Spaces:
Sleeping
Sleeping
| # genesis/api_clients/pubmed_api.py | |
| import os | |
| import requests | |
| import html | |
| from xml.etree import ElementTree as ET | |
| PUBMED_BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" | |
| def search_pubmed_literature(query: str, max_results: int = 10): | |
| """ | |
| Search PubMed literature using NCBI E-utilities API. | |
| Args: | |
| query (str): Search query (e.g. "synthetic biology cancer therapy") | |
| max_results (int): Maximum number of results to return. | |
| Returns: | |
| list[dict]: Each dict has 'title', 'authors', 'link' | |
| """ | |
| if not query.strip(): | |
| return [] | |
| api_key = os.getenv("PUBMED_API_KEY") # optional | |
| params = { | |
| "db": "pubmed", | |
| "term": query, | |
| "retmax": max_results, | |
| "retmode": "xml" | |
| } | |
| if api_key: | |
| params["api_key"] = api_key | |
| try: | |
| # Step 1: Search for IDs | |
| search_url = f"{PUBMED_BASE}/esearch.fcgi" | |
| search_res = requests.get(search_url, params=params, timeout=10) | |
| search_res.raise_for_status() | |
| root = ET.fromstring(search_res.text) | |
| ids = [id_elem.text for id_elem in root.findall(".//Id")] | |
| if not ids: | |
| return [] | |
| # Step 2: Fetch article details | |
| fetch_url = f"{PUBMED_BASE}/efetch.fcgi" | |
| fetch_params = { | |
| "db": "pubmed", | |
| "id": ",".join(ids), | |
| "retmode": "xml" | |
| } | |
| if api_key: | |
| fetch_params["api_key"] = api_key | |
| fetch_res = requests.get(fetch_url, params=fetch_params, timeout=10) | |
| fetch_res.raise_for_status() | |
| fetch_root = ET.fromstring(fetch_res.text) | |
| results = [] | |
| for article in fetch_root.findall(".//PubmedArticle"): | |
| title_elem = article.find(".//ArticleTitle") | |
| title = html.unescape(title_elem.text) if title_elem is not None else "No title" | |
| authors = [] | |
| for author in article.findall(".//Author"): | |
| last = author.find("LastName") | |
| fore = author.find("ForeName") | |
| if last is not None and fore is not None: | |
| authors.append(f"{fore.text} {last.text}") | |
| pmid_elem = article.find(".//PMID") | |
| pmid = pmid_elem.text if pmid_elem is not None else "" | |
| link = f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/" if pmid else "" | |
| results.append({ | |
| "title": title, | |
| "authors": ", ".join(authors) if authors else "N/A", | |
| "link": link | |
| }) | |
| return results | |
| except requests.exceptions.RequestException as e: | |
| print(f"[PubMed API Error] {e}") | |
| return [] | |
| except ET.ParseError as e: | |
| print(f"[PubMed Parse Error] {e}") | |
| return [] | |