module SimpleBioC

SimpleBioC main library

Constants

VERSION

Public Instance Methods

from_xml(file_path, options = {}) click to toggle source

parse a BioC XML file in the given path and convert it into a collection instance

Arguments ↑

  • file_path - file path for parse

  • options - (optional) additional options

Options ↑

  • documents - specify IDs of documents to parse. The result will include only the specified documents

Examples ↑

collection = SimpleBioC.from_xml("./xml/everything.xml")
collection = SimpleBioC.from_xml("./xml/lemma.xml", {documents:[21785578, 21488974]})
# File lib/simple_bioc.rb, line 22
def from_xml(file_path, options = {})
  options[:documents] = options[:documents].map{|e| e.to_s} if options[:documents].kind_of?(Array)
  BioCReader.read(file_path, options)
end
to_xml(collection, options = {}) click to toggle source

convert a collection instance to a BioC XML text. Output will return as string

Arguments ↑

  • collection - Collection instance to process

  • options - (optional) additional options

Options ↑

  • save_with - SaveOption for Nokorigi. If you set this 0, output has no format (no indentation, no whitespace)

Examples ↑

output = SimpleBioC.to_xml(collection)
output = SimpleBioC.to_xml(collection, {save_with: 0})
# File lib/simple_bioc.rb, line 39
def to_xml(collection, options = {})
  BioCWriter.write(collection, options)
end