1#!/usr/bin/env perl
2# -*-Perl-*-
3##
4## @file    addCustomValidator.pl
5## @brief   Example creating a custom validator to be called during validation
6## @author  Frank T. Bergmann
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## NOTE: This example is currently not working as SWIG does not allow for perl
43##       directos yet ... otherwise it would be working as described below.
44##
45
46use LibSBML;
47no strict;
48##
49## Declares a custom validator to be called. This allows you to validate
50## any aspect of an SBML Model that you want to be notified about. You could
51## use this to notify your application that a model contains an unsupported
52## feature of SBML (either as warning).
53##
54## In this example the validator will go through the model and test for the
55## presence of 'fast' reactions and algebraic rules. If either is used a
56## warning will be added to the error log.
57##
58{
59package MyCustomValidator;
60   @ISA = (LibSBML::SBMLValidator);
61   sub new {
62     my $class = shift;
63     bless \$class => $class
64   }
65   sub clone {
66     return new MyCustomValidator()
67   }
68   sub validate{
69     my $self = shift;
70     # if we don't have a model we don't apply this validator.
71     if ($self->getDocument() == undef or $self->getModel() == undef) {
72          return 0;
73     }
74
75     # if we have no rules and reactions we don't apply this validator either
76     if ($self->getModel()->getNumReactions() == 0 and $self->getModel()->getNumRules() == 0) {
77          return 0;
78     }
79
80     $numErrors = 0;
81     # test for algebraic rules
82     for ($i=0; $i< $self->getModel()->getNumRules();$i++) {
83          if ($self->getModel()->getRule($i)->getTypeCode() == $LibSBML::SBML_ALGEBRAIC_RULE) {
84               $self->getErrorLog()->add(new LibSBML::SBMLError(99999, 3, 1,
85                  "This model uses algebraic rules, however this application does not support them.",
86                  0, 0,
87                  $LibSBML::LIBSBML_SEV_WARNING, # or LIBSBML_SEV_ERROR if you want to stop
88                  $LibSBML::LIBSBML_CAT_SBML # or whatever category you prefer
89                  ));
90                $numErrors = $numErrors + 1;
91	  }
92     }
93
94     # test for fast reactions
95     for ($i=0; $i < $self->getModel()->getNumReactions(); $i++) {
96         # test whether value is set, and true
97	 if ($self->getModel()->getReaction($i)->isSetFast() and  $self->getModel()->getReaction($i)->getFast()) {
98             self.getErrorLog().add(new LibSBML::SBMLError(99999, 3, 1,
99                  "This model uses fast reactions, however this application does not support them.",
100                  0, 0,
101                  $LibSBML::LIBSBML_SEV_WARNING, # or LIBSBML_SEV_ERROR if you want to stop
102                  $LibSBML::LIBSBML_CAT_SBML # or whatever category you prefer
103                  ));
104              $numErrors = $numErrors + 1;
105         }
106     }
107     return numErrors;
108   }
109}
110
111if ($#ARGV != 0) {
112  print "Usage: addCustomValidator filename\n";
113  exit 1;
114}
115
116
117# read the file name
118$document = LibSBML::readSBML($ARGV[0]);
119
120# add a custom validator
121$document->addValidator(new MyCustomValidator());
122
123# check consistency like before
124$numErrors = $document->checkConsistency();
125
126# print errors and warnings
127$document->printErrors();
128
129# return number of errors
130exit $numErrors;
131
132