Create literature.py

genesis/literature.py

@@ -0,0 +1,69 @@
+# 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