rule merge_baseline_data:
    input:
        data = expand(config["PARAMS_FOR_ANALYSIS"]["BASELINE"]["FOLDER"] + "/{container}", container=config["PARAMS_FOR_ANALYSIS"]["BASELINE"]["CONTAINER"])
    output:
        "data/raw/baseline_merged.csv"
    script:
        "../src/data/merge_baseline_data.py"

rule download_baseline_data:
    input:
        participant_file = "data/external/participant_files/{pid}.yaml",
        data = "data/raw/baseline_merged.csv"
    output:
        "data/raw/{pid}/participant_baseline_raw.csv"
    script:
        "../src/data/download_baseline_data.py"

rule baseline_features:
    input:
        "data/raw/{pid}/participant_baseline_raw.csv"
    params:
        pid="{pid}",
        features=config["PARAMS_FOR_ANALYSIS"]["BASELINE"]["FEATURES"],
        question_filename=config["PARAMS_FOR_ANALYSIS"]["BASELINE"]["FOLDER"] + "/" + config["PARAMS_FOR_ANALYSIS"]["BASELINE"]["QUESTION_LIST"]
    output:
        interim="data/interim/{pid}/baseline_questionnaires.csv",
        features="data/processed/features/{pid}/baseline_features.csv"
    script:
        "../src/data/baseline_features.py"

rule select_target:
    input:
        cleaned_sensor_features = "data/processed/features/{pid}/all_sensor_features_cleaned_rapids.csv"
    params:
        target_variable = config["PARAMS_FOR_ANALYSIS"]["TARGET"]["LABEL"]
    output:
        "data/processed/models/individual_model/{pid}/input.csv"
    script:
        "../src/models/select_targets.py"

rule merge_features_and_targets_for_population_model:
    input:
        cleaned_sensor_features = "data/processed/features/all_participants/all_sensor_features_cleaned_rapids.csv",
        demographic_features = expand("data/processed/features/{pid}/baseline_features.csv", pid=config["PIDS"]),
    params:
        target_variable=config["PARAMS_FOR_ANALYSIS"]["TARGET"]["LABEL"]
    output:
        "data/processed/models/population_model/input.csv"
    script:
        "../src/models/merge_features_and_targets_for_population_model.py"