Class: BEL::Translator::Plugins::BelScript::Writer

Inherits:
Object
  • Object
show all
Defined in:
lib/bel/translator/plugins/bel_script/writer.rb

Instance Method Summary collapse

Constructor Details

#initialize(data, options = {}) ⇒ Writer

Create a BEL::Translator::Plugins::BelScript::Writer object that serializes Nanopub::Nanopub to BEL Script.

Parameters:

  • data (Enumerator<BEL::Nanopub::Nanopub>) —

    nanopubs iterated using each

  • options (Hash) (defaults to: {}) —

    a customizable set of options

Options Hash (options):



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# File 'lib/bel/translator/plugins/bel_script/writer.rb', line 27

def initialize(data, options = {})
  @data                     = data
  @streaming                = options.fetch(:streaming, false)
  @write_header             = options.fetch(:write_header, true)
  @annotation_reference_map = options.fetch(:annotation_reference_map, nil)
  @namespace_reference_map  = options.fetch(:namespace_reference_map, nil)

  # augment self with BEL serialization stategy.
  serialization = options[:serialization]
  serialization_module =
    case serialization
    when Module
      serialization
    when String, Symbol
      serialization_refs = {
        :discrete => BelDiscreteSerialization,
        :topdown  => BelTopDownSerialization,
        :citation => BelCitationSerialization,
      }
      serialization_module = serialization_refs[serialization.to_sym]
      unless serialization_module
          raise %Q{No BEL serialization strategy for "#{serialization}"}
      end
      serialization_module
    else
      # Default to citation serialization.
      BelCitationSerialization
    end

  self_eigenclass = (class << self; self; end)
  self_eigenclass.send(:include, serialization_module)
end

Instance Method Details

#each ⇒ Object 



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# File 'lib/bel/translator/plugins/bel_script/writer.rb', line 60

def each
  if block_given?
    combiner =
      if @streaming
        BEL::Nanopub::StreamingNanopubCombiner.new(@data)
      elsif @annotation_reference_map && @namespace_reference_map
        BEL::Nanopub::MapReferencesCombiner.new(
          @data,
          BEL::Nanopub::HashMapReferences.new(
            @annotation_reference_map,
            @namespace_reference_map
          )
        )
      else
        BEL::Nanopub::BufferingNanopubCombiner.new(@data)
      end

    header_flag = true
    combiner.each { |nanopub|

      # serialize nanopub
      bel = to_bel(nanopub)

      if @write_header && header_flag
        yield document_header(nanopub.metadata.document_header)
        yield namespaces(combiner.namespace_references)
        yield annotations(combiner.annotation_references)

        yield <<-COMMENT.gsub(/^\s+/, '')
          ###############################################
          # Statements Section
        COMMENT
        header_flag = false
      end

      yield bel
    }

    yield epilogue
  else
    to_enum(:each)
  end
end