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
|
#!/usr/bin/python3
##
## @file flattenModel.py
## @brief Flattens the comp code from the given SBML file.
## @author Frank T. Bergmann
## @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, getopt, os.path
from libsbml import *
# Utility function to make it easier to check the return values from
# libSBML calls.
def check(value, message):
"""If 'value' is None, prints an error message constructed using
'message' and then exits with status code 1. If 'value' is an integer,
it assumes it is a libSBML return status code. If the code value is
LIBSBML_OPERATION_SUCCESS, returns without further action; if it is not,
prints an error message constructed using 'message' along with text from
libSBML explaining the meaning of the code, and exits with status code 1.
"""
if value is None:
raise SystemExit('LibSBML returned a null value trying to ' + message + '.')
elif type(value) is int:
if value == LIBSBML_OPERATION_SUCCESS:
return
else:
err_msg = 'Error encountered trying to ' + message + '.' \
+ 'LibSBML returned error code ' + str(value) + ': "' \
+ OperationReturnValue_toString(value).strip() + '"'
raise SystemExit(err_msg)
else:
return
# The actual program.
def main (argv):
"""Usage: flattenModel.py [-p] MODEL_FILE OUTPUT_FILE
Arguments:
-p (Optional) list unused ports
"""
# Before we begin, check that this copy of libSBML has the 'comp' package
# extension compiled in.
if not SBMLExtensionRegistry.isPackageEnabled("comp"):
err_msg = 'This copy of libSBML does not contain the "comp" extension.' \
+ 'Unable to proceed with flattening the model.'
raise SystemExit(err_msg)
# Read and verify command line arguments.
try:
opts, args = getopt.getopt(argv[1:], "p")
except:
raise SystemExit(main.__doc__)
if len(args) < 2:
raise SystemExit(main.__doc__)
leave_ports = '-p' in opts
input_file = args[0]
output_file = args[1]
if not os.path.exists(input_file):
raise SystemExit('%s : No such file.' % input_file)
# Read the SBML input file.
reader = SBMLReader()
check(reader, 'create an SBMLReader object.')
sbmldoc = reader.readSBML(input_file)
check(sbmldoc, 'create an SBMLDocument object from file input')
if sbmldoc.getNumErrors() > 0:
if sbmldoc.getError(0).getErrorId() == XMLFileUnreadable:
# Handle case of unreadable file here.
sbmldoc.printErrors()
elif sbmldoc.getError(0).getErrorId() == XMLFileOperationError:
# Handle case of other file error here.
sbmldoc.printErrors()
else:
# Handle other error cases here.
sbmldoc.printErrors()
raise SystemExit(2)
# Create the converter options
props = ConversionProperties()
props.addOption("flatten comp", True) # Invokes CompFlatteningConverter
props.addOption("leave_ports", leave_ports) # Indicates whether to leave ports
# Do the conversion.
result = sbmldoc.convert(props)
if result != LIBSBML_OPERATION_SUCCESS:
sbmldoc.printErrors()
raise SystemExit("Conversion failed... ("+ str(result) + ")")
# Write the results to the output file.
writer = SBMLWriter()
check(writer, 'create an SBMLWriter object.')
writer.writeSBML(sbmldoc, output_file)
print("Flattened model written to %s" % output_file)
if __name__ == '__main__':
main(sys.argv)
|
