# genesis/api_clients/pubmed_api.py
import requests
import xml.etree.ElementTree as ET
from typing import List, Dict, Optional
from datetime import datetime

PUBMED_SEARCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
PUBMED_FETCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
NCBI_API_KEY = None  # Optional: Set in Hugging Face secrets for higher rate limits

def search_pubmed(query: str, max_results: int = 20, start_date: Optional[str] = None, end_date: Optional[str] = None) -> List[str]:
    """
    Search PubMed for a given query and return a list of PubMed IDs.
    Optionally filter by start_date and end_date (YYYY/MM/DD format).
    """
    params = {
        "db": "pubmed",
        "term": query,
        "retmax": max_results,
        "retmode": "json",
        "api_key": NCBI_API_KEY
    }
    if start_date and end_date:
        params["mindate"] = start_date
        params["maxdate"] = end_date
        params["datetype"] = "pdat"

    r = requests.get(PUBMED_SEARCH_URL, params=params)
    r.raise_for_status()
    data = r.json()
    return data.get("esearchresult", {}).get("idlist", [])


def fetch_pubmed_details(pmid_list: List[str]) -> List[Dict]:
    """
    Fetch detailed metadata for a list of PubMed IDs.
    Returns title, abstract, authors, journal, and publication date.
    """
    if not pmid_list:
        return []

    params = {
        "db": "pubmed",
        "id": ",".join(pmid_list),
        "retmode": "xml",
        "api_key": NCBI_API_KEY
    }
    r = requests.get(PUBMED_FETCH_URL, params=params)
    r.raise_for_status()

    root = ET.fromstring(r.text)
    results = []

    for article in root.findall(".//PubmedArticle"):
        try:
            title = article.find(".//ArticleTitle").text or "No title"
            abstract = " ".join([t.text for t in article.findall(".//AbstractText") if t.text]) or "No abstract"
            authors = []
            for a in article.findall(".//Author"):
                last = a.findtext("LastName", "")
                first = a.findtext("ForeName", "")
                if last or first:
                    authors.append(f"{first} {last}".strip())

            journal = article.findtext(".//Journal/Title", "Unknown Journal")
            pub_date = article.find(".//PubDate")
            if pub_date is not None:
                year = pub_date.findtext("Year", "")
                month = pub_date.findtext("Month", "")
                day = pub_date.findtext("Day", "")
                date_str = f"{year}-{month}-{day}" if year else "Unknown"
            else:
                date_str = "Unknown"

            results.append({
                "title": title,
                "abstract": abstract,
                "authors": authors,
                "journal": journal,
                "publication_date": date_str,
                "pubmed_link": f"https://pubmed.ncbi.nlm.nih.gov/{article.findtext('.//PMID')}/"
            })
        except Exception:
            continue

    return results


def search_and_fetch_pubmed(query: str, max_results: int = 20, start_date: Optional[str] = None, end_date: Optional[str] = None) -> List[Dict]:
    """
    Search and fetch PubMed results in one call.
    """
    pmids = search_pubmed(query, max_results, start_date, end_date)
    return fetch_pubmed_details(pmids)