bel_parser 1.0.0.alpha.27-java

data/lib/bel_parser/language/version2_0/functions/list.rb

@@ -0,0 +1,114 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # List: Groups a list of terms together.
+        class List
+          extend Function
+
+          SHORT       = :list
+          LONG        = :list
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::List
+          A_ENC       = Version2_0::ValueEncodings::Abundance
+          DESCRIPTION = 'Groups a list of terms together.'.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
+            # ListOfAbundanceEncodingSignature
+            class ListOfAbundanceEncodingSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(List))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(A_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'list(E:abundance...)list'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # ListOfAbundanceSignature
+            class ListOfAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(List))),
+                  variadic_arguments(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'list(F:abundance...)list'.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_0/functions/location.rb

@@ -0,0 +1,83 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # Location: Denotes the cellular location of the abundance.
+        class Location
+          extend Function
+
+          SHORT       = :loc
+          LONG        = :location
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Location
+          L_ENC       = Version2_0::ValueEncodings::Location
+          DESCRIPTION = 'Denotes the 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
+            # LocationSignature
+            class LocationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Location))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(L_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'location(E:location)location'.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_0/functions/micro_rna_abundance.rb

@@ -0,0 +1,163 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # MicroRNAAbundance: Denotes the abundance of a processed,
+        # functional microRNA
+        class MicroRNAAbundance
+          extend Function
+
+          SHORT       = :m
+          LONG        = :microRNAAbundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::MicroRNAAbundance
+          M_ENC       = Version2_0::ValueEncodings::MicroRNAAbundance
+          DESCRIPTION = 'Denotes the abundance of a processed, functional
+          icroRNA'.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
+            # MicroRNAAbundanceSignature
+            class MicroRNAAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(MicroRNAAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(M_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'microRNAAbundance(E:microRNAAbundance)microRNAAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # MicroRNAAbundanceWithLocationSignature
+            class MicroRNAAbundanceWithLocationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(MicroRNAAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(M_ENC)))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'microRNAAbundance(E:microRNAAbundance,F:location)microRNAAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # MicroRNAAbundanceWithVariantSignature
+            class MicroRNAAbundanceWithVariantSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(MicroRNAAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(M_ENC)))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'microRNAAbundance(E:microRNAAbundance,F:variant)microRNAAbundance'.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_0/functions/molecular_activity.rb

@@ -0,0 +1,86 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      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_0::ReturnTypes::MolecularActivity
+          T_ENC       = Version2_0::ValueEncodings::Activity
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member acts as a causal agent at the
+          olecular 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
+            # MolecularActivitySignature
+            class MolecularActivitySignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(MolecularActivity))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(T_ENC)))))
+              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_0/functions/pathology.rb

@@ -0,0 +1,83 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # Pathology: Denotes a disease or pathology process
+        class Pathology
+          extend Function
+
+          SHORT       = :path
+          LONG        = :pathology
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Pathology
+          O_ENC       = Version2_0::ValueEncodings::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
+            # PathologySignature
+            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(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(O_ENC)))))
+              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