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converted setNamesFromIds.cpp example into a python file #312
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#!/usr/bin/env python3 | ||
## | ||
## @file setNamesFromIds.py | ||
## @brief Utility program, renaming all Names to match their ids. | ||
## | ||
## @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 time | ||
import libsbml | ||
|
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# This class implements an identifier transformer, that means it can be used | ||
# to rename all sbase elements. | ||
class SetNamesFromId(libsbml.IdentifierTransformer): | ||
def __init__(self): | ||
# call the constructor of the base class | ||
libsbml.IdentifierTransformer.__init__(self) | ||
|
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# The function actually doing the transforming. This function is called | ||
# once for each SBase element in the model. | ||
def transform(self, element): | ||
# return in case we don't have a valid element | ||
if element is None or element.getTypeCode() == libsbml.SBML_LOCAL_PARAMETER: | ||
return libsbml.LIBSBML_OPERATION_SUCCESS | ||
|
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# or if there is nothing to do | ||
if element.isSetId() == False or element.getId() == element.getName(): | ||
return libsbml.LIBSBML_OPERATION_SUCCESS | ||
|
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# set it | ||
element.setName(element.getId()) | ||
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return libsbml.LIBSBML_OPERATION_SUCCESS | ||
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def main (args): | ||
"""Usage: setNamesFromIds filename output | ||
""" | ||
if len(args) != 3: | ||
print(main.__doc__) | ||
sys.exit(1) | ||
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filename = args[1] | ||
output = args[2] | ||
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# read the document | ||
start = time.time() * 1000 | ||
document = libsbml.readSBMLFromFile(filename) | ||
stop = time.time() * 1000 | ||
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print ("") | ||
print (" filename: {0}".format( filename)) | ||
print (" read time (ms): {0}".format( stop - start)) | ||
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# stop in case of serious errors | ||
errors = document.getNumErrors(libsbml.LIBSBML_SEV_ERROR) | ||
if errors > 0: | ||
print (" error(s): {0}".format(errors)) | ||
document.printErrors() | ||
sys.exit (errors) | ||
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# get a list of all elements, as we will need to know all identifiers | ||
allElements = document.getListOfAllElements() | ||
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# create the transformer | ||
trans = SetNamesFromId() | ||
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# rename the identifiers (using the elements we already gathered before) | ||
start = time.time() * 1000 | ||
document.getModel().renameIDs(allElements, trans) | ||
stop = time.time() * 1000 | ||
print (" rename time (ms): {0}".format(stop - start)) | ||
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# write to file | ||
start = time.time() * 1000 | ||
libsbml.writeSBMLToFile(document, output) | ||
stop = time.time() * 1000 | ||
print (" write time (ms): {0}".format(stop - start)) | ||
print ("") | ||
|
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# if we got here all went well ... | ||
|
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if __name__ == '__main__': | ||
main(sys.argv) |
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this needs to be still
test_python_setIdFromNames
for it to work