Class: BEL::Translator::Plugins::Jgf::JgfTranslator

Inherits:
Object
  • Object
show all
Includes:
BEL::Translator
Defined in:
lib/bel/translator/plugins/jgf/translator.rb

Instance Method Summary collapse

Instance Method Details

#read(data, options = {}) ⇒ Object 



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# File 'lib/bel/translator/plugins/jgf/translator.rb', line 12

def read(data, options = {})
  default_resource_index = options.fetch(:default_resource_index) {
    ResourceIndex.openbel_published_index('20131211')
  }

  ::BEL::JSON.read(data, options).lazy.select { |obj|
    obj.include?(:nodes) && obj.include?(:edges)
  }.flat_map { |graph|
    unwrap(graph, default_resource_index)
  }
end

#write(objects, writer = StringIO.new, options = {}) ⇒ Object 



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# File 'lib/bel/translator/plugins/jgf/translator.rb', line 24

def write(objects, writer = StringIO.new, options = {})
  graph = {
    :type  => 'BEL-V1.0',
    :nodes => [],
    :edges => []
  }

  objects.each do |nanopub|
    unless nanopub.bel_statement.is_a?(::BEL::Nanopub::Statement)
      nanopub.bel_statement = ::BEL::Nanopub::Nanopub.parse_statement(nanopub)
    end

    stmt    = nanopub.bel_statement
    subject = stmt.subject.to_bel

    graph[:nodes] << {
      :id    => subject,
      :label => subject
    }

    if stmt.object
      object  = stmt.object.to_bel
      graph[:nodes] << {
        :id    => object,
        :label => object
      }
      graph[:edges] << {
        :source   => subject,
        :relation => stmt.relationship,
        :target   => object
      }
    end
  end
  graph[:nodes].uniq!

  ::BEL::JSON.write({:graph => graph}, writer, options)
  writer
end