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#!/usr/bin/env perl
# -*-Perl-*-
##
## @file addCustomValidator.pl
## @brief Example creating a custom validator to be called during 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.
## ------------------------------------------------------------------------ -->
##
## NOTE: This example is currently not working as SWIG does not allow for perl
## directos yet ... otherwise it would be working as described below.
##
use LibSBML;
no strict;
##
## Declares a custom validator to be called. This allows you to validate
## any aspect of an SBML Model that you want to be notified about. You could
## use this to notify your application that a model contains an unsupported
## feature of SBML (either as warning).
##
## In this example the validator will go through the model and test for the
## presence of 'fast' reactions and algebraic rules. If either is used a
## warning will be added to the error log.
##
{
package MyCustomValidator;
@ISA = (LibSBML::SBMLValidator);
sub new {
my $class = shift;
bless \$class => $class
}
sub clone {
return new MyCustomValidator()
}
sub validate{
my $self = shift;
# if we don't have a model we don't apply this validator.
if ($self->getDocument() == undef or $self->getModel() == undef) {
return 0;
}
# if we have no rules and reactions we don't apply this validator either
if ($self->getModel()->getNumReactions() == 0 and $self->getModel()->getNumRules() == 0) {
return 0;
}
$numErrors = 0;
# test for algebraic rules
for ($i=0; $i< $self->getModel()->getNumRules();$i++) {
if ($self->getModel()->getRule($i)->getTypeCode() == $LibSBML::SBML_ALGEBRAIC_RULE) {
$self->getErrorLog()->add(new LibSBML::SBMLError(99999, 3, 1,
"This model uses algebraic rules, however this application does not support them.",
0, 0,
$LibSBML::LIBSBML_SEV_WARNING, # or LIBSBML_SEV_ERROR if you want to stop
$LibSBML::LIBSBML_CAT_SBML # or whatever category you prefer
));
$numErrors = $numErrors + 1;
}
}
# test for fast reactions
for ($i=0; $i < $self->getModel()->getNumReactions(); $i++) {
# test whether value is set, and true
if ($self->getModel()->getReaction($i)->isSetFast() and $self->getModel()->getReaction($i)->getFast()) {
self.getErrorLog().add(new LibSBML::SBMLError(99999, 3, 1,
"This model uses fast reactions, however this application does not support them.",
0, 0,
$LibSBML::LIBSBML_SEV_WARNING, # or LIBSBML_SEV_ERROR if you want to stop
$LibSBML::LIBSBML_CAT_SBML # or whatever category you prefer
));
$numErrors = $numErrors + 1;
}
}
return numErrors;
}
}
if ($#ARGV != 0) {
print "Usage: addCustomValidator filename\n";
exit 1;
}
# read the file name
$document = LibSBML::readSBML($ARGV[0]);
# add a custom validator
$document->addValidator(new MyCustomValidator());
# check consistency like before
$numErrors = $document->checkConsistency();
# print errors and warnings
$document->printErrors();
# return number of errors
exit $numErrors;
|
