addCustomValidator.py

Example of creating a custom validator to be called during validation.

#!/usr/bin/env python
##
## @file    addCustomValidator.py
## @brief   Example creating a custom validator to be called during validation
## @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:
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## 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
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import sys
import os.path
import libsbml


##
## Declares a custom validator to be called. This allows you to validate 
## any aspect of an SBML Model that you want to be notified about. You could 
## use this to notify your application that a model contains an unsupported 
## feature of SBML (either as warning). 
## 
## In this example the validator will go through the model and test for the 
## presence of 'fast' reactions and algebraic rules. If either is used a 
## warning will be added to the error log. 
## 

class MyCustomValidator(libsbml.SBMLValidator):
    def __init__(self, orig=None):
        if orig is None:
            super(MyCustomValidator, self).__init__()
        else:
            super(MyCustomValidator, self).__init__(orig)

    def clone(self):
        return MyCustomValidator(self)

    def validate(self):
        # if we don't have a model we don't apply this validator.
        if self.getDocument() is None or self.getModel() is None:
            return 0

        # if we have no rules and reactions we don't apply this validator either
        if self.getModel().getNumReactions() == 0 and self.getModel().getNumRules() == 0:
            return 0

        numErrors = 0
        # test for algebraic rules
        for i in range(0, self.getModel().getNumRules()):
            if self.getModel().getRule(i).getTypeCode() == libsbml.SBML_ALGEBRAIC_RULE:
                self.getErrorLog().add(SBMLError(99999, 3, 1,
                                                 "This model uses algebraic rules, however this application does not support them.",
                                                 0, 0,
                                                 libsbml.LIBSBML_SEV_WARNING,
                                                 # or LIBSBML_SEV_ERROR if you want to stop
                                                 libsbml.LIBSBML_CAT_SBML  # or whatever category you prefer
                                                 ))
        numErrors += 1

        # test for fast reactions
        for i in range(0, self.getModel().getNumReactions()):
            # test whether value is set, and true
            if (self.getModel().getReaction(i).isSetFast() and
                    self.getModel().getReaction(i).getFast()):
                self.getErrorLog().add(SBMLError(99999, 3, 1,
                                                 "This model uses fast reactions, however this application does not support them.",
                                                 0, 0,
                                                 libsbml.LIBSBML_SEV_WARNING,
                                                 # or LIBSBML_SEV_ERROR if you want to stop
                                                 libsbml.LIBSBML_CAT_SBML  # or whatever category you prefer
                                                 ))
                numErrors += 1
        return numErrors


def main(args):
    """Usage: addCustomValidator filename
    """
    if len(args) != 2:
        print(main.__doc__)
        sys.exit(1)

    # read the file name
    document = libsbml.readSBML(args[1])

    # add a custom validator
    document.addValidator(MyCustomValidator())

    # 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)