bio-publisci 0.0.6 → 0.0.7

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

@@ -1,17 +1,17 @@
-module R2RDF
+module PubliSci
   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
+      extend PubliSci::Dataset::DataCube
+      extend PubliSci::Analyzer
+      # extend PubliSci::Metadata
+      extend PubliSci::Query
+      extend PubliSci::Parser
+
+      include PubliSci::Dataset::DataCube
+      include PubliSci::Analyzer
+      include PubliSci::Metadata::Generator
+      include PubliSci::Query
+      include PubliSci::Parser
 
       attr_accessor :labels
       attr_accessor :dimensions

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

@@ -1,4 +1,4 @@
-module R2RDF
+module PubliSci
 		module ORM
 			class Observation
 				attr_accessor :data

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

@@ -0,0 +1,31 @@
+module PubliSci
+  class Dataset
+    class Configuration
+      def self.defaults
+        {
+          interactive: false,
+        }
+      end
+
+      defaults.keys.each{|k|
+        default = defaults[k]
+        define_method(k) do |input=nil|
+          var = instance_variable_get :"@#{k}"
+          if var
+            var
+          else
+            instance_variable_set :"@#{k}", default
+          end
+
+          if input
+            instance_variable_set :"@#{k}", input
+          end
+
+          instance_variable_get :"@#{k}"
+        end
+
+        attr_writer k
+      }
+    end
+  end
+end

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

@@ -5,10 +5,10 @@ class String
   end
 end
 
-module R2RDF
+module PubliSci
   class Dataset
     module DataCube
-      include R2RDF::Parser
+      include PubliSci::Parser
       def defaults
       {
         type: :dataframe,
@@ -60,6 +60,11 @@ module R2RDF
         [newm, newd, newc]
       end
 
+      def component_gen(args,options={})
+        args = Array[args].flatten
+        args.map{|arg| arg.gsub("prop:","cs:").gsub(%r{<#{options[:base_url]}/.+/(\w.+)>$},'cs:'+'\1')}
+      end
+
       def encode_data(codes,data,var,options={})
         codes = sanitize(codes)
         new_data = {}
@@ -101,7 +106,7 @@ module R2RDF
         str = prefixes(var,options)
         str << data_structure_definition(measures, dimensions, codes, var, options)
         str << dataset(var, options)
-        # component_specifications(measures, dimensions, var, options).map{ |c| str << c }
+        component_specifications(measures, dimensions, codes, var, options).map{ |c| str << c }
         dimension_properties(dimensions, codes, var, options).map{|p| str << p}
         measure_properties(measures, var, options).map{|p| str << p}
         code_lists(codes, data, var, options).map{|l| str << l}
@@ -138,14 +143,15 @@ module R2RDF
         var = sanitize([var]).first
         options = defaults().merge(options)
         rdf_measures, rdf_dimensions, rdf_codes  = generate_resources(measures, dimensions, codes, options)
-
+        cs_dims = component_gen(rdf_dimensions,options)  #rdf_dimensions.map{|d| d.gsub('prop:','cs:')}
+        cs_meas = component_gen(rdf_measures,options) #rdf_measures.map!{|m| m.gsub('prop:','cs:')}
         str = "ns:dsd-#{var} a qb:DataStructureDefinition;\n"
-        rdf_dimensions.map{|d|
-          str << "  qb:component [ qb:dimension #{d} ] ;\n"
+        cs_dims.map{|d|
+          str << "  qb:component #{d} ;\n"
         }
 
-        rdf_measures.map{|m|
-          str << "  qb:component [ qb:measure #{m} ] ;\n"
+        cs_meas.map{|m|
+          str << "  qb:component #{m} ;\n"
         }
         str[-2]='.'
         str<<"\n"
@@ -163,24 +169,29 @@ module R2RDF
         EOF
       end
 
-      def component_specifications(measure_names, dimension_names, var, options={})
+      def component_specifications(measure_names, dimension_names, codes, var, options={})
         options = defaults().merge(options)
+        rdf_measures, rdf_dimensions, rdf_codes  = generate_resources(measure_names, dimension_names, codes, options)
+        cs_dims = component_gen(rdf_dimensions,options)
+        cs_meas = component_gen(rdf_measures,options)
+        # cs_dims = rdf_dimensions.map{|d| d.gsub('prop:','cs:')}
+        # cs_meas = rdf_measures.map{|m| m.gsub('prop:','cs:')}
         specs = []
 
-          dimension_names.map{|d|
+          rdf_dimensions.each_with_index.map{|d,i|
           specs << <<-EOF.unindent
-            cs:#{d} a qb:ComponentSpecification ;
-              rdfs:label "#{d} Component" ;
-              qb:dimension prop:#{d} .
+            #{cs_dims[i]} a qb:ComponentSpecification ;
+              rdfs:label "#{strip_prefixes(strip_uri(dimension_names[i]))} Component" ;
+              qb:dimension #{d} .
 
             EOF
           }
 
-          measure_names.map{|n|
+          rdf_measures.each_with_index.map{|n,i|
             specs << <<-EOF.unindent
-              cs:#{n} a qb:ComponentSpecification ;
-                rdfs:label "#{n} Component" ;
-                qb:measure prop:#{n} .
+              #{cs_meas[i]} a qb:ComponentSpecification ;
+                rdfs:label "#{strip_prefixes(strip_uri(measure_names[i]))} Component" ;
+                qb:measure #{n} .
 
               EOF
           }

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

@@ -0,0 +1,11 @@
+module PubliSci
+  class Dataset
+    extend PubliSci::Interactive
+    extend PubliSci::Registry
+
+    def self.configuration
+      @config ||= Dataset::Configuration.new
+    end
+
+  end
+end

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

@@ -1,6 +1,7 @@
-module R2RDF
+require 'open-uri'
+module PubliSci
   class Dataset
-    extend R2RDF::Interactive
+    extend PubliSci::Interactive
 
     def self.for(object, options={}, ask_on_ambiguous=true)
 
@@ -23,10 +24,12 @@ module R2RDF
           when ".RData"
             r_object(object, options, ask_on_ambiguous)
           when /.csv/i
-            R2RDF::Reader::CSV.new.automatic(object,nil,options,ask_on_ambiguous)
+            PubliSci::Reader::CSV.new.automatic(object,nil,options,ask_on_ambiguous)
           end
+        elsif object =~ %r{http[s]://.+}
+          self.for(download(object).path, options, ask_on_ambiguous)
         else
-          raise "Unable to find reader for File or String"
+          raise "Unable to find reader for File or String #{object}"
         end
       elsif object.is_a? Rserve::REXP
         r_object(object, options, ask_on_ambiguous)
@@ -35,6 +38,13 @@ module R2RDF
       end
     end
 
+    def self.download(uri)
+      out = Tempfile.new(uri.split('/').last)
+      out.write open(uri).read
+      out.close
+      out
+    end
+
     def self.r_object(object, options={}, ask_on_ambiguous=true)
       if object.is_a? String
         con = Rserve::Connection.new
@@ -49,7 +59,7 @@ module R2RDF
         r_classes = con.eval("class(#{var})").to_ruby
 
         if r_classes.include? "data.frame"
-          df = R2RDF::Reader::Dataframe.new
+          df = PubliSci::Reader::Dataframe.new
           unless options[:dimensions] || !ask_on_ambiguous
             dims = con.eval("names(#{var})").to_ruby
             puts "Which dimensions? #{dims}"
@@ -70,7 +80,7 @@ module R2RDF
           df.generate_n3(con.eval(var),var,options)
 
         elsif r_classes.include? "cross"
-          bc = R2RDF::Reader::RCross.new
+          bc = PubliSci::Reader::RCross.new
 
           unless options[:measures] || !ask_on_ambiguous
             pheno_names = con.eval("names(#{var}$pheno)").to_ruby
@@ -91,7 +101,7 @@ module R2RDF
           bc.generate_n3(con, var, base, options)
 
         elsif r_classes.include? "matrix"
-          mat = R2RDF::Reader::RMatrix.new
+          mat = PubliSci::Reader::RMatrix.new
 
           unless options[:measures] || !ask_on_ambiguous
             puts "Row label"
@@ -118,13 +128,13 @@ module R2RDF
 
           mat.generate_n3(con, var, base, options)
         else
-          raise "no R2RDF::Reader found for #{r_classes}"
+          raise "no PubliSci::Reader found for #{r_classes}"
         end
 
       elsif object.is_a? Rserve::REXP
         if object.attr.payload["class"].payload.first
 
-          df = R2RDF::Reader::Dataframe.new
+          df = PubliSci::Reader::Dataframe.new
 
           var = nil
 

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

@@ -1,4 +1,4 @@
-module R2RDF
+module PubliSci
   module Interactive
     #to be called by other classes if user input is required
 

data/lib/bio-publisci/dsl/config.rb

@@ -0,0 +1,34 @@
+module PubliSci
+  module DSL
+    class Configuration
+      def self.defaults
+        {
+          output: :generate_n3,
+          abbreviate: false,
+          repository: :in_memory,
+          repository_url: 'http://localhost:8080/'
+        }
+      end
+
+      defaults.keys.each{|k|
+        default = defaults[k]
+        define_method(k) do |input=nil|
+          var = instance_variable_get :"@#{k}"
+          if var
+            var
+          else
+            instance_variable_set :"@#{k}", default
+          end
+
+          if input
+            instance_variable_set :"@#{k}", input
+          end
+
+          instance_variable_get :"@#{k}"
+        end
+
+        attr_writer k
+      }
+    end
+  end
+end

data/lib/bio-publisci/dsl/dataset_dsl.rb

@@ -0,0 +1,91 @@
+module PubliSci
+  class Dataset
+    module DSL
+
+      class Instance
+        include Dataset::DSL
+
+        def initialize
+          Dataset.registry.clear
+        end
+      end
+
+      # def interactive(value=nil)
+      #   set_or_get('interactive',value)
+      # end
+
+      def object(file=nil)
+        set_or_get('object',file)
+      end
+      alias_method :source, :object
+
+      def dimension(*args)
+        if args.size == 0
+          add_or_get('dimension',nil)
+        else
+          args.each{|arg|
+            add_or_get('dimension',arg)
+          }
+        end
+      end
+
+      def measure(*args)
+        if args.size == 0
+          add_or_get('measure',nil)
+        else
+          args.each{|arg|
+            add_or_get('measure',arg)
+          }
+        end
+      end
+
+      def option(opt=nil,value=nil)
+        if opt == nil || value == nil
+          @dataset_generator_options
+        else
+          (@dataset_generator_options ||= {})[opt] = value
+        end
+      end
+      alias_method :options, :option
+
+      def settings
+        Dataset.configuration
+      end
+
+      def generate_n3
+        opts = {}
+        %w{dimension measure}.each{|field|
+          opts[field.to_sym] = send(field.to_sym) if send(field.to_sym)
+        }
+        interact = settings.interactive
+        if options
+          opts = opts.merge(options)
+        end
+        Dataset.for(object,opts,interact)
+      end
+
+      private
+      def set_or_get(var,input=nil)
+        ivar = instance_variable_get("@#{var}")
+
+        if input
+          instance_variable_set("@#{var}", input)
+        else
+          ivar
+        end
+      end
+
+      def add_or_get(var,input)
+        ivar = instance_variable_get("@#{var}")
+
+        if input
+          instance_variable_set("@#{var}", []) unless ivar
+          instance_variable_get("@#{var}") << input
+          instance_variable_get("@#{var}")
+        else
+          ivar
+        end
+      end
+    end
+  end
+end

data/lib/bio-publisci/dsl/dsl.rb

@@ -0,0 +1,69 @@
+module PubliSci
+  module DSL
+    attr_reader :base_url
+
+    # Use to set base url for whole script; helps when referring to dataset
+    # resources from metadata and
+    def base_url=(url)
+      @base_url = url
+      Prov.base_url=url
+    end
+
+    def data(&block)
+      inst=PubliSci::Dataset::DSL::Instance.new
+      inst.instance_eval(&block)
+      @_dsl_data ||= [] << inst
+      inst
+    end
+
+    def metadata(&block)
+      inst=PubliSci::Metadata::DSL::Instance.new
+      inst.instance_eval(&block)
+      @_dsl_metadata = inst
+      inst
+    end
+
+    def provenance(&block)
+      inst=PubliSci::Prov::DSL::Instance.new
+      inst.instance_eval(&block)
+      @_dsl_prov = inst
+      inst
+    end
+
+    def configuration
+      @_dsl_config ||= DSL::Configuration.new
+    end
+
+    def configure
+      yield configuration
+    end
+
+    def settings
+      configuration
+    end
+
+    def generate_n3
+      out = ""
+      @_dsl_data.each{|dat| out << dat.generate_n3 } if @_dsl_data
+      out << @_dsl_metadata.generate_n3 if @_dsl_metadata
+      out << @_dsl_prov.generate_n3 if @_dsl_prov
+      out
+    end
+
+    def to_repository(turtle_string=generate_n3)
+      repo = settings.repository
+      case repo
+      when :in_memory
+        repo = RDF::Repository.new
+      when :fourstore
+        repo = RDF::FourStore::Repository.new('http://localhost:8080')
+      end
+      f=Tempfile.new(['repo','.ttl'])
+      f.write(turtle_string)
+      f.close
+      repo.load(f.path, :format => :ttl).to_s
+      f.unlink
+      repo
+    end
+  end
+end