184 lines
8.0 KiB
Python
184 lines
8.0 KiB
Python
rule restore_sql_file:
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input:
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sql_file = "data/external/rapids_example.sql",
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db_credentials = ".env"
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params:
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group = config["DOWNLOAD_PARTICIPANTS"]["GROUP"]
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output:
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touch("data/interim/restore_sql_file.done")
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script:
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"../src/data/restore_sql_file.py"
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rule create_example_participant_files:
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output:
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expand("data/external/{pid}", pid = ["example01", "example02"])
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shell:
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"echo 'a748ee1a-1d0b-4ae9-9074-279a2b6ba524\nandroid\ntest01\n2020/04/23,2020/05/04\n' >> ./data/external/example01 && echo '13dbc8a3-dae3-4834-823a-4bc96a7d459d\nios\ntest02\n2020/04/23,2020/05/04\n' >> ./data/external/example02"
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rule download_participants:
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params:
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group = config["DOWNLOAD_PARTICIPANTS"]["GROUP"],
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ignored_device_ids = config["DOWNLOAD_PARTICIPANTS"]["IGNORED_DEVICE_IDS"],
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timezone = config["TIMEZONE"]
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priority: 1
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script:
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"../src/data/download_participants.R"
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rule download_dataset:
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input:
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"data/external/{pid}"
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params:
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group = config["DOWNLOAD_DATASET"]["GROUP"],
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table = "{sensor}",
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timezone = config["TIMEZONE"],
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aware_multiplatform_tables = config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"] + "," + config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"] + "," + config["CONVERSATION"]["DB_TABLE"]["ANDROID"] + "," + config["CONVERSATION"]["DB_TABLE"]["IOS"],
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unifiable_sensors = {"calls": config["CALLS"]["DB_TABLE"], "battery": config["BATTERY"]["DB_TABLE"], "screen": config["SCREEN"]["DB_TABLE"], "ios_activity_recognition": config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"], "ios_conversation": config["CONVERSATION"]["DB_TABLE"]["IOS"]}
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output:
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"data/raw/{pid}/{sensor}_raw.csv"
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script:
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"../src/data/download_dataset.R"
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rule compute_day_segments:
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input:
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config["DAY_SEGMENTS"]["FILE"]
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params:
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day_segments_type = config["DAY_SEGMENTS"]["TYPE"],
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pid = "{pid}"
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output:
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segments_file = "data/interim/day_segments/{pid}_day_segments.csv",
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segments_labels_file = "data/interim/day_segments/{pid}_day_segments_labels.csv",
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script:
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"../src/data/compute_day_segments.py"
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PHONE_SENSORS = []
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PHONE_SENSORS.extend([config["MESSAGES"]["DB_TABLE"], config["CALLS"]["DB_TABLE"], config["LOCATIONS"]["DB_TABLE"], config["BLUETOOTH"]["DB_TABLE"], config["BATTERY"]["DB_TABLE"], config["SCREEN"]["DB_TABLE"], config["LIGHT"]["DB_TABLE"], config["ACCELEROMETER"]["DB_TABLE"], config["APPLICATIONS_FOREGROUND"]["DB_TABLE"], config["CONVERSATION"]["DB_TABLE"]["ANDROID"], config["CONVERSATION"]["DB_TABLE"]["IOS"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]])
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PHONE_SENSORS.extend(config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"])
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if len(config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]) > 0:
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PHONE_SENSORS.append(config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"])
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if len(config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]) > 0:
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PHONE_SENSORS.append(config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"])
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rule readable_datetime:
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input:
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sensor_input = "data/raw/{pid}/{sensor}_raw.csv",
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day_segments = "data/interim/day_segments/{pid}_day_segments.csv"
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params:
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timezones = None,
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fixed_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"],
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day_segments_type = config["DAY_SEGMENTS"]["TYPE"],
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include_past_periodic_segments = config["DAY_SEGMENTS"]["INCLUDE_PAST_PERIODIC_SEGMENTS"]
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wildcard_constraints:
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sensor = '.*(' + '|'.join([re.escape(x) for x in PHONE_SENSORS]) + ').*' # only process smartphone sensors, not fitbit
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output:
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"data/raw/{pid}/{sensor}_with_datetime.csv"
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script:
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"../src/data/readable_datetime.R"
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rule phone_sensed_bins:
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input:
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all_sensors = optional_phone_sensed_bins_input
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params:
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bin_size = config["PHONE_VALID_SENSED_BINS"]["BIN_SIZE"]
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output:
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"data/interim/{pid}/phone_sensed_bins.csv"
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script:
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"../src/data/phone_sensed_bins.R"
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rule phone_valid_sensed_days:
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input:
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phone_sensed_bins = "data/interim/{pid}/phone_sensed_bins.csv"
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params:
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min_valid_hours_per_day = "{min_valid_hours_per_day}",
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min_valid_bins_per_hour = "{min_valid_bins_per_hour}"
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output:
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"data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins.csv"
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script:
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"../src/data/phone_valid_sensed_days.R"
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rule unify_ios_android:
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input:
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sensor_data = "data/raw/{pid}/{sensor}_with_datetime.csv",
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participant_info = "data/external/{pid}"
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params:
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sensor = "{sensor}",
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unifiable_sensors = {"calls": config["CALLS"]["DB_TABLE"], "battery": config["BATTERY"]["DB_TABLE"], "screen": config["SCREEN"]["DB_TABLE"], "ios_activity_recognition": config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"], "ios_conversation": config["CONVERSATION"]["DB_TABLE"]["IOS"]}
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output:
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"data/raw/{pid}/{sensor}_with_datetime_unified.csv"
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script:
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"../src/data/unify_ios_android.R"
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rule process_location_types:
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input:
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locations = "data/raw/{pid}/{sensor}_with_datetime.csv",
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phone_sensed_bins = rules.phone_sensed_bins.output,
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day_segments = "data/interim/day_segments/{pid}_day_segments.csv"
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params:
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bin_size = config["PHONE_VALID_SENSED_BINS"]["BIN_SIZE"],
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timezone = config["LOCATIONS"]["TIMEZONE"],
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consecutive_threshold = config["LOCATIONS"]["FUSED_RESAMPLED_CONSECUTIVE_THRESHOLD"],
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time_since_valid_location = config["LOCATIONS"]["FUSED_RESAMPLED_TIME_SINCE_VALID_LOCATION"],
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day_segments_type = config["DAY_SEGMENTS"]["TYPE"],
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locations_to_use = "{locations_to_used}"
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output:
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"data/raw/{pid}/{sensor}_processed_{locations_to_used}.csv"
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script:
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"../src/data/process_location_types.R"
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rule application_genres:
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input:
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"data/raw/{pid}/{sensor}_with_datetime.csv"
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params:
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catalogue_source = config["APPLICATION_GENRES"]["CATALOGUE_SOURCE"],
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catalogue_file = config["APPLICATION_GENRES"]["CATALOGUE_FILE"],
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update_catalogue_file = config["APPLICATION_GENRES"]["UPDATE_CATALOGUE_FILE"],
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scrape_missing_genres = config["APPLICATION_GENRES"]["SCRAPE_MISSING_GENRES"]
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output:
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"data/raw/{pid}/{sensor}_with_datetime_with_genre.csv"
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script:
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"../src/data/application_genres.R"
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rule fitbit_heartrate_with_datetime:
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input:
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expand("data/raw/{{pid}}/{fitbit_table}_raw.csv", fitbit_table=config["HEARTRATE"]["DB_TABLE"])
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params:
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local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"],
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fitbit_sensor = "heartrate"
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output:
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summary_data = "data/raw/{pid}/fitbit_heartrate_summary_with_datetime.csv",
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intraday_data = "data/raw/{pid}/fitbit_heartrate_intraday_with_datetime.csv"
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script:
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"../src/data/fitbit_readable_datetime.py"
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rule fitbit_step_with_datetime:
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input:
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expand("data/raw/{{pid}}/{fitbit_table}_raw.csv", fitbit_table=config["STEP"]["DB_TABLE"])
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params:
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local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"],
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fitbit_sensor = "steps"
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output:
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intraday_data = "data/raw/{pid}/fitbit_step_intraday_with_datetime.csv"
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script:
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"../src/data/fitbit_readable_datetime.py"
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rule fitbit_sleep_with_datetime:
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input:
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expand("data/raw/{{pid}}/{fitbit_table}_raw.csv", fitbit_table=config["SLEEP"]["DB_TABLE"])
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params:
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local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"],
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fitbit_sensor = "sleep"
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output:
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summary_data = "data/raw/{pid}/fitbit_sleep_summary_with_datetime.csv",
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intraday_data = "data/raw/{pid}/fitbit_sleep_intraday_with_datetime.csv"
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script:
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"../src/data/fitbit_readable_datetime.py"
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rule join_wifi_tables:
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input:
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unpack(optional_wifi_input)
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output:
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"data/raw/{pid}/wifi_with_datetime_visibleandconnected.csv"
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script:
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"../src/data/join_visible_and_connected_wifi.R" |