stash more

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
   - id: mixed-line-ending
     args: [ --fix=lf ]
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.5.0
+  rev: v0.8.6
   hooks:
     - id: ruff
     - id: ruff-format

pyproject.toml

@@ -121,6 +121,7 @@ select = [
     "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
     "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
     "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+    "FAST",  # https://docs.astral.sh/ruff/rules/#fastapi-fast
     "PERF",  # https://docs.astral.sh/ruff/rules/#perflint-perf
     "FURB",  # https://docs.astral.sh/ruff/rules/#refurb-furb
     "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
@@ -139,6 +140,7 @@ fixable = [
     "PT",
     "RSE",
     "SIM",
+    "FAST",
     "PERF",
     "FURB",
     "RUF"

src/gene/database/database.py

@@ -9,6 +9,7 @@
 
 import click
 
+from gene.config import config
 from gene.schemas import AwsEnvName, RecordType, RefType, SourceMeta, SourceName
 
 
@@ -62,7 +63,7 @@ def _check_delete_okay() -> bool:
         :raise DatabaseWriteException: if skip confirmation variable is set -- manual
         approval is required.
         """
-        if environ.get(AWS_ENV_VAR_NAME, "") == AwsEnvName.PRODUCTION:
+        if config.env == AwsEnvName.PRODUCTION:
             if environ.get(SKIP_AWS_DB_ENV_NAME, "") == "true":
                 err_msg = f"Must unset {SKIP_AWS_DB_ENV_NAME} env variable to enable drop_db()"
                 raise DatabaseWriteException(err_msg)

src/gene/etl/__init__.py

@@ -10,10 +10,10 @@
 from .ncbi import NCBI
 
 __all__ = [
-    "Ensembl",
     "HGNC",
     "NCBI",
-    "GeneNormalizerEtlError",
+    "Ensembl",
     "GeneFileVersionError",
+    "GeneNormalizerEtlError",
     "GeneSourceFetchError",
 ]

src/gene/main.py

@@ -2,9 +2,12 @@
 
 import html
 import os
+from collections.abc import AsyncGenerator
+from contextlib import asynccontextmanager
 from enum import Enum
+from typing import Annotated
 
-from fastapi import FastAPI, HTTPException, Query
+from fastapi import FastAPI, HTTPException, Query, Request
 
 from gene import __version__
 from gene.database.database import (
@@ -13,6 +16,7 @@
     AwsEnvName,
     create_db,
 )
+from gene.logging import initialize_logs
 from gene.query import InvalidParameterException, QueryHandler
 from gene.schemas import (
     NormalizeService,
@@ -31,8 +35,19 @@ class _Tag(str, Enum):
     META = "Meta"
 
 
-db = create_db()
-query_handler = QueryHandler(db)
+@asynccontextmanager
+async def lifespan(app: FastAPI) -> AsyncGenerator:
+    """Perform operations that interact with the lifespan of the FastAPI instance.
+    See https://fastapi.tiangolo.com/advanced/events/#lifespan.
+
+    :param app: FastAPI instance
+    """
+    initialize_logs()
+
+    db = create_db()
+    app.state.query_handler = QueryHandler(db)
+    yield
+
 
 description = """
 The Gene Normalizer provides tools for resolving ambiguous gene references to
@@ -82,17 +97,19 @@ class _Tag(str, Enum):
     "/gene/search",
     summary=read_query_summary,
     response_description=response_description,
-    response_model=SearchService,
     description=search_description,
     tags=[_Tag.QUERY],
 )
 def search(
-    q: str = Query(..., description=q_descr),
-    incl: str | None = Query(None, description=incl_descr),
-    excl: str | None = Query(None, description=excl_descr),
+    request: Request,
+    q: Annotated[str, Query(..., description=q_descr)],
+    incl: Annotated[str | None, Query(None, description=incl_descr)],
+    excl: Annotated[str | None, Query(None, description=excl_descr)],
 ) -> SearchService:
     """Return strongest match concepts to query string provided by user.
 
+    :param request: the HTTP request context, supplied by FastAPI, used to get
+        query response class
     :param str q: gene search term
     :param Optional[str] incl: comma-separated list of sources to include,
         with all others excluded. Raises HTTPException if both `incl` and
@@ -103,7 +120,9 @@ def search(
     :return: JSON response with matched records and source metadata
     """
     try:
-        resp = query_handler.search(html.unescape(q), incl=incl, excl=excl)
+        resp = request.app.state.query_handler.search(
+            html.unescape(q), incl=incl, excl=excl
+        )
     except InvalidParameterException as e:
         raise HTTPException(status_code=422, detail=str(e)) from e
     return resp
@@ -119,18 +138,22 @@ def search(
     "/gene/normalize",
     summary=normalize_summary,
     response_description=normalize_response_descr,
-    response_model=NormalizeService,
     response_model_exclude_none=True,
     description=normalize_descr,
     tags=[_Tag.QUERY],
 )
-def normalize(q: str = Query(..., description=normalize_q_descr)) -> NormalizeService:
+def normalize(
+    request: Request,
+    q: Annotated[str, Query(..., description=normalize_q_descr)],
+) -> NormalizeService:
     """Return strongest match concepts to query string provided by user.
 
+    :param request: the HTTP request context, supplied by FastAPI, used to get
+        query response class
     :param str q: gene search term
     :return: JSON response with normalized gene concept
     """
-    return query_handler.normalize(html.unescape(q))
+    return request.app.state.query_handler.normalize(html.unescape(q))
 
 
 unmerged_matches_summary = (
@@ -151,25 +174,26 @@ def normalize(q: str = Query(..., description=normalize_q_descr)) -> NormalizeSe
     summary=unmerged_matches_summary,
     operation_id="getUnmergedRecords",
     response_description=unmerged_response_descr,
-    response_model=UnmergedNormalizationService,
     description=unmerged_normalize_description,
     tags=[_Tag.QUERY],
 )
 def normalize_unmerged(
-    q: str = Query(..., description=normalize_q_descr),
+    request: Request,
+    q: Annotated[str, Query(..., description=normalize_q_descr)],
 ) -> UnmergedNormalizationService:
     """Return all individual records associated with a normalized concept.
 
+    :param request: the HTTP request context, supplied by FastAPI, used to get
+        query response class
     :param q: Gene search term
     :returns: JSON response with matching normalized record and source metadata
     """
-    return query_handler.normalize_unmerged(html.unescape(q))
+    return request.app.state.query_handler.normalize_unmerged(html.unescape(q))
 
 
 @app.get(
     "/service_info",
     summary="Get basic service information",
-    response_model=ServiceInfo,
     description="Retrieve service metadata, such as versioning and contact info. Structured in conformance with the [GA4GH service info API specification](https://www.ga4gh.org/product/service-info/)",
     tags=[_Tag.META],
 )

src/gene/schemas.py

@@ -746,6 +746,9 @@ class ServiceType(BaseModel):
     version: Literal[__version__] = __version__
 
 
+LOCAL_DEV_ENV_NAME = "local_dev"
+
+
 class AwsEnvName(str, Enum):
     """AWS environment name that is being used"""
 
@@ -776,5 +779,5 @@ class ServiceInfo(BaseModel):
         "2024-03-04T00:00:00.000000+00:00"
     )
     updatedAt: str | None = None  # noqa: N815
-    environment: AwsEnvName | None = None
+    environment: AwsEnvName | Literal[LOCAL_DEV_ENV_NAME] | None = None
     version: Literal[__version__] = __version__