1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
|
/**
* @file convertSBML.c
* @brief Converts SBML documents between levels
* @author Ben Bornstein
* @author Michael Hucka
*
* <!--------------------------------------------------------------------------
* 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.
* ------------------------------------------------------------------------ -->
*/
#include <stdio.h>
#include <sbml/SBMLTypes.h>
int
main (int argc, char *argv[])
{
unsigned int latestLevel = SBMLDocument_getDefaultLevel();
unsigned int latestVersion = SBMLDocument_getDefaultVersion();
unsigned int errors;
SBMLDocument_t *d;
if (argc != 3)
{
printf("Usage: convertSBML input-filename output-filename\n");
printf("This program will attempt to convert a model either to\n");
printf("SBML Level %d Version %d (if the model is not already) or, if",
latestLevel, latestVersion);
printf("the model is already expressed in Level %d Version %d, this\n",
latestLevel, latestVersion);
printf("program will attempt to convert the model to Level 1 Version 2.\n");
return 1;
}
d = readSBML(argv[1]);
errors = SBMLDocument_getNumErrors(d);
if (errors > 0)
{
printf("Encountered the following SBML error(s):\n");
SBMLDocument_printErrors(d, stdout);
printf("Conversion skipped. Please correct the problems above first.\n");
return errors;
}
else
{
unsigned int olevel = SBMLDocument_getLevel(d);
unsigned int oversion = SBMLDocument_getVersion(d);
int success;
if (olevel < latestLevel || oversion < latestVersion)
{
printf("Attempting to convert model to SBML Level %d Version %d.\n",
latestLevel, latestVersion);
success = SBMLDocument_setLevelAndVersion(d, latestLevel, latestVersion);
}
else
{
printf("Attempting to convert model to SBML Level 1 Version 2.\n");
success = SBMLDocument_setLevelAndVersion(d, 1, 2);
}
errors = SBMLDocument_getNumErrors(d);
if (!success)
{
printf("Unable to perform conversion due to the following:\n");
SBMLDocument_printErrors(d, stdout);
printf("Conversion skipped. Either libSBML does not (yet) have\n");
printf("ability to convert this model, or (automatic) conversion\n");
printf("is not possible in this case.\n");
return errors;
}
if (errors > 0)
{
printf("Information may have been lost in conversion; but a valid model ");
printf("was produced by the conversion.\nThe following information ");
printf("was provided:\n");
SBMLDocument_printErrors(d, stdout);
writeSBML(d, argv[2]);
}
else
{
printf("Conversion completed.\n");
writeSBML(d, argv[2]);
}
}
SBMLDocument_free(d);
return 0;
}
|
