# # @file TestReadFromFile5.py # @brief Reads test-data/l2v1-assignment.xml into memory and tests it. # # @author Akiya Jouraku (Python conversion) # @author Ben Bornstein # # ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ====== # # DO NOT EDIT THIS FILE. # # This file was generated automatically by converting the file located at # src/sbml/test/TestReadFromFile5.cpp # using the conversion program dev/utilities/translateTests/translateTests.pl. # Any changes made here will be lost the next time the file is regenerated. # # ----------------------------------------------------------------------------- # This file is part of libSBML. Please visit http://sbml.org for more # information about SBML, and the latest version of libSBML. # # Copyright 2005-2010 California Institute of Technology. # Copyright 2002-2005 California Institute of Technology and # Japan Science and Technology Corporation. # # This library is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation. A copy of the license agreement is provided # in the file named "LICENSE.txt" included with this software distribution # and also available online as http://sbml.org/software/libsbml/license.html # ----------------------------------------------------------------------------- import sys import unittest import libsbml class TestReadFromFile5(unittest.TestCase): def test_read_l2v1_assignment(self): reader = libsbml.SBMLReader() filename = "../../sbml/test/test-data/" filename += "l2v1-assignment.xml" d = reader.readSBML(filename) if (d == None): pass self.assertTrue( d.getLevel() == 2 ) self.assertTrue( d.getVersion() == 1 ) m = d.getModel() self.assertTrue( m != None ) self.assertTrue( m.getNumCompartments() == 1 ) c = m.getCompartment(0) self.assertTrue( c != None ) self.assertTrue( c.getId() == "cell" ) ud = c.getDerivedUnitDefinition() self.assertTrue( ud.getNumUnits() == 1 ) self.assertTrue( ud.getUnit(0).getKind() == libsbml.UNIT_KIND_LITRE ) loc = m.getListOfCompartments() c1 = loc.get(0) self.assertTrue( c1 == c ) c1 = loc.get("cell") self.assertTrue( c1 == c ) self.assertTrue( m.getNumSpecies() == 5 ) s = m.getSpecies(0) self.assertTrue( s != None ) self.assertTrue( s.getId() == "X0" ) self.assertTrue( s.getCompartment() == "cell" ) self.assertTrue( s.getInitialConcentration() == 1.0 ) los = m.getListOfSpecies() s1 = los.get(0) self.assertTrue( s1 == s ) s1 = los.get("X0") self.assertTrue( s1 == s ) s = m.getSpecies(1) self.assertTrue( s != None ) self.assertTrue( s.getId() == "X1" ) self.assertTrue( s.getCompartment() == "cell" ) self.assertTrue( s.getInitialConcentration() == 0.0 ) s = m.getSpecies(2) self.assertTrue( s != None ) self.assertTrue( s.getId() == "T" ) self.assertTrue( s.getCompartment() == "cell" ) self.assertTrue( s.getInitialConcentration() == 0.0 ) s = m.getSpecies(3) self.assertTrue( s != None ) self.assertTrue( s.getId() == "S1" ) self.assertTrue( s.getCompartment() == "cell" ) self.assertTrue( s.getInitialConcentration() == 0.0 ) s = m.getSpecies(4) self.assertTrue( s != None ) self.assertTrue( s.getId() == "S2" ) self.assertTrue( s.getCompartment() == "cell" ) self.assertTrue( s.getInitialConcentration() == 0.0 ) self.assertTrue( m.getNumParameters() == 1 ) p = m.getParameter(0) self.assertTrue( p != None ) self.assertTrue( p.getId() == "Keq" ) self.assertTrue( p.getValue() == 2.5 ) lop = m.getListOfParameters() p1 = lop.get(0) self.assertTrue( p1 == p ) p1 = lop.get("Keq") self.assertTrue( p1 == p ) ud = p.getDerivedUnitDefinition() self.assertTrue( ud.getNumUnits() == 0 ) self.assertTrue( m.getNumRules() == 2 ) ar = m.getRule(0) self.assertTrue( ar != None ) self.assertTrue( ar.getVariable() == "S1" ) self.assertTrue( ar.getFormula() == "T / (1 + Keq)" ) ud = ar.getDerivedUnitDefinition() self.assertTrue( ud.getNumUnits() == 2 ) self.assertTrue( ud.getUnit(0).getKind() == libsbml.UNIT_KIND_MOLE ) self.assertTrue( ud.getUnit(0).getExponent() == 1 ) self.assertTrue( ud.getUnit(1).getKind() == libsbml.UNIT_KIND_LITRE ) self.assertTrue( ud.getUnit(1).getExponent() == -1 ) self.assertTrue( ar.containsUndeclaredUnits() == True ) lor = m.getListOfRules() ar1 = lor.get(0) self.assertTrue( ar1 == ar ) ar1 = lor.get("S1") self.assertTrue( ar1 == ar ) ar = m.getRule(1) self.assertTrue( ar != None ) self.assertTrue( ar.getVariable() == "S2" ) self.assertTrue( ar.getFormula() == "Keq * S1" ) self.assertTrue( m.getNumReactions() == 2 ) r = m.getReaction(0) self.assertTrue( r != None ) self.assertTrue( r.getId() == "in" ) self.assertTrue( r.getNumReactants() == 1 ) self.assertTrue( r.getNumProducts() == 1 ) sr = r.getReactant(0) self.assertTrue( sr != None ) self.assertTrue( sr.getSpecies() == "X0" ) sr = r.getProduct(0) self.assertTrue( sr != None ) self.assertTrue( sr.getSpecies() == "T" ) kl = r.getKineticLaw() self.assertTrue( kl != None ) self.assertTrue( kl.getFormula() == "k1 * X0" ) self.assertTrue( kl.getNumParameters() == 1 ) r1 = kl.getParentSBMLObject() self.assertTrue( r1 != None ) self.assertTrue( r1.getId() == "in" ) self.assertTrue( r1.getNumReactants() == 1 ) self.assertTrue( r1.getNumProducts() == 1 ) p = kl.getParameter(0) self.assertTrue( p != None ) self.assertTrue( p.getId() == "k1" ) self.assertTrue( p.getValue() == 0.1 ) kl = p.getParentSBMLObject().getParentSBMLObject() self.assertTrue( kl != None ) self.assertTrue( kl.getFormula() == "k1 * X0" ) self.assertTrue( kl.getNumParameters() == 1 ) r = m.getReaction(1) self.assertTrue( r != None ) self.assertTrue( r.getId() == "out" ) self.assertTrue( r.getNumReactants() == 1 ) self.assertTrue( r.getNumProducts() == 1 ) sr = r.getReactant(0) self.assertTrue( sr != None ) self.assertTrue( sr.getSpecies() == "T" ) sr = r.getProduct(0) self.assertTrue( sr != None ) self.assertTrue( sr.getSpecies() == "X1" ) kl = r.getKineticLaw() self.assertTrue( kl != None ) self.assertTrue( kl.getFormula() == "k2 * T" ) self.assertTrue( kl.getNumParameters() == 1 ) p = kl.getParameter(0) self.assertTrue( p != None ) self.assertTrue( p.getId() == "k2" ) self.assertTrue( p.getValue() == 0.15 ) d = None pass def suite(): suite = unittest.TestSuite() suite.addTest(unittest.TestLoader.loadTestsFromTestCase(TestReadFromFile5)) return suite if __name__ == "__main__": if unittest.TextTestRunner(verbosity=1).run(suite()).wasSuccessful() : sys.exit(0) else: sys.exit(1)