bel_parser 1.0.0.alpha.27-java

checksums.yaml

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data/.gemspec-java

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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{2016-05-09}
+  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'
+
+  spec.platform              = 'java'
+  spec.add_runtime_dependency  'dbm-mapdb3', '~> 0.6.0.beta'
+end
+# vim: ft=ruby

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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+
+APPENDIX: How to apply the Apache License to your work
+
+To apply the Apache License to your work, attach the following boilerplate
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data/README.md

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+# bel_parser
+
+Parser for BEL expressions and the BEL Script document format.
+
+### Installation
+
+  gem install bel_parser --pre
+
+### Getting Started
+
+Two tools are available to try out:
+1) bel_script_reader - will read a BEL Script with a specified BEL version and not any warning or errors with the script
+
+2) bel2_validator - will read in lines and validate the BEL Statements
+
+Example script using bel_parser module
+
+  examples/upgrade_kinase.rb
+
+### Design

data/VERSION

@@ -0,0 +1 @@
+1.0.0.alpha.27

data/bin/bel2_validator

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+#!/usr/bin/env ruby
+$LOAD_PATH.unshift(
+  File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
+
+unless ARGV.first
+  program = File.basename($PROGRAM_NAME)
+  $stderr.puts <<-USAGE.gsub(/ {4}/, '')
+    usage: #{program} [BEL specification version] [PREFIX=URI]...
+  USAGE
+  exit 1
+end
+
+def syntax_results(results)
+  results.select do |res|
+    res.is_a? BELParser::Language::Syntax::SyntaxResult
+  end
+end
+
+def semantics_results(results)
+  results.select do |res|
+    res.is_a? BELParser::Language::Semantics::SemanticsResult
+  end
+end
+
+require 'bel_parser'
+require 'bel_parser/expression/validator'
+require 'bel_parser/resource/resource_url_reader'
+
+resource_reader = BELParser::Resource::ResourceURLReader.new(true)
+namespaces      =
+  Hash[
+    ARGV.map do |ns|
+      prefix, identifier = ns.split('=')
+      dataset            = resource_reader.retrieve_resource(identifier)
+      dataset ? [prefix, dataset] : nil
+    end.compact
+  ]
+
+BELParser::Expression::Validator
+  .new(ARGV.first, namespaces, resource_reader)
+  .each($stdin) do |(line_number, line, ast, results)|
+    puts "#{line_number}: #{line}"
+    puts "  AST Type: #{ast.type}"
+
+    puts "  Syntax results:"
+    syntax_results(results).each do |res|
+      puts "    #{res}"
+    end
+
+    puts "  Semantics results:"
+    semantics_results(results).each do |res|
+      if res.is_a?(BELParser::Language::Semantics::SignatureMappingSuccess)
+        puts "    Matched signature: #{res.signature.string_form}"
+      end
+      if res.is_a?(BELParser::Language::Semantics::SignatureMappingWarning)
+        puts "    Failed signature: #{res.signature.string_form}"
+        res.results.select(&:failure?).each do |warning|
+          puts "      #{warning}"
+        end
+      end
+    end
+  end

data/bin/bel_script_reader

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+#!/usr/bin/env ruby
+$LOAD_PATH.unshift(
+  File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
+
+require 'optparse'
+require 'bel_parser'
+require 'bel_parser/resource/resource_url_reader'
+
+options = {
+  spec: BELParser::Language.specification(
+    BELParser::Language.latest_supported_version)
+}
+OptionParser.new do |opts|
+  opts.banner = <<-USAGE.gsub(/^ {4}/, '')
+    Validates BEL Script with support for multiple BEL specifications.
+
+    Read from a BEL file.
+    usage: #$PROGRAM_NAME --file [FILE]
+
+    Read from standard input.
+    usage: #$PROGRAM_NAME
+  USAGE
+
+  opts.on('-f', '--file FILE', 'BEL script file to read.') do |bel|
+    options[:file] = bel
+  end
+
+  opts.on(
+    '-s',
+    '--specification VERSION',
+    'BEL specification version (e.g. 1.0, 2.0)') do |spec|
+
+    unless BELParser::Language.defines_version?(spec)
+      $stderr.puts %(Invalid BEL specification "#{spec}")
+      exit 1
+    end
+
+    options[:spec] = BELParser::Language.specification(spec)
+  end
+
+  opts.on(
+    '-r',
+    '--[no-]reuse-resource-databases',
+    'Enable to reuse resource databases if they exist.') do |reuse|
+
+    options[:reuse] = reuse
+  end
+end.parse!
+
+file, spec = options.values_at(:file, :spec)
+io =
+  if file
+    File.open(file, external_encoding: 'UTF-8')
+  else
+    $stdin
+  end
+
+rr = BELParser::Resource::ResourceURLReader.new(options[:reuse])
+namespaces = Hash[
+  ARGV.map do |ns|
+    prefix, identifier = ns.split('=')
+    dataset            = rr.retrieve_resource(identifier)
+    dataset ? [prefix, dataset] : nil
+  end.compact
+]
+
+initial_state = {
+  resource_reader:       rr,
+  specification:         spec,
+  namespace_definitions: namespaces
+}
+
+module BELParser
+  module Script
+    # Reader assembles a BEL Script reader using the following pipeline:
+    #
+    #   Generate -> Filter -> Pick One -> Aggregate State -> Validate Syntax
+    class Reader
+      SYN_ERR  = BELParser::Language::Syntax::SyntaxError
+      SYN_WARN = BELParser::Language::Syntax::SyntaxWarning
+      SEM_WARN = BELParser::Language::Semantics::SemanticsWarning
+
+      def initialize(initial_state, io)
+        @validator =
+          Validator.new(
+            StateAggregator.new(
+              FirstNode.new(Filter.new(ASTGenerator.new(io))),
+              initial_state))
+      end
+
+      def read
+        @validator.each do |(line_number, line, ast_node, _)|
+          syntax_errors = ast_node.syntax_errors
+          errors        = select(syntax_errors, SYN_ERR)
+          warnings      =
+            select(syntax_errors, SYN_WARN) +
+            select(syntax_errors, SEM_WARN)
+
+          report(line_number, ast_node, errors, warnings)
+
+          unless errors.empty?
+            puts "Exiting due to error on line #{line_number}: #{line}"
+            exit 1
+          end
+        end
+      end
+
+      private
+
+      def select(list, cls)
+        list.select { |item| item.is_a?(cls) }
+      end
+
+      def report(line_number, ast, errors, warnings)
+        log = !errors.empty? || !warnings.empty?
+        if log
+          puts "On line #{line_number} for #{ast.type}"
+          puts "  Errors:"
+          errors.each do |err|
+            puts "    #{err}"
+          end
+          puts "  Warnings:"
+          warnings.each do |warn|
+            puts "    #{warn}"
+          end
+        end
+      end
+    end
+  end
+end
+
+BELParser::Script::Reader.new(initial_state, io).read