bel_parser 1.0.0.alpha.18 → 1.0.0.alpha.19

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 1256e007aca2d5c8449272250647c0cea918c777
-  data.tar.gz: b2744bba741552fd30975cf554f4b91b1d79f9a6
+  metadata.gz: 64448dc49f150b92a0dd2571bfd9f97eff32eda9
+  data.tar.gz: 674d470b18c5195e21570cf3ae28ef75d111a0ff
 SHA512:
-  metadata.gz: a71abfc3ac43e9c87d72d6a5622333b6fbc48d5c15d0944a4addb267d339f638474754068f838147883ead4c913039e78c225e890b34e5684fdd7d7976e59eb3
-  data.tar.gz: c79f00f01c91e3ca4430744e7a2ab9548954c5663129c2947b82cbb47fe78c0c99d1b496d518d46d922c964bd8d8e9f771519737050ef38d3121502c9ea41608
+  metadata.gz: a8854636248e1dd75114b5131920a227bbfacd2d3f2deea6cdc0cd4873d2771b4751c6d4de792e644d671ccfa9213fcc7660d61ecf3ad6f04e90750595e8c1b9
+  data.tar.gz: 880b9595a4daa995594861f84891085762d6ae2b80de61573ac23db73ddb21bb5f5546fbd72e3e397789da559dca7381c4daf76a7f7be1a1e74eb13c2c753551

data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.18
+1.0.0.alpha.19

data/bin/bel_script_reader

@@ -55,28 +55,6 @@ io =
     $stdin
   end
 
-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
 
 rr = BELParser::Resource::ResourceURLReader.new(options[:reuse])
 namespaces = Hash[
@@ -93,18 +71,63 @@ initial_state = {
   namespace_definitions: namespaces
 }
 
-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
+module BELParser
+  module Script
+    # Reader assembles a BEL Script reader using the following pipeline:
+    #
+    #   Generate -> Filter -> Pick One -> Aggregate State -> Validate Syntax
+    class Reader
+      SYN_ERR  = BELParser::Language::Syntax::SyntaxError
+      SYN_WARN = BELParser::Language::Syntax::SyntaxWarning
+      SEM_WARN = BELParser::Language::Semantics::SemanticsWarning
+
+      def initialize(initial_state, io)
+        @validator =
+          Validator.new(
+            StateAggregator.new(
+              FirstNode.new(Filter.new(ASTGenerator.new(io))),
+              initial_state))
+      end
+
+      def read
+        @validator.each do |(line_number, line, ast_node, _)|
+          syntax_errors = ast_node.syntax_errors
+          errors        = select(syntax_errors, SYN_ERR)
+          warnings      =
+            select(syntax_errors, SYN_WARN) +
+            select(syntax_errors, SEM_WARN)
+
+          report(line_number, ast_node, errors, warnings)
+
+          unless errors.empty?
+            puts "Exiting due to error on line #{line_number}: #{line}"
+            exit 1
+          end
+        end
+      end
+
+      private
+
+      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
+    end
   end
 end
+
+BELParser::Script::Reader.new(initial_state, io).read

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

@@ -0,0 +1,35 @@
+# Requires the "bel" gem.
+# This is for the BelScript translator intended to be plugged into bel.rb.
+require 'bel/translator'
+
+module BEL::Translator::Plugins
+  module BelScript
+    # BelScriptTranslator defines a {BEL::Translator} that can read/write
+    # BEL Script using the Nanopub model.
+    class BelScriptTranslator
+      include ::BEL::Translator
+
+      def read(data, options = {})
+        # EvidenceYielder.new(data, options)
+      end
+
+      def write(objects, writer = StringIO.new, options = {})
+        # if block_given?
+        #   BelYielder.new(objects, options).each { |bel_part|
+        #     yield bel_part
+        #   }
+        # else
+        #   if writer
+        #     BelYielder.new(objects, options).each { |bel_part|
+        #       writer << "#{bel_part}"
+        #       writer.flush
+        #     }
+        #     writer
+        #   else
+        #     BelYielder.new(objects, options)
+        #   end
+        # end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,38 @@
+module BEL::Translator::Plugins
+  # BELScript plugs a translator for BEL Script into bel.rb.
+  # Supports multiple BEL specifications by using the
+  # {BELParser::Language::ExpressionValidator expression validator}.
+  module BelScript
+    ID          = :bel_script
+    NAME        = 'BEL Script Translator'
+    DESCRIPTION = 'A translator that can read/write evidence to BEL Script.'
+    MEDIA_TYPES = %i(application/bel)
+    EXTENSIONS  = %i(bel)
+
+    def self.create_translator(options = {})
+      require 'bel'
+      require_relative 'bel_script/translator'
+      BelScriptTranslator.new
+    end
+
+    def self.id
+      ID
+    end
+
+    def self.name
+      NAME
+    end
+
+    def self.description
+      DESCRIPTION
+    end
+
+    def self.media_types
+      MEDIA_TYPES
+    end
+
+    def self.file_extensions
+      EXTENSIONS
+    end
+  end
+end

data/lib/bel_parser/ast_filter.rb

@@ -3,18 +3,19 @@ require_relative 'parsers/ast/node'
 module BELParser
   # ASTFilter filters types of {BELParser::Parsers::AST::Node}.
   class ASTFilter
-    def initialize(*types)
-      @types = types
+    def initialize(ast_enum, *types)
+      @ast_enum = ast_enum
+      @types    = types
     end
 
-    def each(ast_source)
+    def each
       if block_given?
-        ast_source.each do |(line_number, line, ast_results)|
+        @ast_enum.each do |(line_number, line, ast_results)|
           selected = filter(ast_results)
           yield([line_number, line, selected]) unless selected.empty?
         end
       else
-        enum_for(:each, ast_source)
+        enum_for(:each)
       end
     end
 

data/lib/bel_parser/ast_generator.rb

@@ -18,6 +18,10 @@ module BELParser
       map_const.call(BELParser::Parsers::BELScript)
     ].flatten!
 
+    def initialize(io)
+      @io = io
+    end
+
     # Yields AST results for each line of the IO.
     #
     # @example Receive AST results in given block.
@@ -42,9 +46,9 @@ module BELParser
     #         object is returned if a block is given, otherwise an
     #         {Enumerator} object is returned that can be iterated with
     #         {Enumerator#each}
-    def each(io) # rubocop:disable MethodLength
+    def each # rubocop:disable MethodLength
       if block_given?
-        line_enumerator = map_lines(io.each_line.lazy)
+        line_enumerator = map_lines(@io.each_line.lazy)
 
         line_number = 1
         loop do
@@ -62,7 +66,7 @@ module BELParser
           end
         end
       else
-        enum_for(:each, io)
+        enum_for(:each)
       end
     end
   end

data/lib/bel_parser/script/filter.rb

@@ -0,0 +1,35 @@
+module BELParser
+  module Script
+    # Filter will enumerate {BELParser::Parsers::AST::Node AST nodes} that are
+    # relevant to lines in a BEL Script document. It selects the relevant nodes
+    # from an {BELParser::Parsers::AST::Node AST node} enumerator.
+    class Filter
+      # Represents the BEL Script AST Node type.
+      # TODO These could be AST::Node subclasses instead.
+      TYPES = [
+        :simple_statement,
+        :observed_term,
+        :nested_statement,
+        :annotation_definition,
+        :namespace_definition,
+        :set,
+        :document_property,
+        :unset,
+        :blank_line,
+        :comment_line
+      ]
+
+      def initialize(ast_enum)
+        @ast_filter = BELParser::ASTFilter.new(ast_enum, *TYPES)
+      end
+
+      def each(&block)
+        if block_given?
+          @ast_filter.each(&block)
+        else
+          enum_for(:each)
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/script/first_node.rb

@@ -0,0 +1,21 @@
+module BELParser
+  module Script
+    # FirstNode will return the first node from the set of
+    # {BELParser::Parsers::AST::Node AST nodes} provided.
+    class FirstNode
+      def initialize(ast_enum)
+        @ast_enum = ast_enum
+      end
+
+      def each
+        if block_given?
+          @ast_enum.each do |(line_number, line, ast_nodes)|
+            yield [line_number, line, ast_nodes.first]
+          end
+        else
+          enum_for(:each)
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/script/nanopub_mapper.rb

@@ -0,0 +1,8 @@
+module BELParser
+  module Script
+    class NanopubMapper
+
+
+    end
+  end
+end

data/lib/bel_parser/script/state_aggregator.rb

@@ -0,0 +1,49 @@
+module BELParser
+  module Script
+    # StateAggregator aggregates BEL Script state for each
+    # {BELParser::Parsers::AST::Node AST node} it processes.
+    class StateAggregator
+
+      STATE_PATH = 'state'
+
+      def initialize(ast_enum, options = {})
+        @ast_enum        = ast_enum
+        @script_context  = {}.merge(options)
+
+        StateAggregator.require_script_path
+        @state_functions = StateAggregator.state_constants(State)
+      end
+
+      def each
+        if block_given?
+          @ast_enum.each do |(line_number, line, ast_node)|
+            ast_node.traverse.each do |node|
+              @state_functions.each do |func|
+                func.consume(node, @script_context)
+              end
+            end
+            yield [line_number, line, ast_node, @script_context]
+          end
+        else
+          enum_for(:each)
+        end
+      end
+
+      def self.require_script_path
+        base_path = File.expand_path(File.dirname(__FILE__)) + File::SEPARATOR
+        Dir[File.join(base_path, STATE_PATH, '*.rb')]
+          .each do |ruby_file|
+            ruby_file.sub!(/^#{Regexp.escape(base_path)}/, '')
+            require_relative ruby_file
+          end
+      end
+
+      def self.state_constants(mod)
+        mod.constants.collect do |symbol|
+          const = mod.const_get(symbol)
+          const if const.respond_to?(:consume)
+        end.compact
+      end
+    end
+  end
+end

data/lib/bel_parser/script/validator.rb

@@ -12,58 +12,34 @@ require_relative '../language/syntax_function'
 
 module BELParser
   module Script
+    # Validator defines a BEL Script syntax validator. This validator
+    # expects to receive the BEL Script state for each node. This is
+    # accomplished by initializing with a {StateAggregator} that this
+    # will enumerate.
     class Validator
-      include BELParser::Parsers::Common
-      include BELParser::Parsers::Expression
-      include BELParser::Parsers::BELScript
 
-      FILTER = BELParser::ASTFilter.new(
-        :simple_statement,
-        :observed_term,
-        :nested_statement,
-        :annotation_definition,
-        :namespace_definition,
-        :set,
-        :document_property,
-        :unset,
-        :blank_line,
-        :comment_line
-      )
-
-      def initialize(options = {})
-        @script_context = Concurrent::Hash.new.merge(options)
+      def initialize(state_aggregator)
+        @state_aggregator = state_aggregator
 
         Validator.require_script_path
-        @state_functions  = Validator.state_constants(State)
         @syntax_functions = Validator.syntax_constants(Syntax)
       end
 
-      def each(io)
+      def each
         if block_given?
-          filtered_ast = FILTER.each(BELParser::ASTGenerator.new.each(io))
-          filtered_ast.each do |results|
-            line_number, line, ast_results = results
-            ast_node                       = ast_results.first
-
-            syntax_results =
-              ast_node.traverse.flat_map do |node|
-                @syntax_functions.flat_map do |func|
-                  func.map(node, @script_context)
-                end
-              end.compact
-
-            if syntax_results.empty?
-              ast_node.traverse.each do |node|
-                @state_functions.each do |func|
-                  func.consume(node, @script_context)
-                end
+          @state_aggregator.each do |(line_number, line, ast_node, state)|
+            ast_node.traverse.flat_map do |node|
+              @syntax_functions.flat_map do |func|
+                func.map(node, state)
               end
+            end.compact.each do |syntax_result|
+              ast_node.add_syntax_error(syntax_result)
             end
 
-            yield [line_number, line, ast_node, syntax_results, @script_context]
+            yield [line_number, line, ast_node, state]
           end
         else
-          enum_for(:each, io)
+          enum_for(:each)
         end
       end
 
@@ -78,13 +54,6 @@ module BELParser
         end
       end
 
-      def self.state_constants(mod)
-        mod.constants.collect do |symbol|
-          const = mod.const_get(symbol)
-          const if const.respond_to?(:consume)
-        end.compact
-      end
-
       def self.syntax_constants(mod)
         mod.constants.collect do |symbol|
           const = mod.const_get(symbol)
@@ -94,62 +63,3 @@ module BELParser
     end
   end
 end
-
-if __FILE__ == $PROGRAM_NAME
-  $LOAD_PATH.unshift(
-    File.join(File.expand_path(File.dirname(__FILE__)), '..', '..'))
-
-  require 'bel_parser/language'
-  require 'bel_parser/resource/resource_url_reader'
-
-  initial_state = {
-    resource_reader: BELParser::Resource::ResourceURLReader.new,
-    specification:   BELParser::Language.specification(
-      BELParser::Language.latest_supported_version
-    )
-  }
-
-  BELParser::Script::Validator
-  .new(initial_state)
-  .each($stdin) do |(line_number, line, ast, syntax_results, state)|
-    puts "#{line_number}: #{line}"
-    puts ast.to_s(1)
-
-    puts "Syntax errors:"
-    syntax_results
-      .select do |res|
-        res.is_a?(BELParser::Language::Syntax::SyntaxError)
-      end
-      .each do |res|
-        puts "  #{res}"
-      end
-
-    puts "Syntax warnings:"
-    syntax_results
-      .select do |res|
-        res.is_a?(BELParser::Language::Syntax::SyntaxWarning)
-      end
-      .each do |res|
-        puts "  #{res}"
-      end
-
-    puts "Semantics warnings:"
-    syntax_results
-      .select do |res|
-        res.is_a?(BELParser::Language::Semantics::SemanticsWarning)
-      end
-      .each do |res|
-        puts "  #{res}"
-      end
-
-    puts "State:"
-    state.each do |key, value|
-      case value
-      when Hash
-        puts "  #{key}: #{value.keys}"
-      else
-        puts "  #{key}: #{value}"
-      end
-    end
-  end
-end

data/lib/bel_parser/script.rb

@@ -1,5 +1,8 @@
 require_relative 'script/keywords'
 require_relative 'script/state_function'
 
-require_relative 'script/parser'
+require_relative 'script/filter'
+require_relative 'script/first_node'
+require_relative 'script/state_aggregator'
 require_relative 'script/validator'
+require_relative 'script/nanopub_mapper'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.18
+  version: 1.0.0.alpha.19
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -26,6 +26,8 @@ files:
 - VERSION
 - bin/bel2_validator
 - bin/bel_script_reader
+- lib/bel/translator/plugins/bel_script.rb
+- lib/bel/translator/plugins/bel_script/translator.rb
 - lib/bel_parser.rb
 - lib/bel_parser/ast_filter.rb
 - lib/bel_parser/ast_generator.rb
@@ -253,7 +255,6 @@ files:
 - lib/bel_parser/language/version2_0/value_encodings/rna_abundance.rb
 - lib/bel_parser/mixin/line_continuator.rb
 - lib/bel_parser/mixin/line_mapping.rb
-- lib/bel_parser/parser.rb
 - lib/bel_parser/parsers/ast/node.rb
 - lib/bel_parser/parsers/ast/sexp.rb
 - lib/bel_parser/parsers/bel_script.rb
@@ -314,7 +315,10 @@ files:
 - lib/bel_parser/resource/sparql_reader.rb
 - lib/bel_parser/resource/value.rb
 - lib/bel_parser/script.rb
+- lib/bel_parser/script/filter.rb
+- lib/bel_parser/script/first_node.rb
 - lib/bel_parser/script/keywords.rb
+- lib/bel_parser/script/nanopub_mapper.rb
 - lib/bel_parser/script/parser.rb
 - lib/bel_parser/script/state/annotation_definition.rb
 - lib/bel_parser/script/state/bel_version.rb
@@ -322,6 +326,7 @@ files:
 - lib/bel_parser/script/state/namespace_definition.rb
 - lib/bel_parser/script/state/set.rb
 - lib/bel_parser/script/state/unset.rb
+- lib/bel_parser/script/state_aggregator.rb
 - lib/bel_parser/script/state_function.rb
 - lib/bel_parser/script/syntax/expression_validation.rb
 - lib/bel_parser/script/syntax/invalid_regex_pattern.rb

data/lib/bel_parser/parser.rb

@@ -1,54 +0,0 @@
-require_relative 'ast_filter'
-require_relative 'ast_generator'
-require_relative 'parsers/common'
-require_relative 'parsers/expression'
-require_relative 'parsers/bel_script'
-
-module BELParser
-  # Parser is a line parser that supports recognition using all ragel parsers.
-  class Parser
-    include BELParser::Parsers::Common
-    include BELParser::Parsers::Expression
-    include BELParser::Parsers::BELScript
-
-    FILTER = BELParser::ASTFilter.new(
-      :blank_line,
-      :comment_line,
-      :identifier,
-      :string,
-      :list,
-      :comment,
-      :parameter,
-      :term,
-      :relationship,
-      :observed_term,
-      :simple_statement,
-      :nested_statement,
-      :annotation_definition,
-      :namespace_definition,
-      :set,
-      :document_property,
-      :unset
-    )
-
-    def each(io)
-      if block_given?
-        filtered_ast = FILTER.each(BELParser::ASTGenerator.new.each(io))
-        filtered_ast.each do |results|
-          yield results
-        end
-      else
-        enum_for(:each, io)
-      end
-    end
-  end
-end
-
-if __FILE__ == $PROGRAM_NAME
-  BELParser::Parser.new.each($stdin) do |(line_number, line, results)|
-    puts "#{line_number}: #{line}"
-    results.each do |ast|
-      puts ast.to_s(1)
-    end
-  end
-end