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"""Europe PMC search tool - replaces BioRxiv.""" |
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from typing import Any |
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import httpx |
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from tenacity import retry, stop_after_attempt, wait_exponential |
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from src.utils.exceptions import SearchError |
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from src.utils.models import Citation, Evidence |
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class EuropePMCTool: |
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""" |
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Search Europe PMC for papers and preprints. |
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Europe PMC indexes: |
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- PubMed/MEDLINE articles |
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- PMC full-text articles |
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- Preprints from bioRxiv, medRxiv, ChemRxiv, etc. |
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- Patents and clinical guidelines |
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API Docs: https://europepmc.org/RestfulWebService |
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""" |
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BASE_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/search" |
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@property |
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def name(self) -> str: |
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return "europepmc" |
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@retry( |
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stop=stop_after_attempt(3), |
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wait=wait_exponential(multiplier=1, min=1, max=10), |
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reraise=True, |
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) |
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async def search(self, query: str, max_results: int = 10) -> list[Evidence]: |
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""" |
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Search Europe PMC for papers matching query. |
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Args: |
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query: Search keywords |
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max_results: Maximum results to return |
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Returns: |
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List of Evidence objects |
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""" |
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params: dict[str, str | int] = { |
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"query": query, |
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"resultType": "core", |
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"pageSize": min(max_results, 100), |
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"format": "json", |
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} |
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async with httpx.AsyncClient(timeout=30.0) as client: |
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try: |
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response = await client.get(self.BASE_URL, params=params) |
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response.raise_for_status() |
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data = response.json() |
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results = data.get("resultList", {}).get("result", []) |
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return [self._to_evidence(r) for r in results[:max_results]] |
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except httpx.HTTPStatusError as e: |
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raise SearchError(f"Europe PMC API error: {e}") from e |
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except httpx.RequestError as e: |
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raise SearchError(f"Europe PMC connection failed: {e}") from e |
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def _to_evidence(self, result: dict[str, Any]) -> Evidence: |
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"""Convert Europe PMC result to Evidence.""" |
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title = result.get("title", "Untitled") |
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abstract = result.get("abstractText", "No abstract available.") |
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doi = result.get("doi", "") |
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pub_year = result.get("pubYear", "Unknown") |
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author_list = result.get("authorList", {}).get("author", []) |
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authors = [a.get("fullName", "") for a in author_list[:5] if a.get("fullName")] |
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pub_types = result.get("pubTypeList", {}).get("pubType", []) |
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is_preprint = "Preprint" in pub_types |
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source_db = result.get("source", "europepmc") |
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preprint_marker = "[PREPRINT - Not peer-reviewed] " if is_preprint else "" |
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content = f"{preprint_marker}{abstract[:1800]}" |
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if doi: |
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url = f"https://doi.org/{doi}" |
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elif result.get("pmid"): |
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url = f"https://pubmed.ncbi.nlm.nih.gov/{result['pmid']}/" |
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else: |
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url = f"https://europepmc.org/article/{source_db}/{result.get('id', '')}" |
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return Evidence( |
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content=content[:2000], |
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citation=Citation( |
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source="preprint" if is_preprint else "europepmc", |
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title=title[:500], |
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url=url, |
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date=str(pub_year), |
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authors=authors, |
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), |
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relevance=0.75 if is_preprint else 0.9, |
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) |
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