bel_parser 1.0.0.alpha.19 → 1.0.0.alpha.20

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 64448dc49f150b92a0dd2571bfd9f97eff32eda9
-  data.tar.gz: 674d470b18c5195e21570cf3ae28ef75d111a0ff
+  metadata.gz: 5f5c683930e9f6671b818ec184fc5a8a35231984
+  data.tar.gz: 04cb98ee13e3c6f57f2c9ea3a6b2188aba861918
 SHA512:
-  metadata.gz: a8854636248e1dd75114b5131920a227bbfacd2d3f2deea6cdc0cd4873d2771b4751c6d4de792e644d671ccfa9213fcc7660d61ecf3ad6f04e90750595e8c1b9
-  data.tar.gz: 880b9595a4daa995594861f84891085762d6ae2b80de61573ac23db73ddb21bb5f5546fbd72e3e397789da559dca7381c4daf76a7f7be1a1e74eb13c2c753551
+  metadata.gz: 362bc4fd38cb8cb60fcbf3c6a975671192258a9717101b53dd536e68e912d4af15f9c4620506f9782e2cefcab5fbf450586fc988a422e2710a1e8b6e273d41c1
+  data.tar.gz: 6034289be41223dcda961ddafccc4079b62502ab3d4c8376eddee9bc7af109344cc16c2b442a9c4a6aac37186948f530875d3a7275da21bdc1408e5f1d8a5fa3

data/.gemspec

@@ -11,7 +11,7 @@ Gem::Specification.new do |spec|
                                  'Anthony Bargnesi',
                                  'Nick Bargnesi',
                                ]
-  spec.date                  = %q{2016-04-29}
+  spec.date                  = %q{2016-05-01}
   spec.email                 = %q{abargnesi@selventa.com}
   spec.files                 = [
                                  Dir.glob('lib/**/*.{rb,rl}'),

data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.19
+1.0.0.alpha.20

data/bin/bel_script_reader

@@ -55,7 +55,6 @@ io =
     $stdin
   end
 
-
 rr = BELParser::Resource::ResourceURLReader.new(options[:reuse])
 namespaces = Hash[
   ARGV.map do |ns|

data/lib/bel_parser/ast_filter.rb

@@ -30,9 +30,12 @@ end
 if __FILE__ == $PROGRAM_NAME
   require_relative 'ast_generator'
 
-  types = ARGV.map(&:to_sym)
-  ast   = BELParser::ASTGenerator.new.each($stdin)
-  BELParser::ASTFilter.new(*types).each(ast) do |(line_number, line, results)|
+  types     = ARGV.map(&:to_sym)
+  generator = BELParser::ASTGenerator.new($stdin)
+  BELParser::ASTFilter.new(
+    generator,
+    *types
+  ).each do |(line_number, line, results)|
     puts "#{line_number}: #{line}"
     results.each do |result_ast|
       puts result_ast.to_s(1)

data/lib/bel_parser/ast_generator.rb

@@ -73,7 +73,7 @@ module BELParser
 end
 
 if __FILE__ == $PROGRAM_NAME
-  BELParser::ASTGenerator.new.each($stdin) do |line_results|
+  BELParser::ASTGenerator.new($stdin).each do |line_results|
     line_number, line, ast_results = line_results
     puts "#{line_number}: #{line}"
     ast_results.each do |ast|

data/lib/bel_parser/expression/parser.rb

@@ -11,18 +11,20 @@ module BELParser
       include BELParser::Parsers::Common
       include BELParser::Parsers::Expression
 
-      FILTER = BELParser::ASTFilter.new(
+      TYPES = [
         :parameter,
         :term,
         :simple_statement,
         :observed_term,
         :nested_statement
-      )
+      ]
 
       def each(io)
         if block_given?
-          filtered_ast = FILTER.each(BELParser::ASTGenerator.new.each(io))
-          filtered_ast.each do |results|
+          filter = BELParser::ASTFilter.new(
+            BELParser::ASTGenerator.new(io),
+            *TYPES)
+          filter.each do |results|
             yield results
           end
         else

data/lib/bel_parser/expression/validator.rb

@@ -11,12 +11,13 @@ module BELParser
       include BELParser::Parsers::Common
       include BELParser::Parsers::Expression
 
-      FILTER = BELParser::ASTFilter.new(
+      TYPES = [
         :parameter,
         :term,
-        :observed_term,
         :simple_statement,
-        :nested_statement)
+        :observed_term,
+        :nested_statement
+      ]
 
       def initialize(specification_version, namespaces, resource_reader)
         @spec      = BELParser::Language.specification(specification_version)
@@ -26,10 +27,12 @@ module BELParser
 
       def each(io)
         if block_given?
-          filtered_ast = FILTER.each(BELParser::ASTGenerator.new.each(io))
-          filtered_ast.each do |(line_number, line, ast_results)|
-            ast_results.each do |ast|
-              yield [line_number, line, ast, @validator.validate(ast)]
+          filter = BELParser::ASTFilter.new(
+            BELParser::ASTGenerator.new(io),
+            *TYPES)
+          filter.each do |(num, line, results)|
+            results.each do |ast|
+              yield [num, line, ast, @validator.validate(ast)]
             end
           end
         else

data/lib/bel_parser/parsers/serializer.rb

@@ -0,0 +1,205 @@
+require 'bel_parser/vendor/ast'
+
+module BELParser
+  module Parsers
+
+    def serialize(ast_node)
+      serializer = Serializer.new
+      serializer.process(ast_node)
+      serializer.string
+    end
+
+    # Defines an {AST::Processor::Mixin AST processor} that serializes
+    # all {AST::Node AST node} to a string.
+    class Serializer
+      include ::AST::Processor::Mixin
+
+      attr_reader :string
+
+      def initialize
+        @string = ''
+      end
+
+      def on_annotation_definition(annotation_definition_node)
+        @string << 'DEFINE ANNOTATION '
+        process(annotation_definition_node.keyword)
+        @string << ' AS '
+        process(annotation_definition_node.domain)
+      end
+
+      def on_argument(argument_node)
+        @string << ', ' if @separate_by_comma
+
+        process(argument_node.child)
+        @separate_by_comma = true
+      end
+
+      def on_blank_line(blank_line_node)
+        @string << ''
+      end
+
+      def on_comment_line(comment_line_node)
+        @string << %(##{comment_line_node.children[0]})
+      end
+
+      def on_document_property(document_property_node)
+       name  = document_property_node.name.identifier.string_literal
+       value = document_property_node.value.children[0].string_literal
+       @string << %(SET DOCUMENT #{name} = #{value})
+      end
+
+      def on_domain(domain_node)
+        process(domain_node.child)
+      end
+
+      def on_function(function_node)
+        @string << function_node.identifier.string_literal
+      end
+
+      def on_identifier(identifier_node)
+        @string << identifier_node.string_literal
+      end
+
+      def on_keyword(keyword_node)
+        process(keyword_node.identifier)
+      end
+
+      def on_list(list_node)
+        items = list_node.list_items
+        if !items || items.empty?
+          @string << '{}'
+        else
+          @string << '{ '
+          process(items[0])
+          items[1..-1].each do |rest_item|
+            @string << ', '
+            process(rest_item)
+          end
+          @string << ' }'
+        end
+      end
+
+      def on_list_item(list_item_node)
+        process(list_item_node.children[0])
+      end
+
+      def on_name(name_node)
+        process(name_node.identifier)
+      end
+
+      def on_namespace_definition(namespace_definition_node)
+        @string << 'DEFINE NAMESPACE '
+        process(namespace_definition_node.keyword)
+        @string << ' AS '
+        process(namespace_definition_node.domain)
+      end
+
+      def on_nested_statement(nested_statement_node)
+        process(nested_statement_node.statement)
+      end
+
+      def on_object(object_node)
+        process(object_node.child)
+      end
+
+      def on_observed_term(observed_term_node)
+        process(observed_term_node.statement)
+      end
+
+      def on_parameter(param_node)
+        process(param_node.prefix)
+        process(param_node.value)
+      end
+
+      def on_pattern(pattern_node)
+        @string << 'PATTERN '
+        process(pattern_node.string)
+      end
+
+      def on_prefix(prefix_node)
+        prefix = prefix_node.identifier
+        @string << "#{prefix.string_literal}:" unless prefix.nil?
+      end
+
+      def on_relationship(relationship_node)
+        @string << " #{relationship_node.string_literal} "
+      end
+
+      def on_set(set_node)
+        @string << 'SET '
+        process(set_node.name)
+        @string << ' = '
+        process(set_node.value)
+      end
+
+      def on_simple_statement(simple_statement_node)
+        process(simple_statement_node.statement)
+      end
+
+      def on_statement(statement_node)
+        process(statement_node.subject)
+        return if statement_node.object.child.nil?
+
+        process(statement_node.relationship)
+        object_node = statement_node.object
+        if object_node.statement?
+          @string << '('
+          process(object_node)
+          @string << ')'
+        else
+          process(object_node)
+        end
+      end
+
+      def on_string(string_node)
+        @string << string_node.string_literal
+      end
+
+      def on_subject(subject_node)
+        process(subject_node.term)
+      end
+
+      # Called when visiting nodes of type +term+.
+      def on_term(term_node)
+        @separate_by_comma = false
+        process(term_node.function)
+        @string << '('
+        term_node.arguments.each { |arg| process(arg) }
+        @string << ')'
+      end
+
+      def on_unset(unset_node)
+        @string << 'UNSET '
+        process(unset_node.name)
+      end
+
+      def on_url(url_node)
+        @string << 'URL '
+        process(url_node.string)
+      end
+
+      def on_value(value_node)
+        process(value_node.children[0])
+      end
+    end
+  end
+end
+
+if __FILE__ == $PROGRAM_NAME
+  $LOAD_PATH.unshift(
+    File.join(
+      File.expand_path(File.dirname(__FILE__)),
+      '..',
+      '..',
+      '..',
+      'lib'))
+  require 'bel_parser'
+
+  types      = ARGV.map(&:to_sym)
+  generator  = BELParser::ASTGenerator.new($stdin)
+  BELParser::ASTFilter.new(generator, *types).each do |(num, line, results)|
+    serializer = BELParser::Parsers::Serializer.new
+    serializer.process(results.first)
+    puts serializer.string
+  end
+end

data/lib/bel_parser/script/nanopub_mapper.rb

@@ -1,8 +1,68 @@
 module BELParser
   module Script
+    # NanopubMapper maps BEL Script AST nodes to an aggregated nanopub.
     class NanopubMapper
+      STATEMENT_TYPES = [
+        :simple_statement,
+        :nested_statement,
+        :observed_term
+      ]
 
+      def initialize(ast_enum)
+        @ast_enum = ast_enum
+      end
 
+      def each
+        if block_given?
+          @ast_enum.each do |(line_nunber, line, ast_node, state)|
+            next unless STATEMENT_TYPES.include?(ast_node.type)
+
+            # TODO Add StateFunction for capturing :citation.
+            # TODO Add BELSerializer AST processor. Serialize ast_node.
+            # TODO One time: Map annotation and namespace definitions.
+
+            # TODO Collect annotations.
+
+            # TODO Combine into hash. Yield.
+          end
+        else
+          enum_for(:each)
+        end
+      end
     end
   end
 end
+
+if __FILE__ == $PROGRAM_NAME
+  $LOAD_PATH.unshift(
+    File.join(File.expand_path(File.dirname(__FILE__)), '..', '..', '..', 'lib'))
+
+  require 'json'
+  require 'bel_parser/language'
+  require 'bel_parser/script'
+  require 'bel_parser/resource/resource_url_reader'
+  include BELParser::Script
+
+  rr = BELParser::Resource::ResourceURLReader.new(true)
+  namespaces = Hash[
+    ARGV.map do |ns|
+      prefix, identifier = ns.split('=')
+      dataset            = rr.retrieve_resource(identifier)
+      dataset ? [prefix, dataset] : nil
+    end.compact
+  ]
+
+  initial_state = {
+    resource_reader:       rr,
+    specification:         BELParser::Language.specification('2.0'),
+    namespace_definitions: namespaces
+  }
+
+  NanopubMapper.new(
+    Validator.new(
+      StateAggregator.new(
+        FirstNode.new(Filter.new(BELParser::ASTGenerator.new(File.open(ARGV.first)))),
+        initial_state))).each do |nanopub|
+          JSON.dump(nanopub)
+        end
+end

data/lib/bel_parser/script/parser.rb

@@ -12,7 +12,7 @@ module BELParser
       include BELParser::Parsers::Expression
       include BELParser::Parsers::BELScript
 
-      FILTER = BELParser::ASTFilter.new(
+      TYPES = [
         :simple_statement,
         :observed_term,
         :nested_statement,
@@ -23,12 +23,14 @@ module BELParser
         :unset,
         :blank_line,
         :comment_line
-      )
+      ]
 
       def each(io)
         if block_given?
-          filtered_ast = FILTER.each(BELParser::ASTGenerator.new.each(io))
-          filtered_ast.each do |results|
+          filter = BELParser::ASTFilter.new(
+            BELParser::ASTGenerator.new(io),
+            *TYPES)
+          filter.each do |results|
             yield results
           end
         else

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.19
+  version: 1.0.0.alpha.20
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-29 00:00:00.000000000 Z
+date: 2016-05-01 00:00:00.000000000 Z
 dependencies: []
 description: Implements language versions 1.0 and 2.0.
 email: abargnesi@selventa.com
@@ -299,6 +299,7 @@ files:
 - lib/bel_parser/parsers/line_parser.rb
 - lib/bel_parser/parsers/mixin/buffer.rb
 - lib/bel_parser/parsers/nonblocking_io_wrapper.rb
+- lib/bel_parser/parsers/serializer.rb
 - lib/bel_parser/quoting.rb
 - lib/bel_parser/resource/concept.rb
 - lib/bel_parser/resource/concept_scheme.rb