rapids/rules/preprocessing.snakefile

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rule download_dataset:
input:
"data/external/{pid}"
params:
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"
rule readable_datetime:
input:
sensor_input = rules.download_dataset.output
params:
timezones = None,
fixed_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"]
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wildcard_constraints:
sensor = '(' + '|'.join([re.escape(x) for x in config["SENSORS"]]) + ')' # only process smartphone sensors, not fitbit
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output:
"data/raw/{pid}/{sensor}_with_datetime.csv"
script:
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"../src/data/readable_datetime.R"
rule phone_valid_sensed_days:
input:
all_sensors = expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["SENSORS"])
params:
bin_size = config["PHONE_VALID_SENSED_DAYS"]["BIN_SIZE"],
min_valid_hours = config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_HOURS"],
min_bins_per_hour = config["PHONE_VALID_SENSED_DAYS"]["MIN_BINS_PER_HOUR"]
output:
"data/interim/{pid}/phone_valid_sensed_days.csv"
script:
"../src/data/phone_valid_sensed_days.R"
rule phone_sensed_bins:
input:
all_sensors = expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["SENSORS"])
params:
bin_size = config["PHONE_VALID_SENSED_DAYS"]["BIN_SIZE"]
output:
"data/interim/{pid}/phone_sensed_bins.csv"
script:
"../src/data/phone_sensed_bins.R"
rule unify_ios_android:
input:
sensor_data = "data/raw/{pid}/{sensor}_with_datetime.csv",
participant_info = "data/external/{pid}"
params:
sensor = "{sensor}"
output:
"data/raw/{pid}/{sensor}_with_datetime_unified.csv"
script:
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"../src/data/unify_ios_android.R"
rule resample_fused_location:
input:
locations = "data/raw/{pid}/locations_raw.csv",
phone_sensed_bins = rules.phone_sensed_bins.output
params:
bin_size = config["PHONE_VALID_SENSED_DAYS"]["BIN_SIZE"],
timezone = config["RESAMPLE_FUSED_LOCATION"]["TIMEZONE"],
consecutive_threshold = config["RESAMPLE_FUSED_LOCATION"]["CONSECUTIVE_THRESHOLD"],
time_since_valid_location = config["RESAMPLE_FUSED_LOCATION"]["TIME_SINCE_VALID_LOCATION"]
output:
"data/raw/{pid}/locations_resampled.csv"
script:
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"../src/data/resample_fused_location.R"
rule application_genres:
input:
"data/raw/{pid}/applications_foreground_with_datetime.csv"
params:
catalogue_source = config["APPLICATION_GENRES"]["CATALOGUE_SOURCE"],
catalogue_file = config["APPLICATION_GENRES"]["CATALOGUE_FILE"],
update_catalogue_file = config["APPLICATION_GENRES"]["UPDATE_CATALOGUE_FILE"],
scrape_missing_genres = config["APPLICATION_GENRES"]["SCRAPE_MISSING_GENRES"]
output:
"data/interim/{pid}/applications_foreground_with_datetime_with_genre.csv"
script:
"../src/data/application_genres.R"
rule fitbit_with_datetime:
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input:
"data/raw/{pid}/fitbit_data_raw.csv"
params:
local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"],
fitbit_sensor = "{fitbit_sensor}"
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output:
"data/raw/{pid}/fitbit_{fitbit_sensor}_with_datetime.csv"
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script:
"../src/data/fitbit_readable_datetime.py"