wow-inequalities/src/data.py

import io
from pathlib import Path
import sys
try:
    import src.load_yaml as yaml # for quarto document scripts
except ModuleNotFoundError:
    import load_yaml as yaml # for directly running the package
from pandas import DataFrame, read_csv

DEFAULT_YAML_PATH = Path("02-data/processed/relevant")


def to_tsv(studies: list[dict]) -> str:
    if not studies:
        return ""
    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


def from_yml(yml_path: Path | str = DEFAULT_YAML_PATH) -> DataFrame:
    yml_path = Path(yml_path).resolve()
    studies = yaml.load(yml_path)
    if not studies:
        raise ValueError(f"No studies found in directory {yml_path.resolve()}")
    tsv = to_tsv(studies)
    return read_csv(io.StringIO(tsv), sep="\t")


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

    from io import StringIO
    output = StringIO()
    res.to_csv(output)
    output.seek(0)
    print(output.read())