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
127
128
129
|
#!/usr/bin/env python
##
## @file addCustomValidator.py
## @brief Example creating a custom validator to be called during validation
## @author Frank T. Bergmann
##
## <!--------------------------------------------------------------------------
## 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.
## ------------------------------------------------------------------------ -->
import sys
import os.path
import libsbml
##
## Declares a custom validator to be called. This allows you to validate
## any aspect of an SBML Model that you want to be notified about. You could
## use this to notify your application that a model contains an unsupported
## feature of SBML (either as warning).
##
## In this example the validator will go through the model and test for the
## presence of 'fast' reactions and algebraic rules. If either is used a
## warning will be added to the error log.
##
class MyCustomValidator(libsbml.SBMLValidator):
def __init__(self, orig=None):
if orig is None:
super(MyCustomValidator, self).__init__()
else:
super(MyCustomValidator, self).__init__(orig)
def clone(self):
return MyCustomValidator(self)
def validate(self):
# if we don't have a model we don't apply this validator.
if self.getDocument() is None or self.getModel() is None:
return 0
# if we have no rules and reactions we don't apply this validator either
if self.getModel().getNumReactions() == 0 and self.getModel().getNumRules() == 0:
return 0
numErrors = 0
# test for algebraic rules
for i in range(0, self.getModel().getNumRules()):
if self.getModel().getRule(i).getTypeCode() == libsbml.SBML_ALGEBRAIC_RULE:
self.getErrorLog().add(SBMLError(99999, 3, 1,
"This model uses algebraic rules, however this application does not support them.",
0, 0,
libsbml.LIBSBML_SEV_WARNING,
# or LIBSBML_SEV_ERROR if you want to stop
libsbml.LIBSBML_CAT_SBML # or whatever category you prefer
))
numErrors += 1
# test for fast reactions
for i in range(0, self.getModel().getNumReactions()):
# test whether value is set, and true
if (self.getModel().getReaction(i).isSetFast() and
self.getModel().getReaction(i).getFast()):
self.getErrorLog().add(SBMLError(99999, 3, 1,
"This model uses fast reactions, however this application does not support them.",
0, 0,
libsbml.LIBSBML_SEV_WARNING,
# or LIBSBML_SEV_ERROR if you want to stop
libsbml.LIBSBML_CAT_SBML # or whatever category you prefer
))
numErrors += 1
return numErrors
def main(args):
"""Usage: addCustomValidator filename
"""
if len(args) != 2:
print(main.__doc__)
sys.exit(1)
# read the file name
document = libsbml.readSBML(args[1])
# add a custom validator
document.addValidator(MyCustomValidator())
# check consistency like before
numErrors = document.checkConsistency()
# print errors and warnings
document.printErrors()
# return number of errors
return numErrors
if __name__ == '__main__':
main(sys.argv)
|
