bel_parser 1.0.0.alpha.1

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

@@ -0,0 +1,167 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version2
+      module Functions
+        # ProteinModification: Denotes a covalently modified protein abundance
+        class ProteinModification
+          extend Function
+
+          SHORT       = :pmod
+          LONG        = :proteinModification
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::ProteinModification
+          DESCRIPTION = 'Denotes a covalently modified protein 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 ProteinModificationWithType
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              # TODO: More strict prefix validation for modification type?
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(ProteinModification))),
+                argument(
+                  parameter(
+                    prefix(any),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:ModificationType))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinModification(E:modificationType)proteinModification'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class ProteinModificationWithTypeAmino
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              # TODO: More strict prefix validation for modification type?
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(ProteinModification))),
+                argument(
+                  parameter(
+                    prefix(any),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:ModificationType))))),
+                argument(
+                  parameter(
+                    prefix(any),
+                    value(
+                      value_type(
+                        encoding_of(:*))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinModification(E:modificationType,E:*)proteinModification'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class ProteinModificationWithTypeAminoPosition
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              # TODO: More strict prefix validation for modification type?
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(ProteinModification))),
+                argument(
+                  parameter(
+                    prefix(any),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:ModificationType))))),
+                argument(
+                  parameter(
+                    prefix(any),
+                    value(
+                      value_type(
+                        encoding_of(:*))))),
+                argument(
+                  parameter(
+                    prefix(any),
+                    value(
+                      value_type(
+                        encoding_of(:*))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinModification(E:modificationType,E:*,E:*)proteinModification'.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/reactants.rb

@@ -0,0 +1,80 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version2
+      module Functions
+        # Reactants: Denotes the reactants of a reaction
+        class Reactants
+          extend Function
+
+          SHORT       = :reactants
+          LONG        = :reactants
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Reactants
+          DESCRIPTION = 'Denotes the reactants of a reaction'.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 ReactantsSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(Reactants))),
+                variadic_arguments(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'reactants(F:abundance...)reactants'.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/reaction.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
+        # Reaction: Denotes the frequency or abundance of events in a reaction
+        class Reaction
+          extend Function
+
+          SHORT       = :rxn
+          LONG        = :reaction
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Abundance
+          DESCRIPTION = 'Denotes the frequency or abundance of events in a reaction'.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 ReactionSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(Reaction))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Reactants))))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Products))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'reaction(F:reactants,F:products)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/rna_abundance.rb

@@ -0,0 +1,195 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version2
+      module Functions
+        # RNAAbundance: Denotes the abundance of a gene
+        class RNAAbundance
+          extend Function
+
+          SHORT       = :r
+          LONG        = :rnaAbundance
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::GeneAbundance
+          DESCRIPTION = 'Denotes the abundance of a gene'.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 RNAAbundance
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(RNAAbundance))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:RnaAbundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'rnaAbundance(E:rnaAbundance)geneAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class RNAAbundanceWithFusion
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(RNAAbundance))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Fusion))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'rnaAbundance(F:fusion)geneAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class RNAAbundanceWithLocation
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(RNAAbundance))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:RnaAbundance))))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'rnaAbundance(E:rnaAbundance,F:location)geneAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class RNAAbundanceWithVariant
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(RNAAbundance))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:RnaAbundance))))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Variant))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'rnaAbundance(E:rnaAbundance,F:variant)geneAbundance'.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