def test_createInfectedPersonsBestEffort2():
"""
Test that when the population size is less then the amount of people that had been chosen to be infected,
the simulation doesn't crash
"""
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
ageList = [random.randint(19,40) for i in range(10)]
PersonList = list(map(Person, ageList))
env_arr = []
my_world = World(
all_people = PersonList,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.infect_random_set(num_infected = 0, infection_doc = "", per_to_immune = 2,city_name = None,min_age=18,people_per_day =0)
my_simulation.simulate_day()
cnt_immune = 0
cnt_sick = 0
for person in my_world.all_people():
if person.get_disease_state() == DiseaseState.IMMUNE:
cnt_immune += 1
else:
cnt_sick += 1
assert cnt_immune == 10
assert cnt_sick == 0
def test_immune_and_get_events2():
config_path = os.path.join(os.path.dirname(__file__), "..", "src",
"config.json")
Expected = -1
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__), "..", "src",
paramsDataPath),
override=True)
p = Person(30)
ok,events = p.immune_and_get_events(INITIAL_DATE , timedelta(days = 20), \
((DiseaseState.SUSCEPTIBLE,timedelta(10)),(DiseaseState.LATENT,timedelta(5)), \
(DiseaseState.SUSCEPTIBLE,None)))
assert len(events) == 3
assert ok
persons_arr = [p]
env_arr = []
small_world = world.World(all_people=persons_arr,
all_environments=env_arr,
generating_city_name="test",
generating_scale=1)
my_simulation = Simulation(world=small_world,
initial_date=INITIAL_DATE,
interventions=[])
for i in range(10):
my_simulation.simulate_day()
events[0].apply(simulation=my_simulation)
assert p.get_disease_state() == DiseaseState.LATENT
for i in range(5):
my_simulation.simulate_day()
events[1].apply(simulation=my_simulation)
assert p.get_disease_state() == DiseaseState.IMMUNE
def test_createInfectedPersons3():
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
Expected = -1
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
kids = [random.randint(0,17) for i in range(5)]
adults = [random.randint(19,40) for i in range(5)]
ageList = kids + adults
PersonList = list(map(Person, ageList))
env_arr = []
my_world = World(
all_people = PersonList,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.infect_random_set(num_infected = 0, infection_doc = "", per_to_immune = 0.5,Immune_compliance = 0,city_name = None,min_age=18,people_per_day =5)
my_simulation.simulate_day()
#assert events dictionary is not empty
cnt_immune = 0
for person in my_world.all_people():
if person.get_disease_state() == DiseaseState.IMMUNE:
cnt_immune = cnt_immune + 1
assert cnt_immune == 0
def test_createInfectedPersonsOredredASCENDING():
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
Expected = -1
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
kids = [0,4,8,12,16]
adults = [25,29,33]
ageList = kids + adults
youngest = Person(21)
Oldest = Person(37)
PersonList = list(map(Person, ageList))
PersonList = PersonList + [youngest , Oldest]
env_arr = []
my_world = World(
all_people = PersonList,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.infect_random_set(num_infected = 0, infection_doc = "", per_to_immune = 0.5,order= ORDER.ASCENDING,city_name = None,min_age=18,people_per_day =1)
my_simulation.simulate_day()
assert youngest.get_disease_state() == DiseaseState.IMMUNE
#Can't check day by day lots of noise with seir times
for _ in range(4):
my_simulation.simulate_day()
cnt_immune =0
for person in my_world.all_people():
if person.get_disease_state() == DiseaseState.IMMUNE:
cnt_immune = cnt_immune + 1
assert cnt_immune <= 5
def test_createInfectedPersonsByHouseHoldBestEffort2():
"""
Test that when the population size is less then the amount of people that had been chosen to be infected by households,
the simulation doesn't crash
"""
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
#create diff enviroments
KidsHouse = Household(city = None,contact_prob_between_each_two_people=1)
AdultsHouse = Household(city = None,contact_prob_between_each_two_people=1)
MixedHouse = Household(city = None,contact_prob_between_each_two_people=1)
kidsAges = [random.randint(0,17) for i in range(4)]
adultsAges = [random.randint(19,40) for i in range(3)]
KidsLst = list(map(Person, kidsAges))
adultsLst = list(map(Person, adultsAges))
persons_arr = KidsLst + adultsLst
#register people to diff env
KidsHouse.sign_up_for_today(KidsLst[0],1)
KidsHouse.sign_up_for_today(KidsLst[1],1)
AdultsHouse.sign_up_for_today(adultsLst[0],1)
AdultsHouse.sign_up_for_today(adultsLst[1],1)
MixedHouse.sign_up_for_today(adultsLst[2],1)
MixedHouse.sign_up_for_today(KidsLst[2],1)
MixedHouse.sign_up_for_today(KidsLst[3],1)
assert len(KidsHouse.get_people()) == 2
assert len(AdultsHouse.get_people()) == 2
assert len(MixedHouse.get_people()) == 3
env_arr = [KidsHouse,AdultsHouse,MixedHouse]
my_world = World(
all_people = persons_arr,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1,)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.immune_households_infect_others(num_infected = 0, infection_doc = "", per_to_immune = 2 ,city_name = None,min_age=18,people_per_day =5)
my_simulation.simulate_day()
cnt_immune = 0
cnt_sick = 0
for person in my_world.all_people():
if person.get_disease_state() == DiseaseState.IMMUNE:
cnt_immune += 1
elif person.get_disease_state() != DiseaseState.SUSCEPTIBLE:
cnt_sick += 1
assert cnt_immune == 3
assert cnt_sick == 0
def test_createImmunehouseholds4():
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
#create diff enviroments
KidsHouse = Household(city = None,contact_prob_between_each_two_people=1)
AdultsHouse = Household(city = None,contact_prob_between_each_two_people=1)
MixedHouse = Household(city = None,contact_prob_between_each_two_people=1)
kidsAges = [random.randint(0,17) for i in range(4)]
adultsAges = [random.randint(19,40) for i in range(3)]
KidsLst = list(map(Person, kidsAges))
adultsLst = list(map(Person, adultsAges))
persons_arr = KidsLst + adultsLst
#register people to diff env
KidsHouse.sign_up_for_today(KidsLst[0],1)
KidsHouse.sign_up_for_today(KidsLst[1],1)
AdultsHouse.sign_up_for_today(adultsLst[0],1)
AdultsHouse.sign_up_for_today(adultsLst[1],1)
MixedHouse.sign_up_for_today(adultsLst[2],1)
MixedHouse.sign_up_for_today(KidsLst[2],1)
MixedHouse.sign_up_for_today(KidsLst[3],1)
assert len(KidsHouse.get_people()) == 2
assert len(AdultsHouse.get_people()) == 2
assert len(MixedHouse.get_people()) == 3
env_arr = [KidsHouse,AdultsHouse,MixedHouse]
my_world = World(
all_people = persons_arr,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1,)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.immune_households_infect_others(num_infected = 0, infection_doc = "", per_to_immune = 1,Immune_compliance= 0 ,city_name = None,min_age=18,people_per_day= 3 )
my_simulation.simulate_day()
#assert events dictionary is not empty
cnt_immune = 0
for person in my_world.all_people():
if person.get_disease_state() == DiseaseState.IMMUNE:
cnt_immune = cnt_immune + 1
assert cnt_immune == 0
def test_createImmunehouseholds2():
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
#create diff enviroments
house1 = Household(city = None,contact_prob_between_each_two_people=1)
house2 = Household(city = None,contact_prob_between_each_two_people=1)
house1Ages = [98,93,5]
house2Ages = [94,6]
house1Lst = list(map(Person, house1Ages))
house2Lst = list(map(Person, house2Ages))
persons_arr = house1Lst + house2Lst
#register people to diff env
house1.sign_up_for_today(house1Lst[0],1)
house1.sign_up_for_today(house1Lst[1],1)
house1.sign_up_for_today(house1Lst[2],1)
house2.sign_up_for_today(house2Lst[0],1)
house2.sign_up_for_today(house2Lst[1],1)
assert len(house1.get_people()) == 3
assert len(house2.get_people()) == 2
env_arr = [house1,house2]
my_world = World(
all_people = persons_arr,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1,)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.immune_households_infect_others(num_infected = 0, infection_doc = "", per_to_immune = 0.6,Sort_order=ORDER.DESCENDING ,city_name = None,min_age=18,people_per_day= 3 )
my_simulation.simulate_day()
#assert events dictionary is not empty
cnt_immune = 0
for person in my_world.all_people():
if (person.get_age() in [94,93,98]) and (person.get_disease_state() == DiseaseState.IMMUNE):
cnt_immune = cnt_immune + 1
assert cnt_immune == 3
def test_ImmuneGeneralPopulationIntervention():
#pretesting
config_path = os.path.join(os.path.dirname(__file__), "..", "src",
"config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__), "..", "src",
paramsDataPath),
override=True)
my_intervention = ImmuneGeneralPopulationIntervention(
compliance=1,
start_date=INITIAL_DATE,
duration=daysdelta(40),
people_per_day=1,
min_age=15)
assert my_intervention is not None
persons_arr = list(map(Person, [10, 20, 30]))
assert len(persons_arr) == 3
env_arr = []
small_world = World(all_people=persons_arr,
all_environments=env_arr,
generating_city_name="test",
generating_scale=1)
my_simulation = Simulation(world=small_world,
initial_date=INITIAL_DATE,
interventions=[my_intervention])
#test
lst = my_intervention.generate_events(small_world)
#Assert results
assert lst is not None
assert len(lst) == 2
for i in range(1):
assert isinstance(lst[i], DayEvent)
my_simulation.simulate_day()
cnt_immune = sum([
1 for p in persons_arr if p.get_disease_state() == DiseaseState.IMMUNE
])
assert cnt_immune == 1
my_simulation.simulate_day()
cnt_immune = sum([
1 for p in persons_arr if p.get_disease_state() == DiseaseState.IMMUNE
])
assert cnt_immune == 2
my_simulation.simulate_day()
cnt_immune = sum([
1 for p in persons_arr if p.get_disease_state() == DiseaseState.IMMUNE
])
assert cnt_immune == 2
def test_immune_and_get_events5():
"""
Test that a person that is not Susptible nor latent when he should get immuned continues his
usual path to his death
"""
config_path = os.path.join(os.path.dirname(__file__), "..", "src",
"config.json")
Expected = -1
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__), "..", "src",
paramsDataPath),
override=True)
p = Person(30)
ok, events = p.immune_and_get_events(INITIAL_DATE , timedelta(days = 20), \
((DiseaseState.SUSCEPTIBLE,timedelta(10)),(DiseaseState.LATENT,timedelta(5)),\
(DiseaseState.ASYMPTOMATICINFECTIOUS,timedelta(5)),(DiseaseState.DECEASED,timedelta(5)),(DiseaseState.DECEASED,None)))
assert len(events) == 4
assert ok == False
persons_arr = [p]
env_arr = []
small_world = world.World(all_people=persons_arr,
all_environments=env_arr,
generating_city_name="test",
generating_scale=1)
my_simulation = Simulation(world=small_world,
initial_date=INITIAL_DATE,
interventions=[])
for i in range(10):
my_simulation.simulate_day()
events[0].apply(simulation=my_simulation)
assert p.get_disease_state() == DiseaseState.LATENT
for i in range(5):
my_simulation.simulate_day()
events[1].apply(simulation=my_simulation)
assert p.get_disease_state() == DiseaseState.ASYMPTOMATICINFECTIOUS
#Because this person was not susptible nor latent he cannot be immuned
for i in range(5):
my_simulation.simulate_day()
events[2].apply(simulation=my_simulation)
assert p.get_disease_state() == DiseaseState.DECEASED
def test_ImmuneByHouseholdIntervention():
#pretesting
config_path = os.path.join(os.path.dirname(__file__), "..", "src",
"config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__), "..", "src",
paramsDataPath),
override=True)
my_intervention = ImmuneByHouseholdIntervention(compliance=1,
start_date=INITIAL_DATE,
duration=daysdelta(40),
houses_per_day=1,
min_age=18)
assert my_intervention is not None
config_path = os.path.join(os.path.dirname(__file__), "..", "src",
"config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__), "..", "src",
paramsDataPath),
override=True)
#create diff enviroments
KidsHouse = Household(city=None, contact_prob_between_each_two_people=1)
AdultsHouse = Household(city=None, contact_prob_between_each_two_people=1)
MixedHouse = Household(city=None, contact_prob_between_each_two_people=1)
kidsAges = [random.randint(0, 17) for i in range(4)]
adultsAges = [random.randint(19, 40) for i in range(3)]
KidsLst = list(map(Person, kidsAges))
adultsLst = list(map(Person, adultsAges))
persons_arr = KidsLst + adultsLst
#register people to diff env
KidsHouse.sign_up_for_today(KidsLst[0], 1)
KidsHouse.sign_up_for_today(KidsLst[1], 1)
AdultsHouse.sign_up_for_today(adultsLst[0], 1)
AdultsHouse.sign_up_for_today(adultsLst[1], 1)
MixedHouse.sign_up_for_today(adultsLst[2], 1)
MixedHouse.sign_up_for_today(KidsLst[2], 1)
MixedHouse.sign_up_for_today(KidsLst[3], 1)
assert len(KidsHouse.get_people()) == 2
assert len(AdultsHouse.get_people()) == 2
assert len(MixedHouse.get_people()) == 3
env_arr = [KidsHouse, AdultsHouse, MixedHouse]
my_world = World(
all_people=persons_arr,
all_environments=env_arr,
generating_city_name="test",
generating_scale=1,
)
my_simulation = Simulation(world=my_world,
initial_date=INITIAL_DATE,
interventions=[my_intervention])
#test
lst = my_intervention.generate_events(my_world)
#Assert results
assert lst is not None
assert len(lst) == 5
for i in range(1):
assert isinstance(lst[i], DayEvent)
my_simulation.simulate_day()
cnt_immune = sum([
1 for p in persons_arr if p.get_disease_state() == DiseaseState.IMMUNE
])
assert cnt_immune <= 3
my_simulation.simulate_day()
cnt_immune = sum([
1 for p in persons_arr if p.get_disease_state() == DiseaseState.IMMUNE
])
assert cnt_immune == 5
my_simulation.simulate_day()
def test_count_infected_in_hood():
'''
Test that we gather the right data about the infected persons
in each neighborhood.
'''
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
Params.loader()["person"]["state_macine_type"] = "SIR"
DiseaseState.init_infectiousness_list()
#create diff enviroments
house1 = Household(city = None,contact_prob_between_each_two_people=1)
house2 = Household(city = None,contact_prob_between_each_two_people=1)
house1Ages = [98,95,5]
house2Ages = [94,6]
house1Lst = list(map(Person, house1Ages))
house2Lst = list(map(Person, house2Ages))
#register people to diff env
house1.sign_up_for_today(house1Lst[0],1)
house1.sign_up_for_today(house1Lst[1],1)
house1.sign_up_for_today(house1Lst[2],1)
house2.sign_up_for_today(house2Lst[0],1)
house2.sign_up_for_today(house2Lst[1],1)
assert len(house1.get_people()) == 3
assert len(house2.get_people()) == 2
n1 = NeighborhoodCommunity(city= None,contact_prob_between_each_two_people= 1)
n2 = NeighborhoodCommunity(city= None,contact_prob_between_each_two_people= 1)
states_table1 = ((DiseaseState.LATENT,daysdelta(3)),
(DiseaseState.ASYMPTOMATICINFECTIOUS,daysdelta(3)),
(DiseaseState.IMMUNE, daysdelta(3)),
(DiseaseState.IMMUNE, None))
states_table2 = ((DiseaseState.IMMUNE, daysdelta(3)),
(DiseaseState.IMMUNE, None))
events_acc = []
for person in house1.get_people():
person.add_environment(n1)
events = person.gen_and_register_events_from_seir_times(date = INITIAL_DATE,states_and_times= states_table1)
events_acc += events
for person in house2.get_people():
person.add_environment(n2)
events = person.gen_and_register_events_from_seir_times(date = INITIAL_DATE,states_and_times= states_table2)
events_acc += events
env_arr = [house1,house2,n1,n2]
persons_arr = []
persons_arr += house1Lst
persons_arr += house2Lst
my_world = World(
all_people = persons_arr,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1,)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.register_events(events_acc)
for i in range(4):
d1 = my_simulation.stats.get_neiborhood_data(INITIAL_DATE + daysdelta(i),n1.get_neighborhood_id())
d2 = my_simulation.stats.get_neiborhood_data(INITIAL_DATE + daysdelta(i),n2.get_neighborhood_id())
assert d1 == 0 , "Day:" + str(i)
assert d2 == 0 , "Day:" + str(i)
my_simulation.simulate_day()
for i in range(3):
d1 = my_simulation.stats.get_neiborhood_data(INITIAL_DATE + daysdelta(i+3),n1.get_neighborhood_id())
d2 = my_simulation.stats.get_neiborhood_data(INITIAL_DATE + daysdelta(i+3),n2.get_neighborhood_id())
assert d1 == 3 , "Day:" + str(3 + i)
assert d2 == 0 , "Day:" + str(3 + i)
my_simulation.simulate_day()
for i in range(3):
d1 = my_simulation.stats.get_neiborhood_data(INITIAL_DATE,n1.get_neighborhood_id())
d2 = my_simulation.stats.get_neiborhood_data(INITIAL_DATE,n2.get_neighborhood_id())
assert d1 == 0 , "Day:" + str(6 + i)
assert d2 == 0 , "Day:" + str(6 + i)
my_simulation.simulate_day()