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
|
#!/usr/bin/env ruby
#
##
## @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.
## ------------------------------------------------------------------------ -->
##
##
require '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 initialize()
super
end
def clone
return MyCustomValidator.new
end
def validate
# if we don't have a model we don't apply this validator.
if (getDocument == nil or getModel == nil):
return 0;
end
# if we have no rules and reactions we don't apply this validator either
if (getModel.getNumReactions == 0 && getModel.getNumRules == 0):
return 0;
end
numErrors = 0;
# test for algebraic rules
getModel.getNumRules.times do |i|
if getModel.getRule(i).getTypeCode == LibSBML::SBML_ALGEBRAIC_RULE
getErrorLog.add(LibSBML::SBMLError.new(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 = numErrors + 1;
end
end
# test for fast reactions
getModel.getNumReactions.times do |i|
# test whether value is set, and true
if getModel.getReaction(i).isSetFast && getModel.getReaction(i).getFast
getErrorLog.add(LibSBML::SBMLError.new(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 = numErrors + 1;
end
end
return numErrors;
end
end
if ARGV.size != 1
puts "Usage: addCustomValidator filename"
puts ""
exit(1)
end
# read the file name
document = LibSBML::readSBML(ARGV[0])
# add a custom validator
document.addValidator(MyCustomValidator.new)
# check consistency like before
numErrors = document.checkConsistency
# print errors and warnings
document.printErrors
# return number of errors
exit(numErrors)
|
