1#!/usr/bin/env perl
2# -*-Perl-*-
3##
4## @file    promoteParameters.pl
5## @brief   promotes all local to global paramters
6## @author  Frank T. Bergmann
7##
8##
9## <!--------------------------------------------------------------------------
10## This sample program is distributed under a different license than the rest
11## of libSBML.  This program uses the open-source MIT license, as follows:
12##
13## Copyright (c) 2013-2018 by the California Institute of Technology
14## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
15## and the University of Heidelberg (Germany), with support from the National
16## Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
17##
18## Permission is hereby granted, free of charge, to any person obtaining a
19## copy of this software and associated documentation files (the "Software"),
20## to deal in the Software without restriction, including without limitation
21## the rights to use, copy, modify, merge, publish, distribute, sublicense,
22## and/or sell copies of the Software, and to permit persons to whom the
23## Software is furnished to do so, subject to the following conditions:
24##
25## The above copyright notice and this permission notice shall be included in
26## all copies or substantial portions of the Software.
27##
28## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
29## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
30## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
31## THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
32## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
33## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
34## DEALINGS IN THE SOFTWARE.
35##
36## Neither the name of the California Institute of Technology (Caltech), nor
37## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
38## of Heidelberg, nor the names of any contributors, may be used to endorse
39## or promote products derived from this software without specific prior
40## written permission.
41## ------------------------------------------------------------------------ -->
42
43use File::Basename;
44use LibSBML;
45no strict;
46
47if ($#ARGV != 1) {
48   print  "usage: promoteParameters.pl input-filename output-filename\n";
49   exit 1;
50}
51
52$infile  = $ARGV[0];
53$outfile = $ARGV[1];
54
55unless (-e $infile) {
56  print("[Error] ", $infile, ": No such file.", "\n");
57  exit 1;
58}
59$reader  = new LibSBML::SBMLReader();
60$writer  = new LibSBML::SBMLWriter();
61$sbmldoc = $reader->readSBML($infile);
62
63if ($sbmldoc->getNumErrors() > 0) {
64  if ($sbmldoc->getError(0)->getErrorId() == $LibSBML::XMLFileUnreadable) {
65    # Handle case of unreadable file here.
66    $sbmldoc->printErrors();
67  }
68  elsif ($sbmldoc->getError(0)->getErrorId() == $LibSBML::XMLFileOperationError) {
69    # Handle case of other file error here.
70    $sbmldoc->printErrors();
71  }
72  else {
73    # Handle other error cases here.
74    $sbmldoc->printErrors();
75  }
76  exit 1;
77}
78$props = new LibSBML::ConversionProperties();
79$props->addOption("promoteLocalParameters", true, "Promotes all Local Parameters to Global ones");
80if ($sbmldoc->convert($props) != $LibSBML::LIBSBML_OPERATION_SUCCESS)
81{
82  print("[Error] Conversion failed.", "\n");
83  exit 3;
84}
85$writer->writeSBML($sbmldoc, $outfile);
86print("[OK] done, wrote ", $outfile, "\n");
87
88