class TestSimpleSBML(unittest.TestCase):
def setUp(self):
self.simple = SimpleSBML()
self.simple.initialize(cn.TEST_FILE)
def testInitialize(self):
if IGNORE_TEST:
return
simple = SimpleSBML()
simple.initialize(cn.TEST_FILE)
self.assertEqual(len(simple.reactions), cn.NUM_REACTIONS)
self.assertEqual(len(simple.molecules), len(simple.moietys))
def testGetMolecule(self):
if IGNORE_TEST:
return
molecule1 = self.simple.molecules[0]
name = molecule1.name
molecule2 = self.simple.getMolecule(name)
self.assertTrue(molecule1.isEqual(molecule2))
self.assertIsNone(self.simple.getMolecule(NO_NAME))
def testAdd(self):
if IGNORE_TEST:
return
def test():
self.assertEqual(len(self.simple.reactions), 2)
for reaction in [reaction0, reaction1]:
self.assertTrue(reaction in self.simple.reactions)
#
reaction0 = self.simple.reactions[0]
reaction1 = self.simple.reactions[1]
self.simple.reactions = [reaction0]
self.simple.add(reaction1)
test()
self.simple.add(reaction1)
test()
def testRemove(self):
num_reactions = len(self.simple.reactions)
reaction0 = self.simple.reactions[0]
reaction1 = self.simple.reactions[1]
self.simple.remove(reaction0)
self.assertTrue(reaction0 not in self.simple.reactions)
self.assertTrue(reaction1 in self.simple.reactions)
self.simple.add(reaction0)
self.assertTrue(len(self.simple.reactions), num_reactions)
def testGetReaction(self):
if IGNORE_TEST:
return
reaction = self.simple.reactions[0]
label = reaction.label
reaction1 = self.simple.getReaction(label)
self.assertTrue(reaction.isEqual(reaction1))
class TestSOM(unittest.TestCase):
def setUp(self):
self.simple = SimpleSBML()
self.simple.initialize(cn.TEST_FILE3)
self.molecules = self.simple.molecules
self.soms = []
for mole in self.molecules:
self.soms.append(SOM({mole}))
def testConstructor(self):
if IGNORE_TEST:
return
self.assertEqual(len(self.soms), len(self.molecules))
self.assertEqual(self.soms[0].molecules, {self.molecules[0]})
def testMakeId(self):
if IGNORE_TEST:
return
som = self.soms[0]
self.assertTrue(som.molecules.intersection(self.molecules))
molecule = list(re.findall(NAMEFILTER, som.identifier))[0]
self.assertEqual(
list(som.molecules)[0], self.simple.getMolecule(molecule))
def testMerge(self):
if IGNORE_TEST:
return
som1 = self.soms[0]
som2 = self.soms[1]
molecule1 = list(som1.molecules)[0]
molecule2 = list(som2.molecules)[0]
new_som = som1.merge(som2)
self.assertEqual(len(new_som.molecules), NUM_MERGED_SOMS)
self.assertTrue(molecule1 in new_som.molecules)
self.assertTrue(molecule2 in new_som.molecules)
class TestMESGraph(unittest.TestCase):
def setUp(self):
# SimpleSBML with type I error
self.simple = SimpleSBML()
self.simple.initialize(cn.TEST_FILE6)
# SimpleSBML with type II error
self.simple2 = SimpleSBML()
self.simple2.initialize(cn.TEST_FILE7)
# SimpleSBML for type III error
self.simple3 = SimpleSBML()
self.simple3.initialize(cn.TEST_FILE10)
# SimpleSBML for type IV error
self.simple4 = SimpleSBML()
self.simple4.initialize(cn.TEST_FILE11)
# simple5 for type V error
self.simple5 = SimpleSBML()
self.simple5.initialize(cn.TEST_FILE12)
# simple6 will test multi-multi model with no errors
self.simple6 = SimpleSBML()
self.simple6.initialize(cn.TEST_FILE3)
self.mesgraph = MESGraph(self.simple)
def testConstructor(self):
if IGNORE_TEST:
return
self.assertEqual(len(self.mesgraph.nodes), INITIAL_NODES)
self.assertEqual(len(self.mesgraph.edges), INITIAL_EDGES)
dfg = self.simple.getMolecule(DFG)
# molecules is a list of one-molecule sets
molecules = [som.molecules for som in self.mesgraph.nodes]
self.assertTrue({self.simple.getMolecule(DFG)} in molecules)
self.assertEqual(len(self.mesgraph.type_one_errors), 0)
self.assertEqual(len(self.mesgraph.type_two_errors), 0)
self.assertEqual(len(self.mesgraph.type_three_errors), 0)
self.assertEqual(len(self.mesgraph.type_four_errors), 0)
self.assertEqual(len(self.mesgraph.type_five_errors), 0)
def testInitializeSOMs(self):
if IGNORE_TEST:
return
for node in self.mesgraph.nodes:
self.assertEqual(type(node), SOM)
def testMakeId(self):
if IGNORE_TEST:
return
identifier = ""
for key, som in enumerate(self.mesgraph.nodes):
identifier = identifier + som.identifier
if key < len(self.mesgraph.nodes)-1:
identifier = identifier + ";"
self.assertEqual(identifier, self.mesgraph.identifier)
def testGetNode(self):
if IGNORE_TEST:
return
aa = self.simple.getMolecule(AA)
aa_node = self.mesgraph.getNode(aa)
self.assertEqual(type(aa_node), SOM)
self.assertEqual(aa_node.molecules, {aa})
def testMergeNodes(self):
if IGNORE_TEST:
return
m3 = MESGraph(self.simple3)
v1_reaction = self.simple3.getReaction(V1)
v2_reaction = self.simple3.getReaction(V2)
amp_molecule = self.simple3.getMolecule(AMP)
adp_molecule = self.simple3.getMolecule(ADP)
atp_molecule = self.simple3.getMolecule(ATP)
amp_som = m3.getNode(amp_molecule)
adp_som = m3.getNode(adp_molecule)
atp_som = m3.getNode(atp_molecule)
ampatp_som = m3.mergeNodes(amp_som, atp_som, v1_reaction)
self.assertTrue(amp_molecule in ampatp_som.molecules)
self.assertTrue(atp_molecule in ampatp_som.molecules)
self.assertTrue(ampatp_som in m3.nodes)
# tests if anohter merge will remove previous nodes
ampadpatp_som = m3.mergeNodes(ampatp_som, adp_som, v2_reaction)
self.assertFalse(ampatp_som in m3.nodes)
self.assertFalse(adp_som in m3.nodes)
self.assertTrue(ampadpatp_som in m3.nodes)
def testProcessUniUniReaction(self):
if IGNORE_TEST:
return
self.mesgraph.processUniUniReaction(
self.simple.reactions[UNIUNI0])
dfg = self.mesgraph.getNode(self.simple.getMolecule(DFG))
e1 = self.mesgraph.getNode(self.simple.getMolecule(E1))
self.assertTrue(self.mesgraph.has_node(dfg))
self.assertTrue(self.mesgraph.has_node(e1))
self.assertEqual(dfg, e1)
def testProcessUniMultiReaction(self):
if IGNORE_TEST:
return
unimulti_reaction = self.simple.reactions[UNIMULTI]
self.mesgraph.processUniMultiReaction(unimulti_reaction)
prods = [self.mesgraph.getNode(product.molecule) for product in unimulti_reaction.products]
dfg = self.mesgraph.getNode(self.simple.getMolecule(DFG))
for prod in prods:
self.assertTrue(self.mesgraph.has_edge(prod, dfg))
def testProcessMultiUniReaction(self):
if IGNORE_TEST:
return
multiuni_reaction = self.simple.reactions[MULTIUNI]
self.mesgraph.processMultiUniReaction(multiuni_reaction)
reacts = [self.mesgraph.getNode(reactant.molecule) for reactant in multiuni_reaction.reactants]
mel = self.mesgraph.getNode(self.simple.getMolecule(MEL))
for react in reacts:
self.assertTrue(self.mesgraph.has_edge(react, mel))
def testAddMultiMultiReaction(self):
if IGNORE_TEST:
return
m3 = MESGraph(self.simple3)
v2 = self.simple3.getReaction(V2)
m3.addMultiMultiReaction(v2)
self.assertTrue(v2 in m3.multimulti_reactions)
def testAddTypeThreeError(self):
if IGNORE_TEST:
return
m3 = MESGraph(self.simple3)
v1 = self.simple3.getReaction(V1)
v2 = self.simple3.getReaction(V2)
v3 = self.simple3.getReaction(V3)
m3.processUniUniReaction(v1)
m3.processUniMultiReaction(v3)
amp = m3.getNode(self.simple3.getMolecule(AMP))
atp = m3.getNode(self.simple3.getMolecule(ATP))
self.assertTrue(m3.addTypeThreeError(amp, atp, v2))
self.assertTrue(len(m3.type_three_errors), 1)
error = m3.type_three_errors[0]
self.assertEqual(error.node1, amp)
self.assertEqual(error.node2, atp)
self.assertEqual(error.reactions, [v2.label])
def testCheckTypeThreeError(self):
if IGNORE_TEST:
return
m3 = MESGraph(self.simple3)
v1 = self.simple3.getReaction(V1)
v2 = self.simple3.getReaction(V2)
v3 = self.simple3.getReaction(V3)
m3.processUniUniReaction(v1)
adp = m3.getNode(self.simple3.getMolecule(ADP))
atp = m3.getNode(self.simple3.getMolecule(ATP))
self.assertFalse(m3.checkTypeThreeError(adp, atp, v3))
m3.processUniMultiReaction(v3)
self.assertTrue(m3.checkTypeThreeError(adp, atp, v2))
self.assertTrue(m3.checkTypeThreeError(atp, adp, v2))
def testReduceReaction(self):
if IGNORE_TEST:
return
m4 = MESGraph(self.simple4)
atpase = m4.simple.getReaction(ATPASE)
lower = m4.simple.getReaction(LOWER)
self.assertFalse(m4.reduceReaction(atpase))
m4.processUniUniReaction(atpase)
reduced_reaction = m4.reduceReaction(lower)
self.assertEqual(type(reduced_reaction), Reaction)
self.assertEqual(len(reduced_reaction.reactants), 1)
self.assertEqual(reduced_reaction.products, [])
self.assertEqual(reduced_reaction.reactants[0].molecule.name, FRU16P2)
def testProcessMultiMultiReactions(self):
if IGNORE_TEST:
return
# type III error
m3 = MESGraph(self.simple3)
v1 = self.simple3.getReaction(V1)
v2 = self.simple3.getReaction(V2)
v3 = self.simple3.getReaction(V3)
m3.processUniUniReaction(v1)
m3.processUniMultiReaction(v3)
self.assertEqual(m3.type_three_errors, [])
self.assertTrue(m3.processMultiMultiReaction(v2))
self.assertEqual(len(m3.type_three_errors), 1)
# type IV error
m4 = MESGraph(self.simple4)
atpase = m4.simple.getReaction(ATPASE)
lower = m4.simple.getReaction(LOWER)
m4.processUniUniReaction(atpase)
self.assertEqual(m4.type_four_errors, [])
self.assertTrue(m4.processMultiMultiReaction(lower))
self.assertEqual(len(m4.type_four_errors), 1)
# no error
m6 = MESGraph(self.simple6)
r5 = m6.simple.getReaction(R5)
r12 = m6.simple.getReaction(R12)
m6.processUniUniReaction(r12)
ac = m6.getNode(self.simple6.getMolecule(AC))
acp = m6.getNode(self.simple6.getMolecule(ACP))
self.assertFalse(ac==acp)
self.assertTrue(m6.processMultiMultiReaction(r5))
ac = m6.getNode(self.simple6.getMolecule(AC))
acp = m6.getNode(self.simple6.getMolecule(ACP))
self.assertTrue(ac==acp)
def testAddArc(self):
if IGNORE_TEST:
return
source = [self.mesgraph.getNode(self.simple.getMolecule(FRU)),
self.mesgraph.getNode(self.simple.getMolecule(GLY))]
destination = [self.mesgraph.getNode(self.simple.getMolecule(E2))]
dummy_reaction = self.simple.reactions[INEQUAL2]
self.mesgraph.addArc(source[0], destination[0], dummy_reaction)
self.mesgraph.addArc(source[1], destination[0], dummy_reaction)
arc1 = [source[0], destination[0]]
arc2 = [source[1], destination[0]]
self.assertTrue(self.mesgraph.has_edge(arc1[0], arc1[1]))
self.assertTrue(self.mesgraph.has_edge(arc2[0], arc2[1]))
reaction_label1 = self.mesgraph.get_edge_data(arc1[0], arc1[1])[cn.REACTION][0]
reaction_label2 = self.mesgraph.get_edge_data(arc2[0], arc1[1])[cn.REACTION][0]
self.assertEqual(reaction_label1, dummy_reaction.label)
self.assertEqual(reaction_label1, reaction_label2)
def testGetSOMPath(self):
if IGNORE_TEST:
return
uniuni_reaction = self.simple.reactions[UNIUNI0]
self.mesgraph.processUniUniReaction(uniuni_reaction)
dfg = self.simple.getMolecule(DFG)
e1 = self.simple.getMolecule(E1)
som = self.mesgraph.getNode(dfg)
som_path = self.mesgraph.getSOMPath(som, e1, dfg)
self.assertEqual(type(som_path[0]), cn.PathComponents)
self.assertEqual(som_path[0].reactions, [uniuni_reaction.label])
self.assertEqual(len(som_path), 1)
def testPrintSOMPath(self):
if IGNORE_TEST:
return
uniuni_reaction = self.simple.reactions[UNIUNI0]
self.mesgraph.processUniUniReaction(uniuni_reaction)
self.assertTrue(type(self.mesgraph.printSOMPath(DFG, E1))==str)
self.assertFalse(self.mesgraph.printSOMPath(GLY, MEL))
def testCheckTypeOneError(self):
if IGNORE_TEST:
return
uniuni_reaction1 = self.simple.reactions[UNIUNI1]
uniuni_reaction2 = self.simple.reactions[UNIUNI2]
inequality_reaction1 = self.simple.reactions[INEQUAL1]
inequality_reaction2 = self.simple.reactions[INEQUAL2]
self.mesgraph.processUniUniReaction(uniuni_reaction1)
self.mesgraph.processUniUniReaction(uniuni_reaction2)
aa = self.simple.getMolecule(AA)
cn = self.simple.getMolecule(CN)
mg = self.simple.getMolecule(MG)
self.assertTrue(self.mesgraph.checkTypeOneError((aa, cn), inequality_reaction1))
self.assertFalse(self.mesgraph.checkTypeOneError((mg, aa), inequality_reaction2))
self.assertTrue(len(self.mesgraph.type_one_errors)>0)
self.assertFalse(len(self.mesgraph.type_two_errors)>0)
def testCheckTypeTwoError(self):
if IGNORE_TEST:
return
mesgraph2 = MESGraph(self.simple2)
mesgraph2.processUniUniReaction(self.simple2.getReaction(REACTION1))
mesgraph2.processMultiUniReaction(self.simple2.getReaction(REACTION2))
mesgraph2.processMultiUniReaction(self.simple2.getReaction(REACTION3))
self.assertTrue(mesgraph2.checkTypeTwoError())
self.assertFalse(len(mesgraph2.type_one_errors)>0)
self.assertTrue(len(mesgraph2.type_two_errors)>0)
def testAnalyze(self):
if IGNORE_TEST:
return
mesgraph1 = MESGraph(self.simple)
mesgraph1.analyze(self.simple.reactions)
self.assertEqual(len(mesgraph1.nodes), FINAL_NODES)
self.assertEqual(len(mesgraph1.edges), FINAL_EDGES)
self.assertTrue(len(mesgraph1.type_one_errors)>0)
self.assertFalse(len(mesgraph1.type_two_errors)>0)
#
mesgraph2 = MESGraph(self.simple2)
mesgraph2.analyze(self.simple2.reactions)
self.assertTrue(len(mesgraph2.type_one_errors)>0)
self.assertTrue(len(mesgraph2.type_two_errors)>0)
#
mesgraph3 = MESGraph(self.simple3)
mesgraph3.analyze(self.simple3.reactions)
self.assertTrue(len(mesgraph3.type_three_errors)>0)
#
mesgraph4 = MESGraph(self.simple4)
mesgraph4.analyze(self.simple4.reactions)
self.assertTrue(len(mesgraph4.type_four_errors)>0)
#
# mesgraph5 = MESGraph(self.simple5)
# mesgraph5.analyze(self.simple5.reactions)
# dih = mesgraph5.getNode(self.simple5.getMolecule(DIH))
# din = mesgraph5.getNode(self.simple5.getMolecule(DIN))
# self.assertTrue(mesgraph5.has_edge(dih, din))
# self.assertTrue(mesgraph5.has_edge(din, dih))
# self.assertEqual(len(mesgraph5.type_five_errors), 1)
#
mesgraph6 = MESGraph(self.simple6)
mesgraph6.analyze(self.simple6.reactions)
total_errors = len(mesgraph6.type_one_errors) + \
len(mesgraph6.type_two_errors) + \
len(mesgraph6.type_three_errors) + \
len(mesgraph6.type_four_errors) +\
len(mesgraph6.type_five_errors)
self.assertTrue(total_errors==0)
class TestGAMESReport(unittest.TestCase):
def setUp(self):
self.simple1 = SimpleSBML()
self.simple2 = SimpleSBML()
self.simple3 = SimpleSBML()
self.simple4 = SimpleSBML()
# BIOMD0000000248 - canceling_error
self.simple1.initialize(cn.TEST_FILE_GAMESREPORT1)
# BIOMD0000000007 - Type I error
self.simple2.initialize(cn.TEST_FILE_GAMESREPORT2)
# BIOMD0000000018 - Type II error
self.simple3.initialize(cn.TEST_FILE_GAMES_PP2)
# BIOMD0000000167 - Echelon, Type III error
self.simple4.initialize(cn.TEST_FILE_GAMESREPORT3)
def testReportCancelingError(self):
if IGNORE_TEST:
return
m = GAMES_PP(self.simple1)
m.analyze(error_details=False)
gr = GAMESReport(m)
report, error_num = gr.reportCancelingError(m.canceling_errors,
explain_details=True)
extended_report = NULL_STR
extended_report = extended_report + "We detected a mass imbalance\n"
extended_report = extended_report + ": OxidativePhosphorylation: CTtis -> \n\n"
extended_report = extended_report + "from the following reaction isolation set:\n\n"
extended_report = extended_report + "1. OxidativePhosphorylation: 6.00 ADP + CTtis -> 6.00 ATP\n"
extended_report = extended_report + "2. ATPase: ATP -> ADP\n"
extended_report = extended_report + "*ATP and ADP have the same mass according to the above reaction\n"
extended_report = extended_report + "\n%s%s\n" % (PARAGRAPH_DIVIDER,
PARAGRAPH_DIVIDER)
extended_report = extended_report + "\n%s\n" % REPORT_DIVIDER
self.assertEqual(extended_report, report)
self.assertEqual(error_num, [2])
def testGetMoleculeEqualityPath(self):
if IGNORE_TEST:
return
m = GAMES_PP(self.simple2)
m.analyze(error_details=False)
gr = GAMESReport(m)
som = m.getNode(self.simple2.getMolecule(G2K))
equality_path = gr.getMoleculeEqualityPath(som, G2K, PG2R)
self.assertTrue(len(equality_path) == 2)
self.assertEqual(type(equality_path[0]), cn.PathComponents)
self.assertEqual(equality_path[0].node1, G2K)
self.assertEqual(equality_path[0].reactions, [CDC2PHOS])
self.assertEqual(equality_path[1].node2, PG2R)
self.assertEqual(equality_path[1].reactions, [RUM1DEGINPG2R])
def testGetMoleculeEqualityPathReport(self):
if IGNORE_TEST:
return
m = GAMES_PP(self.simple2)
m.analyze(error_details=False)
gr = GAMESReport(m)
count, report1 = gr.getMoleculeEqualityPathReport(
G2K, PG2R, 0, explain_details=False)
self.assertEqual(count, 2)
self.assertEqual(
report1,
"1. Cdc2Phos: G2K -> PG2\n2. Rum1DegInPG2R: PG2R -> PG2\n")
count, report2 = gr.getMoleculeEqualityPathReport(G2K,
PG2R,
0,
explain_details=True)
self.assertEqual(count, 2)
self.assertEqual(
report2,
"\nG2K = PG2 by reaction(s):\n1. Cdc2Phos: G2K -> PG2\n\nPG2 = PG2R by reaction(s):\n2. Rum1DegInPG2R: PG2R -> PG2\n"
)
def testGetMoleculeInequalityPathReport(self):
if IGNORE_TEST:
return
m = GAMES_PP(self.simple2)
m.analyze(error_details=False)
gr = GAMESReport(m)
count, report1 = gr.getMoleculeInequalityPathReport(
G2K, PG2R, ["G2R_Creation"], 0, explain_details=False)
self.assertEqual(count, 1)
self.assertEqual(report1, "1. G2R_Creation: G2K + R -> G2R\n")
count, report2 = gr.getMoleculeInequalityPathReport(
G2K, PG2R, ["G2R_Creation"], 0, explain_details=True)
self.assertEqual(count, 1)
self.assertEqual(
report2,
"G2K < PG2R by reaction(s):\n1. G2R_Creation: G2K + R -> G2R\n")
def testReportTypeOneError(self):
if IGNORE_TEST:
return
m = GAMES_PP(self.simple2)
m.analyze(error_details=False)
gr = GAMESReport(m)
error = [
cn.PathComponents(node1=G2K, node2=G2R, reactions=[G2R_CREATION])
]
report, error_num = gr.reportTypeOneError(error, explain_details=True)
self.assertEqual(error_num, [2])
extended_report = NULL_STR
extended_report = extended_report + "\nG2K = G2R by reaction(s):\n1. Rum1DegInG2R: G2R -> G2K\n\n"
extended_report = extended_report + "However, G2K < G2R by reaction(s):\n2. G2R_Creation: G2K + R -> G2R\n\n"
extended_report = extended_report + "\n----------------------------------------------------------------------\n\n"
extended_report = extended_report + "\n\n**********************************************************************\n\n"
self.assertEqual(report, extended_report)
def testReportTypeTwoError(self):
if IGNORE_TEST:
return
m = GAMES_PP(self.simple3)
m.analyze(error_details=False)
gr = GAMESReport(m)
som1 = m.getNode(self.simple3.getMolecule(CH3FH4))
som2 = m.getNode(self.simple3.getMolecule(FH4))
error = [[som1, som2]]
report, error_num = gr.reportTypeTwoError(error, explain_details=True)
self.assertEqual(error_num, [5])
LOC_START = 241
extended_report = NULL_STR
extended_report = extended_report + "{CH3FH4} < {CH2FH4=FFH2=FH2f=FH4} < {CH3FH4}\n\n"
extended_report = extended_report + "This indicates a mass conflict between reactions.\n"
extended_report = extended_report + "%s%s\n" % (PARAGRAPH_DIVIDER,
PARAGRAPH_DIVIDER)
self.assertEqual(report[-LOC_START:], extended_report)
def testConvertOperationSeriesToReactionOperations(self):
if IGNORE_TEST:
return
m = GAMES_PP(self.simple4)
m.analyze(error_details=False)
gr = GAMESReport(m)
op = pd.Series([1.0, 0.5, 0.0],
index=[
STATPHOSPHORYLATION, PSTATDIMERISATION,
PSTATDIMERISATIONNUC
])
ro = gr.convertOperationSeriesToReactionOperations(op)
self.assertEqual(len(ro), 2)
self.assertEqual(ro[0].reaction, STATPHOSPHORYLATION)
self.assertEqual(ro[0].operation, 1.0)
self.assertEqual(ro[1].reaction, PSTATDIMERISATION)
self.assertEqual(ro[1].operation, 0.5)
def testGetOperationMatrix(self):
if IGNORE_TEST:
return
m1 = GAMES_PP(self.simple1)
m1.analyze(error_details=False)
gr1 = GAMESReport(m1)
self.assertTrue(gr1.getOperationMatrix() is None)
m4 = GAMES_PP(self.simple4)
m4.analyze(error_details=False)
gr4 = GAMESReport(m4)
op_mat = gr4.getOperationMatrix()
self.assertEqual(op_mat.loc[STATPHOSPHORYLATION, STATPHOSPHORYLATION],
1.0)
self.assertEqual(op_mat.loc[PSTATDIMERISATION, PSTATDIMERISATION], 1.0)
self.assertEqual(
op_mat.loc[PSTATDIMERISATIONNUC, PSTATDIMERISATIONNUC], 1.0)
self.assertEqual(op_mat.loc[PSTATDIMERISATIONNUC, STATPHOSPHORYLATION],
0.0)
self.assertEqual(op_mat.loc[STATPHOSPHORYLATION, PSTATDIMERISATIONNUC],
-0.5)
def testGetResultingSeries(self):
if IGNORE_TEST:
return
m = GAMES_PP(self.simple4)
m.analyze(error_details=False)
gr = GAMESReport(m)
resulting_series = gr.getResultingSeries(STATPHOSPHORYLATION)
print(resulting_series)
self.assertEqual(resulting_series["{" + SPECIES_TEST + "}"], 1.0)
self.assertEqual(resulting_series["{" + PSTAT_SOL + "}"], 0.0)
self.assertEqual(
resulting_series[m.getNode(
m.simple.getMolecule(PSTATDIMER_NUC)).identifier], 0.0)
self.assertEqual(
resulting_series[m.getNode(
m.simple.getMolecule(PSTAT_NUC)).identifier], 0.0)
def testGetOperationStoichiometryMatrix(self):
if IGNORE_TEST:
return
m = GAMES_PP(self.simple4)
m.analyze(error_details=False)
gr = GAMESReport(m)
op = pd.Series([1.0, 0.5, 0.0],
index=[
STATPHOSPHORYLATION, PSTATDIMERISATION,
PSTATDIMERISATIONNUC
])
ro = gr.convertOperationSeriesToReactionOperations(op)
osm = gr.getOperationStoichiometryMatrix(ro)
self.assertEqual(osm.loc[SPECIES_TEST, STATPHOSPHORYLATION], 1.0)
self.assertEqual(osm.loc[SPECIES_TEST, PSTATDIMERISATION], 0.0)
self.assertEqual(osm.loc[PSTAT_SOL, STATPHOSPHORYLATION], 1.0)
self.assertEqual(osm.loc[PSTAT_SOL, PSTATDIMERISATION], -2.0)
def testGeInferredReaction(self):
if IGNORE_TEST:
return
m = GAMES_PP(self.simple4)
m.analyze(error_details=False)
gr = GAMESReport(m)
op = pd.Series([1.0, 0.5, 0.0],
index=[
STATPHOSPHORYLATION, PSTATDIMERISATION,
PSTATDIMERISATIONNUC
])
ro = gr.convertOperationSeriesToReactionOperations(op)
inferred_reaction = gr.getInferredReaction(ro)
self.assertEqual(len(inferred_reaction.reactants), 1)
self.assertEqual(len(inferred_reaction.products), 2)
self.assertEqual(inferred_reaction.reactants[0].molecule.name,
STAT_SOL)
self.assertTrue(inferred_reaction.products[0].molecule.name in
{PSTATDIMER_SOL, SPECIES_TEST})
self.assertTrue(inferred_reaction.products[1].molecule.name in
{PSTATDIMER_SOL, SPECIES_TEST})
self.assertEqual(inferred_reaction.reactants[0].stoichiometry, 1.0)
self.assertEqual({p.stoichiometry
for p in inferred_reaction.products}, {0.5, 1.0})
def testReportReactionsInSOM(self):
if IGNORE_TEST:
return
m = GAMES_PP(self.simple4)
m.analyze(error_details=False)
gr = GAMESReport(m)
som = m.getNode(m.simple.getMolecule(PSTATDIMER_NUC))
report, error_num = gr.reportReactionsInSOM(som, 0)
common_part = "1. PstatDimer__import: PstatDimer_sol -> PstatDimer_nuc\n"
self.assertEqual(error_num, 1)
self.assertTrue(report == common_part)
def testReportEchelonError(self):
if IGNORE_TEST:
return
m = GAMES_PP(self.simple4)
m.analyze(error_details=False)
gr = GAMESReport(m)
report, error_num = gr.reportEchelonError(m.echelon_errors,
explain_details=True)
self.assertEqual(error_num, [3])
extended_report = NULL_STR
extended_report = extended_report + "will result in empty reactant with zero mass:\n\n: -> {species_test}\n\n"
extended_report = extended_report + "\n----------------------------------------------------------------------\n"
extended_report = extended_report + "\n----------------------------------------------------------------------\n\n"
extended_report = extended_report + "\n\n**********************************************************************\n\n"
self.assertEqual(report[-288:], extended_report)
def testReportTypeThreeError(self):
if IGNORE_TEST:
return
m = GAMES_PP(self.simple4)
m.analyze(error_details=False)
gr = GAMESReport(m)
report, error_num = gr.reportTypeThreeError(m.type_three_errors,
explain_details=True)
self.assertEqual(error_num, [3])
pseudo_inequality_report = NULL_STR
pseudo_inequality_report = pseudo_inequality_report + "6. statPhosphorylation: stat_sol -> Pstat_sol + species_test\n"
pseudo_inequality_report = pseudo_inequality_report + "(pseudo 6.) statPhosphorylation: {Pstat_nuc=stat_nuc=stat_sol} -> "
pseudo_inequality_report1 = pseudo_inequality_report + "{species_test} + {Pstat_sol}"
pseudo_inequality_report2 = pseudo_inequality_report + "{Pstat_sol} + {species_test}"
inference_report1 = "the masses of {Pstat_sol} and {Pstat_nuc=stat_nuc=stat_sol} are unequal."
inference_report2 = "the masses of {Pstat_nuc=stat_nuc=stat_sol} and {Pstat_sol} are unequal."
self.assertTrue(report[-460:-305] == pseudo_inequality_report1
or report[-460:-305] == pseudo_inequality_report2)
self.assertTrue(report[-293:-221] == inference_report1
or report[-293:-221] == inference_report2)