junifer 0.0.7.dev332__py3-none-any.whl → 0.0.8__py3-none-any.whl

junifer/datagrabber/tests/test_dmcc13_benchmark.py

@@ -2,105 +2,128 @@
 
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
-
-from typing import Optional, Union
+from collections.abc import Iterator
+from pathlib import Path
 
 import pytest
+from pydantic import AnyUrl
+
+from junifer.datagrabber import DataType, DMCC13Benchmark
+from junifer.testing import config_override
+
+
+URI = AnyUrl(
+    "https://cerebra.fz-juelich.de/junifer/datalad-example-dmcc13-benchmark.git"
+)
 
-from junifer.datagrabber import DMCC13Benchmark
 
+@pytest.fixture(scope="module")
+def dmcc13_datadir(tmp_path_factory) -> Iterator[Path]:
+    """Return the path to the DMCC13 benchmark data directory.
 
-URI = "https://gin.g-node.org/synchon/datalad-example-dmcc13-benchmark"
+    Parameters
+    ----------
+    tmp_path_factory : pathlib.Path
+        The path to the test directory.
+
+    Returns
+    -------
+    pathlib.Path
+        The path to the DMCC13 benchmark data directory.
+
+    """
+    datadir = tmp_path_factory.mktemp("dmcc13_datadir")
+    datadir.mkdir(parents=True, exist_ok=True)
+    dg = DMCC13Benchmark(uri=URI, types=["T1w"], datadir=datadir)
+    with config_override("datagrabber.skipidcheck", True), dg:
+        yield datadir
 
 
 @pytest.mark.parametrize(
     "sessions, tasks, phase_encodings, runs, native_t1w",
     [
-        (None, None, None, None, False),
-        ("ses-wave1bas", "Rest", "AP", "1", False),
-        ("ses-wave1bas", "Axcpt", "AP", "1", False),
-        ("ses-wave1bas", "Cuedts", "AP", "1", False),
-        ("ses-wave1bas", "Stern", "AP", "1", False),
-        ("ses-wave1bas", "Stroop", "AP", "1", False),
-        ("ses-wave1bas", "Rest", "PA", "2", False),
-        ("ses-wave1bas", "Axcpt", "PA", "2", False),
-        ("ses-wave1bas", "Cuedts", "PA", "2", False),
-        ("ses-wave1bas", "Stern", "PA", "2", False),
-        ("ses-wave1bas", "Stroop", "PA", "2", False),
-        ("ses-wave1bas", "Rest", "AP", "1", True),
-        ("ses-wave1bas", "Axcpt", "AP", "1", True),
-        ("ses-wave1bas", "Cuedts", "AP", "1", True),
-        ("ses-wave1bas", "Stern", "AP", "1", True),
-        ("ses-wave1bas", "Stroop", "AP", "1", True),
-        ("ses-wave1bas", "Rest", "PA", "2", True),
-        ("ses-wave1bas", "Axcpt", "PA", "2", True),
-        ("ses-wave1bas", "Cuedts", "PA", "2", True),
-        ("ses-wave1bas", "Stern", "PA", "2", True),
-        ("ses-wave1bas", "Stroop", "PA", "2", True),
-        ("ses-wave1pro", "Rest", "AP", "1", False),
-        ("ses-wave1pro", "Rest", "PA", "2", False),
-        ("ses-wave1pro", "Rest", "AP", "1", True),
-        ("ses-wave1pro", "Rest", "PA", "2", True),
-        ("ses-wave1rea", "Rest", "AP", "1", False),
-        ("ses-wave1rea", "Rest", "PA", "2", False),
-        ("ses-wave1rea", "Rest", "AP", "1", True),
-        ("ses-wave1rea", "Rest", "PA", "2", True),
+        (["ses-wave1bas"], ["Rest"], ["AP"], ["1"], False),
+        (["ses-wave1bas"], ["Axcpt"], ["AP"], ["1"], False),
+        (["ses-wave1bas"], ["Cuedts"], ["AP"], ["1"], False),
+        (["ses-wave1bas"], ["Stern"], ["AP"], ["1"], False),
+        (["ses-wave1bas"], ["Stroop"], ["AP"], ["1"], False),
+        (["ses-wave1bas"], ["Rest"], ["PA"], ["2"], False),
+        (["ses-wave1bas"], ["Axcpt"], ["PA"], ["2"], False),
+        (["ses-wave1bas"], ["Cuedts"], ["PA"], ["2"], False),
+        (["ses-wave1bas"], ["Stern"], ["PA"], ["2"], False),
+        (["ses-wave1bas"], ["Stroop"], ["PA"], ["2"], False),
+        (["ses-wave1bas"], ["Rest"], ["AP"], ["1"], True),
+        (["ses-wave1bas"], ["Axcpt"], ["AP"], ["1"], True),
+        (["ses-wave1bas"], ["Cuedts"], ["AP"], ["1"], True),
+        (["ses-wave1bas"], ["Stern"], ["AP"], ["1"], True),
+        (["ses-wave1bas"], ["Stroop"], ["AP"], ["1"], True),
+        (["ses-wave1bas"], ["Rest"], ["PA"], ["2"], True),
+        (["ses-wave1bas"], ["Axcpt"], ["PA"], ["2"], True),
+        (["ses-wave1bas"], ["Cuedts"], ["PA"], ["2"], True),
+        (["ses-wave1bas"], ["Stern"], ["PA"], ["2"], True),
+        (["ses-wave1bas"], ["Stroop"], ["PA"], ["2"], True),
+        (["ses-wave1pro"], ["Rest"], ["AP"], ["1"], False),
+        (["ses-wave1pro"], ["Rest"], ["PA"], ["2"], False),
+        (["ses-wave1pro"], ["Rest"], ["AP"], ["1"], True),
+        (["ses-wave1pro"], ["Rest"], ["PA"], ["2"], True),
+        (["ses-wave1rea"], ["Rest"], ["AP"], ["1"], False),
+        (["ses-wave1rea"], ["Rest"], ["PA"], ["2"], False),
+        (["ses-wave1rea"], ["Rest"], ["AP"], ["1"], True),
+        (["ses-wave1rea"], ["Rest"], ["PA"], ["2"], True),
     ],
 )
 def test_DMCC13Benchmark(
-    sessions: Optional[str],
-    tasks: Optional[str],
-    phase_encodings: Optional[str],
-    runs: Optional[str],
+    sessions: list[str],
+    tasks: list[str],
+    phase_encodings: list[str],
+    runs: list[str],
     native_t1w: bool,
+    dmcc13_datadir: Path,
 ) -> None:
     """Test DMCC13Benchmark DataGrabber.
 
     Parameters
     ----------
-    sessions : str or None
+    sessions : list of str
         The parametrized session values.
-    tasks : str or None
+    tasks : list of str
         The parametrized task values.
-    phase_encodings : str or None
+    phase_encodings : list of str
         The parametrized phase encoding values.
-    runs : str or None
+    runs : list of str
         The parametrized run values.
     native_t1w : bool
         The parametrized values for fetching native T1w.
+    dmcc13_datadir : pathlib.Path
+        The path to the DMCC13 benchmark data directory.
 
     """
     dg = DMCC13Benchmark(
+        uri=URI,
         sessions=sessions,
         tasks=tasks,
         phase_encodings=phase_encodings,
         runs=runs,
         native_t1w=native_t1w,
+        datadir=dmcc13_datadir,
     )
-    # Set URI to Gin
-    dg.uri = URI
-
     with dg:
-        # Get all elements
         all_elements = dg.get_elements()
-        # Get test element
         test_element = all_elements[0]
-        # Get test element's access values
         _, ses, task, phase, run = test_element
-        # Access data
         out = dg[("sub-01", ses, task, phase, run)]
 
         # Available data types
         data_types = [
-            "BOLD",
-            "VBM_CSF",
-            "VBM_GM",
-            "VBM_WM",
-            "T1w",
+            DataType.BOLD,
+            DataType.VBM_CSF,
+            DataType.VBM_GM,
+            DataType.VBM_WM,
+            DataType.T1w,
         ]
         # Add Warp if native T1w is accessed
         if native_t1w:
-            data_types.append("Warp")
+            data_types.append(DataType.Warp)
 
         # Data type file name formats
         data_file_names = [
@@ -129,11 +152,13 @@ def test_DMCC13Benchmark(
                 "sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz"
             )
 
-        for data_type, data_file_name in zip(data_types, data_file_names):
+        for data_type, data_file_name in zip(
+            data_types, data_file_names, strict=False
+        ):
             # Assert data type
-            assert data_type in out
+            assert data_type in out.keys()
             # Conditional for Warp
-            if data_type == "Warp":
+            if data_type is DataType.Warp:
                 for idx, fname in enumerate(data_file_name):
                     # Assert data file path exists
                     assert out[data_type][idx]["path"].exists()
@@ -166,6 +191,7 @@ def test_DMCC13Benchmark(
                     "desc-confounds_regressors.tsv"
                 ),
             ),
+            strict=False,
         ):
             # Assert data type
             assert type_ in out["BOLD"]
@@ -199,15 +225,15 @@ def test_DMCC13Benchmark(
 @pytest.mark.parametrize(
     "types, native_t1w",
     [
-        ("BOLD", True),
+        (["BOLD"], True),
         ("BOLD", False),
-        ("T1w", True),
+        (["T1w"], True),
         ("T1w", False),
-        ("VBM_CSF", True),
+        (["VBM_CSF"], True),
         ("VBM_CSF", False),
-        ("VBM_GM", True),
+        (["VBM_GM"], True),
         ("VBM_GM", False),
-        ("VBM_WM", True),
+        (["VBM_WM"], True),
         ("VBM_WM", False),
         (["BOLD", "VBM_CSF"], True),
         (["BOLD", "VBM_CSF"], False),
@@ -218,8 +244,9 @@ def test_DMCC13Benchmark(
     ],
 )
 def test_DMCC13Benchmark_partial_data_access(
-    types: Union[str, list[str]],
+    types: str | list[str],
     native_t1w: bool,
+    dmcc13_datadir: Path,
 ) -> None:
     """Test DMCC13Benchmark DataGrabber partial data access.
 
@@ -229,68 +256,29 @@ def test_DMCC13Benchmark_partial_data_access(
         The parametrized types.
     native_t1w : bool
         The parametrized values for fetching native T1w.
+    dmcc13_datadir : pathlib.Path
+        The path to the DMCC13 benchmark data directory.
 
     """
-    dg = DMCC13Benchmark(types=types, native_t1w=native_t1w)
-    # Set URI to Gin
-    dg.uri = URI
-
+    dg = DMCC13Benchmark(
+        uri=URI,
+        types=types,
+        native_t1w=native_t1w,
+        datadir=dmcc13_datadir,
+    )
     with dg:
-        # Get all elements
         all_elements = dg.get_elements()
-        # Get test element
         test_element = all_elements[0]
-        # Get test element's access values
-        _, ses, task, phase, run = test_element
-        # Access data
-        out = dg[("sub-01", ses, task, phase, run)]
-        # Assert data type
-        if isinstance(types, list):
-            for type_ in types:
-                assert type_ in out
+        # Elements only have the subject if no data type of the tasks is
+        # grabbed
+        if isinstance(test_element, tuple):
+            out = dg[("sub-01", *test_element[1:])]
         else:
-            assert types in out
-
-
-def test_DMCC13Benchmark_incorrect_data_type() -> None:
-    """Test DMCC13Benchmark DataGrabber incorrect data type."""
-    with pytest.raises(
-        ValueError, match="`patterns` must contain all `types`"
-    ):
-        _ = DMCC13Benchmark(types="Orcus")
-
-
-def test_DMCC13Benchmark_invalid_sessions():
-    """Test DMCC13Benchmark DataGrabber invalid sessions."""
-    with pytest.raises(
-        ValueError,
-        match=("phonyses is not a valid session in the DMCC dataset"),
-    ):
-        DMCC13Benchmark(sessions="phonyses")
-
-
-def test_DMCC13Benchmark_invalid_tasks():
-    """Test DMCC13Benchmark DataGrabber invalid tasks."""
-    with pytest.raises(
-        ValueError,
-        match=("thisisnotarealtask is not a valid task in the DMCC dataset"),
-    ):
-        DMCC13Benchmark(tasks="thisisnotarealtask")
-
-
-def test_DMCC13Benchmark_phase_encodings():
-    """Test DMCC13Benchmark DataGrabber invalid phase encodings."""
-    with pytest.raises(
-        ValueError,
-        match=("moonphase is not a valid phase encoding in the DMCC dataset"),
-    ):
-        DMCC13Benchmark(phase_encodings="moonphase")
-
-
-def test_DMCC13Benchmark_runs():
-    """Test DMCC13Benchmark DataGrabber invalid runs."""
-    with pytest.raises(
-        ValueError,
-        match=("cerebralrun is not a valid run in the DMCC dataset"),
-    ):
-        DMCC13Benchmark(runs="cerebralrun")
+            out = dg["sub-01"]
+        # Assert data type
+        if isinstance(types, str):
+            types = [types]
+        for type_ in types:
+            assert type_ in out
+            element = out[type_]["meta"]["element"]
+            assert list(element) == dg.get_element_keys()