callExternalValidator.py

Example that shows how to call an external program for validation.

#!/usr/bin/env python
##
## @file    callExternalValidator.py
## @brief   Example that shows how to call an external program for validation
## @author  Frank T. Bergmann
##
## <!--------------------------------------------------------------------------
## This sample program is distributed under a different license than the rest
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## Copyright (c) 2013-2018 by the California Institute of Technology
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import sys
import os.path
from libsbml import *

def main (args):
  """Usage: callExternalValidator filename externalValidator [ tempSBMLFile outputFile [ ADDITIONAL-ARGS] ]
     calls an external validator
  """
  if len(args) < 3:
    print(main.__doc__)
    sys.exit(1)
  
  filename = args[1]

  # read additional args
  externalValidator = args[2]

  tempSBMLFileName = filename + "_temp.xml"
  if len(args) > 3:
      tempSBMLFileName = args[3]

  outputFile = filename + "_out.xml"
  if len(args) > 4:
      outputFile = args[4]

  additionalArgs = []
  for i in range (5, len(args)):
      additionalArgs += [args[i]]
  
  # add the output file as additional arg
  additionalArgs += [outputFile]
  
  # read the file name
  document = readSBML(filename)

  # create a external validator that will write the model to 
  # tempFile, then call teh externalValidator with the given number of arguments
  # to produce the output file. This output file will then be parsed and its
  # errors will be added to the error log.
  validator = SBMLExternalValidator()

  validator.setProgram(externalValidator)
  validator.setSBMLFileName(tempSBMLFileName)
  validator.setOutputFileName(outputFile)
  for item in additionalArgs:
      validator.addArgument(item)

  # this means that the external program will be called with the following arguments
  # 
  #    externalValidator tempSBMLFileName additionalArgs
  #
  # (where additionalArgs contains the output file as last argument)
  #
  # The output file that is generated should be an XML document following the 
  # Validator XML format as described here: http://sbml.org/validator/api/#xml
  #
  
  # disable all regular checks
  document.setApplicableValidators(0)

  # add a custom validator
  document.addValidator(validator)

  # check consistency like before
  numErrors = document.checkConsistency()

  # print errors and warnings
  document.printErrors()

  # return number of errors
  return numErrors


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