printUnits.py

A command-line program that prints information about the units of measurement used in a given SBML file.

#!/usr/bin/env python
##
## @file    printUnits.py
## @brief   Prints some unit information about the model
## @author  Sarah Keating
## @author  Michael Hucka
##
##
## <!--------------------------------------------------------------------------
## 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
from libsbml import *

def main (args):
    """Usage: printUnits filename
    """

    if len(args) != 2:
        print("Usage: printUnits filename")
        return 1

    filename = args[1]
    document = readSBML(filename)

    if document.getNumErrors() > 0:
        print("Encountered the following SBML errors:")
        document.printErrors()
        return 1

    model = document.getModel()

    if model is None:
        print("No model present.")
        return 1

    for i in range(0, model.getNumSpecies()):
        s = model.getSpecies(i)
        print("Species " + str(i) + ": "
              + UnitDefinition.printUnits(s.getDerivedUnitDefinition()))

    for i in range(0,model.getNumCompartments()):
        c = model.getCompartment(i)
        print("Compartment " + str(i) + ": "
              + UnitDefinition.printUnits(c.getDerivedUnitDefinition()))

    for i in range(0,model.getNumParameters()):
        p = model.getParameter(i)
        print("Parameter " + str(i) + ": "
              + UnitDefinition.printUnits(p.getDerivedUnitDefinition()))

    for i in range(0,model.getNumInitialAssignments()):
        ia = model.getInitialAssignment(i)
        print("InitialAssignment " + str(i) + ": "
              + UnitDefinition.printUnits(ia.getDerivedUnitDefinition()))
        tmp = "no"
        if ia.containsUndeclaredUnits():
            tmp = "yes"
        print("        undeclared units: " + tmp)

    for i in range(0,model.getNumEvents()):
        e = model.getEvent(i)
        print("Event " + str(i) + ": ")

        if e.isSetDelay():
            print("Delay: "
                  + UnitDefinition.printUnits(e.getDelay().getDerivedUnitDefinition()))
            tmp = "no"
            if e.getDelay().containsUndeclaredUnits():
                tmp = "yes"
            print("        undeclared units: " + tmp)

        for j in range(0,e.getNumEventAssignments()):
            ea = e.getEventAssignment(j)
            print("EventAssignment " + str(j) + ": "
                  + UnitDefinition.printUnits(ea.getDerivedUnitDefinition()))
            tmp = "no"
            if ea.containsUndeclaredUnits():
                tmp = "yes"
            print("        undeclared units: " + tmp)

    for i in range(0,model.getNumReactions()):
        r = model.getReaction(i)

        print("Reaction " + str(i) + ": ")

        if r.isSetKineticLaw():
            print("Kinetic Law: "
                  + UnitDefinition.printUnits(r.getKineticLaw().getDerivedUnitDefinition()))
            tmp = "no"
            if r.getKineticLaw().containsUndeclaredUnits():
                tmp = "yes"
            print("        undeclared units: " + tmp)

        for j in range(0,r.getNumReactants()):
            sr = r.getReactant(j)

            if sr.isSetStoichiometryMath():
                print("Reactant stoichiometryMath" + str(j) + ": "
                      + UnitDefinition.printUnits(sr.getStoichiometryMath().getDerivedUnitDefinition()))
                tmp = "no"
                if sr.getStoichiometryMath().containsUndeclaredUnits():
                    tmp = "yes"
                print("        undeclared units: " + tmp)

        for j in range(0,r.getNumProducts()):
            sr = r.getProduct(j)

            if sr.isSetStoichiometryMath():
                print("Product stoichiometryMath" + str(j) + ": "
                      + UnitDefinition.printUnits(sr.getStoichiometryMath().getDerivedUnitDefinition()))
                tmp = "no"
                if sr.getStoichiometryMath().containsUndeclaredUnits():
                    tmp = "yes"
                print("        undeclared units: " + tmp)

    for i in range(0,model.getNumRules()):
        r = model.getRule(i)
        print("Rule " + str(i) + ": "
              + UnitDefinition.printUnits(r.getDerivedUnitDefinition()))
        tmp = "no"
        if r.getStoichiometryMath().containsUndeclaredUnits():
            tmp = "yes"
        print("        undeclared units: " + tmp)

    return 0


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