Class: BEL::Extension::Format::FormatJGF

Inherits:
Object
  • Object
show all
Includes:
Formatter
Defined in:
lib/bel/extensions/jgf.rb

Constant Summary collapse

ID = 
:jgf
MEDIA_TYPES = 
%i(application/vnd.jgf+json)
EXTENSIONS = 
%i(jgf.json)
ResourceIndex = 
::BEL::Namespace::ResourceIndex

Instance Method Summary collapse

Methods included from Formatter

#evidence_hash

Constructor Details

#initialize ⇒ FormatJGF

Returns a new instance of FormatJGF.



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# File 'lib/bel/extensions/jgf.rb', line 14

def initialize
  json_module = load_implementation_module!
  @json_reader = json_module::JSONReader
  @json_writer = json_module::JSONWriter
end

Instance Method Details

#deserialize(data, options = {}, &block) ⇒ Object 



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# File 'lib/bel/extensions/jgf.rb', line 32

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

  @json_reader.new(data).each.lazy.select { |obj|
    obj.include?(:nodes) && obj.include?(:edges)
  }.flat_map { |graph|
    unwrap(graph, default_resource_index)
  }
end

#file_extensions ⇒ Object 



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# File 'lib/bel/extensions/jgf.rb', line 28

def file_extensions
  EXTENSIONS
end

#id ⇒ Object 



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# File 'lib/bel/extensions/jgf.rb', line 20

def id
  ID
end

#media_types ⇒ Object 



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

def media_types
  MEDIA_TYPES
end

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



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# File 'lib/bel/extensions/jgf.rb', line 44

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

  objects.each do |evidence|
    stmt    = evidence.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!

  json_writer = @json_writer.new
  writer     << json_writer.write_json_object(
    {
      :graph => graph
    }
  )
  writer
end