bel_parser 1.0.0.alpha.56 → 1.0.0.alpha.57

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: a0348eda0d0560bcd6162c0dfcd64cf3c3090c79
+  metadata.gz: a20eb6e58c9d1083ddb40267f95ec6bd49c41019
+  data.tar.gz: eed51687c5ea0aa8d6f3bf6a1ab442bbcd130344
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+  metadata.gz: 8cb211f34198ea310d4b2fe9fa0972cf5a51b75c6b2b82be05b47d4cf23c0347b0fbb38644b8de2684663373aef1fb9c09fbc3e0b1460b6a3c3771efa3048a70
+  data.tar.gz: 13d3ccf6bec4c7f7b485bc97b67c89124a6be2ebaa699de6bab29a1be9af37a2e75ed9cf6ffea821e4f79268b8c69eb268dd6877f771723f1b7359a724c28409

data/.gemspec

@@ -11,7 +11,7 @@ Gem::Specification.new do |spec|
                                  'Anthony Bargnesi',
                                  'Nick Bargnesi',
                                ]
-  spec.date                  = %q{2016-06-01}
+  spec.date                  = %q{2016-06-06}
   spec.email                 = %q{abargnesi@selventa.com}
   spec.files                 = [
                                  Dir.glob('lib/**/*.{rb,rl}'),

data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.56
+1.0.0.alpha.57

data/lib/bel/translator/plugins/bel_script/reader.rb

@@ -11,12 +11,18 @@ module BEL::Translator::Plugins
 
       def initialize(io, options = {})
         @io    = io
+        require 'pry'; binding.pry
+
+        options = {
+          :language => '1.0'
+        }.merge(options)
+
         @state = {
           uri_reader:            BELParser::Resource.default_uri_reader,
           url_reader:            BELParser::Resource.default_url_reader,
-          specification:         BELParser::Language.specification('2.0'),
+          specification:         BELParser::Language.specification(options[:language]),
           namespace_definitions: {}
-        }
+        }.merge(options)
       end
 
       def each

data/lib/bel/translator/plugins/bel_script/translator.rb

@@ -12,7 +12,7 @@ module BEL::Translator::Plugins
       include ::BEL::Translator
 
       def read(data, options = {})
-        Reader.new(data)
+        Reader.new(data, options)
       end
 
       def write(objects, writer = StringIO.new, options = {})

data/lib/bel_parser/expression/model/statement.rb

@@ -80,7 +80,7 @@ module BELParser
         end
 
         def validation(
-          spec       = BELParser::Language.latest_supported_specification,
+          spec       = BELParser::Language.default_specification,
           uri_reader = BELParser::Resource.default_uri_reader,
           url_reader = BELParser::Resource.default_url_reader)
 
@@ -153,7 +153,7 @@ module BELParser
             end
           return nil if statement.nil?
 
-          spec  ||= BELParser::Language.latest_supported_specification
+          spec  ||= BELParser::Language.default_specification
           comment = statement.comment && statement.comment.children[0]
 
           Statement.new(

data/lib/bel_parser/expression/model/term.rb

@@ -52,7 +52,7 @@ module BELParser
         end
 
         def validation(
-          spec       = BELParser::Language.latest_supported_specification,
+          spec       = BELParser::Language.default_specification,
           uri_reader = BELParser::Resource.default_uri_reader,
           url_reader = BELParser::Resource.default_url_reader)
 
@@ -67,7 +67,7 @@ module BELParser
         end
 
         def valid?(
-          spec       = BELParser::Language.latest_supported_specification,
+          spec       = BELParser::Language.default_specification,
           uri_reader = BELParser::Resource.default_uri_reader,
           url_reader = BELParser::Resource.default_url_reader)
 
@@ -75,7 +75,7 @@ module BELParser
         end
 
         def invalid?(
-          spec = BELParser::Language.latest_supported_specification,
+          spec = BELParser::Language.default_specification,
           uri_reader = BELParser::Resource.default_uri_reader,
           url_reader = BELParser::Resource.default_url_reader)
 
@@ -117,7 +117,7 @@ module BELParser
         def ast_to_term(ast, spec, namespaces = {})
           return nil if ast.nil? ||
             !ast.is_a?(BELParser::Parsers::AST::Term)
-          spec    ||= BELParser::Language.latest_supported_specification
+          spec    ||= BELParser::Language.default_specification
           convert   = method(:convert_argument).to_proc.curry[spec][namespaces]
 
           Term.new(

data/lib/bel_parser/expression/parser.rb

@@ -11,7 +11,7 @@ module BELParser
 
     def self.parse(
       input,
-      spec       = BELParser::Language.latest_supported_specification,
+      spec       = BELParser::Language.default_specification,
       namespaces = {})
 
       parser = Parser.new(input, Expression.filter, spec, namespaces)
@@ -20,7 +20,7 @@ module BELParser
 
     def self.parse_parameters(
       input,
-      spec       = BELParser::Language.latest_supported_specification,
+      spec       = BELParser::Language.default_specification,
       namespaces = {})
 
       parser = Parser.new(input, Expression.parameter_filter, spec, namespaces)
@@ -29,7 +29,7 @@ module BELParser
 
     def self.parse_terms(
       input,
-      spec       = BELParser::Language.latest_supported_specification,
+      spec       = BELParser::Language.default_specification,
       namespaces = {})
 
       parser = Parser.new(input, Expression.term_filter, spec, namespaces)
@@ -38,7 +38,7 @@ module BELParser
 
     def self.parse_statements(
       input,
-      spec       = BELParser::Language.latest_supported_specification,
+      spec       = BELParser::Language.default_specification,
       namespaces = {})
 
       parser = Parser.new(input, Expression.statement_filter, spec, namespaces)
@@ -53,7 +53,7 @@ module BELParser
       def initialize(
         input,
         filter     = Expression.filter,
-        spec       = BELParser::Language.latest_supported_specification,
+        spec       = BELParser::Language.default_specification,
         namespaces = {})
 
         @input      = input

data/lib/bel_parser/language.rb

@@ -25,6 +25,8 @@ module BELParser
     LOCK = Mutex.new
     private_constant :LOCK
 
+    DEFAULT_VERSION = '1.0'
+
     # Indicates if +version+ is a defined BEL specification.
     #
     # @param  [#to_s] version the BEL version string (e.g. +"2.0"+)
@@ -53,6 +55,14 @@ module BELParser
       end.sort
     end
 
+    def self.default_version
+      DEFAULT_VERSION
+    end
+
+    def self.default_specification
+      specification(DEFAULT_VERSION)
+    end
+
     # Returns the latest supported version string according to the
     # _MAJOR.MINOR_ pattern.
     #

data/lib/bel_parser/parsers/common/comment_line.rb

@@ -45,7 +45,7 @@ class << self
 end
 self._bel_trans_keys = [
 	0, 0, 9, 35, 9, 35, 
-	9, 32, 10, 10, 0, 
+	10, 10, 10, 10, 0, 
 	0, 0
 ]
 
@@ -54,7 +54,7 @@ class << self
 	private :_bel_key_spans, :_bel_key_spans=
 end
 self._bel_key_spans = [
-	0, 27, 27, 24, 1, 0
+	0, 27, 27, 1, 1, 0
 ]
 
 class << self
@@ -62,7 +62,7 @@ class << self
 	private :_bel_index_offsets, :_bel_index_offsets=
 end
 self._bel_index_offsets = [
-	0, 0, 28, 56, 81, 83
+	0, 0, 28, 56, 58, 60
 ]
 
 class << self
@@ -77,10 +77,7 @@ self._bel_indicies = [
 	1, 1, 1, 1, 1, 1, 1, 1, 
 	1, 1, 1, 1, 1, 1, 1, 1, 
 	1, 1, 1, 0, 1, 1, 2, 1, 
-	5, 6, 4, 4, 4, 4, 4, 4, 
-	4, 4, 4, 4, 4, 4, 4, 4, 
-	4, 4, 4, 4, 4, 4, 4, 5, 
-	4, 3, 7, 1, 0
+	5, 4, 3, 6, 1, 0
 ]
 
 class << self
@@ -88,7 +85,7 @@ class << self
 	private :_bel_trans_targs, :_bel_trans_targs=
 end
 self._bel_trans_targs = [
-	1, 0, 3, 5, 4, 3, 5, 4
+	1, 0, 3, 5, 4, 5, 4
 ]
 
 class << self
@@ -96,7 +93,7 @@ class << self
 	private :_bel_trans_actions, :_bel_trans_actions=
 end
 self._bel_trans_actions = [
-	0, 0, 0, 1, 3, 3, 4, 5
+	0, 0, 0, 1, 3, 4, 5
 ]
 
 class << self

data/lib/bel_parser/parsers/common/comment_line.rl

@@ -20,7 +20,7 @@
     yield comment_line(utf8_string(cl), complete: completed)
   }
 
-  comment_start = SP* NUMBER_SIGN SP*;
+  comment_start = SP* NUMBER_SIGN;
   comment = comment_start (any - NL)*
             >comment_line_start
             $comment_line_more;

data/lib/bel_parser/script/state/set.rb

@@ -60,7 +60,7 @@ module BELParser
         def self.handle_annotation(name_string, value_node, script_context)
           # add to annotation state
           script_context[:annotations]              ||= Concurrent::Hash.new
-          script_context[:annotations][name_string]   = value_node.children[0].string_literal
+          script_context[:annotations][name_string]   = value_node.children[0]
         end
         private_class_method :handle_annotation
 

data/lib/bel_parser/script/syntax/unsupported_bel_version.rb

@@ -25,9 +25,7 @@ module BELParser
             BELParser::Language.specification(value_string)
             nil
           rescue ArgumentError
-            latest_version = BELParser::Language.latest_supported_version
-            latest_spec    = BELParser::Language.specification(latest_version)
-            script_context[:specification] = latest_spec
+            script_context[:specification] = BELParser::Language.default_specification
             UnsupportedBELVersionWarning.new(ast_node, value_string)
           end
         end
@@ -42,13 +40,13 @@ module BELParser
         def initialize(document_property_node, unsupported_version)
           super(document_property_node, nil)
           @unsupported_version = unsupported_version
-          @latest              = BELParser::Language.latest_supported_version
+          @default             = BELParser::Language.default_version
         end
 
         def msg
           <<-MSG.gsub(/^ +/, '').delete("\n")
             Unsupported BEL version "#@unsupported_version". 
-            Setting BEL version to the latest supported version "#@latest".
+            Setting BEL version to the default version "#@default".
           MSG
         end
       end

metadata

@@ -1,25 +1,25 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.56
+  version: 1.0.0.alpha.57
 platform: ruby
 authors:
 - Anthony Bargnesi
 - Nick Bargnesi
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-06-01 00:00:00.000000000 Z
+date: 2016-06-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
+  name: sparql-client
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 2.0.0
-  name: sparql-client
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
@@ -381,7 +381,7 @@ homepage: https://github.com/OpenBEL/bel_parser
 licenses:
 - Apache-2.0
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -396,9 +396,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: 1.3.1
 requirements: []
-rubyforge_project:
-rubygems_version: 2.6.4
-signing_key:
+rubyforge_project: 
+rubygems_version: 2.5.1
+signing_key: 
 specification_version: 4
 summary: Parser for Biolgical Expression Language.
 test_files: []
+has_rdoc: