Module: PubAnnWriter

Defined in:
lib/simple_bioc/pub_ann_writer.rb

Class Method Summary collapse

Class Method Details

.write(collection, options = {}) ⇒ Object 



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# File 'lib/simple_bioc/pub_ann_writer.rb', line 7

def write(collection, options = {})
  Jbuilder.new do |json|
    write_collection(json, collection, options)
  end.target!
end

.write_collection(json, collection, options) ⇒ Object 



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# File 'lib/simple_bioc/pub_ann_writer.rb', line 13

def write_collection(json, collection, options)
  json.array! collection.documents do |d|
    write_document(json, d, options)
  end
end

.write_document(json, document, options) ⇒ Object 



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# File 'lib/simple_bioc/pub_ann_writer.rb', line 19

def write_document(json, document, options)
  json.sourceid document.id
  json.sourcedb options[:sourcedb] || ""
  json.project options[:project] || ""
  json.target options[:target] || ""
  json.text document.all_texts
  json.denotations document.all_annotations do |a|
    a.locations.each do |l|
      json.span do 
        json.begin l.offset.to_i
        json.end l.offset.to_i + l.length.to_i
      end
      json.obj a.infons.map{|k,v| v}.join(",")
      json.id a.id unless a.id.nil?
    end
  end
  json.relations document.all_relations do |r|
    json.pred r.infons.map{|k,v| v}.join(",")
    first = true
    r.nodes.each do |n|
      if first 
        json.obj n.refid
        first = false
      else
        json.subj n.refid
      end
    end
    json.id r.id unless r.id.nil?
  end
end