# # @file TestReadFromFile6.py # @brief Reads test-data/l2v2-newComponents.xml into memory and tests it. # # @author Akiya Jouraku (Python conversion) # @author Sarah Keating # # ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ====== # # DO NOT EDIT THIS FILE. # # This file was generated automatically by converting the file located at # src/sbml/test/TestReadFromFile6.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 TestReadFromFile6(unittest.TestCase): def test_read_l2v2_newComponents(self): reader = libsbml.SBMLReader() filename = "../../sbml/test/test-data/" filename += "l2v2-newComponents.xml" d = reader.readSBML(filename) if (d == None): pass self.assertTrue( d.getLevel() == 2 ) self.assertTrue( d.getVersion() == 2 ) m = d.getModel() self.assertTrue( m != None ) self.assertTrue( m.getId() == "l2v2_newComponents" ) self.assertTrue( m.getSBOTerm() == 4 ) self.assertTrue( m.getSBOTermID() == "SBO:0000004" ) self.assertTrue( m.getNumCompartments() == 2 ) c = m.getCompartment(0) self.assertTrue( c != None ) self.assertTrue( c.getId() == "cell" ) self.assertTrue( c.getCompartmentType() == "mitochondria" ) self.assertTrue( c.getOutside() == "m" ) self.assertTrue( c.getSBOTerm() == -1 ) self.assertTrue( c.getSBOTermID() == "" ) c = m.getCompartment(1) self.assertTrue( c != None ) self.assertTrue( c.getId() == "m" ) self.assertTrue( c.getCompartmentType() == "mitochondria" ) self.assertTrue( m.getNumCompartmentTypes() == 1 ) ct = m.getCompartmentType(0) self.assertTrue( ct != None ) self.assertTrue( ct.getId() == "mitochondria" ) loct = m.getListOfCompartmentTypes() ct1 = loct.get(0) self.assertTrue( ct1 == ct ) ct1 = loct.get("mitochondria") self.assertTrue( ct1 == ct ) self.assertTrue( m.getNumSpeciesTypes() == 1 ) st = m.getSpeciesType(0) self.assertTrue( st != None ) self.assertTrue( st.getId() == "Glucose" ) self.assertTrue( m.getNumSpecies() == 2 ) s = m.getSpecies(0) self.assertTrue( s != None ) self.assertTrue( s.getId() == "X0" ) self.assertTrue( s.getSpeciesType() == "Glucose" ) self.assertTrue( s.getCompartment() == "cell" ) self.assertEqual( False, s.isSetInitialAmount() ) self.assertEqual( False, s.isSetInitialConcentration() ) s = m.getSpecies(1) self.assertTrue( s != None ) self.assertTrue( s.getId() == "X1" ) self.assertEqual( False, s.isSetSpeciesType() ) self.assertTrue( s.getCompartment() == "cell" ) self.assertTrue( s.getInitialConcentration() == 0.013 ) self.assertEqual( False, s.isSetInitialAmount() ) self.assertEqual( True, s.isSetInitialConcentration() ) self.assertTrue( m.getNumParameters() == 1 ) p = m.getParameter(0) self.assertTrue( p != None ) self.assertTrue( p.getId() == "y" ) self.assertTrue( p.getValue() == 2 ) self.assertTrue( p.getUnits() == "dimensionless" ) self.assertTrue( p.getId() == "y" ) self.assertTrue( p.getSBOTerm() == 2 ) self.assertTrue( p.getSBOTermID() == "SBO:0000002" ) self.assertTrue( m.getNumConstraints() == 1 ) con = m.getConstraint(0) self.assertTrue( con != None ) self.assertTrue( con.getSBOTerm() == 64 ) self.assertTrue( con.getSBOTermID() == "SBO:0000064" ) ast = con.getMath() self.assertTrue(( "lt(1, cell)" == libsbml.formulaToString(ast) )) locon = m.getListOfConstraints() con1 = locon.get(0) self.assertTrue( con1 == con ) self.assertTrue( m.getNumInitialAssignments() == 1 ) ia = m.getInitialAssignment(0) self.assertTrue( ia != None ) self.assertTrue( ia.getSBOTerm() == 64 ) self.assertTrue( ia.getSBOTermID() == "SBO:0000064" ) self.assertTrue( ia.getSymbol() == "X0" ) ast = ia.getMath() self.assertTrue(( "y * X1" == libsbml.formulaToString(ast) )) loia = m.getListOfInitialAssignments() ia1 = loia.get(0) self.assertTrue( ia1 == ia ) ia1 = loia.get("X0") self.assertTrue( ia1 == ia ) self.assertTrue( m.getNumReactions() == 1 ) r = m.getReaction(0) self.assertTrue( r != None ) self.assertTrue( r.getSBOTerm() == 231 ) self.assertTrue( r.getSBOTermID() == "SBO:0000231" ) self.assertTrue( r.getId() == "in" ) lor = m.getListOfReactions() r1 = lor.get(0) self.assertTrue( r1 == r ) r1 = lor.get("in") self.assertTrue( r1 == r ) self.assertEqual( True, r.isSetKineticLaw() ) kl = r.getKineticLaw() self.assertTrue( kl != None ) self.assertTrue( kl.getSBOTerm() == 1 ) self.assertTrue( kl.getSBOTermID() == "SBO:0000001" ) self.assertEqual( True, kl.isSetMath() ) ast = kl.getMath() self.assertTrue(( "v * X0 / t" == libsbml.formulaToString(ast) )) self.assertTrue( kl.getNumParameters() == 2 ) p = kl.getParameter(0) self.assertTrue( p != None ) self.assertTrue( p.getSBOTerm() == 2 ) self.assertTrue( p.getSBOTermID() == "SBO:0000002" ) self.assertTrue( p.getId() == "v" ) self.assertTrue( p.getUnits() == "litre" ) self.assertTrue( r.getNumReactants() == 1 ) self.assertTrue( r.getNumProducts() == 0 ) self.assertTrue( r.getNumModifiers() == 0 ) sr = r.getReactant(0) self.assertTrue( sr != None ) self.assertTrue( sr.getName() == "sarah" ) self.assertTrue( sr.getId() == "me" ) self.assertTrue( sr.getSpecies() == "X0" ) losr = r.getListOfReactants() sr1 = losr.get(0) self.assertTrue( sr1 == sr ) sr1 = losr.get("me") self.assertTrue( sr1 == sr ) d = None pass def suite(): suite = unittest.TestSuite() suite.addTest(unittest.TestLoader.loadTestsFromTestCase(TestReadFromFile6)) return suite if __name__ == "__main__": if unittest.TextTestRunner(verbosity=1).run(suite()).wasSuccessful() : sys.exit(0) else: sys.exit(1)