add unit tests

test/unittests/iotools/utils/test_center_nifti.py

@@ -0,0 +1,78 @@
+from os import PathLike
+from pathlib import Path
+from typing import Iterable, List, Optional
+from unittest.mock import patch
+
+import pytest
+
+
+def test_center_nifti_error(tmp_path):
+    from clinica.iotools.utils import center_nifti
+    from clinica.utils.exceptions import ClinicaExistingDatasetError
+
+    (tmp_path / "out").mkdir()
+    (tmp_path / "out" / "foo.txt").touch()
+
+    with pytest.raises(
+        ClinicaExistingDatasetError,
+        match=f"Dataset located at {tmp_path / 'out'} already contain some files.",
+    ):
+        center_nifti(tmp_path / "bids", tmp_path / "out")
+
+
+def center_all_nifti_mock(
+    bids_dir: PathLike,
+    output_dir: PathLike,
+    modalities: Optional[Iterable[str]] = None,
+    center_all_files: bool = False,
+) -> List[Path]:
+    result = []
+    for filename in ("foo.txt", "bar.tsv", "baz.nii.gz"):
+        (Path(output_dir) / filename).touch()
+        result.append(Path(output_dir) / filename)
+    return result
+
+
+def test_center_nifti_log_file_creation_error(tmp_path, mocker):
+    from clinica.iotools.utils import center_nifti
+
+    (tmp_path / "bids").mkdir()
+    (tmp_path / "out").mkdir()
+    mocker.patch(
+        "clinica.iotools.utils.data_handling.write_list_of_files", return_value=False
+    )
+    with patch(
+        "clinica.iotools.utils.data_handling.center_all_nifti",
+        wraps=center_all_nifti_mock,
+    ) as mock:
+        with pytest.raises(
+            IOError,
+            match="Could not create log file",
+        ):
+            center_nifti(tmp_path / "bids", tmp_path / "out", center_all_files=True)
+        mock.assert_called_once_with(tmp_path / "bids", tmp_path / "out", None, True)
+
+
+def test_center_nifti(tmp_path):
+    from clinica.iotools.utils import center_nifti
+
+    (tmp_path / "bids").mkdir()
+    output_dir = tmp_path / "out"
+    output_dir.mkdir()
+
+    with patch(
+        "clinica.iotools.utils.data_handling.center_all_nifti",
+        wraps=center_all_nifti_mock,
+    ) as mock:
+        center_nifti(tmp_path / "bids", tmp_path / "out", ("anat", "pet", "dwi"))
+        mock.assert_called_once_with(
+            tmp_path / "bids", tmp_path / "out", ("anat", "pet", "dwi"), False
+        )
+        assert (
+            len([f for f in output_dir.iterdir()]) == 4
+        )  # 3 files written by mock and 1 log file
+        logs = [f for f in output_dir.glob("centered_nifti_list_*.txt")]
+        assert len(logs) == 1
+        assert logs[0].read_text() == "\n".join(
+            [str(tmp_path / "out" / f) for f in ("foo.txt", "bar.tsv", "baz.nii.gz")]
+        )