bel_parser 1.0.0.alpha.1

data/lib/bel_parser/language/version1/return_types/ribosylation_activity.rb

@@ -0,0 +1,20 @@
+require_relative 'molecular_activity'
+
+module BELParser
+  module Language
+    module Version1
+      module ReturnTypes
+        # RibosylationActivity return type.
+        class RibosylationActivity < MolecularActivity
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != RibosylationActivity
+            :ribosylation_activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1/return_types/rna_abundance.rb

@@ -0,0 +1,17 @@
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version1
+      module ReturnTypes
+        # RNA abundance return type.
+        class RNAAbundance < Abundance
+          def self.to_sym
+            raise_not_implemented(__method__) if self != RNAAbundance
+            :rnaAbundance
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1/return_types/substitution.rb

@@ -0,0 +1,17 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1
+      module ReturnTypes
+        # Substitution return type.
+        class Substitution < Any
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Substitution
+            :substitution
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1/return_types/transcriptional_activity.rb

@@ -0,0 +1,20 @@
+require_relative 'molecular_activity'
+
+module BELParser
+  module Language
+    module Version1
+      module ReturnTypes
+        # TransportActivity return type.
+        class TranscriptionalActivity < MolecularActivity
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != TranscriptionalActivity
+            :transcriptional_activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1/return_types/transport_activity.rb

@@ -0,0 +1,20 @@
+require_relative 'molecular_activity'
+
+module BELParser
+  module Language
+    module Version1
+      module ReturnTypes
+        # TransportActivity return type.
+        class TransportActivity < MolecularActivity
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != TransportActivity
+            :transport_activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1/return_types/truncation.rb

@@ -0,0 +1,17 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1
+      module ReturnTypes
+        # Truncation return type.
+        class Truncation < Any
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Truncation
+            :truncation
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2.rb

@@ -0,0 +1,50 @@
+require_relative 'function'
+require_relative 'specification'
+
+# Require all version 2.0 return types
+Dir[
+  File.join(
+    File.dirname(File.expand_path(__FILE__)),
+    'version2', 'return_types', '*.rb')
+].each do |path|
+  require_relative "version2/return_types/#{File.basename(path)}"
+end
+
+# Require all version 2.0 functions.
+Dir[
+  File.join(
+    File.dirname(File.expand_path(__FILE__)),
+    'version2', 'functions', '*.rb')
+].each do |path|
+  require_relative "version2/functions/#{File.basename(path)}"
+end
+
+module BELParser
+  module Language
+    module Version2
+      # Version2Specification defines the BEL, version 2.0 specification.
+      class Specification
+        include BELParser::Language::Specification
+        def initialize
+          # Establish functions
+          function_classes = Version2::Functions.constants.collect do |symbol|
+            const = Version2::Functions.const_get(symbol)
+            const if
+              const.respond_to?(:short) &&
+              const.respond_to?(:long)
+          end
+          @functions = function_classes.compact
+          @indexed_functions = index_functions(@functions)
+
+          # Establish return types
+          ret_classes = Version2::ReturnTypes.constants.collect do |symbol|
+            const = Version2::ReturnTypes.const_get(symbol)
+            const if const.respond_to?(:subtypes)
+          end
+          @return_types = ret_classes.compact
+          @indexed_return_types = index_return_types(@return_types)
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2/functions/abundance.rb

@@ -0,0 +1,165 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version2
+      module Functions
+        # Abundance: Denotes the abundance of an entity.
+        class Abundance
+          extend Function
+
+          SHORT       = :a
+          LONG        = :abundance
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Abundance
+          DESCRIPTION = 'Denotes the abundance of an entity.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.return_type
+            RETURN_TYPE
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.signatures
+            SIGNATURES
+          end
+
+          module Signatures
+  
+            class AbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(Abundance))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:Abundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'abundance(E:abundance)abundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class AbundanceWithLocationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(Abundance))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:Abundance))))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'abundance(E:abundance,F:location)abundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class AbundanceWithMolecularActivitySignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(Abundance))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:Abundance))))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::MolecularActivity))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'abundance(E:abundance, F:molecularActivity)abundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+          end
+
+          SIGNATURES = Signatures.constants.map do |const|
+            Signatures.const_get(const)
+          end.freeze
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2/functions/activity.rb

@@ -0,0 +1,115 @@
+require_relative '../../version2'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version2
+      module Functions
+        # Activity: Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale.
+        class Activity
+          extend BELParser::Language::Function
+
+          SHORT       = :act
+          LONG        = :activity
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Activity
+          DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.return_type
+            RETURN_TYPE
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.signatures
+            SIGNATURES
+          end
+
+          module Signatures
+  
+            class ActivitySignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Activity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'activity(F:abundance)activity'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class ActivityWithSpecificActivityTypeSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Activity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2::ReturnTypes::MolecularActivity))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'activity(F:abundance, F:molecularActivity)activity'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+          end
+
+          SIGNATURES = Signatures.constants.map do |const|
+            Signatures.const_get(const)
+          end.freeze
+        end
+      end
+    end
+  end
+end