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#!/usr/bin/python3
##
## @file stripPackage.py
## @brief Strips the given package from the given SBML file.
## @author Frank T. Bergmann
##
## <!--------------------------------------------------------------------------
## 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: stripPackage.py input-filename package-to-strip output-filename
"""
if len(args) != 4:
print(main.__doc__)
sys.exit(1)
infile = args[1]
package = args[2]
outfile = args[3]
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)
props = libsbml.ConversionProperties()
props.addOption("stripPackage", True, "Strip SBML Level 3 package constructs from the model")
props.addOption("package", package, "Name of the SBML Level 3 package to be stripped")
if sbmldoc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS:
print("[Error] Conversion failed...")
sys.exit(1)
writer.writeSBML(sbmldoc, outfile)
print("[OK] stripped package '%s' from %s to %s" % (package, infile, outfile))
if __name__ == '__main__':
main(sys.argv)
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