166 lines
5.8 KiB
Python
166 lines
5.8 KiB
Python
#!/usr/bin/env python3
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"""PubMed 生物医学文献搜索。通过 NCBI E-utilities API。"""
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from __future__ import annotations
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import sys
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import xml.etree.ElementTree as ET
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from search_utils import build_parser, get_client, make_item, make_result, print_json
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ESEARCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
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EFETCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
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def search(query: str, limit: int, api_key: str | None = None) -> list[dict]:
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"""执行 PubMed 搜索（两步：esearch 获取 PMID，efetch 获取完整记录含摘要）。"""
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base_params: dict = {"api_key": api_key} if api_key else {}
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# Step 1: esearch 获取 PMID 列表
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with get_client(timeout=30) as client:
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resp = client.get(ESEARCH_URL, params={
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**base_params,
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"db": "pubmed",
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"term": query,
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"retmax": min(limit, 100),
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"retmode": "json",
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"sort": "relevance",
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})
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resp.raise_for_status()
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pmids = resp.json().get("esearchresult", {}).get("idlist", [])
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if not pmids:
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return []
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# Step 2: efetch 获取完整 XML 记录（含摘要）
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with get_client(timeout=30) as client:
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resp = client.get(EFETCH_URL, params={
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**base_params,
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"db": "pubmed",
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"id": ",".join(pmids[:limit]),
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"rettype": "xml",
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"retmode": "xml",
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})
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resp.raise_for_status()
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root = ET.fromstring(resp.text)
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items = []
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for article in root.findall(".//PubmedArticle"):
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medline = article.find("MedlineCitation")
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if medline is None:
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continue
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pmid_elem = medline.find("PMID")
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pmid = pmid_elem.text if pmid_elem is not None else ""
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article_data = medline.find("Article")
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if article_data is None:
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continue
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# 标题
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title_elem = article_data.find("ArticleTitle")
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title = "".join(title_elem.itertext()) if title_elem is not None else ""
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# 摘要（支持结构化摘要，如 BACKGROUND/METHODS/RESULTS/CONCLUSIONS）
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abstract_parts = []
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abstract_elem = article_data.find("Abstract")
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if abstract_elem is not None:
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for ab in abstract_elem.findall("AbstractText"):
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label = ab.get("Label")
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text = "".join(ab.itertext()).strip()
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if label:
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abstract_parts.append(f"{label}: {text}")
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else:
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abstract_parts.append(text)
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abstract = " ".join(abstract_parts)
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# 作者
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authors = []
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author_list = article_data.find("AuthorList")
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if author_list is not None:
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for author in author_list.findall("Author"):
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last = author.findtext("LastName", "")
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fore = author.findtext("ForeName", "")
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name = f"{fore} {last}".strip() if fore else last
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if name:
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authors.append(name)
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# 期刊信息
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journal = article_data.find("Journal")
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journal_name = ""
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pub_date = ""
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volume = ""
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issue = ""
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if journal is not None:
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journal_name = journal.findtext("Title", "") or journal.findtext("ISOAbbreviation", "")
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ji = journal.find("JournalIssue")
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if ji is not None:
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volume = ji.findtext("Volume", "")
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issue = ji.findtext("Issue", "")
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pd = ji.find("PubDate")
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if pd is not None:
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year = pd.findtext("Year", "")
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month = pd.findtext("Month", "")
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day = pd.findtext("Day", "")
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pub_date = " ".join(filter(None, [year, month, day]))
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# 页码
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pages = article_data.findtext(".//MedlinePgn", "")
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# DOI 和 PMC ID（从 ArticleIdList 提取）
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doi = None
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pmc_id = None
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for id_elem in article.findall(".//ArticleId"):
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id_type = id_elem.get("IdType", "")
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if id_type == "doi":
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doi = id_elem.text
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elif id_type == "pmc" and id_elem.text:
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# 规范化：去掉 "PMC" 前缀，只保留数字
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pmc_id = id_elem.text.lstrip("PMCpmc").strip() or id_elem.text
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# MeSH 关键词
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keywords = [kw.text for kw in medline.findall(".//Keyword") if kw.text]
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# 文献类型
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pub_types = [pt.text for pt in article_data.findall(".//PublicationType") if pt.text]
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url = f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/"
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pmc_url = f"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC{pmc_id}/" if pmc_id else None
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items.append(make_item(
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title=title,
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url=url,
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snippet=abstract,
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authors=authors,
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pmid=pmid,
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pmc_id=f"PMC{pmc_id}" if pmc_id else None,
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pmc_url=pmc_url,
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journal=journal_name if journal_name else None,
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pub_date=pub_date if pub_date else None,
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volume=volume if volume else None,
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issue=issue if issue else None,
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pages=pages if pages else None,
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keywords=keywords if keywords else None,
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pub_types=pub_types if pub_types else None,
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doi=doi,
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))
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return items
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def main():
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parser = build_parser("搜索 PubMed 生物医学文献")
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parser.add_argument("--api-key", help="NCBI API Key（可选，限额从 3 req/s 提升至 10 req/s）")
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args = parser.parse_args()
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try:
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items = search(args.query, args.limit, getattr(args, "api_key", None))
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print_json(make_result(True, args.query, "pubmed", items))
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except Exception as e:
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print_json(make_result(False, args.query, "pubmed", [], str(e)))
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sys.exit(1)
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if __name__ == "__main__":
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main()
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