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

data/lib/bel_parser/language/version1_0/value_encodings/any.rb

@@ -0,0 +1,74 @@
+require 'English'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/value_encodings/biological_process.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/value_encodings/complex_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/value_encodings/gene_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/value_encodings/micro_rna_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'rna_abundance'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/value_encodings/pathology.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'biological_process'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/value_encodings/protein_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/value_encodings/rna_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0.rb

@@ -1,101 +1,20 @@
 require_relative 'function'
 require_relative 'specification'
+require_relative 'base_specification'
 
 module BELParser
   module Language
     module Version1_0
-      # Specification defines the BEL, version 1.0 specification.
-      class Specification
-        include BELParser::Language::Specification
+      # Version1_0 specification defines the BEL 1.0 specification.
+      class Specification < BaseSpecification
+        BaseSpecification.load_version_path('version1_0')
+
         def initialize
           @version = '1.0'.freeze
-          load_return_types
-          load_functions
-          load_relationships
-          load_syntax
+          load_language_constants(Version1_0)
           freeze
         end
-
-        def load_return_types
-          # Collect return types
-          ret_classes = Version1_0::ReturnTypes.constants.collect do |symbol|
-            const = Version1_0::ReturnTypes.const_get(symbol)
-            const if const.respond_to?(:subtypes)
-          end
-          @return_types         = ret_classes.compact
-          @indexed_return_types = index_sym(@return_types)
-        end
-
-        def load_functions
-          # Collect functions
-          function_classes = Version1_0::Functions.constants.collect do |symbol|
-            const = Version1_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)
-        end
-
-        def load_relationships
-          # Collect relationships
-          rel_classes = Version1_0::Relationships.constants.collect do |symbol|
-            const = Version1_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)
-        end
-
-        def load_syntax
-          # Collect syntax checkers.
-          syntax_classes = Version1_0::Syntax.constants.collect do |symbol|
-            const = Version1_0::Syntax.const_get(symbol)
-            const if const.respond_to?(:match)
-          end
-          @syntax = syntax_classes.compact
-        end
       end
     end
   end
 end
-
-# Require all version 1.0 return types
-Dir[
-  File.join(
-    File.dirname(File.expand_path(__FILE__)),
-    'version1_0', 'return_types', '*.rb')
-].each do |path|
-  require_relative "version1_0/return_types/#{File.basename(path)}"
-end
-
-# Require all version 1.0 functions.
-Dir[
-  File.join(
-    File.dirname(File.expand_path(__FILE__)),
-    'version1_0', 'functions', '*.rb')
-].each do |path|
-  require_relative "version1_0/functions/#{File.basename(path)}"
-end
-
-# Require all version 1.0 relationships.
-Dir[
-  File.join(
-    File.dirname(File.expand_path(__FILE__)),
-    'version1_0', 'relationships', '*.rb')
-].each do |path|
-  require_relative "version1_0/relationships/#{File.basename(path)}"
-end
-
-# Require all version 1.0 syntax checkers.
-Dir[
-  File.join(
-    File.dirname(File.expand_path(__FILE__)),
-    'version1_0', 'syntax', '*.rb')
-].each do |path|
-  require_relative "version1_0/syntax/#{File.basename(path)}"
-end

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

@@ -14,6 +14,7 @@ module BELParser
           SHORT       = :a
           LONG        = :abundance
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
+          A_ENC       = Version2_0::ValueEncodings::Abundance
           DESCRIPTION = 'Denotes the abundance of an entity.'.freeze
 
           def self.short
@@ -51,13 +52,11 @@ module BELParser
                   argument(
                     parameter(
                       prefix(
-                        identifier(
-                          has_namespace,
-                          namespace_of(:*))),
+                        has_namespace,
+                        namespace_of(:*)),
                       value(
-                        value_type(
-                          has_encoding,
-                          encoding_of(:Abundance))))))
+                        has_encoding,
+                        encoding_of(A_ENC)))))
               end
               private_constant :AST
 
@@ -87,13 +86,11 @@ module BELParser
                   argument(
                     parameter(
                       prefix(
-                        identifier(
-                          has_namespace,
-                          namespace_of(:*))),
+                        has_namespace,
+                        namespace_of(:*)),
                       value(
-                        value_type(
-                          has_encoding,
-                          encoding_of(:Abundance))))),
+                        has_encoding,
+                        encoding_of(A_ENC)))),
                   argument(
                     term(
                       function(
@@ -128,13 +125,11 @@ module BELParser
                   argument(
                     parameter(
                       prefix(
-                        identifier(
-                          has_namespace,
-                          namespace_of(:*))),
+                        has_namespace,
+                        namespace_of(:*)),
                       value(
-                        value_type(
-                          has_encoding,
-                          encoding_of(:Abundance))))),
+                        has_encoding,
+                        encoding_of(A_ENC)))),
                   argument(
                     term(
                       function(

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

@@ -14,6 +14,7 @@ module BELParser
           SHORT       = :bp
           LONG        = :biologicalProcess
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::BiologicalProcess
+          B_ENC       = Version2_0::ValueEncodings::BiologicalProcess
           DESCRIPTION = 'Denotes a process or population of
           vents.'.freeze
 
@@ -52,13 +53,11 @@ module BELParser
                   argument(
                     parameter(
                       prefix(
-                        identifier(
-                          has_namespace,
-                          namespace_of(:*))),
+                        has_namespace,
+                        namespace_of(:*)),
                       value(
-                        value_type(
-                          has_encoding,
-                          encoding_of(:BiologicalProcess))))))
+                        has_encoding,
+                        encoding_of(B_ENC)))))
               end
               private_constant :AST
 

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

@@ -14,6 +14,7 @@ module BELParser
           SHORT       = :complex
           LONG        = :complexAbundance
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ComplexAbundance
+          C_ENC       = Version2_0::ValueEncodings::ComplexAbundance
           DESCRIPTION = 'Denotes the abundance of a molecular
           omplex.'.freeze
 
@@ -52,13 +53,11 @@ module BELParser
                   argument(
                     parameter(
                       prefix(
-                        identifier(
-                          has_namespace,
-                          namespace_of(:*))),
+                        has_namespace,
+                        namespace_of(:*)),
                       value(
-                        value_type(
-                          has_encoding,
-                          encoding_of(:Abundance))))))
+                        has_encoding,
+                        encoding_of(C_ENC)))))
               end
               private_constant :AST
 
@@ -88,13 +87,11 @@ module BELParser
                   argument(
                     parameter(
                       prefix(
-                        identifier(
-                          has_namespace,
-                          namespace_of(:*))),
+                        has_namespace,
+                        namespace_of(:*)),
                       value(
-                        value_type(
-                          has_encoding,
-                          encoding_of(:Abundance))))),
+                        has_encoding,
+                        encoding_of(C_ENC)))),
                   argument(
                     term(
                       function(

data/lib/bel_parser/language/version2_0/functions/fragment.rb

@@ -54,8 +54,7 @@ module BELParser
                     parameter(
                       prefix(any),
                       value(
-                        value_type(
-                          is_amino_acid_range_pattern)))))
+                        is_amino_acid_range_pattern))))
               end
               private_constant :AST
 
@@ -86,15 +85,11 @@ module BELParser
                     parameter(
                       prefix(any),
                       value(
-                        value_type(
-                          is_amino_acid_range_pattern)))),
+                        is_amino_acid_range_pattern))),
                   argument(
                     parameter(
-                      prefix(
-                        any),
-                      value(
-                        value_type(
-                          encoding_of(:*))))))
+                      prefix(any),
+                      value(any))))
               end
               private_constant :AST
 

data/lib/bel_parser/language/version2_0/functions/from_location.rb

@@ -15,6 +15,7 @@ module BELParser
           SHORT       = :fromLoc
           LONG        = :fromLocation
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::FromLocation
+          L_ENC       = Version2_0::ValueEncodings::Location
           DESCRIPTION = 'Denotes the from cellular location of the
           bundance.'.freeze
 
@@ -53,13 +54,11 @@ module BELParser
                   argument(
                     parameter(
                       prefix(
-                        identifier(
-                          has_namespace,
-                          namespace_of(:*))),
+                        has_namespace,
+                        namespace_of(:*)),
                       value(
-                        value_type(
-                          has_encoding,
-                          encoding_of(:Location))))))
+                        has_encoding,
+                        encoding_of(L_ENC)))))
               end
               private_constant :AST