bel_parser 1.0.0.alpha.14 → 1.0.0.alpha.15

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 07332e2aff2a9b3ba75e7570c13dd4b5be14d340
+  metadata.gz: 5a99bbde75e5c199ecf2dd8be815f1405e9eb5e4
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data/.gemspec

@@ -11,7 +11,7 @@ Gem::Specification.new do |spec|
                                  'Anthony Bargnesi',
                                  'Nick Bargnesi',
                                ]
-  spec.date                  = %q{2016-04-27}
+  spec.date                  = %q{2016-04-28}
   spec.email                 = %q{abargnesi@selventa.com}
   spec.files                 = [
                                  Dir.glob('lib/**/*.{rb,rl}'),

data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.14
+1.0.0.alpha.15

data/bin/bel2_validator

@@ -4,7 +4,7 @@ $LOAD_PATH.unshift(
 
 unless ARGV.first
   program = File.basename($PROGRAM_NAME)
-  $stderr.puts <<-USAGE.gsub(/ {6}/, '')
+  $stderr.puts <<-USAGE.gsub(/ {4}/, '')
     usage: #{program} [BEL specification version] [PREFIX=URI]...
   USAGE
   exit 1

data/bin/bel_script_reader

@@ -0,0 +1,70 @@
+#!/usr/bin/env ruby
+$LOAD_PATH.unshift(
+  File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
+
+bel_specification_version, file = ARGV
+
+unless bel_specification_version
+  program = File.basename($PROGRAM_NAME)
+  $stderr.puts <<-USAGE.gsub(/ {4}/, '')
+    usage: #{program} [BEL specification version]
+  USAGE
+  exit 1
+end
+
+io =
+  if file
+    File.open(ARGV.first, external_encoding: 'UTF-8')
+  else
+    $stdin
+  end
+
+require 'bel_parser/language'
+require 'bel_parser/script/validator'
+require 'bel_parser/resource/resource_file_reader'
+
+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
+
+SYN_ERR  = BELParser::Language::Syntax::SyntaxError
+SYN_WARN = BELParser::Language::Syntax::SyntaxWarning
+SEM_WARN = BELParser::Language::Semantics::SemanticsWarning
+
+initial_state = {
+  resource_reader: BELParser::Resource::ResourceFileReader.new,
+  specification:   BELParser::Language.specification(
+    bel_specification_version
+  )
+}
+
+BELParser::Script::Validator
+.new(initial_state)
+.each(io) do |(line_number, line, ast, syntax_results, state)|
+  errors   = select(syntax_results, SYN_ERR)
+  warnings =
+    select(syntax_results, SYN_WARN) +
+    select(syntax_results, SEM_WARN)
+
+  report(line_number, ast, errors, warnings)
+
+  unless errors.empty?
+    puts "Exiting due to error on line #{line_number}: #{line}"
+    exit 1
+  end
+end

data/lib/bel_parser/expression/validator.rb

@@ -48,14 +48,25 @@ if __FILE__ == $PROGRAM_NAME
     USAGE
     exit 1
   end
-  namespaces = Hash[ARGV[1..-1].map { |ns| ns.split('=') }]
+
+  require 'bel_parser/resource/resource_file_reader'
+
+  resource_reader = BELParser::Resource::ResourceFileReader.new
+  namespaces      =
+    Hash[
+      ARGV[1..-1]
+      .map do |ns|
+        prefix, identifier = ns.split('=')
+        [prefix, resource_reader.retrieve_resource(identifier)]
+      end
+    ]
   BELParser::Expression::Validator
-    .new(ARGV.first, namespaces)
-    .each($stdin) do |(line_number, line, ast, messages)|
+    .new(ARGV.first, namespaces, resource_reader)
+    .each($stdin) do |(line_number, line, ast, results)|
       results.select { |res| res.is_a? BELParser::Language::Syntax::SyntaxError }
       puts "#{line_number}: #{line}"
       puts "  AST Type: #{ast.type}"
-      puts messages
+      puts results
         .map { |r| "#{r}\n" }
         .join
         .each_line

data/lib/bel_parser/language/apply_namespace_encoding.rb

@@ -8,9 +8,9 @@ module BELParser
       include AST::Processor::Mixin
       include BELParser::Quoting
 
-      def initialize(language_spec, identifier_hash, resource_reader)
+      def initialize(language_spec, namespace_hash, resource_reader)
         @language_spec   = language_spec
-        @identifier_hash = identifier_hash
+        @namespace_hash  = namespace_hash
         @resource_reader = resource_reader
       end
 
@@ -61,10 +61,9 @@ module BELParser
         return prefix_node unless prefix_node.identifier
 
         @prefix    = prefix_node.identifier.string_literal
-        identifier = @identifier_hash[@prefix].identifier
-        return prefix_node unless identifier
+        dataset    = @namespace_hash[@prefix]
+        return prefix_node unless dataset
 
-        dataset               = @resource_reader.retrieve_resource(identifier)
         @resolved_dataset     = dataset
         prefix_node.namespace = dataset
 

data/lib/bel_parser/language/semantics/signature_mapping.rb

@@ -22,8 +22,9 @@ module BELParser
 
           function_name = term_node.function.identifier.string_literal
           function      = spec.function(function_name.to_sym)
-          mapsig        = method(:map_signature).to_proc.curry[term_node][spec]
+          return nil unless function
 
+          mapsig = method(:map_signature).to_proc.curry[term_node][spec]
           function.signatures.map(&mapsig)
         end
 

data/lib/bel_parser/language/semantics_ast.rb

@@ -717,7 +717,7 @@ module BELParser
         end
 
         def match(value_node, spec)
-          string_literal_sym = value_node.children[0].to_sym
+          string_literal_sym = value_node.children[0].string_literal.to_sym
           return success(value_node, spec) if @hashed[:*]
 
           if @hashed.key?(string_literal_sym)
@@ -760,7 +760,7 @@ module BELParser
         end
 
         def match(value_node, spec)
-          string_literal = unquote(value_node.string_literal)
+          string_literal = unquote(value_node.children[0].string_literal)
           integer_position =
             begin
               Integer(string_literal)

data/lib/bel_parser/language/version1_0/functions/rna_abundance.rb

@@ -14,7 +14,7 @@ module BELParser
           SHORT       = :r
           LONG        = :rnaAbundance
           RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::GeneAbundance
-          R_ENC       = Version1_0::ReturnTypes::GeneAbundance
+          R_ENC       = Version1_0::ValueEncodings::RNAAbundance
           DESCRIPTION = 'Denotes the abundance of a gene'.freeze
 
           def self.short

data/lib/bel_parser/resource/lru_reader.rb

@@ -24,10 +24,7 @@ module BELParser
         end
 
         concepts = resources[resource_identifier]
-        concepts.getset(value) {
-          puts "retrieving from RDF..."
-          super
-        }
+        concepts.getset(value) { super }
       end
 
       def retrieve_values_from_resource(resource_identifier)

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

@@ -21,7 +21,6 @@ module BELParser
           keyword, domain = ast_node.children
           if domain.url?
             url = unquote(domain.child.string.string_literal)
-            puts resource_reader.retrieve_resource(url)
             unless resource_reader.retrieve_resource(url)
               prefix = keyword.identifier.string_literal
               return UnresolvableNamespaceError.new(ast_node, prefix, url)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.14
+  version: 1.0.0.alpha.15
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -9,12 +9,13 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-27 00:00:00.000000000 Z
+date: 2016-04-28 00:00:00.000000000 Z
 dependencies: []
 description: Implements language versions 1.0 and 2.0.
 email: abargnesi@selventa.com
 executables:
 - bel2_validator
+- bel_script_reader
 extensions: []
 extra_rdoc_files: []
 files:
@@ -24,6 +25,7 @@ files:
 - README.md
 - VERSION
 - bin/bel2_validator
+- bin/bel_script_reader
 - lib/bel_parser.rb
 - lib/bel_parser/ast_filter.rb
 - lib/bel_parser/ast_generator.rb