bel_parser 1.0.0.alpha.1

checksums.yaml

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data/.gemspec

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+Gem::Specification.new do |spec|
+  spec.name                  = 'bel_parser'
+  spec.version               = File.read(
+                                 File.join(
+                                   File.expand_path(File.dirname(__FILE__)),
+                                   'VERSION'))
+  spec.summary               = %q{Parser for Biolgical Expression Language.}
+  spec.description           = %q{Implements language versions 1.0 and 2.0.}
+  spec.license               = 'Apache-2.0'
+  spec.authors               = [
+                                 'Anthony Bargnesi',
+                                 'Nick Bargnesi',
+                               ]
+  spec.date                  = %q{2016-04-05}
+  spec.email                 = %q{abargnesi@selventa.com}
+  spec.files                 = [
+                                 Dir.glob('lib/**/*.{rb,rl}'),
+                                 __FILE__,
+                                 'VERSION',
+                                 'CHANGELOG.md',
+                                 'LICENSE',
+                                 'README.md'
+                               ].flatten!
+  spec.executables           = Dir.glob('bin/*').map(&File.method(:basename))
+  spec.homepage              = 'https://github.com/OpenBEL/bel_parser'
+  spec.require_paths         = ['lib']
+  spec.required_ruby_version = '>= 2.0.0'
+end

data/CHANGELOG.md

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+# Change Log
+All notable changes to bel_parser will be documented in this file. The curated log begins at changes to version 1.0.0.
+
+This project adheres to [Semantic Versioning](http://semver.org/).
+
+## [1.0.0][1.0.0] - TBD
+
+### Added
+
+[1.0.0]:    https://github.com/OpenBEL/bel_parser/compare/0.0.0...1.0.0

data/LICENSE

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data/README.md

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+# bel_parser
+
+Parser for BEL expressions and the BEL Script document format.
+
+### Installation
+
+### Getting Started
+
+### Design

data/VERSION

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+1.0.0.alpha.1

data/bin/bel2_termcheck

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+#!/usr/bin/env ruby
+$:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
+
+require 'bel_parser'
+require 'bel_parser/language/version2'
+require 'bel_parser/language/semantics/analyzer'
+
+module BELParser
+  module Expression
+    # Parser for BEL Expression.
+    class TermSemanticsParser
+      include BELParser::Parsers::Common
+      include BELParser::Parsers::Expression
+
+      FILTER = BELParser::ASTFilter.new(:term)
+
+      def each(io)
+        if block_given?
+          v2           = BELParser::Language::Version2::Specification.new
+          filtered_ast = FILTER.each(BELParser::ASTGenerator.new.each(io))
+          filtered_ast.each do |results|
+            term = results.last.first
+            yield BELParser::Language::Semantics.check_term(term, v2)
+          end
+        else
+          enum_for(:each, io)
+        end
+      end
+    end
+  end
+end
+
+BELParser::Expression::TermSemanticsParser.new.each($stdin) do |signature|
+  valid_signatures = signature.compact
+  puts 'Signatures:'
+  valid_signatures.each do |sig|
+    puts "  #{sig}"
+  end
+end

data/lib/bel_parser.rb

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+# vendored 'ast' gem
+require 'bel_parser/vendor/ast'
+
+# AST model
+require 'bel_parser/parsers/ast/node'
+
+# ragel parsers
+require 'bel_parser/parsers/common'
+require 'bel_parser/parsers/expression'
+require 'bel_parser/parsers/bel_script'
+
+# AST processors
+require 'bel_parser/ast_generator'
+require 'bel_parser/ast_filter'
+
+# Language; version-independent classes
+require 'bel_parser/language'

data/lib/bel_parser/ast_filter.rb

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+require_relative 'parsers/ast/node'
+
+module BELParser
+  # ASTFilter filters types of {BELParser::Parsers::AST::Node}.
+  class ASTFilter
+    def initialize(*types)
+      @types = types
+    end
+
+    def each(ast_source)
+      if block_given?
+        ast_source.each do |(line_number, line, ast_results)|
+          selected = filter(ast_results)
+          yield([line_number, line, selected]) unless selected.empty?
+        end
+      else
+        enum_for(:each, ast_source)
+      end
+    end
+
+    def filter(ast_enum)
+      ast_enum.select do |node|
+        @types.include?(node.type)
+      end
+    end
+  end
+end

data/lib/bel_parser/ast_generator.rb

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+require_relative 'parsers/common'
+require_relative 'parsers/expression'
+require_relative 'parsers/bel_script'
+require_relative 'mixin/line_mapping'
+require_relative 'mixin/line_continuator'
+
+module BELParser
+  # ASTGenerator yields AST results for each line in some {IO}.
+  # See #{ASTGenerator#each}.
+  class ASTGenerator
+    include LineMapping
+    include LineContinuator
+
+    map_const = ->(x) { x.constants.map { |c| x.const_get(c) } }
+    PARSERS = [
+      map_const.call(BELParser::Parsers::Common),
+      map_const.call(BELParser::Parsers::Expression),
+      map_const.call(BELParser::Parsers::BELScript)
+    ].flatten!
+
+    # Yields AST results for each line of the IO.
+    #
+    # @example Receive AST results in given block.
+    #   # doctest setup
+    #   require 'bel_parser'
+    #   self.class.include AST::Sexp
+    #
+    #   # example usage
+    #   line_io = StringIO.new("\"AKT1\"\n")
+    #   line    = nil
+    #   ast_res = nil
+    #   ::BELParser::ASTGenerator.new.each(line_io) { |(line_number, line, results)|
+    #     # do something
+    #   }
+    #
+    # @example Receive AST results as an enumerator.
+    #   # doctest setup
+    #   require 'bel_parser'
+    #   self.class.include AST::Sexp
+    #
+    #   # example usage
+    #   line_io = StringIO.new("\"AKT1\"\n")
+    #   line, ast_res = ::BELParser::ASTGenerator.new.each(line_io).first.to_a
+    #
+    # @param  [IO] io the IO-object to read each line from
+    # @yield  [[Integer, String, Array<AST::Node>]] yields line number, line,
+    #         and AST results as an {Array}
+    # @return [IO, #<Enumerator: #<BELParser::ASTGenerator#each>] the {IO}
+    #         object is returned if a block is given, otherwise an
+    #         {Enumerator} object is returned that can be iterated
+    #         with {Enumerator#each}
+    def each(io) # rubocop:disable MethodLength
+      if block_given?
+        line_enumerator = map_lines(io.each_line.lazy)
+
+        line_number = 1
+        loop do
+          begin
+            line = expand_line_continuator(line_enumerator)
+
+            ast_results = []
+            PARSERS.map do |parser|
+              parser.parse(line) { |ast| ast_results << ast }
+            end
+            yield([line_number, line, ast_results])
+            line_number += 1
+          rescue StopIteration
+            return
+          end
+        end
+      else
+        enum_for(:each, io)
+      end
+    end
+  end
+end
+
+if __FILE__ == $PROGRAM_NAME
+  BELParser::ASTGenerator.new.each($stdin) do |line_results|
+    line_number, line, ast_results = line_results
+    puts "#{line_number}: #{line}"
+    ast_results.each do |ast|
+      puts ast.to_s(1)
+    end
+  end
+end

data/lib/bel_parser/ast_validator.rb

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+require_relative 'ast_generator'
+require_relative 'parsers/ast/node'
+require_relative 'parsers/ast/sexp'
+require_relative 'parsers/ast/mapped_traversal'
+
+module BELParser
+  # ASTValidator applies observers to an AST traversal.
+  class ASTValidator
+    def initialize(observers: [])
+      @observers = observers
+    end
+
+    def each(ast_source, &block)
+      if block_given?
+        traversal = observable_traversal
+        ast_source.each do |(line_number, line, ast_results)|
+          traverse(traversal, line_number, line, ast_results, &block)
+        end
+      else
+        enum_for(:each, ast_source)
+      end
+    end
+
+    def traverse(traversal, line_number, line, ast_results)
+      ast_results.each do |ast|
+        traversal.traverse(ast) do |node, results|
+          yield([line_number, line, node, (results && results.compact)])
+        end
+      end
+    end
+
+    def observable_traversal
+      traversal = BELParser::Parsers::AST::MappedTraversal.new
+      @observers.each do |observer|
+        traversal.add_observer(observer)
+      end
+      traversal
+    end
+  end
+end