cortexio-grammar 1.0.0

checksums.yaml

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+SHA1:
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data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+**/.DS_Store

data/Gemfile

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+source 'https://rubygems.org'
+ruby '2.0.0'
+
+gemspec

data/README.md

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+CortexIO Grammer
+====
+A sample grammar using citrus. Run:
+
+    cql_grammar_console
+
+..for interactive grammar validadtion.
+
+
+Credit
+----
+Written by Preston Lee. @prestonism http://prestonlee.com

data/Rakefile

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+#!/usr/bin/env rake
+require "bundler/gem_tasks"
+ 
+require 'rake/testtask'
+ 
+Rake::TestTask.new do |t|
+  t.libs << 'lib/cortexio-grammar'
+  t.test_files = FileList['test/lib/cortexio-grammar/*_test.rb']
+  t.verbose = true
+end
+ 
+task :default => :test

data/bin/cql_grammar_console

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+#!/usr/bin/env ruby
+
+require 'citrus'
+
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', 'lib')
+require 'cortexio-grammar' # Citrus.load 'grammar', :force => true
+
+valid = true
+invalid = false
+prompt = '> '
+
+puts "\n#{__FILE__}. Copyright (C) 2011 TGen. All rights reserved."
+puts "Enter one statement per line."
+puts "'#{valid}' will be returned iff the statment is syntactically and grammatically correct."
+print "The grammar definition will be reloaded before parsing each statement.\n\n#{prompt}"
+
+begin
+	while(line = STDIN.readline.chop)
+		break if line.match /(quit)|(exit)/
+		begin
+			CortexIOGrammar.parse line
+			puts valid
+		rescue Exception => e
+			puts e
+			puts invalid
+		end
+		print prompt
+	end
+rescue EOFError => e
+	# Probably just hit CTRL-D or something. Regardless, time to go!
+	puts ""
+end
+
+puts "Later!"
+

data/cortexio-grammar.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'cortexio-grammar/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "cortexio-grammar"
+  spec.version       = CortexIO::Grammar::VERSION
+  spec.authors       = ["Preston Lee"]
+  spec.email         = ["preston.lee@prestonlee.com"]
+  spec.description   = %q{A proof-of-concept CortexIO Query Language grammar using Ruby and citrus.}
+  spec.summary       = %q{A proof-of-concept grammar.}
+  spec.homepage      = "http://github.com/preston/cortexio-grammar"
+  spec.license       = "Apache 2"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "rake"
+  spec.add_development_dependency "citrus"
+  spec.add_development_dependency "minitest"
+end

data/lib/cortexio-grammar.rb

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+require 'citrus'
+Citrus.load File.join(File.dirname(__FILE__), 'cortexio-grammar', 'parse', 'grammar'), :force => true
+
+module CortexIO
+	module Grammar
+	end
+end

data/lib/cortexio-grammar/parse/grammar.citrus

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+grammar CortexIOGrammar
+	
+	rule statement
+		space? (recover | create | modify | remove | context | expand) space?
+	end
+	
+	rule context
+		`context` space (level space)? (uuid | uuid_set | `with` space expression)
+	end
+	
+	rule expand
+		`expand` space (level space)? (uuid | uuid_set | `with` space expression)
+	end
+	
+	rule recover
+		`recover` space (level space)? (uuid | uuid_set)
+	end
+	
+	rule modify
+		`modify` # entity
+	end
+	
+	rule remove
+		`remove` space `element` space (uuid | uuid_set)
+	end
+	
+	rule set_external
+		`set(e)` space? '=' uuid_set		
+	end
+	
+	rule set_internal
+		`set(i)` space? '=' uuid_set
+	end
+
+	rule set_attribute
+		`set(a)` space? '=' attribute_set
+	end
+	
+	
+	rule attribute_set		
+		space? '{' space? (attribute (',' space? attribute)* space?)? '}' space?
+	end
+	
+	rule attribute
+		attribute_key space? '=' space? attribute_value space?
+	end
+	
+	rule expression
+		expression_either (space? (`and` | `or`) space? expression_either)? space?
+	end
+
+	rule expression_either
+		(attribute | expression_precedent)
+	end
+	
+	
+	rule expression_precedent
+		'(' space? expression ')' space?
+	end
+	
+	rule attribute_key
+		quoted_string
+	end
+
+	rule attribute_value
+		quoted_string
+	end
+
+	rule level
+		(numeric | `max`)
+	end
+
+	rule uuid_set
+		space? '{' space? (uuid (space? ',' space? uuid)* space?)? '}' space?
+	end
+	
+	rule uuid
+		numeric
+	end
+
+	rule quote
+		"\""
+	end
+	
+	rule quoted_string
+		/".*?"/ 
+	end
+	
+	rule numeric
+		[0-9]+
+	end
+	
+	rule alphanumeric
+		[a-zA-Z0-9]+
+	end
+	
+	rule create
+		(create_element | create_attribute)
+	end
+	
+	rule create_element
+		`create` space `element` space set_internal? space? set_external? space? set_attribute?
+	end
+	
+	rule create_attribute
+		`create` space `attribute` space (attribute | attribute_set)
+	end
+
+  rule space
+    [ \t]+
+  end
+
+end

data/lib/cortexio-grammar/version.rb

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+module CortexIO
+
+	module Grammar
+		VERSION = '1.0.0'
+	end
+
+end

data/test/lib/cortexio-grammar/grammar_test.rb

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+# Copyright 2011 TGen. All rights reserved.
+# Author: Preston Lee <plee@tgen.org>
+
+require_relative '../../test_helper'
+
+
+class GrammarTest < Minitest::Test
+
+	# Helper function for batch rule validation.
+	def assert_rule_with_data(rule = 'statement', good, bad)
+		good.each do |line|
+			refute_nil @g.parse line, :root => rule
+		end
+		
+		bad.each do |line|
+			assert_raises(Citrus::ParseError) { @g.parse line, :root => rule }
+		end
+	end
+	
+	
+	def setup
+		# puts 'setup!!!!'
+		@g = CortexIOGrammar
+	end
+	
+  def test_grammar_loaded
+    assert defined?(CortexIOGrammar), "Grammar was not preloaded!"
+  end
+
+
+
+	# create element set(i)={235, 452, 786} set(a)={"symbol"="BRCA1", "source"="ncbi"}
+	# create attribute "type"="node"
+	# create attribute {"type"="node", "source"="ncbi"}
+	# modify element 456 set(x)={578}
+	# modify element with {"symbol"="DLC1", "foo"="bar"} set(i)={345, 87, 673, 4829}
+	# remove element 6574
+	# remove element {157}
+	# remove element {157, 239842, 23}
+	# recover 9875
+	# recover 1 {235, 9875, 98}
+	# recover max {42}
+	# context 1 with "type"="equivalence" and "chromosome"="14"
+	# context max 345
+	# expand 1 element with "symbol" = "BRC*"
+	# expand 2 {578, 418}
+	
+	
+	def test_context
+		good = [
+			'context 0 42',
+			'context 1 1234',
+			'context 42 12341234',
+			'context 42 {}',
+			'context 42 {1}',
+			'context 42 {1,2}',
+			'context 42 { 1 , 2 }', 
+			'context max 42',
+			'context max with "type" = "equivalence" and "chromosome"="14" ',
+			'Context Max WITH ("type" = "equivalence" AND "chromosome"="14")',
+			'  CONTEXT   MAX   WITH "type" = "equivalence" and ("foo"="bar" OR "chromosome"="14") ',
+			]
+		bad = [
+			"context",
+			"context 1 {,}",
+			"context 1 aoeu",
+			"context 1 with"
+			]
+		assert_rule_with_data('statement', good, bad)
+	end
+	
+	def test_expand
+		good = [
+			'expand 0 42',
+			'expand 1 1234',
+			'expand 42 12341234',
+			'expand max 42',
+			'expand max with "type" = "equivalence" and "chromosome"="14" ',
+			'Expand Max WITH ("type" = "equivalence" AND "chromosome"="14")',
+			'  EXPAND   MAX   WITH "type" = "equivalence" and ("foo"="bar" OR "chromosome"="14") ',
+			]
+		bad = [
+			"expand",
+			"expand 1 {,}",
+			"expand 1 aoeu",
+			"expand 1 with"
+		]
+		assert_rule_with_data('statement', good, bad)
+	end
+	
+	
+	def test_create_attribute
+		good = [
+			'create attribute "type"="node"',
+			'create attribute {"type"="node"}',
+			'create attribute {"type"="node", "name"="bob"}',
+			'create attribute {}',
+			'   create      attribute {  }   ',
+			'CREATE ATTRIBUTE {"type"="node", "name"="bob"}',
+			'Create Attribute {"type"="node", "name"="bob"}',
+			]
+		bad = [
+			'create attribute',
+			'create attribute {,}',
+			'create attribute {"bob"}',
+			'create attribute {aoeu}',
+			'create attribute {aoeu,}',
+			'create attribute {, 1234}',
+			'create attribute {1234 2345}'
+			]
+		assert_rule_with_data('statement', good, bad)
+	end
+	
+	def test_create_element
+		good = [
+			'create element set(i)={235, 452, 786}',
+			'create element set(e)={42}',
+			'create element set(a)={"symbol"="BRCA1", "source"="ncbi"}',
+			'create element set(i)={} set(a)={}',
+			'create element SET(I)={235, 452, 786} SET(E)={42} SET(A)={"symbol"="BRCA1", "source"="ncbi"}',
+			'  CREATE   ELEMENT set(e)={}',
+			'Create ELEMENT set(a)={"type"="node", "name"="bob"}',
+			]
+		bad = [
+			'create element',
+			'create element {,}',
+			'create element {"bob"}',
+			'create element {aoeu}',
+			'create element {aoeu,}',
+			'create element {, 1234}',
+			'create element {1234 2345}'
+			]
+		assert_rule_with_data('statement', good, bad)
+	end
+	
+	def test_recover
+		good = [
+			'recover 1234',
+			'recover 0 1234',
+			'recover 42 1234',
+			'recover max 1234',
+			'recover {}',
+			'recover {1234}',
+			'recover   {1234, 1234}',
+			' recover    {1234, 2345}  ',
+			'    recover {1234, 2345 }',
+			'RECOVER 1 { 1234,2345 }',
+			"Recover 33 {\t 1234, 2345 }",
+			"rEcOveR MAX {1234,    2345\t}"
+			]
+		bad = [
+			'recover',
+			'recover element {,}',
+			'recover element {1234,}',
+			'recover element {aoeu}',
+			'recover element {aoeu,}',
+			'recover element {, 1234}',
+			'recover element {1234 2345}'
+			]
+		assert_rule_with_data('statement', good, bad)
+	end
+
+	def test_remove_element
+		good = [
+			"remove element 1234",
+			"remove element {}",
+			"remove element {1234}",
+			"remove element   {1234, 1234}",
+			" remove   element {1234, 2345}  ",
+			"    remove element {1234, 2345 }",
+			"REMOVE ELEMENT { 1234,2345 }",
+			"Remove Element {\t 1234, 2345 }",
+			"REmoVE ELEMent {1234,    2345\t}"
+			]
+		bad = [
+			"remove",
+			"remove element {,}",
+			"remove element {1234,}",
+			"remove element {aoeu}",
+			"remove element {aoeu,}",
+			"remove element {, 1234}",
+			"remove element {1234 2345}"
+			]
+		assert_rule_with_data('statement', good, bad)
+	end
+	
+	def test_uuid_set
+		good = [
+			"{}",
+			"{1234}",
+			"{1234, 2345}",
+			"  {1234,2345}    ",
+			"{1234, 2345, 3456}",
+			]
+		bad = [
+			"",
+			"1234",
+			"{1234",
+			"1234}",
+			"{,}",
+			"{1234}}",
+			"{{1234}}",
+			]
+		assert_rule_with_data('uuid_set', good, bad)
+	end
+	
+	def test_expression
+		good = [
+			'"name"="alice"',
+			'"name" = "alice"',
+			'"name" ="alice"',
+			"\"name\"=\t\"alice\"",
+			'("name"="alice")',
+			'( ("name"="alice"))',
+			'( "name" = "alice" )',
+			'"name" = "alice" AND "type"="user"  ',
+			'("name" = "alice" AND "type"="user")',
+			'("name" = "alice") AND ("type"="user")',
+			'"name" = "alice" AND ("type"="admin")',
+			'"name" = "alice" AND ("type"="admin" or "type"="manager")',
+			'("name" = "alice" OR "email"="alice@example.com") and ("type"="admin" or "type"="manager")',
+			'(("name" = "alice" OR "email"="alice@example.com") and ("type"="admin" or "type"="manager"))',
+			'( ( "name" = "alice" OR "email"="alice@example.com") and ("type"="admin" or "type"="manager" ) ) '
+		]
+
+
+		bad = [
+			'name',
+			'"name"',
+			'"name" =',
+			'"name"=',
+			'("name" = "alice" AND "type"="user" ',
+			'("name" = "alice" AND "type"="user") )'
+		]
+		assert_rule_with_data('expression', good, bad)
+	end
+
+
+
+	
+end

data/test/test_helper.rb

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+require 'minitest/autorun'
+require 'minitest/pride'
+require File.expand_path('../../lib/cortexio-grammar.rb', __FILE__)

metadata

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+--- !ruby/object:Gem::Specification
+name: cortexio-grammar
+version: !ruby/object:Gem::Version
+  version: 1.0.0
+platform: ruby
+authors:
+- Preston Lee
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-07-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: citrus
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: A proof-of-concept CortexIO Query Language grammar using Ruby and citrus.
+email:
+- preston.lee@prestonlee.com
+executables:
+- cql_grammar_console
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- README.md
+- Rakefile
+- bin/cql_grammar_console
+- cortexio-grammar.gemspec
+- lib/cortexio-grammar.rb
+- lib/cortexio-grammar/parse/grammar.citrus
+- lib/cortexio-grammar/version.rb
+- test/lib/cortexio-grammar/grammar_test.rb
+- test/test_helper.rb
+homepage: http://github.com/preston/cortexio-grammar
+licenses:
+- Apache 2
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.0.3
+signing_key: 
+specification_version: 4
+summary: A proof-of-concept grammar.
+test_files:
+- test/lib/cortexio-grammar/grammar_test.rb
+- test/test_helper.rb