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from Bio import Entrez
import os # For environment variables and file paths
# ---------------------------- Configuration ----------------------------
# ---------------------------- Helper Functions ----------------------------
def log_error(message: str):
"""Logs an error message to the console and a file (if possible)."""
print(f"ERROR: {message}")
try:
with open("error_log.txt", "a") as f:
f.write(f"{message}\n")
except:
print("Couldn't write to error log file.") #If logging fails, still print to console
# ---------------------------- Tool Functions ----------------------------
def search_pubmed(query: str) -> list:
"""Searches PubMed and returns a list of article IDs."""
try:
Entrez.email = os.environ.get("ENTREZ_EMAIL", "[email protected]")
handle = Entrez.esearch(db="pubmed", term=query, retmax="5")
record = Entrez.read(handle)
handle.close()
return record["IdList"]
except Exception as e:
log_error(f"PubMed search error: {e}")
return [f"Error during PubMed search: {e}"]
def fetch_abstract(article_id: str) -> str:
"""Fetches the abstract for a given PubMed article ID."""
try:
Entrez.email = os.environ.get("ENTREZ_EMAIL", "[email protected]")
handle = Entrez.efetch(db="pubmed", id=article_id, rettype="abstract", retmode="text")
abstract = handle.read()
handle.close()
return abstract
except Exception as e:
log_error(f"Error fetching abstract for {article_id}: {e}")
return f"Error fetching abstract for {article_id}: {e}"
# ---------------------------- Agent Function ----------------------------
def medai_agent(query: str) -> str:
"""Orchestrates the medical literature review and presents abstract."""
article_ids = search_pubmed(query)
if isinstance(article_ids, list) and article_ids:
results = []
for article_id in article_ids:
abstract = fetch_abstract(article_id)
if "Error" not in abstract:
results.append(f"<div class='article'>\n"
f" <h3 class='article-id'>Article ID: {article_id}</h3>\n"
f" <p class='abstract'><strong>Abstract:</strong> {abstract}</p>\n"
f"</div>\n")
else:
results.append(f"<div class='article error'>\n"
f" <h3 class='article-id'>Article ID: {article_id}</h3>\n"
f" <p class='error-message'>Error processing article: {abstract}</p>\n"
f"</div>\n")
return "\n".join(results)
else:
return f"No articles found or error occurred: {article_ids}" |