getAllElementsWithNotes.py

Demonstrates how to use the element filter class to search the model for elements with specific attributes .

#!/usr/bin/env python
##
## @file    getAllElementsWithNotes.py
## @brief   Utility program, demonstrating how to use the element filter
##          class to search the model for elements with specific attributes
##          in this example, we look for elements with notes
##
## @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
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## and the University of Heidelberg (Germany), with support from the National
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import sys
import os.path
import time 
import libsbml

# This class implements an element filter, that can be used to find elements
# with notes
class NotesFilter(libsbml.ElementFilter):
    def __init__(self):
        # call the constructor of the base class
        libsbml.ElementFilter.__init__(self)

    # The function performing the filtering, here we just check 
    # that we have a valid element, and that it has notes. 
    def filter(self, element):
        # return in case we don't have a valid element
        if element is None or element.isSetNotes() == False:
            return False
        # otherwise we have notes set and want to keep the element
        if element.isSetId():
            print ("                     found : {0}".format(element.getId()))
        else: 
            print ("                     found element without id")
        return True

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

    filename = args[1]

    # 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)

    # create the filter we want to use
    filter = NotesFilter()

    # get a list of all elements with notes
    start = time.time() * 1000
    print ("    searching ......:")
    allElements = document.getListOfAllElements(filter)
    stop = time.time() * 1000
    print ("    search time (ms): {0}".format(stop - start))

    print (" elements with notes: {0}".format(allElements.getSize()))

    # if we got here all went well ... 

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