import sys
from typing import cast
import yaml
from pathlib import Path

DEFAULT_YAML_PATH = Path("../02-data/intermediate/relevant")


def _get_all_yml(path: Path) -> list:
    """Returns list of all yml files."""
    return list(path.rglob(r"*.y*ml"))


def _read_yml(path: Path) -> dict | None:
    try:
        with open(path, "r") as f:
            return yaml.safe_load(f)
    except FileNotFoundError as e:
        print(e)
    return None


def from_yml(
    yml_path: Path | str = DEFAULT_YAML_PATH,
) -> list[dict]:
    """Main data process routine.
    Extracts all necessary data from yaml files returns it.
    """
    contents = [_read_yml(source) for source in _get_all_yml(Path(yml_path))]
    if not contents:
        return []
    contents = cast(list[dict], contents)
    for study in contents:
        del study["annotation"]
    return contents


def to_tsv(studies: list[dict]) -> str:
    tsv = ""
    tab = "\t"
    tsv += (
        f"{tab.join(studies[0].keys())}{tab}"
        f"{tab.join(studies[0]['observation'][0].keys())}\n"
    )
    for study in studies:
        study_list = [str(val).replace("\n", "") for val in study.values()]
        for obs in study["observation"]:
            obs_list = [str(val).replace("\n", "") for val in obs.values()]
            tsv += f"{tab.join(study_list)}{tab}{tab.join(obs_list)}\n"
    return tsv


if __name__ == "__main__":
    if len(sys.argv) == 2:
        res = from_yml(Path(sys.argv[1]))
    else:
        res = from_yml()

    print(to_tsv(res))