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57272d3 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 | """PubMed source: NCBI E-utilities esearch + efetch."""
import datetime
import logging
import time
from xml.etree import ElementTree
from ._http import _http
from .base import Capability, PaperSource, RateLimitHint, paper_dict
logger = logging.getLogger(__name__)
_ESEARCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
_EFETCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
def _parse_pubmed_date(pub_date_elem) -> datetime.datetime | None:
if pub_date_elem is None:
return None
year = pub_date_elem.findtext("Year")
month = pub_date_elem.findtext("Month") or "Jan"
day = pub_date_elem.findtext("Day") or "1"
if not year:
return None
for fmt in ("%Y %b %d", "%Y %m %d"):
try:
return datetime.datetime.strptime(f"{year} {month} {day}", fmt)
except ValueError:
continue
try:
return datetime.datetime(int(year), 1, 1)
except (ValueError, TypeError):
return None
def _parse_pubmed_article(article) -> dict | None:
"""Parse a `<PubmedArticle>` element into the standard paper dict."""
try:
medline = article.find("MedlineCitation")
if medline is None:
return None
pmid = medline.findtext("PMID") or ""
article_elem = medline.find("Article")
if article_elem is None:
return None
title = (article_elem.findtext("ArticleTitle") or "").strip()
if not title or not pmid:
return None
abstract_parts = article_elem.findall(".//AbstractText")
abstract = " ".join(
(e.text or "") for e in abstract_parts if e.text
).strip() or None
author_list = article_elem.findall(".//Author")
author_names = []
for a in author_list:
last = a.findtext("LastName") or ""
first = a.findtext("ForeName") or ""
if last:
author_names.append(f"{last} {first}".strip())
authors = ", ".join(author_names) if author_names else None
pub_date_elem = article_elem.find(".//Journal/JournalIssue/PubDate")
mesh = medline.findall(".//MeshHeading/DescriptorName")
topics = [m.text for m in mesh if m.text][:10]
doi = None
for id_elem in article.findall(".//ArticleIdList/ArticleId"):
if id_elem.get("IdType") == "doi":
doi = id_elem.text
break
return paper_dict(
title=title,
abstract=abstract,
authors=authors,
publication_date=_parse_pubmed_date(pub_date_elem),
source="pubmed",
source_id=pmid,
url=f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/",
doi=doi,
topics=topics,
)
except Exception as exc:
logger.warning("Skipping malformed PubMed article: %s", exc)
return None
def fetch_pubmed(query: str = "machine learning", max_results: int = 20) -> list[dict]:
"""Fetch papers from PubMed via NCBI E-utilities."""
search_params = {
"db": "pubmed",
"term": query,
"retmax": max_results,
"retmode": "json",
"sort": "pub_date",
}
try:
resp = _http.get(_ESEARCH_URL, params=search_params, timeout=15)
resp.raise_for_status()
id_list = resp.json().get("esearchresult", {}).get("idlist", [])
except Exception as exc:
logger.warning("PubMed search failed: %s", exc)
return []
if not id_list:
return []
time.sleep(0.4)
fetch_params = {
"db": "pubmed",
"id": ",".join(id_list),
"retmode": "xml",
"rettype": "abstract",
}
try:
resp = _http.get(_EFETCH_URL, params=fetch_params, timeout=30)
resp.raise_for_status()
root = ElementTree.fromstring(resp.content)
except Exception as exc:
logger.warning("PubMed fetch failed: %s", exc)
return []
papers = []
for article in root.findall(".//PubmedArticle"):
parsed = _parse_pubmed_article(article)
if parsed:
papers.append(parsed)
return papers
def fetch_pubmed_by_id(pmid: str) -> dict | None:
"""Fetch a single PubMed article by its PMID."""
fetch_params = {
"db": "pubmed",
"id": pmid,
"retmode": "xml",
"rettype": "abstract",
}
try:
resp = _http.get(_EFETCH_URL, params=fetch_params, timeout=15)
resp.raise_for_status()
root = ElementTree.fromstring(resp.content)
except Exception as exc:
logger.warning("PubMed get_by_id failed for %s: %s", pmid, exc)
return None
article = root.find(".//PubmedArticle")
if article is None:
return None
return _parse_pubmed_article(article)
class PubmedSource(PaperSource):
"""NCBI PubMed via E-utilities. Search + PMID lookup only."""
name = "pubmed"
def search(
self,
query: str,
max_results: int = 20,
filters: dict | None = None,
) -> list[dict]:
return fetch_pubmed(query=query, max_results=max_results)
def get_by_id(self, identifier: str) -> dict | None:
return fetch_pubmed_by_id(identifier)
def supports(self, capability: Capability) -> bool:
# E-utilities can do elink for refs, but we don't expose that today.
return False
def rate_limit_hint(self) -> RateLimitHint:
return RateLimitHint(
min_interval_seconds=0.34, # 3 req/s without an API key
daily_quota=None,
notes="NCBI E-utilities: 3 req/s without API key, 10 req/s with NCBI_API_KEY",
)
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