module BioCWriter

# File lib/simple_bioc/bioc_writer.rb, line 8
def write(collection, options = {})
  options[:save_with] = 1 if options[:save_with].nil?
  builder = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') do |xml|
    xml.doc.create_internal_subset( 'collection', nil, 'BioC.dtd' )
    write_collection(xml, collection)
  end
  builder.to_xml(options)
end

# File lib/simple_bioc/bioc_writer.rb, line 65
def write_annotation(xml, annotation) 
  if annotation.id.nil?
    attribute = nil
  else
    attribute = {id: annotation.id}
  end
  xml.annotation(attribute) {
    write_infon(xml, annotation)
    annotation.locations.each{|l| write_location(xml, l)}
    xml.text_ annotation.text
  }
end

# File lib/simple_bioc/bioc_writer.rb, line 25
def write_collection(xml, collection)
  xml.collection {
    xml.source collection.source
    xml.date collection.date
    xml.key collection.key
    write_infon(xml, collection)
    collection.documents.each{|d| write_document(xml, d)}
  }
end

# File lib/simple_bioc/bioc_writer.rb, line 35
def write_document(xml, document)
  xml.document {
    xml.id_ document.id
    write_infon(xml, document)
    document.passages.each{|p| write_passage(xml, p)}
    document.relations.each{|r| write_relation(xml, r)}
  }
end

# File lib/simple_bioc/bioc_writer.rb, line 17
def write_infon(xml, obj)
  obj.infons.each do |k, v| 
    xml.infon(:key => k) {
      xml.text v
    }
  end
end

# File lib/simple_bioc/bioc_writer.rb, line 90
def write_location(xml, location) 
  xml.location(:offset => location.offset, :length => location.length)
end

# File lib/simple_bioc/bioc_writer.rb, line 94
def write_node(xml, node)
  xml.node_(:refid => node.refid, :role => node.role)
end

# File lib/simple_bioc/bioc_writer.rb, line 44
def write_passage(xml, passage)
  xml.passage {
    write_infon(xml, passage)
    xml.offset passage.offset
    xml.text_ passage.text unless passage.text.nil?
    passage.annotations.each{|a| write_annotation(xml, a)}
    passage.sentences.each{|s| write_sentence(xml, s)}
    passage.relations.each{|r| write_relation(xml, r)}
  }
end

# File lib/simple_bioc/bioc_writer.rb, line 78
def write_relation(xml, relation) 
  if relation.id.nil?
    attribute = nil
  else
    attribute = {id: relation.id}
  end
  xml.relation(attribute) {
    write_infon(xml, relation)
    relation.nodes.each{|n| write_node(xml, n)}
  }
end

# File lib/simple_bioc/bioc_writer.rb, line 55
def write_sentence(xml, sentence)
  xml.sentence {
    write_infon(xml, sentence)
    xml.offset sentence.offset
    xml.text_ sentence.text unless sentence.text.nil?
    sentence.annotations.each{|a| write_annotation(xml, a)}
    sentence.relations.each{|r| write_relation(xml, r)}
  }
end