bel 0.4.0.beta.4 → 0.4.0.beta.5

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/bel/resource.rb

@@ -18,6 +18,9 @@ module BEL
   end
 end
 
+require_relative 'resource/annotations'
+require_relative 'resource/annotation'
+require_relative 'resource/annotation_value'
 require_relative 'resource/namespaces'
 require_relative 'resource/namespace'
 require_relative 'resource/namespace_value'

data/lib/bel/resource/annotation.rb

@@ -0,0 +1,122 @@
+require          'rdf'
+require_relative 'annotation_value'
+
+module BEL
+  module Resource
+
+    # TODO Document
+    class Annotation
+
+      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,
+          :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.
+					query(@concept_query) { |solution|
+						yield AnnotationValue.new(@rdf_repository, solution.subject)
+					}
+      end
+
+      def find(*values)
+        return to_enum(:find, *values) unless block_given?
+
+        values.flatten.each do |v|
+          yield find_value(v)
+				end
+			end
+
+      def hash
+        @uri_hash
+      end
+
+      def ==(other)
+        return false if other == nil
+        @uri == other.uri
+      end
+      alias_method :eql?, :'=='
+
+      protected
+
+      def find_value(value)
+        # nil input always yield nil
+        return nil if value == nil
+
+        # RDF::URI input handled as a special case
+        return find_annotation_value_uri(value) if value.is_a?(RDF::URI)
+
+        # input handled as literal identifier; empty literals match in a
+        # pattern as if it was nil so return nil if empty string
+        vstr  = value.to_s
+        return nil if vstr.empty?
+
+        # match input as annotation value prefLabel
+				vlit  = RDF::Literal(vstr)
+				label = value_query(
+					:predicate => RDF::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,
+					:object    => vlit
+				)
+				return AnnotationValue.new(@rdf_repository, ident.subject) if ident
+
+        # match input as annotation value title
+				title = value_query(
+					:predicate => RDF::DC.title,
+					:object    => vlit
+				)
+				return AnnotationValue.new(@rdf_repository, title.subject) if title
+      end
+
+      def find_annotation_value_uri(uri)
+        in_annotation_check = @rdf_repository.has_statement?(
+          RDF::Statement(uri, RDF::SKOS.inScheme, @uri)
+        )
+        return nil if !in_annotation_check
+
+        type_check = RDF::Statement(uri, RDF.type, BELV.AnnotationConcept)
+				if @rdf_repository.has_statement?(type_check)
+          return AnnotationValue.new(@rdf_repository, uri)
+        end
+			end
+
+      def value_query(pattern)
+				@rdf_repository.query(pattern).find { |solution|
+				  @rdf_repository.has_statement?(
+						RDF::Statement(solution.subject, RDF::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

@@ -0,0 +1,84 @@
+require          'rdf'
+require_relative 'annotation'
+require_relative 'annotations'
+
+module BEL
+  module Resource
+
+    # TODO Document
+    class AnnotationValue
+
+      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
+        ]
+        @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)
+      end
+
+      def equivalents(target_annotations = :all)
+        return to_enum(:equivalents, target_annotations) unless block_given?
+        if target_annotations == :all
+          @rdf_repository.
+            query(@eq_query) { |solution|
+              yield AnnotationValue.new(@rdf_repository, solution.object)
+            }
+        else
+          target_annotations = Annotations.new(@rdf_repository).
+            find([target_annotations].flatten).to_a
+          target_annotations.compact!
+          target_annotations.map! { |ns| ns.uri }
+
+          @rdf_repository.
+            query(@eq_query).map { |solution|
+              AnnotationValue.new(@rdf_repository, solution.object)
+            }.select { |value|
+              scheme_uri = value.inScheme
+              target_annotations.include?(scheme_uri)
+            }.each { |value|
+              yield value
+            }
+        end
+			end
+
+      def hash
+        @uri_hash
+      end
+
+      def ==(other)
+        return false if other == nil
+        @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

@@ -0,0 +1,82 @@
+require_relative 'annotation'
+
+module BEL
+  module Resource
+
+    # TODO Document
+    class Annotations
+
+      # TODO Document
+      QUERY_ANNOTATIONS = RDF::Query.new do
+        pattern [:uri, RDF.type, BELV.AnnotationConceptScheme]
+      end
+
+      # 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)
+					}
+      end
+
+      def find(*annotations)
+        return to_enum(:find, *annotations) unless block_given?
+
+        annotations.flatten.each do |an|
+          yield find_annotation(an)
+				end
+			end
+
+      protected
+
+      def find_annotation(annotation)
+        # nil input always yield nil
+        return nil if annotation == nil
+
+        # RDF::URI input handled as a special case
+        return find_annotation_uri(annotation) if annotation.is_a?(RDF::URI)
+
+        # input handled as literal identifier; empty literals will match
+        # in a pattern as if it was nil so return nil if empty string
+        nstr  = annotation.to_s
+        return nil if nstr.empty?
+
+        # match input as annotation prefix
+				nlit   = RDF::Literal(nstr)
+				prefix = annotation_query(
+					:predicate => BELV.prefix,
+					:object    => nlit
+				)
+			  return Annotation.new(@rdf_repository, prefix.subject) if prefix
+
+        # match input as annotation prefLabel
+				label  = annotation_query(
+					:predicate => RDF::SKOS.prefLabel,
+					:object    => nlit
+				)
+				return Annotation.new(@rdf_repository, label.subject) if label
+      end
+
+      def find_annotation_uri(uri)
+        type_check = RDF::Statement(uri, RDF.type, BELV.AnnotationConceptScheme)
+				if @rdf_repository.has_statement?(type_check)
+          return Annotation.new(@rdf_repository, uri)
+        end
+			end
+
+      def annotation_query(pattern)
+				@rdf_repository.query(pattern).find { |solution|
+				  @rdf_repository.has_statement?(
+						RDF::Statement(solution.subject, RDF.type, BELV.AnnotationConceptScheme)
+					)
+				}
+      end
+    end
+  end
+end

data/lib/bel/resource/namespace.rb

@@ -1,5 +1,4 @@
 require          'rdf'
-require_relative '../resource'
 require_relative 'namespace_value'
 
 module BEL

data/lib/bel/resource/namespace_value.rb

@@ -1,4 +1,5 @@
 require          'rdf'
+require_relative 'namespace'
 require_relative 'namespaces'
 
 module BEL
@@ -26,6 +27,10 @@ module BEL
                             each.map(&:predicate).uniq
       end
 
+      def namespace
+        Namespace.new(@rdf_repository, self.inScheme)
+      end
+
       def equivalents(target_namespaces = :all)
         return to_enum(:equivalents, target_namespaces) unless block_given?
         if target_namespaces == :all

data/lib/bel/resource/namespaces.rb

@@ -1,3 +1,4 @@
+require          'rdf'
 require_relative 'namespace'
 
 module BEL

data/lib/bel/version.rb

@@ -1,3 +1,3 @@
 module BEL
-  VERSION = '0.4.0.beta.4'
+  VERSION = '0.4.0.beta.5'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel
 version: !ruby/object:Gem::Version
-  version: 0.4.0.beta.4
+  version: 0.4.0.beta.5
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -127,6 +127,9 @@ files:
 - lib/bel/rdf_repository/plugins/memory.rb
 - lib/bel/rdf_repository/plugins/mongo.rb
 - lib/bel/resource.rb
+- lib/bel/resource/annotation.rb
+- lib/bel/resource/annotation_value.rb
+- lib/bel/resource/annotations.rb
 - lib/bel/resource/namespace.rb
 - lib/bel/resource/namespace_value.rb
 - lib/bel/resource/namespaces.rb