readSBML.py

A simple command-line program that reads an SBML file and prints some statistics about it.

#!/usr/bin/env python
##
## @file    readSBML.py
## @brief   Similar to validateSBML, but without the validation
## @author  Sarah Keating
## @author  Ben Bornstein
##
## <!--------------------------------------------------------------------------
## This sample program is distributed under a different license than the rest
## of libSBML.  This program uses the open-source MIT license, as follows:
##
## Copyright (c) 2013-2018 by the California Institute of Technology
## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
## and the University of Heidelberg (Germany), with support from the National
## Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
##
## Permission is hereby granted, free of charge, to any person obtaining a
## copy of this software and associated documentation files (the "Software"),
## to deal in the Software without restriction, including without limitation
## the rights to use, copy, modify, merge, publish, distribute, sublicense,
## and/or sell copies of the Software, and to permit persons to whom the
## Software is furnished to do so, subject to the following conditions:
##
## The above copyright notice and this permission notice shall be included in
## all copies or substantial portions of the Software.
##
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
## THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
## DEALINGS IN THE SOFTWARE.
##
## Neither the name of the California Institute of Technology (Caltech), nor
## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
## of Heidelberg, nor the names of any contributors, may be used to endorse
## or promote products derived from this software without specific prior
## written permission.
## ------------------------------------------------------------------------ -->

import sys
import time
import os
import os.path
from libsbml import *

def main (args):
  """Usage: readSBML filename
  """
  
  if len(args) != 2:
      print("Usage: readSBML filename")
      return 1

  filename = args[1]
  current = time.clock()
  document = readSBML(filename)

  errors = document.getNumErrors()

  print()
  print("            filename: " + filename)
  print("           file size: " + str(os.stat(filename).st_size))
  print("      read time (ms): " + str(time.clock() - current))
  print(" validation error(s): " + str(errors))
  print()
  document.printErrors()

  return errors


if __name__ == '__main__':
  main(sys.argv)