bel_parser 1.0.0.alpha.1

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

@@ -0,0 +1,85 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version2
+      module Functions
+        # ToLocation: Denotes the to cellular location of the abundance.
+        class ToLocation
+          extend Function
+
+          SHORT       = :toLoc
+          LONG        = :toLocation
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::ToLocation
+          DESCRIPTION = 'Denotes the to cellular location of the abundance.'.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 ToLocationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(ToLocation))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:Location))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'toLocation(E:location)toLocation'.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/translocation.rb

@@ -0,0 +1,90 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version2
+      module Functions
+        # Translocation: Denotes the frequency or abundance of events in which members move between locations
+        class Translocation
+          extend Function
+
+          SHORT       = :tloc
+          LONG        = :translocation
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Abundance
+          DESCRIPTION = 'Denotes the frequency or abundance of events in which members move between locations'.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 Translocation
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(Translocation))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::FromLocation))))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::ToLocation))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'translocation(F:abundance,F:fromLocation,F:toLocation)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/variant.rb

@@ -0,0 +1,83 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version2
+      module Functions
+        # Variant: Denotes a sequence variant of the specified abundance.
+        class Variant
+          extend Function
+
+          SHORT       = :var
+          LONG        = :variant
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Variant
+          DESCRIPTION = 'Denotes a sequence variant of the specified abundance.'.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 VariantSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              # TODO: More strict prefix validation for variant namespace?
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(Variant))),
+                argument(
+                  parameter(
+                    prefix(any),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:HgvsVariantDescription))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'variant(E:hgvsVariantDescription)variant'.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/return_types/abundance.rb

@@ -0,0 +1,20 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version2
+      module ReturnTypes
+        # Abundance return type.
+        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
+            :abundance
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,20 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version2
+      module ReturnTypes
+        # Activity return type.
+        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
+            :activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2/return_types/any.rb

@@ -0,0 +1,74 @@
+require 'English'
+
+module BELParser
+  module Language
+    module Version2
+      module ReturnTypes
+        # The any type.
+        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/return_types/biological_process.rb

@@ -0,0 +1,17 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version2
+      module ReturnTypes
+        # Biological process return type.
+        class BiologicalProcess < Any
+          def self.to_sym
+            raise_not_implemented(__method__) if self != BiologicalProcess
+            :biologicalProcess
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2/return_types/complex_abundance.rb

@@ -0,0 +1,17 @@
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version2
+      module ReturnTypes
+        # Complex abundance return type.
+        class ComplexAbundance < Abundance
+          def self.to_sym
+            raise_not_implemented(__method__) if self != ComplexAbundance
+            :complexAbundance
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2/return_types/fragment.rb

@@ -0,0 +1,20 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version2
+      module ReturnTypes
+        # Fragment return type.
+        class Fragment < Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Fragment
+            :fragment
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2/return_types/from_location.rb

@@ -0,0 +1,20 @@
+require_relative 'location'
+
+module BELParser
+  module Language
+    module Version2
+      module ReturnTypes
+        # FromLocation return type.
+        class FromLocation < Location
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != FromLocation
+            :fromLocation
+          end
+        end
+      end
+    end
+  end
+end