bids-mriqc not usable with datalad dataset

[bpinsard]

same error for 23.1.1 and 24.0.2 (don't believe the logs for the version: nipreps/mriqc#1354 )

It seems that mriqc calls datalad even if all files were fetch beforehand outside of the container.

[INFO   ] == Command start (output follows) =====                                                                                                             
------------------------------------------------------------------
  Running MRIQC version 24.1.0.dev0+gd5b13cb5.d20240826
  ----------------------------------------------------------------

  NOTICE
  Copyright © The NiPreps Developers.
  
  This product includes software developed by
  the NiPreps Community (https://nipreps.org/).
  
  Portions of this software were developed at the Department of
  Psychology at Stanford University, Stanford, CA, US.
  
  This software contains code ultimately derived from the
  PCP Quality Assessment Protocol (QAP;
  http://preprocessed-connectomes-project.org/quality-assessment-protocol)
  by C. Craddock, S. Giavasis, D. Clark, Z. Shezhad, and J. Pellman.
  
  This software is also distributed as a Docker container image.
  The bootstrapping file for the image ("Dockerfile") is licensed
  under the MIT License.

  ----------------------------------------------------------------

  * BIDS dataset path: /home/basile/data/tests/mriqc/sourcedata/bids.
  * Output folder: ..
  * Analysis levels: ['participant'].
------------------------------------------------------------------

2024-11-01 18:24:05 | IMPORTANT | mriqc            | DataLad dataset identified, attempting to `datalad get` unavailable files.
Traceback (most recent call last):
  File "/opt/conda/lib/python3.11/pathlib.py", line 1116, in mkdir
    os.mkdir(self, mode)
FileNotFoundError: [Errno 2] No such file or directory: '/home/mriqc/.cache/datalad/sockets'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/conda/lib/python3.11/pathlib.py", line 1116, in mkdir
    os.mkdir(self, mode)
FileNotFoundError: [Errno 2] No such file or directory: '/home/mriqc/.cache/datalad'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/conda/bin/mriqc", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/mriqc/cli/run.py", line 43, in main
    parse_args(argv)
  File "/opt/conda/lib/python3.11/site-packages/mriqc/cli/parser.py", line 658, in parse_args
    initialize_meta_and_data()
  File "/opt/conda/lib/python3.11/site-packages/mriqc/utils/misc.py", line 447, in initialize_meta_and_data
    _datalad_get(dataset)
  File "/opt/conda/lib/python3.11/site-packages/mriqc/utils/misc.py", line 282, in _datalad_get
    return get(
           ^^^^
  File "/opt/conda/lib/python3.11/site-packages/datalad/interface/base.py", line 773, in eval_func
    return return_func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/datalad/interface/base.py", line 763, in return_func
    results = list(results)
              ^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/datalad_next/patches/interface_utils.py", line 197, in _execute_command_
    hooks = get_jsonhooks_from_config(ds.config if ds else dlcfg)
                                      ^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/datalad/distribution/dataset.py", line 331, in config
    repo = self.repo
           ^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/datalad/distribution/dataset.py", line 273, in repo
    self._repo = repo_from_path(self._path)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/datalad/core/local/repo.py", line 61, in repo_from_path
    repo = cls(path, create=False, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/datalad/dataset/repo.py", line 163, in __call__
    instance = type.__call__(cls, *new_args, **new_kwargs)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/datalad/support/annexrepo.py", line 198, in __init__
    super(AnnexRepo, self).__init__(
  File "/opt/conda/lib/python3.11/site-packages/datalad/support/gitrepo.py", line 938, in __init__
    ssh_manager.ensure_initialized()
  File "/opt/conda/lib/python3.11/site-packages/datalad/support/sshconnector.py", line 738, in ensure_initialized
    self._socket_dir.mkdir(exist_ok=True, parents=True)
  File "/opt/conda/lib/python3.11/pathlib.py", line 1120, in mkdir
    self.parent.mkdir(parents=True, exist_ok=True)
  File "/opt/conda/lib/python3.11/pathlib.py", line 1120, in mkdir
    self.parent.mkdir(parents=True, exist_ok=True)
  File "/opt/conda/lib/python3.11/pathlib.py", line 1116, in mkdir
    os.mkdir(self, mode)
OSError: [Errno 30] Read-only file system: '/home/mriqc/.cache'
[INFO   ] == Command exit (modification check follows) ===== 

[bpinsard]

This behavior is only in MRIQC, no other nipreps tool AFAIK
So maybe we should set the repronim/containers datalad config to include --no-datalad-get by default, as datalad operations are supposed to be taken care of outside of the container in that setting.

[yarikoptic]

So maybe we should set the repronim/containers datalad config to include --no-datalad-get by default, as datalad operations are supposed to be taken care of outside of the container in that setting.

indeed, let's just do that....

[bpinsard]

ok I just have to find in which version that option was introduced

[bpinsard]

nipreps/mriqc#1278 24.0.0, so the older versions in repronim/containers will remain broken unless this is backported. @oesteban

[yarikoptic]

old versions would remain "as working" as they were used ;) (ppl might have bind-mounted things up etc). Let's fix current/new ones.

[yarikoptic]

@bpinsard please check/review #133 (I sent an invite as well)