bio-publisci 0.0.3 → 0.0.4

data/lib/bio-publisci/dataset/ORM/data_cube_orm.rb

@@ -1,241 +1,239 @@
 module R2RDF
-	class Dataset
-		module ORM
-			class DataCube
-				extend R2RDF::Dataset::DataCube
-				extend R2RDF::Analyzer
-				extend R2RDF::Metadata
-				extend R2RDF::Query
-				extend R2RDF::Parser
-
-				include R2RDF::Dataset::DataCube
-				include R2RDF::Analyzer
-				include R2RDF::Metadata
-				include R2RDF::Query
-				include R2RDF::Parser
-				
-				attr_accessor :labels
-				attr_accessor :dimensions
-				attr_accessor :measures
-	      attr_accessor :obs
-				attr_accessor :meta
-
-				def initialize(options={},do_parse = true)
-					@dimensions = {}
-					@measures = []
-					@obs = []
-					@generator_options = {}
-					@options = {}
-
-	        @meta = {}
-
-					parse_options options if do_parse
-				end
-
-				def self.load(graph,options={},verbose=false)
-
-          
-          graph = create_graph(graph) unless graph =~ /^http/
-
-          # puts get_hashes(execute_from_file('dimension_ranges.rq',graph))
-          dimensions = Hash[get_hashes(execute_from_file('dimension_ranges.rq',graph),"to_s").map{|solution|
-						#TODO coded properties should be found via SPARQL queries
-						if solution[:range].split('/')[-2] == "code"
-							type = :coded
-						else
-							type = solution[:range].to_s
-						end
-						[solution[:dimension], {type: type}]
-					}]
-					puts "dimensions: #{dimensions}" if verbose
-
-          codes = execute_from_file('code_resources.rq',graph).to_h.map{|sol|
-            [sol[:dimension].to_s, sol[:codeList].to_s, sol[:class].to_s]
+  module ORM
+    class DataCube
+      extend R2RDF::Dataset::DataCube
+      extend R2RDF::Analyzer
+      extend R2RDF::Metadata
+      extend R2RDF::Query
+      extend R2RDF::Parser
+
+      include R2RDF::Dataset::DataCube
+      include R2RDF::Analyzer
+      include R2RDF::Metadata
+      include R2RDF::Query
+      include R2RDF::Parser
+
+      attr_accessor :labels
+      attr_accessor :dimensions
+      attr_accessor :measures
+      attr_accessor :obs
+      attr_accessor :meta
+
+      def initialize(options={},do_parse = true)
+        @dimensions = {}
+        @measures = []
+        @obs = []
+        @generator_options = {}
+        @options = {}
+
+        @meta = {}
+
+        parse_options options if do_parse
+      end
+
+      def self.load(graph,options={},verbose=false)
+
+
+        graph = create_graph(graph) unless graph =~ /^http/
+
+        # puts get_hashes(execute_from_file('dimension_ranges.rq',graph))
+        dimensions = Hash[get_hashes(execute_from_file('dimension_ranges.rq',graph),"to_s").map{|solution|
+          #TODO coded properties should be found via SPARQL queries
+          if solution[:range].split('/')[-2] == "code"
+            type = :coded
+          else
+            type = solution[:range].to_s
+          end
+          [solution[:dimension], {type: type}]
+        }]
+        puts "dimensions: #{dimensions}" if verbose
+
+        codes = execute_from_file('code_resources.rq',graph).to_h.map{|sol|
+          [sol[:dimension].to_s, sol[:codeList].to_s, sol[:class].to_s]
+        }
+        puts "codes: #{codes}" if verbose
+
+        measures = execute_from_file('measures.rq',graph).to_h.map{|m| m[:measure].to_s}
+        puts "measures: #{measures}" if verbose
+
+        name = execute_from_file('dataset.rq',graph).to_h.first[:label]
+        puts "dataset: #{name}" if verbose
+
+        obs = execute_from_file('observations.rq',graph)
+        observations = observation_hash(obs)
+        puts "observations: #{observations}" if verbose
+
+        # simple_observations = observation_hash(obs,true)
+
+        labels = execute_from_file('observation_labels.rq', graph)
+        labels = Hash[labels.map{|sol|
+          [sol[:observation].to_s, sol[:label].to_s]
+        }]
+
+        new_opts = {
+          measures: measures,
+          dimensions: dimensions,
+          observations: observations.values,
+          name: name,
+          labels: labels.values,
+          codes: codes
+        }
+
+        options = options.merge(new_opts)
+        puts "creating #{options}" if verbose
+        self.new(options)
+      end
+
+      def parse_options(options)
+        if options[:dimensions]
+          options[:dimensions].each{|name,details|
+            add_dimension(name, details[:type] || :coded)
           }
-					puts "codes: #{codes}" if verbose
-          
-          measures = execute_from_file('measures.rq',graph).to_h.map{|m| m[:measure].to_s}
-          puts "measures: #{measures}" if verbose
-          
-          name = execute_from_file('dataset.rq',graph).to_h.first[:label]
-          puts "dataset: #{name}" if verbose
-          
-          obs = execute_from_file('observations.rq',graph)
-          observations = observation_hash(obs)
-          puts "observations: #{observations}" if verbose
-
-          # simple_observations = observation_hash(obs,true)
-
-          labels = execute_from_file('observation_labels.rq', graph)
-          labels = Hash[labels.map{|sol|
-            [sol[:observation].to_s, sol[:label].to_s]
-          }]
-
-					new_opts = {
-						measures: measures,
-						dimensions: dimensions,
-						observations: observations.values,
-						name: name,
-            labels: labels.values,
-            codes: codes
-					}
-
-					options = options.merge(new_opts)
-					puts "creating #{options}" if verbose
-					self.new(options)
-				end
-				
-				def parse_options(options)
-					if options[:dimensions]
-						options[:dimensions].each{|name,details|
-							add_dimension(name, details[:type] || :coded)
-						}
-					end
-
-					if options[:measures]
-						options[:measures].each{|m| @measures << m}
-					end
-
-					if options[:observations]
-						options[:observations].each{|obs_data| add_observation obs_data}
-					end
-
-					@generator_options = options[:generator_options] if options[:generator_options]
-					@options[:skip_metadata] = options[:skip_metadata] if options[:skip_metadata]
-
-					if options[:name]
-						@name = options[:name]
-					else
-						raise "No dataset name specified!"
-					end
-
-					if options[:validate_each]
-						@options[:validate_each] = options[:validate_each]
-					end
-
-          if options[:labels]
-            @labels = options[:labels]
+        end
+
+        if options[:measures]
+          options[:measures].each{|m| @measures << m}
+        end
+
+        if options[:observations]
+          options[:observations].each{|obs_data| add_observation obs_data}
+        end
+
+        @generator_options = options[:generator_options] if options[:generator_options]
+        @options[:skip_metadata] = options[:skip_metadata] if options[:skip_metadata]
+
+        if options[:name]
+          @name = options[:name]
+        else
+          raise "No dataset name specified!"
+        end
+
+        if options[:validate_each]
+          @options[:validate_each] = options[:validate_each]
+        end
+
+        if options[:labels]
+          @labels = options[:labels]
+        end
+
+        if options[:codes]
+          @codes = options[:codes]
+        end
+      end
+
+      def to_n3
+
+        #create labels if not specified
+        unless @labels.is_a?(Array) && @labels.size == @obs.size
+          if @labels.is_a? Symbol
+            #define some automatic labeling methods
+          else
+            @labels = (1..@obs.size).to_a.map(&:to_s)
           end
+        end
+        data = {}
 
-          if options[:codes]
-            @codes = options[:codes]
-          end
-				end
-
-				def to_n3
-
-					#create labels if not specified
-					unless @labels.is_a?(Array) && @labels.size == @obs.size
-						if @labels.is_a? Symbol
-							#define some automatic labeling methods
-						else
-							@labels = (1..@obs.size).to_a.map(&:to_s)
-						end
-					end
-					data = {}
-
-
-					#collect observation data
-					check_integrity(@obs.map{|o| o.data}, @dimensions.keys, @measures)
-					@obs.map{|obs|
-						(@measures | @dimensions.keys).map{ |component|
-						 (data[component] ||= []) <<  obs.data[component]
-						}
-					}
-					
-
-					@codes = @dimensions.map{|d,v| d if v[:type] == :coded}.compact unless @codes
-					str = generate(@measures, @dimensions.keys, @codes, data, @labels, @name, @generator_options)
-					unless @options[:skip_metadata]
-		        fields = {
-		          publishers: publishers(),
-		          subject: subjects(),
-		          author: author(),
-		          description: description(),
-		          date: date(),
-		          var: @name,
-		        }
-		        # puts basic(fields,@generator_options)
-		        str += "\n" + basic(fields,@generator_options)
-	      	end
-	        str
-				end
-
-				def add_dimension(name, type=:coded)
-					@dimensions[name.to_s] = {type: type}
-				end
-
-				def add_measure(name)
-					@measures << name
-				end
-
-				def add_observation(data)
-					data = Hash[data.map{|k,v| [k.to_s, v]}]
-					obs = Observation.new(data)
-					check_integrity([obs.data],@dimensions.keys,@measures) if @options[:validate_each]
-					@obs << obs
-				end
-
-				def insert(observation)
-					@obs << observation
-				end
-
-	      def publishers
-	        @meta[:publishers] ||= []
-	      end
-
-	      def publishers=(publishers)
-	        @meta[:publishers] = publishers
-	      end
-
-	      def subjects
-	        @meta[:subject] ||= []
-	      end
-
-	      def subjects=(subjects)
-	        @meta[:subject]=subjects
-	      end
-
-	      def add_publisher(label,uri)
-	        publishers << {label: label, uri: uri}
-	      end
-
-	      def add_subject(id)
-	        subject << id
-	      end
-
-	      def author
-	        @meta[:creator] ||= ""
-	      end
-
-	      def author=(author)
-	        @meta[:creator] = author
-	      end
-
-	      def description
-	        @meta[:description] ||= ""
-	      end
-
-	      def description=(description)
-	        @meta[:description] = description
-	      end
-
-	      def date
-	        @meta[:date] ||= "#{Time.now.day}-#{Time.now.month}-#{Time.now.year}"
-	      end
-
-	      def date=(date)
-	        @meta[:date] =  date
-	      end
-
-	      def to_h
-					{
-						measures: @measures,
-						dimensions: @dimensions,
-						observations: @obs.map{|o| o.data}
-					}
-				end
-			end
-		end
-	end
+
+        #collect observation data
+        check_integrity(@obs.map{|o| o.data}, @dimensions.keys, @measures)
+        @obs.map{|obs|
+          (@measures | @dimensions.keys).map{ |component|
+           (data[component] ||= []) <<  obs.data[component]
+          }
+        }
+
+
+        @codes = @dimensions.map{|d,v| d if v[:type] == :coded}.compact unless @codes
+        str = generate(@measures, @dimensions.keys, @codes, data, @labels, @name, @generator_options)
+        unless @options[:skip_metadata]
+          fields = {
+            publishers: publishers(),
+            subject: subjects(),
+            author: author(),
+            description: description(),
+            date: date(),
+            var: @name,
+          }
+          # puts basic(fields,@generator_options)
+          str += "\n" + basic(fields)
+        end
+        str
+      end
+
+      def add_dimension(name, type=:coded)
+        @dimensions[name.to_s] = {type: type}
+      end
+
+      def add_measure(name)
+        @measures << name
+      end
+
+      def add_observation(data)
+        data = Hash[data.map{|k,v| [k.to_s, v]}]
+        obs = Observation.new(data)
+        check_integrity([obs.data],@dimensions.keys,@measures) if @options[:validate_each]
+        @obs << obs
+      end
+
+      def insert(observation)
+        @obs << observation
+      end
+
+      def publishers
+        @meta[:publishers] ||= []
+      end
+
+      def publishers=(publishers)
+        @meta[:publishers] = publishers
+      end
+
+      def subjects
+        @meta[:subject] ||= []
+      end
+
+      def subjects=(subjects)
+        @meta[:subject]=subjects
+      end
+
+      def add_publisher(label,uri)
+        publishers << {label: label, uri: uri}
+      end
+
+      def add_subject(id)
+        subject << id
+      end
+
+      def author
+        @meta[:creator] ||= ""
+      end
+
+      def author=(author)
+        @meta[:creator] = author
+      end
+
+      def description
+        @meta[:description] ||= ""
+      end
+
+      def description=(description)
+        @meta[:description] = description
+      end
+
+      def date
+        @meta[:date] ||= "#{Time.now.day}-#{Time.now.month}-#{Time.now.year}"
+      end
+
+      def date=(date)
+        @meta[:date] =  date
+      end
+
+      def to_h
+        {
+          measures: @measures,
+          dimensions: @dimensions,
+          observations: @obs.map{|o| o.data}
+        }
+      end
+    end
+  end
 end

data/lib/bio-publisci/dataset/ORM/observation.rb

@@ -1,8 +1,7 @@
 module R2RDF
-	class Dataset
 		module ORM
 			class Observation
-				attr_accessor :data			
+				attr_accessor :data
 				def initialize(data={})
 					@data = data
 				end
@@ -15,6 +14,5 @@ module R2RDF
 
 				end
 			end
-		end
 	end
 end

data/lib/bio-publisci/dataset/data_cube.rb

@@ -1,4 +1,4 @@
-  #monkey patch to make rdf string w/ heredocs prettier ;)  
+  #monkey patch to make rdf string w/ heredocs prettier ;)
 class String
   def unindent
     gsub /^#{self[/\A\s*/]}/, ''
@@ -25,7 +25,7 @@ module R2RDF
             m
           else
             "prop:#{m}"
-          end            
+          end
         }
 
         newc = []
@@ -54,13 +54,14 @@ module R2RDF
           }
         else
           newc = codes.map{|c|
-              ["#{c}","code:#{c.downcase}","code:#{c.downcase.capitalize}"]
+              ["#{sanitize(c).first}","code:#{sanitize(c).first.downcase}","code:#{sanitize(c).first.downcase.capitalize}"]
           }
         end
         [newm, newd, newc]
       end
 
       def encode_data(codes,data,var,options={})
+        codes = sanitize(codes)
         new_data = {}
         data.map{|k,v|
           if codes.include? k
@@ -89,7 +90,7 @@ module R2RDF
           nil
         end
       end
-     
+
       def generate(measures, dimensions, codes, data, observation_labels, var, options={})
         # dimensions = sanitize(dimensions)
         # codes = sanitize(codes)
@@ -154,7 +155,7 @@ module R2RDF
       def dataset(var,options={})
         var = sanitize([var]).first
         options = defaults().merge(options)
-        <<-EOF.unindent    
+        <<-EOF.unindent
         ns:dataset-#{var} a qb:DataSet ;
           rdfs:label "#{var}"@en ;
           qb:structure ns:dsd-#{var} .
@@ -165,7 +166,7 @@ module R2RDF
       def component_specifications(measure_names, dimension_names, var, options={})
         options = defaults().merge(options)
         specs = []
-        
+
           dimension_names.map{|d|
           specs << <<-EOF.unindent
             cs:#{d} a qb:ComponentSpecification ;
@@ -183,7 +184,7 @@ module R2RDF
 
               EOF
           }
-        
+
         specs
       end
 
@@ -192,10 +193,10 @@ module R2RDF
         rdf_measures, rdf_dimensions, rdf_codes  = generate_resources([], dimensions, codes, options)
         props = []
 
-        dimension_codes = rdf_codes.map{|c| 
+        dimension_codes = rdf_codes.map{|c|
           if c[0]=~/^<http:/
-            c[0][1..-2] 
-          else 
+            c[0][1..-2]
+          else
             c[0]
           end
         }
@@ -218,7 +219,7 @@ module R2RDF
             EOF
           end
           }
-        
+
         props
       end
 
@@ -226,43 +227,45 @@ module R2RDF
         options = defaults().merge(options)
         rdf_measures = generate_resources(measures, [], [], options)[0]
         props = []
-        
+
           rdf_measures.map{ |m|
-              
+
             props <<  <<-EOF.unindent
             #{m} a rdf:Property, qb:MeasureProperty ;
               rdfs:label "#{strip_prefixes(strip_uri(m))}"@en .
 
             EOF
             }
-        
+
         props
       end
 
-      def observations(measures, dimensions, codes, data, observation_labels, var, options={})  
+      def observations(measures, dimensions, codes, data, observation_labels, var, options={})
         var = sanitize([var]).first
+        measures = sanitize(measures)
+        dimensions = sanitize(dimensions)
         options = defaults().merge(options)
         rdf_measures, rdf_dimensions, rdf_codes  = generate_resources(measures, dimensions, codes, options)
         data = encode_data(codes, data, var, options)
         obs = []
-        
-        dimension_codes = rdf_codes.map{|c| 
+
+        dimension_codes = rdf_codes.map{|c|
           if c[0]=~/^<http:/
-            c[0][1..-2] 
-          else 
+            c[0][1..-2]
+          else
             c[0]
           end
         }
 
         observation_labels.each_with_index.map{|r, i|
           contains_nulls = false
-          str = <<-EOF.unindent 
+          str = <<-EOF.unindent
           ns:obs#{r} a qb:Observation ;
             qb:dataSet ns:dataset-#{var} ;
           EOF
 
           str << "  rdfs:label \"#{r}\" ;\n" unless options[:no_labels]
-          
+
           dimensions.each_with_index{|d,j|
             contains_nulls = contains_nulls | (data[d][i] == nil)
 
@@ -276,8 +279,8 @@ module R2RDF
 
           measures.each_with_index{|m,j|
             contains_nulls = contains_nulls | (data[m][i] == nil)
-            str << "  #{rdf_measures[j]} #{to_literal(data[m][i], options)} ;\n" 
-            
+            str << "  #{rdf_measures[j]} #{to_literal(data[m][i], options)} ;\n"
+
           }
 
           str << "  .\n\n"
@@ -288,7 +291,7 @@ module R2RDF
               puts "missing component for observation, skipping: #{str}, "
             end
           else
-            obs << str 
+            obs << str
           end
         }
         obs
@@ -323,11 +326,11 @@ module R2RDF
               str << "  skos:hasTopConcept #{to_resource(value,options)} ;\n"
             end
           }
-          
+
           str << "  .\n\n"
           lists << str
         }
-        
+
 
         lists
       end
@@ -362,6 +365,7 @@ module R2RDF
 
       def abbreviate_known(turtle_string)
         #debug method
+        # puts turtle_string
         turtle_string.gsub(/<http:\/\/www\.rqtl\.org\/dc\/properties\/(\S+)>/, 'prop:\1').gsub(/<http:\/\/www.rqtl.org\/ns\/dc\/code\/(\S+)\/(\S+)>/, '<code/\1/\2>').gsub(/<http:\/\/www.rqtl.org\/dc\/dataset\/(\S+)\/code\/(\S+)>/, 'code:\2')
       end
     end