module SimpleBioC
SimpleBioC
main library
Constants
- VERSION
Public Instance Methods
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 23 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
parse a BioC XML file and convert it into a collection instance
Arguments¶ ↑
-
file_path
- file object for parse -
options
- (optional) additional options
Options¶ ↑
-
documents
- specify IDs of documents to parse. The result will include only the specified documents
Examples¶ ↑
file = File.open(path) collection = SimpleBioC.from_xml(file) collection = SimpleBioC.from_xml(file, {documents:[21785578, 21488974]})
# File lib/simple_bioc.rb, line 41 def from_xml_file(file, options = {}) options[:documents] = options[:documents].map{|e| e.to_s} if options[:documents].kind_of?(Array) BioCReader.read_from_file_or_string(file, options) end
parse a BioC XML string and convert it into a collection instance
Arguments¶ ↑
-
string
- xml string (text) for parse -
options
- (optional) additional options
Options¶ ↑
-
documents
- specify IDs of documents to parse. The result will include only the specified documents
Examples¶ ↑
content = "<?xml version=\"1.0\" encoding=\"UTF-8\"?> ..." collection = SimpleBioC.from_xml(content) collection = SimpleBioC.from_xml(content, {documents:[21785578, 21488974]})
# File lib/simple_bioc.rb, line 59 def from_xml_string(string, options = {}) options[:documents] = options[:documents].map{|e| e.to_s} if options[:documents].kind_of?(Array) BioCReader.read_from_file_or_string(string, options) end
# File lib/simple_bioc.rb, line 85 def to_pubann(collection, options = {}) PubAnnWriter.write(collection, options) end
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 81 def to_xml(collection, options = {}) BioCWriter.write(collection, options) end