minor improvements to code readability (#110)

* minor improvements to code readability

* pass in uuids as fixture

api/src/models/repository.py

@@ -8,7 +8,7 @@
     AsyncIOMotorDatabase,
 )
 import pydantic
-from typing import List, Any, Callable, Type, Union
+from typing import List, Any, Type, Union
 from enum import Enum
 import uuid
 import pymongo
@@ -535,8 +535,7 @@ async def validate_object_dependency(
             if isinstance(getattr(doc_to_verify, field), uuid.UUID):
                 uuid_to_check = getattr(doc_to_verify, field)
                 await self.validate_uuid_type(uuid_to_check, doc_type.__name__)
-
-            if isinstance(getattr(doc_to_verify, field), List):
+            elif isinstance(getattr(doc_to_verify, field), List):
                 for uuid_to_check in getattr(doc_to_verify, field):
                     await self.validate_uuid_type(uuid_to_check, doc_type.__name__)
 
@@ -607,34 +606,36 @@ async def validate_uuid_type(self, target_uuid: uuid.UUID, expected_type_name: s
 
         return
 
+    @staticmethod
     def append_dependency(
-        self,
-        dependency_map: dict,
+        dependency_map_collector: dict,
         dependency: Union[uuid.UUID, List[uuid.UUID]],
         index: int,
         expected_type: Type[models.DocumentMixin],
     ):
         if isinstance(dependency, uuid.UUID):
-            if dependency_map.get(dependency, None) is None:
-                dependency_map[dependency] = {
+            if dependency_map_collector.get(dependency, None) is None:
+                dependency_map_collector[dependency] = {
                     "index": [index],
                     "type": {expected_type.__name__},
                 }
             else:
-                dependency_map[dependency]["index"].append(index)
+                dependency_map_collector[dependency]["index"].append(index)
                 # We expect a single unique doc type but will sort out throwing an error below
-                dependency_map[dependency]["type"].add(expected_type.__name__)
+                dependency_map_collector[dependency]["type"].add(expected_type.__name__)
         elif isinstance(dependency, List):
             for dependency_uuid in dependency:
-                if dependency_map.get(dependency_uuid, None) is None:
-                    dependency_map[dependency_uuid] = {
+                if dependency_map_collector.get(dependency_uuid, None) is None:
+                    dependency_map_collector[dependency_uuid] = {
                         "index": [index],
                         "type": {expected_type.__name__},
                     }
                 else:
-                    dependency_map[dependency_uuid]["index"].append(index)
+                    dependency_map_collector[dependency_uuid]["index"].append(index)
                     # We expect a single unique doc type but will sort out throwing an error below
-                    dependency_map[dependency_uuid]["type"].add(expected_type.__name__)
+                    dependency_map_collector[dependency_uuid]["type"].add(
+                        expected_type.__name__
+                    )
         return
 
 

api/src/tests/test_biosample_specimen_image_acquisition.py

@@ -9,6 +9,8 @@
 from fastapi.testclient import TestClient
 from .util import (
     get_template_biosample,
+    get_template_specimen,
+    get_template_image_acquisition,
 )
 import pytest
 
@@ -36,20 +38,9 @@ def test_biosample_create_retrieve_update(api_client: TestClient, uuid: str):
 
 
 def test_specimen_create_retrieve_update(
-    api_client: TestClient, uuid: str, existing_biosample: dict
+    api_client: TestClient, existing_biosample: dict, uuid: str
 ):
-    specimen = {
-        "uuid": uuid,
-        "version": 0,
-        "biosample_uuid": existing_biosample["uuid"],
-        "title": "placeholder_title",
-        "sample_preparation_protocol": "placeholder_sample_preparation_protocol",
-        "growth_protocol": "placeholder_growth_protocol",
-        "attributes": {},
-        "annotations": [],
-        "annotations_applied": False,
-        "@context": "https://placeholder/context",
-    }
+    specimen = get_template_specimen(existing_biosample) | {"uuid": uuid}
     rsp = api_client.post(f"private/specimens", json=specimen)
     assert rsp.status_code == 201, rsp.json()
 
@@ -70,28 +61,18 @@ def test_specimen_create_retrieve_update(
 
 
 def test_image_acquisition_create_retrieve_update(
-    api_client: TestClient, uuid: str, existing_specimen: dict
+    api_client: TestClient, existing_specimen: dict, uuid: str
 ):
-    image_acquisition = {
-        "uuid": uuid,
-        "version": 0,
-        "specimen_uuid": existing_specimen["uuid"],
-        "title": "placeholder_title",
-        "imaging_instrument": "placeholder_imaging_instrument",
-        "image_acquisition_parameters": "placeholder_image_acquisition_parameters",
-        "imaging_method": "placeholder_imaging_method",
-        "attributes": {},
-        "annotations": [],
-        "annotations_applied": False,
-        "@context": "https://placeholder/context",
+    image_acquisition = get_template_image_acquisition(existing_specimen) | {
+        "uuid": uuid
     }
     rsp = api_client.post(f"private/image_acquisitions", json=image_acquisition)
     assert rsp.status_code == 201, rsp.json()
 
     rsp = api_client.get(f"image_acquisitions/{uuid}")
-    specimen_fetched = rsp.json()
-    del specimen_fetched["model"]
-    assert specimen_fetched == image_acquisition
+    image_acquisition_fetched = rsp.json()
+    del image_acquisition_fetched["model"]
+    assert image_acquisition_fetched == image_acquisition
 
     image_acquisition["title"] = "title_updated"
     image_acquisition["version"] += 1
@@ -106,24 +87,12 @@ def test_image_acquisition_create_retrieve_update(
 
 def test_create_update_with_badly_typed_uuid(
     api_client: TestClient,
-    uuid: str,
     existing_specimen: dict,
     existing_image_acquisition: dict,
     existing_study: dict,
+    uuid: str,
 ):
-    image_acquisition = {
-        "uuid": uuid,
-        "version": 0,
-        "specimen_uuid": existing_study["uuid"],
-        "title": "placeholder_title",
-        "imaging_instrument": "placeholder_imaging_instrument",
-        "image_acquisition_parameters": "placeholder_image_acquisition_parameters",
-        "imaging_method": "placeholder_imaging_method",
-        "attributes": {},
-        "annotations": [],
-        "annotations_applied": False,
-        "@context": "https://placeholder/context",
-    }
+    image_acquisition = get_template_image_acquisition(existing_study) | {"uuid": uuid}
     rsp = api_client.post(f"private/image_acquisitions", json=image_acquisition)
     assert rsp.status_code == 400, rsp.json()
 
@@ -134,18 +103,7 @@ def test_create_update_with_badly_typed_uuid(
     )
     assert rsp.status_code == 400, rsp.json()
 
-    specimen = {
-        "uuid": uuid,
-        "version": 0,
-        "biosample_uuid": existing_study["uuid"],
-        "title": "placeholder_title",
-        "sample_preparation_protocol": "placeholder_sample_preparation_protocol",
-        "growth_protocol": "placeholder_growth_protocol",
-        "attributes": {},
-        "annotations": [],
-        "annotations_applied": False,
-        "@context": "https://placeholder/context",
-    }
+    specimen = get_template_specimen(existing_study, add_uuid=True)
     rsp = api_client.post(f"private/specimens", json=specimen)
     assert rsp.status_code == 400, rsp.json()