def application(output_folder="output", csv_name="ReportNodeDemographics.csv", config_filename="config.json",
report_name=sft.sft_output_filename, debug=False):
if debug:
print("output_folder: " + output_folder + "\n")
print("csv_name: " + csv_name + "\n")
print("config_name: " + config_filename + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
with open(config_filename) as infile:
test_config_name = json.load(infile)["parameters"]["Config_Name"]
sft.start_report_file(report_name, test_config_name)
all_data_df = pd.read_csv(path.join(output_folder, csv_name))
all_data_df.rename(columns={' NodeID': 'NodeID', ' Gender': 'Gender',
' AgeYears': 'AgeYears', ' NumIndividuals': 'NumIndividuals',
' NumInfected': 'NumInfected'}, inplace=True)
all_data_df.drop(['NumInfected'], axis=1, inplace=True)
if debug:
all_data_df.to_csv("DEBUG_all_data_cleaned.csv")
last_day_df = all_data_df.loc[all_data_df['Time']==399]
if debug:
last_day_df.to_csv("DEBUG_day_399_data_cleaned.csv")
northern_nodes = last_day_df[last_day_df['NodeID'].isin([1,2,3])]
southern_nodes = last_day_df[last_day_df['NodeID'].isin([7,8,9])]
eastern_nodes = last_day_df[last_day_df['NodeID'].isin([3,6,9])]
western_nodes = last_day_df[last_day_df['NodeID'].isin([1,4,7])]
create_report_file(sft_filename=report_name, n_nodes=northern_nodes,
s_nodes=southern_nodes, e_nodes=eastern_nodes,
w_nodes=western_nodes)
def application(config_filename="config.json", debug=False):
with open(config_filename) as infile:
config_json = json.load(infile)
config_params = config_json[d_ss.ConfigKeys.PARAMETERS_KEY]
config_object = d_ss.load_config_file(config_filename=config_filename, debug=debug)
sft.start_report_file(output_filename=sft.sft_output_filename,
config_name=config_object[d_ss.ConfigKeys.CONFIGNAME_KEY])
d_ss.start_serialization_test()
expected_dtk_filepath = config_params[d_ss.ConfigKeys.Serialization.POPULATION_PATH]
expected_dtk_filename = config_params[d_ss.ConfigKeys.Serialization.POPULATION_FILENAMES_KEY][0]
expected_dtk_fullpath = path.join(expected_dtk_filepath, expected_dtk_filename)
dtk_file = d_ss.DtkFile(expected_dtk_fullpath, file_suffix="old")
dtk_file.write_node_to_disk(node_index=0)
dtk_file.write_simulation_to_disk()
found_people={}
ignored_people=[]
testable_infections = 5
remaining_sim_duration = config_object[d_ss.ConfigKeys.Serialization.TIMESTEPS_KEY][0]
while len(found_people) < testable_infections:
maybe_person = dtk_file.find_human_from_node(node_index=0, min_infections=1, ignore_suids=ignored_people)
human_suid = maybe_person["suid"]["id"]
if debug:
print(f"Trying human {human_suid}.\n")
acceptable_infection = has_acceptable_infection(maybe_person, remaining_sim_duration)
if acceptable_infection:
dtk_file.write_human_to_disk(node_index=0, suid=human_suid)
found_people[human_suid] = acceptable_infection
ignored_people.append(human_suid)
dtk_file.write_json_file(found_people, "DEBUG_found_infected_persons.json")
def application(output_folder="output",
config_filename="config.json",
jsonreport_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder + "\n")
print("config_filename: " + config_filename + "\n")
print("insetchart_name: " + jsonreport_name + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
config_object = dtk_iis.load_config_file(config_filename=config_filename,
debug=debug)
demographics_overlay_name = config_object[
dtk_iis.ConfigKeys.DEMOGRAPHIC_FILENAMES][-1]
campaign_name = config_object[dtk_iis.ConfigKeys.CAMPAIGN_FILENAME]
test_config_name = config_object[dtk_iis.ConfigKeys.CONFIG_NAME]
campaign_object = dtk_iis.load_campaign_file(campaign_name, debug)
outbreak_day = campaign_object[dtk_iis.CampaignKeys.START_DAY]
demographics_object = dtk_iis.load_demographics_file(
demographics_filename=demographics_overlay_name,
susceptibility_initialization_type=config_object[
dtk_iis.ConfigKeys.SUS_INIT_DIST_TYPE],
debug=debug)
average_immunity = demographics_object[
dtk_iis.DemographicFileKeys.KEY_AVERAGE_IMMUNITY]
sft.start_report_file(report_name, test_config_name)
report_data_object = dtk_iis.parse_json_report(output_folder=output_folder,
report_name=jsonreport_name,
debug=debug)
statistical_population_channel = report_data_object[
dtk_iis.InsetChannels.STATISTICAL_POPULATION]
new_infections_channel = report_data_object[
dtk_iis.InsetChannels.NEW_INFECTIONS]
expected_infections_obj = dtk_iis.get_expected_infections(
statistical_population_channel,
average_immunity,
campaign_object,
debug=debug)
actual_infections = dtk_iis.get_actual_infections(new_infections_channel,
outbreak_day)
dtk_iis.create_report_file(expected_infections_obj,
actual_infections,
outbreak_day,
report_name,
debug=debug)
def application(output_folder="output", config_filename="config.json",
jsonreport_name="InsetChart.json", stdout_filename="test.txt",
report_name=sft.sft_output_filename, debug=False):
if debug:
print("output_folder: " + output_folder)
print("config_filename: " + config_filename)
print("insetchart_name: " + jsonreport_name)
print("report_name: " + report_name)
print("debug: " + str(debug))
sft.wait_for_done()
config_object = dtk_iis.load_config_file(config_filename=config_filename,
debug=debug)
demographics_overlay_name = config_object[dtk_iis.ConfigKeys.DEMOGRAPHIC_FILENAMES][-1]
campaign_name = config_object[dtk_iis.ConfigKeys.CAMPAIGN_FILENAME]
test_config_name = config_object[dtk_iis.ConfigKeys.CONFIG_NAME]
campaign_object = dtk_iis.load_campaign_file(campaign_name, debug)
outbreak_day = campaign_object[dtk_iis.CampaignKeys.START_DAY]
demographics_object = dtk_iis.load_demographics_file(
demographics_filename=demographics_overlay_name,
susceptibility_initialization_type=config_object[dtk_iis.ConfigKeys.SUS_INIT_DIST_TYPE],
debug=debug)
average_immunity = demographics_object[dtk_iis.DemographicFileKeys.KEY_AVERAGE_IMMUNITY]
sft.start_report_file(report_name, test_config_name)
individual_df = dtk_iis.parse_stdout_file(stdout_filename, debug=debug)
dtk_iis.test_immunity_within_age_range(individual_df, max_age=365,
expected_immunity=0.0)
dtk_iis.test_immunity_within_age_range(individual_df, max_age=730,
expected_immunity=0.4)
report_data_object = dtk_iis.parse_json_report(output_folder=output_folder,
report_name=jsonreport_name,
debug=debug)
statistical_population_channel = report_data_object[dtk_iis.InsetChannels.STATISTICAL_POPULATION]
new_infections_channel = report_data_object[dtk_iis.InsetChannels.NEW_INFECTIONS]
expected_infections_obj = dtk_iis.get_expected_infections(statistical_population_channel,
average_immunity,
campaign_object,
debug=debug)
actual_infections = dtk_iis.get_actual_infections(new_infections_channel,
outbreak_day)
dtk_iis.create_report_file(expected_infections_obj, actual_infections,
outbreak_day, report_name,
debug=debug)
def application(output_folder="output", config_filename="config.json",
report_name=sft.sft_output_filename, debug=False):
if debug:
print("output_folder: {0}".format(output_folder))
print("config_filename: {0}".format(config_filename))
print("report_name: {0}".format(report_name))
print("debug: {0}".format(debug))
config_object = d_ss.load_config_file(config_filename=config_filename, debug=debug)
sft.start_report_file(output_filename=report_name,
config_name=config_object[d_ss.ConfigKeys.CONFIGNAME_KEY],
already_started=True)
dtk_filename = path.join(output_folder, 'state-00070.dtk')
dtk_file = d_ss.DtkFile(dtk_filename)
dtk_file.write_node_to_disk(node_index=0)
dtk_file.write_simulation_to_disk()
dtk_file.write_human_to_disk(node_index=0, suid=10)
dtk_file.write_human_to_disk(node_index=0, suid=100)
dtk_file.write_human_to_disk(node_index=0, suid=1000)
#TODO: make sure each individual is Simulation_Duration days older
human_1_first = d_ss.SerializedHuman.from_file('human-10-old.json')
human_1_second = d_ss.SerializedHuman.from_file('human-10-new.json')
human_100_first = d_ss.SerializedHuman.from_file('human-100-old.json')
human_100_second = d_ss.SerializedHuman.from_file('human-100-new.json')
human_1000_first = d_ss.SerializedHuman.from_file('human-1000-old.json')
human_1000_second = d_ss.SerializedHuman.from_file('human-1000-new.json')
messages = []
expected_age_delta = config_object[d_ss.ConfigKeys.SIMULATION_DURATION_KEY]
human_1_messages = human_1_first.compare_to_older(human_1_second, expected_age_delta)
human_100_messages = human_100_first.compare_to_older(human_100_second, expected_age_delta)
human_1000_messages = human_1000_first.compare_to_older(human_1000_second, expected_age_delta)
messages += human_1_messages if human_1_messages else ["GOOD: Human 1 checks out"]
messages += human_100_messages if human_100_messages else ["GOOD: Human 100 checks out"]
messages += human_1000_messages if human_1000_messages else ["GOOD: Human 1000 checks out"]
#TODO: compare the simulation objects
#TODO: compare the node objects
success_message_formatter = sft.format_success_msg
d_ss.generate_report_file(config_object, report_name, output_folder=output_folder,
messages=messages, success_formatter=success_message_formatter,
debug=debug)
d_ss.clean_serialization_test(debug)
def application(output_folder="output", config_filename="config.json",
report_name=sft.sft_output_filename, debug=False):
if debug:
print("output_folder: {0}".format(output_folder))
print("config_filename: {0}".format(config_filename))
print("report_name: {0}".format(report_name))
print("debug: {0}".format(debug))
config_object = d_ss.load_config_file(config_filename=config_filename, debug=debug)
sft.start_report_file(output_filename=report_name, config_name=config_object[d_ss.ConfigKeys.CONFIGNAME_KEY])
success_message_formatter = sft.format_success_msg
d_ss.generate_report_file(config_object, report_name, output_folder=output_folder,
success_formatter=success_message_formatter,
debug=debug)
def application(config_filename="config.json", debug=False):
with open(config_filename) as infile:
config_json = json.load(infile)
config_params = config_json[d_ss.ConfigKeys.PARAMETERS_KEY]
config_object = d_ss.load_config_file(config_filename=config_filename, debug=debug)
sft.start_report_file(output_filename=sft.sft_output_filename,
config_name=config_object[d_ss.ConfigKeys.CONFIGNAME_KEY])
d_ss.start_serialization_test()
expected_dtk_filepath = config_params[d_ss.ConfigKeys.Serialization.POPULATION_PATH]
expected_dtk_filename = config_params[d_ss.ConfigKeys.Serialization.POPULATION_FILENAMES_KEY][0]
expected_dtk_fullpath = path.join(expected_dtk_filepath, expected_dtk_filename)
dtk_file = d_ss.DtkFile(expected_dtk_fullpath, file_suffix="old")
dtk_file.write_node_to_disk(node_index=0)
# dtk_file.drop_simulation() # TODO: Figure out how to drop random number generator parts
dtk_file.write_human_to_disk(node_index=0, suid=10)
dtk_file.write_human_to_disk(node_index=0, suid=100)
dtk_file.write_human_to_disk(node_index=0, suid=1000)
def application(config_filename="config.json", debug=False):
with open(config_filename) as infile:
config_json = json.load(infile)
config_params = config_json[d_ss.ConfigKeys.PARAMETERS_KEY]
config_object = d_ss.load_config_file(config_filename=config_filename, debug=debug)
sft.start_report_file(output_filename=sft.sft_output_filename,
config_name=config_object[d_ss.ConfigKeys.CONFIGNAME_KEY])
d_ss.start_serialization_test()
expected_dtk_filepath = config_params[d_ss.ConfigKeys.Serialization.POPULATION_PATH]
expected_dtk_filename = config_params[d_ss.ConfigKeys.Serialization.POPULATION_FILENAMES_KEY][0]
expected_dtk_fullpath = path.join(expected_dtk_filepath, expected_dtk_filename)
dtk_file = d_ss.DtkFile(expected_dtk_fullpath, file_suffix="old")
dtk_file.write_node_to_disk(node_index=0)
dtk_file.write_simulation_to_disk()
dtk_file.write_human_to_disk(node_index=0, suid=10)
dtk_file.write_human_to_disk(node_index=0, suid=100)
dtk_file.write_human_to_disk(node_index=0, suid=1000)
def application(output_folder="output",
csv_name="ReportNodeDemographics.csv",
config_filename="config.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder + "\n")
print("csv_name: " + csv_name + "\n")
print("config_name: " + config_filename + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
with open(config_filename) as infile:
test_config_name = json.load(infile)["parameters"]["Config_Name"]
sft.start_report_file(report_name, test_config_name)
all_data_df = pd.read_csv(path.join(output_folder, csv_name))
all_data_df.rename(columns={
' NodeID': 'NodeID',
' Gender': 'Gender',
' AgeYears': 'AgeYears',
' NumIndividuals': 'NumIndividuals',
' NumInfected': 'NumInfected'
},
inplace=True)
all_data_df.drop(['NumInfected'], axis=1, inplace=True)
if debug:
all_data_df.to_csv("DEBUG_all_data_cleaned.csv")
last_day_df = all_data_df.loc[all_data_df['Time'] == 399]
if debug:
last_day_df.to_csv("DEBUG_day_399_data_cleaned.csv")
northern_nodes = last_day_df[last_day_df['NodeID'].isin([1, 2, 3])]
southern_nodes = last_day_df[last_day_df['NodeID'].isin([7, 8, 9])]
eastern_nodes = last_day_df[last_day_df['NodeID'].isin([3, 6, 9])]
western_nodes = last_day_df[last_day_df['NodeID'].isin([1, 4, 7])]
create_report_file(sft_filename=report_name,
n_nodes=northern_nodes,
s_nodes=southern_nodes,
e_nodes=eastern_nodes,
w_nodes=western_nodes)
def application(output_folder="output", config_filename="config.json",
jsonreport_name="InsetChart.json", stdout_filename="test.txt",
report_name=sft.sft_output_filename, debug=False):
if debug:
print("output_folder: " + output_folder + "\n")
print("config_filename: " + config_filename + "\n")
print("insetchart_name: " + jsonreport_name + "\n")
print("stdout filename:" + stdout_filename + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
config_object = dtk_iis.load_config_file(config_filename=config_filename,
debug=debug)
demographics_overlay_name = config_object[dtk_iis.ConfigKeys.DEMOGRAPHIC_FILENAMES][-1]
campaign_name = config_object[dtk_iis.ConfigKeys.CAMPAIGN_FILENAME]
test_config_name = config_object[dtk_iis.ConfigKeys.CONFIG_NAME]
demographics_object = dtk_iis.load_demographics_file(
demographics_filename=demographics_overlay_name,
susceptibility_initialization_type=config_object[dtk_iis.ConfigKeys.SUS_INIT_DIST_TYPE],
debug=debug)
sft.start_report_file(report_name, test_config_name)
i_df = dtk_iis.parse_stdout_file(stdout_filename, debug=debug)
distribution_object = demographics_object[dtk_iis.DemographicFileKeys.SusceptibilityDistribution.KEY]
distro_values = \
distribution_object[dtk_iis.DemographicFileKeys.SusceptibilityDistribution.ComplexKeys.DistributionValues][0]
distro_results = \
distribution_object[dtk_iis.DemographicFileKeys.SusceptibilityDistribution.ComplexKeys.ResultValues][0]
if debug:
print("Sus distribution type: {0}\n".format(config_object[dtk_iis.ConfigKeys.SUS_INIT_DIST_TYPE]))
print("Distribution object: {0}\n".format(distribution_object))
print("Distro values: {0}\n".format(distro_values))
with open(report_name, "a") as outfile:
messages = dtk_iis.validate_complex_initialization_numpy(
individual_dataframe=i_df, susceptibility_distribution=distribution_object,
outfile=outfile, debug=debug)
pass
def application(config_filename="config.json", debug=False):
with open(config_filename) as infile:
config_json = json.load(infile)
config_params = config_json[d_ss.ConfigKeys.PARAMETERS_KEY]
config_object = d_ss.load_config_file(config_filename=config_filename,
debug=debug)
sft.start_report_file(
output_filename=sft.sft_output_filename,
config_name=config_object[d_ss.ConfigKeys.CONFIGNAME_KEY])
d_ss.start_serialization_test()
expected_dtk_filepath = config_params[
d_ss.ConfigKeys.Serialization.POPULATION_PATH]
expected_dtk_filename = config_params[
d_ss.ConfigKeys.Serialization.POPULATION_FILENAMES_KEY][0]
expected_dtk_fullpath = path.join(expected_dtk_filepath,
expected_dtk_filename)
dtk_file = d_ss.DtkFile(expected_dtk_fullpath, file_suffix="old")
dtk_file.write_node_to_disk(node_index=0)
dtk_file.write_simulation_to_disk()
found_people = {}
ignored_people = []
testable_infections = 5
remaining_sim_duration = config_object[
d_ss.ConfigKeys.Serialization.TIMESTEPS_KEY][0]
while len(found_people) < testable_infections:
maybe_person = dtk_file.find_human_from_node(
node_index=0, min_infections=1, ignore_suids=ignored_people)
human_suid = maybe_person["suid"]["id"]
if debug:
print(f"Trying human {human_suid}.\n")
acceptable_infection = has_acceptable_infection(
maybe_person, remaining_sim_duration)
if acceptable_infection:
dtk_file.write_human_to_disk(node_index=0, suid=human_suid)
found_people[human_suid] = acceptable_infection
ignored_people.append(human_suid)
dtk_file.write_json_file(found_people, "DEBUG_found_infected_persons.json")
def application(output_folder="output",
config_filename="config.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: {0}".format(output_folder))
print("config_filename: {0}".format(config_filename))
print("report_name: {0}".format(report_name))
print("debug: {0}".format(debug))
config_object = d_ss.load_config_file(config_filename=config_filename,
debug=debug)
sft.start_report_file(
output_filename=report_name,
config_name=config_object[d_ss.ConfigKeys.CONFIGNAME_KEY],
already_started=True)
dtk_filename = path.join(output_folder, 'state-00300.dtk')
dtk_file = d_ss.DtkFile(dtk_filename)
dtk_file.write_node_to_disk(node_index=0)
# dtk_file.drop_simulation() # TODO: remove random number generator parts
dtk_file.write_human_to_disk(node_index=0, suid=10)
dtk_file.write_human_to_disk(node_index=0, suid=100)
dtk_file.write_human_to_disk(node_index=0, suid=1000)
#TODO: make sure each individual is Simulation_Duration days older
human_1_first = d_ss.SerializedHuman.from_file('human-10-old.json')
human_1_second = d_ss.SerializedHuman.from_file('human-10-new.json')
human_100_first = d_ss.SerializedHuman.from_file('human-100-old.json')
human_100_second = d_ss.SerializedHuman.from_file('human-100-new.json')
human_1000_first = d_ss.SerializedHuman.from_file('human-1000-old.json')
human_1000_second = d_ss.SerializedHuman.from_file('human-1000-new.json')
messages = []
expected_age_delta = config_object[d_ss.ConfigKeys.SIMULATION_DURATION_KEY]
human_1_messages = human_1_first.compare_to_older(human_1_second,
expected_age_delta)
human_100_messages = human_100_first.compare_to_older(
human_100_second, expected_age_delta)
human_1000_messages = human_1000_first.compare_to_older(
human_1000_second, expected_age_delta)
messages += human_1_messages if human_1_messages else [
"GOOD: Human 1 checks out"
]
messages += human_100_messages if human_100_messages else [
"GOOD: Human 100 checks out"
]
messages += human_1000_messages if human_1000_messages else [
"GOOD: Human 1000 checks out"
]
#TODO: compare the simulation objects
#TODO: compare the node objects
success_message_formatter = sft.format_success_msg
d_ss.generate_report_file(config_object,
report_name,
output_folder=output_folder,
messages=messages,
success_formatter=success_message_formatter,
debug=debug)
d_ss.clean_serialization_test(debug)
def application(output_folder="output", config_filename="config.json",
report_name=sft.sft_output_filename, debug=False):
if debug:
print("output_folder: {0}".format(output_folder))
print("config_filename: {0}".format(config_filename))
print("report_name: {0}".format(report_name))
print("debug: {0}".format(debug))
config_object = d_ss.load_config_file(config_filename=config_filename, debug=debug)
sft.start_report_file(output_filename=report_name,
config_name=config_object[d_ss.ConfigKeys.CONFIGNAME_KEY],
already_started=True)
sft.wait_for_done()
dtk_filename = path.join(output_folder, 'state-00005.dtk')
dtk_file = d_ss.DtkFile(dtk_filename)
dtk_file.write_node_to_disk(node_index=0)
dtk_file.write_simulation_to_disk()
infected_people_to_check = []
with open("DEBUG_found_infected_persons.json") as infile:
infected_people_to_check = json.load(infile)
if debug:
print(f"Infected_people_to_check: {infected_people_to_check}")
infected_people_first={}
infected_people_second={}
for suid in infected_people_to_check:
suid_int = int(suid)
print("Trying suid: {0}".format(suid_int))
infected_people_first[suid] = d_ss.SerializedHuman.from_file(f"human-{suid_int}-old.json")
dtk_file.write_human_to_disk(node_index=0, suid=suid_int, debug=debug)
infected_people_second[suid] = d_ss.SerializedHuman.from_file(f"human-{suid_int}-new.json")
# Make sure each individual is Simulation_Duration days older
messages = []
expected_age_delta = config_object[d_ss.ConfigKeys.Serialization.TIMESTEPS_KEY][0]
for person in infected_people_to_check:
infection_suid = infected_people_to_check[person]
if debug:
# print(f"X is: {x}")
print(f"person is: {person}")
print(f"infection is: {infection_suid}")
print(f"infected_people_first[person] = {infected_people_first[person]}")
print(f"infected_people_second[person] = {infected_people_second[person]}")
aging_messages = infected_people_first[person].compare_to_older(infected_people_second[person], expected_age_delta)
messages += aging_messages if aging_messages else [f"GOOD: human {person} checks out"]
older_infection = infected_people_first[person].get_infection_by_suid(infection_suid)
newer_infection = infected_people_second[person].get_infection_by_suid(infection_suid)
messages += newer_infection.compare_to_older(older_infection, expected_age_delta)
messages += newer_infection.validate_own_timers()
# Make sure each infection is Simulation_Duration days older
#TODO: compare the simulation objects
#TODO: compare the node objects
success_message_formatter = sft.format_success_msg
d_ss.generate_report_file(config_object, report_name, output_folder=output_folder,
messages=messages, success_formatter=success_message_formatter,
debug=debug)
d_ss.clean_serialization_test(debug)
def application(output_folder="output",
config_filename="config.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: {0}".format(output_folder))
print("config_filename: {0}".format(config_filename))
print("report_name: {0}".format(report_name))
print("debug: {0}".format(debug))
config_object = d_ss.load_config_file(config_filename=config_filename,
debug=debug)
sft.start_report_file(
output_filename=report_name,
config_name=config_object[d_ss.ConfigKeys.CONFIGNAME_KEY],
already_started=True)
sft.wait_for_done()
dtk_filename = path.join(output_folder, 'state-00005.dtk')
dtk_file = d_ss.DtkFile(dtk_filename)
dtk_file.write_node_to_disk(node_index=0)
dtk_file.write_simulation_to_disk()
infected_people_to_check = []
with open("DEBUG_found_infected_persons.json") as infile:
infected_people_to_check = json.load(infile)
if debug:
print(f"Infected_people_to_check: {infected_people_to_check}")
infected_people_first = {}
infected_people_second = {}
for suid in infected_people_to_check:
suid_int = int(suid)
print("Trying suid: {0}".format(suid_int))
infected_people_first[suid] = d_ss.SerializedHuman.from_file(
f"human-{suid_int}-old.json")
dtk_file.write_human_to_disk(node_index=0, suid=suid_int, debug=debug)
infected_people_second[suid] = d_ss.SerializedHuman.from_file(
f"human-{suid_int}-new.json")
# Make sure each individual is Simulation_Duration days older
messages = []
expected_age_delta = config_object[
d_ss.ConfigKeys.Serialization.TIMESTEPS_KEY][0]
for person in infected_people_to_check:
infection_suid = infected_people_to_check[person]
if debug:
# print(f"X is: {x}")
print(f"person is: {person}")
print(f"infection is: {infection_suid}")
print(
f"infected_people_first[person] = {infected_people_first[person]}"
)
print(
f"infected_people_second[person] = {infected_people_second[person]}"
)
aging_messages = infected_people_first[person].compare_to_older(
infected_people_second[person], expected_age_delta)
messages += aging_messages if aging_messages else [
f"GOOD: human {person} checks out"
]
older_infection = infected_people_first[person].get_infection_by_suid(
infection_suid)
newer_infection = infected_people_second[person].get_infection_by_suid(
infection_suid)
messages += newer_infection.compare_to_older(older_infection,
expected_age_delta)
messages += newer_infection.validate_own_timers()
# Make sure each infection is Simulation_Duration days older
#TODO: compare the simulation objects
#TODO: compare the node objects
success_message_formatter = sft.format_success_msg
d_ss.generate_report_file(config_object,
report_name,
output_folder=output_folder,
messages=messages,
success_formatter=success_message_formatter,
debug=debug)
d_ss.clean_serialization_test(debug)