bel_parser 1.0.0.alpha.12 → 1.0.0.alpha.13

data/lib/bel_parser/language/version2_0/value_encodings/abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version2_0'
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ValueEncodings
+        # Abundance value encoding.
+        class Abundance < Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Abundance
+            :A
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/value_encodings/activity.rb

@@ -0,0 +1,21 @@
+require_relative '../../version2_0'
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ValueEncodings
+        # Activity value encoding.
+        class Activity < Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Activity
+            :T
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/value_encodings/any.rb

@@ -0,0 +1,74 @@
+require 'English'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ValueEncodings
+        # The Any value encoding.
+        class Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Any
+            :*
+          end
+
+          # Returns +true+ if I am a subtype of +other_return_type+; otherwise
+          # return +false+.
+          #
+          # @param  [Class]   other_return_type to compare to
+          # @return [Boolean] +true+ if I am a subtype; +false+ if not
+          def self.subtype_of?(other_return_type)
+            self <= other_return_type
+          end
+
+          # Retrieve my immediate subtypes.
+          #
+          # @return [Array<Class>] my immediate subtypes
+          def self.subtypes
+            (@subtypes ||= []).freeze
+          end
+
+          # Retrieve my transitive subtypes.
+          #
+          # @return [Array<Class>] my transitive subtypes
+          def self.transitive_subtypes
+            transitive_subtypes =
+              (@subtypes ||= []).flat_map do |subtype|
+                [subtype, subtype.subtypes]
+              end.flatten
+            transitive_subtypes << self
+            transitive_subtypes.freeze
+          end
+
+          # Inherited hook overridden to keep track of descendants. This method
+          # is inherited by all descendants.
+          #
+          # @param [Class] cls the subclass that is inheriting me
+          # @see .subtypes
+          def self.inherited(cls)
+            (@subtypes ||= []) << cls
+          end
+          private_class_method
+
+          # Raise {NotImplementedError} for +method+. Alters the exception
+          # backtrace to exclude this method.
+          #
+          # @param [#to_s] the method name
+          # @raise [NotImplementedError] for +method+
+          def self.raise_not_implemented(method)
+            msg = "#{name} must implement the #{method} method"
+            raise NotImplementedError, msg
+          rescue StandardError
+            raise(
+              $ERROR_INFO.class,
+              $ERROR_INFO.message,
+              $ERROR_INFO.backtrace[1..-1])
+          end
+          private_class_method
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/value_encodings/biological_process.rb

@@ -0,0 +1,21 @@
+require_relative '../../version2_0'
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ValueEncodings
+        # BiologicalProcess value encoding.
+        class BiologicalProcess < Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != BiologicalProcess
+            :B
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/value_encodings/complex_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version2_0'
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ValueEncodings
+        # ComplexAbundance value encoding.
+        class ComplexAbundance < Abundance
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != ComplexAbundance
+            :C
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/value_encodings/gene_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version2_0'
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ValueEncodings
+        # GeneAbundance value encoding.
+        class GeneAbundance < Abundance
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != GeneAbundance
+            :G
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/value_encodings/location.rb

@@ -0,0 +1,21 @@
+require_relative '../../version2_0'
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ValueEncodings
+        # Location value encoding.
+        class Location < Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Location
+            :L
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/value_encodings/micro_rna_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version2_0'
+require_relative 'rna_abundance'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ValueEncodings
+        # Micro RNA abundance value encoding.
+        class MicroRNAAbundance < RNAAbundance
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != MicroRNAAbundance
+            :M
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/value_encodings/pathology.rb

@@ -0,0 +1,21 @@
+require_relative '../../version2_0'
+require_relative 'biological_process'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ValueEncodings
+        # Pathology value encoding.
+        class Pathology < BiologicalProcess
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Pathology
+            :O
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/value_encodings/protein_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version2_0'
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ValueEncodings
+        # ProteinAbundance value encoding.
+        class ProteinAbundance < Abundance
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != ProteinAbundance
+            :P
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/value_encodings/protein_modification.rb

@@ -0,0 +1,21 @@
+require_relative '../../version2_0'
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ValueEncodings
+        # ProteinModification value encoding.
+        class ProteinModification < Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != ProteinModification
+            :E
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/value_encodings/rna_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version2_0'
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ValueEncodings
+        # RNAAbundance value encoding.
+        class RNAAbundance < Abundance
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != RNAAbundance
+            :R
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0.rb

@@ -1,74 +1,20 @@
 require_relative 'function'
 require_relative 'specification'
+require_relative 'base_specification'
 
 module BELParser
   module Language
     module Version2_0
-      # Version2_0Specification defines the BEL, version 2.0 specification.
-      class Specification
-        include BELParser::Language::Specification
+      # Version2_0 specification defines the BEL 2.0 specification.
+      class Specification < BaseSpecification
+        BaseSpecification.load_version_path('version2_0')
+
         def initialize
           @version = '2.0'.freeze
-
-          # Establish functions
-          function_classes = Version2_0::Functions.constants.collect do |symbol|
-            const = Version2_0::Functions.const_get(symbol)
-            const if
-              const.respond_to?(:short) &&
-              const.respond_to?(:long)
-          end
-          @functions         = function_classes.compact
-          @indexed_functions = index_long_short(@functions)
-
-          # Collect relationships
-          rel_classes = Version2_0::Relationships.constants.collect do |symbol|
-            const = Version2_0::Relationships.const_get(symbol)
-            const if
-              const.respond_to?(:short) &&
-              const.respond_to?(:long)
-          end
-          @relationships         = rel_classes.compact
-          @indexed_relationships = index_long_short(@relationships)
-          assign_relationship_categories(@relationships)
-
-          # Establish return types
-          ret_classes = Version2_0::ReturnTypes.constants.collect do |symbol|
-            const = Version2_0::ReturnTypes.const_get(symbol)
-            const if const.respond_to?(:subtypes)
-          end
-          @return_types         = ret_classes.compact
-          @indexed_return_types = index_sym(@return_types)
-
+          load_language_constants(Version2_0)
           freeze
         end
       end
     end
   end
 end
-
-# Require all version 2.0 return types
-Dir[
-  File.join(
-    File.dirname(File.expand_path(__FILE__)),
-    'version2_0', 'return_types', '*.rb')
-].each do |path|
-  require_relative "version2_0/return_types/#{File.basename(path)}"
-end
-
-# Require all version 2.0 functions.
-Dir[
-  File.join(
-    File.dirname(File.expand_path(__FILE__)),
-    'version2_0', 'functions', '*.rb')
-].each do |path|
-  require_relative "version2_0/functions/#{File.basename(path)}"
-end
-
-# Require all version 1.0 relationships.
-Dir[
-  File.join(
-    File.dirname(File.expand_path(__FILE__)),
-    'version2_0', 'relationships', '*.rb')
-].each do |path|
-  require_relative "version2_0/relationships/#{File.basename(path)}"
-end

data/lib/bel_parser/language.rb

@@ -1,5 +1,4 @@
 require_relative 'language/function'
-require_relative 'language/quoting'
 require_relative 'language/syntax'
 require_relative 'language/semantics'
 require_relative 'language/signature'
@@ -68,13 +67,13 @@ module BELParser
     #         supported
     # @see    {.defines?}
     def self.specification(version)
-      version_string = version.to_s
-      unless version_string =~ /^[0-9]+\.[0-9]+/
+      version_string         =  version.to_s
+      unless version_string  =~ /^[0-9]+\.[0-9]+/
         raise ArgumentError, 'Version format incorrect; expecting MAJOR.MINOR'
       end
 
       LOCK.synchronize do
-        version_sym = version_string.to_sym
+        version_sym           = version_string.to_sym
         @specs              ||= {}
         @specs[version_sym] ||= create_specification(version_string)
         @specs[version_sym]

data/lib/bel_parser/parsers/ast/node.rb

@@ -428,6 +428,9 @@ module BELParser
       end
 
       # AST node representing a parameter.
+      #
+      # === Special node properties - _namespace_: {#namespace}
+      #
       class Prefix < Node
         # AST node type
         @ast_type = :prefix
@@ -445,6 +448,9 @@ module BELParser
         def identifier
           children[0]
         end
+
+        # Get/Set the namespace property.
+        attr_accessor :namespace
       end
 
       # AST node representing a parameter.
@@ -814,8 +820,14 @@ module BELParser
           super(Value.ast_type, children, properties)
         end
 
-        # Get the value's encoding.
-        attr_reader :encoding
+        # Get/Set the value's encoding.
+        attr_accessor :encoding
+
+        # Get/Set the value's namespace.
+        attr_accessor :namespace
+
+        # Get/Set the value from the purported namespace.
+        attr_accessor :namespace_value
       end
 
       # Sexp defines a module that creates {BELParser::Parsers::AST::Node

data/lib/bel_parser/{language/quoting.rb → quoting.rb}

@@ -173,61 +173,5 @@ module BELParser
         matcher.match string
       end
     end
-
-    ## Deprecated, remove in [0.6.0].
-
-    # @deprecated Use {#quote_if_needed} instead. Will be removed in a
-    #             future release.
-    def ensure_quotes(identifier)
-      warn <<-DOC.gsub(/^\s+/, '')
-        Deprecation Warning
-        -------------------
-        The BEL::Quoting::ensure_quotes method is deprecated and
-        will be removed in a future release.
-        Call module method BEL::Quoting.quote_if_needed instead.
-      DOC
-      quote_if_needed(identifier)
-    end
-
-    # @deprecated Use {#unquote} instead. Will be removed in a
-    #             future release.
-    def remove_quotes(identifier)
-      warn <<-DOC.gsub(/^\s+/, '')
-        Deprecation Warning
-        -------------------
-        The BEL::Quoting::remove_quotes method is deprecated and
-        will be removed in a future release.
-        Call module method BEL::Quoting.unquote instead.
-      DOC
-      unquote(identifier)
-    end
-
-    # @deprecated Use {#quote} instead. Will be removed in a
-    #             future release.
-    def always_quote(identifier)
-      warn <<-DOC.gsub(/^\s+/, '')
-        Deprecation Warning
-        -------------------
-        The BEL::Quoting::always_quote method is deprecated and
-        will be removed in a future release.
-        Call module method BEL::Quoting.quote instead.
-      DOC
-      quote(identifier)
-    end
-
-    # @deprecated Use {#quoted?} or {#unquoted?} instead. Will be removed
-    #             in a future release.
-    def quotes_required?(identifier)
-      warn <<-DOC.gsub(/^\s+/, '')
-        Deprecation Warning
-        -------------------
-        The BEL::Quoting::quotes_required? method is deprecated and
-        will be removed in a future release. Use BEL::Quoting.quoted? and
-        BEL::Quoting.unquoted?.
-      DOC
-      [NonWordMatcher, KeywordMatcher].any? do |m|
-        m.match identifier.to_s
-      end
-    end
   end
 end

data/lib/bel_parser/resource/concept.rb

@@ -0,0 +1,56 @@
+require_relative 'value'
+
+module BELParser
+  module Resource
+    # Concept
+    class Concept
+      include Value
+
+      attr_reader :dataset, :uri, :name, :identifier,
+                  :title,   :synonyms, :encodings
+
+      def initialize(dataset, uri, pref_label, identifier,
+                     title,   alt_labels, types)
+
+        @dataset    = dataset
+        @uri        = uri
+        @name       = pref_label.to_s
+        @identifier = identifier.to_s
+        @title      = title.to_s
+        @synonyms   = alt_labels.to_s.split('|')
+        @encodings  = convert_encoding_types(types.to_s)
+      end
+
+      private
+
+      def convert_encoding_types(types)
+        types.split('|').map do |type|
+          case type
+          when /AbundanceConcept$/
+            :A
+          when /BiologicalProcessConcept$/
+            :B
+          when /ComplexConcept$/
+            :C
+          when /GeneConcept$/
+            :G
+          when /LocationConcept$/
+            :L
+          when /MicroRNAConcept$/
+            :M
+          when /MolecularActivityConcept$/
+            :T
+          when /PathologyConcept$/
+            :O
+          when /ProteinConcept$/
+            :P
+          when /ProteinModificationConcept$/
+            :E
+          when /RNAConcept$/
+            :R
+          end
+        end.compact
+      end
+    end
+  end
+end

data/lib/bel_parser/resource/concept_scheme.rb

@@ -0,0 +1,35 @@
+require_relative 'dataset'
+
+module BELParser
+  module Resource
+    #ConceptScheme
+    class ConceptScheme
+      include Dataset
+
+      attr_reader :identifier, :domain, :keyword, :name, :types
+
+      def initialize(identifier, domain, prefix, name, types)
+        @identifier = identifier.to_s
+        @domain     = domain.to_s
+        @keyword    = prefix.to_s
+        @name       = name.to_s
+        @types      = convert_types(types.to_s)
+      end
+
+      private
+
+      def convert_types(types)
+        types.split('|').map do |type|
+          case type
+          when /NamespaceConceptScheme$/
+            Dataset::NAMESPACE
+          when /AnnotationConceptScheme$/
+            Dataset::ANNOTATION
+          else
+            nil
+          end
+        end.compact
+      end
+    end
+  end
+end

data/lib/bel_parser/resource/dataset.rb

@@ -0,0 +1,34 @@
+module BELParser
+  module Resource
+    # Dataset
+    module Dataset
+
+      ANNOTATION = :annotation
+      NAMESPACE  = :namespace
+
+      def identifier
+        raise NotImplementedError, "#{__method__} is not implemented."
+      end
+
+      def keyword
+        raise NotImplementedError, "#{__method__} is not implemented."
+      end
+
+      def domain
+        raise NotImplementedError, "#{__method__} is not implemented."
+      end
+
+      def annotation_resource?
+        types.include?(ANNOTATION)
+      end
+
+      def namespace_resource?
+        types.include?(NAMESPACE)
+      end
+
+      def types
+        raise NotImplementedError, "#{__method__} is not implemented."
+      end
+    end
+  end
+end