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app.py

@@ -215,23 +215,101 @@ def new_chat(): return [], "", "New chat started"
 
 def get_pubmed(query, n=5):
     try:
+        forced = query + " AND (heart valve OR hemodynamics OR microfluidic OR thrombogen OR creatinine OR PIV OR CKD)"
         r = requests.get("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi",
-            params={"db":"pubmed","term":query+" AND (mechanical heart valve OR microfluidic OR CKD OR thrombogenicity)","retmax":n,"retmode":"json","sort":"date"},timeout=10)
+            params={"db":"pubmed","term":forced,"retmax":n,"retmode":"json","sort":"date","field":"tiab"},timeout=10)
         ids = r.json()["esearchresult"]["idlist"]
         if not ids: return ""
         return chr(10).join(["https://pubmed.ncbi.nlm.nih.gov/"+i for i in ids])
     except: return ""
 
-def quick_search(query):
-    if not query.strip(): return "Please enter a topic."
-    pubmed = get_pubmed(query, n=8)
+def expand_query(query):
+    if not GROQ_KEY: return query
+    try:
+        client = Groq(api_key=GROQ_KEY)
+        system_msg = ("You are a biomedical engineering PubMed search expert for SJSU CardioLab. "
+            "Convert the user query into optimized PubMed keywords. "
+            "Focus on: mechanical heart valves, hemodynamics, blood flow, PIV, thrombogenicity, FSI, CFD, microfluidics, CKD, creatinine. "
+            "Return ONLY the search terms, no explanation, no dashes, no punctuation.")
+        resp = client.chat.completions.create(
+            model="llama-3.3-70b-versatile",
+            messages=[
+                {"role":"system","content":system_msg},
+                {"role":"user","content":"Optimize for PubMed: "+query}
+            ],
+            max_tokens=60
+        )
+        expanded = resp.choices[0].message.content.strip()
+        return expanded if expanded else query
+    except: return query
+
+def search_pubmed_smart(query, n=8):
     try:
+        expanded = expand_query(query)
+        biomedical_filter = " AND (heart valve OR hemodynamics OR microfluidic OR thrombogen OR creatinine OR PIV OR CFD OR fluid structure OR CKD)"
+        forced = expanded + biomedical_filter
+        r = requests.get("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi",
+            params={"db":"pubmed","term":forced,"retmax":n,"retmode":"json","sort":"date","field":"tiab"},timeout=10)
+        ids = r.json()["esearchresult"]["idlist"]
+        if not ids:
+            return "No PubMed results found for this topic.", expanded
+        r2 = requests.get("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi",
+            params={"db":"pubmed","id":",".join(ids),"retmode":"xml","rettype":"abstract"},timeout=10)
+        lines = []
+        try:
+            import xml.etree.ElementTree as ET
+            root = ET.fromstring(r2.content)
+            for article in root.findall(".//PubmedArticle"):
+                try:
+                    title_el = article.find(".//ArticleTitle")
+                    title = title_el.text if title_el is not None else "No title"
+                    pmid_el = article.find(".//PMID")
+                    pmid = pmid_el.text if pmid_el is not None else ""
+                    year_el = article.find(".//PubDate/Year")
+                    year = year_el.text if year_el is not None else ""
+                    url = "https://pubmed.ncbi.nlm.nih.gov/"+pmid
+                    lines.append(str(title)[:90]+" ("+year+")"+chr(10)+"  "+url)
+                except: continue
+        except:
+            lines = ["https://pubmed.ncbi.nlm.nih.gov/"+i for i in ids]
+        return chr(10)+chr(10).join(lines), expanded
+    except Exception as e:
+        return "PubMed error: "+str(e), query
+
+def search_scholar_smart(query, n=8):
+    try:
+        expanded = expand_query(query)
         r = requests.get("https://api.semanticscholar.org/graph/v1/paper/search",
-            params={"query":query+" biomedical","limit":5,"fields":"title,year,url"},timeout=10)
+            params={"query":expanded,"limit":n,"fields":"title,year,url,citationCount"},
+            timeout=15)
         papers = r.json().get("data",[])
-        scholar = chr(10).join([p.get("title","")[:80]+" ("+str(p.get("year",""))+")"+chr(10)+"   "+p.get("url","") for p in papers if p.get("url","")])
-    except: scholar = ""
-    return "PUBMED:"+chr(10)+pubmed+chr(10)+chr(10)+"SCHOLAR:"+chr(10)+scholar
+        if not papers:
+            return "No Semantic Scholar results found."
+        out = []
+        for p in papers:
+            title = p.get("title","")
+            year = str(p.get("year",""))
+            url = p.get("url","")
+            citations = str(p.get("citationCount",0))
+            if url:
+                out.append(str(title)[:90]+" ("+year+") | "+citations+" citations"+chr(10)+"  "+url)
+        return chr(10)+chr(10).join(out) if out else "No results."
+    except Exception as e:
+        return "Scholar error: "+str(e)
+
+def quick_search(query):
+    if not query.strip(): return "Please enter a research topic."
+    pubmed_results, expanded = search_pubmed_smart(query, n=8)
+    scholar_results = search_scholar_smart(query, n=6)
+    result = "YOUR QUERY: " + query + chr(10)
+    result += "AI EXPANDED: " + expanded + chr(10)
+    result += "="*45 + chr(10) + chr(10)
+    result += "PUBMED RESULTS (titles + verified links):" + chr(10)
+    result += pubmed_results + chr(10) + chr(10)
+    result += "="*45 + chr(10)
+    result += "SEMANTIC SCHOLAR RESULTS:" + chr(10)
+    result += scholar_results
+    return result
 
 def research_chat(message, history):
     if not GROQ_KEY: