Fix optional input files for phone sensed bins
JulioV
parent
8c5497ebc0
commit
3f48a47a14
27
Snakefile
27
Snakefile
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@ -15,15 +15,18 @@ files_to_compute = []
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if len(config["PIDS"]) == 0:
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raise ValueError("Add participants IDs to PIDS in config.yaml. Remember to create their participant files in data/external")
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if config["PHONE_VALID_SENSED_BINS"]["COMPUTE"]:
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if len(config["PHONE_VALID_SENSED_BINS"]["TABLES"]) == 0:
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raise ValueError("If you want to compute PHONE_VALID_SENSED_BINS, you need to add at least one table to [PHONE_VALID_SENSED_BINS][TABLES] in config.yaml")
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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
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if len(config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"]) == 0:
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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")
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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
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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
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for pids,table in zip([pids_android, pids_ios], [tables_android, tables_ios]):
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=pids, sensor=table))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=pids, sensor=table))
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files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
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if config["PHONE_VALID_SENSED_DAYS"]["COMPUTE"]:
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if len(config["PHONE_VALID_SENSED_BINS"]["TABLES"]) == 0:
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raise ValueError("If you want to compute PHONE_VALID_SENSED_DAYS, you need to add at least one table to [PHONE_VALID_SENSED_BINS][TABLES] in config.yaml")
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files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
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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",
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pid=config["PIDS"],
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min_valid_hours_per_day=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_HOURS_PER_DAY"],
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@ -42,11 +45,11 @@ if config["CALLS"]["COMPUTE"]:
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if config["BARNETT_LOCATION"]["COMPUTE"]:
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if config["BARNETT_LOCATION"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED":
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if config["BARNETT_LOCATION"]["DB_TABLE"] in config["PHONE_VALID_SENSED_BINS"]["TABLES"]:
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if config["BARNETT_LOCATION"]["DB_TABLE"] in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"]:
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files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_resampled.csv", pid=config["PIDS"], sensor=config["BARNETT_LOCATION"]["DB_TABLE"]))
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else:
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raise ValueError("Error: Add your locations table (and as many sensor tables as you have) to [PHONE_VALID_SENSED_BINS][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)")
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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)")
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["BARNETT_LOCATION"]["DB_TABLE"]))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["BARNETT_LOCATION"]["DB_TABLE"]))
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files_to_compute.extend(expand("data/processed/{pid}/location_barnett_{day_segment}.csv", pid=config["PIDS"], day_segment = config["BARNETT_LOCATION"]["DAY_SEGMENTS"]))
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@ -72,10 +75,10 @@ if config["BATTERY"]["COMPUTE"]:
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files_to_compute.extend(expand("data/processed/{pid}/battery_{day_segment}.csv", pid = config["PIDS"], day_segment = config["BATTERY"]["DAY_SEGMENTS"]))
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if config["SCREEN"]["COMPUTE"]:
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if config["SCREEN"]["DB_TABLE"] in config["PHONE_VALID_SENSED_BINS"]["TABLES"]:
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if config["SCREEN"]["DB_TABLE"] in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"]:
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files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
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else:
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raise ValueError("Error: Add your screen table (and as many sensor tables as you have) to [PHONE_VALID_SENSED_BINS][TABLES] in config.yaml. This is necessary to compute phone_sensed_bins (bins of time when the smartphone was sensing data)")
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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)")
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["SCREEN"]["DB_TABLE"]))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["SCREEN"]["DB_TABLE"]))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime_unified.csv", pid=config["PIDS"], sensor=config["SCREEN"]["DB_TABLE"]))
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@ -135,11 +138,11 @@ if config["CONVERSATION"]["COMPUTE"]:
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if config["DORYAB_LOCATION"]["COMPUTE"]:
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if config["DORYAB_LOCATION"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED":
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if config["DORYAB_LOCATION"]["DB_TABLE"] in config["PHONE_VALID_SENSED_BINS"]["TABLES"]:
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if config["DORYAB_LOCATION"]["DB_TABLE"] in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"]:
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files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_resampled.csv", pid=config["PIDS"], sensor=config["DORYAB_LOCATION"]["DB_TABLE"]))
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else:
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raise ValueError("Error: Add your locations table (and as many sensor tables as you have) to [PHONE_VALID_SENSED_BINS][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)")
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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)")
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["DORYAB_LOCATION"]["DB_TABLE"]))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["DORYAB_LOCATION"]["DB_TABLE"]))
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files_to_compute.extend(expand("data/processed/{pid}/location_doryab_{segment}.csv", pid=config["PIDS"], segment = config["DORYAB_LOCATION"]["DAY_SEGMENTS"]))
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@ -32,7 +32,7 @@ PHONE_VALID_SENSED_BINS:
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BIN_SIZE: &bin_size 5 # (in minutes)
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# Add as many sensor tables as you have, they all improve the computation of PHONE_VALID_SENSED_BINS and PHONE_VALID_SENSED_DAYS.
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# If you are extracting screen or Barnett's location features, screen and locations tables are mandatory.
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TABLES: []
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DB_TABLES: []
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PHONE_VALID_SENSED_DAYS:
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COMPUTE: False
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@ -1,3 +1,22 @@
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def optional_phone_sensed_bins_input(wildcards):
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with open("data/external/"+wildcards.pid, encoding="ISO-8859-1") as external_file:
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external_file_content = external_file.readlines()
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platforms = external_file_content[1].strip().split(",")
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if platforms[0] == "multiple" or (len(platforms) > 1 and "android" in platforms and "ios" in platforms):
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platform = "android"
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else:
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platform = platforms[0]
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if platform not in ["android", "ios"]:
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raise ValueError("Platform (line 2) in a participant file should be 'android', 'ios', or 'multiple'. You typed '" + platforms + "'")
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if platform == "android":
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tables_platform = [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
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elif platform == "ios":
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tables_platform = [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
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return expand("data/raw/{{pid}}/{table}_with_datetime.csv", table = tables_platform)
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rule restore_sql_file:
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input:
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sql_file = "data/external/rapids_example.sql",
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@ -40,7 +59,7 @@ rule download_dataset:
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PHONE_SENSORS = []
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PHONE_SENSORS.extend([config["MESSAGES"]["DB_TABLE"], config["CALLS"]["DB_TABLE"], config["BARNETT_LOCATION"]["DB_TABLE"], config["DORYAB_LOCATION"]["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"]["TABLES"])
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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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@ -63,7 +82,7 @@ rule readable_datetime:
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rule phone_sensed_bins:
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input:
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all_sensors = expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["PHONE_VALID_SENSED_BINS"]["TABLES"])
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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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@ -22,10 +22,10 @@ if config["CALLS"]["COMPUTE"]:
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files_to_compute.extend(expand("data/processed/{pid}/calls_{call_type}_{segment}.csv", pid=config["PIDS"], call_type=config["CALLS"]["TYPES"], segment = config["CALLS"]["DAY_SEGMENTS"]))
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if config["SCREEN"]["COMPUTE"]:
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if config["SCREEN"]["DB_TABLE"] in config["PHONE_VALID_SENSED_BINS"]["TABLES"]:
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if config["SCREEN"]["DB_TABLE"] in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"]:
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files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
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else:
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raise ValueError("Error: Add your screen table (and as many sensor tables as you have) to [PHONE_VALID_SENSED_BINS][TABLES] in config.yaml. This is necessary to compute phone_sensed_bins (bins of time when the smartphone was sensing data)")
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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)")
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["SCREEN"]["DB_TABLE"]))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["SCREEN"]["DB_TABLE"]))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime_unified.csv", pid=config["PIDS"], sensor=config["SCREEN"]["DB_TABLE"]))
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