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
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
|
#!/usr/bin/python3
##
## @file validateSBML.py
## @brief Validates one or more SBML files
## @author Akiya Jouraku (translated from libSBML C++ examples)
## @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.
## ------------------------------------------------------------------------ -->
import sys
import os.path
import time
import libsbml
class validateSBML:
def __init__(self, ucheck):
self.reader = libsbml.SBMLReader()
self.ucheck = ucheck
self.numinvalid = 0
def validate(self, file):
if not os.path.exists(file):
print("[Error] %s : No such file." % infile)
self.numinvalid += 1
return
start = time.time()
sbmlDoc = libsbml.readSBML(file)
stop = time.time()
timeRead = (stop - start)*1000
errors = sbmlDoc.getNumErrors()
seriousErrors = False
numReadErr = 0
numReadWarn = 0
errMsgRead = ""
if errors > 0:
for i in range(errors):
severity = sbmlDoc.getError(i).getSeverity()
if (severity == libsbml.LIBSBML_SEV_ERROR) or (severity == libsbml.LIBSBML_SEV_FATAL):
seriousErrors = True
numReadErr += 1
else:
numReadWarn += 1
errMsgRead = sbmlDoc.getErrorLog().toString()
# If serious errors are encountered while reading an SBML document, it
# does not make sense to go on and do full consistency checking because
# the model may be nonsense in the first place.
numCCErr = 0
numCCWarn = 0
errMsgCC = ""
skipCC = False
timeCC = 0.0
if seriousErrors:
skipCC = True
errMsgRead += "Further consistency checking and validation aborted."
self.numinvalid += 1
else:
sbmlDoc.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, self.ucheck)
start = time.time()
failures = sbmlDoc.checkConsistency()
stop = time.time()
timeCC = (stop - start)*1000
if failures > 0:
isinvalid = False
for i in range(failures):
severity = sbmlDoc.getError(i).getSeverity()
if (severity == libsbml.LIBSBML_SEV_ERROR) or (severity == libsbml.LIBSBML_SEV_FATAL):
numCCErr += 1
isinvalid = True
else:
numCCWarn += 1
if isinvalid:
self.numinvalid += 1
errMsgCC = sbmlDoc.getErrorLog().toString()
#
# print results
#
print(" filename : %s" % file)
print(" file size (byte) : %d" % (os.path.getsize(file)))
print(" read time (ms) : %f" % timeRead)
if not skipCC :
print( " c-check time (ms) : %f" % timeCC)
else:
print( " c-check time (ms) : skipped")
print( " validation error(s) : %d" % (numReadErr + numCCErr))
if not skipCC :
print( " (consistency error(s)): %d" % numCCErr)
else:
print( " (consistency error(s)): skipped")
print( " validation warning(s) : %d" % (numReadWarn + numCCWarn))
if not skipCC :
print( " (consistency warning(s)): %d" % numCCWarn)
else:
print( " (consistency warning(s)): skipped")
if errMsgRead or errMsgCC:
print()
print( "===== validation error/warning messages =====\n")
if errMsgRead :
print( errMsgRead)
if errMsgCC :
print( "*** consistency check ***\n")
print( errMsgCC)
def main (args):
"""usage: validateSBML.py [-u] inputfile1 [inputfile2 ...]
-u skips unit consistency check
"""
if len(args) < 2:
print( main.__doc__)
sys.exit(1)
elif (len(args) == 1) and (args[1] == "-u"):
print( main.__doc__)
sys.exit(1)
enableUnitCCheck = True
if args[1] == "-u":
enableUnitCCheck = False
validator = validateSBML(enableUnitCCheck)
fnum = 0
for i in range(1,len(args)):
if args[i] == "-u":
continue
print( "---------------------------------------------------------------------------")
validator.validate(args[i])
fnum += 1
numinvalid = validator.numinvalid
print( "---------------------------------------------------------------------------")
print( "Validated %d files, %d valid files, %d invalid files" % (fnum, fnum - numinvalid, numinvalid))
if not enableUnitCCheck:
print( "(Unit consistency checks skipped)")
if numinvalid > 0:
sys.exit(1)
if __name__ == '__main__':
main(sys.argv)
|
