docs/changes/latest.inc

@@ -71,6 +71,8 @@ Bugs
 
 - Fix a bug in which :func:`junifer.stats.count` will not be correctly applied across an axis (:gh:`195` by `Fede Raimondo`_).
 
+- Fix an issue with datalad cache and locks in which the overriden settings in Junifer were not propagated to subprocesses, resulting in using the default settings (:gh:`199` by `Fede Raimondo`_).
+
 API changes
 ~~~~~~~~~~~
 

junifer/api/cli.py

@@ -74,6 +74,45 @@ def _parse_elements(element: str, config: Dict) -> Union[List, None]:
     return elements
 
 
+def _validate_verbose(
+    ctx: click.Context, param: str, value: str
+) -> Union[str, int]:
+    """Validate verbose option.
+
+    Parameters
+    ----------
+    ctx : click.Context
+        The context of the command.
+    param : str
+        The parameter to validate.
+    value : str
+        The value to validate.
+
+    Returns
+    -------
+    str or int
+        The validated value.
+    """
+    if isinstance(value, int):
+        return value
+
+    valid_strings = ["error", "warning", "info", "debug"]
+    if isinstance(value, str) and value.lower() in valid_strings:
+        return value.upper()
+
+    try:
+        value = int(value)  # type: ignore
+        return value
+    except ValueError:
+        # If we get here, the value is not a valid integer.
+        pass
+
+    # If we get here, the value is not valid.
+    raise click.BadParameter(
+        f"verbose must be one of {valid_strings} or an integer"
+    )
+
+
 @click.group()
 def cli() -> None:  # pragma: no cover
     """CLI for JUelich NeuroImaging FEature extractoR."""
@@ -90,10 +129,11 @@ def cli() -> None:  # pragma: no cover
 @click.option(
     "-v",
     "--verbose",
-    type=click.Choice(["warning", "info", "debug"], case_sensitive=False),
+    type=click.UNPROCESSED,
+    callback=_validate_verbose,
     default="info",
 )
-def run(filepath: click.Path, element: str, verbose: click.Choice) -> None:
+def run(filepath: click.Path, element: str, verbose: Union[str, int]) -> None:
     """Run command for CLI.
     \f
     Parameters
@@ -106,7 +146,7 @@ def run(filepath: click.Path, element: str, verbose: click.Choice) -> None:
         The verbosity level: warning, info or debug (default "info").
 
     """
-    configure_logging(level=str(verbose).upper())
+    configure_logging(level=verbose)
     # TODO: add validation
     config = parse_yaml(filepath)  # type: ignore
     workdir = config["workdir"]
@@ -136,10 +176,11 @@ def run(filepath: click.Path, element: str, verbose: click.Choice) -> None:
 @click.option(
     "-v",
     "--verbose",
-    type=click.Choice(["warning", "info", "debug"], case_sensitive=False),
+    type=click.UNPROCESSED,
+    callback=_validate_verbose,
     default="info",
 )
-def collect(filepath: click.Path, verbose: click.Choice) -> None:
+def collect(filepath: click.Path, verbose: Union[str, int]) -> None:
     """Collect command for CLI.
     \f
     Parameters
@@ -150,7 +191,7 @@ def collect(filepath: click.Path, verbose: click.Choice) -> None:
         The verbosity level: warning, info or debug (default "info").
 
     """
-    configure_logging(level=str(verbose).upper())
+    configure_logging(level=verbose)
     # TODO: add validation
     config = parse_yaml(filepath)  # type: ignore
     storage = config["storage"]
@@ -171,7 +212,8 @@ def collect(filepath: click.Path, verbose: click.Choice) -> None:
 @click.option(
     "-v",
     "--verbose",
-    type=click.Choice(["warning", "info", "debug"], case_sensitive=False),
+    type=click.UNPROCESSED,
+    callback=_validate_verbose,
     default="info",
 )
 def queue(
@@ -179,7 +221,7 @@ def queue(
     element: str,
     overwrite: bool,
     submit: bool,
-    verbose: click.Choice,
+    verbose: Union[str, int],
 ) -> None:
     """Queue command for CLI.
     \f
@@ -197,7 +239,7 @@ def queue(
         The verbosity level: warning, info or debug (default "info").
 
     """
-    configure_logging(level=str(verbose).upper())
+    configure_logging(level=verbose)
     # TODO: add validation
     config = parse_yaml(filepath)  # type: ignore
     elements = _parse_elements(element, config)

junifer/datagrabber/datalad_base.py

@@ -6,6 +6,7 @@
 # License: AGPL
 
 import atexit
+import os
 import shutil
 import tempfile
 from pathlib import Path
@@ -13,6 +14,7 @@ from typing import Dict, Optional, Tuple, Union
 
 import datalad
 import datalad.api as dl
+from datalad.support.exceptions import IncompleteResultsError
 from datalad.support.gitrepo import GitRepo
 
 from ..api.decorators import register_datagrabber
@@ -82,21 +84,10 @@ class DataladDataGrabber(BaseDataGrabber):
             sockets_dir.mkdir(parents=True, exist_ok=False)
             locks_dir.mkdir(parents=True, exist_ok=False)
             logger.debug(f"Setting datalad cache to {cache_dir}")
-            datalad.cfg.set(
+            os.environ["DATALAD_LOCATIONS_CACHE"] = cache_dir.as_posix()
-                "datalad.locations.cache",
+            os.environ["DATALAD_LOCATIONS_SOCKETS"] = sockets_dir.as_posix()
-                cache_dir.as_posix(),
+            os.environ["DATALAD_LOCATIONS_LOCKS"] = locks_dir.as_posix()
-                scope="override",
+            datalad.cfg.reload()
-            )
-            datalad.cfg.set(
-                "datalad.locations.sockets",
-                sockets_dir.as_posix(),
-                scope="override",
-            )
-            datalad.cfg.set(
-                "datalad.locations.locks",
-                locks_dir.as_posix(),
-                scope="override",
-            )
             logger.debug(
                 "Datalad cache set to "
                 f"{datalad.cfg.get('datalad.locations.cache')}"
@@ -184,7 +175,12 @@ class DataladDataGrabber(BaseDataGrabber):
             for fname in to_get:
                 logger.debug(f"\t: {fname}")
 
-            dl_out = self._dataset.get(to_get, result_renderer="disabled")
+            try:
+                dl_out = self._dataset.get(to_get, result_renderer="disabled")
+            except IncompleteResultsError as e:
+                raise_error(
+                    f"Failed to get from dataset: {e.failed}"
+                )
             if not self._was_cloned:
                 # If the dataset was already installed, check that the
                 # file was actually downloaded to avoid removing a

junifer/datagrabber/tests/test_datalad_base.py

@@ -160,6 +160,49 @@ def test_datalad_clone_cleanup(
     assert len(list(datadir.glob("*"))) == 0
 
 
+def test_datalad_clone_create_cleanup(concrete_datagrabber: Type) -> None:
+    """Test datalad base tempdir clone and remove.
+
+    Parameters
+    ----------
+    concrete_datagrabber : DataladDataGrabber
+        A concrete datagrabber class to use.
+    """
+
+    # Clone whole dataset
+    uri = _testing_dataset["example_bids"]["uri"]
+    with concrete_datagrabber(datadir=None, uri=uri) as dg:
+        datadir = dg._tmpdir / "datadir"
+        elem1_bold = (
+            datadir / "example_bids/sub-01/func/sub-01_task-rest_bold.nii.gz"
+        )
+        elem1_t1w = datadir / "example_bids/sub-01/anat/sub-01_T1w.nii.gz"
+
+        assert elem1_bold.is_file() is False
+        assert elem1_t1w.is_file() is False
+        assert datadir.exists() is True
+        assert dg._was_cloned is True
+        assert elem1_bold.is_file() is False
+        assert elem1_bold.is_symlink() is True
+        assert elem1_t1w.is_file() is False
+        assert elem1_t1w.is_symlink() is True
+        elem1 = dg["sub-01"]
+        assert "meta" in elem1["BOLD"]
+        meta = elem1["BOLD"]["meta"]
+        assert "datagrabber" in meta
+        assert "datalad_dirty" in meta["datagrabber"]
+        assert meta["datagrabber"]["datalad_dirty"] is False
+        assert hasattr(dg, "_got_files") is False
+        assert datadir.exists() is True
+        assert elem1_bold.is_file() is True
+        assert elem1_bold.is_symlink() is True
+        assert elem1_t1w.is_file() is True
+        assert elem1_t1w.is_symlink() is True
+
+    assert datadir.exists() is False
+    assert len(list(datadir.glob("*"))) == 0
+
+
 def test_datalad_previously_cloned(
     tmp_path: Path, concrete_datagrabber: Type
 ) -> None: