MedAdapt Content Server

import requests import xml.etree.ElementTree as ET import os from dotenv import load_dotenv # Load environment variables for API key load_dotenv() API_KEY = os.getenv('NCBI_API_KEY', '') def search_pubmed(query, max_results=10): """ Search PubMed for articles matching query Args: query: Search terms max_results: Maximum number of results to return Returns: List of article metadata """ base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/" api_params = f"&api_key={API_KEY}" if API_KEY else "" # Step 1: Search for article IDs search_url = f"{base_url}esearch.fcgi?db=pubmed&term={query}&retmode=json&retmax={max_results}{api_params}" try: response = requests.get(search_url) data = response.json() if 'esearchresult' not in data or 'idlist' not in data['esearchresult']: return [] pmids = data['esearchresult']['idlist'] if not pmids: return [] # Step 2: Fetch article details fetch_url = f"{base_url}efetch.fcgi?db=pubmed&id={','.join(pmids)}&retmode=xml{api_params}" fetch_response = requests.get(fetch_url) # Parse XML response root = ET.fromstring(fetch_response.text) articles = [] for article in root.findall('.//PubmedArticle'): # Extract article metadata pmid_elem = article.find('.//PMID') if pmid_elem is None: continue pmid = pmid_elem.text # Title title_elem = article.find('.//ArticleTitle') title = title_elem.text if title_elem is not None else "Unknown Title" # Abstract abstract_elem = article.find('.//AbstractText') abstract = abstract_elem.text if abstract_elem is not None else None # Journal journal_elem = article.find('.//Journal/Title') journal = journal_elem.text if journal_elem is not None else "Unknown Journal" # Year year_elem = article.find('.//PubDate/Year') year = year_elem.text if year_elem is not None else None # Authors authors = [] for author_elem in article.findall('.//Author'): last_name = author_elem.find('LastName') fore_name = author_elem.find('ForeName') if last_name is not None: author_name = last_name.text if fore_name is not None: author_name = f"{fore_name.text} {author_name}" authors.append(author_name) articles.append({ 'id': f"pubmed-{pmid}", 'title': title, 'abstract': abstract, 'journal': journal, 'year': year, 'authors': authors, 'source_type': 'pubmed', 'source_id': pmid, 'content_type': 'article', 'url': f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/" }) return articles except Exception as e: print(f"Error searching PubMed: {e}") return [] def fetch_pubmed_article(pmid): """ Fetch complete article details by PubMed ID Args: pmid: PubMed ID Returns: Complete article metadata """ base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/" api_params = f"&api_key={API_KEY}" if API_KEY else "" fetch_url = f"{base_url}efetch.fcgi?db=pubmed&id={pmid}&retmode=xml{api_params}" try: response = requests.get(fetch_url) root = ET.fromstring(response.text) article_elem = root.find('.//PubmedArticle') if article_elem is None: return {"error": "Article not found"} # Extract article metadata title_elem = article_elem.find('.//ArticleTitle') abstract_elem = article_elem.find('.//AbstractText') journal_elem = article_elem.find('.//Journal/Title') year_elem = article_elem.find('.//PubDate/Year') authors = [] for author_elem in article_elem.findall('.//Author'): last_name = author_elem.find('LastName') fore_name = author_elem.find('ForeName') if last_name is not None: author_name = last_name.text if fore_name is not None: author_name = f"{fore_name.text} {author_name}" authors.append(author_name) # Extract mesh terms mesh_terms = [] for mesh_elem in article_elem.findall('.//MeshHeading'): descriptor = mesh_elem.find('DescriptorName') if descriptor is not None: mesh_terms.append(descriptor.text) return { 'id': f"pubmed-{pmid}", 'title': title_elem.text if title_elem is not None else "Unknown Title", 'abstract': abstract_elem.text if abstract_elem is not None else "No abstract available", 'authors': authors, 'journal': journal_elem.text if journal_elem is not None else "Unknown Journal", 'year': year_elem.text if year_elem is not None else "Unknown Year", 'mesh_terms': mesh_terms, 'source_type': 'pubmed', 'source_id': pmid, 'content_type': 'article', 'url': f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/" } except Exception as e: print(f"Error fetching PubMed article: {e}") return {"error": f"Error fetching article: {e}"}