# api_clients/pubmed_client.py """ Client for the PubMed API via NCBI's Entrez E-utilities. This module is expertly crafted to perform a two-step search: first finding relevant article IDs (PMIDs) and then fetching their structured summaries. It intelligently prioritizes review articles to provide high-quality, synthesized information to the main orchestrator. """ import aiohttp from .config import PUBMED_BASE_URL, REQUEST_HEADERS async def search_pubmed(session: aiohttp.ClientSession, query: str, max_results: int = 5) -> list[dict]: """ Searches PubMed and returns a list of article summaries. This function implements an intelligent search strategy: 1. It searches for article IDs (PMIDs) matching the query within the title/abstract. 2. It specifically filters for "review" articles, which are ideal for summarization. 3. It then fetches concise summaries for the found PMIDs. Args: session (aiohttp.ClientSession): The active HTTP session. query (str): The search term, likely a combination of concepts (e.g., "Migraine AND Aura"). max_results (int): The maximum number of article summaries to return. Returns: list[dict]: A list of dictionaries, each containing summary data for an article. Returns an empty list if no results are found or an error occurs. """ if not query: return [] # --- Step 1: ESearch - Find relevant article PMIDs --- # We construct a powerful query to get the most relevant results. # - `[Title/Abstract]`: Focuses the search on the most important parts of the paper. # - `AND review[Publication Type]`: Narrows results to high-value review articles. # - `sort=relevance`: Ensures the best matches appear first. search_term = f"({query}) AND review[Publication Type]" esearch_params = { 'db': 'pubmed', 'term': search_term, 'retmode': 'json', 'retmax': max_results, 'sort': 'relevance' } esearch_url = f"{PUBMED_BASE_URL}/esearch.fcgi" pmids = [] try: async with session.get(esearch_url, params=esearch_params, headers=REQUEST_HEADERS, timeout=10) as resp: resp.raise_for_status() data = await resp.json() pmids = data.get('esearchresult', {}).get('idlist', []) if not pmids: # If no review articles are found, try a broader search as a fallback print(f"No review articles found for '{query}'. Broadening search...") esearch_params['term'] = query # Remove the review filter async with session.get(esearch_url, params=esearch_params, headers=REQUEST_HEADERS) as fallback_resp: fallback_resp.raise_for_status() fallback_data = await fallback_resp.json() pmids = fallback_data.get('esearchresult', {}).get('idlist', []) if not pmids: print(f"No PubMed results found for query: {query}") return [] # --- Step 2: ESummary - Fetch summaries for the found PMIDs --- esummary_params = { 'db': 'pubmed', 'id': ",".join(pmids), # E-utilities can take a comma-separated list of IDs 'retmode': 'json' } esummary_url = f"{PUBMED_BASE_URL}/esummary.fcgi" async with session.get(esummary_url, params=esummary_params, headers=REQUEST_HEADERS, timeout=15) as resp: resp.raise_for_status() summary_data = await resp.json() # The result is a dict with a 'result' key, which contains another dict # where keys are the PMIDs. We'll parse this into a clean list. results = summary_data.get('result', {}) # A robust way to parse, ensuring order and handling missing data parsed_articles = [] for pmid in pmids: if pmid in results: article = results[pmid] parsed_articles.append({ 'uid': article.get('uid', pmid), 'title': article.get('title', 'Title Not Available'), 'pubdate': article.get('pubdate', 'N/A'), 'authors': [author['name'] for author in article.get('authors', [])], 'journal': article.get('source', 'N/A'), 'url': f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/" }) return parsed_articles except aiohttp.ClientError as e: print(f"An error occurred while fetching from PubMed: {e}") return [] except Exception as e: print(f"A general error occurred in the pubmed_client: {e}") return []