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#!/usr/bin/env perl
# -*-Perl-*-
##
## @file callExternalValidator.pl
## @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.
## ------------------------------------------------------------------------ -->
##
use File::Basename;
use LibSBML;
no strict;
if ($#ARGV < 1){
print "Usage: callExternalValidator filename externalValidator [ tempSBMLFile outputFile [ ADDITIONAL-ARGS] ]\n";
print "calls an external validator\n";
exit 1;
}
$filename = $ARGV[0];
# read additional args
$externalValidator = $ARGV[1];
$tempSBMLFileName = $filename . "_temp.xml";
if ($#ARGV > 1){
$tempSBMLFileName = $ARGV[2];
}
$outputFile = $filename. "_out.xml";
if ($#ARGV > 2) {
$outputFile = $ARGV[3];
}
@additionalArgs = ();
for ($i=4; $i < $#additionalArgs; $i++) {
push(@additionalArgs, $ARGV[i] );
}
# add the output file as additional arg
push(@additionalArgs, $outputFile );
print "Number of arguments: ", $#ARGV, "\n";
print "Name of external validator: ", $externalValidator, "\n";
print " file to validate: ", $filename, "\n";
print " temp file : ", $tempSBMLFileName, "\n";
print " out file : ", $outputFile, "\n";
# read the file name
$document = LibSBML::readSBML($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 = new LibSBML::SBMLExternalValidator();
$validator->setProgram($externalValidator);
$validator->setSBMLFileName($tempSBMLFileName);
$validator->setOutputFileName($outputFile);
for ($i = 0; $i < $#additionalArgs; $i++) {
$validator->addArgument($additionalArgs[$i]);
}
# 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
exit $numErrors;
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