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| import logging | |
| import os | |
| import sentry_sdk | |
| from dotenv import load_dotenv | |
| load_dotenv() | |
| from fastapi import FastAPI, HTTPException, Request | |
| from fastapi.middleware.cors import CORSMiddleware | |
| from fastapi.responses import JSONResponse | |
| from slowapi import Limiter, _rate_limit_exceeded_handler | |
| from slowapi.util import get_remote_address | |
| from slowapi.errors import RateLimitExceeded | |
| from app.config import settings | |
| from app.routers import pipelines, pipeline_v2, ai, jobs, share, profile, sequences, uniprot, alignment, structures, pathways, domains, interactions, primers, structure_analysis, phylo, export, api_keys, cache_stats, docking | |
| from app.services.cache import init_redis | |
| logger = logging.getLogger(__name__) | |
| limiter = Limiter(key_func=get_remote_address, default_limits=["30/minute"]) | |
| app = FastAPI(title="Bio Nexus API", version="0.2.0") | |
| app.state.limiter = limiter | |
| app.add_exception_handler(RateLimitExceeded, _rate_limit_exceeded_handler) | |
| PROD_ORIGIN = settings.CORS_ORIGIN | |
| app.add_middleware( | |
| CORSMiddleware, | |
| allow_origins=[ | |
| "http://localhost:3000", | |
| "http://localhost:3001", | |
| PROD_ORIGIN, | |
| "https://bioai-platform.vercel.app", | |
| ], | |
| allow_credentials=True, | |
| allow_methods=["*"], | |
| allow_headers=["*"], | |
| ) | |
| app.include_router(pipelines.router, prefix="/api/pipelines", tags=["pipelines"]) | |
| app.include_router(pipeline_v2.router, prefix="/api/pipeline/v2", tags=["pipeline_v2"]) | |
| app.include_router(ai.router, prefix="/api/ai", tags=["ai"]) | |
| app.include_router(jobs.router, prefix="/api/jobs", tags=["jobs"]) | |
| app.include_router(share.router, prefix="/api/share", tags=["share"]) | |
| app.include_router(profile.router, prefix="/api/profile", tags=["profile"]) | |
| app.include_router(sequences.router, prefix="/api/sequences", tags=["sequences"]) | |
| app.include_router(uniprot.router, prefix="/api/uniprot", tags=["uniprot"]) | |
| app.include_router(alignment.router, prefix="/api/alignment", tags=["alignment"]) | |
| app.include_router(structures.router, prefix="/api/structures", tags=["structures"]) | |
| app.include_router(pathways.router, prefix="/api/pathways", tags=["pathways"]) | |
| app.include_router(domains.router) | |
| app.include_router(interactions.router) | |
| app.include_router(primers.router) | |
| app.include_router(structure_analysis.router) | |
| app.include_router(phylo.router) | |
| app.include_router(export.router, prefix="/api/export", tags=["export"]) | |
| app.include_router(api_keys.router, prefix="/api/keys", tags=["api_keys"]) | |
| app.include_router(cache_stats.router) | |
| app.include_router(docking.router) | |
| TERMINAL_STATUSES = {"complete", "failed"} | |
| NON_TERMINAL_STATUSES = { | |
| "submitted_to_ncbi", "polling_ncbi", "parsing", | |
| "fetching_uniprot", "fetching_alphafold", "interpreting", | |
| } | |
| async def _fail_stuck_jobs(): | |
| try: | |
| import httpx | |
| from app.config import settings | |
| headers = { | |
| "apikey": settings.SUPABASE_SERVICE_ROLE_KEY, | |
| "Authorization": f"Bearer {settings.SUPABASE_SERVICE_ROLE_KEY}", | |
| "Content-Type": "application/json", | |
| "Prefer": "return=minimal", | |
| } | |
| url = f"{settings.SUPABASE_URL}/rest/v1/jobs" | |
| quoted = ",".join(f'"{s}"' for s in NON_TERMINAL_STATUSES) | |
| select_url = f"{url}?select=id&status=in.({quoted})" | |
| async with httpx.AsyncClient(timeout=10) as client: | |
| resp = await client.get(select_url, headers=headers) | |
| if resp.status_code != 200: | |
| logger.warning(f"Startup resume: failed to query jobs ({resp.status_code})") | |
| return | |
| stuck = resp.json() | |
| for job in stuck: | |
| jid = job["id"] | |
| logger.info(f"Startup resume: marking stuck job {jid} as failed") | |
| await client.patch( | |
| f"{url}?id=eq.{jid}", | |
| headers=headers, | |
| json={"status": "failed", "error": "Worker lost on restart — please re-run"}, | |
| ) | |
| if stuck: | |
| logger.info(f"Startup resume: marked {len(stuck)} stuck job(s) as failed") | |
| except Exception as e: | |
| logger.warning(f"Startup resume: error: {e}") | |
| async def startup(): | |
| sentry_sdk.init( | |
| dsn=settings.SENTRY_DSN, | |
| environment=os.getenv("ENVIRONMENT", "development"), | |
| traces_sample_rate=0.1, | |
| ) | |
| init_redis() | |
| await _fail_stuck_jobs() | |
| async def health(): | |
| from app.services.cache import get_cache_stats | |
| stats = get_cache_stats() | |
| return {"status": "ok", "cache": stats} | |
| async def global_exception_handler(request: Request, exc: Exception): | |
| if isinstance(exc, HTTPException): | |
| return JSONResponse(status_code=exc.status_code, content={"detail": exc.detail}) | |
| logger.exception("Unhandled exception") | |
| return JSONResponse( | |
| status_code=500, | |
| content={"detail": "Internal server error"}, | |
| ) | |