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from snakemake.utils import validate
configfile: "config.yaml"
validate(config, "tools/config.schema.yaml")
include: "rules/common.smk"
include: "rules/renv.smk"
include: "rules/preprocessing.smk"
include: "rules/features.smk"
include: "rules/models.smk"
include: "rules/reports.smk"
import itertools
files_to_compute = []
if len(config["PIDS"]) == 0:
raise ValueError("Add participants IDs to PIDS in config.yaml. Remember to create their participant files in data/external")
for provider in config["PHONE_DATA_YIELD"]["PROVIDERS"].keys():
if config["PHONE_DATA_YIELD"]["PROVIDERS"][provider]["COMPUTE"]:
allowed_phone_sensors = get_phone_sensor_names()
if not (set(config["PHONE_DATA_YIELD"]["SENSORS"]) <= set(allowed_phone_sensors)):
raise ValueError('\nInvalid sensor(s) for PHONE_DATA_YIELD. config["PHONE_DATA_YIELD"]["SENSORS"] can have '
'one or more of the following phone sensors: {}.\nInstead you provided "{}".\n'
'Keep in mind that the sensors\' CONTAINER attribute must point to a valid database table or file'\
.format(', '.join(allowed_phone_sensors),
', '.join(set(config["PHONE_DATA_YIELD"]["SENSORS"]) - set(allowed_phone_sensors))))
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=map(str.lower, config["PHONE_DATA_YIELD"]["SENSORS"])))
files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_data_yield_features/phone_data_yield_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_DATA_YIELD"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_data_yield.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_MESSAGES"]["PROVIDERS"].keys():
if config["PHONE_MESSAGES"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_messages_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_messages_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_messages_features/phone_messages_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_MESSAGES"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_messages.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_CALLS"]["PROVIDERS"].keys():
if config["PHONE_CALLS"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_calls_raw.csv", pid=config["PIDS"]))
if (provider == "RAPIDS") and (config["PHONE_CALLS"]["PROVIDERS"][provider]["FEATURES_TYPE"] == "EPISODES"):
files_to_compute.extend(expand("data/interim/{pid}/phone_calls_episodes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_calls_episodes_resampled.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_calls_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
else:
files_to_compute.extend(expand("data/raw/{pid}/phone_calls_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_calls_features/phone_calls_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_CALLS"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_calls.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_BLUETOOTH"]["PROVIDERS"].keys():
if config["PHONE_BLUETOOTH"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_bluetooth_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_bluetooth_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_bluetooth_features/phone_bluetooth_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_BLUETOOTH"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_bluetooth.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"].keys():
if config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_activity_recognition_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_activity_recognition_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_episodes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_episodes_resampled.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_features/phone_activity_recognition_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_activity_recognition.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_BATTERY"]["PROVIDERS"].keys():
if config["PHONE_BATTERY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_battery_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_battery_episodes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_battery_episodes_resampled.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_battery_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_battery_features/phone_battery_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_BATTERY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_battery.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_SCREEN"]["PROVIDERS"].keys():
if config["PHONE_SCREEN"]["PROVIDERS"][provider]["COMPUTE"]:
# if "PHONE_SCREEN" in config["PHONE_DATA_YIELD"]["SENSORS"]:# not used for now because we took episodepersensedminutes out of the list of supported features
# files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps.csv", pid=config["PIDS"]))
# else:
# raise ValueError("Error: Add PHONE_SCREEN (and as many PHONE_SENSORS as you have in your database) to [PHONE_DATA_YIELD][SENSORS] in config.yaml. This is necessary to compute phone_yielded_timestamps (time when the smartphone was sensing data)")
files_to_compute.extend(expand("data/raw/{pid}/phone_screen_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_screen_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_screen_episodes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_screen_episodes_resampled.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_screen_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_screen_features/phone_screen_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_SCREEN"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_screen.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_LIGHT"]["PROVIDERS"].keys():
if config["PHONE_LIGHT"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_light_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_light_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_light_features/phone_light_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_LIGHT"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_light.csv", pid=config["PIDS"],))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_ACCELEROMETER"]["PROVIDERS"].keys():
if config["PHONE_ACCELEROMETER"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_accelerometer_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_accelerometer_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_accelerometer_features/phone_accelerometer_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_ACCELEROMETER"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_accelerometer.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"].keys():
if config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_foreground_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_foreground_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_foreground_with_datetime_with_categories.csv", pid=config["PIDS"]))
if config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"][provider]["INCLUDE_EPISODE_FEATURES"]:
files_to_compute.extend(expand("data/interim/{pid}/phone_app_episodes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_app_episodes_resampled.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_app_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_applications_foreground_features/phone_applications_foreground_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_applications_foreground.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_WIFI_VISIBLE"]["PROVIDERS"].keys():
if config["PHONE_WIFI_VISIBLE"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_visible_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_visible_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_wifi_visible_features/phone_wifi_visible_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_WIFI_VISIBLE"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_wifi_visible.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_WIFI_CONNECTED"]["PROVIDERS"].keys():
if config["PHONE_WIFI_CONNECTED"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_connected_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_connected_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_wifi_connected_features/phone_wifi_connected_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_WIFI_CONNECTED"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_wifi_connected.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_CONVERSATION"]["PROVIDERS"].keys():
if config["PHONE_CONVERSATION"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_conversation_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_conversation_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_conversation_features/phone_conversation_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_CONVERSATION"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_conversation.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_ESM"]["PROVIDERS"].keys():
if config["PHONE_ESM"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_esm_raw.csv",pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_esm_with_datetime.csv",pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_esm_clean.csv",pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_esm_features/phone_esm_{language}_{provider_key}.csv",pid=config["PIDS"],language=get_script_language(config["PHONE_ESM"]["PROVIDERS"][provider]["SRC_SCRIPT"]),provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_esm.csv", pid=config["PIDS"]))
#files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv",pid=config["PIDS"]))
#files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
# We can delete these if's as soon as we add feature PROVIDERS to any of these sensors
if isinstance(config["PHONE_APPLICATIONS_CRASHES"]["PROVIDERS"], dict):
for provider in config["PHONE_APPLICATIONS_CRASHES"]["PROVIDERS"].keys():
if config["PHONE_APPLICATIONS_CRASHES"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_crashes_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_crashes_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_crashes_with_datetime_with_categories.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_applications_crashes_features/phone_applications_crashes_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_APPLICATIONS_CRASHES"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_applications_crashes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if isinstance(config["PHONE_APPLICATIONS_NOTIFICATIONS"]["PROVIDERS"], dict):
for provider in config["PHONE_APPLICATIONS_NOTIFICATIONS"]["PROVIDERS"].keys():
if config["PHONE_APPLICATIONS_NOTIFICATIONS"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_notifications_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_notifications_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_notifications_with_datetime_with_categories.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_applications_notifications_features/phone_applications_notifications_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_APPLICATIONS_NOTIFICATIONS"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_applications_notifications.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if isinstance(config["PHONE_KEYBOARD"]["PROVIDERS"], dict):
for provider in config["PHONE_KEYBOARD"]["PROVIDERS"].keys():
if config["PHONE_KEYBOARD"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_keyboard_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_keyboard_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_keyboard_features/phone_keyboard_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_KEYBOARD"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_keyboard.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if isinstance(config["PHONE_LOG"]["PROVIDERS"], dict):
for provider in config["PHONE_LOG"]["PROVIDERS"].keys():
if config["PHONE_LOG"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_log_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_log_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_log_features/phone_log_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_LOG"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_log.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_LOCATIONS"]["PROVIDERS"].keys():
if config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["COMPUTE"]:
if config["PHONE_LOCATIONS"]["LOCATIONS_TO_USE"] in ["FUSED_RESAMPLED","ALL_RESAMPLED"]:
if "PHONE_LOCATIONS" in config["PHONE_DATA_YIELD"]["SENSORS"]:
files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps.csv", pid=config["PIDS"]))
else:
raise ValueError("Error: Add PHONE_LOCATIONS (and as many PHONE_SENSORS as you have) to [PHONE_DATA_YIELD][SENSORS] in config.yaml. This is necessary to compute phone_yielded_timestamps (time when the smartphone was sensing data) which is used to resample fused location data (ALL_RESAMPLED and RESAMPLED_FUSED)")
if provider == "BARNETT":
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_barnett_daily.csv", pid=config["PIDS"]))
if provider == "DORYAB":
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed_with_datetime_with_doryab_columns_episodes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed_with_datetime_with_doryab_columns_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_locations_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_features/phone_locations_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_locations.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_CALORIES_INTRADAY"]["PROVIDERS"].keys():
if config["FITBIT_CALORIES_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_calories_intraday_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_calories_intraday_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_calories_intraday_features/fitbit_calories_intraday_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["FITBIT_CALORIES_INTRADAY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_calories_intraday.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_DATA_YIELD"]["PROVIDERS"].keys():
if config["FITBIT_DATA_YIELD"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_intraday_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_intraday_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_data_yield.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_HEARTRATE_SUMMARY"]["PROVIDERS"].keys():
if config["FITBIT_HEARTRATE_SUMMARY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_summary_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_summary_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_heartrate_summary_features/fitbit_heartrate_summary_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["FITBIT_HEARTRATE_SUMMARY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_heartrate_summary.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_HEARTRATE_INTRADAY"]["PROVIDERS"].keys():
if config["FITBIT_HEARTRATE_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_intraday_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_intraday_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_heartrate_intraday_features/fitbit_heartrate_intraday_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["FITBIT_HEARTRATE_INTRADAY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_heartrate_intraday.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_SLEEP_SUMMARY"]["PROVIDERS"].keys():
if config["FITBIT_SLEEP_SUMMARY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_summary_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_summary_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_sleep_summary_features/fitbit_sleep_summary_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["FITBIT_SLEEP_SUMMARY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_sleep_summary.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_SLEEP_INTRADAY"]["PROVIDERS"].keys():
if config["FITBIT_SLEEP_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_intraday_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_intraday_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_sleep_intraday_episodes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_sleep_intraday_episodes_resampled.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_sleep_intraday_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_sleep_intraday_features/fitbit_sleep_intraday_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["FITBIT_SLEEP_INTRADAY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_sleep_intraday.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"].keys():
if config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_summary_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_summary_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_steps_summary_features/fitbit_steps_summary_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_steps_summary.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"].keys():
if config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
if config["FITBIT_STEPS_INTRADAY"]["EXCLUDE_SLEEP"]["TIME_BASED"]["EXCLUDE"] or config["FITBIT_STEPS_INTRADAY"]["EXCLUDE_SLEEP"]["FITBIT_BASED"]["EXCLUDE"]:
if config["FITBIT_STEPS_INTRADAY"]["EXCLUDE_SLEEP"]["FITBIT_BASED"]["EXCLUDE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_summary_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_steps_intraday_with_datetime_exclude_sleep.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_intraday_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_intraday_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_steps_intraday_features/fitbit_steps_intraday_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_steps_intraday.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["EMPATICA_ACCELEROMETER"]["PROVIDERS"].keys():
if config["EMPATICA_ACCELEROMETER"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_accelerometer_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_accelerometer_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_ACCELEROMETER"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_accelerometer.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["EMPATICA_HEARTRATE"]["PROVIDERS"].keys():
if config["EMPATICA_HEARTRATE"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_heartrate_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_heartrate_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_heartrate_features/empatica_heartrate_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_HEARTRATE"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_heartrate.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["EMPATICA_TEMPERATURE"]["PROVIDERS"].keys():
if config["EMPATICA_TEMPERATURE"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_temperature_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_temperature_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_temperature_features/empatica_temperature_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_TEMPERATURE"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_temperature.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["EMPATICA_ELECTRODERMAL_ACTIVITY"]["PROVIDERS"].keys():
if config["EMPATICA_ELECTRODERMAL_ACTIVITY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_electrodermal_activity_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_electrodermal_activity_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_ELECTRODERMAL_ACTIVITY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_electrodermal_activity.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["EMPATICA_BLOOD_VOLUME_PULSE"]["PROVIDERS"].keys():
if config["EMPATICA_BLOOD_VOLUME_PULSE"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_blood_volume_pulse_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_blood_volume_pulse_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_BLOOD_VOLUME_PULSE"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_blood_volume_pulse.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"].keys():
if config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_inter_beat_interval_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_inter_beat_interval_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_inter_beat_interval.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if isinstance(config["EMPATICA_TAGS"]["PROVIDERS"], dict):
for provider in config["EMPATICA_TAGS"]["PROVIDERS"].keys():
if config["EMPATICA_TAGS"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_tags_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_tags_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_tags_features/empatica_tags_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_TAGS"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_tags.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
# Visualization for Data Exploration
if config["HISTOGRAM_PHONE_DATA_YIELD"]["PLOT"]:
files_to_compute.append("reports/data_exploration/histogram_phone_data_yield.html")
if config["HEATMAP_SENSORS_PER_MINUTE_PER_TIME_SEGMENT"]["PLOT"]:
files_to_compute.extend(expand("reports/interim/{pid}/heatmap_sensors_per_minute_per_time_segment.html", pid=config["PIDS"]))
files_to_compute.append("reports/data_exploration/heatmap_sensors_per_minute_per_time_segment.html")
if config["HEATMAP_SENSOR_ROW_COUNT_PER_TIME_SEGMENT"]["PLOT"]:
files_to_compute.extend(expand("reports/interim/{pid}/heatmap_sensor_row_count_per_time_segment.html", pid=config["PIDS"]))
files_to_compute.append("reports/data_exploration/heatmap_sensor_row_count_per_time_segment.html")
if config["HEATMAP_PHONE_DATA_YIELD_PER_PARTICIPANT_PER_TIME_SEGMENT"]["PLOT"]:
if not config["PHONE_DATA_YIELD"]["PROVIDERS"]["RAPIDS"]["COMPUTE"]:
raise ValueError("Error: [PHONE_DATA_YIELD][PROVIDERS][RAPIDS][COMPUTE] must be True in config.yaml to get heatmaps of overall data yield.")
files_to_compute.append("reports/data_exploration/heatmap_phone_data_yield_per_participant_per_time_segment.html")
if config["HEATMAP_FEATURE_CORRELATION_MATRIX"]["PLOT"]:
files_to_compute.append("reports/data_exploration/heatmap_feature_correlation_matrix.html")
# Data Cleaning
for provider in config["ALL_CLEANING_INDIVIDUAL"]["PROVIDERS"].keys():
if config["ALL_CLEANING_INDIVIDUAL"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features_cleaned_" + provider.lower() +".csv", pid=config["PIDS"]))
for provider in config["ALL_CLEANING_OVERALL"]["PROVIDERS"].keys():
if config["ALL_CLEANING_OVERALL"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/processed/features/all_participants/all_sensor_features_cleaned_" + provider.lower() +".csv"))
# Baseline features
if config["PARAMS_FOR_ANALYSIS"]["BASELINE"]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/baseline_merged.csv"))
files_to_compute.extend(expand("data/raw/{pid}/participant_baseline_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/baseline_questionnaires.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/baseline_features.csv", pid=config["PIDS"]))
# Targets (labels)
if config["PARAMS_FOR_ANALYSIS"]["TARGET"]["COMPUTE"]:
files_to_compute.extend(expand("data/processed/models/individual_model/{pid}/input.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/models/population_model/input.csv"))
#files_to_compute.extend(expand("data/processed/models/individual_model/{pid}/output_{cv_method}/baselines.csv", pid=config["PIDS"], cv_method=config["PARAMS_FOR_ANALYSIS"]["CV_METHODS"]))
rule all:
input:
files_to_compute
rule clean:
shell:
"rm -rf data/raw/* && rm -rf data/interim/* && rm -rf data/processed/* && rm -rf reports/figures/* && rm -rf reports/*.zip && rm -rf reports/compliance/*"