check-omero-data

#!/usr/bin/env python
# -*- coding: utf-8 -*-

## Copyright (C) 2016 Carnë Draug
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 3 of the License, or
## (at your option) any later version.
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with this program; if not, see <http://www.gnu.org/licenses/>.

import os.path
import sys
import fileinput

import omero.util

def main(argv):
  """Check if omero data file exists.

  SYNOPSIS
    check-omero-data OMERO-DIR DATA-TYPE [FILES-IDS] [-]

  DESCRIPTION
    Prints back ids of missing files.
  """
  omero_dir = argv[1]
  if not os.path.isdir(omero_dir):
    sys.exit("confirm-data: OMERO-DIR '%s' is not a directory" % omero_dir)

  data_type = argv[2]
  data_dir = os.path.join(omero_dir, data_type)
  if not os.path.isdir(data_dir):
    sys.exit("confirm-data: OMERO-DIR/DATA-TYPE '%s' is not a directory"
              % data_dir)

  for id in fileinput.input(argv[3:]):
    id = id.strip()
    path = omero.util.long_to_path(long(id))
    path = os.path.join(data_dir, path)
    if not os.path.isfile(path):
      print id

  return 0

if __name__ == "__main__":
  sys.exit(main(sys.argv))