def get_script_language(script_path): from pathlib import Path script_path = Path(script_path) if not script_path.exists(): raise ValueError("The following provider feature script does not exist: " + str(script_path)) if script_path.name.endswith(".py"): return "python" elif script_path.name.endswith(".R"): return "r" # Features.smk ######################################################################################################### def find_features_files(wildcards): feature_files = [] for provider_key, provider in config[(wildcards.sensor_key).upper()]["PROVIDERS"].items(): if provider["COMPUTE"]: feature_files.extend(expand("data/interim/{{pid}}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", sensor_key=wildcards.sensor_key.lower(), language=get_script_language(provider["SRC_SCRIPT"]), provider_key=provider_key.lower())) return(feature_files) def optional_steps_sleep_input(wildcards): if config["STEP"]["EXCLUDE_SLEEP"]["EXCLUDE"] == True and config["STEP"]["EXCLUDE_SLEEP"]["TYPE"] == "FITBIT_BASED": return "data/raw/{pid}/fitbit_sleep_summary_with_datetime.csv" else: return [] def input_merge_sensor_features_for_individual_participants(wildcards): feature_files = [] for config_key in config.keys(): if config_key.startswith(("PHONE", "FITBIT", "EMPATICA")) and "PROVIDERS" in config[config_key] and isinstance(config[config_key]["PROVIDERS"], dict): for provider_key, provider in config[config_key]["PROVIDERS"].items(): if "COMPUTE" in provider.keys() and provider["COMPUTE"]: feature_files.append("data/processed/features/{pid}/" + config_key.lower() + ".csv") break return feature_files def get_phone_sensor_names(): phone_sensor_names = [] for config_key in config.keys(): if config_key.startswith(("PHONE")) and "PROVIDERS" in config[config_key]: if config_key != "PHONE_DATA_YIELD" and config_key not in phone_sensor_names: phone_sensor_names.append(config_key) return phone_sensor_names def pull_phone_data_input_with_mutation_scripts(wilcards): from pathlib import Path import yaml input = dict() phone_stream = config["PHONE_DATA_STREAMS"]["USE"] input["participant_file"] = "data/external/participant_files/{pid}.yaml" input["rapids_schema_file"] = "src/data/streams/rapids_columns.yaml" input["stream_format"] = "src/data/streams/" + phone_stream + "/format.yaml" if Path("src/data/streams/"+ phone_stream + "/container.R").exists(): input["stream_container"] = "src/data/streams/"+ phone_stream + "/container.R" elif Path("src/data/streams/"+ phone_stream + "/container.py").exists(): input["stream_container"] = "src/data/streams/"+ phone_stream + "/container.py" else: raise ValueError("The container script for {stream} is missing: src/data/streams/{stream}/container.[py|R]".format(stream=empatica_stream)) schema = yaml.load(open(input.get("stream_format"), 'r'), Loader=yaml.FullLoader) sensor = ("phone_" + wilcards.sensor).upper() if sensor not in schema: raise ValueError("{sensor} is not defined in the schema {schema}".format(sensor=sensor, schema=input.get("stream_format"))) for device_os in schema[sensor].keys(): if "MUTATION" not in schema[sensor][device_os]: raise ValueError("MUTATION is missing from [{sensor}][{device_os}] of {schema}".format(sensor=sensor, device_os=device_os,schema=input.get("stream_format"))) if "COLUMN_MAPPINGS" not in schema[sensor][device_os]["MUTATION"]: raise ValueError("COLUMN_MAPPINGS is missing from [{sensor}][{device_os}][MUTATION] of {schema}".format(sensor=sensor, device_os=device_os, schema=input.get("stream_format"))) if "SCRIPTS" not in schema[sensor][device_os]["MUTATION"]: raise ValueError("SCRIPTS is missing from [{sensor}][{device_os}][MUTATION] of {schema}".format(sensor=sensor, device_os=device_os, schema=input.get("stream_format"))) scripts = schema[sensor][device_os]["MUTATION"]["SCRIPTS"] if isinstance(scripts, list): for idx, script in enumerate(scripts): if not script.lower().endswith((".py", ".r")): 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("stream_format"))) input["mutationscript"+str(idx)] = script return input def input_tzcodes_file(wilcards): from pathlib import Path if config["TIMEZONE"]["TYPE"] == "MULTIPLE": if not config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"].lower().endswith(".csv"): raise ValueError("[TIMEZONE][MULTIPLE][TZCODES_FILE] should point to a CSV file, instead you typed: " + config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"]) if not Path(config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"]).exists(): 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"]) return [config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"]] return [] def pull_wearable_data_input_with_mutation_scripts(wilcards): import yaml from pathlib import Path input = dict() device = wilcards.device_type.upper() device_stream = config[device+"_DATA_STREAMS"]["USE"] input["participant_file"] = "data/external/participant_files/{pid}.yaml" input["rapids_schema_file"] = "src/data/streams/rapids_columns.yaml" input["stream_format"] = "src/data/streams/" + device_stream + "/format.yaml" if Path("src/data/streams/"+ device_stream + "/container.R").exists(): input["stream_container"] = "src/data/streams/"+ device_stream + "/container.R" elif Path("src/data/streams/"+ device_stream + "/container.py").exists(): input["stream_container"] = "src/data/streams/"+ device_stream + "/container.py" else: raise ValueError("The container script for {stream} is missing: src/data/streams/{stream}/container.[py|R]".format(stream=device_stream)) schema = yaml.load(open(input.get("stream_format"), 'r'), Loader=yaml.FullLoader) sensor = (device + "_" + wilcards.sensor).upper() if sensor not in schema: raise ValueError("{sensor} is not defined in the schema {schema}".format(sensor=sensor, schema=input.get("stream_format"))) if "MUTATION" not in schema[sensor]: raise ValueError("MUTATION is missing from [{sensor}] of {schema}".format(sensor=sensor, schema=input.get("stream_format"))) if "COLUMN_MAPPINGS" not in schema[sensor]["MUTATION"]: raise ValueError("COLUMN_MAPPINGS is missing from [{sensor}][MUTATION] of {schema}".format(sensor=sensor, schema=input.get("stream_format"))) if "SCRIPTS" not in schema[sensor]["MUTATION"]: raise ValueError("SCRIPTS is missing from [{sensor}][MUTATION] of {schema}".format(sensor=sensor, schema=input.get("stream_format"))) scripts = schema[sensor]["MUTATION"]["SCRIPTS"] if isinstance(scripts, list): for idx, script in enumerate(scripts): if not script.lower().endswith((".py", ".r")): raise ValueError("Mutate scripts can only be Python or R scripts (.py, .R).\n Instead we got {script} in [{sensor}] of {schema}".format(script=script, sensor=sensor, schema=input.get("stream_format"))) input["mutationscript"+str(idx)] = script return input