def testConstructorWithError(self):
if IGNORE_TEST:
return
shim = SBMLShim(sbmlstr="", is_ignore_errors=True)
self.assertIsNone(shim._exception)
with self.assertRaises(Exception):
SBMLShim(sbmlstr="")
def testCreateReaction(self):
if IGNORE_TEST:
return
reactants = ["A"]
products = ["B", "C"]
sbmlstr = SBMLShim.createSBMLReaction(reactants, products)
shim = SBMLShim(sbmlstr=sbmlstr)
self.assertTrue(len(shim.getReactants(0)), len(reactants))
self.assertTrue(len(shim.getProducts(0)), len(products))
def _testTransformStatistic(self, reactants, products, key, value):
"""
:param list-of-str reactants:
:param list-of-str products:
:param str key: key in the result
:param float value: value in the result
"""
sbmlstr = SBMLShim.createSBMLReaction(reactants, products)
shim = SBMLShim(sbmlstr=sbmlstr)
complex = ComplexTransformationReactionStatistic(shim)
self.assertEqual(complex._addValues({}, 0)[key], [value])
def testGetReactionIndicies(self):
antimonystr = '''
A -> B; 1
C -> D; 1
A = 1
B = 1
C = 1
D =1
'''
sbmlstr = SBMLShim.createSBML(antimonystr)
shim = SBMLShim(sbmlstr=sbmlstr)
reaction_indicies = shim.getReactionIndicies()
self.assertEqual(len(reaction_indicies), 2)
def next(self):
"""
:return SBMLShim: next bio model
:raises StopIteration:
"""
if self._idx < len(self._ids):
shim = SBMLShim.getShimForBiomodel(self._ids[self._idx])
self._idx += 1
return shim
else:
raise StopIteration()
def testcreateSBML(self):
if IGNORE_TEST:
return
sbmlstr = SBMLShim.createSBML("A + B -> C; 1")
shim = SBMLShim(sbmlstr=sbmlstr)
reaction = shim.getReactions()[0]
reactants = set([r.getSpecies() for r in shim.getReactants(reaction)])
self.assertEqual(reactants, set(["A", "B"]))
self.assertEqual(shim.getProducts(reaction)[0].getSpecies(), "C")
def setUp(self):
self.shim = SBMLShim(filepath=TEST_FILE)
def testStatisticError(self):
shim = SBMLShim.getShimForBiomodel("BIOMD0000000020")
statistics = Statistic.getAllStatistics(self.shim)
self.assertTrue(len(statistics.keys()) > 10)
def testReactionStatisticError(self):
#if IGNORE_TEST:
# return
shim = SBMLShim.getShimForBiomodel("BIOMD0000000020")
statistics = Statistic.getAllStatistics(shim)
self.assertEqual(statistics["Num_Reactions"], 0)
def testGetShimForBiomodel(self):
if IGNORE_TEST:
return
shim = SBMLShim.getShimForBiomodel(BIOMODEL)
self.assertTrue(len(shim.getReactions()) > 0)
self.assertEqual(shim.getBiomodelId(), BIOMODEL)
class TestSBMLShim(unittest.TestCase):
def setUp(self):
self.shim = SBMLShim(filepath=TEST_FILE)
def testConstructorWithFile(self):
if IGNORE_TEST:
return
self.assertEqual(len(self.shim.getReactions()), NUM_REACTIONS)
for reaction in self.shim.getReactions():
self.assertTrue(isinstance(reaction, libsbml.Reaction))
self.assertLessEqual(reaction.getNumReactants(), MAX_REACTANTS)
self.assertEqual(len(self.shim.getParameters()), NUM_PARAMETERS)
for parameter in self.shim.getParameters():
self.assertTrue(isinstance(parameter, libsbml.Parameter))
def testConstructorWithError(self):
if IGNORE_TEST:
return
shim = SBMLShim(sbmlstr="", is_ignore_errors=True)
self.assertIsNone(shim._exception)
with self.assertRaises(Exception):
SBMLShim(sbmlstr="")
def testGetShimForBiomodel(self):
if IGNORE_TEST:
return
shim = SBMLShim.getShimForBiomodel(BIOMODEL)
self.assertTrue(len(shim.getReactions()) > 0)
self.assertEqual(shim.getBiomodelId(), BIOMODEL)
def testcreateSBML(self):
if IGNORE_TEST:
return
sbmlstr = SBMLShim.createSBML("A + B -> C; 1")
shim = SBMLShim(sbmlstr=sbmlstr)
reaction = shim.getReactions()[0]
reactants = set([r.getSpecies() for r in shim.getReactants(reaction)])
self.assertEqual(reactants, set(["A", "B"]))
self.assertEqual(shim.getProducts(reaction)[0].getSpecies(), "C")
def testCreateReaction(self):
if IGNORE_TEST:
return
reactants = ["A"]
products = ["B", "C"]
sbmlstr = SBMLShim.createSBMLReaction(reactants, products)
shim = SBMLShim(sbmlstr=sbmlstr)
self.assertTrue(len(shim.getReactants(0)), len(reactants))
self.assertTrue(len(shim.getProducts(0)), len(products))
def testGetReactionIndicies(self):
antimonystr = '''
A -> B; 1
C -> D; 1
A = 1
B = 1
C = 1
D =1
'''
sbmlstr = SBMLShim.createSBML(antimonystr)
shim = SBMLShim(sbmlstr=sbmlstr)
reaction_indicies = shim.getReactionIndicies()
self.assertEqual(len(reaction_indicies), 2)
def testExecFunction(self):
num_errors = self.shim.execFunction("getNumErrors")
self.assertEqual(num_errors, 0)
num_params = self.shim.execFunction("getNumParameters",
attribute="model")
self.assertGreater(num_params, 0)