Shared models v2 (#114)

* Add tests to create all models defined in bia_data_model

* Change type of size_t in ImageRepresentation to int

* Fix minor issues before merging PR

* Use conlist for Specimen, make description mandatory for Study

bia-shared-datamodels/pyproject.toml

@@ -7,11 +7,14 @@ license = "Apache Software License 2.0"
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = "^3.9"
+python = "^3.10"
 pydantic = {version = "^2", extras = ["email"]}
 pydantic-2-mermaid = "^0.7"
 pytest = "^7"
 
+[tool.poetry.group.dev.dependencies]
+ipython = "^8.25.0"
+
 [tool.poetry-dynamic-versioning]
 enable = true
 vcs = "git"

bia-shared-datamodels/src/bia_models/bia_data_model.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 import semantic_models
-from pydantic import BaseModel, Field, AnyUrl
+from pydantic import BaseModel, Field, AnyUrl, conlist
 from typing import List, Optional, Union
 from uuid import UUID
 
@@ -26,6 +26,8 @@ class Study(
 ):
     experimental_imaging_component: List[UUID] = Field()
     annotation_component: List[UUID] = Field()
+    author: conlist(item_type=semantic_models.Contributor, min_length=1) = Field()
+    description: str = Field()
 
 
 class FileReference(
@@ -57,8 +59,8 @@ class ExperimentalImagingDataset(
 
 
 class Specimen(semantic_models.Specimen):
-    preparation_method: List[UUID] = Field()
-    sample_of: List[UUID] = Field()
+    preparation_method: conlist(item_type=UUID, min_length=1) = Field()
+    sample_of: conlist(item_type=UUID, min_length=1) = Field()
 
 
 class ExperimentallyCapturedImage(

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

@@ -130,6 +130,10 @@ class Study(DocumentMixin):
     attribute: dict = Field(
         description="""Freeform key-value pairs from user provided metadata (e.g. filelist data) and experimental fields."""
     )
+    # Override optional description in DocumentMixin
+    description: str = Field(
+        None, description="""Brief description of the scientific document."""
+    )
 
 
 class Publication(DocumentMixin):
@@ -296,9 +300,9 @@ class ImageRepresentation(BaseModel):
         None,
         description="""Number of channels of the image.""",
     )
-    size_t: Optional[float] = Field(
+    size_t: Optional[int] = Field(
         None,
-        description="""temporal dimension of the data array of the image (in seconds???).""",
+        description="""Size of temporal dimension of the data array of the image).""",
     )
     image_viewer_setting: Optional[List[RenderedView]] = Field(
         None,
@@ -404,7 +408,7 @@ class ImageAcquisition(BaseModel):
     imaging_instrument_description: str = Field(
         description="""Names, types, or description of how the instruments used to create the image."""
     )
-    image_acquistion_parameters: str = Field(
+    image_acquisition_parameters: str = Field(
         description="""Parameters relevant to how the image was taken, such as instrument settings."""
     )
     fbbi_id: List[str] = Field(

bia-shared-datamodels/test/test_shared_models.py

@@ -0,0 +1,59 @@
+from uuid import uuid4
+import pytest
+from pydantic import ValidationError
+from . import utils
+from .utils import (
+    bia_data_model,
+    semantic_models,
+)
+
+
+@pytest.mark.parametrize(
+    ("expected_model_type", "model_creation_func",),
+    (
+        (bia_data_model.Study, utils.get_template_study,),
+        (bia_data_model.FileReference, utils.get_template_file_reference,),
+        (bia_data_model.ImageRepresentation, utils.get_template_image_representation,),
+        (
+            bia_data_model.ExperimentalImagingDataset,
+            utils.get_template_experimental_imaging_dataset,
+        ),
+        (bia_data_model.Specimen, utils.get_template_specimen,),
+        (
+            bia_data_model.ExperimentallyCapturedImage,
+            utils.get_template_experimentally_captured_image,
+        ),
+        (bia_data_model.ImageAcquisition, utils.get_template_image_acquisition,),
+        (
+            bia_data_model.SpecimenPrepartionProtocol,
+            utils.get_template_specimen_preparation_protocol,
+        ),
+        (bia_data_model.BioSample, utils.get_template_biosample,),
+        (
+            bia_data_model.ImageAnnotationDataset,
+            utils.get_template_image_annotation_dataset,
+        ),
+        (
+            bia_data_model.AnnotationFileReference,
+            utils.get_template_annotation_file_reference,
+        ),
+        (bia_data_model.DerivedImage, utils.get_template_derived_image,),
+        (bia_data_model.AnnotationMethod, utils.get_template_annotation_method,),
+    ),
+)
+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_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()],}
+        )