From 9f20cc9615c03e36ed6e6ae4282a7fc7f89abaa5 Mon Sep 17 00:00:00 2001 From: VibhavSetlur Date: Fri, 20 Feb 2026 18:04:38 -0600 Subject: [PATCH] fix: replace hardcoded kb_env defaults with settings.KB_ENV --- app/models.py | 3 ++- app/routes.py | 14 +++++++------- app/utils/workspace.py | 14 +++++++------- 3 files changed, 16 insertions(+), 15 deletions(-) diff --git a/app/models.py b/app/models.py index 3022f80..8e71a09 100644 --- a/app/models.py +++ b/app/models.py @@ -2,6 +2,7 @@ from typing import Any, Literal from pydantic import BaseModel, Field +from app.config import settings from app.config_constants import MAX_LIMIT @@ -71,7 +72,7 @@ class TableDataRequest(BaseModel): examples=[{"gene_name": "kinase", "organism": "E. coli"}] ) kb_env: str = Field( - "appdev", + settings.KB_ENV, description="KBase environment" ) diff --git a/app/routes.py b/app/routes.py index a5fb072..2a2d26d 100644 --- a/app/routes.py +++ b/app/routes.py @@ -472,7 +472,7 @@ async def upload_database( ) async def list_tables_by_object( ws_ref: str = Path(..., description="KBase workspace object reference (UPA format: workspace_id/object_id/version)", examples=["76990/7/2"]), - kb_env: str = Query("appdev", description="KBase environment", examples=["appdev"]), + kb_env: str = Query(settings.KB_ENV, description="KBase environment", examples=["appdev", "prod"]), authorization: str | None = Header(None, description="KBase authentication token (Bearer token or plain token)", examples=["Bearer YOUR_KBASE_TOKEN"]), kbase_session: str | None = Cookie(None, description="KBase session cookie", examples=["YOUR_KBASE_TOKEN"]) ): @@ -651,7 +651,7 @@ async def get_table_data_by_object( sort_column: str | None = Query(None, description="Column name to sort by", examples=["gene_name"]), sort_order: str | None = Query("ASC", description="Sort order: ASC or DESC", examples=["ASC"]), search: str | None = Query(None, description="Global text search across all columns", examples=["kinase"]), - kb_env: str = Query("appdev", description="KBase environment", examples=["appdev"]), + kb_env: str = Query(settings.KB_ENV, description="KBase environment", examples=["appdev", "prod"]), authorization: str | None = Header(None, description="KBase authentication token", examples=["Bearer YOUR_KBASE_TOKEN"]), kbase_session: str | None = Cookie(None, description="KBase session cookie", examples=["YOUR_KBASE_TOKEN"]) ): @@ -701,7 +701,7 @@ async def get_table_data_by_object( async def get_table_stats( ws_ref: str = Path(..., description="KBase workspace object reference (UPA format)", examples=["76990/7/2"]), table_name: str = Path(..., description="Name of the table to analyze", examples=["Genes"]), - kb_env: str = Query("appdev", description="KBase environment", examples=["appdev"]), + kb_env: str = Query(settings.KB_ENV, description="KBase environment", examples=["appdev", "prod"]), authorization: str | None = Header(None, description="KBase authentication token", examples=["Bearer YOUR_KBASE_TOKEN"]), kbase_session: str | None = Cookie(None, description="KBase session cookie", examples=["YOUR_KBASE_TOKEN"]) ): @@ -761,7 +761,7 @@ async def get_table_stats( ) async def list_databases_in_object( upa: str = Query(..., description="KBase workspace object reference (UPA format)", examples=["76990/7/2", "76990/Test2"]), - kb_env: str = Query("appdev", description="KBase environment", examples=["appdev"]), + kb_env: str = Query(settings.KB_ENV, description="KBase environment", examples=["appdev", "prod"]), authorization: str | None = Header(None, description="KBase authentication token"), kbase_session: str | None = Cookie(None, description="KBase session cookie") ): @@ -884,7 +884,7 @@ async def list_databases_in_object( async def list_tables_in_database( db_name: str = Path(..., description="Database name within the object", examples=["pg_ecoli_k12", "GCF_000368685.1"]), upa: str = Query(..., description="KBase workspace object reference (UPA format)", examples=["76990/7/2", "76990/Test2"]), - kb_env: str = Query("appdev", description="KBase environment"), + kb_env: str = Query(settings.KB_ENV, description="KBase environment"), authorization: str | None = Header(None, description="KBase authentication token"), kbase_session: str | None = Cookie(None, description="KBase session cookie") ): @@ -979,7 +979,7 @@ async def get_table_data_from_database( sort_column: str | None = Query(None, description="Column to sort by"), sort_order: str | None = Query("ASC", description="Sort order: ASC or DESC"), search: str | None = Query(None, description="Global text search"), - kb_env: str = Query("appdev", description="KBase environment"), + kb_env: str = Query(settings.KB_ENV, description="KBase environment"), authorization: str | None = Header(None, description="KBase authentication token"), kbase_session: str | None = Cookie(None, description="KBase session cookie") ): @@ -1083,7 +1083,7 @@ async def query_table_data( try: token = get_auth_token(authorization, kbase_session) cache_dir = get_cache_dir() - kb_env = getattr(request, 'kb_env', 'appdev') or 'appdev' + kb_env = getattr(request, 'kb_env', settings.KB_ENV) or settings.KB_ENV filters = request.col_filter if request.col_filter else request.query_filters diff --git a/app/utils/workspace.py b/app/utils/workspace.py index 9cdf632..8bfd38e 100644 --- a/app/utils/workspace.py +++ b/app/utils/workspace.py @@ -28,7 +28,7 @@ class KBaseClient: def __init__( self, token: str | None, - kb_env: str = "appdev", + kb_env: str = settings.KB_ENV, cache_dir: Path | None = None ): """ @@ -269,7 +269,7 @@ def get_object_with_type(self, ref: str) -> tuple[dict[str, Any], str]: def get_berdl_table_data( berdl_table_id: str, auth_token: str, - kb_env: str = "appdev" + kb_env: str = settings.KB_ENV ) -> dict[str, Any]: client = KBaseClient(auth_token, kb_env) return client.get_object(berdl_table_id) @@ -278,7 +278,7 @@ def get_berdl_table_data( def get_object_type( berdl_table_id: str, auth_token: str, - kb_env: str = "appdev" + kb_env: str = settings.KB_ENV ) -> str: if berdl_table_id.startswith("local:"): return "LocalDatabase" @@ -288,7 +288,7 @@ def get_object_type( def get_object_info( object_ref: str, auth_token: str, - kb_env: str = "appdev" + kb_env: str = settings.KB_ENV ) -> dict[str, Any]: client = KBaseClient(auth_token, kb_env) return client.get_object(object_ref) @@ -298,7 +298,7 @@ def download_db( berdl_table_id: str, auth_token: str, cache_dir: Path, - kb_env: str = "appdev" + kb_env: str = settings.KB_ENV ) -> Path: cache_dir = Path(cache_dir) db_dir = get_upa_cache_path(cache_dir, berdl_table_id) @@ -339,7 +339,7 @@ def download_multi_dbs( berdl_table_id: str, auth_token: str, cache_dir: Path, - kb_env: str = "appdev" + kb_env: str = settings.KB_ENV ) -> list[dict]: cache_dir = Path(cache_dir) base_dir = get_upa_cache_path(cache_dir, berdl_table_id) @@ -401,7 +401,7 @@ def download_db_multi( db_name: str, auth_token: str, cache_dir: Path, - kb_env: str = "appdev" + kb_env: str = settings.KB_ENV ) -> dict[str, Any]: cache_dir = Path(cache_dir) base_dir = get_upa_cache_path(cache_dir, berdl_table_id)