bel_parser 1.0.0.alpha.44-java → 1.0.0.alpha.45-java

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: 69df1fed65007b73516917a30f7db3d8bd7afbad
+  data.tar.gz: 4ef2f2d87fae044628aea867fba96e240a9f64f0
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data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.44
+1.0.0.alpha.45

data/bin/bel2_validator

@@ -2,13 +2,69 @@
 $LOAD_PATH.unshift(
   File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
 
-unless ARGV.first
-  program = File.basename($PROGRAM_NAME)
-  $stderr.puts <<-USAGE.gsub(/ {4}/, '')
-    usage: #{program} [BEL specification version] [PREFIX=URI]...
+require 'optparse'
+require 'bel_parser'
+
+options = {
+  uri_reader: BELParser::Resource.default_uri_reader,
+  url_reader: BELParser::Resource.default_url_reader,
+  spec: BELParser::Language.specification(
+    BELParser::Language.latest_supported_version)
+}
+OptionParser.new do |opts|
+  opts.banner = <<-USAGE.gsub(/^ {4}/, '')
+    Validates BEL 2.0 expressions.
+
+    Read from a BEL file.
+    usage: #$PROGRAM_NAME --file [FILE]
+
+    Read from standard input.
+    usage: #$PROGRAM_NAME
   USAGE
-  exit 1
-end
+
+  opts.on('-f', '--file FILE', 'BEL script file to read.') do |bel|
+    options[:file] = bel
+  end
+
+  opts.on(
+    '-v',
+    '--[no-]verbose',
+    'Enable verbose logging.') do |verbose|
+      options[:verbose] = verbose
+    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(
+    '-q',
+    '--sparql-endpoint URL',
+    'SPARQL endpoint URL containing BEL RDF resources.') do |sparql|
+
+      require 'bel_parser/resource/sparql_reader'
+      options[:uri_reader] = BELParser::Resource::SPARQLReader.new(sparql)
+    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)
+      end
+  end
+end.parse!
 
 def syntax_results(results)
   results.select do |res|
@@ -22,22 +78,22 @@ def semantics_results(results)
   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      =
+uri_reader, url_reader = options.values_at(:uri_reader, :url_reader)
+
+namespaces =
   Hash[
     ARGV.map do |ns|
       prefix, identifier = ns.split('=')
-      dataset            = resource_reader.retrieve_resource(identifier)
-      dataset ? [prefix, dataset] : nil
+      dataset            = uri_reader.retrieve_resource(identifier)
+      dataset ? [prefix, [:uri, dataset]] : nil
     end.compact
   ]
 
 BELParser::Expression::Validator
-  .new(ARGV.first, namespaces, resource_reader)
+  .new(options[:spec], namespaces, uri_reader, url_reader)
   .each($stdin) do |(line_number, line, ast, results)|
     puts "#{line_number}: #{line}"
     puts "  AST Type: #{ast.type}"

data/bin/bel_script_reader

@@ -4,9 +4,10 @@ $LOAD_PATH.unshift(
 
 require 'optparse'
 require 'bel_parser'
-require 'bel_parser/resource/resource_url_reader'
 
 options = {
+  uri_reader: BELParser::Resource.default_uri_reader,
+  url_reader: BELParser::Resource.default_url_reader,
   spec: BELParser::Language.specification(
     BELParser::Language.latest_supported_version)
 }
@@ -25,25 +26,43 @@ OptionParser.new do |opts|
     options[:file] = bel
   end
 
+  opts.on(
+    '-v',
+    '--[no-]verbose',
+    'Enable verbose logging.') do |verbose|
+      options[:verbose] = verbose
+    end
+
   opts.on(
     '-s',
     '--specification VERSION',
-    'BEL specification version (e.g. 1.0, 2.0)') do |spec|
+    '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
 
-    unless BELParser::Language.defines_version?(spec)
-      $stderr.puts %(Invalid BEL specification "#{spec}")
-      exit 1
+      options[:spec] = BELParser::Language.specification(spec)
     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|
+    '-q',
+    '--sparql-endpoint URL',
+    'SPARQL endpoint URL containing BEL RDF resources.') do |sparql|
 
-    options[:reuse] = reuse
+      require 'bel_parser/resource/sparql_reader'
+      options[:uri_reader] = BELParser::Resource::SPARQLReader.new(sparql)
+    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)
+      end
   end
 end.parse!
 
@@ -55,17 +74,20 @@ io =
     $stdin
   end
 
-rr = BELParser::Resource::ResourceURLReader.new(options[:reuse])
+uri_reader = options[:uri_reader]
+url_reader = options[:url_reader]
+
 namespaces = Hash[
   ARGV.map do |ns|
     prefix, identifier = ns.split('=')
-    dataset            = rr.retrieve_resource(identifier)
+    dataset            = uri_reader.retrieve_resource(identifier)
     dataset ? [prefix, dataset] : nil
   end.compact
 ]
 
 initial_state = {
-  resource_reader:       rr,
+  uri_reader:            uri_reader,
+  url_reader:            url_reader,
   specification:         spec,
   namespace_definitions: namespaces
 }
@@ -80,7 +102,8 @@ module BELParser
       SYN_WARN = BELParser::Language::Syntax::SyntaxWarning
       SEM_WARN = BELParser::Language::Semantics::SemanticsWarning
 
-      def initialize(initial_state, io)
+      def initialize(initial_state, io, verbose)
+        @verbose   = verbose
         @validator =
           Validator.new(
             StateAggregator.new(
@@ -96,7 +119,7 @@ module BELParser
             select(syntax_errors, SYN_WARN) +
             select(syntax_errors, SEM_WARN)
 
-          report(line_number, ast_node, errors, warnings)
+          report(line_number, line, ast_node, errors, warnings)
 
           unless errors.empty?
             puts "Exiting due to error on line #{line_number}: #{line}"
@@ -111,22 +134,30 @@ module BELParser
         list.select { |item| item.is_a?(cls) }
       end
 
-      def report(line_number, ast, errors, warnings)
+      def report(line_number, line, 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}"
+          puts '  Line:'
+          puts "    #{line}"
+          unless errors.empty?
+            puts '  Errors:'
+            errors.each do |err|
+              puts "    #{err}"
+            end
           end
-          puts "  Warnings:"
-          warnings.each do |warn|
-            puts "    #{warn}"
+          unless warnings.empty?
+            puts '  Warnings:'
+            warnings.each do |warn|
+              puts "    #{warn}"
+            end
           end
+        else
+          puts "Line OK: #{line}" if @verbose
         end
       end
     end
   end
 end
 
-BELParser::Script::Reader.new(initial_state, io).read
+BELParser::Script::Reader.new(initial_state, io, options[:verbose]).read

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

@@ -12,7 +12,8 @@ module BEL::Translator::Plugins
       def initialize(io, options = {})
         @io    = io
         @state = {
-          resource_reader:       BELParser::Resource::ResourceURLReader.new(true),
+          uri_reader:            BELParser::Resource.default_uri_reader,
+          url_reader:            BELParser::Resource.default_url_reader,
           specification:         BELParser::Language.specification('2.0'),
           namespace_definitions: {}
         }

data/lib/bel_parser/expression/validator.rb

@@ -19,10 +19,10 @@ module BELParser
         :nested_statement
       ]
 
-      def initialize(specification_version, namespaces, resource_reader)
-        @spec      = BELParser::Language.specification(specification_version)
+      def initialize(specification, namespaces, uri_reader, url_reader)
+        @spec      = specification
         @validator = BELParser::Language::ExpressionValidator.new(
-          @spec, namespaces, resource_reader)
+          @spec, namespaces, uri_reader, url_reader)
       end
 
       def each(io)
@@ -52,19 +52,18 @@ if __FILE__ == $PROGRAM_NAME
     exit 1
   end
 
-  require 'bel_parser/resource/resource_url_reader'
-
-  resource_reader = BELParser::Resource::ResourceURLReader.new
+  uri_reader = BELParser::Resource.default_uri_reader
+  url_reader = BELParser::Resource.default_url_reader
   namespaces      =
     Hash[
       ARGV[1..-1]
       .map do |ns|
         prefix, identifier = ns.split('=')
-        [prefix, resource_reader.retrieve_resource(identifier)]
+        [prefix, uri_reader.retrieve_resource(identifier)]
       end
     ]
   BELParser::Expression::Validator
-    .new(ARGV.first, namespaces, resource_reader)
+    .new(ARGV.first, namespaces, uri_reader, url_reader)
     .each($stdin) do |(line_number, line, ast, results)|
       results.select { |res| res.is_a? BELParser::Language::Syntax::SyntaxError }
       puts "#{line_number}: #{line}"

data/lib/bel_parser/language/apply_namespace_encoding.rb

@@ -1,17 +1,15 @@
-require 'bel_parser/quoting'
-
 module BELParser
   module Language
     # ApplyNamespaceEncoding applies _namespace_ and _encoding_ properties to
     # {BELParser::Parsers::AST::Parameter} child nodes.
     class ApplyNamespaceEncoding
       include AST::Processor::Mixin
-      include BELParser::Quoting
 
-      def initialize(language_spec, namespace_hash, resource_reader)
-        @language_spec   = language_spec
-        @namespace_hash  = namespace_hash
-        @resource_reader = resource_reader
+      def initialize(language_spec, namespace_hash, uri_reader, url_reader)
+        @language_spec  = language_spec
+        @namespace_hash = namespace_hash
+        @uri_reader     = uri_reader
+        @url_reader     = url_reader
       end
 
       def on_observed_term(observed_term_node)
@@ -51,8 +49,9 @@ module BELParser
       end
 
       def on_parameter(parameter_node)
-        @resolved_dataset = nil
-        @prefix           = nil
+        @type    = nil
+        @dataset = nil
+        @prefix  = nil
         process(parameter_node.prefix)
         process(parameter_node.value)
       end
@@ -60,28 +59,26 @@ module BELParser
       def on_prefix(prefix_node)
         return prefix_node unless prefix_node.identifier
 
-        @prefix    = prefix_node.identifier.string_literal
-        dataset    = @namespace_hash[@prefix]
-        return prefix_node unless dataset
-
-        @resolved_dataset     = dataset
-        prefix_node.namespace = dataset
+        @prefix         = prefix_node.identifier.string_literal
+        @type, @dataset = @namespace_hash[@prefix]
+        return prefix_node unless @dataset
 
+        prefix_node.namespace = @dataset
         prefix_node
       end
 
       def on_value(value_node)
-        return value_node unless @resolved_dataset
-        value_node.namespace = @resolved_dataset
-        identifier           = @resolved_dataset.identifier
-        value_literal        = unquote(value_node.children[0].string_literal)
+        return value_node unless @dataset
+        value_node.namespace = @dataset
+        identifier           = @dataset.identifier
+        value_literal        = value_node.children[0].string_literal
 
-        value =
-          @resource_reader
-          .retrieve_value_from_resource(identifier, value_literal)
+        reader = @type == :uri ? @uri_reader : @url_reader
+        values = reader.retrieve_value_from_resource(identifier, value_literal)
 
         value_node.prefix = @prefix
-        if value
+        if values
+          value = values.first
           value_node.encoding =
             value
             .encodings

data/lib/bel_parser/language/expression_validator.rb

@@ -8,13 +8,13 @@ module BELParser
     # when supplied a {BELParser::Language::Specification} and Hash of
     # namespaces.
     class ExpressionValidator
-      def initialize(spec, namespaces, resource_reader)
+      def initialize(spec, namespaces, uri_reader, url_reader)
         @spec                = spec
         @namespaces          = namespaces || {}
         @syntax_functions    = Syntax.syntax_functions
         @semantics_functions = Semantics.semantics_functions
         @transform           =
-          ApplyNamespaceEncoding.new(@spec, @namespaces, resource_reader)
+          ApplyNamespaceEncoding.new(@spec, @namespaces, uri_reader, url_reader)
       end
 
       # Validate the syntax and semantics of

data/lib/bel_parser/parsers/ast/node.rb

@@ -266,6 +266,9 @@ module BELParser
         def domain
           children[1]
         end
+
+        # Get/Set the uri property.
+        attr_accessor :uri
       end
 
       # AST node representing the function of a BEL term.
@@ -317,6 +320,9 @@ module BELParser
         def domain
           children[1]
         end
+
+        # Get/Set the uri property.
+        attr_accessor :uri
       end
 
       # AST node representing a keyword (e.g. definitions).
@@ -363,6 +369,11 @@ module BELParser
           children[0] && children[0].is_a?(Pattern)
         end
 
+        # Determine if this is a URI domain.
+        def uri?
+          children[0] && children[0].is_a?(Uri)
+        end
+
         # Determine if this is a URL domain.
         def url?
           children[0] && children[0].is_a?(Url)
@@ -394,6 +405,26 @@ module BELParser
         end
       end
 
+      # AST node representing a URI.
+      class Uri < Node
+        # AST node type
+        @ast_type = :uri
+        # Urls have semantic meaning
+        @has_semantics = true
+
+        # New Uri AST node.
+        #
+        # @see Node#initialize Node class for basic properties
+        def initialize(children = [], properties = {})
+          super(Uri.ast_type, children, properties)
+        end
+
+        # Get the uri's string.
+        def string
+          children[0]
+        end
+      end
+
       # AST node representing a Pattern.
       class Pattern < Node
         # AST node type
@@ -1029,6 +1060,10 @@ module BELParser
           Url.new(children, props)
         end
 
+        def uri(*children, **props)
+          Uri.new(children, props)
+        end
+
         def pattern(*children, **props)
           Pattern.new(children, props)
         end