refactor: allow instrument_id to be included in device.name fields (#1663)

* refactor: allow instrument_id to be included in device.name fields

* test: add coverage for the new instrumentID check

* chore: lint

* chore: fix bad active devices

* tests: ensure that exaspim acq/inst are compatible

* tests: fix broken test

* chore: lint

Author: dbirman

examples/exaspim_acquisition.py

@@ -49,14 +49,14 @@
 )
 
 imaging_config = ImagingConfig(
-    device_name="ExaSPIM",
+    device_name="exaSPIM1",
     channels=[
         Channel(
             channel_name="488",
             intended_measurement="GFP signal",
             light_sources=[
                 LaserConfig(
-                    device_name="LAS_08308",
+                    device_name="LAS-08307",
                     wavelength=488,
                     wavelength_unit=SizeUnit.NM,
                     power=200,
@@ -115,7 +115,7 @@
     experimenters=["John Smith"],
     specimen_id="123456-123",
     subject_id="123456",
-    instrument_id="###",
+    instrument_id="exaSPIM1",
     maintenance=[
         Maintenance(
             maintenance_date=t,
@@ -149,8 +149,11 @@
             stream_end_time=t,
             modalities=[Modality.SPIM],
             active_devices=[
-                "LAS_08308",
+                "LAS-08307",
                 "539251",
+                "Multiband filter",
+                "PMT_1",
+                "Sample chamber",
             ],
             configurations=[
                 imaging_config,

examples/exaspim_instrument.py

@@ -37,7 +37,7 @@
 
 detectors = [
     Detector(
-        name="Camera 1",
+        name="PMT_1",
         detector_type="Camera",
         data_interface="Coax",
         cooling="Air",
@@ -193,6 +193,13 @@
         model="L6Cc",
         serial_number="L6CC-00513",
     ),
+    AdditionalImagingDevice(
+        name="Sample chamber",
+        imaging_device_type="Sample Chamber",
+        manufacturer=Organization.AI,
+        model="Custom exaspim chamber",
+        serial_number="01",
+    ),
 ]
 
 laser_launch = Device(

src/aind_data_schema/core/instrument.py

@@ -173,6 +173,9 @@ def get_component_names(self) -> List[str]:
             names.extend(recursive_get_all_names(component))
         names = [name for name in names if name is not None]
 
+        # Include the instrument ID as a valid name
+        names = names + [self.instrument_id]
+
         return names
 
     @field_validator("modalities", mode="before")

tests/test_acquisition.py

@@ -550,7 +550,7 @@ def test_datastream_add_with_exaspim_example(self):
 
         self.assertIsNotNone(combined_stream)
         self.assertIn(Modality.SPIM, combined_stream.modalities)
-        self.assertEqual(len(combined_stream.active_devices), 3)
+        self.assertEqual(len(combined_stream.active_devices), 6)
 
 
 if __name__ == "__main__":

tests/test_compatibility_check.py

@@ -8,6 +8,9 @@
 from aind_data_schema.core.instrument import Instrument
 from aind_data_schema.utils.compatibility_check import InstrumentAcquisitionCompatibility
 
+from examples.exaspim_acquisition import acq
+from examples.exaspim_instrument import inst
+
 
 class TestInstrumentAcquisitionCompatibility(unittest.TestCase):
     """Unit tests for InstrumentAcquisitionCompatibility class."""
@@ -34,6 +37,11 @@ def setUp(self):
         self.mock_acquisition.data_streams = [MagicMock(active_devices=["component_1"])]
         self.mock_acquisition.stimulus_epochs = [MagicMock(active_devices=["component_2"])]
 
+    def test_exaspim_example_compatibility(self):
+        """Test compatibility of the exaspim example instrument and acquisition."""
+        checker = InstrumentAcquisitionCompatibility(inst, acq)
+        self.assertIsNone(checker.run_compatibility_check())
+
     def test_compare_instrument_id_success(self):
         """Test that instrument IDs match."""
         checker = InstrumentAcquisitionCompatibility(self.mock_instrument, self.mock_acquisition)

tests/test_inst_acq_compatibility.py

@@ -5,6 +5,8 @@
 from aind_data_schema.utils.compatibility_check import InstrumentAcquisitionCompatibility
 from examples.ephys_acquisition import acquisition as ephys_acquisition
 from examples.ephys_instrument import inst as ephys_instrument
+from examples.exaspim_acquisition import acq as exaspim_acquisition
+from examples.exaspim_instrument import inst as exaspim_instrument
 from examples.fip_ophys_instrument import instrument as ophys_instrument
 from examples.ophys_acquisition import a as ophys_acquisition
 
@@ -16,6 +18,8 @@ def setUp(self):
         """Set up test data"""
         self.ephys_instrument = ephys_instrument.model_copy()
         self.ephys_acquisition = ephys_acquisition.model_copy()
+        self.exaspim_instrument = exaspim_instrument.model_copy()
+        self.exaspim_acquisition = exaspim_acquisition.model_copy()
         self.ophys_instrument = ophys_instrument.model_copy()
         self.ophys_acquisition = ophys_acquisition.model_copy()
 
@@ -27,6 +31,12 @@ def test_check_examples_compatibility(self):
         )
         self.assertIsNone(example_ephys_check.run_compatibility_check())
 
+        # check that exaspim acquisition and instrument are synced
+        example_exaspim_check = InstrumentAcquisitionCompatibility(
+            instrument=self.exaspim_instrument, acquisition=self.exaspim_acquisition
+        )
+        self.assertIsNone(example_exaspim_check.run_compatibility_check())
+
         # check that ophys acquisition and instrument are synced
         example_ophys_check = InstrumentAcquisitionCompatibility(
             instrument=self.ophys_instrument, acquisition=self.ophys_acquisition

tests/test_instrument.py

@@ -354,6 +354,7 @@ def test_constructors(self):
             Instrument()
 
         self.assertIsNotNone(ephys_instrument)
+        self.assertIn(ephys_instrument.instrument_id, ephys_instrument.get_component_names())
 
     def test_other_camera_target(self):
         """Test that the camera_target being set to Other throws a validation error without notes"""