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from phi.assistant import Assistant | ||
from phi.tools.pubmed import Pubmed | ||
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assistant = Assistant(tools=[Pubmed()], debug_mode=True, show_tool_calls=True) | ||
assistant.print_response( | ||
"ulcerative colitis.", | ||
markdown=True, | ||
) |
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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 | ||
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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 | ||
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self.register(self.search_pubmed) | ||
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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] | ||
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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) | ||
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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 | ||
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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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