| |
| """ |
| Unpack the output of an HADDOCK3 run directory. |
| |
| The unpack process performs file unpacking and file decompressing |
| operations. File with extension `seed` and `con` are unpacked from |
| their `.tgz` files. While files with `.pdb.gz` and `.psf.gz` extension |
| are uncompressed. If `--all` is given, unpack also `.inp.gz` and |
| `.out.gz` files. |
| |
| This CLI performs the opposite operations as the ``haddock3-clean`` |
| command-line. |
| |
| The <run_directory> can either be a whole HADDOCK3 run folder or a |
| specific folder of the workflow step. <ncores> defined the number of |
| threads to use. |
| |
| Usage:: |
| |
| haddock3-unpack -h |
| haddock3-unpack -r <run_directory> |
| haddock3-unpack run1 |
| haddock3-unpack run1/1_rigidbody |
| haddock3-unpack run1 -n # uses all cores |
| haddock3-unpack run1 -n 2 # uses 2 cores |
| haddock3-unpack run1 -n 2 -a |
| haddock3-unpack run1 -n 2 --all |
| """ |
| import argparse |
| import sys |
|
|
| from haddock.core.typing import ( |
| ArgumentParser, |
| Callable, |
| FilePath, |
| Namespace, |
| Optional, |
| ) |
| from haddock.libs import libcli |
|
|
|
|
| |
| ap = argparse.ArgumentParser( |
| description=__doc__, |
| formatter_class=argparse.RawDescriptionHelpFormatter, |
| ) |
|
|
| libcli.add_rundir_arg(ap) |
|
|
| ap.add_argument( |
| "--all", |
| "-a", |
| dest="dec_all", |
| help="Unpack all files (includes `.inp` and `.out`).", |
| action="store_true", |
| ) |
|
|
| libcli.add_ncores_arg(ap) |
| libcli.add_version_arg(ap) |
|
|
|
|
| def _ap() -> ArgumentParser: |
| return ap |
|
|
|
|
| def load_args(ap: ArgumentParser) -> Namespace: |
| """Load argument parser args.""" |
| return ap.parse_args() |
|
|
|
|
| def cli(ap: ArgumentParser, main: Callable[..., None]) -> None: |
| """Command-line interface entry point.""" |
| cmd = load_args(ap) |
| main(**vars(cmd)) |
|
|
|
|
| def maincli() -> None: |
| """Execute main client.""" |
| cli(ap, main) |
|
|
|
|
| def main(run_dir: FilePath, ncores: Optional[int] = 1, dec_all: bool = False) -> None: |
| """ |
| Unpack a HADDOCK3 run directory step folders. |
| |
| Usually, this concerns uncompressing and unpacking files. |
| |
| It performs the oposity function as |
| :py:func:`haddock.clis.cli_clean.main`. |
| |
| Parameters |
| ---------- |
| run_dir : str or :external:py:class:`pathlib.Path`. |
| The path to the run directory or to a folder of a specific step |
| of the workflow. |
| |
| ncores : int, or None |
| The number of cores to use. If ``None``, use all possible threads. |
| Defaults to 1. |
| |
| See Also |
| -------- |
| `haddock.gear.clean_steps` |
| """ |
| |
| from pathlib import Path |
|
|
| from haddock import log |
| from haddock.gear.clean_steps import unpack_compressed_and_archived_files |
| from haddock.libs.libtimer import log_time |
| from haddock.libs.libutil import parse_ncores |
| from haddock.modules import get_module_steps_folders, is_step_folder |
|
|
| log.info(f"Unpacking {str(run_dir)!r} folder") |
| ncores = parse_ncores(ncores) |
|
|
| if is_step_folder(run_dir): |
| with log_time("unpacking took"): |
| unpack_compressed_and_archived_files( |
| [run_dir], |
| ncores, |
| dec_all=dec_all, |
| ) |
|
|
| else: |
| step_folders = [Path(run_dir, p) for p in get_module_steps_folders(run_dir)] |
| with log_time("unpacking took"): |
| unpack_compressed_and_archived_files( |
| step_folders, |
| ncores, |
| dec_all=dec_all, |
| ) |
|
|
| return |
|
|
|
|
| if __name__ == "__main__": |
| sys.exit(maincli()) |
|
|
