fix: properly handle modalit*ies* list, fixing tests

AllenNeuralDynamics · Sep 26, 2024 · 51a36d6 · 51a36d6
1 parent 4ae43c2
commit 51a36d6
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Showing 2 changed files with 32 additions and 22 deletions.
diff --git a/src/aind_data_schema/core/metadata.py b/src/aind_data_schema/core/metadata.py
@@ -198,23 +198,24 @@ def validate_metadata(self):
     def validate_expected_files_by_modality(self):
         """Validator checks that all required/excluded files match the metadata model"""
         if self.data_description:
-            modality = self.data_description.modality
+            modalities = self.data_description.modality
 
-            for file in CORE_FILES:
-                #  For each field, check if this is a required/excluded file
-                file_requirement = getattr(getattr(ExpectedFiles, str(modality.abbreviation).upper()), file)
-
-                # Check required case
-                if file_requirement == FileRequirement.REQUIRED and not getattr(self, file):
-                    raise ValueError(
-                        f"{modality.abbreviation} metadata missing required file: {file}"
-                    )
+            for modality in modalities:
+                for file in CORE_FILES:
+                    #  For each field, check if this is a required/excluded file
+                    file_requirement = getattr(getattr(ExpectedFiles, str(modality.abbreviation).upper()), file)
+
+                    # Check required case
+                    if file_requirement == FileRequirement.REQUIRED and not getattr(self, file):
+                        raise ValueError(
+                            f"{modality.abbreviation} metadata missing required file: {file}"
+                        )
 
-                # Check excluded case
-                if file_requirement == FileRequirement.EXCLUDED and getattr(self, file):
-                    raise ValueError(
-                        f"{modality.abbreviation} metadata includes excluded file: {file}"
-                    )
+                    # Check excluded case
+                    if file_requirement == FileRequirement.EXCLUDED and getattr(self, file):
+                        raise ValueError(
+                            f"{modality.abbreviation} metadata includes excluded file: {file}"
+                        )
 
         return self
 

diff --git a/tests/test_metadata.py b/tests/test_metadata.py
@@ -7,6 +7,7 @@
 
 from aind_data_schema_models.organizations import Organization
 from aind_data_schema_models.platforms import Platform
+from aind_data_schema_models.modalities import Modality
 from pydantic import ValidationError
 from pydantic import __version__ as pyd_version
 
@@ -140,13 +141,16 @@ def test_validate_smartspim_metadata(self):
                 name="ecephys_655019_2023-04-03_18-17-09",
                 location="bucket",
                 data_description=DataDescription.model_construct(
-                    label="some label", platform=Platform.SMARTSPIM, creation_time=time(12, 12, 12)
+                    label="some label",
+                    platform=Platform.SMARTSPIM, 
+                    creation_time=time(12, 12, 12),
+                    modality=[Modality.SPIM],
                 ),
                 procedures=Procedures.model_construct(subject_procedures=[surgery1]),
                 acquisition=Acquisition.model_construct(),
             )
         self.assertIn(
-            "Missing some metadata for SmartSpim. Requires subject, procedures, acquisition, and instrument.",
+            "SPIM metadata missing required file: subject",
             str(context.exception),
         )
 
@@ -157,12 +161,14 @@ def test_validate_smartspim_metadata(self):
                 name="ecephys_655019_2023-04-03_18-17-09",
                 location="bucket",
                 data_description=DataDescription.model_construct(
-                    label="some label", platform=Platform.SMARTSPIM, creation_time=time(12, 12, 12)
+                    label="some label", platform=Platform.SMARTSPIM, creation_time=time(12, 12, 12),
+                    modality=[Modality.SPIM]
                 ),
                 subject=Subject.model_construct(),
                 procedures=Procedures.model_construct(subject_procedures=[surgery2]),
                 acquisition=Acquisition.model_construct(),
                 instrument=Instrument.model_construct(),
+                processing=Processing.model_construct()
             )
         self.assertIn("Injection is missing injection_materials.", str(context.exception))
 
@@ -179,13 +185,14 @@ def test_validate_ecephys_metadata(self):
                 name="ecephys_655019_2023-04-03_18-17-09",
                 location="bucket",
                 data_description=DataDescription.model_construct(
-                    label="some label", platform=Platform.ECEPHYS, creation_time=time(12, 12, 12)
+                    label="some label", platform=Platform.ECEPHYS, creation_time=time(12, 12, 12),
+                    modality=[Modality.ECEPHYS],
                 ),
                 procedures=Procedures.model_construct(subject_procedures=[surgery1]),
                 rig=Rig.model_construct(),
             )
         self.assertIn(
-            "Missing some metadata for Ecephys. Requires subject, procedures, session, rig, and processing.",
+            "ecephys metadata missing required file: subject",
             str(context.exception),
         )
 
@@ -196,7 +203,8 @@ def test_validate_ecephys_metadata(self):
                 name="ecephys_655019_2023-04-03_18-17-09",
                 location="bucket",
                 data_description=DataDescription.model_construct(
-                    label="some label", platform=Platform.ECEPHYS, creation_time=time(12, 12, 12)
+                    label="some label", platform=Platform.ECEPHYS, creation_time=time(12, 12, 12),
+                    modality=[Modality.ECEPHYS],
                 ),
                 subject=Subject.model_construct(),
                 procedures=Procedures.model_construct(subject_procedures=[surgery2]),
@@ -216,7 +224,8 @@ def test_validate_rig_session_compatibility(self):
                 name="ecephys_655019_2023-04-03_18-17-09",
                 location="bucket",
                 data_description=DataDescription.model_construct(
-                    label="some label", platform=Platform.ECEPHYS, creation_time=time(12, 12, 12)
+                    label="some label", platform=Platform.ECEPHYS, creation_time=time(12, 12, 12),
+                    modality=[Modality.ECEPHYS]
                 ),
                 subject=Subject.model_construct(),
                 procedures=Procedures.model_construct(),