bel_parser 1.0.0.alpha.7 → 1.0.0.alpha.8

data/lib/bel_parser/language/signature.rb

@@ -16,17 +16,17 @@ module BELParser
       def size
         count = 0
         nodes = [semantic_ast]
-        while !nodes.empty?
+        until nodes.empty?
           n = nodes.shift
           if n
-            count += 1 
+            count += 1
             nodes.concat(n.children) if n.respond_to?(:children)
           end
         end
         count
       end
 
-      def <=> (other)
+      def <=>(other)
         return 1 if other.nil?
         size <=> other.size
       end

data/lib/bel_parser/language/syntax/invalid_function.rb

@@ -10,7 +10,7 @@ module BELParser
 
         private_class_method :new
 
-        def self.map(func_node, spec, namespaces)
+        def self.map(func_node, spec, _namespaces)
           return nil unless func_node.is_a?(BELParser::Parsers::AST::Function)
 
           function_name = func_node.identifier.string_literal
@@ -31,7 +31,7 @@ module BELParser
         end
 
         def msg
-          %Q{Invalid function "#{invalid_function}".}
+          %(Invalid function "#{invalid_function}".)
         end
       end
     end

data/lib/bel_parser/language/syntax/invalid_relationship.rb

@@ -10,7 +10,7 @@ module BELParser
 
         private_class_method :new
 
-        def self.map(stmt_node, spec, namespaces)
+        def self.map(stmt_node, spec, _namespaces)
           return nil unless stmt_node.is_a?(BELParser::Parsers::AST::Statement)
 
           rel_name = stmt_node.relationship.string_literal
@@ -34,7 +34,7 @@ module BELParser
         end
 
         def msg
-          %Q{Invalid relationship "#{relationship}".}
+          %(Invalid relationship "#{relationship}".)
         end
       end
     end

data/lib/bel_parser/language/syntax/undefined_namespace.rb

@@ -47,4 +47,3 @@ module BELParser
     end
   end
 end
-

data/lib/bel_parser/language/syntax.rb

@@ -4,16 +4,21 @@ require_relative 'syntax_warning'
 
 module BELParser
   module Language
+    # Syntax module aggregates the generic {SyntaxFunction}
+    # implementations that apply to all
+    # {BELParser::Language::Specification BEL specifications}.
     module Syntax
       def self.syntax_functions
-        self.constants.collect do |symbol|
-          const = self.const_get(symbol)
+        constants.collect do |symbol|
+          const = const_get(symbol)
           const if
             const.respond_to?(:include?) &&
             const.include?(SyntaxFunction)
         end.compact
       end
 
+      # Valid defines a {SyntaxResult} that indicates successful syntax
+      # validation.
       class Valid < SyntaxResult
         def msg
           'Syntax is valid.'

data/lib/bel_parser/language/syntax_error.rb

@@ -3,6 +3,8 @@ require_relative 'syntax_result'
 module BELParser
   module Language
     module Syntax
+      # SyntaxError defines a {SyntaxResult} that should be regarded as an
+      # error with the expression.
       class SyntaxError < SyntaxResult
         def initialize(expression_node, specification)
           super(expression_node, specification)

data/lib/bel_parser/language/syntax_function.rb

@@ -1,10 +1,13 @@
 module BELParser
   module Language
     module Syntax
+      # SyntaxFunction provides a {#map} function that maps a
+      # {BELParser::Parsers::AST::Node} to one or more
+      # {SyntaxResult syntax results}.
       module SyntaxFunction
         # @abstract Include {SyntaxFunction} and override {#map} to check
         # expression syntax.
-        def self.map(expression_ast, spec, namespaces)
+        def self.map(_expression_ast, _spec, _namespaces)
           raise NotImplementedError, "#{__method__} is not implemented."
         end
       end

data/lib/bel_parser/language/syntax_result.rb

@@ -1,6 +1,7 @@
 module BELParser
   module Language
     module Syntax
+      # SyntaxResult represents the result of running a {SyntaxFunction}.
       class SyntaxResult
         attr_reader :expression_node, :specification
 

data/lib/bel_parser/language/syntax_warning.rb

@@ -3,6 +3,8 @@ require_relative 'syntax_result'
 module BELParser
   module Language
     module Syntax
+      # SyntaxWarning defines a {SyntaxResult} that should be regarded as an
+      # warning with the expression.
       class SyntaxWarning < SyntaxResult
         attr_reader :target_node
 

data/lib/bel_parser/language/version1_0/functions/abundance.rb

@@ -37,7 +37,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # AbundanceSignature
             class AbundanceSignature
               extend BELParser::Language::Signature
 
@@ -45,19 +45,19 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(Abundance))),
-                argument(
-                  parameter(
-                    prefix(
-                      identifier(
-                        has_namespace,
-                        namespace_of(:*))),
-                    value(
-                      value_type(
-                        has_encoding,
-                        encoding_of(:Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(Abundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        identifier(
+                          has_namespace,
+                          namespace_of(:*))),
+                      value(
+                        value_type(
+                          has_encoding,
+                          encoding_of(:Abundance))))))
               end
               private_constant :AST
 
@@ -72,7 +72,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version1_0/functions/biological_process.rb

@@ -37,7 +37,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # BiologicalProcessSignature
             class BiologicalProcessSignature
               extend BELParser::Language::Signature
 
@@ -45,19 +45,19 @@ module BELParser
 
               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))))))              
+                  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
 
@@ -72,7 +72,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version1_0/functions/catalytic_activity.rb

@@ -7,14 +7,18 @@ module BELParser
   module Language
     module Version1_0
       module Functions
-        # CatalyticActivity: Denotes the frequency or abundance of events where a member acts as an enzymatic catalyst of biochecmial reactions
+        # CatalyticActivity: Denotes the frequency or abundance of events
+        # where a member acts as an enzymatic catalyst of biochecmial
+        # reactions
         class CatalyticActivity
           extend Function
 
           SHORT       = :cat
           LONG        = :catalyticActivity
           RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::CatalyticActivity
-          DESCRIPTION = 'Denotes the frequency or abundance of events where a member acts as an enzymatic catalyst of biochecmial reactions'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          here a member acts as an enzymatic catalyst of
+          iochecmial reactions'.freeze
 
           def self.short
             SHORT
@@ -37,7 +41,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # CatalyticActivityOfComplexAbundanceSignature
             class CatalyticActivityOfComplexAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +49,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(CatalyticActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(CatalyticActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
               end
               private_constant :AST
 
@@ -67,7 +71,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # CatalyticActivityOfProteinAbundanceSignature
             class CatalyticActivityOfProteinAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -75,14 +80,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(CatalyticActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(CatalyticActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
               end
               private_constant :AST
 
@@ -97,7 +102,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version1_0/functions/cell_secretion.rb

@@ -7,14 +7,18 @@ module BELParser
   module Language
     module Version1_0
       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
+        # 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::Version1_0::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
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which members of an abundance move from cells
+          o regions outside of the cells'.freeze
 
           def self.short
             SHORT
@@ -37,7 +41,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # CellSecretionSignature
             class CellSecretionSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +49,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(CellSecretion))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(CellSecretion))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST
 
@@ -67,7 +71,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version1_0/functions/cell_surface_expression.rb

@@ -7,14 +7,18 @@ module BELParser
   module Language
     module Version1_0
       module Functions
-        # CellSurfaceExpression: Denotes the frequency or abundance of events in which members of an abundance move to the surface of cells
+        # 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::Version1_0::ReturnTypes::Abundance
-          DESCRIPTION = 'Denotes the frequency or abundance of events in which members of an abundance move to the surface of cells'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events in
+          hich members of an abundance move to the surface
+          f cells'.freeze
 
           def self.short
             SHORT
@@ -37,7 +41,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # CellSurfaceExpressionSignature
             class CellSurfaceExpressionSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +49,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(CellSurfaceExpression))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(CellSurfaceExpression))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST
 
@@ -67,7 +71,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version1_0/functions/chaperone_activity.rb

@@ -7,14 +7,18 @@ module BELParser
   module Language
     module Version1_0
       module Functions
-        # ChaperoneActivity: Denotes the frequency or abundance of events in which a member binds to some substrate and acts as a chaperone for the substrate
+        # ChaperoneActivity: Denotes the frequency or abundance of
+        # events in which a member binds to some substrate and acts as
+        # a chaperone for the substrate
         class ChaperoneActivity
           extend Function
 
           SHORT       = :chap
           LONG        = :chaperoneActivity
           RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::ChaperoneActivity
-          DESCRIPTION = 'Denotes the frequency or abundance of events in which a member binds to some substrate and acts as a chaperone for the substrate'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member binds to some substrate and acts
+          s a chaperone for the substrate'.freeze
 
           def self.short
             SHORT
@@ -37,7 +41,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # ChaperoneActivityOfComplexAbundanceSignature
             class ChaperoneActivityOfComplexAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +49,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(ChaperoneActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(ChaperoneActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
               end
               private_constant :AST
 
@@ -67,7 +71,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # ChaperoneActivityOfProteinAbundanceSignature
             class ChaperoneActivityOfProteinAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -75,14 +80,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(ChaperoneActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(ChaperoneActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
               end
               private_constant :AST
 
@@ -97,7 +102,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version1_0/functions/complex_abundance.rb

@@ -14,7 +14,8 @@ module BELParser
           SHORT       = :complex
           LONG        = :complexAbundance
           RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance
-          DESCRIPTION = 'Denotes the abundance of a molecular complex'.freeze
+          DESCRIPTION = 'Denotes the abundance of a molecular
+          omplex'.freeze
 
           def self.short
             SHORT
@@ -37,7 +38,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # NamedComplexAbundanceSignature
             class NamedComplexAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -45,19 +46,19 @@ module BELParser
 
               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))))))              
+                  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
 
@@ -72,7 +73,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # ComposedComplexAbundanceSignature
             class ComposedComplexAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -80,14 +82,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(ComplexAbundance))),
-                variadic_arguments(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(ComplexAbundance))),
+                  variadic_arguments(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST
 
@@ -102,7 +104,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|