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#!/usr/bin/python3
##
## @file convertSBML.py
## @brief Converts SBML documents between levels
## @author Michael Hucka
## @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 os.path
from libsbml import *
def main (args):
"""Usage: convertSBML input-filename output-filename
This program will attempt to convert a model either to
SBML Level 3 Version 1 (if the model is not already) or, if
the model is already expressed in Level 3 Version 1, this
program will attempt to convert the model to Level 1 Version 2.
"""
latestLevel = SBMLDocument.getDefaultLevel()
latestVersion = SBMLDocument.getDefaultVersion()
if len(args) != 3:
print(main.__doc__)
sys.exit(1)
inputFile = args[1]
outputFile = args[2]
document = readSBML(inputFile)
errors = document.getNumErrors()
if errors > 0:
print("Encountered the following SBML errors:" + "\n")
document.printErrors()
print("Conversion skipped. Please correct the problems above first."
+ "\n")
return errors
#
# If the given model is not already L2v4, assume that the user wants to
# convert it to the latest release of SBML (which is L2v4 currently).
# If the model is already L2v4, assume that the user wants to attempt to
# convert it down to Level 1 (specifically L1v2).
#
olevel = document.getLevel()
oversion = document.getVersion()
success = False
if olevel < latestLevel or oversion < latestVersion:
print ("Attempting to convert Level " + str(olevel) + " Version " + str(oversion)
+ " model to Level " + str(latestLevel)
+ " Version " + str(latestVersion) + "." + "\n")
success = document.setLevelAndVersion(latestLevel, latestVersion)
else:
print ("Attempting to convert Level " + str(olevel) + " Version " + str(oversion)
+ " model to Level 1 Version 2." + "\n")
success = document.setLevelAndVersion(1, 2)
errors = document.getNumErrors()
if not success:
print("Unable to perform conversion due to the following:" + "\n")
document.printErrors()
print("\n")
print("Conversion skipped. Either libSBML does not (yet)" + "\n"
+ "have the ability to convert this model or (automatic)" + "\n"
+ "conversion is not possible in this case." + "\n")
return errors
elif errors > 0:
print("Information may have been lost in conversion; but a valid model ")
print("was produced by the conversion.\nThe following information ")
print("was provided:\n")
document.printErrors()
writeSBML(document, outputFile)
else:
print("Conversion completed." + "\n")
writeSBML(document, outputFile)
return 0
if __name__ == '__main__':
main(sys.argv)
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