Verify Checksums in a FDA eCTD Submission

ectdmd5.rb

#!/usr/bin/env ruby
#
# Expects path to the root folder of the submission sequence to be passed as param 1
#
# ectdmd5.rb (PATH)
#


args = ARGV.dup
ARGV.clear
path = args.shift.strip rescue 'help'
puts "Checking all Leafs of Submission #{path}"

require 'nokogiri'
require 'digest/md5'

files_to_check = Dir["#{path}/**/*.xml"]
count_failed_files = 0
files_to_check.each do |file|
  f = File.open(file)
  
  save_flag = false
  doc = Nokogiri::XML(f)
  leafs =  doc.css('leaf')
  
  leafs.each do |leaf|
    leaf_href_full_path = "#{File.dirname(file)}/#{leaf.attribute('href')}"
    calculated_checksum = Digest::MD5.hexdigest(File.read(leaf_href_full_path))
    leaf_checksum = leaf.attribute("checksum")
    
    if calculated_checksum.to_s.chomp != leaf_checksum.to_s.chomp
      save_flag = true
      count_failed_files += 1
      leaf['checksum'] = calculated_checksum
      puts "md5 mismatch #{calculated_checksum} !=  #{leaf_checksum}   for file #{leaf.attribute('href')}"
    end
  end
  
  if save_flag  
    puts ARGV 
    puts "Checkusm Errors Found in #{file}.   Would you like us to update them (Y/n)?"
    user_confirm = $stdin.gets.chomp
    if user_confirm == "Y"
      puts "updating bad checksums in #{file}"
      File.open(file, 'w') {|f| f.write(doc.to_xml) }
    end
    user_confirm = nil
  end
  
  f.close
end

index_calculated_checksum = Digest::MD5.file("#{path}/index.xml")
index_checksum = File.read("#{path}/index-md5.txt")

if index_calculated_checksum != index_checksum
  count_failed_files += 1
  puts "index.xml md5 mismatch. Would you like us to update them (Y/n)?"
  user_confirm = $stdin.gets.chomp
  if user_confirm == "Y"
    puts "updating bad checksums in #{path}/index-md5.txt"
    File.open("#{path}/index-md5.txt", 'w') {|f| f.write(index_calculated_checksum) }
  end
end

puts "#{count_failed_files} bad checksums"