Enable zarr backend testing in data tests [1] (#1056)

Co-authored-by: Cody Baker <[email protected]>

CHANGELOG.md

@@ -13,6 +13,7 @@
 * Added automated EFS volume creation and mounting to the `submit_aws_job` helper function. [PR #1018](https://github.com/catalystneuro/neuroconv/pull/1018)
 
 ## Improvements
+* Add writing to zarr test for to the test on data [PR #1056](https://github.com/catalystneuro/neuroconv/pull/1056)
 * Modified the CI to avoid running doctests twice [PR #1077](https://github.com/catalystneuro/neuroconv/pull/#1077)
 
 ## v0.6.3

src/neuroconv/datainterfaces/behavior/video/videodatainterface.py

@@ -97,7 +97,7 @@ def get_metadata(self):
         metadata = super().get_metadata()
         behavior_metadata = {
             self.metadata_key_name: [
-                dict(name=f"Video: {Path(file_path).stem}", description="Video recorded by camera.", unit="Frames")
+                dict(name=f"Video {Path(file_path).stem}", description="Video recorded by camera.", unit="Frames")
                 for file_path in self.source_data["file_paths"]
             ]
         }

src/neuroconv/tools/testing/data_interface_mixins.py

@@ -67,9 +67,8 @@ class DataInterfaceTestMixin:
 
     @pytest.fixture
     def setup_interface(self, request):
-
+        """Add this as a fixture when you want freshly created interface in the test."""
         self.test_name: str = ""
-        self.conversion_options = self.conversion_options or dict()
         self.interface = self.data_interface_cls(**self.interface_kwargs)
 
         return self.interface, self.test_name
@@ -88,31 +87,26 @@ def check_conversion_options_schema_valid(self):
         schema = self.interface.get_conversion_options_schema()
         Draft7Validator.check_schema(schema=schema)
 
-    def check_metadata_schema_valid(self):
+    def test_metadata_schema_valid(self, setup_interface):
         schema = self.interface.get_metadata_schema()
         Draft7Validator.check_schema(schema=schema)
 
     def check_metadata(self):
-        schema = self.interface.get_metadata_schema()
+        # Validate metadata now happens on the class itself
         metadata = self.interface.get_metadata()
-        if "session_start_time" not in metadata["NWBFile"]:
-            metadata["NWBFile"].update(session_start_time=datetime.now().astimezone())
-        # handle json encoding of datetimes and other tricky types
-        metadata_for_validation = json.loads(json.dumps(metadata, cls=_NWBMetaDataEncoder))
-        validate(metadata_for_validation, schema)
         self.check_extracted_metadata(metadata)
 
-    def check_no_metadata_mutation(self):
-        """Ensure the metadata object was not altered by `add_to_nwbfile` method."""
-        metadata = self.interface.get_metadata()
-        metadata["NWBFile"].update(session_start_time=datetime.now().astimezone())
-
-        metadata_in = deepcopy(metadata)
+    def test_no_metadata_mutation(self, setup_interface):
+        """Ensure the metadata object is not altered by `add_to_nwbfile` method."""
 
         nwbfile = mock_NWBFile()
+
+        metadata = self.interface.get_metadata()
+        metadata_before_add_method = deepcopy(metadata)
+
         self.interface.add_to_nwbfile(nwbfile=nwbfile, metadata=metadata, **self.conversion_options)
 
-        assert metadata == metadata_in
+        assert metadata == metadata_before_add_method
 
     def check_run_conversion_with_backend(self, nwbfile_path: str, backend: Literal["hdf5", "zarr"] = "hdf5"):
         metadata = self.interface.get_metadata()
@@ -223,6 +217,26 @@ def run_custom_checks(self):
         """Override this in child classes to inject additional custom checks."""
         pass
 
+    @pytest.mark.parametrize("backend", ["hdf5", "zarr"])
+    def test_run_conversion_with_backend(self, setup_interface, tmp_path, backend):
+
+        nwbfile_path = str(tmp_path / f"conversion_with_backend{backend}-{self.test_name}.nwb")
+
+        metadata = self.interface.get_metadata()
+        if "session_start_time" not in metadata["NWBFile"]:
+            metadata["NWBFile"].update(session_start_time=datetime.now().astimezone())
+
+        self.interface.run_conversion(
+            nwbfile_path=nwbfile_path,
+            overwrite=True,
+            metadata=metadata,
+            backend=backend,
+            **self.conversion_options,
+        )
+
+        if backend == "zarr":
+            self.check_basic_zarr_read(nwbfile_path)
+
     def test_all_conversion_checks(self, setup_interface, tmp_path):
         interface, test_name = setup_interface
 
@@ -231,16 +245,13 @@ def test_all_conversion_checks(self, setup_interface, tmp_path):
         self.nwbfile_path = nwbfile_path
 
         # Now run the checks using the setup objects
-        self.check_metadata_schema_valid()
         self.check_conversion_options_schema_valid()
         self.check_metadata()
-        self.check_no_metadata_mutation()
         self.check_configure_backend_for_equivalent_nwbfiles()
 
         self.check_run_conversion_in_nwbconverter_with_backend(nwbfile_path=nwbfile_path, backend="hdf5")
         self.check_run_conversion_in_nwbconverter_with_backend_configuration(nwbfile_path=nwbfile_path, backend="hdf5")
 
-        self.check_run_conversion_with_backend(nwbfile_path=nwbfile_path, backend="hdf5")
         self.check_run_conversion_with_backend_configuration(nwbfile_path=nwbfile_path, backend="hdf5")
 
         self.check_read_nwb(nwbfile_path=nwbfile_path)
@@ -733,16 +744,13 @@ def test_all_conversion_checks(self, setup_interface, tmp_path):
         nwbfile_path = str(tmp_path / f"{self.__class__.__name__}_{self.test_name}.nwb")
 
         # Now run the checks using the setup objects
-        self.check_metadata_schema_valid()
         self.check_conversion_options_schema_valid()
         self.check_metadata()
-        self.check_no_metadata_mutation()
         self.check_configure_backend_for_equivalent_nwbfiles()
 
         self.check_run_conversion_in_nwbconverter_with_backend(nwbfile_path=nwbfile_path, backend="hdf5")
         self.check_run_conversion_in_nwbconverter_with_backend_configuration(nwbfile_path=nwbfile_path, backend="hdf5")
 
-        self.check_run_conversion_with_backend(nwbfile_path=nwbfile_path, backend="hdf5")
         self.check_run_conversion_with_backend_configuration(nwbfile_path=nwbfile_path, backend="hdf5")
 
         self.check_read_nwb(nwbfile_path=nwbfile_path)
@@ -813,7 +821,7 @@ def check_read_nwb(self, nwbfile_path: str):
         with NWBHDF5IO(path=nwbfile_path, mode="r", load_namespaces=True) as io:
             nwbfile = io.read()
             video_type = Path(self.interface_kwargs["file_paths"][0]).suffix[1:]
-            assert f"Video: video_{video_type}" in nwbfile.acquisition
+            assert f"Video video_{video_type}" in nwbfile.acquisition
 
     def check_interface_set_aligned_timestamps(self):
         all_unaligned_timestamps = self.interface.get_original_timestamps()
@@ -883,6 +891,29 @@ class MedPCInterfaceMixin(DataInterfaceTestMixin, TemporalAlignmentMixin):
     A mixin for testing MedPC interfaces.
     """
 
+    def test_metadata_schema_valid(self):
+        pass
+
+    def test_run_conversion_with_backend(self):
+        pass
+
+    def test_no_metadata_mutation(self):
+        pass
+
+    def check_metadata_schema_valid(self):
+        schema = self.interface.get_metadata_schema()
+        Draft7Validator.check_schema(schema=schema)
+
+    def check_metadata(self):
+        schema = self.interface.get_metadata_schema()
+        metadata = self.interface.get_metadata()
+        if "session_start_time" not in metadata["NWBFile"]:
+            metadata["NWBFile"].update(session_start_time=datetime.now().astimezone())
+        # handle json encoding of datetimes and other tricky types
+        metadata_for_validation = json.loads(json.dumps(metadata, cls=_NWBMetaDataEncoder))
+        validate(metadata_for_validation, schema)
+        self.check_extracted_metadata(metadata)
+
     def check_no_metadata_mutation(self, metadata: dict):
         """Ensure the metadata object was not altered by `add_to_nwbfile` method."""
 
@@ -1220,6 +1251,22 @@ def check_read_nwb(self, nwbfile_path: str):
 class TDTFiberPhotometryInterfaceMixin(DataInterfaceTestMixin, TemporalAlignmentMixin):
     """Mixin for testing TDT Fiber Photometry interfaces."""
 
+    def test_metadata_schema_valid(self):
+        pass
+
+    def test_no_metadata_mutation(self):
+        pass
+
+    def test_run_conversion_with_backend(self):
+        pass
+
+    def test_no_metadata_mutation(self):
+        pass
+
+    def check_metadata_schema_valid(self):
+        schema = self.interface.get_metadata_schema()
+        Draft7Validator.check_schema(schema=schema)
+
     def check_no_metadata_mutation(self, metadata: dict):
         """Ensure the metadata object was not altered by `add_to_nwbfile` method."""
 

tests/test_behavior/test_video_interface.py

@@ -137,8 +137,8 @@ def test_video_external_mode(self):
             nwbfile = io.read()
             module = nwbfile.acquisition
             metadata = self.nwb_converter.get_metadata()
-            self.assertListEqual(list1=list(module["Video: test1"].external_file[:]), list2=self.video_files[0:2])
-            self.assertListEqual(list1=list(module["Video: test3"].external_file[:]), list2=[self.video_files[2]])
+            self.assertListEqual(list1=list(module["Video test1"].external_file[:]), list2=self.video_files[0:2])
+            self.assertListEqual(list1=list(module["Video test3"].external_file[:]), list2=[self.video_files[2]])
 
     def test_video_irregular_timestamps(self):
         aligned_timestamps = [np.array([1.0, 2.0, 4.0]), np.array([5.0, 6.0, 7.0])]
@@ -157,7 +157,7 @@ def test_video_irregular_timestamps(self):
         expected_timestamps = timestamps = np.array([1.0, 2.0, 4.0, 55.0, 56.0, 57.0])
         with NWBHDF5IO(path=self.nwbfile_path, mode="r") as io:
             nwbfile = io.read()
-            np.testing.assert_array_equal(expected_timestamps, nwbfile.acquisition["Video: test1"].timestamps[:])
+            np.testing.assert_array_equal(expected_timestamps, nwbfile.acquisition["Video test1"].timestamps[:])
 
     def test_starting_frames_type_error(self):
         timestamps = [np.array([2.2, 2.4, 2.6]), np.array([3.2, 3.4, 3.6])]

tests/test_on_data/ecephys/test_recording_interfaces.py

@@ -1,7 +1,6 @@
 from datetime import datetime
 from platform import python_version
 from sys import platform
-from typing import Literal
 
 import numpy as np
 import pytest
@@ -180,32 +179,30 @@ class TestEDFRecordingInterface(RecordingExtractorInterfaceTestMixin):
     def check_extracted_metadata(self, metadata: dict):
         assert metadata["NWBFile"]["session_start_time"] == datetime(2022, 3, 2, 10, 42, 19)
 
-    def test_interface_alignment(self):
-        interface_kwargs = self.interface_kwargs
+    def test_all_conversion_checks(self, setup_interface, tmp_path):
+        # Create a unique test name and file path
+        nwbfile_path = str(tmp_path / f"{self.__class__.__name__}.nwb")
+        self.nwbfile_path = nwbfile_path
+
+        # Now run the checks using the setup objects
+        self.check_conversion_options_schema_valid()
+        self.check_metadata()
 
-        # TODO - debug hanging I/O from pyedflib
-        # self.check_interface_get_original_timestamps()
-        # self.check_interface_get_timestamps()
-        # self.check_align_starting_time_internal()
-        # self.check_align_starting_time_external()
-        # self.check_interface_align_timestamps()
-        # self.check_shift_timestamps_by_start_time()
-        # self.check_interface_original_timestamps_inmutability()
+        self.check_run_conversion_with_backend(nwbfile_path=nwbfile_path, backend="hdf5")
 
-        self.check_nwbfile_temporal_alignment()
+        self.check_read_nwb(nwbfile_path=nwbfile_path)
 
     # EDF has simultaneous access issues; can't have multiple interfaces open on the same file at once...
-    def check_run_conversion_in_nwbconverter_with_backend(
-        self, nwbfile_path: str, backend: Literal["hdf5", "zarr"] = "hdf5"
-    ):
+    def test_metadata_schema_valid(self):
         pass
 
-    def check_run_conversion_in_nwbconverter_with_backend_configuration(
-        self, nwbfile_path: str, backend: Literal["hdf5", "zarr"] = "hdf5"
-    ):
+    def test_no_metadata_mutation(self):
         pass
 
-    def check_run_conversion_with_backend(self, nwbfile_path: str, backend: Literal["hdf5", "zarr"] = "hdf5"):
+    def test_run_conversion_with_backend(self):
+        pass
+
+    def test_interface_alignment(self):
         pass