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#!/usr/bin/python3
##
## @file setIdFromNames.py
## @brief Utility program, renaming all SIds that also has
## names specified. The new id will be derived from
## the name, with all invalid characters removed.
##
## @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
# This class implements an identifier transformer, that means it can be used
# to rename all sbase elements.
class SetIdFromNames(libsbml.IdentifierTransformer):
def __init__(self, ids):
# call the constructor of the base class
libsbml.IdentifierTransformer.__init__(self)
# remember existing ids ...
self.existingIds = ids
# 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
# or if there is nothing to do
if element.isSetName() == False or element.getId() == element.getName():
return libsbml.LIBSBML_OPERATION_SUCCESS
# find the new id
newId = self.getValidIdForName(element.getName())
# set it
element.setId(newId)
# remember it
self.existingIds.append(newId)
return libsbml.LIBSBML_OPERATION_SUCCESS
def nameToSbmlId(self, name):
IdStream = []
count = 0
end = len(name)
if '0' <= name[count] and name[count] <= '9':
IdStream.append('_')
for count in range (0, end):
if (('0' <= name[count] and name[count] <= '9') or
('a' <= name[count] and name[count] <= 'z') or
('A' <= name[count] and name[count] <= 'Z')):
IdStream.append(name[count])
else:
IdStream.append('_')
Id = ''.join(IdStream)
if Id[len(Id) - 1] != '_':
return Id
return Id[:-1]
#
# Generates the id out of the name, and ensures it is unique.
# It does so by appending numbers to the original name.
#
def getValidIdForName(self, name):
baseString = self.nameToSbmlId(name)
id = baseString
count = 1
while self.existingIds.count(id) != 0:
id = "{0}_{1}".format(baseString, count)
count += 1
return id
#
# Returns a list of all ids from the given list of elements
#
def getAllIds(allElements):
result = []
if allElements is None or allElements.getSize() == 0:
return result
for i in range (0, allElements.getSize()):
current = allElements.get(i)
if current.isSetId() and current.getTypeCode() != libsbml.SBML_LOCAL_PARAMETER:
result.append(current.getId())
return result
def main (args):
"""Usage: setIdFromNames filename output
"""
if len(args) != 3:
print(main.__doc__)
sys.exit(1)
filename = args[1]
output = args[2]
# read the document
start = time.time() * 1000
document = libsbml.readSBMLFromFile(filename)
stop = time.time() * 1000
print ("")
print (" filename: {0}".format( filename))
print (" read time (ms): {0}".format( stop - start))
# 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)
# get a list of all elements, as we will need to know all identifiers
# so that we don't create duplicates.
allElements = document.getListOfAllElements()
# get a list of all ids
allIds = getAllIds(allElements)
# create the transformer with the ids
trans = SetIdFromNames(allIds)
# 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))
# write to file
start = time.time() * 1000
libsbml.writeSBMLToFile(document, output)
stop = time.time() * 1000
print (" write time (ms): {0}".format(stop - start))
print ("")
# if we got here all went well ...
if __name__ == '__main__':
main(sys.argv)
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