/csv.rb
+- lib/bio-publisci/readers/dataframe.rb
+- lib/bio-publisci/readers/maf.rb
+- lib/bio-publisci/readers/r_cross.rb
+- lib/bio-publisci/readers/r_matrix.rb
+- lib/bio-publisci/store.rb
+- lib/bio-publisci/writers/arff.rb
+- lib/bio-publisci/writers/base.rb
+- lib/bio-publisci/writers/csv.rb
+- lib/bio-publisci/writers/dataframe.rb
+- lib/bio-publisci/writers/json.rb
+- lib/r2rdf.rb
+- lib/template_bak.rb
+- lib/template_bak/publisci.rb
+- lib/vocabs/cc.rb
+- lib/vocabs/cert.rb
+- lib/vocabs/dc.rb
+- lib/vocabs/dc11.rb
+- lib/vocabs/doap.rb
+- lib/vocabs/exif.rb
+- lib/vocabs/foaf.rb
+- lib/vocabs/geo.rb
+- lib/vocabs/http.rb
+- lib/vocabs/ma.rb
+- lib/vocabs/owl.rb
+- lib/vocabs/rdfs.rb
+- lib/vocabs/rsa.rb
+- lib/vocabs/rss.rb
+- lib/vocabs/sioc.rb
+- lib/vocabs/skos.rb
+- lib/vocabs/wot.rb
+- lib/vocabs/xhtml.rb
+- lib/vocabs/xsd.rb
+- resources/maf_example.maf
+- resources/maf_rdf.ttl
+- resources/primer.ttl
+- resources/queries/code_resources.rq
+- resources/queries/codes.rq
+- resources/queries/dataset.rq
+- resources/queries/dimension_ranges.rq
+- resources/queries/dimensions.rq
+- resources/queries/gene.rq
+- resources/queries/hugo_to_ensembl.rq
+- resources/queries/maf_column.rq
+- resources/queries/measures.rq
+- resources/queries/observation_labels.rq
+- resources/queries/observations.rq
+- resources/queries/patient.rq
+- resources/queries/patient_list.rq
+- resources/queries/patients_with_mutation.rq
+- resources/queries/properties.rq
+- resources/queries/test.rq
+- resources/weather.numeric.arff
+- scripts/get_gene_lengths.rb
+- scripts/islet_mlratio.rb
+- scripts/scan_islet.rb
+- scripts/update_reference.rb
+- server/helpers.rb
+- server/public/src-min-noconflict/LICENSE
+- server/public/src-min-noconflict/ace.js
+- server/public/src-min-noconflict/ext-chromevox.js
+- server/public/src-min-noconflict/ext-elastic_tabstops_lite.js
+- server/public/src-min-noconflict/ext-emmet.js
+- server/public/src-min-noconflict/ext-keybinding_menu.js
+- server/public/src-min-noconflict/ext-language_tools.js
+- server/public/src-min-noconflict/ext-modelist.js
+- server/public/src-min-noconflict/ext-old_ie.js
+- server/public/src-min-noconflict/ext-searchbox.js
+- server/public/src-min-noconflict/ext-settings_menu.js
+- server/public/src-min-noconflict/ext-spellcheck.js
+- server/public/src-min-noconflict/ext-split.js
+- server/public/src-min-noconflict/ext-static_highlight.js
+- server/public/src-min-noconflict/ext-statusbar.js
+- server/public/src-min-noconflict/ext-textarea.js
+- server/public/src-min-noconflict/ext-themelist.js
+- server/public/src-min-noconflict/ext-whitespace.js
+- server/public/src-min-noconflict/keybinding-emacs.js
+- server/public/src-min-noconflict/keybinding-vim.js
+- server/public/src-min-noconflict/mode-ruby.js
+- server/public/src-min-noconflict/snippets/ruby.js
+- server/public/src-min-noconflict/theme-twilight.js
+- server/public/src-min-noconflict/worker-coffee.js
+- server/public/src-min-noconflict/worker-css.js
+- server/public/src-min-noconflict/worker-javascript.js
+- server/public/src-min-noconflict/worker-json.js
+- server/public/src-min-noconflict/worker-lua.js
+- server/public/src-min-noconflict/worker-php.js
+- server/public/src-min-noconflict/worker-xquery.js
+- server/routes.rb
+- server/views/dsl.haml
+- server/views/dump.haml
+- server/views/import.haml
+- server/views/new_repository.haml
+- server/views/query.haml
+- server/views/repository.haml
+- spec/ORM/data_cube_orm_spec.rb
+- spec/ORM/prov_model_spec.rb
+- spec/analyzer_spec.rb
+- spec/bnode_spec.rb
+- spec/csv/bacon.csv
+- spec/csv/moar_bacon.csv
+- spec/data_cube_spec.rb
+- spec/dataset_for_spec.rb
+- spec/dsl_spec.rb
+- spec/generators/csv_spec.rb
+- spec/generators/dataframe_spec.rb
+- spec/generators/maf_spec.rb
+- spec/generators/r_cross_spec.rb
+- spec/generators/r_matrix_spec.rb
+- spec/length_lookup_spec.rb
+- spec/maf_query_spec.rb
+- spec/metadata/metadata_dsl_spec.rb
+- spec/prov/activity_spec.rb
+- spec/prov/agent_spec.rb
+- spec/prov/association_spec.rb
+- spec/prov/config_spec.rb
+- spec/prov/derivation_spec.rb
+- spec/prov/entity_spec.rb
+- spec/prov/role_spec.rb
+- spec/prov/usage_spec.rb
+- spec/queries/integrity/1.rq
+- spec/queries/integrity/11.rq
+- spec/queries/integrity/12.rq
+- spec/queries/integrity/14.rq
+- spec/queries/integrity/19_1.rq
+- spec/queries/integrity/19_2.rq
+- spec/queries/integrity/2.rq
+- spec/queries/integrity/3.rq
+- 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
+- spec/turtle/weather
+- spec/writer_spec.rb
+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
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.0.3
+signing_key: 
+specification_version: 4
+summary: Publish scientific results to the semantic web
+test_files: []