bel_parser 1.0.0.alpha.9 → 1.0.0.alpha.10

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: ae09c0ccf3a4ad7edad1288aa2b557dfc8496f60
+  metadata.gz: 56e97fd6f3c7806fa34aea964a08dbceb7c03d91
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data/.gemspec

@@ -11,7 +11,7 @@ Gem::Specification.new do |spec|
                                  'Anthony Bargnesi',
                                  'Nick Bargnesi',
                                ]
-  spec.date                  = %q{2016-04-13}
+  spec.date                  = %q{2016-04-14}
   spec.email                 = %q{abargnesi@selventa.com}
   spec.files                 = [
                                  Dir.glob('lib/**/*.{rb,rl}'),

data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.9
+1.0.0.alpha.10

data/lib/bel_parser/language/amino_acid.rb

@@ -0,0 +1,68 @@
+module BELParser
+  module Language
+    # AminoAcid defines a controlled vocabulary of twenty Amino Acids that are
+    # encoded by the universal genetic code. It does not contain the additional
+    # Amino Acids incorporated into proteins by synthetic means.
+    #
+    # see https://en.wikipedia.org/wiki/Amino_acid
+    module AminoAcid
+      Alanine       = [:Alanine, :A, :Ala].freeze
+      Arginine      = [:Arginine, :R, :Arg].freeze
+      Asparagine    = [:Asparagine, :N, :Asn].freeze
+      AsparticAcid  = [:'Aspartic Acid', :D, :Asp].freeze
+      Cysteine      = [:Cysteine, :C, :Cys].freeze
+      GlutamicAcid  = [:'Glutamic Acid', :E, :Glu].freeze
+      Glutamine     = [:Glutamine, :Q, :Gln].freeze
+      Glycine       = [:Glycine, :G, :Gly].freeze
+      Histidine     = [:Histidine, :H, :His].freeze
+      Isoleucine    = [:Isoleucine, :I, :Ile].freeze
+      Leucine       = [:Leucine, :L, :Leu].freeze
+      Lysine        = [:Lysine, :K, :Lys].freeze
+      Methionine    = [:Methionine, :M, :Met].freeze
+      Phenylalanine = [:Phenylalanine, :F, :Phe].freeze
+      Proline       = [:Proline, :P, :Pro].freeze
+      Serine        = [:Serine, :S, :Ser].freeze
+      Threonine     = [:Threonine, :T, :Thr].freeze
+      Tryptophan    = [:Tryptophan, :W, :Trp].freeze
+      Tyrosine      = [:Tyrosine, :Y, :Tyr].freeze
+      Valine        = [:Valine, :V, :Val].freeze
+
+      # Determines if +sym+ represents an amino acid code.
+      #
+      # @param [#to_sym] sym amino acid code
+      # @return [Boolean] +true+ if +sym+ amino acid code is included in
+      # supported amino acids; +false+ if not supported
+      def self.includes?(sym)
+        @hash.key?(sym.to_sym)
+      end
+
+      # Gets all supported amino acid names.
+      def self.names
+        @names
+      end
+
+      # Gets all supported amino acid codes (i.e. name, 1-Letter, 3-Letter).
+      def self.values
+        @values
+      end
+
+      unless defined? @hash
+        @hash = {}
+        constants.map(&method(:const_get)).each do |values|
+          @hash.update(
+            Hash[values.map { |v| [v, values.first] }]
+          )
+        end
+        @hash.freeze
+			end
+
+      unless defined? @names
+        @names = constants.map(&method(:const_get)).map(&:first).sort.freeze
+			end
+
+      unless defined? @values
+        @values = constants.map(&method(:const_get)).map(&:to_a).flatten.freeze
+      end
+    end
+  end
+end

data/lib/bel_parser/language/semantics/function_deprecation.rb

@@ -3,6 +3,10 @@ require 'bel_parser/parsers/ast/node'
 module BELParser
   module Language
     module Semantics
+      # FunctionDeprecation implements a {SemanticsFunction} that maps a
+      # {BELParser::Parsers::AST::Function} to a {SemanticsWarning} if the
+      # referenced function is deprecated for the
+      # {BELParser::Language::Specification}.
       class FunctionDeprecation
         include SemanticsFunction
 
@@ -19,6 +23,9 @@ module BELParser
         end
       end
 
+      # Represents a {SemanticsWarning} when a
+      # {BELParser::Parsers::AST::Function} references a deprecated function
+      # for the {BELParser::Language::Specification}.
       class FunctionDeprecationWarning < SemanticsWarning
         attr_reader :deprecated_function
 
@@ -28,7 +35,7 @@ module BELParser
         end
 
         def to_s
-          %Q{Function "#{deprecated_function}" is deprecated.}
+          %(Function "#{deprecated_function}" is deprecated.)
         end
       end
     end

data/lib/bel_parser/language/semantics/multiple_subject_object.rb

@@ -0,0 +1,55 @@
+require 'bel_parser/parsers/ast/node'
+
+module BELParser
+  module Language
+    module Semantics
+      # MultipleSubjectObject implements a {SemanticsFunction} that maps a
+      # {BELParser::Parsers::AST::Statement} to a {SemanticsWarning} if the
+      # subject term is referenced as an argument of the object list term.
+      class MultipleSubjectObject
+        include SemanticsFunction
+
+        private_class_method :new
+
+        def self.map(stmt_node, spec, _namespaces)
+          return nil unless stmt_node.is_a?(BELParser::Parsers::AST::Statement)
+          return nil unless stmt_node.relationship?
+          rel = spec.relationship(stmt_node.relationship.string_literal.to_sym)
+          return nil unless rel.listable?
+
+          list_func = spec.function(:list)
+          return nil unless list_func
+          return nil unless stmt_node.object.term?
+
+          map_subject_object(stmt_node, rel, spec)
+        end
+
+        def self.map_subject_object(stmt_node, rel, spec)
+          sub_term  = stmt_node.subject.term
+          list_term = stmt_node.object.child
+
+          if list_term.arguments.any? { |arg| sub_term == arg.child }
+            MultipleSubjectObjectWarning.new(stmt_node, spec, rel)
+          end
+        end
+      end
+
+      # Represents a {SemanticsWarning} when a
+      # {BELParser::Parsers::AST::Statement} includes the subject term as an
+      # argument of an object list term.
+      class MultipleSubjectObjectWarning < SemanticsWarning
+        def initialize(stmt_node, spec, rel)
+          super(stmt_node, spec)
+          @rel = rel
+        end
+
+        def to_s
+          <<-MSG.gsub(/ {12}/, '').gsub(/\n/, '')
+            A "#{@rel.long}" statement cannot use the subject term as an
+             object list() argument.
+          MSG
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/semantics/non_causal_nested_statement.rb

@@ -44,11 +44,6 @@ module BELParser
              Causal Relationships: #{causal_relationships}
           MSG
         end
-
-        private
-
-        def causal_relationships
-        end
       end
     end
   end

data/lib/bel_parser/language/semantics/non_object_list.rb

@@ -0,0 +1,56 @@
+require 'bel_parser/parsers/ast/node'
+
+module BELParser
+  module Language
+    module Semantics
+      # NonObjectList implements a {SemanticsFunction} that maps a
+      # {BELParser::Parsers::AST::Object} to a {SemanticsWarning} if the
+      # object of a multiple relationship *is not* a list term.
+      class NonObjectList
+        include SemanticsFunction
+
+        private_class_method :new
+
+        def self.map(stmt_node, spec, _namespaces)
+          return nil unless stmt_node.is_a?(BELParser::Parsers::AST::Statement)
+          return nil unless stmt_node.relationship?
+
+          list_func = spec.function(:list)
+          return nil unless list_func
+
+          rel = spec.relationship(stmt_node.relationship.string_literal.to_sym)
+          return nil unless rel.listable?
+
+          map_object(stmt_node.object, rel, list_func, spec)
+        end
+
+        def self.map_object(obj_node, rel, list_func, spec)
+          return NonObjectListWarning.new(
+            obj_node,
+            spec,
+            rel) unless obj_node.term?
+
+          obj_func = obj_node.child.function.identifier.string_literal
+          NonObjectListWarning.new(
+            obj_node,
+            spec,
+            rel) unless spec.function(obj_func.to_sym) == list_func
+        end
+      end
+
+      # Represents a {SemanticsWarning} when a
+      # multiple relationship {BELParser::Parsers::AST::Statement} does not
+      # reference an object list term.
+      class NonObjectListWarning < SemanticsWarning
+        def initialize(statement_node, spec, rel)
+          super(statement_node, spec)
+          @rel = rel
+        end
+
+        def to_s
+          %(The "#{@rel.long}" relationship must take a list() object term.)
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/semantics/relationship_deprecation.rb

@@ -3,6 +3,10 @@ require 'bel_parser/parsers/ast/node'
 module BELParser
   module Language
     module Semantics
+      # RelationshipDeprecation implements a {SemanticsFunction} that maps a
+      # {BELParser::Parsers::AST::Relationship} to a {SemanticsWarning} if the
+      # referenced relationship is deprecated for the
+      # {BELParser::Language::Specification}.
       class RelationshipDeprecation
         include SemanticsFunction
 
@@ -19,6 +23,9 @@ module BELParser
         end
       end
 
+      # Represents a {SemanticsWarning} when a
+      # {BELParser::Parsers::AST::Relationship} references a deprecated
+      # relationship for the {BELParser::Language::Specification}.
       class RelationshipDeprecationWarning < SemanticsWarning
         attr_reader :deprecated_relationship
 
@@ -28,7 +35,7 @@ module BELParser
         end
 
         def to_s
-          %Q{Relationship "#{deprecated_relationship}" is deprecated.}
+          %(Relationship "#{deprecated_relationship}" is deprecated.)
         end
       end
     end

data/lib/bel_parser/language/semantics/relationship_not_listable.rb

@@ -0,0 +1,60 @@
+require 'bel_parser/parsers/ast/node'
+
+module BELParser
+  module Language
+    module Semantics
+      # RelationshipNotListable implements a {SemanticsFunction} that maps a
+      # {BELParser::Parsers::AST::Statement} to a {SemanticsWarning} if the
+      # relationship cannot be used for multiple terms in a list.
+      class RelationshipNotListable
+        include SemanticsFunction
+
+        private_class_method :new
+
+        def self.map(node, spec, _namespaces)
+          return nil unless node.is_a?(BELParser::Parsers::AST::Statement)
+          return nil unless node.relationship?
+          return nil unless node.object.term?
+
+          map_statement(node, spec)
+        end
+
+        def self.map_statement(stmt_node, spec)
+          list_func = spec.function(:list)
+          return nil unless list_func
+
+          obj_func = stmt_node.object.child.function.identifier.string_literal
+          return nil unless spec.function(obj_func.to_sym) == list_func
+
+          rel = spec.relationship(stmt_node.relationship.string_literal.to_sym)
+          return nil unless rel
+
+          RelationshipNotMultipleWarning.new(stmt_node, spec, rel) unless
+            rel.listable?
+        end
+      end
+
+      # Represents a {SemanticsWarning} when a statement has a relationship
+      # that cannot reference multiple objects.
+      class RelationshipNotMultipleWarning < SemanticsWarning
+        def initialize(statement_node, spec, rel)
+          super(statement_node, spec)
+          @rel = rel
+        end
+
+        def to_s
+          multiple_relationships =
+            @specification
+            .listable_relationships
+            .map(&:long)
+            .join(', ')
+          <<-MSG.gsub(/ {12}/, '').strip
+            Statement must use a multiple relationship with a list object.
+              The "#{@rel.long}" relationship cannot reference multiple objects.
+              Multiple Relationships: #{multiple_relationships}
+          MSG
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/semantics_ast.rb

@@ -210,8 +210,33 @@ module BELParser
           super(:term, children, properties)
         end
 
+        def function
+          children[0]
+        end
+
+        def variadic_arguments?
+          children[1].type == :variadic_arguments
+        end
+
+        def arguments
+          children[1..-1]
+        end
+
         def match(parse_node, _)
-          type == parse_node.type ? success(parse_node) : failure(parse_node)
+          return failure(nil) if parse_node.nil?
+          return failure(parse_node) unless parse_node.type == type
+
+          # Return success if semantic AST does not supply argument patterns.
+          if arguments.empty? || variadic_arguments?
+            success(parse_node)
+          else
+            # Otherwise, check argument length.
+            if arguments.length == parse_node.arguments.length
+              success(parse_node)
+            else
+              failure(parse_node)
+            end
+          end
         end
       end
 

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

@@ -1,6 +1,7 @@
 require_relative '../../version1_0'
 require_relative '../../function'
 require_relative '../../signature'
+require_relative '../../amino_acid'
 require_relative '../../semantics'
 
 module BELParser
@@ -63,7 +64,7 @@ module BELParser
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))),
+                          amino_acid_of(*AminoAcid.values))))),
                   argument(
                     parameter(
                       prefix(
@@ -74,7 +75,9 @@ module BELParser
               end
               private_constant :AST
 
-              STRING_FORM = 'proteinModification(E:*,E:*,E:*)proteinModification'.freeze
+              STRING_FORM =
+                'proteinModification(E:*,T:AminoAcid,E:*)proteinModification'
+                .freeze
               private_constant :STRING_FORM
 
               def self.semantic_ast
@@ -110,11 +113,13 @@ module BELParser
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))))
+                          amino_acid_of(*AminoAcid.values))))))
               end
               private_constant :AST
 
-              STRING_FORM = 'proteinModification(E:*,E:*)proteinModification'.freeze
+              STRING_FORM =
+                'proteinModification(E:*,T:AminoAcid)proteinModification'
+                .freeze
               private_constant :STRING_FORM
 
               def self.semantic_ast

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

@@ -56,7 +56,7 @@ module BELParser
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))),
+                          amino_acid_of(*AminoAcid.values))))),
                   argument(
                     parameter(
                       prefix(
@@ -70,11 +70,12 @@ module BELParser
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))))
+                          amino_acid_of(*AminoAcid.values))))))
               end
               private_constant :AST
 
-              STRING_FORM = 'substitution(E:*,E:*,E:*)substitution'.freeze
+              STRING_FORM =
+                'substitution(T:AminoAcid,E:*,T:AminoAcid)substitution'.freeze
               private_constant :STRING_FORM
 
               def self.semantic_ast

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

@@ -1,6 +1,7 @@
 require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
+require_relative '../../amino_acid'
 require_relative '../../semantics'
 
 module BELParser
@@ -14,7 +15,8 @@ module BELParser
 
           SHORT       = :pmod
           LONG        = :proteinModification
-          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ProteinModification
+          RETURN_TYPE =
+            BELParser::Language::Version2_0::ReturnTypes::ProteinModification
           DESCRIPTION = 'Denotes a covalently modified protein
           bundance'.freeze
 
@@ -61,7 +63,9 @@ module BELParser
               end
               private_constant :AST
 
-              STRING_FORM = 'proteinModification(E:modificationType)proteinModification'.freeze
+              STRING_FORM =
+                'proteinModification(E:modificationType)proteinModification'
+                .freeze
               private_constant :STRING_FORM
 
               def self.semantic_ast
@@ -97,11 +101,13 @@ module BELParser
                       prefix(any),
                       value(
                         value_type(
-                          encoding_of(:*))))))
+                          amino_acid_of(*AminoAcid.values))))))
               end
               private_constant :AST
 
-              STRING_FORM = 'proteinModification(E:modificationType,E:*)proteinModification'.freeze
+              STRING_FORM =
+                'proteinModification(E:modificationType,T:AminoAcid)proteinModification'
+                .freeze
               private_constant :STRING_FORM
 
               def self.semantic_ast
@@ -137,7 +143,7 @@ module BELParser
                       prefix(any),
                       value(
                         value_type(
-                          encoding_of(:*))))),
+                          amino_acid_of(*AminoAcid.values))))),
                   argument(
                     parameter(
                       prefix(any),
@@ -147,7 +153,9 @@ module BELParser
               end
               private_constant :AST
 
-              STRING_FORM = 'proteinModification(E:modificationType,E:*,E:*)proteinModification'.freeze
+              STRING_FORM =
+                'proteinModification(E:modificationType,T:AminoAcid,E:*)proteinModification'
+                .freeze
               private_constant :STRING_FORM
 
               def self.semantic_ast

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.9
+  version: 1.0.0.alpha.10
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-13 00:00:00.000000000 Z
+date: 2016-04-14 00:00:00.000000000 Z
 dependencies: []
 description: Implements language versions 1.0 and 2.0.
 email: abargnesi@selventa.com
@@ -30,6 +30,7 @@ files:
 - lib/bel_parser/expression/parser.rb
 - lib/bel_parser/expression/validator.rb
 - lib/bel_parser/language.rb
+- lib/bel_parser/language/amino_acid.rb
 - lib/bel_parser/language/expression_validator.rb
 - lib/bel_parser/language/function.rb
 - lib/bel_parser/language/quoting.rb
@@ -38,8 +39,11 @@ files:
 - lib/bel_parser/language/semantics/deeply_nested_statement.rb
 - lib/bel_parser/language/semantics/function_deprecation.rb
 - lib/bel_parser/language/semantics/list_function_subject.rb
+- lib/bel_parser/language/semantics/multiple_subject_object.rb
 - lib/bel_parser/language/semantics/non_causal_nested_statement.rb
+- lib/bel_parser/language/semantics/non_object_list.rb
 - lib/bel_parser/language/semantics/relationship_deprecation.rb
+- lib/bel_parser/language/semantics/relationship_not_listable.rb
 - lib/bel_parser/language/semantics/signature_mapping.rb
 - lib/bel_parser/language/semantics_ast.rb
 - lib/bel_parser/language/semantics_function.rb