100 lines
3.3 KiB
Plaintext
100 lines
3.3 KiB
Plaintext
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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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 readable_datetime:
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input:
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sensor_input = rules.download_dataset.output
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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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wildcard_constraints:
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sensor = "^fitbit.*" # ignoring fitbit sensors
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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_valid_sensed_days:
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input:
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all_sensors = expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["SENSORS"])
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params:
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bin_size = config["PHONE_VALID_SENSED_DAYS"]["BIN_SIZE"],
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min_valid_hours = config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_HOURS"],
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min_bins_per_hour = config["PHONE_VALID_SENSED_DAYS"]["MIN_BINS_PER_HOUR"]
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output:
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"data/interim/{pid}/phone_valid_sensed_days.csv"
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script:
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"../src/data/phone_valid_sensed_days.R"
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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["SENSORS"])
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params:
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bin_size = config["PHONE_VALID_SENSED_DAYS"]["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 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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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 resample_fused_location:
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input:
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locations = "data/raw/{pid}/locations_raw.csv",
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phone_sensed_bins = rules.phone_sensed_bins.output
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params:
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bin_size = config["PHONE_VALID_SENSED_DAYS"]["BIN_SIZE"],
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timezone = config["RESAMPLE_FUSED_LOCATION"]["TIMEZONE"],
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consecutive_threshold = config["RESAMPLE_FUSED_LOCATION"]["CONSECUTIVE_THRESHOLD"],
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time_since_valid_location = config["RESAMPLE_FUSED_LOCATION"]["TIME_SINCE_VALID_LOCATION"]
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output:
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"data/raw/{pid}/locations_resampled.csv"
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script:
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"../src/data/resample_fused_location.R"
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rule fitbit_heartrate_with_datetime:
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input:
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"data/raw/{pid}/fitbit_data_raw.csv"
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params:
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local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"],
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output:
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"data/raw/{pid}/fitbit_heartrate_with_datetime.csv"
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script:
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"../src/data/fitbit_heartrate_with_datetime.py"
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rule fitbit_steps_with_datetime:
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input:
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"data/raw/{pid}/fitbit_data_raw.csv"
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params:
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local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"]
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output:
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"data/raw/{pid}/fitbit_steps_with_datetime.csv"
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script:
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"../src/data/fitbit_steps_with_datetime.py"
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rule fitbit_sleep_with_datetime:
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input:
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"data/raw/{pid}/fitbit_data_raw.csv"
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params:
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local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"]
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output:
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"data/raw/{pid}/fitbit_sleep_with_datetime.csv"
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script:
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"../src/data/fitbit_sleep_with_datetime.py" |