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from typing import Optional, List, Dict, Any
import json
import requests
from xml.etree import ElementTree
from phi.tools import Toolkit
class Pubmed(Toolkit):
def __init__(
self,
email: str = "[email protected]",
max_results: Optional[int] = None,
):
super().__init__(name="pubmed")
self.max_results: Optional[int] = max_results
self.email: str = email
self.register(self.search_pubmed)
def fetch_pubmed_ids(self, query: str, max_results: int, email: str) -> List[str]:
url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
params = {
"db": "pubmed",
"term": query,
"retmax": max_results,
"email": email,
"usehistory": "y",
}
response = requests.get(url, params=params)
root = ElementTree.fromstring(response.content)
return [id_elem.text for id_elem in root.findall(".//Id") if id_elem.text is not None]
def fetch_details(self, pubmed_ids: List[str]) -> ElementTree.Element:
url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
params = {"db": "pubmed", "id": ",".join(pubmed_ids), "retmode": "xml"}
response = requests.get(url, params=params)
return ElementTree.fromstring(response.content)
def parse_details(self, xml_root: ElementTree.Element) -> List[Dict[str, Any]]:
articles = []
for article in xml_root.findall(".//PubmedArticle"):
pub_date = article.find(".//PubDate/Year")
title = article.find(".//ArticleTitle")
abstract = article.find(".//AbstractText")
articles.append(
{
"Published": (pub_date.text if pub_date is not None else "No date available"),
"Title": title.text if title is not None else "No title available",
"Summary": (abstract.text if abstract is not None else "No abstract available"),
}
)
return articles
def search_pubmed(self, query: str, max_results: int = 10) -> str:
"""Use this function to search PubMed for articles.
Args:
query (str): The search query.
max_results (int): The maximum number of results to return.
Returns:
str: A JSON string containing the search results.
"""
try:
ids = self.fetch_pubmed_ids(query, self.max_results or max_results, self.email)
details_root = self.fetch_details(ids)
articles = self.parse_details(details_root)
results = [
f"Published: {article.get('Published')}\nTitle: {article.get('Title')}\nSummary:\n{article.get('Summary')}"
for article in articles
]
return json.dumps(results)
except Exception as e:
return f"Cound not fetch articles. Error: {e}"
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