bio-publisci 0.0.6 → 0.0.7

data/lib/bio-publisci/metadata/prov/model/prov_models.rb

@@ -1,10 +1,10 @@
 require 'rdf/4store'
 
-begin
-  require 'spira'
+# begin
+  # require 'spira'
 
 module PubliSci
-  module Prov
+  class Prov
     module Model
       PROV ||= RDF::Vocabulary.new(RDF::URI.new('http://www.w3.org/ns/prov#'))
 
@@ -51,19 +51,18 @@ module PubliSci
         has_many :qualifiedAssociation, predicate: PROV.qualifiedAssociation
       end
 
-
       class Association < Spira::Base
         type PROV.Association
         property :label, predicate: RDF::RDFS.label
         property :agent, predicate: PROV.agent
-        property :hadPlan, predicate: PROV.plan
+        property :hadPlan, predicate: PROV.hadPlan
       end
 
       class Derivation < Spira::Base
         type PROV.Derivation
         property :label, predicate: RDF::RDFS.label
         property :agent, predicate: PROV.agent
-        property :hadPlan, predicate: PROV.plan
+        property :hadPlan, predicate: PROV.hadPlan
       end
 
       class Plan < Spira::Base
@@ -74,6 +73,6 @@ module PubliSci
     end
   end
 end
-rescue LoadError
-  # puts "spira not installed, ORM unavailable"
-end
+# rescue LoadError
+#   puts "spira not installed, ORM unavailable"
+# end

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

@@ -1,5 +1,5 @@
 module PubliSci
-module Prov
+class Prov
   class Plan
     include Prov::Element
 

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

@@ -1,39 +1,41 @@
 module PubliSci
-  module Prov
-    def self.register(name,object)
-      # puts "register #{name} #{object} #{associations.size}"
-      name = name.to_sym if name
+  class Prov
+    extend PubliSci::Registry
+
+    def self.configuration
+      @config ||= Configuration.new
+    end
+
+    def self.symbol_for(object)
       if object.is_a? Agent
-        sub = :agents
+        :agents
       elsif object.is_a? Entity
-        sub = :entities
+        :entities
       elsif object.is_a? Activity
-        sub = :activities
+        :activities
       elsif object.is_a? Association
-        sub = :associations
+        :associations
       elsif object.is_a? Plan
-        sub = :plans
-      else
-        sub = object.class.to_s.split('::').last.downcase.to_sym
-        # raise "UnknownElement: unkown object type for #{object}"
-      end
-      if name
-        (registry[sub] ||= {})[name] = object
+        :plans
       else
-        (registry[sub] ||= []) << object
+        false
       end
     end
 
-    def self.registry
-      @registry ||= {}
-    end
 
     def self.run(string)
+      sing =DSL::Instance.new
       if File.exists? string
-        DSL::Singleton.new.instance_eval(IO.read(string),string)
+        sing.instance_eval(IO.read(string),string)
       else
-        DSL::Singleton.new.instance_eval(string)
+        sing.instance_eval(string)
       end
+      sing.output
+    end
+
+    def self.reset_settings
+      Configuration.defaults.map{|k,v| configuration.send("#{k}=",v)}
+      @base_url=nil
     end
 
     def self.agents

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

@@ -1,5 +1,5 @@
 module PubliSci
-  module Prov
+  class Prov
     class Role
       # attr_writer :comment
 

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

@@ -1,5 +1,5 @@
 module PubliSci
-  module Prov
+  class Prov
     class Usage
       include Prov::Element
 

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

@@ -0,0 +1,25 @@
+module PubliSci
+  class Metadata
+    class Publisher
+
+      def uri(uri=nil)
+        if uri
+          @uri = uri
+        else
+          @uri
+        end
+      end
+      alias_method :url, :uri
+
+      def label(label=nil)
+        if label
+          @label = label
+        else
+          @label
+        end
+      end
+      alias_method :name, :label
+
+    end
+  end
+end

data/lib/bio-publisci/mixins/dereferencable.rb

@@ -1,5 +1,5 @@
 module PubliSci
-  module Prov
+  class Prov
     module Dereferencable
       def dereference
         self.map{|x|

data/lib/bio-publisci/mixins/registry.rb

@@ -0,0 +1,27 @@
+module PubliSci
+  module Registry
+    def register(name,object)
+      # puts "register #{name} #{object} #{associations.size}"
+      name = name.to_sym if name
+      if symbol_for(object)
+        sub = symbol_for(object)
+      else
+        sub = object.class.to_s.split('::').last.downcase.to_sym
+      end
+      if name
+        (registry[sub] ||= {})[name] = object
+      else
+        (registry[sub] ||= []) << object
+      end
+    end
+
+    def registry
+      @registry ||= {}
+    end
+
+    #should be overridden
+    def symbol_for(object)
+      false
+    end
+  end
+end

data/lib/bio-publisci/output.rb

@@ -1,4 +1,4 @@
-module R2RDF
+module PubliSci
   module Reader
     module Output
       def output(string, options={},append=false)

data/lib/bio-publisci/parser.rb

@@ -1,4 +1,4 @@
-module R2RDF
+module PubliSci
 	module Parser
 
     def is_uri?(string)

data/lib/bio-publisci/query/query_helper.rb

@@ -16,7 +16,7 @@ module RDF
 	end
 end
 
-module R2RDF
+module PubliSci
   #.gsub(/^\s+/,'')
   module Query
     def vocabulary
@@ -30,19 +30,19 @@ module R2RDF
       }
     end
 
-    
+
 
     # def execute_internal(query,repo)
     #   SPARQL.execute(query,repo)
     # end
 
     def execute(string,store,type=:fourstore)
-    	if type == :graph || store.is_a?(RDF::Graph) || store.is_a?(RDF::Repository)    		
+    	if type == :graph || store.is_a?(RDF::Graph) || store.is_a?(RDF::Repository)
 				sparql = SPARQL::Client.new(store)
-			elsif store.is_a? R2RDF::Store
-				sparql = SPARQL::Client.new(store.url+"/sparql/")				
+			elsif store.is_a? PubliSci::Store
+				sparql = SPARQL::Client.new(store.url+"/sparql/")
 			elsif type == :fourstore
-				sparql = SPARQL::Client.new(store+"/sparql/")				
+				sparql = SPARQL::Client.new(store+"/sparql/")
       end
       sparql.query(string)
     end
@@ -62,13 +62,13 @@ module R2RDF
 
 #     def prefixes
 #       <<-EOF
-# PREFIX ns:     <http://www.rqtl.org/ns/#> 
-# 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://www.rqtl.org/dc/properties/> 
+# PREFIX ns:     <http://www.rqtl.org/ns/#>
+# 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://www.rqtl.org/dc/properties/>
 # PREFIX cs:   <http://www.rqtl.org/dc/cs/>
-# PREFIX skos: <http://www.w3.org/2004/02/skos/core#> 
+# PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
 
 #       EOF
 #     end
@@ -109,6 +109,6 @@ SELECT DISTINCT ?label WHERE {
   end
 
   class QueryHelper
-    include R2RDF::Query
-  end  
+    include PubliSci::Query
+  end
 end

data/lib/bio-publisci/r_client.rb

@@ -1,6 +1,6 @@
-module R2RDF
+module PubliSci
 	module Rconnect
-		
+
 		def connect(address=nil)
 			if address
 				Rserve::Connection.new(address)
@@ -22,12 +22,12 @@ module R2RDF
 			connection.eval("ls()")
 		end
 
-	end 
+	end
 
 	class Client
-		include R2RDF::Rconnect
+		include PubliSci::Rconnect
     attr :R
-    
+
 		def initialize(auto=true, loc=Dir.home)
       @R = connect
 			@loc = loc

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

@@ -1,15 +1,15 @@
-module R2RDF
+module PubliSci
 		module Reader
 		class ARFF
-			include R2RDF::Dataset::DataCube
+			include PubliSci::Dataset::DataCube
 			def generate_n3(arff, options={})
-				arff = IO.read(arff) if File.exist? arff	
+				arff = IO.read(arff) if File.exist? arff
 				options[:no_labels] = true # unless options[:no_labels] == nil
 				@options = options
 				comps =  components(arff)
 				obs = data(arff, comps.keys)
 				repl = generate(comps.reject{|c| comps[c][:codes]}.keys, comps.select{|c| comps[c][:codes]}.keys, comps.select{|c| comps[c][:codes]}.keys, obs, (1..obs.first[1].size).to_a, relation(arff), options)
-				
+
 			end
 
 			def relation(arff)
@@ -52,7 +52,7 @@ module R2RDF
 		# 			[@options[:row_label]]
 		# 		else
 		# 			["refRow"]
-		# 		end	
+		# 		end
 		# 	end
 
 		# 	def measures

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

@@ -1,8 +1,8 @@
-module R2RDF
+module PubliSci
 	module Reader
 		class CSV
-      include R2RDF::Dataset::DataCube
-			include R2RDF::Interactive
+      include PubliSci::Dataset::DataCube
+			include PubliSci::Interactive
 
       def automatic(file=nil,dataset_name=nil,options={},interactive=true)
         #to do

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

@@ -1,8 +1,8 @@
-module R2RDF
+module PubliSci
 		module Reader
 		class Dataframe
-      include R2RDF::Dataset::DataCube
-			include R2RDF::Reader::Output
+      include PubliSci::Dataset::DataCube
+			include PubliSci::Reader::Output
 
 			# def initialize(var)
 			# 	@var = var

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

@@ -1,8 +1,8 @@
-module R2RDF
+module PubliSci
   module Reader
     class RCross
-      include R2RDF::Dataset::DataCube
-      include R2RDF::Reader::Output
+      include PubliSci::Dataset::DataCube
+      include PubliSci::Reader::Output
 
       def generate_n3(client, var, outfile_base, options={})
         meas = measures(client,var,options)
@@ -42,7 +42,7 @@ module R2RDF
         str = prefixes(var,options)
         str << data_structure_definition(meas,dim,codes,var,options)
         str << dataset(var,options)
-        component_specifications(meas, dim, var, options).map{ |c| str << c }
+        component_specifications(meas, dim, codes, var, options).map{ |c| str << c }
         measure_properties(meas,var,options).map{|m| str << m}
 
         str

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

@@ -1,7 +1,7 @@
-module R2RDF
+module PubliSci
 	module Reader
 		class RMatrix
-			include R2RDF::Dataset::DataCube
+			include PubliSci::Dataset::DataCube
 
 			#NOTE; this is pretty much hard coded for Karl's application right now, and doesn't
 			# do any dimension or code generation. Since its a set of LOD scores indexed by dimension
@@ -76,7 +76,7 @@ module R2RDF
 				str = prefixes(var, options)
 				str << data_structure_definition(meas,[],codes,outvar,options)
 				str << dataset(outvar,options)
-    		component_specifications(meas, dim, var, options).map{ |c| str << c }
+    		component_specifications(meas, dim, codes, var, options).map{ |c| str << c }
 				measure_properties(meas,var,options).map{|m| str << m}
 
 				str

data/lib/bio-publisci/store.rb

@@ -1,7 +1,7 @@
-module R2RDF
+module PubliSci
   # handles connection and messaging to/from the triple store
   class Store
-    include R2RDF::Query
+    include PubliSci::Query
 
     def defaults
       {
@@ -27,7 +27,7 @@ module R2RDF
     end
 
     def add_all(dir, graph, pattern=nil)
-      pattern = /.+\.ttl/ if pattern == :turtle || pattern == :ttl 
+      pattern = /.+\.ttl/ if pattern == :turtle || pattern == :ttl
 
       files = Dir.entries(dir) - %w(. ..)
       files = files.grep(pattern) if pattern.is_a? Regexp

data/lib/bio-publisci/writers/arff.rb

@@ -1,9 +1,9 @@
-module R2RDF
+module PubliSci
   module Writer
     class ARFF
-      include R2RDF::Query
-      include R2RDF::Parser
-      include R2RDF::Analyzer
+      include PubliSci::Query
+      include PubliSci::Parser
+      include PubliSci::Analyzer
 
       def build_arff(relation, attributes, data, source)
         str = <<-EOS
@@ -11,7 +11,7 @@ module R2RDF
 %
 % 2. Sources:
 %    (a) Generated from RDF source #{source}
-%     
+%
 @RELATION #{relation}
 
 EOS
@@ -30,7 +30,7 @@ EOS
         puts "loading #{turtle_file}" if verbose
         repo = RDF::Repository.load(turtle_file)
         puts "loaded #{repo.size} statements into temporary repo" if verbose
-        
+
         dims = execute_from_file("dimensions.rq",repo,:graph).to_h.map{|d| [d[:dimension].to_s, d[:label].to_s]}
         meas = execute_from_file("measures.rq",repo,:graph).to_h.map{|m| [m[:measure].to_s, m[:label].to_s]}
         relation = execute_from_file("dataset.rq",repo,:graph).to_h.first[:label].to_s