bel 0.7.0 → 1.0.0

data/lib/bel/{evidence_model/summary_text.rb → nanopub/support.rb}

@@ -1,8 +1,8 @@
 require 'forwardable'
 
 module BEL
-  module Model
-    class SummaryText
+  module Nanopub
+    class Support
       extend Forwardable
 
       attr_accessor :value
@@ -11,6 +11,12 @@ module BEL
         @value = value
       end
 
+      def ==(other)
+        return false if other.nil?
+        @value == other.value
+      end
+      alias eql? ==
+
       def_delegators :@value, :to_s
     end
   end

data/lib/bel/{evidence_model → nanopub}/util.rb

@@ -1,8 +1,8 @@
 module BEL
-  module Model
+  module Nanopub
 
     def self.union_namespace_references(destination, source, suffix = 'incr')
-      BEL::Model.union_by_keyword(
+      BEL::Nanopub.union_by_keyword(
         destination,
         source,
         suffix
@@ -10,7 +10,7 @@ module BEL
     end
 
     def self.union_annotation_references(destination, source, suffix = 'incr')
-      BEL::Model.union_by_keyword(
+      BEL::Nanopub.union_by_keyword(
         destination,
         source,
         suffix
@@ -36,21 +36,20 @@ module BEL
       remap_result   = {}
 
       combined = destination + new.map { |new_obj|
-        new_key = new_obj[:keyword].to_s
+        new_key = new_obj.keyword
 
         # find a match where the keyword differs
-        new_value      = new_obj.reject { |key, value| key == :keyword }
         match_by_value = destination.find { |dest|
-          new_value == dest.reject { |key, value| key == :keyword }
+          new_obj.domain_equal?(dest)
         }
 
         rewrite_key =
           if match_by_value
-            match_by_value[:keyword]
+            match_by_value.keyword
           else
             # find max suffix match
             max_suffix = destination.map { |dest|
-              key, suffix_number = dest[:keyword].to_s.split(suffix_pattern)
+              key, suffix_number = dest.keyword.to_s.split(suffix_pattern)
               if new_key == key
                 suffix_number
               else
@@ -63,7 +62,7 @@ module BEL
             if max_suffix
               new_key + suffix + max_suffix.next
             else
-              if destination.any? { |dest| dest[:keyword] == new_key }
+              if destination.any? { |dest| dest.keyword == new_key }
                 "#{new_key}#{suffix}1"
               else
                 new_key
@@ -71,7 +70,8 @@ module BEL
             end
           end
 
-        rewrite_obj           = new_obj.merge({:keyword => rewrite_key})
+        rewrite_obj           = new_obj.dup
+        rewrite_obj.keyword   = rewrite_key
         remap_result[new_obj] = rewrite_obj
         rewrite_obj
       }

data/lib/bel/resource/annotation.rb

@@ -1,28 +1,31 @@
 require          'rdf'
+require          'rdf/vocab'
+require_relative 'concept_scheme'
 require_relative 'annotation_value'
 
 module BEL
   module Resource
-
-    # TODO Document
+    # Annotation represents a AnnotationConceptScheme RDF Resource and
+    # associated properties.
     class Annotation
+      include ConceptScheme
+
+      DC   = RDF::Vocab::DC
+      SKOS = RDF::Vocab::SKOS
+      BELV = RDF::Vocabulary.new('http://www.openbel.org/vocabulary/')
 
       attr_reader :uri
 
-      # TODO Document
       def initialize(rdf_repository, uri)
         @rdf_repository = rdf_repository
         @uri            = RDF::URI(uri.to_s)
         @uri_hash       = @uri.hash
         @concept_query  = [
-          :predicate => RDF::SKOS.inScheme,
+          :predicate => SKOS.inScheme,
           :object    => @uri
         ]
-        @predicates     = @rdf_repository.query(:subject => @uri).
-                            each.map(&:predicate)
       end
 
-      # TODO Document
       def each
         return to_enum(:each) unless block_given?
 				@rdf_repository.
@@ -66,21 +69,21 @@ module BEL
         # match input as annotation value prefLabel
 				vlit  = RDF::Literal(vstr)
 				label = value_query(
-					:predicate => RDF::SKOS.prefLabel,
+					:predicate => SKOS.prefLabel,
 					:object    => vlit
 				)
 			  return AnnotationValue.new(@rdf_repository, label.subject) if label
 
         # match input as annotation value identifier
 				ident = value_query(
-					:predicate => RDF::DC.identifier,
+					:predicate => DC.identifier,
 					:object    => vlit
 				)
 				return AnnotationValue.new(@rdf_repository, ident.subject) if ident
 
         # match input as annotation value title
 				title = value_query(
-					:predicate => RDF::DC.title,
+					:predicate => DC.title,
 					:object    => vlit
 				)
 				return AnnotationValue.new(@rdf_repository, title.subject) if title
@@ -88,7 +91,7 @@ module BEL
 
       def find_annotation_value_uri(uri)
         in_annotation_check = @rdf_repository.has_statement?(
-          RDF::Statement(uri, RDF::SKOS.inScheme, @uri)
+          RDF::Statement(uri, SKOS.inScheme, @uri)
         )
         return nil if !in_annotation_check
 
@@ -101,22 +104,10 @@ module BEL
       def value_query(pattern)
 				@rdf_repository.query(pattern).find { |solution|
 				  @rdf_repository.has_statement?(
-						RDF::Statement(solution.subject, RDF::SKOS.inScheme, @uri)
+						RDF::Statement(solution.subject, SKOS.inScheme, @uri)
 					)
 				}
       end
-
-      def method_missing(method)
-        method_predicate = @predicates.find { |p|
-          p.qname[1].to_sym == method.to_sym
-        }
-        return nil unless method_predicate
-        objects = @rdf_repository.query(
-          :subject   => @uri,
-          :predicate => method_predicate
-        ).each.map(&:object)
-        objects.size == 1 ? objects.first : objects.to_a
-      end
     end
   end
 end

data/lib/bel/resource/annotation_value.rb

@@ -1,34 +1,52 @@
 require          'rdf'
+require          'rdf/vocab'
+require_relative 'concept'
 require_relative 'annotation'
 require_relative 'annotations'
 
 module BEL
   module Resource
 
-    # TODO Document
+    # AnnotationValue represents a AnnotationConcept RDF Resource and
+    # associated properties.
     class AnnotationValue
+      include Concept
+
+      DC   = RDF::Vocab::DC
+      SKOS = RDF::Vocab::SKOS
+      BELV = RDF::Vocabulary.new('http://www.openbel.org/vocabulary/')
 
       attr_reader :uri
 
-      # TODO Document
       def initialize(rdf_repository, uri)
         @rdf_repository = rdf_repository
         @uri            = RDF::URI(uri.to_s)
         @uri_hash       = @uri.hash
         @eq_query       = [
           :subject   => @uri,
-          :predicate => RDF::SKOS.exactMatch
+          :predicate => SKOS.exactMatch
         ]
         @ortho_query    = [
           :subject   => @uri,
           :predicate => BELV.orthologousMatch
         ]
-        @predicates     = @rdf_repository.query(:subject => @uri).
-                            each.map(&:predicate).uniq
       end
 
       def annotation
-        Annotation.new(@rdf_repository, self.inScheme)
+        schemes = in_scheme
+        return nil if schemes.empty?
+        Annotation.new(@rdf_repository, schemes.first)
+      end
+
+      def in_scheme
+        @rdf_repository
+        .query([:subject => @uri, :predicate => SKOS.inScheme])
+        .select { |solution|
+          scheme_uri = solution.object
+          @rdf_repository.has_statement?(
+            RDF::Statement(scheme_uri, RDF.type, BELV.AnnotationConceptScheme)
+          )
+        }.map { |solution| solution.object.to_s }
       end
 
       def equivalents(target_annotations = :all)
@@ -65,20 +83,6 @@ module BEL
         @uri == other.uri
       end
       alias_method :eql?, :'=='
-
-      protected
-
-      def method_missing(method)
-        method_predicate = @predicates.find { |p|
-          p.qname[1].to_sym == method.to_sym
-        }
-        return nil unless method_predicate
-        objects = @rdf_repository.query(
-          :subject   => @uri,
-          :predicate => method_predicate
-        ).each.map(&:object)
-        objects.size == 1 ? objects.first : objects.to_a
-      end
     end
   end
 end

data/lib/bel/resource/annotations.rb

@@ -1,27 +1,28 @@
+require          'rdf'
+require          'rdf/vocab'
 require_relative 'annotation'
 
 module BEL
   module Resource
-
-    # TODO Document
+    # Annotations allows access to all AnnotationConceptScheme RDF Resources
+    # available in the resources dataset.
     class Annotations
 
-      # TODO Document
-      QUERY_ANNOTATIONS = RDF::Query.new do
-        pattern [:uri, RDF.type, BELV.AnnotationConceptScheme]
-      end
+      BELV = RDF::Vocabulary.new('http://www.openbel.org/vocabulary/')
+      SKOS = RDF::Vocab::SKOS
 
-      # TODO Document
       def initialize(rdf_repository)
         @rdf_repository = rdf_repository
       end
 
-      # TODO Document
       def each
         return to_enum(:each) unless block_given?
 				@rdf_repository.
-					query(QUERY_ANNOTATIONS) { |solution|
-						yield Annotation.new(@rdf_repository, solution.uri)
+					query(
+            :predicate => RDF.type,
+            :object => BELV.AnnotationConceptScheme) { |solution|
+
+						yield Annotation.new(@rdf_repository, solution.subject)
 					}
       end
 
@@ -57,7 +58,7 @@ module BEL
 
         # match input as annotation prefLabel
 				label  = annotation_query(
-					:predicate => RDF::SKOS.prefLabel,
+					:predicate => SKOS.prefLabel,
 					:object    => nlit
 				)
 				return Annotation.new(@rdf_repository, label.subject) if label

data/lib/bel/resource/concept.rb

@@ -0,0 +1,62 @@
+require 'rdf'
+require 'rdf/vocab'
+
+module BEL
+  module Resource
+    # Concept captures the properties available on an RDF Annotation or
+    # Namespace Concept.
+    module Concept
+      DC   = RDF::Vocab::DC
+      SKOS = RDF::Vocab::SKOS
+      BELV = RDF::Vocabulary.new('http://www.openbel.org/vocabulary/')
+
+      def type
+        @rdf_repository
+        .query([:subject => @uri, :predicate => RDF.type])
+        .map do |solution|
+          solution.object.to_s
+        end
+      end
+
+      def pref_label
+        @rdf_repository
+        .query([:subject => @uri, :predicate => SKOS.prefLabel])
+        .map do |solution|
+          solution.object.to_s
+        end
+      end
+
+      def identifier
+        @rdf_repository
+        .query([:subject => @uri, :predicate => DC.identifier])
+        .map do |solution|
+          solution.object.to_s
+        end
+      end
+
+      def title
+        @rdf_repository
+        .query([:subject => @uri, :predicate => DC.title])
+        .map do |solution|
+          solution.object.to_s
+        end
+      end
+
+      def alt_label
+        @rdf_repository
+        .query([:subject => @uri, :predicate => SKOS.altLabel])
+        .map do |solution|
+          solution.object.to_s
+        end
+      end
+
+      def from_species
+        @rdf_repository
+        .query([:subject => @uri, :predicate => BELV.fromSpecies])
+        .map do |solution|
+          solution.object.to_s
+        end
+      end
+    end
+  end
+end

data/lib/bel/resource/concept_scheme.rb

@@ -0,0 +1,49 @@
+require 'rdf'
+require 'rdf/vocab'
+
+module BEL
+  module Resource
+    # ConceptScheme captures the properties available on an RDF Annotation or
+    # Namespace ConceptScheme.
+    module ConceptScheme
+      SKOS = RDF::Vocab::SKOS
+      BELV = RDF::Vocabulary.new('http://www.openbel.org/vocabulary/')
+
+      def type
+        solution =
+          @rdf_repository
+          .query([:subject => @uri, :predicate => RDF.type])
+          .map do |solution|
+            solution.object.to_s
+          end
+      end
+
+      def pref_label
+        solution =
+          @rdf_repository
+          .query([:subject => @uri, :predicate => SKOS.prefLabel])
+          .map do |solution|
+            solution.object.to_s
+          end
+      end
+
+      def domain
+        solution =
+          @rdf_repository
+          .query([:subject => @uri, :predicate => BELV.domain])
+          .map do |solution|
+            solution.object.to_s
+          end
+      end
+
+      def prefix
+        solution =
+          @rdf_repository
+          .query([:subject => @uri, :predicate => BELV.prefix])
+          .map do |solution|
+            solution.object.to_s
+          end
+      end
+    end
+  end
+end

data/lib/bel/resource/namespace.rb

@@ -1,28 +1,31 @@
 require          'rdf'
+require          'rdf/vocab'
+require_relative 'concept_scheme'
 require_relative 'namespace_value'
 
 module BEL
   module Resource
-
-    # TODO Document
+    # Namespace represents a NamespaceConceptScheme RDF Resource and
+    # associated properties.
     class Namespace
+      include ConceptScheme
 
       attr_reader :uri
 
-      # TODO Document
+      DC   = RDF::Vocab::DC
+      SKOS = RDF::Vocab::SKOS
+      BELV = RDF::Vocabulary.new('http://www.openbel.org/vocabulary/')
+
       def initialize(rdf_repository, uri)
         @rdf_repository = rdf_repository
         @uri            = RDF::URI(uri.to_s)
         @uri_hash       = @uri.hash
         @concept_query  = [
-          :predicate => RDF::SKOS.inScheme,
+          :predicate => SKOS.inScheme,
           :object    => @uri
         ]
-        @predicates     = @rdf_repository.query(:subject => @uri).
-                            each.map(&:predicate)
       end
 
-      # TODO Document
       def each
         return to_enum(:each) unless block_given?
 				@rdf_repository.
@@ -66,21 +69,21 @@ module BEL
         # match input as namespace value prefLabel
 				vlit  = RDF::Literal(vstr)
 				label = value_query(
-					:predicate => RDF::SKOS.prefLabel,
+					:predicate => SKOS.prefLabel,
 					:object    => vlit
 				)
 			  return NamespaceValue.new(@rdf_repository, label.subject) if label
 
         # match input as namespace value identifier
 				ident = value_query(
-					:predicate => RDF::DC.identifier,
+					:predicate => DC.identifier,
 					:object    => vlit
 				)
 				return NamespaceValue.new(@rdf_repository, ident.subject) if ident
 
         # match input as namespace value title
 				title = value_query(
-					:predicate => RDF::DC.title,
+					:predicate => DC.title,
 					:object    => vlit
 				)
 				return NamespaceValue.new(@rdf_repository, title.subject) if title
@@ -89,7 +92,7 @@ module BEL
       def find_namespace_value_uri(uri_s)
         subject            = RDF::URI(uri_s)
         in_namespace_check = @rdf_repository.has_statement?(
-          RDF::Statement(subject, RDF::SKOS.inScheme, @uri)
+          RDF::Statement(subject, SKOS.inScheme, @uri)
         )
         return nil if !in_namespace_check
 
@@ -102,22 +105,10 @@ module BEL
       def value_query(pattern)
 				@rdf_repository.query(pattern).find { |solution|
 				  @rdf_repository.has_statement?(
-						RDF::Statement(solution.subject, RDF::SKOS.inScheme, @uri)
+						RDF::Statement(solution.subject, SKOS.inScheme, @uri)
 					)
 				}
       end
-
-      def method_missing(method)
-        method_predicate = @predicates.find { |p|
-          p.qname[1].to_sym == method.to_sym
-        }
-        return nil unless method_predicate
-        objects = @rdf_repository.query(
-          :subject   => @uri,
-          :predicate => method_predicate
-        ).each.map(&:object)
-        objects.size == 1 ? objects.first : objects.to_a
-      end
     end
   end
 end