bio-publisci 0.0.2 → 0.0.3

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

@@ -0,0 +1,150 @@
+module R2RDF
+  class Dataset
+    extend R2RDF::Interactive
+
+    def self.for(object, options={}, ask_on_ambiguous=true)
+      if object.is_a? String
+        if File.exist? object
+          if File.extname(object).size > 0
+            extension = File.extname(object)
+          elsif File.basename(object)[0] == '.' && File.basename(object).count('.') == 1
+            extension = File.basename(object)
+          else
+            raise "Can't load file #{object}; type inference not yet implemented"
+          end
+
+          case extension
+          when ".RData"
+            r_object(object, options, ask_on_ambiguous)
+          when /.csv/i
+            R2RDF::Reader::CSV.new.automatic(object,nil,options,ask_on_ambiguous)
+          end
+        else
+          raise "Unable to find reader for File or String"
+        end 
+      elsif object.is_a? Rserve::REXP
+        r_object(object, options, ask_on_ambiguous)
+      else
+        raise "not recognize Ruby objects of this type yet (#{object})"
+      end
+    end
+
+    def self.r_object(object, options={}, ask_on_ambiguous=true)
+      if object.is_a? String
+        con = Rserve::Connection.new
+        vars = con.eval("load('#{File.absolute_path object}')")
+        if vars.to_ruby.size > 1 && ask_on_ambiguous
+          puts "Which variable? #{vars.to_ruby}"
+          var = vars.to_ruby[gets.to_i]
+        else
+          var = vars.to_ruby[0]
+        end
+
+        r_classes = con.eval("class(#{var})").to_ruby
+
+        if r_classes.include? "data.frame"
+          df = R2RDF::Reader::Dataframe.new
+          unless options[:dimensions] || !ask_on_ambiguous
+            dims = con.eval("names(#{var})").to_ruby
+            puts "Which dimensions? #{dims}"
+            selection = gets.chomp
+            if selection.size > 0
+              options[:dimensions] = selection.split(',').map(&:to_i).map{|i| dims[i]}
+            end
+          end
+          unless options[:measures] || !ask_on_ambiguous
+            meas = con.eval("names(#{var})").to_ruby
+            puts "Which measures? #{meas} "
+            selection = gets.chomp
+            if selection.size > 0
+              options[:measures] = selection.split(',').map(&:to_i).map{|i| meas[i]}
+            end
+          end
+          
+          df.generate_n3(con.eval(var),var,options)
+        
+        elsif r_classes.include? "cross"
+          bc = R2RDF::Reader::BigCross.new
+
+          unless options[:measures] || !ask_on_ambiguous
+            pheno_names = con.eval("names(#{var}$pheno)").to_ruby
+            puts "Which phenotype traits? #{pheno_names}"
+            selection = gets.chomp
+            if selection.size > 0
+              options[:measures] = selection.split(',').map(&:to_i).map{|i| pheno_names[i]}
+            end
+          end
+
+          base = var
+          if ask_on_ambiguous
+            puts "Output file base?"
+            base = gets.chomp
+            base = var unless base.size > 0
+          end
+
+          bc.generate_n3(con, var, base, options)
+
+        elsif r_classes.include? "matrix"
+          mat = R2RDF::Reader::RMatrix.new
+
+          unless options[:measures] || !ask_on_ambiguous  
+            puts "Row label"
+            rows = gets.chomp
+            rows = "row" unless rows.size > 0
+
+            puts "Column label"
+            cols = gets.chomp
+            cols = "column" unless cols.size > 0
+
+            puts "Entry label"
+            vals = gets.chomp
+            vals = "value" unless vals.size > 0
+
+            options[:measures] = [cols,rows,vals]
+          end
+          
+          base = var
+          if ask_on_ambiguous
+            puts "Output file base?"
+            base = gets.chomp
+            base = var unless base.size > 0
+          end
+
+          mat.generate_n3(con, var, base, options)
+        else
+          raise "no R2RDF::Reader found for #{r_classes}"
+        end
+
+      elsif object.is_a? Rserve::REXP
+        if object.attr.payload["class"].payload.first
+          
+          df = R2RDF::Reader::Dataframe.new
+
+          var = nil
+
+          if ask_on_ambiguous
+            var = interact("Dataset name?",nil)
+          end
+
+          unless options[:dimensions] || !ask_on_ambiguous
+            dims = object.payload.names
+            selection = interact("Which dimensions?","row",dims){|s| puts s; nil}
+            options[:dimensions] = selection if selection
+          end
+
+          unless options[:measures] || !ask_on_ambiguous
+            meas = object.payload.names
+            options[:measures] = interact("Which measures?",meas,meas)
+          end
+          
+          df.generate_n3(object,var,options)
+        else
+          raise "support for other Rserve objects coming shortly"
+        end
+
+      else
+        raise "#{object} is not an R object"
+      end
+    end
+  end
+end

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

@@ -1,57 +1,72 @@
 module R2RDF
-	module Dataset
-		module Interactive
-			#to be called by other classes if user input is required
-			def defaults
-				{
-					load_from_file: false
-				}
-			end
-
-			def interactive(options={})
-				options = defaults.merge(options)
-				qb = {}
-
-				puts "load config from file? [y/N]"
-				if gets.chomp == "y"
-					#use yaml or DSL file to configure
-				else
-					qb[:dimensions] = dimensions()
-					qb[:measures] = measures()
-				end
-
-				puts "load data from file? [y/N]"
-				if gets.chomp == "y"
-					#attempt to load dataset from file, ask user to resolve problems or ambiguity
-				else
-				end
-				qb
-			end
-
-			def dimensions
-				puts "Enter a list of dimensions, separated by commas"
-				arr = gets.chomp.split(",")
-				dims = {}
-
-				arr.map{|dim|
-					puts "What is the range of #{dim.chomp.strip}? [:coded]"
-					type = gets.chomp
-					type = :coded if type == ":coded" || type == ""
-					dims[dim.chomp.strip] = {type: type}
-				}
-
-				dims
-			end
-
-			def measures
-				puts "Enter a list of measures, separated by commas"
-				arr = gets.chomp.split(",")
-				meas = []
-
-				arr.map{|m| meas << m.chomp.strip}
-
-				meas
-			end
-		end
-	end
+  module Interactive
+    #to be called by other classes if user input is required
+
+    #take message, options, defaults. can be passed block to handle default as well
+    def interact(message, default, options=nil)
+      puts message + " (#{default})\n[#{options}]"
+      str = gets.chomp
+      if str.size > 0
+        if options
+          if str.split(',').all?{|s| Integer(s) rescue nil}
+            str.split(',').map(&:to_i).map{|i| options[i]}
+          else
+            str.split(',').each{|s| raise "unkown selection #{s}" unless options.include? s.strip}
+            str.split(',').map(&:strip)
+          end
+        else
+          str
+        end
+      elsif block_given?
+        yield str
+      else
+        default
+      end
+    end
+
+    # def interactive(options={})
+    #   options = defaults.merge(options)
+    #   qb = {}
+
+    #   puts "load config from file? [y/N]"
+    #   if gets.chomp == "y"
+    #     #use yaml or DSL file to configure
+    #   else
+    #     qb[:dimensions] = dimensions()
+    #     qb[:measures] = measures()
+    #   end
+
+    #   puts "load data from file? [y/N]"
+    #   if gets.chomp == "y"
+    #     #attempt to load dataset from file, ask user to resolve problems or ambiguity
+    #   else
+    #   end
+    #   qb
+    # end
+
+    # def dimensions
+    #   puts "Enter a list of dimensions, separated by commas"
+    #   arr = gets.chomp.split(",")
+    #   dims = {}
+
+    #   arr.map{|dim|
+    #     puts "What is the range of #{dim.chomp.strip}? [:coded]"
+    #     type = gets.chomp
+    #     type = :coded if type == ":coded" || type == ""
+    #     dims[dim.chomp.strip] = {type: type}
+    #   }
+
+    #   dims
+    # end
+
+    # def measures
+    #   puts "Enter a list of measures, separated by commas"
+    #   arr = gets.chomp.split(",")
+    #   meas = []
+
+    #   arr.map{|m| meas << m.chomp.strip}
+
+    #   meas
+    # end
+  end
 end

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

@@ -6,6 +6,8 @@ end
 
 module R2RDF
   module Metadata
+    include R2RDF::Parser
+
     def defaults
     {
       encode_nulls: false,
@@ -18,7 +20,20 @@ module R2RDF
       #make it just "var", and try to make that clear to calling classes
 
       fields[:var] = sanitize([fields[:var]]).first
+
+      unless fields[:creator]
+        if ENV['USER']
+          fields[:creator] = ENV['USER']
+        elsif ENV['USERNAME']
+          fields[:creator] = ENV['USERNAME']
+        end
+      end
+
+      fields[:date] = Time.now.strftime("%Y-%m-%d") unless fields[:date]
+
       options = defaults().merge(options)
+
+      #TODO some of these should probably be resources, eg dct:creator, or put under DC namespace
       str = <<-EOF.unindent
       ns:dataset-#{fields[:var]} rdfs:label "#{fields[:title]}";
         dct:title "#{fields[:title]}";
@@ -52,19 +67,77 @@ module R2RDF
     def provenance(fields, options={})
       #TODO: should either add a prefixes method or replace some with full URIs
       var = sanitize([fields[:var]]).first
+      creator = fields[:creator] if fields[:creator] #should be URI
+      org = fields[:organization] if fields[:organization] #should be URI
       source_software = fields[:software] # software name, object type, optionally steps list for, eg, R
+      str = "ns:dataset-#{var} a prov:Entity.\n\n"
+      assoc_id = Time.now.nsec.to_s(32)
+      endstr = <<-EOF.unindent      
+        </ns/R2RDF> a prov:Agent .
+        ns:dataset-#{var} prov:wasGeneratredBy ns:activity-0 .
+
+        ns:activity-0 a prov:Activity ;
+          prov:qualifiedAssociation ns:assoc-0_#{assoc_id};
+          prov:generated ns:dataset-#{var} .
+
+        ns:assoc-0_#{assoc_id} a prov:Assocation ;
+          prov:entity </ns/R2RDF>;
+          prov:hadPlan ns:plan-0.
+
+        ns:plan-0 a prov:Plan ;
+          rdfs:comment "generation of dataset-#{var} by R2RDF gem".
+
+      EOF
+
+      if creator
+        str << "<#{creator}> a prov:Agent, prov:Person .\n"
+        str << "</ns/R2RDF> prov:actedOnBehalfOf <#{creator}> .\n\n"
+
+        if org
+          str << "<#{org}> a prov:Agent, prov:Organization .\n"
+          str << "<#{creator}> prov:actedOnBehalfOf <#{org}> .\n"
+        end
+      end
 
-      str = "qb:dataset-#{var} a prov:Entity.\n"
-      endstr = "qb:dataset-#{var} prov:wasGeneratredBy <#{options[:base_url]}/ns/R2RDF>\n" #replace once gem has an actual name
       if source_software
-        source_software = [source_software] unless source_software.respond_to? :map
-        source_software.map{|soft|
-          str << "<#{options[:base_url]}/ns/prov/software/#{soft}> a prov:Entity .\n"
+        source_software = [source_software] unless source_software.is_a? Array
+        source_software.each_with_index.map{|soft,i|
+          str << "</ns/prov/software/#{soft[:name]}> a prov:Agent .\n"
 
-          #Note: probably should say derived from the software object, then software object from software.
-          endstr << "qb:dataset-#{var} prov:wasDerivedFrom <#{options[:base_url]}/ns/prov/#{soft}> .\n"
+          endstr << "ns:activity-0 prov:used </ns/dataset/#{var}#var> .\n"
+          endstr << "ns:dataset-#{var} prov:wasDerivedFrom </ns/dataset/#{var}#var> .\n\n"
+
+          if soft[:process]
+            if File.exist? soft[:process]
+              soft[:process] = IO.read(soft[:process])
+            end
+            endstr << "</ns/dataset/#{var}#var> prov:wasGeneratredBy ns:activity-#{i+1} .\n" 
+            endstr << process(i+1, soft[:process],"/ns/prov/software/#{soft[:name]}", var)
+          end
         }
       end
+      str + "\n" + endstr
+    end
+
+    def process(id, step_string, software_resource, software_var, options={})      
+      #TODO a better predicate for the steplist than rdfs:comment
+      # and make sure it looks good.
+      steps = '"' + step_string.split("\n").join('" "') + '"'
+      assoc_id = Time.now.nsec.to_s(32)
+      str = <<-EOF.unindent     
+        ns:activity-#{id} a prov:Activity ;
+          prov:qualifiedAssociation ns:assoc-#{assoc_id} ;
+          prov:used </ns/dataset/#{software_var}#var>.
+
+        ns:assoc-#{id}_#{assoc_id} a prov:Assocation ;
+          prov:entity <#{software_resource}>;
+          prov:hadPlan ns:plan-#{id}.
+
+        ns:plan-#{id} a prov:Plan ;
+          rdfs:comment (#{steps});
+
+      EOF
+
     end
 
     def r2rdf_metadata
@@ -77,7 +150,7 @@ module R2RDF
 
     def org_metadata
       str <<-EOF.unindent
-        <http://sciruby.com/> a org:Organization;
+        <http://sciruby.com/> a org:Organization, prov:Organization;
           skos:prefLabel "SciRuby";
           rdfs:description "A Project to Build and Improve Tools for Scientific Computing in Ruby".
       EOF

data/lib/bio-publisci/parser.rb

@@ -1,5 +1,34 @@
 module R2RDF
 	module Parser
+
+    def sanitize(array)
+      #remove spaces and other special characters
+      processed = []
+      array.map{|entry|
+        if entry.is_a? String
+          processed << entry.gsub(/[\s\.]/,'_')
+        else
+          processed << entry
+        end
+      }
+      processed
+    end
+
+    def sanitize_hash(h)
+      mappings = {}
+      h.keys.map{|k| 
+        if(k.is_a? String)
+          mappings[k] = k.gsub(' ','_')
+        end
+      }
+
+      h.keys.map{|k|
+        h[mappings[k]] = h.delete(k) if mappings[k]
+      }
+
+      h
+    end
+
 		def create_graph(string)
 			f = Tempfile.new('graph')
 			f.write(string)
@@ -57,8 +86,54 @@ module R2RDF
 	    end
     end
 
+    def to_resource(obj, options)
+      if obj.is_a? String
+        obj = "<#{obj}>" if obj =~ /^http:\/\//
+          
+        #TODO decide the right way to handle missing values, since RDF has no null
+        #probably throw an error here since a missing resource is a bigger problem
+        obj = "NA" if obj.empty?
+        
+        #TODO  remove special characters (faster) as well (eg '?')
+        obj.gsub(' ','_').gsub('?','')
+      elsif obj == nil && options[:encode_nulls]
+        '"NA"'
+      elsif obj.is_a? Numeric
+        #resources cannot be referred to purely by integer (?)
+        "n"+obj.to_s
+      else
+        obj
+      end
+    end
+
+    def to_literal(obj, options)
+      if obj.is_a? String
+        # Depressing that there's no more elegant way to check if a string is 
+        # a number...
+        if val = Integer(obj) rescue nil
+          val
+        elsif val = Float(obj) rescue nil
+          val
+        else
+          '"'+obj+'"'
+        end
+      elsif obj == nil && options[:encode_nulls]
+        #TODO decide the right way to handle missing values, since RDF has no null
+        '"NA"'
+      else
+        obj
+      end
+    end
+
     def strip_uri(uri)
-    	uri.to_s.split('/').last.split('#').last
+      uri = uri.to_s.dup
+      uri[-1] = '' if uri[-1] == '>'
+      uri.to_s.split('/').last.split('#').last
+    end
+
+    def strip_prefixes(string)
+      string.to_s.split(':').last
     end
+
 	end
 end