1#!/usr/bin/env perl
2# -*-Perl-*-
3##
4## \file    addingEvidenceCodes_1.pl
5## \brief   adds controlled vocabulary terms to a reaction in a model
6## \author  Sarah Keating
7##
8## <!--------------------------------------------------------------------------
9## This sample program is distributed under a different license than the rest
10## of libSBML.  This program uses the open-source MIT license, as follows:
11##
12## Copyright (c) 2013-2018 by the California Institute of Technology
13## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
14## and the University of Heidelberg (Germany), with support from the National
15## Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
16##
17## Permission is hereby granted, free of charge, to any person obtaining a
18## copy of this software and associated documentation files (the "Software"),
19## to deal in the Software without restriction, including without limitation
20## the rights to use, copy, modify, merge, publish, distribute, sublicense,
21## and/or sell copies of the Software, and to permit persons to whom the
22## Software is furnished to do so, subject to the following conditions:
23##
24## The above copyright notice and this permission notice shall be included in
25## all copies or substantial portions of the Software.
26##
27## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
28## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
29## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
30## THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
31## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
32## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
33## DEALINGS IN THE SOFTWARE.
34##
35## Neither the name of the California Institute of Technology (Caltech), nor
36## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
37## of Heidelberg, nor the names of any contributors, may be used to endorse
38## or promote products derived from this software without specific prior
39## written permission.
40## ------------------------------------------------------------------------ -->
41##
42
43
44use LibSBML;
45no strict;
46
47if ($#ARGV != 1) {
48  print "usage: addingEvidenceCodes_1 <input-filename> <output-filename>\n";
49  print "       Adds controlled vocabulary term to a reaction\n";
50  exit 2;
51}
52
53$d = LibSBML::readSBML($ARGV[0]);
54$errors = $d->getNumErrors();
55
56if ($errors > 0) {
57  print("Read Error(s):\n");
58  $d->printErrors();
59
60  print("Correct the above and re-run.\n");
61  exit $errors;
62}
63
64$n = $d->getModel()->getNumReactions();
65
66if ($n <= 0) {
67    print("Model has no reactions.\n Cannot add CV terms\n");
68    exit 0;
69}
70
71$r = $d->getModel()->getReaction(0);
72
73# check that the reaction has a metaid
74# no CVTerms will be added if there is no metaid to reference
75#
76if ( not $r->isSetMetaId()) {
77    $r->setMetaId("metaid_0000052");
78}
79
80$cv1 = new LibSBML::CVTerm($LibSBML::BIOLOGICAL_QUALIFIER);
81$cv1->setBiologicalQualifierType($LibSBML::BQB_IS_DESCRIBED_BY);
82$cv1->addResource("urn:miriam:obo.eco:ECO%3A0000183");
83
84$r->addCVTerm($cv1);
85
86$cv2 = new LibSBML::CVTerm($LibSBML::BIOLOGICAL_QUALIFIER);
87$cv2->setBiologicalQualifierType($LibSBML::BQB_IS);
88$cv2->addResource("urn:miriam:kegg.reaction:R00756");
89$cv2->addResource("urn:miriam:reactome:REACT_736");
90
91$r->addCVTerm($cv2);
92
93LibSBML::writeSBML($d, $ARGV[1]);
94exit $errors;
95
96