Issue #39: Update pre-commit to run type checking; fix some type errors (#45)

Author: groybal

.pre-commit-config.yaml

@@ -23,3 +23,12 @@ repos:
     hooks:
       - id: cspell
         exclude: cspell.json
+  - repo: local
+    hooks:
+      - id: ty-check
+        name: ty-check
+        entry: uv run ty check --error-on-warning
+        language: system
+        types: [python]
+        pass_filenames: false
+        always_run: true

bases/lif/identity_mapper_restapi/core.py

@@ -2,7 +2,7 @@
 from typing import List
 from uuid import uuid4
 
-from fastapi import FastAPI, Request, Response, status
+from fastapi import FastAPI, Request, status
 from fastapi.responses import JSONResponse
 from sqlalchemy.orm import sessionmaker, Session
 
@@ -49,8 +49,10 @@ def shutdown():
     status_code=status.HTTP_200_OK,
     response_model=List[IdentityMapping],
 )
-async def do_save_mappings(org_id: str, person_id: str, mappings: List[IdentityMapping]) -> Response:
+async def do_save_mappings(org_id: str, person_id: str, mappings: List[IdentityMapping]) -> List[IdentityMapping]:
     logger.info(f"CALL RECEIVED TO (POST) /organizations/{org_id}/persons/{person_id}/mappings API")
+    if service is None:
+        raise RuntimeError("Service is not initialized")
     mappings_created: List[IdentityMapping] = await service.save_mappings(org_id, person_id, mappings)
     logger.info(f"Mappings saved successfully for person {person_id} in organization {org_id}")
     return mappings_created
@@ -63,6 +65,8 @@ async def do_save_mappings(org_id: str, person_id: str, mappings: List[IdentityM
 )
 async def do_get_mappings(org_id: str, person_id: str) -> List[IdentityMapping]:
     logger.info(f"CALL RECEIVED TO (GET) /organizations/{org_id}/persons/{person_id}/mappings API")
+    if service is None:
+        raise RuntimeError("Service is not initialized")
     mappings = await service.get_mappings(org_id, person_id)
     logger.info(f"Mappings retrieved successfully for person {person_id} in organization {org_id}")
     return mappings
@@ -71,6 +75,8 @@ async def do_get_mappings(org_id: str, person_id: str) -> List[IdentityMapping]:
 @app.delete("/organizations/{org_id}/persons/{person_id}/mappings/{mapping_id}", status_code=status.HTTP_204_NO_CONTENT)
 async def do_delete_mapping(org_id: str, person_id: str, mapping_id: str):
     logger.info(f"CALL RECEIVED TO (DELETE) /organizations/{org_id}/persons/{person_id}/mappings/{mapping_id} API")
+    if service is None:
+        raise RuntimeError("Service is not initialized")
     await service.delete_mapping(org_id, person_id, mapping_id)
     logger.info(f"Mapping {mapping_id} deleted successfully for person {person_id} in organization {org_id}")
 

components/lif/auth/core.py

@@ -1,5 +1,5 @@
 import os
-from datetime import datetime, timedelta
+from datetime import datetime, timedelta, timezone
 
 import jwt
 from fastapi import HTTPException, Security
@@ -19,15 +19,15 @@
 def create_access_token(data: dict) -> str:
     """Create a JWT access token with expiration."""
     to_encode = data.copy()
-    expire = datetime.utcnow() + timedelta(minutes=ACCESS_TOKEN_EXPIRE_MINUTES)
+    expire = datetime.now(timezone.utc) + timedelta(minutes=ACCESS_TOKEN_EXPIRE_MINUTES)
     to_encode.update({"exp": expire})
     return jwt.encode(to_encode, SECRET_KEY, algorithm=ALGORITHM)
 
 
 def create_refresh_token(data: dict) -> str:
     """Create a JWT refresh token with expiration."""
     to_encode = data.copy()
-    expire = datetime.utcnow() + timedelta(days=REFRESH_TOKEN_EXPIRE_DAYS)
+    expire = datetime.now(timezone.utc) + timedelta(days=REFRESH_TOKEN_EXPIRE_DAYS)
     to_encode.update({"exp": expire})
     return jwt.encode(to_encode, SECRET_KEY, algorithm=ALGORITHM)
 

components/lif/datatypes/core.py

@@ -78,12 +78,6 @@ class LIFQueryFilter(RootModel[LIFQueryPersonFilter]):
 
     root: LIFQueryPersonFilter
 
-    def __iter__(self):
-        return iter(self.root)
-
-    def __getitem__(self, item):
-        return self.root[item]
-
 
 class LIFQuery(BaseModel):
     """
@@ -112,10 +106,12 @@ class LIFQueryStatusResponse(BaseModel):
     Attributes:
         query_id (str): Query ID for the query.
         status (str): Status of the query (e.g., 'PENDING').
+        error_message (str | None): Error message if the query failed.
     """
 
     query_id: str = Field(..., description="Query ID for the query")
     status: str = Field(..., description="Status of the query (e.g., 'PENDING', 'COMPLETED)")
+    error_message: str | None = Field(None, description="Error message if the query failed")
 
 
 class LIFUpdatePersonPayload(BaseModel):

components/lif/identity_mapper_storage_sql/model.py

@@ -1,6 +1,7 @@
 from uuid import uuid4
 
-from sqlalchemy import Column, String, UniqueConstraint
+from sqlalchemy import String, UniqueConstraint
+from sqlalchemy.orm import Mapped, mapped_column
 from lif.identity_mapper_storage_sql.db import Base
 from lif.datatypes import IdentityMapping
 
@@ -10,12 +11,12 @@ class IdentityMappingModel(Base):
 
     __tablename__ = "identity_mappings"
 
-    mapping_id: Column[String] = Column(String(36), primary_key=True, index=True, default=lambda: str(uuid4()))
-    lif_organization_id: Column[String] = Column(String(255), index=True, nullable=False)
-    lif_organization_person_id: Column[String] = Column(String(255), index=True, nullable=False)
-    target_system_id: Column[String] = Column(String(255), index=True, nullable=False)
-    target_system_person_id_type: Column[String] = Column(String(100), index=True, nullable=False)
-    target_system_person_id: Column[String] = Column(String(255), index=True, nullable=False)
+    mapping_id: Mapped[str] = mapped_column(String(36), primary_key=True, index=True, default=lambda: str(uuid4()))
+    lif_organization_id: Mapped[str] = mapped_column(String(255), index=True, nullable=False)
+    lif_organization_person_id: Mapped[str] = mapped_column(String(255), index=True, nullable=False)
+    target_system_id: Mapped[str] = mapped_column(String(255), index=True, nullable=False)
+    target_system_person_id_type: Mapped[str] = mapped_column(String(100), index=True, nullable=False)
+    target_system_person_id: Mapped[str] = mapped_column(String(255), index=True, nullable=False)
     __table_args__ = (
         UniqueConstraint(
             "lif_organization_id",

components/lif/query_cache_service/core.py

@@ -275,7 +275,7 @@ async def add(lif_record: LIFRecord) -> LIFRecord:
         result = await collection.insert_one(lif_record.model_dump())
         if result.inserted_id:
             added_record = await collection.find_one({"_id": result.inserted_id})
-            return LIFRecord(**added_record)
+            return LIFRecord(**added_record)  # type: ignore
         raise ResourceNotFoundException("Failed to add record, no inserted ID returned.")
     except Exception as e:
         logger.exception("Add Exception: %s", e)

components/lif/query_planner_service/core.py

@@ -111,7 +111,7 @@ async def run_query(self, query: LIFQuery, first_run: bool) -> List[LIFRecord] |
 
                 orchestrator_job_request: OrchestratorJobRequest = OrchestratorJobRequest(
                     lif_query_plan=lif_query_plan,
-                    async_=True,  # Run the orchestration asynchronously
+                    async_=True,  # ty: ignore[unknown-argument]
                 )
 
                 try:

pyproject.toml

@@ -116,8 +116,8 @@ line-length = 120
 required-version = "~=0.11.13"
 
 [tool.ruff.format]
-# use '\n' line endings for all files (*nix/mac default)
 docstring-code-format = true
+# use '\n' line endings for all files (*nix/mac default)
 line-ending = "lf"
 skip-magic-trailing-comma = true
 
@@ -130,3 +130,22 @@ ignore = [
   "TD002",
   "TD003"
 ]
+
+[tool.ty.src]
+exclude = [
+  "scripts/",
+  "test/",
+  "bases/lif/advisor_restapi/",
+  "bases/lif/api_graphql/",
+  "bases/lif/mdr_restapi/",
+  "bases/lif/semantic_search_mcp_server",
+  "components/lif/langchain_agent/",
+  "components/lif/mdr_dto/",
+  "components/lif/mdr_services/",
+  "components/lif/mdr_utils/",
+  "components/lif/openapi_to_graphql/",
+  "components/lif/orchestrator_clients/",
+  "components/lif/semantic_search_service/",
+  "development/"
+]
+