bel_parser 1.0.0.alpha.10 → 1.0.0.alpha.11

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 79712252a5ee0abbb4c92ccbfe1291b3e5dd657a
+  metadata.gz: 102eb6c434bb351a77b6c48cb79819b4bbd6c02d
+  data.tar.gz: a018453c3f5a83b1ec952460c58462f9086b05c5
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+  data.tar.gz: d85096c8ffacc3b2887b43907949c36c155d26a925f7fa41e0ccee3138c902858be4898e9689d67c4db3c18e2e4d84b5d5b90df6cdb379718d7358571d7382f3

data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.10
+1.0.0.alpha.11

data/bin/bel2_validator

@@ -15,6 +15,13 @@ require 'bel_parser'
 require 'bel_parser/expression/validator'
 BELParser::Expression::Validator
   .new(ARGV.first, namespaces)
-  .each($stdin) do |res|
-    puts res.map { |r| "#{r}\n" }.join.each_line.map { |l| "  #{l}" }.join
+  .each($stdin) do |(line_number, line, ast, messages)|
+    puts "#{line_number}: #{line}"
+    puts "  AST Type: #{ast.type}"
+    puts messages
+      .map { |r| "#{r}\n" }
+      .join
+      .each_line
+      .map { |l| "  #{l}" }
+      .join
   end

data/lib/bel_parser/ast_generator.rb

@@ -55,7 +55,7 @@ module BELParser
             PARSERS.map do |parser|
               parser.parse(line) { |ast| ast_results << ast }
             end
-            yield([line_number, line, ast_results])
+            yield [line_number, line, ast_results]
             line_number += 1
           rescue StopIteration
             return

data/lib/bel_parser/expression/validator.rb

@@ -20,15 +20,17 @@ module BELParser
 
       def initialize(specification_version, namespaces)
         @spec      = BELParser::Language.specification(specification_version)
-        @validator = BELParser::Language::ExpressionValidator.new(@spec, namespaces)
+        @validator = BELParser::Language::ExpressionValidator.new(
+          @spec, namespaces)
       end
 
       def each(io)
         if block_given?
           filtered_ast = FILTER.each(BELParser::ASTGenerator.new.each(io))
-          filtered_ast.each do |results|
-            term = results.last.first
-            yield @validator.validate(term)
+          filtered_ast.each do |(line_number, line, ast_results)|
+            ast_results.each do |ast|
+              yield [line_number, line, ast, @validator.validate(ast)]
+            end
           end
         else
           enum_for(:each, io)
@@ -46,8 +48,17 @@ if __FILE__ == $PROGRAM_NAME
     USAGE
     exit 1
   end
-  ns = Hash[ARGV[1..-1].map { |ns| ns.split('=') }]
-  BELParser::Expression::Validator.new(ARGV.first, ns).each($stdin) do |res|
-    puts res.map { |r| "#{r}\n" }.join.each_line.map { |l| "  #{l}" }.join
-  end
+  namespaces = Hash[ARGV[1..-1].map { |ns| ns.split('=') }]
+  BELParser::Expression::Validator
+    .new(ARGV.first, namespaces)
+    .each($stdin) do |(line_number, line, ast, messages)|
+      puts "#{line_number}: #{line}"
+      puts "  AST Type: #{ast.type}"
+      puts messages
+        .map { |r| "#{r}\n" }
+        .join
+        .each_line
+        .map { |l| "  #{l}" }
+        .join
+    end
 end

data/lib/bel_parser/language/amino_acid.rb

@@ -54,11 +54,11 @@ module BELParser
           )
         end
         @hash.freeze
-			end
+      end
 
       unless defined? @names
         @names = constants.map(&method(:const_get)).map(&:first).sort.freeze
-			end
+      end
 
       unless defined? @values
         @values = constants.map(&method(:const_get)).map(&:to_a).flatten.freeze

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

@@ -13,7 +13,7 @@ module BELParser
 
         def self.map(stmt_node, spec, _namespaces)
           return nil unless stmt_node.is_a?(BELParser::Parsers::AST::Statement)
-          return nil unless stmt_node.relationship?
+          return nil if stmt_node.relationship.string_literal.nil?
           rel = spec.relationship(stmt_node.relationship.string_literal.to_sym)
           return nil unless rel.listable?
 
@@ -44,7 +44,7 @@ module BELParser
         end
 
         def to_s
-          <<-MSG.gsub(/ {12}/, '').gsub(/\n/, '')
+          <<-MSG.gsub(/ {12}/, '').delete("\n")
             A "#{@rel.long}" statement cannot use the subject term as an
              object list() argument.
           MSG

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

@@ -13,7 +13,7 @@ module BELParser
 
         def self.map(stmt_node, spec, _namespaces)
           return nil unless stmt_node.is_a?(BELParser::Parsers::AST::Statement)
-          return nil unless stmt_node.relationship?
+          return nil if stmt_node.relationship.string_literal.nil?
 
           list_func = spec.function(:list)
           return nil unless list_func

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

@@ -14,6 +14,7 @@ module BELParser
 
         def self.map(node, spec, _namespaces)
           return nil unless node.is_a?(BELParser::Parsers::AST::Relationship)
+          return nil if node.string_literal.nil?
 
           relationship_name = node.string_literal
           rel               = spec.relationship(relationship_name.to_sym)

data/lib/bel_parser/language/semantics_ast.rb

@@ -166,6 +166,10 @@ module BELParser
           SemanticIsAminoAcidRange.new(**properties)
         end
 
+        def is_sequence_position(**properties)
+          SemanticIsSequencePosition.new(**properties)
+        end
+
         def variadic_arguments(*params_or_terms, **properties)
           SemanticVariadicArguments.new(params_or_terms, **properties)
         end
@@ -229,13 +233,11 @@ module BELParser
           # Return success if semantic AST does not supply argument patterns.
           if arguments.empty? || variadic_arguments?
             success(parse_node)
+          # Or, check argument length.
+          elsif arguments.length == parse_node.arguments.length
+            success(parse_node)
           else
-            # Otherwise, check argument length.
-            if arguments.length == parse_node.arguments.length
-              success(parse_node)
-            else
-              failure(parse_node)
-            end
+            failure(parse_node)
           end
         end
       end
@@ -612,6 +614,30 @@ module BELParser
           end
         end
       end
+
+      # AST node for IsSequencePosition is a semantic AST.
+      class SemanticIsSequencePosition < SemanticASTNode
+        include BELParser::Quoting
+
+        def initialize(**properties)
+          super(:is_sequence_position, [], properties)
+        end
+
+        def match(value_type, _)
+          string_literal = unquote(value_type.string_literal)
+          integer_position =
+            begin
+              Integer(string_literal)
+            rescue
+              nil
+            end
+          if integer_position && integer_position > 0
+            success(value_type)
+          else
+            failure(value_type)
+          end
+        end
+      end
     end
   end
 end

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

@@ -66,14 +66,14 @@ module BELParser
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))),
+                          is_sequence_position)))),
                   argument(
                     parameter(
                       prefix(
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))))
+                          is_sequence_position)))))
               end
               private_constant :AST
 
@@ -152,14 +152,14 @@ module BELParser
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))),
+                          is_sequence_position)))),
                   argument(
                     parameter(
                       prefix(
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))))
+                          is_sequence_position)))))
               end
               private_constant :AST
 
@@ -238,14 +238,14 @@ module BELParser
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))),
+                          is_sequence_position)))),
                   argument(
                     parameter(
                       prefix(
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))))
+                          is_sequence_position)))))
               end
               private_constant :AST
 

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

@@ -71,7 +71,7 @@ module BELParser
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))))
+                          is_sequence_position)))))
               end
               private_constant :AST
 

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

@@ -63,7 +63,7 @@ module BELParser
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))),
+                          is_sequence_position)))),
                   argument(
                     parameter(
                       prefix(

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

@@ -56,7 +56,7 @@ module BELParser
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))))
+                          is_sequence_position)))))
               end
               private_constant :AST
 

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

@@ -149,7 +149,7 @@ module BELParser
                       prefix(any),
                       value(
                         value_type(
-                          encoding_of(:*))))))
+                          is_sequence_position)))))
               end
               private_constant :AST
 

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

@@ -911,6 +911,10 @@ module BELParser
           Set.new(children)
         end
 
+        def unset(*children)
+          Unset.new(children)
+        end
+
         def document_property(*children)
           DocumentProperty.new(children)
         end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.10
+  version: 1.0.0.alpha.11
 platform: ruby
 authors:
 - Anthony Bargnesi