4394e7d6f9
Tools added: - Wikipedia: search, get article, get full article - News: Hacker News, Reddit, aggregated news search - Finance: stocks (yfinance), crypto (CoinGecko), exchange rates - Medical: PubMed, FDA, disease data, health topics - Weather: current, forecast, air quality (Open-Meteo) - Science: arXiv, Semantic Scholar, DOAJ - Web: DuckDuckGo search, instant answers, page content All tools use completely free APIs with no authentication required.
509 lines
15 KiB
Python
509 lines
15 KiB
Python
"""
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Medical/Health Tool - Search medical literature and health data
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Free sources used:
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- PubMed/NCBI E-utilities API (completely free, no key required for basic use)
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- Disease.sh API (completely free, open disease data)
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- Health.gov API (free government health data)
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- OpenFDA API (free FDA data)
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All APIs are free and most don't require authentication.
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"""
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from __future__ import annotations
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import logging
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from datetime import datetime
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from typing import Optional
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import requests
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log = logging.getLogger(__name__)
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# Free medical API endpoints
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PUBMED_EUTILS_API = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"
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DISEASE_API = "https://disease.sh/v3"
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OPENFDA_API = "https://api.fda.gov"
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HEALTH_GOV_API = "https://health.gov"
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def medical_search_pubmed(
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query: str,
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max_results: int = 10,
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) -> dict:
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"""
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Search PubMed for medical/health research articles.
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Args:
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query: Search query (medical terms, diseases, treatments, etc.)
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max_results: Maximum number of results (default: 10)
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Returns:
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Dictionary with PubMed search results
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"""
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try:
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# First, search for article IDs
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search_url = f"{PUBMED_EUTILS_API}/esearch.fcgi"
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search_params = {
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"db": "pubmed",
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"term": query,
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"retmax": max_results,
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"retmode": "json",
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"sort": "relevance",
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}
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search_response = requests.get(search_url, params=search_params, timeout=15)
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search_response.raise_for_status()
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search_data = search_response.json()
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id_list = search_data.get("esearchresult", {}).get("idlist", [])
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if not id_list:
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return {
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"success": True,
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"source": "pubmed",
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"query": query,
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"results": [],
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"count": 0,
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"message": "No articles found for this query",
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}
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# Fetch article summaries
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fetch_url = f"{PUBMED_EUTILS_API}/esummary.fcgi"
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fetch_params = {
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"db": "pubmed",
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"id": ",".join(id_list),
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"retmode": "json",
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}
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fetch_response = requests.get(fetch_url, params=fetch_params, timeout=15)
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fetch_response.raise_for_status()
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fetch_data = fetch_response.json()
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results = []
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for article_id in id_list:
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article = fetch_data.get("result", {}).get(article_id, {})
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if article and "error" not in article:
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results.append({
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"pmid": article_id,
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"title": article.get("title", ""),
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"authors": [a.get("name", "") for a in article.get("authors", [])],
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"journal": article.get("fulljournalname", article.get("source", "")),
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"pub_date": article.get("pubdate", ""),
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"doi": article.get("elocationid", ""),
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"url": f"https://pubmed.ncbi.nlm.nih.gov/{article_id}/",
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"abstract_available": "abstract" in article,
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})
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return {
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"success": True,
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"source": "pubmed",
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"query": query,
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"results": results,
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"count": len(results),
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"total_found": int(search_data.get("esearchresult", {}).get("count", 0)),
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}
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except Exception as e:
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log.error(f"PubMed search failed: {e}")
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return {
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"success": False,
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"error": str(e),
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"source": "pubmed",
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}
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def medical_get_pubmed_abstract(
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pmid: str,
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) -> dict:
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"""
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Get the abstract of a PubMed article.
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Args:
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pmid: PubMed ID
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Returns:
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Dictionary with article abstract
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"""
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try:
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fetch_url = f"{PUBMED_EUTILS_API}/efetch.fcgi"
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params = {
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"db": "pubmed",
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"id": pmid,
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"rettype": "abstract",
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"retmode": "text",
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}
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response = requests.get(fetch_url, params=params, timeout=15)
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response.raise_for_status()
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abstract_text = response.text.strip()
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return {
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"success": True,
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"source": "pubmed",
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"pmid": pmid,
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"abstract": abstract_text,
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"url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/",
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}
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except Exception as e:
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log.error(f"PubMed abstract fetch failed: {e}")
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return {
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"success": False,
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"error": str(e),
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"source": "pubmed",
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"pmid": pmid,
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}
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def medical_get_disease_data(
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disease: str = "covid",
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) -> dict:
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"""
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Get current disease statistics from Disease.sh API.
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Args:
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disease: Disease type (covid, influenza, or all)
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Returns:
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Dictionary with disease statistics
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"""
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try:
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disease = disease.lower()
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if disease in ["covid", "covid-19", "coronavirus"]:
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url = f"{DISEASE_API}/covid-19/all"
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elif disease in ["influenza", "flu"]:
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url = f"{DISEASE_API}/influenza/cdc"
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elif disease == "all":
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url = f"{DISEASE_API}/all"
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else:
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# Try COVID-19 countries data
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url = f"{DISEASE_API}/covid-19/countries/{disease}"
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response = requests.get(url, timeout=10)
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response.raise_for_status()
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data = response.json()
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return {
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"success": True,
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"source": "disease.sh",
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"disease": disease,
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"data": data,
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"timestamp": datetime.now().isoformat(),
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}
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except Exception as e:
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log.error(f"Disease data fetch failed: {e}")
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return {
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"success": False,
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"error": str(e),
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"source": "disease.sh",
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}
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def medical_get_covid_country(
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country: str = "usa",
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) -> dict:
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"""
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Get COVID-19 statistics for a specific country.
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Args:
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country: Country name or ISO code (e.g., usa, uk, germany, china)
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Returns:
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Dictionary with country COVID-19 data
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"""
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try:
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url = f"{DISEASE_API}/covid-19/countries/{country}"
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response = requests.get(url, timeout=10)
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response.raise_for_status()
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data = response.json()
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return {
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"success": True,
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"source": "disease.sh",
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"country": data.get("country", country),
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"cases": data.get("cases"),
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"today_cases": data.get("todayCases"),
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"deaths": data.get("deaths"),
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"today_deaths": data.get("todayDeaths"),
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"recovered": data.get("recovered"),
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"active": data.get("active"),
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"critical": data.get("critical"),
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"cases_per_million": data.get("casesPerOneMillion"),
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"deaths_per_million": data.get("deathsPerOneMillion"),
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"tests": data.get("tests"),
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"tests_per_million": data.get("testsPerOneMillion"),
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"population": data.get("population"),
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"continent": data.get("continent"),
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"updated": datetime.fromtimestamp(data.get("updated", 0) / 1000).isoformat() if data.get("updated") else None,
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}
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except Exception as e:
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log.error(f"COVID country data fetch failed: {e}")
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return {
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"success": False,
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"error": str(e),
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"source": "disease.sh",
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}
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def medical_search_fda(
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query: str,
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database: str = "drug",
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limit: int = 10,
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) -> dict:
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"""
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Search FDA drug, device, or food databases.
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Args:
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query: Search query
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database: Database to search (drug, device, food, other)
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limit: Maximum results (default: 10)
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Returns:
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Dictionary with FDA search results
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"""
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try:
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# Map database names to FDA endpoints
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db_map = {
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"drug": "drug/label",
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"device": "device/510k",
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"food": "food/enforcement",
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"other": "other/substance",
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}
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endpoint = db_map.get(database.lower(), "drug/label")
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url = f"{OPENFDA_API}/{endpoint}.json"
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params = {
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"search": query,
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"limit": limit,
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}
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response = requests.get(url, params=params, timeout=15)
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response.raise_for_status()
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data = response.json()
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results = []
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for item in data.get("results", []):
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if database.lower() == "drug":
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results.append({
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"brand_name": item.get("openfda", {}).get("brand_name", [""])[0] if item.get("openfda") else "",
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"generic_name": item.get("openfda", {}).get("generic_name", [""])[0] if item.get("openfda") else "",
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"manufacturer": item.get("openfda", {}).get("manufacturer_name", [""])[0] if item.get("openfda") else "",
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"purpose": item.get("purpose", [""])[0] if item.get("purpose") else "",
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"indications": item.get("indications_and_usage", [""])[0][:500] if item.get("indications_and_usage") else "",
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"warnings": item.get("warnings", [""])[0][:500] if item.get("warnings") else "",
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})
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else:
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results.append(item)
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return {
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"success": True,
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"source": "openfda",
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"database": database,
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"query": query,
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"results": results,
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"count": len(results),
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}
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except Exception as e:
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log.error(f"FDA search failed: {e}")
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return {
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"success": False,
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"error": str(e),
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"source": "openfda",
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}
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def medical_get_health_topics(
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topic: Optional[str] = None,
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limit: int = 10,
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) -> dict:
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"""
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Get health topics from Health.gov.
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Args:
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topic: Health topic to search (optional)
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limit: Maximum results (default: 10)
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Returns:
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Dictionary with health topics
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"""
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try:
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url = f"{HEALTH_GOV_API}/myhealthfinder/api/v3/topicsearch.json"
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params = {"lang": "en"}
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if topic:
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params["topic"] = topic
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else:
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params["pageSize"] = limit
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response = requests.get(url, params=params, timeout=10)
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response.raise_for_status()
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data = response.json()
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topics = data.get("Result", {}).get("Resources", {}).get("Resource", [])
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results = []
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for item in topics[:limit]:
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results.append({
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"title": item.get("Title", ""),
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"url": item.get("AccessibleVersion", item.get("MyHealthfinder", "")),
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"image_url": item.get("ImageAltUrl", ""),
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"image_alt": item.get("ImageAltText", ""),
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"categories": item.get("Categories", ""),
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"content": item.get("Sections", {}).get("section", [{}])[0].get("Content", "")[:500] if item.get("Sections") else "",
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})
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return {
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"success": True,
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"source": "health.gov",
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"topic": topic,
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"results": results,
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"count": len(results),
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}
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except Exception as e:
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log.error(f"Health topics fetch failed: {e}")
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return {
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"success": False,
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"error": str(e),
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"source": "health.gov",
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}
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# Tool schemas for OpenAI function calling
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MEDICAL_SEARCH_PUBMED_SCHEMA = {
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"type": "function",
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"function": {
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"name": "medical_search_pubmed",
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"description": "Search PubMed for medical and health research articles. Use for scientific medical literature.",
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"parameters": {
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"type": "object",
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"properties": {
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"query": {
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"type": "string",
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"description": "Medical search query (disease, treatment, drug, symptom)",
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},
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"max_results": {
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"type": "integer",
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"description": "Maximum number of results (default: 10)",
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"default": 10,
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},
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},
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"required": ["query"],
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},
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},
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}
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MEDICAL_GET_PUBMED_ABSTRACT_SCHEMA = {
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"type": "function",
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"function": {
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"name": "medical_get_pubmed_abstract",
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"description": "Get the full abstract of a PubMed article. Use after medical_search_pubmed to get detailed content.",
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"parameters": {
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"type": "object",
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"properties": {
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"pmid": {
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"type": "string",
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"description": "PubMed ID from search results",
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},
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},
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"required": ["pmid"],
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},
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},
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}
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MEDICAL_GET_DISEASE_DATA_SCHEMA = {
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"type": "function",
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"function": {
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"name": "medical_get_disease_data",
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"description": "Get current disease statistics (COVID-19, influenza). Use for outbreak data and statistics.",
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"parameters": {
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"type": "object",
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"properties": {
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"disease": {
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"type": "string",
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"description": "Disease type (covid, influenza, all)",
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"default": "covid",
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},
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},
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"required": [],
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},
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},
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}
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MEDICAL_GET_COVID_COUNTRY_SCHEMA = {
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"type": "function",
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"function": {
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"name": "medical_get_covid_country",
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"description": "Get COVID-19 statistics for a specific country. Use for country-specific pandemic data.",
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"parameters": {
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"type": "object",
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"properties": {
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"country": {
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"type": "string",
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"description": "Country name or ISO code (e.g., usa, uk, germany)",
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},
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},
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"required": [],
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},
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},
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}
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MEDICAL_SEARCH_FDA_SCHEMA = {
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"type": "function",
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"function": {
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"name": "medical_search_fda",
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"description": "Search FDA databases for drug information, device approvals, and food safety. Use for medication info.",
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"parameters": {
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"type": "object",
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"properties": {
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"query": {
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"type": "string",
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"description": "Search query (drug name, ingredient, etc.)",
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},
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"database": {
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"type": "string",
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"description": "Database to search (drug, device, food)",
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"default": "drug",
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"enum": ["drug", "device", "food"],
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},
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"limit": {
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"type": "integer",
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"description": "Maximum results (default: 10)",
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"default": 10,
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},
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},
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"required": ["query"],
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},
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},
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}
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MEDICAL_GET_HEALTH_TOPICS_SCHEMA = {
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"type": "function",
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"function": {
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"name": "medical_get_health_topics",
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"description": "Get health information and topics from Health.gov. Use for general health advice and wellness topics.",
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"parameters": {
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"type": "object",
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"properties": {
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"topic": {
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"type": "string",
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"description": "Health topic to search (optional)",
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},
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"limit": {
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"type": "integer",
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"description": "Maximum results (default: 10)",
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"default": 10,
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},
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},
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"required": [],
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},
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},
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}
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