Upload 5 files
Browse files- src/api/admin.py +0 -0
- src/api/agent.py +57 -47
- src/api/feedback.py +8 -3
- src/api/search.py +188 -176
src/api/admin.py
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src/api/agent.py
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@@ -1,52 +1,62 @@
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"""Authenticated agent endpoint; Cloudflare is the only intended caller."""
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import html
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import
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import
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from src.agentcore.
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from src.agentcore.
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from src.services.html_sanitizer import sanitize_answer_html
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async def agent_query(request: Request, req: AgentRequest):
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start_time = time.time()
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question = _normalize_whitespace(req.question)
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response
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return
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"""Authenticated agent endpoint; Cloudflare is the only intended caller."""
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import html
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import re
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import time
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import uuid
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from fastapi import APIRouter, HTTPException, Request
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from src.agentcore.models import AgentRequest, AgentResponse
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from src.agentcore.orchestrator import _agent_query_inner, _log_agent_query
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from src.agentcore.utils import _get_runtime_config, _normalize_whitespace, _safe_metrics_increment, _sanitize_llm_response
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from src.services.html_sanitizer import sanitize_answer_html
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from src.config import get_settings
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router = APIRouter()
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@router.post("", response_model=AgentResponse)
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async def agent_query(request: Request, req: AgentRequest):
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start_time = time.time()
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settings = get_settings()
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if (len(req.question) > settings.max_question_chars or
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len(req.history) > settings.max_history_messages or
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any(len(message.content) > settings.max_message_chars for message in req.history)):
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raise HTTPException(status_code=422, detail="Question or history exceeds the configured text limit.")
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supplied_id = request.headers.get("x-request-id", "")
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request_id = supplied_id if re.fullmatch(r"[A-Za-z0-9_-]{8,80}", supplied_id) else str(uuid.uuid4())
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question = _normalize_whitespace(req.question)
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if not question:
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raise HTTPException(status_code=422, detail="Question must contain text.")
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history = list(req.history)
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if history and history[-1].role == "user" and _normalize_whitespace(history[-1].content) == question:
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history.pop()
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is_canary = request.headers.get("x-libbee-canary") == "1"
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if not is_canary:
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_safe_metrics_increment("agent_requests")
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response = await _agent_query_inner(question, history, req.model, req.client_state, start_time)
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response.request_id = request_id
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response.answer = _sanitize_llm_response(response.answer)
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runtime_config = _get_runtime_config()
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announcement = str(runtime_config.get("announcement", "")).strip()
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if announcement and response.intent not in {"social_greeting", "social"}:
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response.answer += '<div class="libbee-announcement" role="note"><strong>Announcement:</strong> ' + html.escape(announcement) + "</div>"
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response.answer = sanitize_answer_html(response.answer)
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if not is_canary:
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_log_agent_query(question, response, start_time)
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return response
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@router.get("/test")
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async def test():
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return {"status": "ok"}
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@router.get("/rag-status")
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async def rag_status():
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try:
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from app import get_rag_service
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return get_rag_service().get_stats()
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except Exception:
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return {"ready": False}
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src/api/feedback.py
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@@ -12,9 +12,12 @@ router = APIRouter()
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class FeedbackRequest(BaseModel):
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model_config = ConfigDict(extra="forbid")
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request_id: str = Field(pattern=r"^[A-Za-z0-
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feedback: str
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comment: str = Field(default="", max_length=500)
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@field_validator("feedback")
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@classmethod
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@router.post("")
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async def save_feedback(req: FeedbackRequest):
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settings = get_settings()
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payload = {
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"timestamp": time.time(),
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"request_id": req.request_id,
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"feedback": req.feedback,
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"comment":
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}
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settings.feedback_path.parent.mkdir(parents=True, exist_ok=True)
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with settings.feedback_path.open("a", encoding="utf-8") as handle:
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class FeedbackRequest(BaseModel):
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model_config = ConfigDict(extra="forbid")
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request_id: str = Field(pattern=r"^[A-Za-z0-9_-]{8,80}$")
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feedback: str
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comment: str = Field(default="", max_length=500)
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# The existing LibGuides client sends this field to its Worker. Accept it
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# if forwarded, but do not store it in the local feedback fallback.
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session_id: str | None = Field(default=None, pattern=r"^[A-Za-z0-9_-]{8,80}$")
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@field_validator("feedback")
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@classmethod
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@router.post("")
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async def save_feedback(req: FeedbackRequest):
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settings = get_settings()
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comment = re.sub(r"[\w.+-]+@[\w-]+\.[\w.-]+", "[email]", req.comment)
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comment = re.sub(r"\b\d{6,}\b", "[number]", comment)
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payload = {
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"timestamp": time.time(),
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"request_id": req.request_id,
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"feedback": req.feedback,
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"comment": comment[:500],
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}
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settings.feedback_path.parent.mkdir(parents=True, exist_ok=True)
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with settings.feedback_path.open("a", encoding="utf-8") as handle:
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src/api/search.py
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"""
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Search approach: send the full boolean query as a single q=any,contains,<boolean>
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parameter — exactly how the PRIMO web UI works. This preserves phrase quotes,
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parentheses, AND/OR operators, and gives results identical to the web UI.
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Earlier versions split the boolean into multiple q= params (one per AND group),
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but PRIMO does not reliably handle OR within a single q= value in multi-param mode.
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The correct approach is a single q= with the full boolean, URL-encoded.
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"""
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import re
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import logging
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from typing import Optional
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from fastapi import APIRouter
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from pydantic import BaseModel, ConfigDict, Field
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from urllib.parse import quote
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logger = logging.getLogger(__name__)
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router = APIRouter()
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# ── Models ─────────────────────────────────────────────────────────────────────
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class SearchRequest(BaseModel):
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model_config = ConfigDict(extra="forbid")
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query: str = Field(min_length=1, max_length=1000)
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boolean_query: Optional[str] = Field(default=None, max_length=1500)
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source: str = Field(default="primo", pattern=r"^(primo|pubmed)$")
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limit: int = Field(default=5, ge=1, le=20)
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peer_reviewed: bool = False
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open_access: bool = False
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year_from: Optional[str] = Field(default=None, pattern=r"^
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year_to: Optional[str] = Field(default=None, pattern=r"^
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resource_type: str = Field(default="articles", pattern=r"^(articles|books|both)$")
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# ── PRIMO query builder ────────────────────────────────────────────────────────
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def _boolean_to_primo_params(boolean_query: str) -> str:
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"""
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Sends the full boolean as: q=any,contains,<url-encoded boolean>
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This matches exactly how the PRIMO web UI constructs advanced search URLs.
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Examples:
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'("machine learning" OR "deep learning") AND ("healthcare")'
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→ 'q=any,contains,%28%22machine+learning%22+OR+%22deep+learning%22%29...'
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'"climate change"'
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→ 'q=any,contains,%22climate+change%22'
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"""
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if not boolean_query or not boolean_query.strip():
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return "q=any,contains,library"
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# Send the full boolean as a single q= parameter — PRIMO parses it correctly
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return f"q=any,contains,{quote(boolean_query.strip())}"
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# ── PRIMO helpers ──────────────────────────────────────────────────────────────
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def _build_primo_search_link(title: str, record_id: Optional[str] = None) -> Optional[str]:
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base =
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if record_id:
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return f"{base}/fulldisplay?docid={quote(str(record_id))}&vid=971KUOSTAR_INST:KU"
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clean_title = (title or
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if not clean_title:
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return None
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return (
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f"{base}/search?query=any,contains,{quote(clean_title)}"
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"&tab=Everything&search_scope=MyInst_and_CI&vid=971KUOSTAR_INST:KU&lang=en"
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)
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async def search_primo(req: SearchRequest, api_key: str) -> dict:
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"""
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Search the PRIMO API.
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Prefers req.boolean_query (LLM-built) over req.query for structured results.
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Converts boolean to multi-q-param format for accurate PRIMO results.
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"""
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import httpx
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if not api_key:
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return {"error": "PRIMO_API_KEY not configured", "results": [], "total": 0}
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raw_query = (req.boolean_query or req.query or "").strip()
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has_bool = bool(re.search(r'\b(AND|OR)\b', raw_query)) and '(' in raw_query
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else:
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clean = re.sub(r'["\']', '', raw_query).strip()
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query_params = f"q=any,contains,{quote(clean)}"
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facets = ""
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if req.peer_reviewed:
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facets
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if req.open_access:
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facets
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if req.year_from or req.year_to:
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vid = "971KUOSTAR_INST:KU"
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qs = (
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f"&{query_params}"
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f"
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f"&apikey={api_key}{facets}"
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)
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for region in ["api-eu", "api-na", "api-ap"]:
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url = base.replace("api-eu", region) + qs
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try:
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return {"error": "PRIMO API unavailable", "results": [], "total": 0, "source": "PRIMO"}
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async def search_pubmed(req: SearchRequest) -> dict:
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"""Search PubMed
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import httpx
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base = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"
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yt = req.year_to or str(datetime.now().year)
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query = f"({query}) AND ({yf}:{yt}[dp])"
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try:
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async with httpx.AsyncClient(timeout=
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f"{base}/esearch.fcgi",
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params={
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ids = esearch.get("idlist"
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query_translation = esearch.get("querytranslation", "")
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count = int(esearch.get("count", 0))
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if not ids:
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return {"total":
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f"{base}/esummary.fcgi",
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params={"db": "pubmed", "id": ",".join(ids), "retmode": "json"}
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)
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if
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results = []
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for pid in ids:
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if not isinstance(
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continue
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authors_list =
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authors = ", ".join(
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if len(authors_list) > 3:
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authors += " et al."
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results.append({
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"title":
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"creator": authors,
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"date":
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"source":
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"doi": doi,
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"pmid": pid,
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"link": f"https://pubmed.ncbi.nlm.nih.gov/{pid}/",
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"type": "
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"_source": "PubMed",
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})
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except Exception as e:
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return {"error": f"PubMed: {str(e)}", "results": [], "source": "PubMed"}
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-
# ── FastAPI endpoint ───────────────────────────────────────────────────────────
|
| 244 |
|
| 245 |
@router.post("")
|
| 246 |
async def search_endpoint(req: SearchRequest):
|
| 247 |
-
"""
|
| 248 |
-
Search PRIMO or PubMed.
|
| 249 |
-
Accepts boolean_query (preferred, LLM-built) or falls back to query.
|
| 250 |
-
"""
|
| 251 |
from src.config import get_settings
|
| 252 |
-
settings = get_settings()
|
| 253 |
|
| 254 |
-
|
| 255 |
-
|
| 256 |
-
if source == "pubmed":
|
| 257 |
return await search_pubmed(req)
|
| 258 |
-
|
| 259 |
-
return await search_primo(req, settings.primo_api_key)
|
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|
| 1 |
+
"""PRIMO and PubMed search, with explicit filters and bounded upstream waits."""
|
| 2 |
+
import asyncio
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|
| 3 |
import logging
|
| 4 |
+
import re
|
| 5 |
from typing import Optional
|
| 6 |
+
from urllib.parse import quote
|
| 7 |
|
| 8 |
from fastapi import APIRouter
|
| 9 |
+
from pydantic import BaseModel, ConfigDict, Field, model_validator
|
|
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|
| 10 |
|
| 11 |
logger = logging.getLogger(__name__)
|
| 12 |
router = APIRouter()
|
| 13 |
+
PRIMO_REQUEST_TIMEOUT = 5.0
|
| 14 |
+
PUBMED_REQUEST_TIMEOUT = 8.0
|
| 15 |
|
| 16 |
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|
| 17 |
class SearchRequest(BaseModel):
|
| 18 |
+
model_config = ConfigDict(extra="forbid", str_strip_whitespace=True)
|
| 19 |
query: str = Field(min_length=1, max_length=1000)
|
| 20 |
boolean_query: Optional[str] = Field(default=None, max_length=1500)
|
| 21 |
source: str = Field(default="primo", pattern=r"^(primo|pubmed)$")
|
| 22 |
limit: int = Field(default=5, ge=1, le=20)
|
| 23 |
peer_reviewed: bool = False
|
| 24 |
open_access: bool = False
|
| 25 |
+
year_from: Optional[str] = Field(default=None, pattern=r"^[0-9]{4}$")
|
| 26 |
+
year_to: Optional[str] = Field(default=None, pattern=r"^[0-9]{4}$")
|
| 27 |
resource_type: str = Field(default="articles", pattern=r"^(articles|books|both)$")
|
| 28 |
|
| 29 |
+
@model_validator(mode="after")
|
| 30 |
+
def validate_search(self):
|
| 31 |
+
self.boolean_query = self.boolean_query or None
|
| 32 |
+
for year in (self.year_from, self.year_to):
|
| 33 |
+
if year == "0000":
|
| 34 |
+
raise ValueError("Publication years must be between 0001 and 9999")
|
| 35 |
+
if self.year_from and self.year_to and self.year_from > self.year_to:
|
| 36 |
+
raise ValueError("year_from must not be later than year_to")
|
| 37 |
+
# Primo reserves semicolons for additional field clauses, even when
|
| 38 |
+
# percent-encoded; accepting one here changes the meaning of a query.
|
| 39 |
+
if self.source == "primo" and ";" in (self.boolean_query or self.query):
|
| 40 |
+
raise ValueError("PRIMO search terms cannot contain semicolons")
|
| 41 |
+
return self
|
| 42 |
|
|
|
|
| 43 |
|
| 44 |
def _boolean_to_primo_params(boolean_query: str) -> str:
|
| 45 |
+
"""Preserve exact phrases and all Boolean operators in one Primo q value."""
|
| 46 |
+
return f"q=any,contains,{quote(boolean_query.strip(), safe='')}"
|
|
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|
| 47 |
|
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|
| 48 |
|
| 49 |
+
def _year_bounds(req: SearchRequest) -> tuple[str, str]:
|
| 50 |
+
"""Represent an omitted bound without silently excluding older/future works."""
|
| 51 |
+
return req.year_from or "0001", req.year_to or "9999"
|
|
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|
| 52 |
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|
| 53 |
|
| 54 |
def _build_primo_search_link(title: str, record_id: Optional[str] = None) -> Optional[str]:
|
| 55 |
+
base = "https://khalifa.primo.exlibrisgroup.com/discovery"
|
| 56 |
if record_id:
|
| 57 |
+
return f"{base}/fulldisplay?docid={quote(str(record_id), safe='')}&vid=971KUOSTAR_INST:KU"
|
| 58 |
+
clean_title = (title or "").strip()
|
| 59 |
if not clean_title:
|
| 60 |
return None
|
| 61 |
return (
|
| 62 |
+
f"{base}/search?query=any,contains,{quote(clean_title, safe='')}"
|
| 63 |
"&tab=Everything&search_scope=MyInst_and_CI&vid=971KUOSTAR_INST:KU&lang=en"
|
| 64 |
)
|
| 65 |
|
| 66 |
|
| 67 |
+
def _first(value, default=""):
|
| 68 |
+
"""PNX values are normally arrays; tolerate scalar/missing metadata."""
|
| 69 |
+
if isinstance(value, list):
|
| 70 |
+
value = value[0] if value else default
|
| 71 |
+
return value if isinstance(value, str) else default
|
| 72 |
+
|
| 73 |
+
|
| 74 |
+
def _result_link(raw_link: str, fallback: Optional[str]) -> Optional[str]:
|
| 75 |
+
# PNX link fields can contain $$U<url>$$D<label>, rather than a bare URL.
|
| 76 |
+
match = re.match(r"(?:\$\$U)?(https?://[^\s]+?)(?:\$\$|$)", raw_link)
|
| 77 |
+
return match.group(1) if match else fallback
|
| 78 |
+
|
| 79 |
+
|
| 80 |
async def search_primo(req: SearchRequest, api_key: str) -> dict:
|
| 81 |
+
"""Search Primo using the full preferred query and documented facet syntax."""
|
|
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|
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|
|
|
|
| 82 |
import httpx
|
| 83 |
|
| 84 |
if not api_key:
|
| 85 |
+
return {"error": "PRIMO_API_KEY not configured", "results": [], "total": 0, "source": "PRIMO"}
|
|
|
|
|
|
|
|
|
|
| 86 |
|
| 87 |
+
query_params = _boolean_to_primo_params(req.boolean_query or req.query)
|
| 88 |
+
facets = []
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 89 |
if req.peer_reviewed:
|
| 90 |
+
facets.append("facet_tlevel,exact,peer_reviewed")
|
| 91 |
if req.open_access:
|
| 92 |
+
facets.append("facet_tlevel,exact,open_access")
|
| 93 |
if req.year_from or req.year_to:
|
| 94 |
+
year_from, year_to = _year_bounds(req)
|
| 95 |
+
facets.append(f"facet_searchcreationdate,exact,[{year_from} TO {year_to}]")
|
| 96 |
+
if req.resource_type != "both":
|
| 97 |
+
facets.append(f"facet_rtype,exact,{req.resource_type}")
|
| 98 |
+
|
| 99 |
+
# qInclude accepts one value, joining ANDed facets with |,|. Repeated
|
| 100 |
+
# qInclude keys are not its documented API contract.
|
| 101 |
+
facet_params = f"&qInclude={quote('|,|'.join(facets), safe='')}" if facets else ""
|
|
|
|
| 102 |
qs = (
|
| 103 |
+
"?vid=971KUOSTAR_INST:KU&tab=Everything&scope=MyInst_and_CI"
|
| 104 |
+
f"&{query_params}&lang=en&sort=rank&limit={req.limit}&offset=0"
|
| 105 |
+
f"{facet_params}"
|
|
|
|
| 106 |
)
|
| 107 |
|
| 108 |
+
async with httpx.AsyncClient(timeout=PRIMO_REQUEST_TIMEOUT) as client:
|
| 109 |
+
for region in ("api-eu", "api-na", "api-ap"):
|
| 110 |
+
url = f"https://{region}.hosted.exlibrisgroup.com/primo/v1/search{qs}"
|
|
|
|
|
|
|
| 111 |
try:
|
| 112 |
+
# httpx read timeouts reset per chunk. wait_for additionally
|
| 113 |
+
# bounds the complete request, including a slowly streamed body.
|
| 114 |
+
response = await asyncio.wait_for(
|
| 115 |
+
client.get(url, headers={"Accept": "application/json", "Authorization": f"apikey {api_key}"}),
|
| 116 |
+
timeout=PRIMO_REQUEST_TIMEOUT,
|
| 117 |
+
)
|
| 118 |
+
if response.status_code != 200:
|
| 119 |
+
logger.warning("PRIMO region %s returned HTTP %s", region, response.status_code)
|
| 120 |
+
if response.status_code == 429:
|
| 121 |
+
return {"error": "PRIMO request limit reached; try again later", "results": [], "total": 0, "source": "PRIMO"}
|
| 122 |
+
if response.status_code == 400:
|
| 123 |
+
return {"error": "PRIMO could not process this search; check the search terms", "results": [], "total": 0, "source": "PRIMO"}
|
| 124 |
+
continue
|
| 125 |
+
data = response.json()
|
| 126 |
+
if not isinstance(data, dict) or not isinstance(data.get("docs"), list):
|
| 127 |
+
raise ValueError("Invalid PRIMO response")
|
| 128 |
+
results = []
|
| 129 |
+
for doc in data.get("docs", []):
|
| 130 |
+
if not isinstance(doc, dict):
|
| 131 |
+
continue
|
| 132 |
+
pnx = doc.get("pnx") or {}
|
| 133 |
+
if not isinstance(pnx, dict):
|
| 134 |
+
continue
|
| 135 |
+
display = pnx.get("display") or {}
|
| 136 |
+
addata = pnx.get("addata") or {}
|
| 137 |
+
search = pnx.get("search") or {}
|
| 138 |
+
control = pnx.get("control") or {}
|
| 139 |
+
links = pnx.get("links") or {}
|
| 140 |
+
record_id = _first(control.get("recordid"), None)
|
| 141 |
+
title = _first(display.get("title"), "Untitled")
|
| 142 |
+
primo_url = _build_primo_search_link(title, record_id)
|
| 143 |
+
creators = display.get("creator") or display.get("contributor") or []
|
| 144 |
+
if isinstance(creators, str):
|
| 145 |
+
creators = [creators]
|
| 146 |
+
raw_link = _first(links.get("openurl") or links.get("linktorsrc"))
|
| 147 |
+
results.append({
|
| 148 |
+
"record_id": record_id,
|
| 149 |
+
"title": title,
|
| 150 |
+
"creator": "; ".join(str(creator) for creator in creators) or "Unknown",
|
| 151 |
+
"date": _first(search.get("creationdate") or addata.get("risdate") or addata.get("date")),
|
| 152 |
+
"type": _first(display.get("type")),
|
| 153 |
+
"source": _first(display.get("source") or addata.get("jtitle")),
|
| 154 |
+
"description": _first(display.get("description"))[:400],
|
| 155 |
+
"doi": _first(addata.get("doi"), None),
|
| 156 |
+
"primo_url": primo_url,
|
| 157 |
+
"link": _result_link(raw_link, primo_url),
|
| 158 |
+
"open_access": _first(display.get("oa")) == "free_for_read",
|
| 159 |
+
"_source": "PRIMO",
|
| 160 |
+
})
|
| 161 |
+
return {"total": (data.get("info") or {}).get("total", 0), "results": results, "source": "PRIMO"}
|
| 162 |
+
except (httpx.HTTPError, TimeoutError, ValueError, TypeError, AttributeError) as exc:
|
| 163 |
+
# Exception strings from HTTP clients can include the full URL,
|
| 164 |
+
# including the API key. Never put them in logs or responses.
|
| 165 |
+
logger.warning("PRIMO region %s failed (%s)", region, type(exc).__name__)
|
| 166 |
|
| 167 |
return {"error": "PRIMO API unavailable", "results": [], "total": 0, "source": "PRIMO"}
|
| 168 |
|
| 169 |
|
| 170 |
+
def _pubmed_query(req: SearchRequest) -> str:
|
| 171 |
+
query = req.boolean_query or req.query
|
| 172 |
+
if req.year_from or req.year_to:
|
| 173 |
+
year_from, year_to = _year_bounds(req)
|
| 174 |
+
query = f"({query}) AND ({year_from}:{year_to}[dp])"
|
| 175 |
+
if req.open_access:
|
| 176 |
+
query = f"({query}) AND free full text[sb]"
|
| 177 |
+
if req.resource_type == "books":
|
| 178 |
+
query = f'({query}) AND "pubmed books"[sb]'
|
| 179 |
+
elif req.resource_type == "articles":
|
| 180 |
+
query = f'({query}) NOT "pubmed books"[sb]'
|
| 181 |
+
return query
|
| 182 |
+
|
| 183 |
|
| 184 |
async def search_pubmed(req: SearchRequest) -> dict:
|
| 185 |
+
"""Search PubMed; free availability does not establish an open-access licence."""
|
| 186 |
import httpx
|
| 187 |
|
| 188 |
base = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"
|
| 189 |
+
warnings = []
|
| 190 |
+
if req.peer_reviewed:
|
| 191 |
+
warnings.append("PubMed has no general peer-reviewed-only filter; peer review must be checked for each record.")
|
| 192 |
+
if req.open_access:
|
| 193 |
+
warnings.append("The PubMed access filter finds free full text; it does not verify an open-access licence.")
|
| 194 |
+
common = {"source": "PubMed", "warnings": warnings}
|
| 195 |
|
| 196 |
+
def failed(message):
|
| 197 |
+
return {**common, "error": message, "results": [], "total": 0}
|
|
|
|
|
|
|
| 198 |
|
| 199 |
try:
|
| 200 |
+
async with httpx.AsyncClient(timeout=PUBMED_REQUEST_TIMEOUT) as client:
|
| 201 |
+
response = await asyncio.wait_for(client.get(
|
| 202 |
f"{base}/esearch.fcgi",
|
| 203 |
+
params={"db": "pubmed", "term": _pubmed_query(req), "retmax": req.limit,
|
| 204 |
+
"retmode": "json", "sort": "relevance"},
|
| 205 |
+
), timeout=PUBMED_REQUEST_TIMEOUT)
|
| 206 |
+
if response.status_code != 200:
|
| 207 |
+
return failed("PubMed search failed")
|
| 208 |
+
payload = response.json()
|
| 209 |
+
esearch = payload.get("esearchresult", {})
|
| 210 |
+
if payload.get("error") or esearch.get("ERROR") or esearch.get("errorlist"):
|
| 211 |
+
return failed("PubMed could not process this search; check the search terms")
|
| 212 |
+
ids = esearch.get("idlist")
|
| 213 |
+
if not isinstance(ids, list):
|
| 214 |
+
return failed("PubMed returned an unreadable search response; try again")
|
| 215 |
query_translation = esearch.get("querytranslation", "")
|
| 216 |
count = int(esearch.get("count", 0))
|
| 217 |
if not ids:
|
| 218 |
+
return {**common, "total": count, "results": [], "query_translation": query_translation}
|
| 219 |
|
| 220 |
+
summary = await asyncio.wait_for(client.get(
|
| 221 |
f"{base}/esummary.fcgi",
|
| 222 |
+
params={"db": "pubmed", "id": ",".join(ids), "retmode": "json"},
|
| 223 |
+
), timeout=PUBMED_REQUEST_TIMEOUT)
|
| 224 |
+
if summary.status_code != 200:
|
| 225 |
+
return failed("PubMed fetch failed")
|
| 226 |
+
summary_payload = summary.json()
|
| 227 |
+
if summary_payload.get("error"):
|
| 228 |
+
return failed("PubMed fetch failed")
|
| 229 |
+
data = summary_payload.get("result", {})
|
| 230 |
results = []
|
| 231 |
for pid in ids:
|
| 232 |
+
record = data.get(pid)
|
| 233 |
+
if not isinstance(record, dict) or record.get("error"):
|
| 234 |
continue
|
| 235 |
+
authors_list = record.get("authors") or []
|
| 236 |
+
authors = ", ".join(author.get("name", "") for author in authors_list[:3])
|
| 237 |
if len(authors_list) > 3:
|
| 238 |
authors += " et al."
|
| 239 |
+
doi = next((article.get("value") for article in record.get("articleids", [])
|
| 240 |
+
if article.get("idtype") == "doi"), None)
|
| 241 |
+
if not doi:
|
| 242 |
+
match = re.search(r"\bdoi:\s*(\S+)", record.get("elocationid", ""), re.IGNORECASE)
|
| 243 |
+
doi = match.group(1) if match else None
|
| 244 |
results.append({
|
| 245 |
+
"title": record.get("title", ""),
|
| 246 |
"creator": authors,
|
| 247 |
+
"date": record.get("pubdate", ""),
|
| 248 |
+
"source": record.get("fulljournalname", record.get("source", "")),
|
| 249 |
"doi": doi,
|
| 250 |
"pmid": pid,
|
| 251 |
"link": f"https://pubmed.ncbi.nlm.nih.gov/{pid}/",
|
| 252 |
+
"type": "; ".join(record.get("pubtype") or []) or "PubMed record",
|
| 253 |
+
"free_full_text": True if req.open_access else None,
|
| 254 |
"_source": "PubMed",
|
| 255 |
})
|
| 256 |
+
if ids and not results:
|
| 257 |
+
return failed("PubMed returned no readable record details; try again")
|
| 258 |
+
return {**common, "total": count, "results": results, "query_translation": query_translation}
|
| 259 |
+
except (httpx.HTTPError, TimeoutError, ValueError, TypeError, AttributeError) as exc:
|
| 260 |
+
logger.warning("PubMed search failed (%s)", type(exc).__name__)
|
| 261 |
+
return failed("PubMed is temporarily unavailable; try again")
|
| 262 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 263 |
|
| 264 |
@router.post("")
|
| 265 |
async def search_endpoint(req: SearchRequest):
|
| 266 |
+
"""Search PRIMO or PubMed, preferring boolean_query when supplied."""
|
|
|
|
|
|
|
|
|
|
| 267 |
from src.config import get_settings
|
|
|
|
| 268 |
|
| 269 |
+
if req.source == "pubmed":
|
|
|
|
|
|
|
| 270 |
return await search_pubmed(req)
|
| 271 |
+
return await search_primo(req, get_settings().primo_api_key)
|
|
|