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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}" | |