def addTypeOneError(self, mole1, mole2, reaction):
"""
Add Type I Error components to self.type_one_errors
All components of resulting PathComponents are str
:param Molecule mole1:
:param Molecule mole2:
:param Reaction reaction:
:return bool flag:
"""
flag = False
for component in self.type_one_errors:
if (component.node1 == mole1.name) and (component.node2
== mole2.name):
new_component = cn.PathComponents(
node1=mole1.name,
node2=mole2.name,
reactions=component.reactions + [reaction.label])
self.type_one_errors.remove(component)
self.type_one_errors.append(new_component)
flag = True
break
if not flag:
self.type_one_errors.append(
cn.PathComponents(node1=mole1.name,
node2=mole2.name,
reactions=[reaction.label]))
flag = True
return flag
def addTypeThreeError(self, som1, som2, reaction):
"""
Add Type III Error components to self.type_three_errors
All components of resulting PathComponents are str
:param SOM som1:
:param SOM som2:
:param Reaction reaction:
:return bool flag:
"""
flag = False
for component in self.type_three_errors:
if (component.node1 == som1) and (component.node2 == som2):
new_component = cn.PathComponents(
node1=som1,
node2=som2,
reactions=component.reactions + [reaction.label])
self.type_three_errors.remove(component)
self.type_three_errors.append(new_component)
flag = True
break
if not flag:
self.type_three_errors.append(
cn.PathComponents(node1=som1,
node2=som2,
reactions=[reaction.label]))
flag = True
return flag
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 getMoleculeEqualityPath(self, som, molecule1, molecule2):
"""
Create an undirected graph between
two molecules within a SOM
and find the shortest path
:param SOM som:
:param Molecule mole1:
:param Molecule mole2:
:return PathComponents: som_path
"""
# molecule1 = mole1.name
# molecule2 = mole2.name
# construct undirected graph
subg = nx.Graph()
# here, every reaction is 1-1 reaction
for reaction in list(som.reactions):
node1 = reaction.reactants[0].molecule.name
node2 = reaction.products[0].molecule.name
if subg.has_edge(node1, node2):
reaction_label = subg.get_edge_data(node1, node2)[cn.REACTION]
# if reaction.label is not included in the attribute, add its label
if reaction.label not in set(reaction_label):
reaction_label = reaction_label + [reaction.label]
else:
reaction_label = [reaction.label]
subg.add_edge(node1, node2, reaction=reaction_label)
path = [short_p for short_p in nx.shortest_path(subg,
source=molecule1,
target=molecule2
)
]
som_path = []
for idx in range(len(path)-1):
edge_reactions = subg.get_edge_data(path[idx], path[idx+1])[cn.REACTION]
som_path.append(cn.PathComponents(node1=path[idx],
node2=path[idx+1],
reactions=edge_reactions
)
)
return som_path
def addTypeTwoError(self, cycle):
"""
Add Type II Error components to self.type_two_errors
which is a list of lists
All components of resulting PathComponents are str
:param list-SOM cycle:
"""
# exceptionally, here PathComponents are
# node1=[], node2=[], reactions=[] and their index
# of each component will match. All elements within nodes
# are in the same SOM
error_cycle = []
for node_idx in range(len(cycle) - 1):
som1 = cycle[node_idx]
som2 = cycle[node_idx + 1]
som1_moles = {mole.name for mole in list(som1.molecules)}
som2_moles = {mole.name for mole in list(som2.molecules)}
reactions = self.get_edge_data(som1, som2)[cn.REACTION]
# all reactions (in an edge), should create a single PathComponent
nodes1 = []
nodes2 = []
reaction_labels = []
for r in reactions:
reaction = self.simple.getReaction(r)
if reaction.category == cn.REACTION_n_1:
sources = {r.molecule.name for r in reaction.reactants}
destinations = {p.molecule.name for p in reaction.products}
elif reaction.category == cn.REACTION_1_n:
sources = {p.molecule.name for p in reaction.products}
destinations = {
r.molecule.name
for r in reaction.reactants
}
# for any reaction that addes arcs, len(nodes2)==1
node2 = list(destinations.intersection(som2_moles))[0]
for node1 in list(sources.intersection(som1_moles)):
nodes1.append(node1)
nodes2.append(node2)
reaction_labels.append(reaction.label)
error_cycle.append(
cn.PathComponents(node1=nodes1,
node2=nodes2,
reactions=reaction_labels))
som1 = cycle[-1]
som2 = cycle[0]
som1_moles = {mole.name for mole in list(som1.molecules)}
som2_moles = {mole.name for mole in list(som2.molecules)}
reactions = self.get_edge_data(som1, som2)[cn.REACTION]
# all reactions (in an edge), should create a single PathComponent
nodes1 = []
nodes2 = []
reaction_labels = []
for r in reactions:
reaction = self.simple.getReaction(r)
if reaction.category == cn.REACTION_n_1:
sources = {r.molecule.name for r in reaction.reactants}
destinations = {p.molecule.name for p in reaction.products}
elif reaction.category == cn.REACTION_1_n:
sources = {p.molecule.name for p in reaction.products}
destinations = {r.molecule.name for r in reaction.reactants}
# for any reaction that addes arcs, len(nodes2)==1
node2 = list(destinations.intersection(som2_moles))[0]
for node1 in list(sources.intersection(som1_moles)):
nodes1.append(node1)
nodes2.append(node2)
reaction_labels.append(reaction.label)
error_cycle.append(
cn.PathComponents(node1=nodes1,
node2=nodes2,
reactions=reaction_labels))
self.type_two_errors.append(error_cycle)