echoSBML.py

Echos (and in the process, pretty prints) an SBML model.

#!/usr/bin/env python
##
## @file    echoSBML.py
## @brief   Echos an SBML model.
## @author  Akiya Jouraku (translated from libSBML C++ examples)
## @author  Ben Bornstein
## @author  Michael Hucka
## 
##
## <!--------------------------------------------------------------------------
## 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 os.path
import libsbml

def main (args):
  """usage: echoSBML.py input-filename output-filename
  """
  if len(args) != 3:
    print(main.__doc__)
    sys.exit(1)

  infile  = args[1]
  outfile = args[2]

  if not os.path.exists(infile):
    print("[Error] %s : No such file." % infile)
    sys.exit(1)

  reader  = libsbml.SBMLReader()
  writer  = libsbml.SBMLWriter()
  sbmldoc = reader.readSBML(infile)

  if sbmldoc.getNumErrors() > 0:
    if sbmldoc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
      # Handle case of unreadable file here.
      sbmldoc.printErrors()
    elif sbmldoc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
      # Handle case of other file error here.
      sbmldoc.printErrors()
    else:
      # Handle other error cases here.
      sbmldoc.printErrors()

    sys.exit(1)
    
  writer.writeSBML(sbmldoc, outfile)
  print("[OK] Echoed %s to %s" % (infile, outfile))

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