bel_parser 1.1.2 → 1.1.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -8,3 +8,6 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ### Added
 
 [1.0.0]:    https://github.com/OpenBEL/bel_parser/compare/0.0.0...1.0.0
+
+[1.1.3]:    https://github.com/OpenBEL/bel_parser/compare/1.0.0...1.1.3
+

data/VERSION

@@ -1 +1 @@
-1.1.2
+1.1.3

data/bin/bel2_validator

@@ -87,7 +87,11 @@ uri_reader, url_reader = options.values_at(:uri_reader, :url_reader)
 namespaces = Hash[
   ARGV.map do |ns|
     keyword, identifier = ns.split('=')
-    [keyword, BELParser::Expression::Model::Namespace.new(keyword, identifier, nil)]
+    if identifier.end_with?('.belns')
+      [keyword, BELParser::Expression::Model::Namespace.new(keyword, nil, identifier)]
+    else
+      [keyword, BELParser::Expression::Model::Namespace.new(keyword, identifier, nil)]
+    end
   end.compact
 ]
 

data/bin/bel_script_reader

@@ -81,7 +81,11 @@ url_reader = options[:url_reader]
 namespaces = Hash[
   ARGV.map do |ns|
     keyword, identifier = ns.split('=')
-    [keyword, BELParser::Expression::Model::Namespace.new(keyword, identifier, nil)]
+    if identifier.end_with?('.belns')
+      [keyword, BELParser::Expression::Model::Namespace.new(keyword, nil, identifier)]
+    else
+      [keyword, BELParser::Expression::Model::Namespace.new(keyword, identifier, nil)]
+    end
   end.compact
 ]
 

data/lib/bel_parser/language/apply_default_namespace.rb

@@ -0,0 +1,48 @@
+require 'bel_parser/language/term_transformation'
+
+module BELParser
+  module Language
+    # ApplyDefaultNamespace sets the DEFAULT namespace for values when one is
+    # not provided. Applies to all namespace values within a BEL 2.0 expression.
+    class ApplyDefaultNamespace
+      include BELParser::Language::TermTransformation
+
+      def initialize(language_spec, namespace_hash, uri_reader, url_reader)
+        @language_spec  = language_spec
+        @namespace_hash = namespace_hash
+        @uri_reader     = uri_reader
+        @url_reader     = url_reader
+      end
+
+      def on_term(term_node)
+        term_node.updated([
+            term_node.function,
+            term_node.arguments.map! {|arg| argument(process(arg.child))}
+        ].flatten)
+      end
+
+      def on_argument(argument_node)
+        process(argument_node.child)
+      end
+
+      def on_parameter(parameter_node)
+        parameter_node.updated([
+          process(parameter_node.prefix),
+          parameter_node.value
+        ].flatten)
+      end
+
+      def on_prefix(prefix_node)
+        # guard: return prefix AST node if namespace already supplied
+        return prefix_node if prefix_node.identifier
+
+        # return "DEFAULT" namespace
+        prefix(
+          identifier(
+            'DEFAULT',
+            :complete => true),
+          :complete => true)
+      end
+    end
+  end
+end

data/lib/bel_parser/language/expression_validator.rb

@@ -1,5 +1,6 @@
 require_relative 'syntax'
 require_relative 'semantics'
+require_relative 'apply_default_namespace'
 require_relative 'apply_namespace_encoding'
 
 module BELParser
@@ -9,11 +10,13 @@ module BELParser
     # namespaces.
     class ExpressionValidator
       def initialize(spec, namespaces, uri_reader, url_reader)
-        @spec                = spec
-        @namespaces          = namespaces || {}
-        @syntax_functions    = Syntax.syntax_functions
-        @semantics_functions = Semantics.semantics_functions
-        @transform           =
+        @spec                         = spec
+        @namespaces                   = namespaces || {}
+        @syntax_functions             = Syntax.syntax_functions
+        @semantics_functions          = Semantics.semantics_functions
+        @default_namespace_transform  =
+          ApplyDefaultNamespace.new(@spec, @namespaces, uri_reader, url_reader)
+        @namespace_encoding_transform =
           ApplyNamespaceEncoding.new(@spec, @namespaces, uri_reader, url_reader)
       end
 
@@ -23,7 +26,11 @@ module BELParser
       # @param  [BELParser::Parsers::AST::Node] expression_node to validate
       # @return [BELParser::Language::Syntax::SyntaxResult] syntax results
       def validate(expression_node)
-        @transform.process(expression_node)
+        if @spec.version >= "2.0"
+          expression_node = @default_namespace_transform.process(expression_node)
+        end
+
+        @namespace_encoding_transform.process(expression_node)
 
         case expression_node
         when BELParser::Parsers::AST::SimpleStatement

data/lib/bel_parser/language/semantics_ast.rb

@@ -574,7 +574,7 @@ module BELParser
           unless prefix_node.respond_to?(:namespace) && prefix_node.namespace
             return invalid_namespace(prefix_node, spec, namespaces)
           end
-          
+
           if namespaces.any? { |i| i == :* || i == input_namespace }
             success(prefix_node, spec)
           else
@@ -736,8 +736,16 @@ module BELParser
         end
 
         def match(value_node, spec)
-          string_literal = value_node.children[0]
-          case string_literal
+          ident_or_string = value_node.children[0]
+          value =
+            case ident_or_string
+            when BELParser::Parsers::AST::String
+              ident_or_string.string_value
+            else
+              ident_or_string.string_literal
+            end
+
+          case value
           when START_STOP, UNDETERMINED, UNKNOWN_START_STOP
             success(value_node, spec)
           else

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

@@ -70,6 +70,35 @@ module BELParser
               end
             end
 
+            class FragmentWithAnySignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                    function(
+                        identifier(
+                            function_of(Fragment))),
+                    argument(
+                        parameter(
+                            prefix(any),
+                            value(any))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fragment(E:*)abundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
             # FragmentWithRangeDescriptorSignature
             class FragmentWithRangeDescriptorSignature
               extend BELParser::Language::Signature
@@ -104,6 +133,41 @@ module BELParser
                 STRING_FORM
               end
             end
+
+            # FragmentWithRangeDescriptorSignature
+            class FragmentWithAnyDescriptorSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                    function(
+                        identifier(
+                            function_of(Fragment))),
+                    argument(
+                        parameter(
+                            prefix(any),
+                            value(any))),
+                    argument(
+                        parameter(
+                            prefix(any),
+                            value(any))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fragment(E:*,E:*)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|

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

@@ -15,7 +15,7 @@ module BELParser
           SHORT       = :fromLoc
           LONG        = :fromLocation
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::FromLocation
-          L_ENC       = Version2_0::ValueEncodings::Location
+          A_ENC       = Version2_0::ValueEncodings::Abundance
           DESCRIPTION = 'Denotes the from cellular location of the
           abundance.'.freeze
 
@@ -58,7 +58,7 @@ module BELParser
                         namespace_of(:*)),
                       value(
                         has_encoding,
-                        encoding_of(L_ENC)))))
+                        encoding_of(A_ENC)))))
               end
               private_constant :AST
 
@@ -73,6 +73,36 @@ module BELParser
                 STRING_FORM
               end
             end
+
+            class FromLocationAnySignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                    function(
+                        identifier(
+                            function_of(FromLocation))),
+                    argument(
+                        parameter(
+                            prefix(any),
+                            value(any))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fromLocation(Any)fromLocation'.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|

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

@@ -14,7 +14,7 @@ module BELParser
           SHORT       = :loc
           LONG        = :location
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Location
-          L_ENC       = Version2_0::ValueEncodings::Location
+          A_ENC       = Version2_0::ValueEncodings::Abundance
           DESCRIPTION = 'Denotes the cellular location of the abundance.'.freeze
 
           def self.short
@@ -56,7 +56,7 @@ module BELParser
                         namespace_of(:*)),
                       value(
                         has_encoding,
-                        encoding_of(L_ENC)))))
+                        encoding_of(A_ENC)))))
               end
               private_constant :AST
 
@@ -71,6 +71,39 @@ module BELParser
                 STRING_FORM
               end
             end
+
+            # LocationSignature
+            class LocationAnySignature
+              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(any))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'location(Any)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|

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

@@ -74,8 +74,37 @@ module BELParser
                 STRING_FORM
               end
             end
-          end
 
+            # MolecularActivitySignature
+            class MolecularActivityAnySignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                    function(
+                        identifier(
+                            function_of(MolecularActivity))),
+                    argument(
+                        parameter(
+                            prefix(any),
+                            value(any))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'molecularActivity(Any)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

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

@@ -55,9 +55,10 @@ module BELParser
                   argument(
                     parameter(
                       prefix(any),
-                      value(
-                        has_encoding,
-                        encoding_of(E_ENC)))))
+                      value(any))))
+                      # value(
+                      #   has_encoding,
+                      #   encoding_of(E_ENC)))))
               end
               private_constant :AST
 
@@ -90,9 +91,10 @@ module BELParser
                   argument(
                     parameter(
                       prefix(any),
-                      value(
-                        has_encoding,
-                        encoding_of(E_ENC)))),
+                      value(any))),
+                      # value(
+                      #   has_encoding,
+                      #   encoding_of(E_ENC)))),
                   argument(
                     parameter(
                       prefix(any),
@@ -130,9 +132,10 @@ module BELParser
                   argument(
                     parameter(
                       prefix(any),
-                      value(
-                        has_encoding,
-                        encoding_of(E_ENC)))),
+                      value(any))),
+                      # value(
+                      #   has_encoding,
+                      #   encoding_of(E_ENC)))),
                   argument(
                     parameter(
                       prefix(any),

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

@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :r
           LONG        = :rnaAbundance
-          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::GeneAbundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::RNAAbundance
           R_ENC       = Version2_0::ValueEncodings::RNAAbundance
           DESCRIPTION = 'Denotes the abundance of a gene'.freeze
 

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

@@ -14,7 +14,7 @@ module BELParser
           SHORT       = :toLoc
           LONG        = :toLocation
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ToLocation
-          L_ENC       = Version2_0::ValueEncodings::Location
+          A_ENC       = Version2_0::ValueEncodings::Abundance
           DESCRIPTION = 'Denotes the to cellular location of the
           abundance.'.freeze
 
@@ -57,7 +57,7 @@ module BELParser
                         namespace_of(:*)),
                       value(
                         has_encoding,
-                        encoding_of(L_ENC)))))
+                        encoding_of(A_ENC)))))
               end
               private_constant :AST
 
@@ -72,6 +72,37 @@ module BELParser
                 STRING_FORM
               end
             end
+
+            # ToLocationAnySignature
+            class ToLocationAnySignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                    function(
+                        identifier(
+                            function_of(ToLocation))),
+                    argument(
+                        parameter(
+                            prefix(any),
+                            value(any))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'toLocation(Any)toLocation'.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|

data/lib/bel_parser/language/version2_0/value_encodings/location.rb

@@ -5,7 +5,7 @@ module BELParser
     module Version2_0
       module ValueEncodings
         # Location value encoding.
-        class Location < Any
+        class Location < Abundance
           # Return the {Symbol} value.
           #
           # @note This method should be overridden in subclasses.

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.1.2
+  version: 1.1.3
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -42,11 +42,11 @@ dependencies:
 description: Implements language versions 1.0 and 2.0.
 email: abargnesi@selventa.com
 executables:
+- bel2_compatibility
+- bel2_debug_ast
 - bel2_upgrade
 - bel2_validator
 - bel_script_reader
-- bel2_compatibility
-- bel2_debug_ast
 extensions: []
 extra_rdoc_files: []
 files:
@@ -84,6 +84,7 @@ files:
 - lib/bel_parser/expression/validator.rb
 - lib/bel_parser/language.rb
 - lib/bel_parser/language/amino_acid.rb
+- lib/bel_parser/language/apply_default_namespace.rb
 - lib/bel_parser/language/apply_namespace_encoding.rb
 - lib/bel_parser/language/base_specification.rb
 - lib/bel_parser/language/covalent_protein_modification.rb
@@ -429,7 +430,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.8
+rubygems_version: 2.5.1
 signing_key: 
 specification_version: 4
 summary: Parser for Biolgical Expression Language.