bel_parser 1.0.0.alpha.1 → 1.0.0.alpha.2

data/lib/bel_parser/language/version2_0/relationships/translated_to.rb

@@ -0,0 +1,31 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # TranslatedTo:  +R >> P+ -  For rnaAbundance term R and proteinAbundance term P, +R translatedTo P+ or +R >> P+ indicates that members of P are produced by the translation of members of R. For example: +r(HGNC:AKT1) >> p(HGNC:AKT1)+ indicates that AKT1 protein is produced by translation of AKT1 RNA.
+        class TranslatedTo
+          extend Relationship
+
+          SHORT       = :>>
+          LONG        = :translatedTo
+          DESCRIPTION = ' +R >> P+ -  For rnaAbundance term R and proteinAbundance term P, +R translatedTo P+ or +R >> P+ indicates that members of P are produced by the translation of members of R. For example: +r(HGNC:AKT1) >> p(HGNC:AKT1)+ indicates that AKT1 protein is produced by translation of AKT1 RNA.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/relationships/translocates.rb

@@ -0,0 +1,31 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # Translocates:  +translocation(A, ns1:v1, ns2:v2) translocates A+ -  This relationship links the abundance term in a +translocation()+ to the translocation. This relationship is direct because it is a _self_ relationship. The translocated abundance is directly acted on by the translocation process. This relationship is introduced by the BEL Compiler and may not be used by statements in BEL documents.
+        class Translocates
+          extend Relationship
+
+          SHORT       = :translocates
+          LONG        = :translocates
+          DESCRIPTION = ' +translocation(A, ns1:v1, ns2:v2) translocates A+ -  This relationship links the abundance term in a +translocation()+ to the translocation. This relationship is direct because it is a _self_ relationship. The translocated abundance is directly acted on by the translocation process. This relationship is introduced by the BEL Compiler and may not be used by statements in BEL documents.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/{version1 → version2_0}/return_types/abundance.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version1
+    module Version2_0
       module ReturnTypes
         # Abundance return type.
         class Abundance < Any

data/lib/bel_parser/language/{version2 → version2_0}/return_types/activity.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # Activity return type.
         class Activity < Any

data/lib/bel_parser/language/{version2 → version2_0}/return_types/any.rb

@@ -2,7 +2,7 @@ require 'English'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # The any type.
         class Any

data/lib/bel_parser/language/{version2 → version2_0}/return_types/biological_process.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # Biological process return type.
         class BiologicalProcess < Any

data/lib/bel_parser/language/{version1 → version2_0}/return_types/complex_abundance.rb

@@ -2,7 +2,7 @@ require_relative 'abundance'
 
 module BELParser
   module Language
-    module Version1
+    module Version2_0
       module ReturnTypes
         # Complex abundance return type.
         class ComplexAbundance < Abundance

data/lib/bel_parser/language/{version2 → version2_0}/return_types/fragment.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # Fragment return type.
         class Fragment < Any

data/lib/bel_parser/language/{version2 → version2_0}/return_types/from_location.rb

@@ -2,7 +2,7 @@ require_relative 'location'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # FromLocation return type.
         class FromLocation < Location

data/lib/bel_parser/language/{version2 → version2_0}/return_types/fusion.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # Fusion return type.
         class Fusion < Any

data/lib/bel_parser/language/{version1 → version2_0}/return_types/gene_abundance.rb

@@ -2,7 +2,7 @@ require_relative 'abundance'
 
 module BELParser
   module Language
-    module Version1
+    module Version2_0
       module ReturnTypes
         # Gene abundance return type.
         class GeneAbundance < Abundance

data/lib/bel_parser/language/{version2 → version2_0}/return_types/list.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # List return type.
         class List < Any

data/lib/bel_parser/language/{version2 → version2_0}/return_types/location.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # Location return type.
         class Location < Any

data/lib/bel_parser/language/{version2 → version2_0}/return_types/micro_rna_abundance.rb

@@ -2,7 +2,7 @@ require_relative 'abundance'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # Micro RNA abundance return type.
         class MicroRNAAbundance < Abundance

data/lib/bel_parser/language/{version2 → version2_0}/return_types/molecular_activity.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # MolecularActivity return type.
         class MolecularActivity < Any

data/lib/bel_parser/language/{version2 → version2_0}/return_types/pathology.rb

@@ -2,7 +2,7 @@ require_relative 'biological_process'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # Pathology return type.
         class Pathology < BiologicalProcess

data/lib/bel_parser/language/{version1 → version2_0}/return_types/products.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version1
+    module Version2_0
       module ReturnTypes
         # Products return type.
         class Products < Any

data/lib/bel_parser/language/{version1 → version2_0}/return_types/protein_abundance.rb

@@ -2,7 +2,7 @@ require_relative 'abundance'
 
 module BELParser
   module Language
-    module Version1
+    module Version2_0
       module ReturnTypes
         # Protein abundance return type.
         class ProteinAbundance < Abundance

data/lib/bel_parser/language/{version2 → version2_0}/return_types/protein_modification.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # Protein modification return type.
         class ProteinModification < Any

data/lib/bel_parser/language/{version1 → version2_0}/return_types/reactants.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version1
+    module Version2_0
       module ReturnTypes
         # Reactants return type.
         class Reactants < Any

data/lib/bel_parser/language/{version2 → version2_0}/return_types/rna_abundance.rb

@@ -2,7 +2,7 @@ require_relative 'abundance'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # RNA abundance return type.
         class RNAAbundance < Abundance

data/lib/bel_parser/language/{version2 → version2_0}/return_types/to_location.rb

@@ -2,7 +2,7 @@ require_relative 'location'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # ToLocation return type.
         class ToLocation < Location

data/lib/bel_parser/language/{version2 → version2_0}/return_types/variant.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module ReturnTypes
         # Variant return type.
         class Variant < Any

data/lib/bel_parser/language/version2_0.rb

@@ -0,0 +1,73 @@
+require_relative 'function'
+require_relative 'specification'
+
+module BELParser
+  module Language
+    module Version2_0
+      # Version2_0Specification defines the BEL, version 2.0 specification.
+      class Specification
+        include BELParser::Language::Specification
+        def initialize
+          @version = '2.0'.freeze
+
+          # Establish functions
+          function_classes = Version2_0::Functions.constants.collect do |symbol|
+            const = Version2_0::Functions.const_get(symbol)
+            const if
+              const.respond_to?(:short) &&
+              const.respond_to?(:long)
+          end
+          @functions         = function_classes.compact
+          @indexed_functions = index_long_short(@functions)
+
+          # Collect relationships
+          rel_classes = Version2_0::Relationships.constants.collect do |symbol|
+            const = Version2_0::Relationships.const_get(symbol)
+            const if
+              const.respond_to?(:short) &&
+              const.respond_to?(:long)
+          end
+          @relationships         = rel_classes.compact
+          @indexed_relationships = index_long_short(@relationships)
+
+          # Establish return types
+          ret_classes = Version2_0::ReturnTypes.constants.collect do |symbol|
+            const = Version2_0::ReturnTypes.const_get(symbol)
+            const if const.respond_to?(:subtypes)
+          end
+          @return_types         = ret_classes.compact
+          @indexed_return_types = index_sym(@return_types)
+
+          freeze
+        end
+      end
+    end
+  end
+end
+
+# Require all version 2.0 return types
+Dir[
+  File.join(
+    File.dirname(File.expand_path(__FILE__)),
+    'version2_0', 'return_types', '*.rb')
+].each do |path|
+  require_relative "version2_0/return_types/#{File.basename(path)}"
+end
+
+# Require all version 2.0 functions.
+Dir[
+  File.join(
+    File.dirname(File.expand_path(__FILE__)),
+    'version2_0', 'functions', '*.rb')
+].each do |path|
+  require_relative "version2_0/functions/#{File.basename(path)}"
+end
+
+# Require all version 1.0 relationships.
+Dir[
+  File.join(
+    File.dirname(File.expand_path(__FILE__)),
+    'version2_0', 'relationships', '*.rb')
+].each do |path|
+  require_relative "version2_0/relationships/#{File.basename(path)}"
+end

data/lib/bel_parser/language.rb

@@ -1,7 +1,95 @@
 require_relative 'language/function'
 require_relative 'language/quoting'
-require_relative 'language/semantic_ast'
+require_relative 'language/semantics'
 require_relative 'language/signature'
 require_relative 'language/specification'
+require_relative 'language/expression_validator'
 
-# BEL language/version1 and language/version2 files are loaded when needed.
+module BELParser
+  module Language
+
+    # Mutex to synchronize creation of BEL specifications.
+    LOCK = Mutex.new
+    private_constant :LOCK
+
+    # Indicates if +version+ is a defined BEL specification.
+    #
+    # @param  [#to_s] version the BEL version string (e.g. +"2.0"+)
+    # @return [Boolean] +true+ if +version+ is defined; +false+ if not
+    def self.defines_version?(version)
+      begin
+        specification(version)
+        true
+      rescue ArgumentError, LoadError
+        false
+      end
+    end
+
+    # Returns all version strings that are defined and supported by this
+    # project.
+    #
+    # @return [Array<String>] BEL language versions
+    def self.versions
+      Dir[
+        File.join(
+          File.expand_path('..', __FILE__),
+          'language',
+          'version*.rb'
+        )
+      ].map do |path|
+        file_name = File.basename(path)
+        file_name.scan(/[0-9]+_[0-9]+/).first.sub('_', '.')
+      end.sort
+    end
+
+    # Returns all language {Specification specifications}.
+    #
+    # @return [Array<Specification>] BEL specifications
+    def self.specifications
+      versions.map { |version| specification(version) }
+    end
+
+    # Returns the {Specification} for a BEL specification +version+.
+    #
+    # @param  [#to_s] version the BEL version string (e.g. +"2.0"+)
+    # @return [Specification] the BEL specification
+    # @raise  [ArgumentError] if the version string is malformed or is not
+    #         supported
+    # @see    {.defines?}
+    def self.specification(version)
+      version_string = version.to_s
+      unless version_string =~ /^[0-9]+\.[0-9]+/
+        raise ArgumentError, "Version format incorrect; expecting MAJOR.MINOR"
+      end
+
+      LOCK.synchronize do
+        version_sym = version_string.to_sym
+        @specs              ||= {}
+        @specs[version_sym] ||= create_specification(version_string)
+        @specs[version_sym]
+      end
+    end
+
+    # Create the {Specification} for a BEL +version+.
+    #
+    # @param  [String] version the BEL version string (e.g. +"2.0"+)
+    # @return [Specification] the BEL specification
+    # @raise  [ArgumentError] if the version string is malformed or is not
+    #         supported
+    # @see    {.defines?}
+    def self.create_specification(version)
+      major, minor = version.split('.')
+      version_file = "language/version#{major}_#{minor}"
+
+      begin
+        require_relative version_file
+        version_const  = :"Version#{major}_#{minor}"
+        version_module = BELParser::Language.const_get(version_const)
+        version_module::Specification.new
+      rescue LoadError
+        raise ArgumentError, "Version #{version} is not supported."
+      end
+    end
+    private_class_method :create_specification
+  end
+end

data/lib/bel_parser/parsers/ast/node.rb

@@ -64,6 +64,16 @@ module BELParser
         # of this AST node.
         attr_reader :character_range
 
+        # Get the syntax errors for this AST node.
+        def syntax_errors
+          (@syntax_errors ||= [])
+        end
+
+        # Add a syntax error to thie AST node.
+        def add_syntax_error(syntax_error)
+          syntax_errors << syntax_error
+        end
+
         # Get the start of the character range enclosing this AST node.
         def range_start
           @character_range[0]
@@ -92,10 +102,10 @@ module BELParser
 
         def traverse(&block)
           if block_given?
+            yield self
             children.each do |child_node|
               child_node.traverse(&block) if child_node.respond_to?(:traverse)
             end
-            yield self
           else
             enum_for(:traverse)
           end