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XML Integrity Checking
# frozen_string_literal: true
# https://gist.github.com/remomueller/c853734a2f85937b69b373c46760fcdd
# gem install xml-simple colorize --no-document
# ruby xml_testing.rb
# XML Integrity Checking
# I think checking through all XML for the following would be a good place to
# start on a list to check:
# 1. No scored events at all (<ScoredEvent> area essentially empty, save for
# staging data)
# 2. Arousal <3 seconds in duration (<ScoredEvent> with "Arousal" in <Name> and
# <Duration> less than 3 seconds)
# 3. Respiratory event <10 seconds in duration (<ScoredEvent> with "Apnea",
# "Hypopnea", or "Unsure" in <Name> and <Duration> less than 10 seconds)
# This could sort of work like "edfize" where it checks each individual file for
# any failures and then spits out a warning when it encounters an issue. For #2
# and #3 it might also be nice to have the start time of the event(s) flagged in
# the output to know where to look when inspecting the XML manually.
require "rubygems"
require "colorize"
require "json"
require "xmlsimple"
def extract(hash, key, convert: nil)
value = hash[key] && !hash[key][0].empty? ? hash[key][0] : nil
convert && value ? value.send(convert) : value
end
def starts_with?(search, word)
!(/^#{search}/i =~ word).nil?
end
def contains_word?(search, word)
!(/#{search}/i =~ word).nil?
end
good_count = 0
bad_count = 0
xmls = Dir.glob("**/*.xml", File::FNM_CASEFOLD)
xml_count = xmls.size
xmls.each_with_index do |xml_path, index|
print "\r#{index + 1} of #{xml_count} (#{(index + 1) * 100 / xml_count}%)"
xml = XmlSimple.xml_in(xml_path)
scored_events = \
if xml["ScoredEvents"].nil? || xml["ScoredEvents"][0].nil? || xml["ScoredEvents"][0]["ScoredEvent"].nil?
[]
else
xml["ScoredEvents"][0]["ScoredEvent"].collect do |hash|
{
name: extract(hash, "Name"),
lowest_spo2: extract(hash, "LowestSpO2", convert: :to_f),
desaturation: extract(hash, "Desaturation", convert: :to_f),
start: extract(hash, "Start", convert: :to_f),
duration: extract(hash, "Duration", convert: :to_f),
input: extract(hash, "Input")
}
end
end
arousal_events = scored_events.select do |event|
starts_with?("Arousal", event[:name]) && event[:duration] < 3
end
respiratory_events = scored_events.select do |event|
(
contains_word?("Apnea", event[:name]) ||
contains_word?("Hypopnea", event[:name]) ||
contains_word?("Unsure", event[:name])
) && event[:duration] < 10
end
if !scored_events.empty? && arousal_events.empty? && respiratory_events.empty?
good_count += 1
else
bad_count += 1
puts "\n#{xml_path}"
puts "Empty: No Scored Events" if scored_events.empty?
unless arousal_events.empty?
puts "Detected: Arousal Events <3 seconds"
puts " Start: #{arousal_events.collect { |event| event[:start] }.join(', ')}"
end
unless respiratory_events.empty?
puts "Detected: Respiratory Events <10 seconds"
puts " Start: #{respiratory_events.collect { |event| event[:start] }.join(', ')}"
end
puts "\n"
end
end
puts "\n" + good_count.to_s.colorize(good_count.positive? ? :green : nil) + " XML#{good_count == 1 ? ' ' : 's'} passed"
puts bad_count.to_s.colorize(bad_count.positive? ? :red : nil) + " XML#{bad_count == 1 ? ' ' : 's'} failed"
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