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#!/usr/bin/python3
##
## @file callExternalValidator.py
## @brief Example that shows how to call an external program for validation
## @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
from libsbml import *
def main (args):
"""Usage: callExternalValidator filename externalValidator [ tempSBMLFile outputFile [ ADDITIONAL-ARGS] ]
calls an external validator
"""
if len(args) < 3:
print(main.__doc__)
sys.exit(1)
filename = args[1]
# read additional args
externalValidator = args[2]
tempSBMLFileName = filename + "_temp.xml"
if len(args) > 3:
tempSBMLFileName = args[3]
outputFile = filename + "_out.xml"
if len(args) > 4:
outputFile = args[4]
additionalArgs = []
for i in range (5, len(args)):
additionalArgs += [args[i]]
# add the output file as additional arg
additionalArgs += [outputFile]
# read the file name
document = readSBML(filename)
# create a external validator that will write the model to
# tempFile, then call teh externalValidator with the given number of arguments
# to produce the output file. This output file will then be parsed and its
# errors will be added to the error log.
validator = SBMLExternalValidator()
validator.setProgram(externalValidator)
validator.setSBMLFileName(tempSBMLFileName)
validator.setOutputFileName(outputFile)
for item in additionalArgs:
validator.addArgument(item)
# this means that the external program will be called with the following arguments
#
# externalValidator tempSBMLFileName additionalArgs
#
# (where additionalArgs contains the output file as last argument)
#
# The output file that is generated should be an XML document following the
# Validator XML format as described here: http://sbml.org/validator/api/#xml
#
# disable all regular checks
document.setApplicableValidators(0)
# add a custom validator
document.addValidator(validator)
# check consistency like before
numErrors = document.checkConsistency()
# print errors and warnings
document.printErrors()
# return number of errors
return numErrors
if __name__ == '__main__':
main(sys.argv)
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