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Background job executor for bioinformatics pipelines.
For the prototype, uses asyncio.create_task (not Celery) —
sufficient for single-instance. Raw responses are stored
to R2/local before any parsing occurs.
"""
import asyncio
import logging
from typing import Optional
import httpx
from app.config import settings
from app.integrations.ncbi import blast as ncbi_blast
from app.integrations.ncbi.parser import parse_blast_xml
from app.core.storage import store_raw_response, store_result
from app.data.demo_results import get_demo_result
logger = logging.getLogger(__name__)
DEMO_MODE = settings.DEMO_MODE
STEP_STATUSES = [
"submitted_to_ncbi",
"polling_ncbi",
"parsing",
"interpreting",
"pathway_enrichment",
"fetching_alphafold",
"complete",
]
def _supa_headers() -> dict:
return {
"apikey": settings.SUPABASE_SERVICE_ROLE_KEY,
"Authorization": f"Bearer {settings.SUPABASE_SERVICE_ROLE_KEY}",
"Content-Type": "application/json",
"Prefer": "return=minimal",
}
async def _patch_job(job_id: str, payload: dict) -> None:
url = f"{settings.SUPABASE_URL}/rest/v1/jobs?id=eq.{job_id}"
try:
async with httpx.AsyncClient(timeout=10) as client:
resp = await client.patch(url, headers=_supa_headers(), json=payload)
if resp.status_code not in (200, 204):
logger.error(f"[{job_id}] Supabase PATCH {resp.status_code}: {resp.text[:300]}")
except Exception as e:
logger.error(f"[{job_id}] Supabase PATCH exception: {e}")
def _matches_demo(sequence: str) -> Optional[dict]:
from app.data.demo_results import DEMO_SEQUENCES
seq_clean = "".join(c for c in sequence if c.isalpha()).upper()
for key, info in DEMO_SEQUENCES.items():
demo_clean = "".join(c for c in info["sequence"] if c.isalpha()).upper()
if seq_clean == demo_clean:
return info
return None
async def execute_blast_job(job_id: str, sequence: str, database: str = "nr", max_hits: int = 10) -> None:
steps_completed: list[str] = []
async def _set_step(step: str, progress_pct: int) -> None:
steps_completed.append(step)
await _patch_job(job_id, {
"status": step,
"steps_completed": steps_completed,
"progress_pct": progress_pct,
})
logger.info(f"[{job_id}] Step: {step}")
try:
await _set_step("submitted_to_ncbi", 10)
sequence_clean = "".join(c for c in sequence if c.isalpha()).upper()
seq_for_blast = sequence_clean if len(sequence_clean) > 20 else sequence_clean
demo_info = _matches_demo(sequence)
if DEMO_MODE and demo_info:
logger.info(f"[{job_id}] Demo mode: using cached result for {demo_info['name']}")
await _set_step("polling_ncbi", 30)
await asyncio.sleep(1)
await _set_step("parsing", 50)
demo_result = get_demo_result(sequence)
parsed = demo_result if demo_result else {"error": "Demo result not found", "hits": []}
await _set_step("interpreting", 70)
else:
if DEMO_MODE:
demo_label = _matches_demo(sequence)
if not demo_label:
logger.info(f"[{job_id}] Demo mode ON but sequence doesn't match known demo sequences — falling through to real NCBI call")
await _set_step("polling_ncbi", 30)
submit_result = await ncbi_blast.submit_blast(seq_for_blast, database=database)
if "error" in submit_result:
raise RuntimeError(f"NCBI submission failed: {submit_result['error']}")
rid = submit_result["rid"]
poll_interval = min(submit_result["estimated_seconds"] / 2, 15)
max_polls = 40
await _patch_job(job_id, {
"context_json": {"ncbi_rid": rid, "poll_interval": poll_interval},
})
for attempt in range(max_polls):
await asyncio.sleep(poll_interval)
status_result = await ncbi_blast.check_status(rid)
status = status_result["status"]
if status == "READY":
break
if status in ("ERROR", "FAILED"):
raise RuntimeError(f"NCBI BLAST failed with status: {status}")
else:
raise RuntimeError("NCBI BLAST timed out")
await _set_step("parsing", 50)
results = await ncbi_blast.fetch_results(rid)
if "error" in results:
raise RuntimeError(f"NCBI fetch failed: {results['error']}")
raw_xml = results["raw"]
await store_raw_response(job_id, "blast", "ncbi_blast", raw_xml, "xml")
parsed = parse_blast_xml(raw_xml)
if "error" in parsed:
raise RuntimeError(f"BLAST XML parse error: {parsed['error']}")
await _set_step("interpreting", 70)
await store_result(job_id, "blast_hits", parsed, "json")
top_hit = parsed["hits"][0] if parsed.get("hits") else None
context = {
"query": {
"sequence": sequence,
"length": len(sequence_clean),
},
"blast": {
"count": len(parsed.get("hits", [])),
"source": "demo" if (DEMO_MODE and demo_info) else "ncbi",
"database": parsed.get("database", "nr"),
"top_hit": {
"accession": top_hit["accession"],
"description": top_hit["description"],
"evalue": top_hit["evalue"],
"evalue_raw": top_hit.get("evalue_raw", str(top_hit["evalue"])),
"identity_pct": top_hit["identity_pct"],
"bit_score": top_hit["bit_score"],
"alignment_length": top_hit.get("alignment_length", 0),
} if top_hit else None,
"hits": [
{
"accession": h["accession"],
"description": h["description"],
"evalue": h["evalue"],
"evalue_raw": h.get("evalue_raw", str(h["evalue"])),
"identity_pct": h["identity_pct"],
"bit_score": h["bit_score"],
}
for h in parsed.get("hits", [])[:max_hits]
],
},
}
if top_hit:
try:
from app.tools.uniprot import UniprotTool
from app.services.sequence_utils import map_refseq_to_uniprot, detect_source_from_accession
uniprot = UniprotTool()
accession = demo_info.get("uniprot_accession", top_hit["accession"]) if (DEMO_MODE and demo_info) else top_hit["accession"]
source = detect_source_from_accession(accession)
if source == "ncbi":
mapped = await map_refseq_to_uniprot(accession)
if mapped:
logger.info(f"[{job_id}] Mapped RefSeq {accession} -> UniProt {mapped}")
accession = mapped
uniprot_result = await uniprot.run({"accession": accession})
if "error" not in uniprot_result:
context["uniprot"] = {
"accession": uniprot_result.get("accession", ""),
"full_name": uniprot_result.get("full_name", ""),
"organism": uniprot_result.get("organism", ""),
"gene_names": uniprot_result.get("gene_names", []),
"functions": uniprot_result.get("functions", []),
"keywords": uniprot_result.get("keywords", []),
"subcellular_locations": uniprot_result.get("subcellular_locations", []),
"pdb_ids": uniprot_result.get("pdb_ids", []),
"features": [
f for f in (uniprot_result.get("features", []) or [])
if f.get("type") in ("ACTIVE_SITE", "BINDING", "MUTAGENESIS")
],
"go_terms": uniprot_result.get("go_terms", []),
"sequence_length": uniprot_result.get("sequence_length", 0),
}
except Exception as e:
logger.warning(f"[{job_id}] UniProt fetch failed (non-fatal): {e}")
pathway_enrichment_result = None
try:
gene_names = []
if context.get("uniprot", {}).get("gene_names"):
gene_names = context["uniprot"]["gene_names"][:20]
if not gene_names:
for hit in parsed.get("hits", [])[:10]:
words = (hit.get("description", "") or "").replace("(", " ").replace(")", " ").split()
for w in words:
if w.isupper() and len(w) >= 2 and not w.startswith("OS="):
gene_names.append(w)
break
if gene_names:
from app.services.pathway_enrichment import run_enrichment
pathway_enrichment_result = await run_enrichment(gene_names)
if pathway_enrichment_result:
logger.info(f"[{job_id}] Pathway enrichment found {len(pathway_enrichment_result['pathways'])} pathways")
except Exception as e:
logger.warning(f"[{job_id}] Pathway enrichment failed (non-fatal): {e}")
context["pathway_enrichment"] = pathway_enrichment_result
if pathway_enrichment_result:
await _set_step("pathway_enrichment", 80)
else:
logger.info(f"[{job_id}] Skipping pathway_enrichment step (no enrichment data)")
alphafold_data = None
uniprot_id = context.get("uniprot", {}).get("accession")
if uniprot_id:
try:
await _set_step("fetching_alphafold", 85)
from app.tools.alphafold import AlphaFoldTool
af_result = await AlphaFoldTool().run({"uniprot_accession": uniprot_id})
alphafold_data = af_result
except Exception as e:
logger.warning(f"[{job_id}] AlphaFold fetch failed for {uniprot_id}: {e}")
alphafold_data = {"structure_available": False, "message": str(e)}
context["alphafold"] = alphafold_data
await _patch_job(job_id, {
"status": "complete",
"context_json": context,
"steps_completed": steps_completed,
"progress_pct": 100,
})
logger.info(f"[{job_id}] Pipeline complete (demo={DEMO_MODE})")
except Exception as exc:
logger.error(f"[{job_id}] Pipeline failed: {exc}", exc_info=True)
await _patch_job(job_id, {
"status": "failed",
"error": str(exc),
})
async def _set_job_failed(job_id: str, message: str) -> None:
await _patch_job(job_id, {"status": "failed", "error": message})
def run_pipeline_sync(job_id: str, sequence: str, database: str = "nr", max_hits: int = 10) -> None:
loop = asyncio.new_event_loop()
asyncio.set_event_loop(loop)
try:
loop.run_until_complete(execute_blast_job(job_id, sequence, database=database, max_hits=max_hits))
except Exception:
logger.exception(f"[{job_id}] FATAL: unhandled exception in background thread")
try:
loop.run_until_complete(_set_job_failed(job_id, "Internal pipeline error"))
except Exception:
pass
finally:
loop.close()
asyncio.set_event_loop(None)
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