genesis/literature.py

# genesis/literature.py
import os
import requests
from typing import List, Dict

NCBI_API_KEY = os.getenv("NCBI_API_KEY")
NCBI_EMAIL = os.getenv("NCBI_EMAIL")

def search_pubmed(query: str, max_results: int = 5, sort: str = "relevance") -> List[Dict]:
    """
    Search PubMed for research articles.
    
    sort: "relevance", "pub date", or "most recent"
    Returns: List of dicts with title, authors, journal, year, and link.
    """
    try:
        # Step 1: Search PubMed for IDs
        search_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
        search_params = {
            "db": "pubmed",
            "term": query,
            "retmax": max_results,
            "api_key": NCBI_API_KEY,
            "email": NCBI_EMAIL,
            "sort": "relevance" if sort == "relevance" else "pub+date" if sort == "most recent" else "pub+date",
            "retmode": "json"
        }
        r = requests.get(search_url, params=search_params, timeout=10)
        r.raise_for_status()
        ids = r.json().get("esearchresult", {}).get("idlist", [])
        if not ids:
            return []

        # Step 2: Fetch summaries for IDs
        summary_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"
        summary_params = {
            "db": "pubmed",
            "id": ",".join(ids),
            "retmode": "json"
        }
        s = requests.get(summary_url, params=summary_params, timeout=10)
        s.raise_for_status()
        summaries = s.json().get("result", {})

        papers = []
        for pmid in ids:
            paper = summaries.get(pmid, {})
            authors = [a["name"] for a in paper.get("authors", [])]
            papers.append({
                "title": paper.get("title", "N/A"),
                "authors": ", ".join(authors) if authors else "N/A",
                "journal": paper.get("fulljournalname", "N/A"),
                "year": paper.get("pubdate", "N/A"),
                "pmid": pmid,
                "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/"
            })
        return papers
    except Exception as e:
        print(f"[PubMed] Failed: {e}")
        return []

def format_literature_markdown(papers: List[Dict]) -> str:
    """Format literature list into markdown table."""
    if not papers:
        return "No relevant papers found."
    md = "| Title | Authors | Journal | Year |\n|-------|---------|---------|------|\n"
    for p in papers:
        md += f"| [{p['title']}]({p['url']}) | {p['authors']} | {p['journal']} | {p['year']} |\n"
    return md