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_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 city_curfew_routine(person: Person, city_name):
"""
Create a routine change that represents a city curfew effect on a person routine.
Here we try to represent the changing (decreasing/ increasing of weights) of the weight in all the environment,
due to the closure of the city.
:param person: Person
:return: routine change dict, keys are environment names, values are weight multipliers.
"""
params = Params.loader()["interventions_routines"]["city_curfew"]
routine = {}
has_free_time = False
for env_name, env in person._environments.items():
if env._city is None:
continue
if not ((env._city.get_name() == city_name) ^ (person.get_city_name() == city_name)):
continue
else:
routine[env_name] = params["out_of_city"]
has_free_time = True
if has_free_time:
routine['household'] = params["in_city"]["household"]
routine['city_community'] = params["in_city"]["city_community"]
routine['neighborhood_community'] = params["in_city"]["neighborhood_community"]
return routine
def test_sample_SIRS_seirs_times():
#Pretest
Params.clean()
SIRS.clean()
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)
curr_machine_type = machine_type["SIRS"]
p = Person(94)
final_states = []
for i in range(1000):
table = sample_seir_times(curr_machine_type, p)
assert table[0][0] == DiseaseState.LATENT
final_states.append(table[-1][0])
cnt_table = Counter(final_states)
assert DiseaseState.DECEASED in cnt_table.keys()
assert DiseaseState.SUSCEPTIBLE in cnt_table.keys()
assert len(cnt_table.keys()) == 2
def test_latent_incubating_critical_deceased():
#Pretest
Params.clean()
SIRS.clean()
config_path = os.path.join(
os.path.dirname(__file__), "tests_config_files",
"test_latent_incubating_critical_deceased_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__),
"tests_params_files", paramsDataPath),
override=True)
p = Person(30)
for _ in range(100):
for cur_type in machine_type:
tbl = sample_seir_times(cur_type, p)
assert tbl[0][0] == DiseaseState.LATENT, "{}".format(cur_type.name)
assert tbl[1][0] == DiseaseState.INCUBATINGPOSTLATENT, "{}".format(
cur_type.name)
assert tbl[2][
0] == DiseaseState.SYMPTOMATICINFECTIOUS, "{}".format(
cur_type.name)
assert tbl[3][0] == DiseaseState.CRITICAL, "{}".format(
cur_type.name)
assert tbl[4][0] == DiseaseState.DECEASED, "{}".format(
cur_type.name)
def quarantine_routine(person: Person):
"""
Create a routine change that represents a person being in quarantine.
Here we try to represent the changing (decreasing of weights) of the weight in all the environment, due to the quarantine.
:param person: Person
:return: routine change dict, keys are environment names, values are weight multipliers.
"""
params = Params.loader()["interventions_routines"]["quarantine"]
return {env_name: params["all"] for env_name in person.get_routine()}
def generate_household_in_city(city):
"""
Generates a househeold from a given city (which holds relevant distributions)
:param city: A City object corresponding to where we want to generate a household.
:return: A list of Person objects corresponding to a random household in that city.
"""
assert isinstance(city, City)
household_size = city.household_size_distribution.sample()
return [
Person(city.age_distribution.sample()) for i in range(household_size)
]
def test_SIRS_second_infection():
"""
Test that in SIRS model in case that a person get sick twice,
(and get recovered between them).
He will experience two different time schedule of the illness
"""
#Pretest
Params.clean()
SIRS.clean()
config_path = os.path.join(
os.path.dirname(__file__), "tests_config_files",
"test_latent_incubating_critical_immune_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__),
"tests_params_files", paramsDataPath),
override=True)
Params.loader()["person"]["state_macine_type"] = "SIRS"
p = Person(30)
event_lst = p.infect_and_get_events(INITIAL_DATE,
InitialGroup.initial_group())
p.set_disease_state(DiseaseState.SUSCEPTIBLE)
event_lst2 = p.infect_and_get_events(INITIAL_DATE,
InitialGroup.initial_group())
assert not (event_lst == event_lst2)
def test_sortPersonsDescending():
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)
persons_arr = [Person(random.randint(0, 99)) for _ in range(20)]
persons_arr = sorted(persons_arr,
key=cmp_to_key(Person.person_comperator_DESCENDING))
for i in range(1, 20):
assert persons_arr[i - 1].get_age() >= persons_arr[i].get_age()
def household_isolation_routine(person: Person):
"""
Create a routine change that represents a person being in isolation at home.
Here we try to represent the changing (decreasing/ increasing of weights) of the weight in all the environment,
due to the person staying at home.
:param person: Person
:return: routine change dict, keys are environment names, values are weight multipliers.
"""
params = Params.loader()["interventions_routines"]["household_isolation"]
routine = {}
for env_name in person.get_routine():
if env_name == 'household':
routine['household'] = params["household"]
else:
routine[env_name] = params["other"]
return routine
def workplace_closure_routine(person: Person):
"""
Create a routine change that represents a closure of the person's workplace.
Here we try to represent the changing of the weight in the workplace environment as well as other environments,
due to the closure.
:param person: Person
:return: routine change dict, keys are environment names, values are weight multipliers.
"""
params = Params.loader()["interventions_routines"]["workplace_closure"]
routine = {}
for env_name in person.get_routine():
if env_name == 'workplace':
routine['workplace'] = params["workplace"]
else:
routine[env_name] = params["other"]
return routine
def social_distancing_routine(person: Person):
"""
Create a routine change that represents a social distancing effect on a person routine.
Here we try to represent the changing (decreasing/ increasing of weights) of the weight in all the environment,
due to the closure.
:param person: Person
:return: routine change dict, keys are environment names, values are weight multipliers.
"""
params = Params.loader()["interventions_routines"]["social_distancing"]
routine = {}
for env_name in person.get_routine():
if env_name == 'household':
routine['household'] = params["household"]
elif env_name == 'workplace':
routine['workplace'] = params["workplace"]
elif env_name == 'school':
routine[env_name] = params["school"]
else:
routine[env_name] = params["other"]
return routine
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