bel_parser 1.0.0.alpha.1

data/lib/bel_parser/language/version2/functions/biological_process.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
+        # BiologicalProcess: Denotes a process or population of events.
+        class BiologicalProcess
+          extend Function
+
+          SHORT       = :bp
+          LONG        = :biologicalProcess
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::BiologicalProcess
+          DESCRIPTION = 'Denotes a process or population of events.'.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 BiologicalProcessSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(BiologicalProcess))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:BiologicalProcess))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'biologicalProcess(E:biologicalProcess)biologicalProcess'.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/cell_secretion.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
+        # CellSecretion: Denotes the frequency or abundance of events in which members of an abundance move from cells to regions outside of the cells.
+        class CellSecretion
+          extend Function
+
+          SHORT       = :sec
+          LONG        = :cellSecretion
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Abundance
+          DESCRIPTION = 'Denotes the frequency or abundance of events in which members of an abundance move from cells to regions outside of the cells.'.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 CellSecretionSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(CellSecretion))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'cellSecretion(F:abundance)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/cell_surface_expression.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
+        # CellSurfaceExpression: Denotes the frequency or abundance of events in which members of an abundance move to the surface of cells.
+        class CellSurfaceExpression
+          extend Function
+
+          SHORT       = :surf
+          LONG        = :cellSurfaceExpression
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Abundance
+          DESCRIPTION = 'Denotes the frequency or abundance of events in which members of an abundance move to the surface of cells.'.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 CellSurfaceExpressionSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(CellSurfaceExpression))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'cellSurfaceExpression(F:abundance)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/complex_abundance.rb

@@ -0,0 +1,190 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version2
+      module Functions
+        # ComplexAbundance: Denotes the abundance of a molecular complex.
+        class ComplexAbundance
+          extend Function
+
+          SHORT       = :complex
+          LONG        = :complexAbundance
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::ComplexAbundance
+          DESCRIPTION = 'Denotes the abundance of a molecular complex.'.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 NamedComplexAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(ComplexAbundance))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:Abundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'complexAbundance(E:abundance)complexAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class NamedComplexAbundanceWithLocationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(ComplexAbundance))),
+                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 = 'complexAbundance(E:abundance,F:location)complexAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class ComposedComplexAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(ComplexAbundance))),
+                variadic_arguments(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'complexAbundance(F:abundance...)complexAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class ComposedComplexAbundanceWithLocationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(ComplexAbundance))),
+                variadic_arguments(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'complexAbundance(F:abundance...,F:location)complexAbundance'.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/composite_abundance.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
+        # CompositeAbundance: Denotes the frequency or abundance of events in which members are present.
+        class CompositeAbundance
+          extend Function
+
+          SHORT       = :composite
+          LONG        = :compositeAbundance
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Abundance
+          DESCRIPTION = 'Denotes the frequency or abundance of events in which members are present.'.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 CompositeAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(CompositeAbundance))),
+                variadic_arguments(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'compositeAbundance(F:abundance...)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