libSBML Python API  5.11.0
unsetNotes.py

Unsets the notes for each element in the given SBML file.

1 #!/usr/bin/env python
2 ##
3 ## @file unsetNotes.py
4 ## @brief unset notes for each element
5 ## @author Akiya Jouraku
6 ##
7 ## <!--------------------------------------------------------------------------
8 ## This sample program is distributed under a different license than the rest
9 ## of libSBML. This program uses the open-source MIT license, as follows:
10 ##
11 ## Copyright (c) 2013-2014 by the California Institute of Technology
12 ## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
13 ## and the University of Heidelberg (Germany), with support from the National
14 ## Institutes of Health (USA) under grant R01GM070923. All rights reserved.
15 ##
16 ## Permission is hereby granted, free of charge, to any person obtaining a
17 ## copy of this software and associated documentation files (the "Software"),
18 ## to deal in the Software without restriction, including without limitation
19 ## the rights to use, copy, modify, merge, publish, distribute, sublicense,
20 ## and/or sell copies of the Software, and to permit persons to whom the
21 ## Software is furnished to do so, subject to the following conditions:
22 ##
23 ## The above copyright notice and this permission notice shall be included in
24 ## all copies or substantial portions of the Software.
25 ##
26 ## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
27 ## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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30 ## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
31 ## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
32 ## DEALINGS IN THE SOFTWARE.
33 ##
34 ## Neither the name of the California Institute of Technology (Caltech), nor
35 ## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
36 ## of Heidelberg, nor the names of any contributors, may be used to endorse
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39 ## ------------------------------------------------------------------------ -->
40 
41 import sys
42 import time
43 import os
44 import os.path
45 from libsbml import *
46 
47 def main (args):
48  """Usage: unsetNotes <input-filename> <output-filename>
49  """
50  if (len(args) != 3):
51  print("\n" + "Usage: unsetNotes <input-filename> <output-filename>" + "\n" + "\n");
52  return 1;
53 
54  filename = args[1];
55 
56  document = readSBML(filename);
57 
58 
59  errors = document.getNumErrors();
60 
61  if (errors > 0):
62  document.printErrors();
63  return errors;
64 
65  m = document.getModel();
66  m.unsetNotes();
67 
68  for i in range(0, m.getNumReactions()):
69  re = m.getReaction(i);
70  re.unsetNotes();
71 
72  for j in range(0, re.getNumReactants()):
73  rt = re.getReactant(j);
74  rt.unsetNotes();
75 
76  for j in range(0, re.getNumProducts()):
77  rt = re.getProduct(j);
78  rt.unsetNotes();
79 
80  for j in range(0, re.getNumModifiers()):
81  md = re.getModifier(j);
82  md.unsetNotes();
83 
84  if (re.isSetKineticLaw()):
85  kl = re.getKineticLaw();
86  kl.unsetNotes();
87 
88  for j in range(0, kl.getNumParameters()):
89  pa = kl.getParameter(j);
90  pa.unsetNotes();
91 
92  for i in range(0, m.getNumSpecies()):
93  sp = m.getSpecies(i);
94  sp.unsetNotes();
95 
96  for i in range(0, m.getNumCompartments()):
97  sp = m.getCompartment(i);
98  sp.unsetNotes();
99 
100  for i in range(0, m.getNumFunctionDefinitions()):
101  sp = m.getFunctionDefinition(i);
102  sp.unsetNotes();
103 
104  for i in range(0, m.getNumUnitDefinitions()):
105  sp = m.getUnitDefinition(i);
106  sp.unsetNotes();
107 
108  for i in range(0, m.getNumParameters()):
109  sp = m.getParameter(i);
110  sp.unsetNotes();
111 
112  for i in range(0, m.getNumRules()):
113  sp = m.getRule(i);
114  sp.unsetNotes();
115 
116  for i in range(0, m.getNumInitialAssignments()):
117  sp = m.getInitialAssignment(i);
118  sp.unsetNotes();
119 
120  for i in range(0, m.getNumEvents()):
121  sp = m.getEvent(i);
122  sp.unsetNotes();
123 
124  for j in range(0, sp.getNumEventAssignments()):
125  ea = sp.getEventAssignment(j);
126  ea.unsetNotes();
127 
128  for i in range(0, m.getNumSpeciesTypes()):
129  sp = m.getSpeciesType(i);
130  sp.unsetNotes();
131 
132  for i in range(0, m.getNumConstraints()):
133  sp = m.getConstraint(i);
134  sp.unsetNotes();
135 
136  writeSBML(document, args[2]);
137 
138  return errors;
139 
140 if __name__ == '__main__':
141  main(sys.argv)