tests: more test fixing

AllenNeuralDynamics · Jan 27, 2025 · 1ff075e · 1ff075e
1 parent c45b5e6
commit 1ff075e
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Showing 4 changed files with 31 additions and 34 deletions.
diff --git a/examples/ephys_insturment.py → examples/ephys_instrument.py b/examples/ephys_insturment.py → examples/ephys_instrument.py
diff --git a/tests/test_imaging.py b/tests/test_imaging.py
@@ -29,8 +29,8 @@
 class ImagingTests(unittest.TestCase):
     """test imaging schemas"""
 
-    def test_constructors(self):
-        """testing constructors"""
+    def test_acquisition_constructor(self):
+        """testing Acquisition constructor"""
         with self.assertRaises(ValidationError):
             acq.Acquisition()
 
@@ -76,11 +76,11 @@ def test_constructors(self):
 
         self.assertIsNotNone(a)
 
+    def test_instrument_constructor(self):
+        """testing Instrument constructor"""
         with self.assertRaises(ValidationError):
             Instrument()
 
-        # Generate a valid instrument
-
         objective = Objective(
             name="TLX Objective",
             numerical_aperture=0.2,
@@ -102,7 +102,8 @@ def test_constructors(self):
 
         self.assertIsNotNone(i)
 
-        # Instrument type Other requires notes
+    def test_instrument_type_other_requires_notes(self):
+        """testing Instrument type Other requires notes"""
         with self.assertRaises(ValidationError) as e1:
             Instrument(
                 instrument_id="room_exaSPIM1-1_20231004",
@@ -114,7 +115,8 @@ def test_constructors(self):
 
         self.assertIn("instrument_id", repr(e1.exception))
 
-        # Modality SPIM requirements components
+    def test_modality_spim_requires_components(self):
+        """testing Modality SPIM requires components"""
         with self.assertRaises(ValidationError) as e2:
             Instrument(
                 instrument_id="room_exaSPIM1-1_20231004",
@@ -124,19 +126,7 @@ def test_constructors(self):
                 manufacturer=Organization.OTHER,
             )
 
-        expected_exception2 = (
-            "2 validation errors for Instrument\n"
-            "modification_date\n"
-            "  Field required [type=missing, input_value={'instrument_type': 'diSP...[],"
-            " 'light_sources': []}, input_type=dict]\n"
-            f"    For further information visit https://errors.pydantic.dev/{PYD_VERSION}/v/missing\n"
-            "notes\n"
-            "  Value error, Notes cannot be empty if manufacturer is Other."
-            " Describe the manufacturer in the notes field."
-            " [type=value_error, input_value=None, input_type=NoneType]\n"
-            f"    For further information visit https://errors.pydantic.dev/{PYD_VERSION}/v/value_error"
-        )
-        self.assertEqual(expected_exception2, repr(e2.exception))
+        self.assertIn("modality 'SPIM' requires at least one device", repr(e2.exception))
 
     def test_axis(self):
         """test the axis class"""

diff --git a/tests/test_inst_acq_compatibility.py b/tests/test_inst_acq_compatibility.py
@@ -53,7 +53,7 @@
 from aind_data_schema_models.brain_atlas import CCFStructure
 
 EXAMPLES_DIR = Path(__file__).parents[1] / "examples"
-EPHYS_INST_JSON = EXAMPLES_DIR / "ephys_inst.json"
+EPHYS_INST_JSON = EXAMPLES_DIR / "ephys_instrument.json"
 EPHYS_SESSION_JSON = EXAMPLES_DIR / "ephys_session.json"
 
 behavior_computer = "W10DT72941"
@@ -761,7 +761,7 @@ def read_json(filepath: Path) -> dict:
                 ],
             ),
         ]
-        additional_devices = [d.Device(device_type="Photometry Clock", name="Photometry Clock")]
+        additional_devices = [d.Device(name="Photometry Clock")]
 
         cls.example_ephys_inst = Instrument.model_validate_json(json.dumps(read_json(EPHYS_INST_JSON)))
         cls.example_ephys_session = Session.model_validate_json(json.dumps(read_json(EPHYS_SESSION_JSON)))

diff --git a/tests/test_metadata.py b/tests/test_metadata.py
@@ -32,6 +32,16 @@
 
 PYD_VERSION = re.match(r"(\d+.\d+).\d+", pyd_version).group(1)
 
+ephys_assembly = EphysAssembly(
+    probes=[EphysProbe(probe_model="Neuropixels 1.0", name="Probe A")],
+    manipulator=Manipulator(
+        name="Probe manipulator",
+        manufacturer=Organization.NEW_SCALE_TECHNOLOGIES,
+        serial_number="4321",
+    ),
+    name="Ephys_assemblyA",
+)
+
 
 class TestMetadata(unittest.TestCase):
     """Class to test Metadata model"""
@@ -322,7 +332,12 @@ def test_validate_ecephys_metadata(self):
                     subject_id="655019",
                 ),
                 procedures=Procedures.model_construct(subject_procedures=[surgery1]),
-                instrument=Instrument.model_construct(modalities=modalities),
+                instrument=Instrument.model_construct(
+                    modalities=modalities,
+                    components=[
+                        ephys_assembly,
+                    ],
+                ),
             )
         self.assertIn(
             "ECEPHYS metadata missing required file: subject",
@@ -350,15 +365,6 @@ def test_validate_ecephys_metadata(self):
 
     def test_validate_instrument_session_compatibility(self):
         """Tests that instrument/session compatibility validator works as expected"""
-        ephys_assembly = EphysAssembly(
-            probes=[EphysProbe(probe_model="Neuropixels 1.0", name="Probe A")],
-            manipulator=Manipulator(
-                name="Probe manipulator",
-                manufacturer=Organization.NEW_SCALE_TECHNOLOGIES,
-                serial_number="4321",
-            ),
-            name="Ephys_assemblyA",
-        )
 
         mouse_platform = MousePlatform.model_construct(name="platform1")
         inst = Instrument.model_construct(
@@ -367,7 +373,6 @@ def test_validate_instrument_session_compatibility(self):
             modalities=[Modality.ECEPHYS],
             components=[ephys_assembly],
         )
-        session = Session.model_construct(instrument_id="123_EPHYS2_20230101", mouse_platform_name="platform2")
         with self.assertRaises(ValidationError) as context:
             Metadata(
                 name="655019_2023-04-03_18-17-09",
@@ -381,9 +386,11 @@ def test_validate_instrument_session_compatibility(self):
                 procedures=Procedures.model_construct(),
                 instrument=inst,
                 processing=Processing.model_construct(),
-                session=session,
+                acquisition=Acquisition.model_construct(
+                    instrument_id="123_EPHYS2_20230101",
+                ),
+                session=Session.model_construct(instrument_id="123_EPHYS2_20230101"),
             )
-        print(str(context.exception))
         self.assertIn(
             "Instrument ID in session 123_EPHYS2_20230101 does not match the rig's 123_EPHYS1_20220101.",
             str(context.exception),