rapids/Snakefile

configfile: "config.yaml"
include: "rules/common.smk"
include: "rules/renv.smk"
include: "rules/preprocessing.smk"
include: "rules/features.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")

if config["PHONE_VALID_SENSED_BINS"]["COMPUTE"] or config["PHONE_VALID_SENSED_DAYS"]["COMPUTE"]: # valid sensed bins is necessary for sensed days, so we add these files anyways if sensed days are requested
    if len(config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"]) == 0:
            raise ValueError("If you want to compute PHONE_VALID_SENSED_BINS or PHONE_VALID_SENSED_DAYS, you need to add at least one table to [PHONE_VALID_SENSED_BINS][DB_TABLES] in config.yaml")

    pids_android = list(filter(lambda pid: infer_participant_platform("data/external/" + pid) == "android", config["PIDS"]))
    pids_ios = list(filter(lambda pid: infer_participant_platform("data/external/" + pid) == "ios", config["PIDS"]))
    tables_android = [table for table in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"] if table not in [config["CONVERSATION"]["DB_TABLE"]["IOS"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]]] # for android, discard any ios tables that may exist
    tables_ios = [table for table in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"] if table not in [config["CONVERSATION"]["DB_TABLE"]["ANDROID"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"]]] # for ios, discard any android tables that may exist

    for pids,table in zip([pids_android, pids_ios], [tables_android, tables_ios]):
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=pids, sensor=table))
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=pids, sensor=table))
    files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))

if config["PHONE_VALID_SENSED_DAYS"]["COMPUTE"]:
    files_to_compute.extend(expand("data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins.csv",
                                pid=config["PIDS"],
                                min_valid_hours_per_day=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_HOURS_PER_DAY"],
                                min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]))

for provider in config["MESSAGES"]["PROVIDERS"].keys():
    if config["MESSAGES"]["PROVIDERS"][provider]["COMPUTE"]:
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["MESSAGES"]["DB_TABLE"]))
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["MESSAGES"]["DB_TABLE"]))
        files_to_compute.extend(expand("data/interim/{pid}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["MESSAGES"]["PROVIDERS"][provider]["SRC_LANGUAGE"], provider_key=provider, sensor_key="MESSAGES".lower()))
        files_to_compute.extend(expand("data/processed/features/{pid}/{sensor_key}.csv", pid=config["PIDS"], sensor_key="MESSAGES".lower()))

for provider in config["CALLS"]["PROVIDERS"].keys():
    if config["CALLS"]["PROVIDERS"][provider]["COMPUTE"]:
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["CALLS"]["DB_TABLE"]))
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["CALLS"]["DB_TABLE"]))
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime_unified.csv", pid=config["PIDS"], sensor=config["CALLS"]["DB_TABLE"]))
        files_to_compute.extend(expand("data/interim/{pid}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["CALLS"]["PROVIDERS"][provider]["SRC_LANGUAGE"], provider_key=provider, sensor_key="CALLS".lower()))
        files_to_compute.extend(expand("data/processed/features/{pid}/{sensor_key}.csv", pid=config["PIDS"], sensor_key="CALLS".lower()))

for provider in config["BLUETOOTH"]["PROVIDERS"].keys():
    if config["BLUETOOTH"]["PROVIDERS"][provider]["COMPUTE"]:
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["BLUETOOTH"]["DB_TABLE"]))
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["BLUETOOTH"]["DB_TABLE"]))
        files_to_compute.extend(expand("data/interim/{pid}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["BLUETOOTH"]["PROVIDERS"][provider]["SRC_LANGUAGE"], provider_key=provider, sensor_key="BLUETOOTH".lower()))
        files_to_compute.extend(expand("data/processed/features/{pid}/{sensor_key}.csv", pid=config["PIDS"], sensor_key="BLUETOOTH".lower()))

if config["ACTIVITY_RECOGNITION"]["COMPUTE"]:
    pids_android = list(filter(lambda pid: infer_participant_platform("data/external/" + pid) == "android", config["PIDS"]))
    pids_ios = list(filter(lambda pid: infer_participant_platform("data/external/" + pid) == "ios", config["PIDS"]))
    
    for pids,table in zip([pids_android, pids_ios], [config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]]):
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=pids, sensor=table))
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=pids, sensor=table))
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime_unified.csv", pid=pids, sensor=table))
        files_to_compute.extend(expand("data/processed/{pid}/{sensor}_deltas.csv", pid=pids, sensor=table))
    files_to_compute.extend(expand("data/processed/{pid}/activity_recognition_{day_segment}.csv",pid=config["PIDS"], day_segment = config["ACTIVITY_RECOGNITION"]["DAY_SEGMENTS"]))

if config["BATTERY"]["COMPUTE"]:
    files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["BATTERY"]["DB_TABLE"]))
    files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["BATTERY"]["DB_TABLE"]))
    files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime_unified.csv", pid=config["PIDS"], sensor=config["BATTERY"]["DB_TABLE"]))
    files_to_compute.extend(expand("data/processed/{pid}/battery_deltas.csv", pid=config["PIDS"]))
    files_to_compute.extend(expand("data/processed/{pid}/battery_{day_segment}.csv", pid = config["PIDS"], day_segment = config["BATTERY"]["DAY_SEGMENTS"]))

if config["SCREEN"]["COMPUTE"]:
    if config["SCREEN"]["DB_TABLE"] in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"]:
        files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
    else:
        raise ValueError("Error: Add your screen table (and as many sensor tables as you have) to [PHONE_VALID_SENSED_BINS][DB_TABLES] in config.yaml. This is necessary to compute phone_sensed_bins (bins of time when the smartphone was sensing data)")
    files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["SCREEN"]["DB_TABLE"]))
    files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["SCREEN"]["DB_TABLE"]))
    files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime_unified.csv", pid=config["PIDS"], sensor=config["SCREEN"]["DB_TABLE"]))
    files_to_compute.extend(expand("data/processed/{pid}/screen_deltas.csv", pid=config["PIDS"]))
    files_to_compute.extend(expand("data/processed/{pid}/screen_{day_segment}.csv", pid = config["PIDS"], day_segment = config["SCREEN"]["DAY_SEGMENTS"]))

for provider in config["LIGHT"]["PROVIDERS"].keys():
    if config["LIGHT"]["PROVIDERS"][provider]["COMPUTE"]:
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["LIGHT"]["DB_TABLE"]))
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["LIGHT"]["DB_TABLE"]))
        files_to_compute.extend(expand("data/interim/{pid}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["LIGHT"]["PROVIDERS"][provider]["SRC_LANGUAGE"], provider_key=provider, sensor_key="LIGHT".lower()))
        files_to_compute.extend(expand("data/processed/features/{pid}/{sensor_key}.csv", pid=config["PIDS"], sensor_key="LIGHT".lower()))

if config["ACCELEROMETER"]["COMPUTE"]:
    files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["ACCELEROMETER"]["DB_TABLE"]))
    files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["ACCELEROMETER"]["DB_TABLE"]))
    files_to_compute.extend(expand("data/processed/{pid}/accelerometer_{day_segment}.csv", pid = config["PIDS"], day_segment = config["ACCELEROMETER"]["DAY_SEGMENTS"]))

for provider in config["APPLICATIONS_FOREGROUND"]["PROVIDERS"].keys():
    if config["APPLICATIONS_FOREGROUND"]["PROVIDERS"][provider]["COMPUTE"]:
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["APPLICATIONS_FOREGROUND"]["DB_TABLE"]))
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["APPLICATIONS_FOREGROUND"]["DB_TABLE"]))
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime_with_genre.csv", pid=config["PIDS"], sensor=config["APPLICATIONS_FOREGROUND"]["DB_TABLE"]))
        files_to_compute.extend(expand("data/interim/{pid}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["APPLICATIONS_FOREGROUND"]["PROVIDERS"][provider]["SRC_LANGUAGE"], provider_key=provider, sensor_key="APPLICATIONS_FOREGROUND".lower()))
        files_to_compute.extend(expand("data/processed/features/{pid}/{sensor_key}.csv", pid=config["PIDS"], sensor_key="APPLICATIONS_FOREGROUND".lower()))

for provider in config["WIFI"]["PROVIDERS"].keys():
    if config["WIFI"]["PROVIDERS"][provider]["COMPUTE"]:
        if len(config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]) > 0:
            files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]))
            files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]))
            files_to_compute.extend(expand("data/raw/{pid}/{sensor_key}_with_datetime_visibleandconnected.csv", pid=config["PIDS"], sensor_key="WIFI".lower()))
            files_to_compute.extend(expand("data/interim/{pid}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["WIFI"]["PROVIDERS"][provider]["SRC_LANGUAGE"], provider_key=provider, sensor_key="WIFI".lower()))
            files_to_compute.extend(expand("data/processed/features/{pid}/{sensor_key}.csv", pid=config["PIDS"], sensor_key="WIFI".lower()))
        if len(config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]) > 0:
            files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]))
            files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]))
            files_to_compute.extend(expand("data/raw/{pid}/{sensor_key}_with_datetime_visibleandconnected.csv", pid=config["PIDS"], sensor_key="WIFI".lower()))
            files_to_compute.extend(expand("data/interim/{pid}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["WIFI"]["PROVIDERS"][provider]["SRC_LANGUAGE"], provider_key=provider, sensor_key="WIFI".lower()))
            files_to_compute.extend(expand("data/processed/features/{pid}/{sensor_key}.csv", pid=config["PIDS"], sensor_key="WIFI".lower()))

if config["HEARTRATE"]["COMPUTE"]:
    files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["HEARTRATE"]["DB_TABLE"]))
    files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_{fitbit_data_type}_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["summary", "intraday"]))
    files_to_compute.extend(expand("data/processed/{pid}/fitbit_heartrate_{day_segment}.csv", pid = config["PIDS"], day_segment = config["HEARTRATE"]["DAY_SEGMENTS"]))

if config["STEP"]["COMPUTE"]:
    if config["STEP"]["EXCLUDE_SLEEP"]["EXCLUDE"] == True and config["STEP"]["EXCLUDE_SLEEP"]["TYPE"] == "FITBIT_BASED":
        files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_{fitbit_data_type}_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["summary"]))
    files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["STEP"]["DB_TABLE"]))
    files_to_compute.extend(expand("data/raw/{pid}/fitbit_step_{fitbit_data_type}_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["intraday"]))
    files_to_compute.extend(expand("data/processed/{pid}/fitbit_step_{day_segment}.csv", pid = config["PIDS"], day_segment = config["STEP"]["DAY_SEGMENTS"]))

if config["SLEEP"]["COMPUTE"]:
    files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["SLEEP"]["DB_TABLE"]))
    files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_{fitbit_data_type}_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["intraday", "summary"]))
    files_to_compute.extend(expand("data/processed/{pid}/fitbit_sleep_{day_segment}.csv", pid = config["PIDS"], day_segment = config["SLEEP"]["DAY_SEGMENTS"]))

pids_android = list(filter(lambda pid: infer_participant_platform("data/external/" + pid) == "android", config["PIDS"]))
pids_ios = list(filter(lambda pid: infer_participant_platform("data/external/" + pid) == "ios", config["PIDS"]))

for provider in config["CONVERSATION"]["PROVIDERS"].keys():    
    if config["CONVERSATION"]["PROVIDERS"][provider]["COMPUTE"]:
        for pids,table in zip([pids_android, pids_ios], [config["CONVERSATION"]["DB_TABLE"]["ANDROID"], config["CONVERSATION"]["DB_TABLE"]["IOS"]]):
            files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=pids, sensor=table))
            files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=pids, sensor=table))
            files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime_unified.csv", pid=pids, sensor=table))
        files_to_compute.extend(expand("data/interim/{pid}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["CONVERSATION"]["PROVIDERS"][provider]["SRC_LANGUAGE"], provider_key=provider, sensor_key="CONVERSATION".lower()))
        files_to_compute.extend(expand("data/processed/features/{pid}/{sensor_key}.csv", pid=config["PIDS"], sensor_key="CONVERSATION".lower()))

for provider in config["LOCATIONS"]["PROVIDERS"].keys():
    if config["LOCATIONS"]["PROVIDERS"][provider]["COMPUTE"]:
        if config["LOCATIONS"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED":
            if config["LOCATIONS"]["DB_TABLE"] in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"]:
                files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
            else:
                raise ValueError("Error: Add your locations table (and as many sensor tables as you have) to [PHONE_VALID_SENSED_BINS][DB_TABLES] in config.yaml. This is necessary to compute phone_sensed_bins (bins of time when the smartphone was sensing data) which is used to resample fused location data (RESAMPLED_FUSED)")
            
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["LOCATIONS"]["DB_TABLE"]))
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["LOCATIONS"]["DB_TABLE"]))
        files_to_compute.extend(expand("data/raw/{pid}/{sensor}_processed_{locations_to_use}.csv", pid=config["PIDS"], sensor=config["LOCATIONS"]["DB_TABLE"], locations_to_use=config["LOCATIONS"]["LOCATIONS_TO_USE"]))
        files_to_compute.extend(expand("data/interim/{pid}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["LOCATIONS"]["PROVIDERS"][provider]["SRC_LANGUAGE"], provider_key=provider, sensor_key="LOCATIONS".lower()))
        files_to_compute.extend(expand("data/processed/features/{pid}/{sensor_key}.csv", pid=config["PIDS"], sensor_key="LOCATIONS".lower()))

# visualization for data exploration
if config["HEATMAP_FEATURES_CORRELATIONS"]["PLOT"]:
    files_to_compute.extend(expand("reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/heatmap_features_correlations.html", min_valid_hours_per_day=config["HEATMAP_FEATURES_CORRELATIONS"]["MIN_VALID_HOURS_PER_DAY"], min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]))
    
if config["HISTOGRAM_VALID_SENSED_HOURS"]["PLOT"]:
    files_to_compute.extend(expand("reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/histogram_valid_sensed_hours.html", min_valid_hours_per_day=config["HISTOGRAM_VALID_SENSED_HOURS"]["MIN_VALID_HOURS_PER_DAY"], min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]))

if config["HEATMAP_DAYS_BY_SENSORS"]["PLOT"]:
    files_to_compute.extend(expand("reports/interim/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{pid}/heatmap_days_by_sensors.html", pid=config["PIDS"], min_valid_hours_per_day=config["HEATMAP_DAYS_BY_SENSORS"]["MIN_VALID_HOURS_PER_DAY"], min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]))
    files_to_compute.extend(expand("reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/heatmap_days_by_sensors_all_participants.html", min_valid_hours_per_day=config["HEATMAP_DAYS_BY_SENSORS"]["MIN_VALID_HOURS_PER_DAY"], min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]))

if config["HEATMAP_SENSED_BINS"]["PLOT"]:
    files_to_compute.extend(expand("reports/interim/heatmap_sensed_bins/{pid}/heatmap_sensed_bins.html", pid=config["PIDS"]))
    files_to_compute.extend(["reports/data_exploration/heatmap_sensed_bins_all_participants.html"])

if config["OVERALL_COMPLIANCE_HEATMAP"]["PLOT"]:
    files_to_compute.extend(expand("reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/overall_compliance_heatmap.html", min_valid_hours_per_day=config["OVERALL_COMPLIANCE_HEATMAP"]["MIN_VALID_HOURS_PER_DAY"], min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]))


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/*"