| |
| """Extract finished zip downloads into data/raw, then delete the zip to save disk.""" |
| from __future__ import annotations |
|
|
| import json |
| import subprocess |
| import zipfile |
| from pathlib import Path |
|
|
| ROOT = Path("/opt/dlami/nvme/workspace/skin_disease_classification") |
| LOG = ROOT / "logs" |
| STATE = ROOT / "logs" / "extract_state.json" |
|
|
| JOBS = [ |
| |
| ("skindisnet1", ROOT / "data/downloads/skindisnet/SkinDisNet.zip", ROOT / "data/raw/skindisnet"), |
| ("skindisnet2", ROOT / "data/downloads/skindisnet/SkinDisNet_2.zip", ROOT / "data/raw/skindisnet"), |
| ("pad1", ROOT / "data/downloads/pad_ufes_20/imgs_part_1.zip", ROOT / "data/raw/pad_ufes_20/images"), |
| ("pad2", ROOT / "data/downloads/pad_ufes_20/imgs_part_2.zip", ROOT / "data/raw/pad_ufes_20/images"), |
| ("pad3", ROOT / "data/downloads/pad_ufes_20/imgs_part_3.zip", ROOT / "data/raw/pad_ufes_20/images"), |
| ("isic2016_train", ROOT / "data/downloads/isic2016/ISBI2016_ISIC_Part3_Training_Data.zip", ROOT / "data/raw/isic2016/train"), |
| ("isic2016_test", ROOT / "data/downloads/isic2016/ISBI2016_ISIC_Part3_Test_Data.zip", ROOT / "data/raw/isic2016/test"), |
| ("isic2018_train", ROOT / "data/downloads/isic2018/ISIC2018_Task3_Training_Input.zip", ROOT / "data/raw/ham10000/train"), |
| ("isic2018_train_gt", ROOT / "data/downloads/isic2018/ISIC2018_Task3_Training_GroundTruth.zip", ROOT / "data/raw/ham10000"), |
| ("isic2018_val", ROOT / "data/downloads/isic2018/ISIC2018_Task3_Validation_Input.zip", ROOT / "data/raw/ham10000/val"), |
| ("isic2018_val_gt", ROOT / "data/downloads/isic2018/ISIC2018_Task3_Validation_GroundTruth.zip", ROOT / "data/raw/ham10000"), |
| ("isic2018_test", ROOT / "data/downloads/isic2018/ISIC2018_Task3_Test_Input.zip", ROOT / "data/raw/ham10000/test"), |
| ("isic2018_test_gt", ROOT / "data/downloads/isic2018/ISIC2018_Task3_Test_GroundTruth.zip", ROOT / "data/raw/ham10000"), |
| ("isic2019_train", ROOT / "data/downloads/isic2019/ISIC_2019_Training_Input.zip", ROOT / "data/raw/isic2019/train"), |
| ("isic2019_test", ROOT / "data/downloads/isic2019/ISIC_2019_Test_Input.zip", ROOT / "data/raw/isic2019/test"), |
| ("isic2024_train", ROOT / "data/downloads/isic2024/ISIC_2024_Training_Input.zip", ROOT / "data/raw/isic2024/train"), |
| ("milk_train", ROOT / "data/downloads/milk10k/MILK10k_Training_Input.zip", ROOT / "data/raw/milk10k/train"), |
| ("milk_test", ROOT / "data/downloads/milk10k/MILK10k_Test_Input.zip", ROOT / "data/raw/milk10k/test"), |
| ("isic2020_train_jpeg", ROOT / "data/downloads/isic2020/ISIC_2020_Training_JPEG.zip", ROOT / "data/raw/isic2020/train"), |
| ("isic2020_test_jpeg", ROOT / "data/downloads/isic2020/ISIC_2020_Test_JPEG.zip", ROOT / "data/raw/isic2020/test"), |
| ] |
|
|
|
|
| def job_done(name: str) -> bool: |
| log = LOG / f"{name}.log" |
| if not log.exists(): |
| return False |
| text = log.read_text(errors="replace") |
| if f"END {name} rc=0" in text: |
| return True |
| |
| return " saved [" in text and text.rstrip().endswith("]") |
|
|
|
|
| def load_state() -> dict: |
| if STATE.exists(): |
| return json.loads(STATE.read_text()) |
| return {} |
|
|
|
|
| def save_state(state: dict) -> None: |
| STATE.write_text(json.dumps(state, indent=2)) |
|
|
|
|
| def extract(zip_path: Path, dest: Path) -> None: |
| dest.mkdir(parents=True, exist_ok=True) |
| print(f"EXTRACT {zip_path.name} -> {dest}", flush=True) |
| with zipfile.ZipFile(zip_path) as zf: |
| zf.extractall(dest) |
| zip_path.unlink() |
| print(f"DELETED {zip_path.name}", flush=True) |
|
|
|
|
| def main() -> None: |
| state = load_state() |
| for name, zip_path, dest in JOBS: |
| if state.get(name) == "extracted": |
| continue |
| if not job_done(name): |
| continue |
| if not zip_path.exists(): |
| print(f"MISSING zip for {name}", flush=True) |
| continue |
| extract(zip_path, dest) |
| state[name] = "extracted" |
| save_state(state) |
| print("extract pass complete", json.dumps(state), flush=True) |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
