bel_parser 1.0.0.alpha.2 → 1.0.0.alpha.3

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 87f55444534d215b579b4aec8d657cf38479ae1b
+  metadata.gz: fc1ced9daf61e6924edb4e15fe137e76fac85049
+  data.tar.gz: 1662c4c080eb06306ddc52a0c730bb226fe89e69
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data/.gemspec

@@ -11,7 +11,7 @@ Gem::Specification.new do |spec|
                                  'Anthony Bargnesi',
                                  'Nick Bargnesi',
                                ]
-  spec.date                  = %q{2016-04-08}
+  spec.date                  = %q{2016-04-11}
   spec.email                 = %q{abargnesi@selventa.com}
   spec.files                 = [
                                  Dir.glob('lib/**/*.{rb,rl}'),

data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.2
+1.0.0.alpha.3

data/bin/bel2_validator

@@ -0,0 +1,19 @@
+#!/usr/bin/env ruby
+$:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
+
+unless ARGV.first
+  program = File.basename($PROGRAM_NAME)
+  $stderr.puts <<-USAGE.gsub(/ {6}/, '')
+    usage: #{program} [BEL specification version] [PREFIX=URI]...
+  USAGE
+  exit 1
+end
+namespaces = Hash[ARGV[1..-1].map { |ns| ns.split('=') }]
+
+require 'bel_parser'
+require 'bel_parser/expression/term_validator'
+BELParser::Expression::TermValidator.new(ARGV.first, namespaces).each($stdin) do |res|
+  res.each do |res|
+    puts "  #{res}"
+  end
+end

data/lib/bel_parser/expression/parser.rb

@@ -12,6 +12,8 @@ module BELParser
       include BELParser::Parsers::Expression
 
       FILTER = BELParser::ASTFilter.new(
+        :parameter,
+        :term,
         :statement_simple,
         :observed_term,
         :nested_statement

data/lib/bel_parser/expression/term_validator.rb

@@ -0,0 +1,50 @@
+require_relative '../ast_filter'
+require_relative '../ast_generator'
+require_relative '../parsers/expression'
+require_relative '../language'
+require_relative '../language/expression_validator'
+
+module BELParser
+  module Expression
+    # Parser for BEL Expression.
+    class TermValidator
+      include BELParser::Parsers::Common
+      include BELParser::Parsers::Expression
+
+      FILTER = BELParser::ASTFilter.new(:term)
+
+      def initialize(specification_version, namespaces)
+        @spec      = BELParser::Language.specification(specification_version)
+        @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)
+          end
+        else
+          enum_for(:each, io)
+        end
+      end
+    end
+  end
+end
+
+if __FILE__ == $PROGRAM_NAME
+  unless ARGV.first
+    program = File.basename($PROGRAM_NAME)
+    $stderr.puts <<-USAGE.gsub(/ {6}/, '')
+      usage: #{program} [BEL specification version] [PREFIX=URI]...
+    USAGE
+    exit 1
+  end
+  namespaces = Hash[ARGV[1..-1].map { |ns| ns.split('=') }]
+  BELParser::Expression::TermValidator.new(ARGV.first, namespaces).each($stdin) do |res|
+    res.each do |res|
+      puts "  #{res}"
+    end
+  end
+end

data/lib/bel_parser/language/expression_validator.rb

@@ -1,41 +1,31 @@
+require_relative 'syntax'
+require_relative 'semantics'
+
 module BELParser
   module Language
     class ExpressionValidator
-      def initialize(spec)
-        @spec = spec
+      def initialize(spec, namespaces)
+        @spec             = spec
+        @namespaces       = namespaces
+        @syntax_functions = Syntax.syntax_functions
       end
 
       def validate(expression_ast)
-        node_errors = check_syntax(expression_ast)
-        if !node_errors.empty?
-          node_errors.each do |node_error|
-            puts "Syntax error (#{node_error.syntax_errors}) with #{node_error.type}."
-          end
-        else
-          check_semantics(expression_ast)
-        end
+        syntax_problems = syntax(expression_ast)
+        return syntax_problems unless syntax_problems.empty?
+        [Syntax::Valid.new(expression_ast, @spec)] + semantics(expression_ast)
       end
 
       private
 
-      def check_syntax(ast)
-        # Clear syntax checks.
-        ast.traverse.each do |node|
-          node.syntax_errors.clear
-        end
-
-        # Run syntax checks, sets syntax_errors on nodes.
-        @spec.syntax.each do |syntax|
-          syntax.match(ast)
-        end
-
-        ast.traverse.select do |node|
-          !node.syntax_errors.empty?
+      def syntax(expression_ast)
+        @syntax_functions.flat_map do |syntax_function|
+          syntax_function.map(expression_ast, @spec, @namespaces)
         end
       end
 
-      def check_semantics(ast)
-        BELParser::Language::Semantics.check_term(ast, @spec)
+      def semantics(expression_ast)
+        BELParser::Language::Semantics.check_term(expression_ast, @spec)
       end
     end
   end

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

@@ -0,0 +1,44 @@
+require 'bel_parser/parsers/ast/node'
+
+module BELParser
+  module Language
+    module Syntax
+      # InvalidFunction represents a syntax error with invalid function name
+      # according to a BEL specification.
+      class InvalidFunction
+        include SyntaxFunction
+
+        private_class_method :new
+
+        def self.map(expression_ast, spec, namespaces)
+          errors = []
+          expression_ast.traverse.map do |node|
+            next unless node.is_a?(BELParser::Parsers::AST::Function)
+            function_name = node.identifier.string_literal
+            unless spec.function(function_name.to_sym)
+              errors << InvalidFunctionSyntaxError.new(
+                expression_ast, spec, node, spec.functions)
+            end
+          end
+          errors
+        end
+      end
+
+      # InvalidFunctionSyntaxError indicates a function name was invalid.
+      class InvalidFunctionSyntaxError < SyntaxError
+        # Gets the functions defined by a BEL specification.
+        attr_reader :bel_functions
+
+        def initialize(expression_node, spec, error_node, bel_functions)
+          super(expression_node, spec, error_node)
+          @bel_functions = bel_functions
+        end
+
+        def msg
+          invalid_function = error_node.identifier.string_literal
+          %Q{Invalid function "#{invalid_function}".}
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,48 @@
+require 'bel_parser/parsers/ast/node'
+
+module BELParser
+  module Language
+    module Syntax
+      # Undefined namespace finds parameter prefixes that reference an
+      # undefined namespace.
+      class UndefinedNamespace
+        include SyntaxFunction
+
+        private_class_method :new
+
+        def self.map(expression_ast, spec, namespaces)
+          errors = []
+          expression_ast.traverse.map do |node|
+            next unless node.is_a?(BELParser::Parsers::AST::Prefix)
+            next if node.identifier.nil?
+
+            namespace_prefix = node.identifier.string_literal
+            unless namespaces[namespace_prefix]
+              errors << UndefinedNamespaceError.new(
+                expression_ast, node, namespaces)
+            end
+          end
+          errors
+        end
+      end
+
+      # UndefinedNamespaceError indicates a parameter prefix is referencing
+      # an undefined namespace.
+      class UndefinedNamespaceError < SyntaxError
+        # Gets the defined namespaces.
+        attr_reader :defined_namespaces
+
+        def initialize(expression_node, spec, error_node, defined_namespaces)
+          super(expression_node, spec, error_node)
+          @defined_namespaces = defined_namespaces.dup
+        end
+
+        def msg
+          undefined_namespace = error_node.identifier.string_literal
+          %Q{Undefined namespace "#{undefined_namespace}".}
+        end
+      end
+    end
+  end
+end
+

data/lib/bel_parser/language/syntax.rb

@@ -0,0 +1,33 @@
+require_relative 'syntax_function'
+require_relative 'syntax_error'
+require_relative 'syntax_warning'
+
+module BELParser
+  module Language
+    module Syntax
+      def self.syntax_functions
+        self.constants.collect do |symbol|
+          const = self.const_get(symbol)
+          const if
+            const.respond_to?(:include?) &&
+            const.include?(SyntaxFunction)
+        end.compact
+      end
+
+      class Valid < SyntaxResult
+        def msg
+          'Syntax is valid.'
+        end
+      end
+    end
+  end
+end
+
+# Require all generic syntax functions.
+Dir[
+  File.join(
+    File.dirname(File.expand_path(__FILE__)),
+    'syntax', '*.rb')
+].each do |path|
+  require_relative "syntax/#{File.basename(path)}"
+end

data/lib/bel_parser/language/syntax_error.rb

@@ -0,0 +1,25 @@
+require_relative 'syntax_result'
+
+module BELParser
+  module Language
+    module Syntax
+      class SyntaxError < SyntaxResult
+        attr_reader :expression_node, :target_node
+
+        def initialize(expression_node, specification, target_node)
+          super(expression_node, specification)
+          @target_node = target_node
+        end
+
+        # @abstract Subclass and override {#msg} to provide the message.
+        def msg
+          raise NotImplementedError, "#{__method__} is not implemented."
+        end
+
+        def to_s
+          "Error: #{msg}"
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/syntax_function.rb

@@ -0,0 +1,13 @@
+module BELParser
+  module Language
+    module Syntax
+      module SyntaxFunction
+        # @abstract Include {SyntaxFunction} and override {#map} to check
+        # expression syntax.
+        def self.map(expression_ast, spec, namespaces)
+          raise NotImplementedError, "#{__method__} is not implemented."
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/syntax_result.rb

@@ -0,0 +1,23 @@
+module BELParser
+  module Language
+    module Syntax
+      class SyntaxResult
+        attr_reader :expression_node, :specification
+
+        def initialize(expression_node, specification)
+          @expression_node = expression_node
+          @specification   = specification
+        end
+
+        # @abstract Subclass and override {#msg} to provide the message.
+        def msg
+          raise NotImplementedError, "#{__method__} is not implemented."
+        end
+
+        def to_s
+          "Info: #{msg}"
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/syntax_warning.rb

@@ -0,0 +1,20 @@
+require_relative 'syntax_result'
+
+module BELParser
+  module Language
+    module Syntax
+      class SyntaxWarning < SyntaxResult
+        attr_reader :expression_node, :target_node
+
+        def initialize(expression_node, specification, target_node)
+          super(expression_node, specification)
+          @target_node = target_node
+        end
+
+        def to_s
+          "Warning: #{msg}"
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language.rb

@@ -1,5 +1,6 @@
 require_relative 'language/function'
 require_relative 'language/quoting'
+require_relative 'language/syntax'
 require_relative 'language/semantics'
 require_relative 'language/signature'
 require_relative 'language/specification'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.2
+  version: 1.0.0.alpha.3
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -9,12 +9,12 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-08 00:00:00.000000000 Z
+date: 2016-04-11 00:00:00.000000000 Z
 dependencies: []
 description: Implements language versions 1.0 and 2.0.
 email: abargnesi@selventa.com
 executables:
-- bel2_termcheck
+- bel2_validator
 extensions: []
 extra_rdoc_files: []
 files:
@@ -23,13 +23,13 @@ files:
 - LICENSE
 - README.md
 - VERSION
-- bin/bel2_termcheck
+- bin/bel2_validator
 - lib/bel_parser.rb
 - lib/bel_parser/ast_filter.rb
 - lib/bel_parser/ast_generator.rb
 - lib/bel_parser/ast_validator.rb
 - lib/bel_parser/expression/parser.rb
-- lib/bel_parser/expression/term_semantics.rb
+- lib/bel_parser/expression/term_validator.rb
 - lib/bel_parser/language.rb
 - lib/bel_parser/language/expression_validator.rb
 - lib/bel_parser/language/function.rb
@@ -42,6 +42,12 @@ files:
 - lib/bel_parser/language/signature.rb
 - lib/bel_parser/language/specification.rb
 - lib/bel_parser/language/syntax.rb
+- lib/bel_parser/language/syntax/invalid_function.rb
+- lib/bel_parser/language/syntax/undefined_namespace.rb
+- lib/bel_parser/language/syntax_error.rb
+- lib/bel_parser/language/syntax_function.rb
+- lib/bel_parser/language/syntax_result.rb
+- lib/bel_parser/language/syntax_warning.rb
 - lib/bel_parser/language/version1_0.rb
 - lib/bel_parser/language/version1_0/functions/abundance.rb
 - lib/bel_parser/language/version1_0/functions/biological_process.rb

data/bin/bel2_termcheck

@@ -1,39 +0,0 @@
-#!/usr/bin/env ruby
-$:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
-
-require 'bel_parser'
-require 'bel_parser/language/version2_0'
-require 'bel_parser/language/semantics/analyzer'
-
-module BELParser
-  module Expression
-    # Parser for BEL Expression.
-    class TermSemanticsParser
-      include BELParser::Parsers::Common
-      include BELParser::Parsers::Expression
-
-      FILTER = BELParser::ASTFilter.new(:term)
-
-      def each(io)
-        if block_given?
-          v2           = BELParser::Language::Version2_0::Specification.new
-          filtered_ast = FILTER.each(BELParser::ASTGenerator.new.each(io))
-          filtered_ast.each do |results|
-            term = results.last.first
-            yield BELParser::Language::Semantics.check_term(term, v2)
-          end
-        else
-          enum_for(:each, io)
-        end
-      end
-    end
-  end
-end
-
-BELParser::Expression::TermSemanticsParser.new.each($stdin) do |signature|
-  valid_signatures = signature.compact
-  puts 'Signatures:'
-  valid_signatures.each do |sig|
-    puts "  #{sig}"
-  end
-end

data/lib/bel_parser/expression/term_semantics.rb

@@ -1,36 +0,0 @@
-require_relative '../ast_filter'
-require_relative '../ast_generator'
-require_relative '../parsers/expression'
-require_relative '../language/version2_0'
-require_relative '../language/semantics/analyzer'
-
-module BELParser
-  module Expression
-    # Parser for BEL Expression.
-    class TermSemanticsParser
-      include BELParser::Parsers::Common
-      include BELParser::Parsers::Expression
-
-      FILTER = BELParser::ASTFilter.new(:term)
-
-      def each(io)
-        if block_given?
-          v2           = BELParser::Language::Version2_0::Specification.new
-          filtered_ast = FILTER.each(BELParser::ASTGenerator.new.each(io))
-          filtered_ast.each do |results|
-            term = results.last.first
-            yield BELParser::Language::Semantics.check_term(term, v2)
-          end
-        else
-          enum_for(:each, io)
-        end
-      end
-    end
-  end
-end
-
-if __FILE__ == $PROGRAM_NAME
-  BELParser::Expression::TermSemanticsParser.new.each($stdin) do |semantics|
-    puts semantics.join(", ")
-  end
-end