generalised tests to all classes

bia-shared-datamodels/src/bia_shared_datamodels/semantic_models.py

@@ -367,7 +367,7 @@ class Channel(ConfiguredBaseModel):
 
     colormap_start: float = Field(description="""Start value of colormap""")
     colormap_end: float = Field(description="""End value of colormap""")
-    scale_factor: float = Field(None)
+    scale_factor: Optional[float] = Field(None)
     label: Optional[str] = Field(
         None, description="""Label describing the channel for display."""
     )

bia-shared-datamodels/test/test_shared_models.py

@@ -1,124 +1,94 @@
-from uuid import uuid4
 import pytest
-from pydantic import ValidationError
+from pydantic import ValidationError, BaseModel
 from . import utils
-from bia_shared_datamodels import bia_data_model
-
+from bia_shared_datamodels import bia_data_model, semantic_models
+from typing import Callable
 
 @pytest.mark.parametrize(
+    ("expected_model_type", "dict_creation_func"),
     (
-        "expected_model_type",
-        "model_creation_func",
-    ),
-    (
+        (semantic_models.Taxon, utils.get_taxon_dict),
+        (semantic_models.Channel, utils.get_channel_dict),
+        (semantic_models.RenderedView, utils.get_rendered_view_dict),
         (
-            bia_data_model.FileReference,
-            utils.get_template_file_reference,
+            semantic_models.SignalChannelInformation,
+            utils.get_signal_channel_information_dict,
         ),
         (
-            bia_data_model.ImageRepresentation,
-            utils.get_template_image_representation,
-        ),
-        (
-            bia_data_model.ExperimentalImagingDataset,
-            utils.get_template_experimental_imaging_dataset,
+            bia_data_model.SpecimenImagingPrepartionProtocol,
+            utils.get_specimen_imaging_preparation_protocol_dict,
         ),
         (
-            bia_data_model.Specimen,
-            utils.get_template_specimen,
+            bia_data_model.SpecimenGrowthProtocol,
+            utils.get_specimen_growth_protocol_dict,
         ),
+        (bia_data_model.BioSample, utils.get_biosample_dict),
+        (bia_data_model.Specimen, utils.get_specimen_dict),
+        (bia_data_model.AnnotationMethod, utils.get_annotation_method_dict),
         (
             bia_data_model.ExperimentallyCapturedImage,
-            utils.get_template_experimentally_captured_image,
-        ),
-        (
-            bia_data_model.ImageAcquisition,
-            utils.get_template_image_acquisition,
-        ),
-        (
-            bia_data_model.SpecimenImagingPrepartionProtocol,
-            utils.get_template_specimen_imaging_preparation_protocol,
-        ),
-        (
-            bia_data_model.BioSample,
-            utils.get_template_biosample,
+            utils.get_experimentally_captured_image_dict,
         ),
+        (bia_data_model.DerivedImage, utils.get_derived_image_dict),
         (
             bia_data_model.ImageAnnotationDataset,
-            utils.get_template_image_annotation_dataset,
+            utils.get_image_annotation_dataset_dict,
         ),
+        (bia_data_model.ImageAcquisition, utils.get_image_acquisition_dict),
+        (semantic_models.ImageAnalysisMethod, utils.get_image_analysis_method_dict),
         (
-            bia_data_model.AnnotationFileReference,
-            utils.get_template_annotation_file_reference,
+            semantic_models.ImageCorrelationMethod,
+            utils.get_image_correlation_method_dict,
         ),
         (
-            bia_data_model.DerivedImage,
-            utils.get_template_derived_image,
-        ),
-        (
-            bia_data_model.AnnotationMethod,
-            utils.get_template_annotation_method,
+            bia_data_model.ExperimentalImagingDataset,
+            utils.get_experimental_imaging_dataset_dict,
         ),
         (
-            bia_data_model.SpecimenGrowthProtocol,
-            utils.get_template_specimen_growth_protocol,
+            bia_data_model.AnnotationFileReference,
+            utils.get_annotation_file_reference_dict,
         ),
+        (bia_data_model.FileReference, utils.get_file_reference_dict),
+        (bia_data_model.ImageRepresentation, utils.get_image_representation_dict),
+        (semantic_models.Affiliation, utils.get_affiliation_dict),
+        (semantic_models.Contributor, utils.get_contributor_dict),
+        (bia_data_model.Study, utils.get_study_dict),
     ),
 )
-def test_create_models(expected_model_type, model_creation_func):
-    expected_model = model_creation_func()
-    assert type(expected_model) is expected_model_type
-
-
-def test_create_study():
+def test_create_study(
+    expected_model_type: BaseModel,
+    dict_creation_func: Callable[[utils.Completeness], dict],
+):
 
-    complete_dict = utils.get_study_dict(utils.Completeness.COMPLETE)
-    study_complete = bia_data_model.Study(**complete_dict)
+    complete_dict = dict_creation_func(utils.Completeness.COMPLETE)
+    complete_model: BaseModel = expected_model_type(**complete_dict)
 
     # Check that the model is created
-    assert type(study_complete) is bia_data_model.Study
+    assert type(complete_model) is expected_model_type
     # Check that the dictionary is indeed "Complete" - no optional fields missed
-    assert study_complete.model_dump() == complete_dict
+    assert complete_model.model_dump() == complete_dict
     # Check that there are no inconsistencies in the model definition
     assert (
-        type(bia_data_model.Study(**study_complete.model_dump()))
-        is bia_data_model.Study
+        type(expected_model_type(**complete_model.model_dump())) is expected_model_type
     )
 
-    mimimal_dict = utils.get_study_dict(utils.Completeness.MINIMAL)
-    study_minimal = bia_data_model.Study(**mimimal_dict)
+    mimimal_dict = dict_creation_func(utils.Completeness.MINIMAL)
+    minimal_model: BaseModel = expected_model_type(**mimimal_dict)
 
     # Check that the model is created
-    assert type(study_minimal) is bia_data_model.Study
-    # Check that the dictionary is indeed "Minimal" - no optional fields included
+    assert type(minimal_model) is expected_model_type
+    # Check that the dictionary is indeed "Minimal" - no optional fields included, and list fields are of minimum length
     for key in mimimal_dict:
         less_than_minimal_dict = mimimal_dict.copy()
+        if isinstance(less_than_minimal_dict[key], list) and len(less_than_minimal_dict[key]) > 0:
+            less_than_minimal_dict[key] = []
+            with pytest.raises(ValidationError):
+                expected_model_type(**less_than_minimal_dict)
+
         del less_than_minimal_dict[key]
         with pytest.raises(ValidationError):
-            bia_data_model.Study(**less_than_minimal_dict)
+            expected_model_type(**less_than_minimal_dict)
     # Check that there are no inconsistencies in the model definition's optional fields
     assert (
-        type(bia_data_model.Study(**study_minimal.model_dump())) is bia_data_model.Study
+        type(expected_model_type(**minimal_model.model_dump())) is expected_model_type
     )
-
-
-def test_create_specimen_with_empty_lists_fails():
-    with pytest.raises(ValidationError):
-        specimen = bia_data_model.Specimen.model_validate(
-            {
-                "sample_of": [],
-                "preparation_method": [],
-            }
-        )
-        specimen = bia_data_model.Specimen.model_validate(
-            {
-                "sample_of": [uuid4()],
-                "preparation_method": [],
-            }
-        )
-        specimen = bia_data_model.Specimen.model_validate(
-            {
-                "sample_of": [],
-                "preparation_method": [uuid4()],
-            }
-        )