feat: aws manager (#17)

Author: jtyoung84

aind-sharepoint-service-server/pyproject.toml

@@ -18,11 +18,10 @@ dynamic = ["version"]
 
 dependencies = [
     'pydantic>=2.0',
-    'pydantic-settings>=2.0',
+    'aind-settings-utils>=0.1.0',
     'fastapi[standard]>=0.114.0',
     'fastapi-cache2[redis]>=0.2.2',
     'azure-identity>=1.15.0',
-    'aind-settings-utils>=0.0.3',
     'requests',
 ]
 

aind-sharepoint-service-server/src/aind_sharepoint_service_server/configs.py

@@ -3,14 +3,12 @@
 from typing import ClassVar, Optional
 from urllib.parse import urljoin
 
-from aind_settings_utils.aws import (
-    ParameterStoreAppBaseSettings,
-)
+from aind_settings_utils.aws import SecretsManagerBaseSettings
 from pydantic import Field, RedisDsn, SecretStr
 from pydantic_settings import SettingsConfigDict
 
 
-class Settings(ParameterStoreAppBaseSettings):
+class Settings(SecretsManagerBaseSettings):
     """Settings needed to connect to Sharepoint database"""
 
     model_config = SettingsConfigDict(
@@ -105,6 +103,4 @@ def nsb_present_url(self) -> str:
         )
 
 
-def get_settings() -> Settings:
-    """Return a Settings object."""
-    return Settings()
+settings = Settings()

aind-sharepoint-service-server/src/aind_sharepoint_service_server/main.py

@@ -16,7 +16,7 @@
 from redis.asyncio import from_url  # noqa
 
 from aind_sharepoint_service_server import __version__ as service_version
-from aind_sharepoint_service_server.configs import get_settings
+from aind_sharepoint_service_server.configs import settings
 from aind_sharepoint_service_server.route import router
 
 # The log level can be set by adding an environment variable before launch.
@@ -34,7 +34,6 @@
 @asynccontextmanager
 async def lifespan(_: FastAPI) -> AsyncIterator[None]:
     """Init cache and add to lifespan of app"""
-    settings = get_settings()
     if settings.redis_url is not None:
         redis = from_url(settings.redis_url.unicode_string())
         FastAPICache.init(RedisBackend(redis), prefix="fastapi-cache")

aind-sharepoint-service-server/src/aind_sharepoint_service_server/models/nsb_2023.py

@@ -528,9 +528,7 @@ class NSB2023LimsTaskflow(Enum, metaclass=EnumMeta):
         "Brain Observatory Transgenic Characterization"
     )
     BRAIN_OBSERVATORY_V1_DD = "Brain Observatory V1DD"
-    BRAIN_OBSERVATORY_VISUAL_BEHAVIOR = (
-        "Brain Observatory Visual Behavior"
-    )
+    BRAIN_OBSERVATORY_VISUAL_BEHAVIOR = "Brain Observatory Visual Behavior"
     BRAIN_OBSERVATORY_VISUAL_BEHAVIOR_1B = (
         "Brain Observatory Visual Behavior 1B"
     )
@@ -746,27 +744,21 @@ class NSB2023Procedure(Enum, metaclass=EnumMeta):
     SX_9__GRID_INJ_6_OR_9__MO = "Sx-09 Grid INJ (6 or 9) + Motor Ctx 2P"
     SX_11_19_HP__ONLY = "Sx-11&19 HP Only"
     SX_11_19_HP__TRANSCRANIAL = "Sx-11&19 HP Transcranial"
-    SX_12__STEREOTAXIC__INJEC = (
-        "Sx-12 Stereotaxic Injection (with Headpost)"
-    )
+    SX_12__STEREOTAXIC__INJEC = "Sx-12 Stereotaxic Injection (with Headpost)"
     SX_14__VISUAL__CTX_NP = "Sx-14 Visual Ctx NP"
     SX_15_WHC_NP = "Sx-15 WHC NP"
     SX_16_INJ_WHC_NP = "Sx-16 INJ + WHC NP"
     SX_17_DHC = "Sx-17 DHC"
     SX_18_INJ_DHC = "Sx-18 INJ+DHC"
-    SX_21__FIBER__OPTIC__IMPL = (
-        "Sx-21 Fiber Optic Implant (with Headpost)"
-    )
+    SX_21__FIBER__OPTIC__IMPL = "Sx-21 Fiber Optic Implant (with Headpost)"
     SX_21__INJECTION__FIBER = (
         "Sx-21 Injection + Fiber Optic Implant (with Headpost)"
     )
     SX_24__STEREOTAXIC_INJECT = "Sx-24 Stereotaxic injections: 1 INJ material"
     SX_25__STEREOTAXIC_INJECT = (
         "Sx-25 Stereotaxic injections: 2+ INJ materials"
     )
-    SX_26_ISI_GUIDED__INJECTI = (
-        "Sx-26 ISI-guided Injection (with Headpost)"
-    )
+    SX_26_ISI_GUIDED__INJECTI = "Sx-26 ISI-guided Injection (with Headpost)"
     SX__SPINAL__CORD_INJ = "Sx- Spinal Cord INJ"
     SX_EMG__ARRAY = "Sx- EMG Array"
     SX__TESTES__INJECTION = "Sx- Testes Injection"
@@ -779,9 +771,7 @@ class NSB2023Procedure(Enum, metaclass=EnumMeta):
     FRONTAL_CTX_2_P = "Frontal Ctx 2P"
     HP_ONLY = "HP Only"
     HP_TRANSCRANIAL = "HP Transcranial"
-    INJECTION_FIBER_OPTIC_IMP = (
-        "Injection+Fiber Optic Implant (with Headpost)"
-    )
+    INJECTION_FIBER_OPTIC_IMP = "Injection+Fiber Optic Implant (with Headpost)"
     INJ_MOTOR_CTX = "INJ + Motor Ctx"
     INJ_VISUAL_CTX_2_P = "INJ + Visual Ctx 2P"
     INJ_WHC_NP_1_INJECTION_LO = "INJ + WHC NP (1 Injection Location)"
@@ -5687,9 +5677,7 @@ class NSB2023List(BaseModel, extra="allow"):
     )
     craniotomy_type: Annotated[
         NSB2023CraniotomyType, WrapValidator(optional_enum)
-    ] = Field(
-        default=None, alias="CraniotomyType", title="Craniotomy Type"
-    )
+    ] = Field(default=None, alias="CraniotomyType", title="Craniotomy Type")
     created: Optional[datetime] = Field(
         default=None, alias="Created", title="Created"
     )
@@ -6163,9 +6151,7 @@ class NSB2023List(BaseModel, extra="allow"):
     )
     surgery_status: Annotated[
         NSB2023SurgeryStatus, WrapValidator(optional_enum)
-    ] = Field(
-        default=None, alias="SurgeryStatus", title="Surgery Status"
-    )
+    ] = Field(default=None, alias="SurgeryStatus", title="Surgery Status")
     test1: Optional[str] = Field(
         default=None, alias="Test1", title="Initial Surgeon"
     )
@@ -6175,9 +6161,7 @@ class NSB2023List(BaseModel, extra="allow"):
         title="Follow up Surgeon",
     )
     thermistor: Annotated[NSB2023Thermistor, WrapValidator(optional_enum)] = (
-        Field(
-            default=None, alias="Thermistor", title="Thermistor"
-        )
+        Field(default=None, alias="Thermistor", title="Thermistor")
     )
     title: Optional[str] = Field(default=None, alias="Title", title="Title")
     ui_version_string: Optional[str] = Field(

aind-sharepoint-service-server/src/aind_sharepoint_service_server/route.py

@@ -4,11 +4,11 @@
 
 from azure.core.credentials import AccessToken
 from azure.identity import ClientSecretCredential
-from fastapi import APIRouter, Depends, Path, status
+from fastapi import APIRouter, Path, status
 from fastapi_cache.decorator import cache
 from httpx import AsyncClient
 
-from aind_sharepoint_service_server.configs import Settings, get_settings
+from aind_sharepoint_service_server.configs import settings
 from aind_sharepoint_service_server.handler import SessionHandler
 from aind_sharepoint_service_server.models.core import HealthCheck
 from aind_sharepoint_service_server.models.las_2020 import Las2020List
@@ -19,7 +19,7 @@
 
 
 @cache(expire=3360)
-async def get_access_token(settings: Settings) -> str:
+async def get_access_token() -> str:
     """
     Get access token from either Azure or cache. Token is valid for 60 minutes.
     We set cache lifespan to 56 minutes.
@@ -38,9 +38,9 @@ async def get_access_token(settings: Settings) -> str:
 
 
 @cache(expire=3600)
-async def get_las_2020_list(settings: Settings) -> List[Dict[str, Any]]:
+async def get_las_2020_list() -> List[Dict[str, Any]]:
     """Get the LAS_2020 list items"""
-    bearer_token = await get_access_token(settings=settings)
+    bearer_token = await get_access_token()
     headers = {
         "Authorization": f"Bearer {bearer_token}",
         "Content-Type": "application/json",
@@ -58,11 +58,9 @@ async def get_las_2020_list(settings: Settings) -> List[Dict[str, Any]]:
 
 
 # Not worthwhile to cache results for NSB lists
-async def get_nsb_2019_list(
-    subject_id: str, settings: Settings
-) -> List[Dict[str, Any]]:
+async def get_nsb_2019_list(subject_id: str) -> List[Dict[str, Any]]:
     """Get the NSB_2019 list items"""
-    bearer_token = await get_access_token(settings=settings)
+    bearer_token = await get_access_token()
     headers = {
         "Authorization": f"Bearer {bearer_token}",
         "Content-Type": "application/json",
@@ -79,11 +77,9 @@ async def get_nsb_2019_list(
     return list_items
 
 
-async def get_nsb_2023_list(
-    subject_id: str, settings: Settings
-) -> List[Dict[str, Any]]:
+async def get_nsb_2023_list(subject_id: str) -> List[Dict[str, Any]]:
     """Get the NSB_2023 list items"""
-    bearer_token = await get_access_token(settings=settings)
+    bearer_token = await get_access_token()
     headers = {
         "Authorization": f"Bearer {bearer_token}",
         "Content-Type": "application/json",
@@ -100,11 +96,9 @@ async def get_nsb_2023_list(
     return list_items
 
 
-async def get_nsb_present_list(
-    subject_id: str, settings: Settings
-) -> List[Dict[str, Any]]:
+async def get_nsb_present_list(subject_id: str) -> List[Dict[str, Any]]:
     """Get the NSB Present list items"""
-    bearer_token = await get_access_token(settings=settings)
+    bearer_token = await get_access_token()
     headers = {
         "Authorization": f"Bearer {bearer_token}",
         "Content-Type": "application/json",
@@ -153,14 +147,13 @@ async def get_las_2020(
                 "value": "805811",
             }
         },
-    ),
-    settings=Depends(get_settings),
+    )
 ):
     """
     # LAS 2020 Endpoint
     Retrieve information from the LAS 2020 list for a given subject ID.
     """
-    las_2020_list = await get_las_2020_list(settings=settings)
+    las_2020_list = await get_las_2020_list()
     las_2020_models = [
         Las2020List.model_validate(item["fields"])
         for item in las_2020_list
@@ -183,17 +176,14 @@ async def get_nsb_2019(
                 "value": "656374",
             }
         },
-    ),
-    settings=Depends(get_settings),
+    )
 ):
     """
     # NSB 2019 Endpoint
     Retrieve information from the NSB 2019 list for a given subject ID.
     """
 
-    nsb_2019_list = await get_nsb_2019_list(
-        subject_id=subject_id, settings=settings
-    )
+    nsb_2019_list = await get_nsb_2019_list(subject_id=subject_id)
     nsb_2019_models = [
         NSB2019List.model_validate(item["fields"]) for item in nsb_2019_list
     ]
@@ -214,17 +204,14 @@ async def get_nsb_2023(
                 "value": "657849",
             }
         },
-    ),
-    settings=Depends(get_settings),
+    )
 ):
     """
     # NSB 2023 Endpoint
     Retrieve information from the NSB 2023-Archive list for a given subject ID.
     """
 
-    nsb_2023_list = await get_nsb_2023_list(
-        subject_id=subject_id, settings=settings
-    )
+    nsb_2023_list = await get_nsb_2023_list(subject_id=subject_id)
     nsb_2023_models = [
         NSB2023List.model_validate(item["fields"]) for item in nsb_2023_list
     ]
@@ -245,17 +232,14 @@ async def get_nsb_present(
                 "value": "790025",
             }
         },
-    ),
-    settings=Depends(get_settings),
+    )
 ):
     """
     # NSB Present Endpoint
     Retrieve information from the NSB 2023-Present list for a given subject ID.
     """
 
-    nsb_present_list = await get_nsb_present_list(
-        subject_id=subject_id, settings=settings
-    )
+    nsb_present_list = await get_nsb_present_list(subject_id=subject_id)
     nsb_present_models = [
         NSB2023List.model_validate(item["fields"]) for item in nsb_present_list
     ]

aind-sharepoint-service-server/tests/conftest.py

@@ -10,7 +10,7 @@
 from fastapi.testclient import TestClient
 from pydantic import RedisDsn
 
-from aind_sharepoint_service_server.configs import Settings
+from aind_sharepoint_service_server.configs import settings
 
 RESOURCES_DIR = Path(os.path.dirname(os.path.realpath(__file__))) / "resources"
 
@@ -95,13 +95,12 @@ def client_with_redis() -> Generator[TestClient, Any, None]:
     # Import moved to be able to mock cache
     from aind_sharepoint_service_server.main import app
 
-    settings = Settings()
     settings_with_redis = settings.model_copy(
         update={"redis_url": RedisDsn("redis://example.com:1234")}, deep=True
     )
     with (
         patch(
-            "aind_sharepoint_service_server.main.get_settings",
+            "aind_sharepoint_service_server.main.settings",
             return_value=settings_with_redis,
         ),
         patch(

aind-sharepoint-service-server/tests/test_route.py

@@ -7,7 +7,6 @@
 from azure.core.credentials import AccessToken
 from fastapi.testclient import TestClient
 
-from aind_sharepoint_service_server.configs import Settings
 from aind_sharepoint_service_server.route import (
     get_access_token,
     get_las_2020_list,
@@ -33,7 +32,7 @@ async def test_get_access_token(self, mock_azure_credentials: MagicMock):
         mock_azure_credentials.return_value.get_token.return_value = (
             AccessToken(token="abc", expires_on=100)
         )
-        token = await get_access_token(settings=Settings())
+        token = await get_access_token()
         mock_azure_credentials.assert_has_calls(
             [
                 call(
@@ -61,7 +60,7 @@ async def test_get_las_2020_list(
         """Tests get_las_2020_list method"""
         mock_get_access_token.return_value = "abc"
         mock_get_list_items.return_value = mock_get_las_2020_list_items
-        list_items = await get_las_2020_list(settings=Settings())
+        list_items = await get_las_2020_list()
         mock_client.assert_called_once()
         assert 4 == len(list_items)
 
@@ -93,9 +92,7 @@ async def test_get_nsb_2023_list(
         """Tests get_nsb_2023_list method"""
         mock_get_access_token.return_value = "abc"
         mock_get_list_items.return_value = mock_get_nsb_2023_list_items
-        list_items = await get_nsb_2023_list(
-            settings=Settings(), subject_id="657849"
-        )
+        list_items = await get_nsb_2023_list(subject_id="657849")
         mock_client.assert_called_once()
         assert 1 == len(list_items)
 
@@ -127,9 +124,7 @@ async def test_get_nsb_2019_list(
         """Tests get_nsb_2019_list method"""
         mock_get_access_token.return_value = "abc"
         mock_get_list_items.return_value = mock_get_nsb_2019_list_items
-        list_items = await get_nsb_2019_list(
-            settings=Settings(), subject_id="656374"
-        )
+        list_items = await get_nsb_2019_list(subject_id="656374")
         mock_client.assert_called_once()
         assert 1 == len(list_items)
 
@@ -161,9 +156,7 @@ async def test_get_nsb_present_list(
         """Tests get_nsb_present_list method"""
         mock_get_access_token.return_value = "abc"
         mock_get_list_items.return_value = mock_get_nsb_present_list_items
-        list_items = await get_nsb_present_list(
-            settings=Settings(), subject_id="790025"
-        )
+        list_items = await get_nsb_present_list(subject_id="790025")
         mock_client.assert_called_once()
         assert 1 == len(list_items)