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#!/usr/bin/env perl
# -*-Perl-*-
##
## \file addingEvidenceCodes_1.pl
## \brief adds controlled vocabulary terms to a reaction in a model
## \author Sarah Keating
##
## <!--------------------------------------------------------------------------
## 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 LibSBML;
no strict;
if ($#ARGV != 1) {
print "usage: addingEvidenceCodes_1 <input-filename> <output-filename>\n";
print " Adds controlled vocabulary term to a reaction\n";
exit 2;
}
$d = LibSBML::readSBML($ARGV[0]);
$errors = $d->getNumErrors();
if ($errors > 0) {
print("Read Error(s):\n");
$d->printErrors();
print("Correct the above and re-run.\n");
exit $errors;
}
$n = $d->getModel()->getNumReactions();
if ($n <= 0) {
print("Model has no reactions.\n Cannot add CV terms\n");
exit 0;
}
$r = $d->getModel()->getReaction(0);
# check that the reaction has a metaid
# no CVTerms will be added if there is no metaid to reference
#
if ( not $r->isSetMetaId()) {
$r->setMetaId("metaid_0000052");
}
$cv1 = new LibSBML::CVTerm($LibSBML::BIOLOGICAL_QUALIFIER);
$cv1->setBiologicalQualifierType($LibSBML::BQB_IS_DESCRIBED_BY);
$cv1->addResource("urn:miriam:obo.eco:ECO%3A0000183");
$r->addCVTerm($cv1);
$cv2 = new LibSBML::CVTerm($LibSBML::BIOLOGICAL_QUALIFIER);
$cv2->setBiologicalQualifierType($LibSBML::BQB_IS);
$cv2->addResource("urn:miriam:kegg.reaction:R00756");
$cv2->addResource("urn:miriam:reactome:REACT_736");
$r->addCVTerm($cv2);
LibSBML::writeSBML($d, $ARGV[1]);
exit $errors;
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