def test_createInfectedPersons(helpers):
"""
#create population with 5 people ages [9,19,29,39,49]
#test that each day one of them is getting immuned
"""
helpers.clean_outputs()
#Editig confige file saving is nessery
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
ConfigData = None
#reading the confige file
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 = list(map(Person, [9,19,29,39,49,59]))
assert len(persons_arr) == 6
env_arr = []
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.run_simulation(7,"test_simulation",datas_to_plot = None,extensionsList = ["ImmuneByAgeExtension","EmptyExtension"] )
cnt = sum([1 for p in persons_arr if p.get_disease_state() == DiseaseState.IMMUNE])
assert cnt == 4
def create_and_run_simulation(self,
outdir,
stop_early,
with_population_caching=True,
verbosity=False):
"""
The main function that handles the run of the simulation by the task.
It updated the params changes, loads or creates the population, initializes the simulation and runs it.
:param outdir: the output directory for the task
:param stop_early: only relevant to R computation, see Simulation doc
:param with_population_caching: bool, if False generates the population, else - tries to use the cache and save time.
:param verbosity: bool, if it's True then additional output logs will be printed to the screen
"""
seed.set_random_seed()
config_path = os.path.join(os.path.dirname(__file__), "config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
citiesDataPath = ConfigData['CitiesFilePath']
paramsDataPath = ConfigData['ParamsFilePath']
Extensionslst = ConfigData['ExtensionsNamelst']
Params.load_from(os.path.join(os.path.dirname(__file__),
paramsDataPath),
override=True)
for param, val in self.params_to_change.items():
Params.loader()[param] = val
DiseaseState.init_infectiousness_list()
citiesDataPath = citiesDataPath
population_loader = PopulationLoader(
citiesDataPath,
added_description=Params.loader().description(),
with_caching=with_population_caching,
verbosity=verbosity)
world = population_loader.get_world(city_name=self.city_name,
scale=self.scale,
is_smart=True)
ExtensionType = None
sim = Simulation(world,
self.initial_date,
self.interventions,
verbosity=verbosity,
outdir=outdir,
stop_early=stop_early)
self.infection_params.infect_simulation(sim, outdir)
if len(Extensionslst) > 0:
sim.run_simulation(self.days,
self.scenario_name,
datas_to_plot=self.datas_to_plot,
extensionsList=Extensionslst)
else:
sim.run_simulation(self.days,
self.scenario_name,
datas_to_plot=self.datas_to_plot,
extensionsList=None)
def test_CreateDeltaFile(helpers):
helpers.clean_outputs()
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(0, 40) for i in range(10)]
PersonList = list(map(Person, ageList))
events_acc = []
for person in PersonList:
states_table = ((DiseaseState.LATENT, daysdelta(3)),
(DiseaseState.ASYMPTOMATICINFECTIOUS,
daysdelta(3)), (DiseaseState.IMMUNE, daysdelta(3)),
(DiseaseState.IMMUNE, None))
events = person.gen_and_register_events_from_seir_times(
date=INITIAL_DATE, states_and_times=states_table)
events_acc += events
# person.set_disease_state(DiseaseState.LATENT)
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.register_events(events_acc)
my_simulation.run_simulation(num_days=10, name="test")
#assert events dictionary is not empty
txt = my_simulation.stats.get_state_stratified_summary_table(
table_format=TableFormat.CSV)
test_data = StringIO(txt)
tbl = pd.read_csv(test_data)
assert len(tbl) == 7
print(tbl)
assert tbl.iloc[0, DiseaseState.SUSCEPTIBLE.value] == 10
assert tbl.iloc[3, DiseaseState.ASYMPTOMATICINFECTIOUS.value] == 10
assert tbl.iloc[6, DiseaseState.IMMUNE.value] == 10
def test_SymptomaticIsolationIntervention_Genarete_events(helpers):
#pretesting
helpers.clean_outputs()
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 = SymptomaticIsolationIntervention(compliance=1,
start_date=INITIAL_DATE,
duration=daysdelta(40))
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) == 3
for i in range(1):
assert isinstance(lst[i], DayEvent)
for person in persons_arr:
assert len(list(person.state_to_events.keys())) == (1 + 4)
my_simulation.run_simulation(name="test", num_days=60)
def test_CreateDeltaFileAtlit(helpers):
helpers.clean_outputs()
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)
citiesDataPath = ConfigData['CitiesFilePath']
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()
pop = population_loader.PopulationLoader(citiesDataPath)
my_world = pop.get_world(city_name='Atlit', scale=1, is_smart=False)
sim = Simulation(world=my_world, initial_date=INITIAL_DATE)
sim.infect_random_set(num_infected=500, infection_doc="")
sim.run_simulation(num_days=180, name="test")
#assert events dictionary is not empty
txt = sim.stats.get_state_stratified_summary_table(
table_format=TableFormat.CSV)
test_data = StringIO(txt)
tbl = pd.read_csv(test_data)
cnt_start = tbl.iloc[0, DiseaseState.SUSCEPTIBLE.value] + tbl.iloc[
0, DiseaseState.LATENT.value]
cnt_end = 0
for i in range(len(tbl)):
cnt_end = cnt_end + tbl.iloc[i, DiseaseState.IMMUNE.value] + tbl.iloc[
i, DiseaseState.DECEASED.value]
plug_number = len([
p for p in sim._world.all_people()
if p.get_disease_state() == DiseaseState.SUSCEPTIBLE
])
assert cnt_start >= cnt_end + plug_number