fix broken unit tests

clinica/utils/caps.py

@@ -7,17 +7,13 @@
 from cattr.gen import make_dict_unstructure_fn, override
 from cattr.preconf.json import make_converter
 
-# from clinica.utils.input import DatasetType
 from clinica.utils.bids import BIDS_VERSION
+from clinica.utils.exceptions import ClinicaCAPSError
+from clinica.utils.inputs import DatasetType
 
 CAPS_VERSION = "1.0.0"
 
 
-class DatasetType(str, Enum):
-    RAW = "raw"
-    DERIVATIVE = "derivative"
-
-
 @define
 class CAPSDatasetDescription:
     """Model representing a CAPS dataset description."""
@@ -55,7 +51,7 @@ def from_file(cls, json_file: Path):
                 DatasetType(parsed["DatasetType"]),
             )
         except KeyError:
-            raise ValueError(
+            raise ClinicaCAPSError(
                 f"CAPS dataset_description.json file {json_file} is not valid and "
                 "cannot be parsed as a CAPSDatasetDescription. "
                 "Please verify that the file is well formatted."
@@ -103,17 +99,24 @@ def write_caps_dataset_description(
     caps_version: Optional[str] = None,
 ) -> None:
     """Write `dataset_description.json` at the root of the CAPS directory."""
+    from clinica.utils.stream import cprint
+
     new_desc = CAPSDatasetDescription.from_values(name, bids_version, caps_version)
     if (caps_dir / "dataset_description.json").exists():
-        print(f"The CAPS dataset already contains a dataset_description.json file.")
+        cprint(
+            f"The CAPS dataset {name} already contains a dataset_description.json file.",
+            lvl="info",
+        )
         previous_desc = CAPSDatasetDescription.from_file(
             caps_dir / "dataset_description.json"
         )
         if not previous_desc.is_compatible_with(new_desc):
-            raise ValueError(
+            msg = (
                 f"Impossible to write the dataset_description.json file in {caps_dir} "
                 "because it already exists and it contains incompatible metadata."
             )
+            cprint(msg, lvl="error")
+            raise ClinicaCAPSError(msg)
         if previous_desc.name != new_desc.name:
             new_desc.name = f"{previous_desc.name} + {new_desc.name}"
     with open(caps_dir / "dataset_description.json", "w") as f:

clinica/utils/testing_utils.py

@@ -72,6 +72,11 @@ def build_caps_directory(directory: os.PathLike, configuration: dict) -> None:
     This function is a simple prototype for creating fake datasets for testing.
     """
     directory = Path(directory)
+    with open(directory / "dataset_description.json", "w") as fp:
+        json.dump(
+            {"Name": "Example dataset", "BIDSVersion": "1.0.2", "CAPSVersion": "1.0.0"},
+            fp,
+        )
     _build_groups(directory, configuration)
     _build_subjects(directory, configuration)
 

test/unittests/pipelines/t1_linear/test_anat_linear_pipeline.py

@@ -23,7 +23,7 @@ def test_anat_linear_pipeline_single_bids_input_error(tmp_path):
     with pytest.raises(
         ClinicaBIDSError,
         match=re.escape(
-            f"The BIDS directory ({tmp_path}) you provided "
+            f"The raw directory ({tmp_path}) you provided "
             "is missing a dataset_description.json file."
         ),
     ):
@@ -37,7 +37,7 @@ def test_anat_linear_pipeline_single_caps_input_error(tmp_path):
     with pytest.raises(
         ClinicaCAPSError,
         match=re.escape(
-            f"The CAPS directory ({tmp_path}) you provided "
+            f"The derivative directory ({tmp_path}) you provided "
             "is missing a dataset_description.json file."
         ),
     ):

test/unittests/utils/test_caps.py

@@ -66,6 +66,7 @@ def test_write_caps_dataset_description_error(tmp_path):
         DatasetType,
         write_caps_dataset_description,
     )
+    from clinica.utils.exceptions import ClinicaCAPSError
 
     caps_dir = tmp_path / "caps"
     caps_dir.mkdir()
@@ -91,7 +92,7 @@ def test_write_caps_dataset_description_error(tmp_path):
 
     # But re-writing a different description raises an error
     with pytest.raises(
-        ValueError,
+        ClinicaCAPSError,
         match=(
             f"Impossible to write the dataset_description.json file in {caps_dir} "
             "because it already exists and it contains incompatible metadata."

test/unittests/utils/test_utils_inputs.py

@@ -1,3 +1,4 @@
+import json
 import os
 import re
 from pathlib import Path
@@ -354,6 +355,18 @@ def test_check_caps_folder(tmp_path):
 
     (tmp_path / "subjects").mkdir()
     (tmp_path / "subjects" / "foo.txt").mkdir()
+    with pytest.raises(
+        ClinicaCAPSError,
+        match=re.escape(
+            f"The derivative directory ({tmp_path}) you provided is missing a dataset_description.json file."
+        ),
+    ):
+        check_caps_folder(tmp_path)
+    with open(tmp_path / "dataset_description.json", "w") as fp:
+        json.dump(
+            {"Name": "Example dataset", "BIDSVersion": "1.0.2", "CAPSVersion": "1.0.0"},
+            fp,
+        )
     assert check_caps_folder(tmp_path) is None
     (tmp_path / "sub-01").mkdir()
     with pytest.raises(
@@ -709,6 +722,11 @@ def test_clinica_file_reader_dwi_dti(tmp_path):
         / "native_space"
     )
     dti_folder.mkdir(parents=True)
+    with open(tmp_path / "dataset_description.json", "w") as fp:
+        json.dump(
+            {"Name": "Example dataset", "BIDSVersion": "1.0.2", "CAPSVersion": "1.0.0"},
+            fp,
+        )
     for measure in DTIBasedMeasure:
         (dti_folder / f"sub-01_ses-M000_space-T1w_{measure.value}.nii.gz").touch()
     query = dwi_dti("FA", space="T1w")