79 lines
4.3 KiB
Python
79 lines
4.3 KiB
Python
# Features.smk #########################################################################################################
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def find_features_files(wildcards):
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feature_files = []
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for provider_key, provider in config[(wildcards.sensor_key).upper()]["PROVIDERS"].items():
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if provider["COMPUTE"]:
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feature_files.extend(expand("data/interim/{{pid}}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", sensor_key=wildcards.sensor_key.lower(), language=provider["SRC_LANGUAGE"].lower(), provider_key=provider_key.lower()))
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return(feature_files)
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def optional_steps_sleep_input(wildcards):
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if config["STEP"]["EXCLUDE_SLEEP"]["EXCLUDE"] == True and config["STEP"]["EXCLUDE_SLEEP"]["TYPE"] == "FITBIT_BASED":
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return "data/raw/{pid}/fitbit_sleep_summary_with_datetime.csv"
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else:
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return []
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def input_merge_sensor_features_for_individual_participants(wildcards):
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feature_files = []
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for config_key in config.keys():
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if config_key.startswith(("PHONE", "FITBIT", "EMPATICA")) and "PROVIDERS" in config[config_key] and isinstance(config[config_key]["PROVIDERS"], dict):
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for provider_key, provider in config[config_key]["PROVIDERS"].items():
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if "COMPUTE" in provider.keys() and provider["COMPUTE"]:
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feature_files.append("data/processed/features/{pid}/" + config_key.lower() + ".csv")
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break
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return feature_files
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def get_phone_sensor_names():
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phone_sensor_names = []
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for config_key in config.keys():
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if config_key.startswith(("PHONE")) and "PROVIDERS" in config[config_key]:
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if config_key != "PHONE_DATA_YIELD" and config_key not in phone_sensor_names:
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phone_sensor_names.append(config_key)
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return phone_sensor_names
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def get_zip_suffixes(pid):
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from pathlib import Path
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zipfiles = list((Path("data/external/empatica/") / Path(pid)).rglob("*.zip"))
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suffixes = []
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for zipfile in zipfiles:
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suffixes.append(zipfile.stem)
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return suffixes
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def get_all_raw_empatica_sensor_files(wildcards):
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suffixes = get_zip_suffixes(wildcards.pid)
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files = ["data/raw/{}/empatica_{}_raw_{}.csv".format(wildcards.pid, wildcards.sensor, suffix) for suffix in suffixes]
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return(files)
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def download_phone_data_input_with_mutation_scripts(wilcards):
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import yaml
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input = dict()
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phone_source_type = config["PHONE_DATA_CONFIGURATION"]["SOURCE"]["TYPE"]
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input["participant_file"] = "data/external/participant_files/{pid}.yaml"
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input["rapids_schema_file"] = "src/data/streams/rapids_columns.yaml"
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input["source_schema_file"] = "src/data/streams/" + phone_source_type + "/format.yaml"
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input["source_download_file"] = "src/data/streams/"+ phone_source_type + "/container.R"
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schema = yaml.load(open(input.get("source_schema_file"), 'r'), Loader=yaml.FullLoader)
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sensor = ("phone_" + wilcards.sensor).upper()
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if sensor not in schema:
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raise ValueError("{sensor} is not defined in the schema {schema}".format(sensor=sensor, schema=input.get("source_schema_file")))
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for device_os in ["ANDROID", "IOS"]:
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scripts = schema[sensor][device_os]["MUTATION_SCRIPTS"]
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if isinstance(scripts, list):
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for idx, script in enumerate(scripts):
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if not script.lower().endswith((".py", ".r")):
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raise ValueError("Mutate scripts can only be Python or R scripts (.py, .R).\n Instead we got {script} in \n [{sensor}][{device_os}] of {schema}".format(script=script, sensor=sensor, device_os=device_os, schema=input.get("source_schema_file")))
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input["mutationscript"+str(idx)] = script
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return input
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def input_tzcodes_file(wilcards):
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from pathlib import Path
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if config["TIMEZONE"]["TYPE"] == "MULTIPLE":
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if not config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"].lower().endswith(".csv"):
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raise ValueError("[TIMEZONE][MULTIPLE][TZCODES_FILE] should point to a CSV file, instead you typed: " + config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"])
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if not Path(config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"]).exists():
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raise ValueError("[TIMEZONE][MULTIPLE][TZCODES_FILE] should point to a CSV file, the file in the path you typed does not exist: " + config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"])
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return [config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"]]
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return [] |