Marty Oehme
7241b62efe
Allow loading the script both through quarto using full absolute path and through the command line using (I believe) a relative path.
49 lines
1.4 KiB
Python
49 lines
1.4 KiB
Python
import io
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from pathlib import Path
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import sys
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try:
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import src.load_yaml as yaml # for quarto document scripts
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except ModuleNotFoundError:
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import load_yaml as yaml # for directly running the package
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from pandas import DataFrame, read_csv
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DEFAULT_YAML_PATH = Path("02-data/processed/relevant")
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def to_tsv(studies: list[dict]) -> str:
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if not studies:
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return ""
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tsv = ""
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tab = "\t"
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tsv += (
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f"{tab.join(studies[0].keys())}{tab}"
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f"{tab.join(studies[0]['observation'][0].keys())}\n"
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)
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for study in studies:
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study_list = [str(val).replace("\n", "") for val in study.values()]
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for obs in study["observation"]:
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obs_list = [str(val).replace("\n", "") for val in obs.values()]
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tsv += f"{tab.join(study_list)}{tab}{tab.join(obs_list)}\n"
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return tsv
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def from_yml(yml_path: Path | str = DEFAULT_YAML_PATH) -> DataFrame:
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yml_path = Path(yml_path).resolve()
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studies = yaml.load(yml_path)
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if not studies:
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raise ValueError(f"No studies found in directory {yml_path.resolve()}")
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tsv = to_tsv(studies)
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return read_csv(io.StringIO(tsv), sep="\t")
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if __name__ == "__main__":
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if len(sys.argv) == 2:
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res = from_yml(Path(sys.argv[1]))
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else:
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res = from_yml()
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from io import StringIO
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output = StringIO()
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res.to_csv(output)
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output.seek(0)
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print(output.read())
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