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| import httpx | |
| import json | |
| import hashlib | |
| import logging | |
| from app.services.cache import cache_get, cache_set | |
| logger = logging.getLogger(__name__) | |
| ANALYSIS_BASE = "https://reactome.org/AnalysisService" | |
| async def run_enrichment(identifiers: list[str]) -> dict | None: | |
| raw = json.dumps(sorted(identifiers), sort_keys=True) | |
| key_hash = hashlib.sha256(raw.encode()).hexdigest()[:16] | |
| cache_key = f"enrichment:{key_hash}" | |
| cached = cache_get(cache_key) | |
| if cached is not None: | |
| try: | |
| result = json.loads(cached) | |
| if isinstance(result, dict): | |
| result["from_cache"] = True | |
| return result | |
| except (json.JSONDecodeError, TypeError): | |
| pass | |
| try: | |
| body = "\n".join(identifiers) | |
| async with httpx.AsyncClient(timeout=30) as client: | |
| resp = await client.post( | |
| f"{ANALYSIS_BASE}/identifiers/projection", | |
| content=body, | |
| headers={"Content-Type": "text/plain"}, | |
| params={"pageSize": "20", "page": "1"}, | |
| ) | |
| if resp.status_code != 200: | |
| logger.warning(f"Reactome Analysis Service returned {resp.status_code}") | |
| return None | |
| data = resp.json() | |
| token = data.get("summary", {}).get("token", "") | |
| if not token: | |
| logger.warning("No analysis token returned from Reactome") | |
| return None | |
| # The projection response already carries the enriched pathways; | |
| # the separate /token/{token}/pathways call is unnecessary (and | |
| # currently 404s for tokens returned with a trailing %3D). | |
| pathways_data = data | |
| pathways = [] | |
| for item in pathways_data.get("pathways", []): | |
| species = item.get("species", {}) | |
| species_name = ( | |
| species.get("name", "") | |
| if isinstance(species, dict) | |
| else (species or "") | |
| ) | |
| entities = item.get("entities", {}) | |
| found = entities.get("found", 0) | |
| total = entities.get("total", 0) | |
| pathways.append({ | |
| "stId": item.get("stId", ""), | |
| "name": item.get("name", ""), | |
| "species": species_name, | |
| "entitiesFound": found, | |
| "entitiesTotal": total, | |
| "geneRatio": round(found / total, 4) if total else 0.0, | |
| "entitiesFDR": entities.get("fdr", 1.0), | |
| "entitiesPValue": entities.get("pValue", 1.0), | |
| }) | |
| pathways.sort(key=lambda p: p["entitiesFDR"]) | |
| result = { | |
| "token": token, | |
| "pathways": pathways, | |
| } | |
| try: | |
| cache_set(cache_key, json.dumps(result), ttl=86400) | |
| except (TypeError, ValueError): | |
| pass | |
| result["from_cache"] = False | |
| return result | |
| except Exception as e: | |
| logger.warning(f"Pathway enrichment failed: {e}") | |
| return None | |