module BioCReader

# File lib/simple_bioc/bioc_reader.rb, line 7
def read(path, options) 
  collection = nil
  File.open(path) do |file|
    collection = read_from_file_or_string(file, options)
  end

  collection
end

# File lib/simple_bioc/bioc_reader.rb, line 94
def read_annotation(xml, annotation, options = {}) 
  annotation.id = xml["id"]
  annotation.text = read_text(xml, "text")
  read_infon(xml, annotation)
  read_recursive(xml, annotation, "location")
  true
end

# File lib/simple_bioc/bioc_reader.rb, line 55
def read_collection(xml, collection, options = {})
  collection.source = read_text(xml, "source")
  collection.date = read_text(xml, "date")
  collection.key = read_text(xml, "key")
  read_infon(xml, collection)
  read_recursive(xml, collection, "document", options)
end

# File lib/simple_bioc/bioc_reader.rb, line 63
def read_document(xml, document, options = {})
  document.id = read_text(xml, "id")
  if options[:documents].kind_of?(Array) && !options[:documents].include?(document.id)
    return false
  end
  read_infon(xml, document)
  read_recursive(xml, document, "passage")
  read_recursive(xml, document, "relation")
  document.adjust_ref
  true
end

# File lib/simple_bioc/bioc_reader.rb, line 16
def read_from_file_or_string(file_or_string, options)
  collection = nil

  xml_doc  = Nokogiri::XML(file_or_string) do |config|
    config.noent.strict.noblanks
  end
  xml = xml_doc.at_xpath("//collection")
  if xml.nil?
    fail 'Wrong format'
  end
  collection = SimpleBioC::Collection.new
  read_collection(xml, collection, options)

  collection
end

# File lib/simple_bioc/bioc_reader.rb, line 42
def read_infon(xml, obj)
  xml.xpath("infon").each{ |i| obj.infons[i["key"]] = i.content}
end

# File lib/simple_bioc/bioc_reader.rb, line 37
def read_int(xml, name)
  val = read_text(xml, name) 
  val && val.to_i
end

# File lib/simple_bioc/bioc_reader.rb, line 109
def read_location(xml, location, options = {}) 
  location.offset = xml["offset"]
  location.length = xml["length"]
  true
end

# File lib/simple_bioc/bioc_reader.rb, line 115
def read_node(xml, node, options = {})
  node.refid = xml["refid"]
  node.role = xml["role"]
  true
end

# File lib/simple_bioc/bioc_reader.rb, line 75
def read_passage(xml, passage, options = {})
  passage.text = read_text(xml, "text")
  passage.offset = read_int(xml, "offset")
  read_infon(xml, passage)
  read_recursive(xml, passage, "sentence")
  read_recursive(xml, passage, "annotation")
  read_recursive(xml, passage, "relation")
  true
end

# File lib/simple_bioc/bioc_reader.rb, line 46
def read_recursive(xml, obj, name, options = {})
  target_class = SimpleBioC.const_get(name.capitalize)
  xml.xpath(name).each do |node|
    instance = target_class.new(obj)
    ret = send(:"read_#{name}", node, instance, options)
    obj.instance_variable_get(:"@#{name}s")  << instance if ret
  end
end

# File lib/simple_bioc/bioc_reader.rb, line 102
def read_relation(xml, relation, options = {}) 
  relation.id = xml["id"]
  read_infon(xml, relation)
  read_recursive(xml, relation, "node")
  true
end

# File lib/simple_bioc/bioc_reader.rb, line 85
def read_sentence(xml, sentence, options = {})
  sentence.text = read_text(xml, "text")
  sentence.offset = read_int(xml, "offset")
  read_infon(xml, sentence)
  read_recursive(xml, sentence, "annotation")
  read_recursive(xml, sentence, "relation")
  true
end

# File lib/simple_bioc/bioc_reader.rb, line 32
def read_text(xml, name)
  node = xml.at_xpath(name)
  node && node.content
end