bio-publisci 0.0.3 → 0.0.4

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-publisci
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
 platform: ruby
 authors:
-- wstrinz
+- Will Strinz
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-07-25 00:00:00.000000000 Z
+date: 2013-07-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdf
@@ -178,8 +178,22 @@ dependencies:
     - - ~>
       - !ruby/object:Gem::Version
         version: '3.12'
-description: 'A toolkit for publishing scientific results and datasets using RDF and
-  related technologies '
+- !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'
+description: 'A toolkit for publishing scientific results and datasets using RDF,
+  OWL, and related technologies '
 email: wstrinz@gmail.com
 executables:
 - bio-publisci
@@ -198,6 +212,10 @@ files:
 - README.rdoc
 - Rakefile
 - bin/bio-publisci
+- examples/bio-band_integration.rb
+- examples/no_magic.prov
+- examples/primer.prov
+- examples/prov_dsl.prov
 - features/create_generator.feature
 - features/integration.feature
 - features/integration_steps.rb
@@ -205,6 +223,8 @@ files:
 - 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
@@ -221,15 +241,27 @@ files:
 - lib/bio-publisci/dataset/dataset_for.rb
 - lib/bio-publisci/dataset/interactive.rb
 - lib/bio-publisci/metadata/metadata.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/derivation.rb
+- lib/bio-publisci/metadata/prov/dsl.rb
+- lib/bio-publisci/metadata/prov/element.rb
+- lib/bio-publisci/metadata/prov/entity.rb
+- lib/bio-publisci/metadata/prov/plan.rb
+- lib/bio-publisci/metadata/prov/prov.rb
+- lib/bio-publisci/mixins/custom_predicate.rb
+- lib/bio-publisci/mixins/vocabulary.rb
+- lib/bio-publisci/output.rb
 - lib/bio-publisci/parser.rb
 - lib/bio-publisci/query/query_helper.rb
 - lib/bio-publisci/r_client.rb
 - lib/bio-publisci/readers/arff.rb
-- lib/bio-publisci/readers/big_cross.rb
-- lib/bio-publisci/readers/cross.rb
 - lib/bio-publisci/readers/csv.rb
 - lib/bio-publisci/readers/dataframe.rb
+- lib/bio-publisci/readers/r_cross.rb
 - lib/bio-publisci/readers/r_matrix.rb
+- lib/bio-publisci/spira.rb
 - lib/bio-publisci/store.rb
 - lib/bio-publisci/writers/arff.rb
 - lib/bio-publisci/writers/dataframe.rb
@@ -274,8 +306,10 @@ files:
 - spec/csv/bacon.csv
 - spec/csv/moar_bacon.csv
 - spec/data_cube_spec.rb
+- spec/dataset_for_spec.rb
 - spec/generators/csv_spec.rb
 - spec/generators/dataframe_spec.rb
+- spec/generators/r_cross_spec.rb
 - spec/generators/r_matrix_spec.rb
 - spec/queries/integrity/1.rq
 - spec/queries/integrity/11.rq
@@ -316,5 +350,5 @@ rubyforge_project:
 rubygems_version: 2.0.3
 signing_key: 
 specification_version: 4
-summary: Publish science data using semantic web ontologies
+summary: Publish scientific results to the semantic web
 test_files: []

data/lib/bio-publisci/readers/cross.rb

@@ -1,72 +0,0 @@
-module R2RDF
-	module Reader
-		class Cross
-			include R2RDF::Dataset::DataCube
-
-			def generate_n3(rexp, var, options={})
-				@rexp = rexp
-				@options = options
-				generate(measures, dimensions, codes, observation_data, observation_labels, var, options)
-			end
-
-			def dimensions
-				["individual","chr","sex","marker"]
-			end
-
-			def codes
-				["individual","chr","sex","marker"]
-			end
-
-			def measures
-				((@rexp.payload["pheno"].payload.names - ["sex"]) | ["genotype","markerpos"]) 
-			end
-
-			def observation_labels
-				# row_names = @rexp.attr.payload["row.names"].to_ruby
-				# entries_per_individual = @rexp.payload["geno"].payload[0].payload["map"].payload.size * @rexp.payload["geno"].payload.names.size
-				entries_per_individual = 0
-				@rexp.payload["geno"].payload.to_ruby.map{|v| entries_per_individual += (v["map"].size)}
-				individuals = @rexp.payload["pheno"].payload.first.to_ruby.size
-	      (1..(entries_per_individual * individuals)).to_a
-			end
-
-			def observation_data
-
-				data = {}
-				n_individuals = @rexp.payload["pheno"].payload.first.to_ruby.size
-				entries_per_individual = 0
-				@rexp.payload["geno"].payload.to_ruby.map{|v| entries_per_individual += (v["map"].size)}
-				# entries_per_individual = @rexp.payload["geno"].payload[row_individ].payload["map"].payload.size * @rexp.payload["geno"].payload.names.size
-				data["chr"] = []
-				data["genotype"] = []
-				data["individual"] = []
-				data["marker"] = []
-				data["markerpos"] = []
-				@rexp.payload["pheno"].payload.names.map{|name|
-					data[name] = []
-				}
-				n_individuals.times{|row_individ|
-					# puts row_individ
-					data["individual"] << (1..entries_per_individual).to_a.fill(row_individ)
-					@rexp.payload["pheno"].payload.names.map{|name|
-						data[name] << (1..entries_per_individual).to_a.fill(@rexp.payload["pheno"].payload[name].to_ruby[row_individ])
-					}
-					@rexp.payload["geno"].payload.names.map { |chr|
-						geno_chr = @rexp.payload["geno"].payload[chr]
-						num_markers = geno_chr.payload.first.to_ruby.column_size
-						data["chr"] << (1..num_markers).to_a.fill(chr)
-						data["genotype"] << geno_chr.payload["data"].to_ruby.row(row_individ).to_a
-						data["marker"] << geno_chr.payload["map"].to_ruby.names
-						data["markerpos"] << geno_chr.payload["map"].to_a
-					}
-				}
-				# data["chr"].flatten!
-				# data["genotype"].flatten!
-				data.keys.map{|k| data[k].flatten!}
-
-				#data["refRow"] = observation_labels()
-				data
-			end
-		end
-	end
-end