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[Conformal EEG] Fix TUEV dataset metadata permissions for shared cluster storage - main #787

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[Conformal EEG] Fix TUEV dataset metadata permissions for shared cluster storage - main #787

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57 changes: 50 additions & 7 deletions pyhealth/datasets/tuev.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,24 @@ def __init__(
raise ValueError("subset must be one of 'train', 'eval', or 'both'")

self.prepare_metadata()

# Determine where the CSVs are located (shared directory or cache)
root_path = Path(root)
cache_dir = Path.home() / ".cache" / "pyhealth" / "tuev"

# Check if CSVs exist in cache and not in shared location
use_cache = False
for table in tables:
shared_csv = root_path / f"tuev-{table}-pyhealth.csv"
cache_csv = cache_dir / f"tuev-{table}-pyhealth.csv"
if not shared_csv.exists() and cache_csv.exists():
use_cache = True
break

# Use cache directory as root if CSVs are there
if use_cache:
logger.info(f"Using cached metadata from {cache_dir}")
root = str(cache_dir)

super().__init__(
root=root,
Expand All @@ -107,12 +125,16 @@ def prepare_metadata(self) -> None:
- segment_id = a_ / a_1 / ...
"""
root = Path(self.root)
cache_dir = Path.home() / ".cache" / "pyhealth" / "tuev"

train_rows: list[dict] = []
eval_rows: list[dict] = []

for split in ("train", "eval"):
if os.path.exists(root / f"tuev-{split}-pyhealth.csv"):
# Check if metadata exists in either shared location or cache
shared_csv = root / f"tuev-{split}-pyhealth.csv"
cache_csv = cache_dir / f"tuev-{split}-pyhealth.csv"
if shared_csv.exists() or cache_csv.exists():
continue

split_dir = root / split
Expand Down Expand Up @@ -153,7 +175,9 @@ def prepare_metadata(self) -> None:
}
)

root.mkdir(parents=True, exist_ok=True)
# Setup cache directory as fallback for metadata CSVs
cache_dir = Path.home() / ".cache" / "pyhealth" / "tuev"
cache_dir.mkdir(parents=True, exist_ok=True)

# Write train metadata
if train_rows:
Expand All @@ -162,9 +186,18 @@ def prepare_metadata(self) -> None:
["patient_id", "record_id"], inplace=True, na_position="last"
)
train_df.reset_index(drop=True, inplace=True)
train_csv = root / "tuev-train-pyhealth.csv"
train_df.to_csv(train_csv, index=False)


# Try shared location first, fall back to cache if no write permission
train_csv_shared = root / "tuev-train-pyhealth.csv"
train_csv_cache = cache_dir / "tuev-train-pyhealth.csv"

try:
train_csv_shared.parent.mkdir(parents=True, exist_ok=True)
train_df.to_csv(train_csv_shared, index=False)
logger.info(f"Wrote train metadata to {train_csv_shared}")
except (PermissionError, OSError):
train_df.to_csv(train_csv_cache, index=False)
logger.info(f"Wrote train metadata to cache: {train_csv_cache}")

# Write eval metadata
if eval_rows:
Expand All @@ -175,8 +208,18 @@ def prepare_metadata(self) -> None:
na_position="last",
)
eval_df.reset_index(drop=True, inplace=True)
eval_csv = root / "tuev-eval-pyhealth.csv"
eval_df.to_csv(eval_csv, index=False)

# Try shared location first, fall back to cache if no write permission
eval_csv_shared = root / "tuev-eval-pyhealth.csv"
eval_csv_cache = cache_dir / "tuev-eval-pyhealth.csv"

try:
eval_csv_shared.parent.mkdir(parents=True, exist_ok=True)
eval_df.to_csv(eval_csv_shared, index=False)
logger.info(f"Wrote eval metadata to {eval_csv_shared}")
except (PermissionError, OSError):
eval_df.to_csv(eval_csv_cache, index=False)
logger.info(f"Wrote eval metadata to cache: {eval_csv_cache}")

@property
def default_task(self) -> EEGEventsTUEV:
Expand Down