| """Tools for post-processing haddock3 runs.""" |
|
|
| import os |
| import shutil |
| import tarfile |
| import time |
|
|
| from haddock import log |
| from haddock.clis.cli_analyse import ANA_FOLDER |
| from haddock.core.typing import Optional |
|
|
|
|
| def _robust_rmtree(path: str, retries: int = 3, delay: float = 0.5) -> None: |
| """Delete a directory tree, tolerant of non-local filesystem quirks. |
| |
| On non-local filesystems (NFS, FUSE object-store mounts such as gcsfuse or |
| s3fs, overlayfs in containers, CIFS/SMB) deleting a still-open file does not |
| remove it immediately, and directory listings can be eventually inconsistent. |
| As a result ``shutil.rmtree`` may fail with |
| ``OSError: [Errno 39] Directory not empty`` even when nothing should remain. |
| |
| This retries the removal a few times to absorb transient inconsistency. If |
| the tree still cannot be removed, a warning is logged and the leftover |
| directory is left in place rather than crashing the run — the ``.tgz`` |
| archive has already been written, so no data is lost. |
| |
| The primary safeguard against this situation is closing any open file |
| handles (e.g. the run ``log`` file) *before* calling this function; the |
| retries here are a defensive fallback for whatever filesystem the run |
| happens to live on. |
| """ |
| for attempt in range(1, retries + 1): |
| try: |
| shutil.rmtree(path) |
| return |
| except OSError as err: |
| if attempt == retries: |
| log.warning( |
| f"Could not fully remove '{path}' after archiving " |
| f"({err}). The archive is intact; leaving the directory " |
| "in place. This is typically caused by a non-local " |
| "filesystem (NFS, gcsfuse/s3fs, overlayfs) holding a file " |
| "open or lagging on deletion." |
| ) |
| return |
| time.sleep(delay) |
|
|
|
|
| def archive_run(run_dir: str, delete: bool = True) -> tuple[str, Optional[str]]: |
| """Create an archive of the haddock3 run directory and analysis. |
| |
| Parameters |
| ---------- |
| run_dir : str |
| Path to the run directory |
| delete : bool, optional |
| Should the un-archived directory be deleted?, by default False |
| |
| Returns |
| ------- |
| tuple[str, Optional[str]] |
| run_archive_fname : str |
| Path to the run archive |
| analysis_archive_fname : Optional[str] |
| Path to the run analysis archive |
| """ |
| log.info("Creating an archive of the run") |
| |
| run_archive_fname = f"{run_dir}.tgz" |
| with tarfile.open(run_archive_fname, "w:gz") as tar: |
| tar.add(run_dir, arcname=os.path.basename(run_dir)) |
|
|
| |
| analysis_archive_fname = None |
| if os.path.exists(f"{run_dir}/{ANA_FOLDER}"): |
| analysis_archive_fname = f"{run_dir}_{ANA_FOLDER}.tgz" |
| with tarfile.open(analysis_archive_fname, "w:gz") as tar: |
| tar.add(f"{run_dir}/{ANA_FOLDER}", arcname=f"{run_dir}_{ANA_FOLDER}") |
|
|
| if delete: |
| _robust_rmtree(run_dir) |
|
|
| return run_archive_fname, analysis_archive_fname |
|
|
