File size: 4,080 Bytes
0ea5581 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 | #!/usr/bin/env python3
"""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 = [
# job_log_name, zip_path, dest
("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
# Direct wget jobs print: "... saved [bytes/bytes]"
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()
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