bel_parser 1.0.8 → 1.1.1

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 41e23bc6c3ccbf5ab389986ce481e4ae782997d9
+  metadata.gz: 918e134aad64f9a085893f1efe594fc7c7bc8176
+  data.tar.gz: 58c493d5631689b4230e9055dbe443381abe9e75
 SHA512:
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+  metadata.gz: 747d0dfc27dae01731d43e7d464819d935be23d96a78321a88d6e82947a8a3389745381e1a23343a96494c25d43308807f8af31076e9a09e82598e6ee0ab4924
+  data.tar.gz: ff4584aa710cdba505a0ec05c24d731b8c8b058608178432cbd42d108bf054080372f3d1d6ae0e78a49105fed85dd793c27d3235207e9adec5f2da8ac103bd39

data/.gemspec

@@ -11,7 +11,7 @@ Gem::Specification.new do |spec|
                                  'Anthony Bargnesi',
                                  'Nick Bargnesi',
                                ]
-  spec.date                  = %q{2016-06-17}
+  spec.date                  = %q{2017-01-13}
   spec.email                 = %q{abargnesi@selventa.com}
   spec.files                 = [
                                  Dir.glob('lib/**/*.{rb,rl}'),
@@ -26,5 +26,15 @@ Gem::Specification.new do |spec|
   spec.require_paths         = ['lib']
   spec.required_ruby_version = '>= 2.0.0'
 
-  spec.add_runtime_dependency  'sparql-client', '~> 2.0.0'
+  if RUBY_ENGINE =~ /jruby/
+    spec.platform               = 'java'
+    spec.add_runtime_dependency   'sparql-client',       '~> 2.0.0'
+    spec.add_runtime_dependency   'dbm-mapdb3',          '~> 0.6.0.beta'
+    spec.add_runtime_dependency   'levenshtein-jruby',   '0.1.0'
+  else
+    spec.platform               = 'ruby'
+    spec.add_runtime_dependency   'sparql-client',       '~> 2.0.0'
+    spec.add_runtime_dependency   'damerau-levenshtein', '1.2.0'
+  end
 end
+# vim: ft=ruby

data/VERSION

@@ -1 +1 @@
-1.0.8
+1.1.1

data/bin/bel2_compatibility

@@ -15,6 +15,18 @@ OptionParser.new do |opts|
   opts.banner = <<-USAGE.gsub(/^ {4}/, '')
     Confirm compatibility with BEL 2.0 expressions.
   USAGE
+
+  if RUBY_ENGINE =~ /^jruby/i
+    opts.on(
+      '-t',
+      '--read-jena-tdb DIRECTORY',
+      'Jena TDB directory containing BEL RDF resources.') do |tdb|
+
+        require 'bel_parser/resource/jena_tdb_reader'
+        options[:uri_reader] = BELParser::Resource::JenaTDBReader.new(tdb)
+        BELParser::Resource.default_uri_reader = options[:uri_reader]
+      end
+  end
 end.parse!
 
 def syntax_results(results)
@@ -32,15 +44,6 @@ end
 require 'bel_parser/expression/validator'
 require 'bel_parser/resource/resource_url_reader'
 
-uri_reader, url_reader = options.values_at(:uri_reader, :url_reader)
-
-namespaces = Hash[
-  ARGV.map do |ns|
-    keyword, identifier = ns.split('=')
-    [keyword, BELParser::Expression::Model::Namespace.new(keyword, identifier, nil)]
-  end.compact
-]
-
 def validate(expression)
   v2 = BELParser::Language.specification('2.0')
   ns = {

data/bin/bel2_upgrade

@@ -20,6 +20,18 @@ OptionParser.new do |opts|
   opts.on('-f', '--file FILE', 'BEL script file to read.') do |bel|
     options[:file] = bel
   end
+
+  if RUBY_ENGINE =~ /^jruby/i
+    opts.on(
+      '-t',
+      '--read-jena-tdb DIRECTORY',
+      'Jena TDB directory containing BEL RDF resources.') do |tdb|
+
+        require 'bel_parser/resource/jena_tdb_reader'
+        options[:uri_reader] = BELParser::Resource::JenaTDBReader.new(tdb)
+        BELParser::Resource.default_uri_reader = options[:uri_reader]
+      end
+  end
 end.parse!
 
 file = options[:file]
@@ -49,7 +61,7 @@ puts serialize(
     value(
       string('"2.0"'))))
 BELParser::ASTGenerator.new(io).each do |result|
-  line_number, line, asts = result
+  _, line, asts = result
 
   document_property =
     asts.find { |ast|
@@ -57,17 +69,17 @@ BELParser::ASTGenerator.new(io).each do |result|
     }
   next if document_property && document_property.name.identifier.string_literal.downcase == 'belversion'
 
-  ast =
+  convert_ast =
     asts.find do |ast|
       ast && CONVERSION_TYPES.include?(ast.type)
     end
 
-  if ast
-    ast =
-      upgrades.reduce(ast) do |ast, upgrade|
+  if convert_ast
+    puts serialize(
+      upgrades.reduce(convert_ast) do |ast, upgrade|
         upgrade.process(ast)
       end
-    puts serialize(ast)
+    )
   else
     puts line
   end

data/bin/bel2_validator

@@ -62,6 +62,7 @@ OptionParser.new do |opts|
 
         require 'bel_parser/resource/jena_tdb_reader'
         options[:uri_reader] = BELParser::Resource::JenaTDBReader.new(tdb)
+        BELParser::Resource.default_uri_reader = options[:uri_reader]
       end
   end
 end.parse!
@@ -104,14 +105,16 @@ BELParser::Expression::Validator
 
     puts "  Semantics results:"
     results.semantics_results.each do |res|
-      if res.is_a?(BELParser::Language::Semantics::SignatureMappingSuccess)
+      case res
+      when BELParser::Language::Semantics::SignatureMappingSuccess
         puts "    Matched signature: #{res.signature.string_form}"
-      end
-      if res.is_a?(BELParser::Language::Semantics::SignatureMappingWarning)
+      when BELParser::Language::Semantics::SignatureMappingWarning
         puts "    Failed signature: #{res.signature.string_form}"
         res.results.select(&:failure?).each do |warning|
           puts "      #{warning}"
         end
+      when BELParser::Language::Semantics::SemanticsWarning
+        puts "    Warning: #{res}"
       end
     end
   end

data/bin/bel_script_reader

@@ -62,6 +62,7 @@ OptionParser.new do |opts|
 
         require 'bel_parser/resource/jena_tdb_reader'
         options[:uri_reader] = BELParser::Resource::JenaTDBReader.new(tdb)
+        BELParser::Resource.default_uri_reader = options[:uri_reader]
       end
   end
 end.parse!