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| from fastapi import APIRouter, HTTPException, Depends, Request | |
| from pydantic import BaseModel | |
| from app.services.validators import validate_fasta | |
| from app.pipeline.definitions.protein_analysis import get_pipeline_definition | |
| from app.services.supabase import get_supabase | |
| from app.services.rate_limit import check_daily_limit, check_daily_limit_pipelines | |
| from app.services.auth import get_user_id | |
| from app.models.responses import PipelineRunResponse, PipelineDefinitionResponse | |
| from app.deps import limiter | |
| from datetime import datetime, timezone | |
| import uuid | |
| router = APIRouter() | |
| class PipelineRunRequest(BaseModel): | |
| sequence: str | |
| pipeline_type: str = "protein_analysis" | |
| database: str = "" | |
| program: str = "" | |
| max_hits: int = 100 | |
| query_accession: str = "" | |
| fast_mode: bool = False | |
| async def run_pipeline(request: Request, req: PipelineRunRequest, user_id: str | None = Depends(get_user_id)): | |
| validation = validate_fasta(req.sequence, "blast") | |
| if not validation.valid: | |
| raise HTTPException(status_code=400, detail=validation.error) | |
| seq = str(validation.sequences[0].seq).upper() | |
| clean = "".join(c for c in seq if c.isalpha()) | |
| job_id = str(uuid.uuid4()) | |
| supabase = get_supabase() | |
| supabase.table("jobs").insert({ | |
| "id": job_id, | |
| "user_id": user_id, | |
| "tool": "pipeline", | |
| "query_preview": clean, | |
| "status": "queued", | |
| "pipeline_type": req.pipeline_type, | |
| "steps_completed": [], | |
| "context_json": { | |
| "sequence": clean, | |
| "fast_mode": req.fast_mode, | |
| "database": req.database, | |
| "program": req.program, | |
| "max_hits": req.max_hits, | |
| "query_accession": req.query_accession, | |
| }, | |
| "progress_pct": 0, | |
| "created_at": datetime.now(timezone.utc).isoformat(), | |
| "completed_at": None, | |
| "error": None, | |
| "share_token": None, | |
| }).execute() | |
| return {"job_id": job_id, "status": "queued"} | |
| async def list_pipeline_definitions(): | |
| return {"pipelines": [get_pipeline_definition()]} | |
| async def get_pipeline_definition_endpoint(pipeline_type: str): | |
| if pipeline_type == "protein_analysis": | |
| return get_pipeline_definition() | |
| raise HTTPException(status_code=404, detail=f"Unknown pipeline: {pipeline_type}") | |