bel_parser 1.0.0.alpha.1

data/lib/bel_parser/language/version2/functions/molecular_activity.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
+        # MolecularActivity: Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale
+        class MolecularActivity
+          extend Function
+
+          SHORT       = :ma
+          LONG        = :molecularActivity
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::MolecularActivity
+          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 MolecularActivitySignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              # TODO: More constraints on prefix for activity namespace?
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(MolecularActivity))),
+                argument(
+                  parameter(
+                    prefix(any),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:Activity))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'molecularActivity(E:activity)molecularActivity'.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/pathology.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
+        # Pathology: Denotes a disease or pathology process
+        class Pathology
+          extend Function
+
+          SHORT       = :path
+          LONG        = :pathology
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Pathology
+          DESCRIPTION = 'Denotes a disease or pathology process'.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 PathologySignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(Pathology))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:Pathology))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'pathology(E:pathology)pathology'.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/products.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
+        # Products: Denotes the products of a reaction
+        class Products
+          extend Function
+
+          SHORT       = :products
+          LONG        = :products
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Products
+          DESCRIPTION = 'Denotes the products 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 ProductsSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(Products))),
+                variadic_arguments(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'products(F:abundance...)products'.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/protein_abundance.rb

@@ -0,0 +1,285 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version2
+      module Functions
+        # ProteinAbundance: Denotes the abundance of a protein
+        class ProteinAbundance
+          extend Function
+
+          SHORT       = :p
+          LONG        = :proteinAbundance
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::ProteinAbundance
+          DESCRIPTION = 'Denotes the abundance of a protein'.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 ProteinAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(ProteinAbundance))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:ProteinAbundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinAbundance(E:proteinAbundance)proteinAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class ProteinAbundanceWithFragmentSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(ProteinAbundance))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:ProteinAbundance))))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Fragment))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinAbundance(E:proteinAbundance,F:fragment)proteinAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class ProteinAbundanceWithFusionSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(ProteinAbundance))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:ProteinAbundance))))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Fusion))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinAbundance(E:proteinAbundance,F:fusion)proteinAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class ProteinAbundanceWithLocationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(ProteinAbundance))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:ProteinAbundance))))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinAbundance(E:proteinAbundance,F:location)proteinAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class ProteinAbundanceWithProteinModificationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(ProteinAbundance))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:ProteinAbundance))))),
+                variadic_arguments(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::ProteinModification))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinAbundance(E:proteinAbundance,F:proteinModification...)proteinAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class ProteinAbundanceWithVariantSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(ProteinAbundance))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:ProteinAbundance))))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Variant))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinAbundance(E:proteinAbundance,F:variant)proteinAbundance'.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