| """Normalize the GenomeQA eukaryote_cls configuration to the mcq schema.""" |
|
|
| import argparse |
| import ast |
| import json |
| from pathlib import Path |
|
|
| from datasets import load_dataset |
| from huggingface_hub import CommitOperationAdd, HfApi, hf_hub_download |
|
|
|
|
| DATASET_ID = "HuggingFaceBio/genomeqa" |
| PARQUET_PATH = "mcq/eukaryote_cls_mcq.parquet" |
|
|
|
|
| def main() -> None: |
| parser = argparse.ArgumentParser() |
| parser.add_argument("--source-revision", required=True) |
| parser.add_argument("--output-dataset", default=DATASET_ID) |
| parser.add_argument("--output-dir", type=Path, default=Path.cwd()) |
| parser.add_argument("--publish", action="store_true") |
| args = parser.parse_args() |
|
|
| reference = load_dataset(DATASET_ID, "mcq", split="train", revision=args.source_revision) |
| source = load_dataset(DATASET_ID, "eukaryote_cls", split="train", revision=args.source_revision) |
| normalized = source.map(lambda row: {"metadata": json.dumps(ast.literal_eval(row["metadata"]))}) |
| normalized = normalized.cast(reference.features) |
|
|
| parquet_path = args.output_dir / PARQUET_PATH |
| parquet_path.parent.mkdir(parents=True, exist_ok=True) |
| normalized.to_parquet(parquet_path) |
|
|
| api = HfApi() |
| head = api.repo_info(args.output_dataset, repo_type="dataset").sha |
| card = Path(hf_hub_download(args.output_dataset, "README.md", repo_type="dataset", revision=head)).read_text() |
| if "- config_name: eukaryote_cls\n features:" not in card: |
| info = f"""- config_name: eukaryote_cls |
| features: |
| - name: id |
| dtype: int64 |
| - name: subtask |
| dtype: string |
| - name: question |
| dtype: string |
| - name: options |
| list: string |
| - name: answer_index |
| dtype: int64 |
| - name: answer_text |
| dtype: string |
| - name: metadata |
| dtype: string |
| splits: |
| - name: train |
| num_bytes: {normalized.data.nbytes} |
| num_examples: {len(normalized)} |
| download_size: {parquet_path.stat().st_size} |
| dataset_size: {normalized.data.nbytes} |
| """ |
| card = card.replace("- config_name: binary_600\n", info + "- config_name: binary_600\n", 1) |
|
|
| if "The `eukaryote_cls` configuration uses the `mcq` feature schema" not in card: |
| note = "The `eukaryote_cls` configuration uses the `mcq` feature schema, including JSON-serialized `metadata`.\n\n" |
| card = card.replace("The `binary_600` and `mcq_600` configurations", note + "The `binary_600` and `mcq_600` configurations", 1) |
|
|
| if "scripts/create_eukaryote_cls.py" not in card: |
| card += f""" |
| ## Reproducing |
| |
| To rebuild and publish the normalized `eukaryote_cls` configuration from the pinned source revision, run: |
| |
| ```bash |
| python scripts/create_eukaryote_cls.py --source-revision {args.source_revision} --output-dataset {args.output_dataset} --publish |
| ``` |
| |
| The script preserves the source rows, converts `metadata` from Python dictionary strings to JSON, and casts the |
| columns to the `mcq` feature schema. It publishes the Parquet file, this card, and the builder script in one commit. |
| """ |
|
|
| card_path = args.output_dir / "README.md" |
| card_path.write_text(card) |
| print(f"Prepared {len(normalized)} rows at {parquet_path}") |
| if args.publish: |
| commit = api.create_commit( |
| repo_id=args.output_dataset, |
| repo_type="dataset", |
| parent_commit=head, |
| commit_message="Normalize eukaryote_cls schema and metadata", |
| operations=[ |
| CommitOperationAdd(path_in_repo=PARQUET_PATH, path_or_fileobj=parquet_path), |
| CommitOperationAdd(path_in_repo="README.md", path_or_fileobj=card_path), |
| CommitOperationAdd(path_in_repo="scripts/create_eukaryote_cls.py", path_or_fileobj=__file__), |
| ], |
| ) |
| print(f"Published {commit.commit_url}") |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
