unsetAnnotation.py

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

#!/usr/bin/env python
## 
## @file    unsetAnnotation.py
## @brief   unset annotation for each element
## @author  Akiya Jouraku
## 
## <!--------------------------------------------------------------------------
## 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
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## ------------------------------------------------------------------------ -->
## 

import sys
import time
import os
import os.path
from libsbml import *

def main (args):
  """Usage: unsetAnnotation <input-filename> <output-filename>
  """
  if len(args) != 3:
      print("\n" + "Usage: unsetAnnotation <input-filename> <output-filename>" + "\n" + "\n")
      return 1

  filename = args[1]

  document = readSBML(filename)

  errors = document.getNumErrors()

  if errors > 0:
      document.printErrors()
      return errors

  m = document.getModel()
  m.unsetAnnotation()

  for i in range(0, m.getNumReactions()):
      re = m.getReaction(i)
      re.unsetAnnotation()

      for j in range(0, re.getNumReactants()):
          rt = re.getReactant(j)
          rt.unsetAnnotation()

      for j in range(0, re.getNumProducts()):
          rt = re.getProduct(j)
          rt.unsetAnnotation()

      for j in range(0, re.getNumModifiers()):
          md = re.getModifier(j)
          md.unsetAnnotation()

      if re.isSetKineticLaw():
          kl = re.getKineticLaw()
          kl.unsetAnnotation()

          for j in range(0, kl.getNumParameters()):
              pa = kl.getParameter(j)
              pa.unsetAnnotation()

  for i in range(0, m.getNumSpecies()):
      sp = m.getSpecies(i)
      sp.unsetAnnotation()

  for i in range(0, m.getNumCompartments()):
      sp = m.getCompartment(i)
      sp.unsetAnnotation()

  for i in range(0, m.getNumFunctionDefinitions()):
      sp = m.getFunctionDefinition(i)
      sp.unsetAnnotation()

  for i in range(0, m.getNumUnitDefinitions()):
      sp = m.getUnitDefinition(i)
      sp.unsetAnnotation()

  for i in range(0, m.getNumParameters()):
      sp = m.getParameter(i)
      sp.unsetAnnotation()

  for i in range(0, m.getNumRules()):
      sp = m.getRule(i)
      sp.unsetAnnotation()

  for i in range(0, m.getNumInitialAssignments()):
      sp = m.getInitialAssignment(i)
      sp.unsetAnnotation()

  for i in range(0, m.getNumEvents()):
      sp = m.getEvent(i)
      sp.unsetAnnotation()

      for j in range(0, sp.getNumEventAssignments()):
          ea = sp.getEventAssignment(j)
          ea.unsetAnnotation()

  for i in range(0, m.getNumSpeciesTypes()):
      sp = m.getSpeciesType(i)
      sp.unsetAnnotation()

  for i in range(0, m.getNumConstraints()):
      sp = m.getConstraint(i)
      sp.unsetAnnotation()

  writeSBML(document, args[2])

  return errors


if __name__ == '__main__':
  main(sys.argv)