components/pubmed_search.py

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}"