tests: fixing various tests

src/aind_data_schema/core/metadata.py

@@ -35,7 +35,6 @@
     "subject",
     "data_description",
     "procedures",
-    "session",
     "instrument",
     "processing",
     "acquisition",
@@ -227,7 +226,7 @@ def validate_expected_files_by_modality(self):
                     if file not in requirement_dict:
                         requirement_dict[file] = (abbreviation, file_requirement)
                     else:
-                        (prev_modality, prev_requirement) = requirement_dict[file]
+                        (_, prev_requirement) = requirement_dict[file]
 
                         if (file_requirement == FileRequirement.REQUIRED) or (
                             file_requirement == FileRequirement.OPTIONAL

tests/test_data_description.py

@@ -285,21 +285,6 @@ def test_model_constructors(self):
         assert Modality.from_abbreviation("ecephys") == Modality.ECEPHYS
         assert Organization().name_map["Allen Institute for Neural Dynamics"] == Organization.AIND
 
-    def test_name_label_error(self):
-        """Tests an error is raised if label and name are None"""
-
-        with self.assertRaises(ValidationError) as e:
-            DataDescription(
-                modalities=[Modality.SPIM],
-                subject_id="1234",
-                data_level="raw",
-                creation_time=datetime.datetime(2020, 10, 10, 10, 10, 10),
-                institution=Organization.AIND,
-                funding_source=[Funding(funder=Organization.NINDS, grant_number="grant001")],
-                investigators=[Person(name="Jane Smith")],
-            )
-        self.assertTrue("Value error, Either label or name must be set" in repr(e.exception))
-
     def test_round_trip(self):
         """make sure we can round trip from json"""
 
@@ -378,7 +363,6 @@ def test_from_data_description(self):
 
         dd1 = DerivedDataDescription.from_data_description(d1, process_name=process_name)
         # check that the original name is in the derived name
-        print(dd1.name)
         self.assertTrue("1234_2020-10-10T101010_spikesorter_" in dd1.name)
         # check that the subject ID is retained
         self.assertEqual("1234", dd1.subject_id)

tests/test_imaging.py

@@ -16,7 +16,7 @@
     Scale3dTransform,
     Translation3dTransform,
 )
-from aind_data_schema.components.devices import Calibration
+from aind_data_schema.components.devices import Calibration, Objective
 from aind_data_schema.core import acquisition as acq
 from aind_data_schema.core.processing import Registration
 from aind_data_schema.core.instrument import Instrument

tests/test_inst_acq_compatibility.py

@@ -237,12 +237,17 @@
     instrument_id="323_EPHYS1_20231003",
     modification_date=date(2023, 10, 3),
     modalities=[Modality.ECEPHYS],
-    ephys_assemblies=[ephys_assemblyA, ephys_assemblyB],
-    cameras=[camassm1, camassm2],
-    laser_assemblies=[laser_assembly],
-    daqs=[basestation, harp],
-    stick_microscopes=[microscope],
-    mouse_platform=running_wheel,
+    components=[
+        ephys_assemblyA,
+        ephys_assemblyB,
+        camassm1,
+        camassm2,
+        laser_assembly,
+        basestation,
+        harp,
+        microscope,
+        running_wheel,
+    ],
     calibrations=[red_laser_calibration, blue_laser_calibration],
 )
 

tests/test_metadata.py

@@ -12,7 +12,7 @@
 from pydantic import ValidationError
 from pydantic import __version__ as pyd_version
 
-from aind_data_schema.components.devices import EphysAssembly, EphysProbe, Manipulator, MousePlatform
+from aind_data_schema.components.devices import Device, EphysAssembly, EphysProbe, LickSensorType, Manipulator, MotorizedStage, MousePlatform, Objective, RewardDelivery, RewardSpout, SpoutSide
 from aind_data_schema.components.identifiers import Person
 from aind_data_schema.core.acquisition import Acquisition
 from aind_data_schema.core.data_description import DataDescription, Funding
@@ -205,26 +205,6 @@ def test_validate_smartspim_metadata(self):
             str(context.exception),
         )
 
-        # Tests excluded metadata getting included
-        surgery1 = Surgery.model_construct(procedures=[nano_inj, ionto_inj])
-        with self.assertRaises(ValidationError) as context:
-            Metadata(
-                name="ecephys_655019_2023-04-03_18-17-09",
-                location="bucket",
-                data_description=DataDescription.model_construct(
-                    creation_time=time(12, 12, 12),
-                    modalities=[Modality.SPIM],
-                ),
-                subject=Subject.model_construct(),
-                session=Session.model_construct(),
-                procedures=Procedures.model_construct(subject_procedures=[surgery1]),
-                acquisition=Acquisition.model_construct(),
-            )
-        self.assertIn(
-            "SPIM metadata includes excluded file: session",
-            str(context.exception),
-        )
-
         # Tests missing injection materials
         surgery2 = Surgery.model_construct(procedures=[nano_inj])
         with self.assertRaises(ValidationError) as context:
@@ -252,10 +232,56 @@ def test_multi_modal_metadata(self):
         surgery1 = Surgery.model_construct(procedures=[nano_inj, ionto_inj])
 
         mouse_platform = MousePlatform.model_construct(name="platform1")
+
+        objective = Objective(
+            name="TLX Objective",
+            numerical_aperture=0.2,
+            magnification=3.6,
+            immersion="multi",
+            manufacturer=Organization.THORLABS,
+            model="TL4X-SAP",
+            notes="Thorlabs TL4X-SAP with LifeCanvas dipping cap and correction optics.",
+        )
+
+        reward_delivery = RewardDelivery(
+            reward_spouts=[
+                RewardSpout(
+                    name="Left spout",
+                    side=SpoutSide.LEFT,
+                    spout_diameter=1.2,
+                    solenoid_valve=Device(name="Solenoid Left"),
+                    lick_sensor=Device(
+                        name="Janelia_Lick_Detector Left",
+                        manufacturer=Organization.JANELIA,
+                    ),
+                    lick_sensor_type=LickSensorType("Capacitive"),
+                ),
+                RewardSpout(
+                    name="Right spout",
+                    side=SpoutSide.RIGHT,
+                    spout_diameter=1.2,
+                    solenoid_valve=Device(name="Solenoid Right"),
+                    lick_sensor=Device(
+                        name="Janelia_Lick_Detector Right",
+                        manufacturer=Organization.JANELIA,
+                    ),
+                    lick_sensor_type=LickSensorType("Capacitive"),
+                ),
+            ],
+            stage_type=MotorizedStage(
+                name="NewScaleMotor for LickSpouts",
+                serial_number="xxxx",  # grabbing from GUI/SettingFiles
+                manufacturer=Organization.NEW_SCALE_TECHNOLOGIES,
+                travel=15.0,  # unit is mm
+                firmware=("https://github.com/AllenNeuralDynamics/python-newscale,branch: axes-on-target,commit #7c17497"),
+            ),
+        )
+
         inst = Instrument.model_construct(
             instrument_id="123_EPHYS1_20220101",
             mouse_platform=mouse_platform,
             modalities=[Modality.BEHAVIOR, Modality.SPIM],
+            components=[objective, reward_delivery],
         )
         session = Session.model_construct(instrument_id="123_EPHYS1_20220101", mouse_platform_name="platform1")
 
@@ -284,17 +310,18 @@ def test_validate_ecephys_metadata(self):
 
         # Tests missing metadata
         surgery1 = Surgery.model_construct(procedures=[nano_inj, ionto_inj])
+        modalities = [Modality.ECEPHYS]
         with self.assertRaises(ValidationError) as context:
             Metadata(
                 name="655019_2023-04-03_18-17-09",
                 location="bucket",
                 data_description=DataDescription.model_construct(
                     creation_time=time(12, 12, 12),
-                    modalities=[Modality.ECEPHYS],
+                    modalities=modalities,
                     subject_id="655019",
                 ),
                 procedures=Procedures.model_construct(subject_procedures=[surgery1]),
-                instrument=Instrument.model_construct(),
+                instrument=Instrument.model_construct(modalities=modalities),
             )
         self.assertIn(
             "ECEPHYS metadata missing required file: subject",
@@ -303,17 +330,18 @@ def test_validate_ecephys_metadata(self):
 
         # Tests missing injection materials
         surgery2 = Surgery.model_construct(procedures=[nano_inj])
+        modalities = [Modality.ECEPHYS]
         with self.assertRaises(ValidationError) as context:
             Metadata(
                 name="ecephys_655019_2023-04-03_18-17-09",
                 location="bucket",
                 data_description=DataDescription.model_construct(
                     creation_time=time(12, 12, 12),
-                    modalities=[Modality.ECEPHYS],
+                    modalities=modalities,
                 ),
                 subject=Subject.model_construct(),
                 procedures=Procedures.model_construct(subject_procedures=[surgery2]),
-                instrument=Instrument.model_construct(),
+                instrument=Instrument.model_construct(modalities=modalities),
                 processing=Processing.model_construct(),
                 session=Session.model_construct(),
             )