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import requests
import json
from bs4 import BeautifulSoup
import logging
# Setup logging
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
def test_pubmed_search():
"""Test PubMed search API"""
base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
search_url = f"{base_url}esearch.fcgi"
# Test query
query = "clinical notes"
search_params = {
"db": "pubmed",
"term": query,
"retmax": 10, # Just get 10 results for testing
"retmode": "json",
"sort": "relevance"
}
logger.info(f"Testing PubMed search with query: {query}")
logger.info(f"Search URL: {search_url}")
logger.info(f"Search params: {search_params}")
try:
response = requests.get(search_url, params=search_params)
response.raise_for_status()
search_results = response.json()
logger.info(f"Response status code: {response.status_code}")
logger.info(f"Response headers: {dict(response.headers)}")
logger.info(f"Search results: {json.dumps(search_results, indent=2)}")
if "esearchresult" in search_results:
id_list = search_results["esearchresult"]["idlist"]
logger.info(f"Found {len(id_list)} article IDs")
# Test fetching one article
if id_list:
test_id = id_list[0]
fetch_url = f"{base_url}efetch.fcgi"
fetch_params = {
"db": "pubmed",
"id": test_id,
"retmode": "xml"
}
logger.info(f"\nTesting article fetch for ID: {test_id}")
logger.info(f"Fetch URL: {fetch_url}")
logger.info(f"Fetch params: {fetch_params}")
response = requests.get(fetch_url, params=fetch_params)
response.raise_for_status()
logger.info(f"Fetch response status code: {response.status_code}")
logger.info(f"Fetch response headers: {dict(response.headers)}")
logger.info(f"First 500 chars of response: {response.text[:500]}")
soup = BeautifulSoup(response.text, 'lxml')
article = soup.find('PubmedArticle')
if article:
logger.info("\nArticle structure:")
logger.info(f"Title: {article.find('ArticleTitle').get_text() if article.find('ArticleTitle') else 'Not found'}")
logger.info(f"Abstract: {article.find('Abstract').get_text()[:200] + '...' if article.find('Abstract') else 'Not found'}")
else:
logger.error("No PubmedArticle found in response")
except Exception as e:
logger.error(f"Error during test: {str(e)}", exc_info=True)
if __name__ == "__main__":
test_pubmed_search() |