Fix analyze chat: skip diagram analysis call and show user query

frontend/app/analyze/[id]/page.tsx

@@ -65,8 +65,9 @@ export default function AnalysisResultsPage({
   const [results, setResults] = useState<AnalysisResults | null>(null);
   const [isAnalysisLoading, setIsAnalysisLoading] = useState(!conversationId);
   const [diagramAnalysis, setDiagramAnalysis] = useState("");
-  const [analysisError, setAnalysisError] = useState("");
-  const [combinedMessages, setCombinedMessages] = useState<string[]>([]);
+  const [combinedMessages, setCombinedMessages] = useState<
+    { role: "user" | "assistant"; content: string }[]
+  >([]);
   const [biomodelData, setBiomodelData] = useState<BiomodelDetail | null>(null);
   const [biomodelLoading, setBiomodelLoading] = useState(true);
   const [showLoginDialog, setShowLoginDialog] = useState(false);
@@ -135,32 +136,15 @@ export default function AnalysisResultsPage({
     // is already part of the stored history, no need to regenerate it.
     if (conversationId) return;
 
+    // Diagram analyses are being precomputed and stored for all biomodels
+    // instead of generated on demand per request, so skip the /diagram
+    // call for now and show a placeholder instead.
     const fetchDiagramAnalysis = async () => {
       setIsAnalysisLoading(true);
-      setAnalysisError("");
-      try {
-        const token = await getAccessToken();
-        const apiUrl = process.env.NEXT_PUBLIC_API_URL;
-        const res = await fetch(`${apiUrl}/analyse/${id}/diagram`, {
-          method: "POST",
-          headers: {
-            Authorization: `Bearer ${token}`,
-            "Content-Type": "application/json",
-          },
-        });
-
-        if (res.ok) {
-          const data = await res.json();
-          setDiagramAnalysis(data.response || "");
-        } else {
-          const errorData = await res.json();
-          setAnalysisError(errorData.detail || "Failed to analyze diagram.");
-        }
-      } catch (err) {
-        setAnalysisError("Failed to fetch diagram analysis.");
-      } finally {
-        setIsAnalysisLoading(false);
-      }
+      setDiagramAnalysis(
+        "AI generated summary/analysis of this biomodel will be displayed here.",
+      );
+      setIsAnalysisLoading(false);
     };
 
     const fetchAnalysis = async () => {
@@ -206,21 +190,27 @@ export default function AnalysisResultsPage({
   // Create combined messages when analyses are ready
   useEffect(() => {
     if (diagramAnalysis || results?.aiAnalysis) {
-      const messageParts: string[] = [];
+      const newMessages: { role: "user" | "assistant"; content: string }[] = [];
 
       if (diagramAnalysis) {
-        const diagramMessage = `# Diagram Analysis \n ${diagramAnalysis}`;
-        messageParts.push(diagramMessage);
+        newMessages.push({
+          role: "assistant",
+          content: `# Diagram Analysis \n ${diagramAnalysis}`,
+        });
       }
 
-      if (results?.aiAnalysis) {
-        const aiMessage = `# Biomodel Analysis \n ${results.aiAnalysis}`;
-        messageParts.push(aiMessage);
+      if (prompt.trim()) {
+        newMessages.push({ role: "user", content: prompt });
       }
 
-      const joined_messages = messageParts.join("\n\n");
+      if (results?.aiAnalysis) {
+        newMessages.push({
+          role: "assistant",
+          content: `# Biomodel Analysis \n ${results.aiAnalysis}`,
+        });
+      }
 
-      setCombinedMessages([joined_messages]);
+      setCombinedMessages(newMessages);
     }
   }, [diagramAnalysis, results?.aiAnalysis, id]);
 

frontend/app/search/[bmid]/page.tsx

@@ -29,7 +29,7 @@ import {
   Briefcase,
   Cog,
 } from "lucide-react";
-import { getAccessToken, useUser } from "@auth0/nextjs-auth0/client";
+import { useUser } from "@auth0/nextjs-auth0/client";
 import { LoginRequiredDialog } from "@/components/login-required-dialog";
 import { SignInOutButton } from "@/components/sign-in-out-button";
 import { getOptionalAccessToken } from "@/lib/get-optional-access-token";
@@ -98,7 +98,6 @@ export default function BiomodelDetailPage() {
     conversationId ? "analysis" : "overview",
   );
   const [diagramAnalysis, setDiagramAnalysis] = useState("");
-  const [analysisError, setAnalysisError] = useState("");
   const [combinedMessages, setCombinedMessages] = useState<string[]>([]);
   const [showLoginDialog, setShowLoginDialog] = useState(false);
   const [diagramImageUrl, setDiagramImageUrl] = useState("");
@@ -205,28 +204,13 @@ export default function BiomodelDetailPage() {
     if (diagramFetchTriggeredRef.current) return;
     diagramFetchTriggeredRef.current = true;
 
+    // Diagram analyses are being precomputed and stored for all biomodels
+    // instead of generated on demand per request, so skip the /diagram
+    // call for now and show a placeholder instead.
     const fetchDiagramAnalysis = async () => {
-      try {
-        const token = await getAccessToken();
-        const apiUrl = process.env.NEXT_PUBLIC_API_URL;
-        const res = await fetch(`${apiUrl}/analyse/${data.bmKey}/diagram`, {
-          method: "POST",
-          headers: {
-            Authorization: `Bearer ${token}`,
-            "Content-Type": "application/json",
-          },
-        });
-
-        if (res.ok) {
-          const responseData = await res.json();
-          setDiagramAnalysis(responseData.response || "");
-        } else {
-          const errorData = await res.json();
-          setAnalysisError(errorData.detail || "Failed to analyze diagram.");
-        }
-      } catch (err) {
-        setAnalysisError("Failed to fetch diagram analysis.");
-      }
+      setDiagramAnalysis(
+        "AI generated summary/analysis of this biomodel will be displayed here.",
+      );
     };
 
     fetchDiagramAnalysis();

frontend/components/ChatBox.tsx

@@ -46,8 +46,10 @@ interface ChatParameters {
   llmMode: string;
 }
 
+type SeedMessage = string | { role: "user" | "assistant"; content: string };
+
 interface ChatBoxProps {
-  startMessage: string | string[];
+  startMessage: string | SeedMessage[];
   quickActions: QuickAction[];
   supplementalActions?: QuickAction[];
   cardTitle: string;
@@ -61,12 +63,12 @@ interface ChatBoxProps {
 }
 
 // Pure helpers — no dependency on component state/props.
-const createInitialMessages = (startMsg: string | string[]): Message[] => {
+const createInitialMessages = (startMsg: string | SeedMessage[]): Message[] => {
   if (Array.isArray(startMsg)) {
-    return startMsg.map((content, index) => ({
+    return startMsg.map((seed, index) => ({
       id: (index + 1).toString(),
-      role: "assistant" as const,
-      content,
+      role: typeof seed === "string" ? ("assistant" as const) : seed.role,
+      content: typeof seed === "string" ? seed : seed.content,
       timestamp: new Date(),
     }));
   } else if (startMsg) {
@@ -166,10 +168,7 @@ export const ChatBox: React.FC<ChatBoxProps> = ({
   useEffect(() => {
     if (boundConversationId) return;
     if (!startMessage || isInitialLoading) return;
-    setLocalSeedMessages((prev) => {
-      if (prev.some((m) => m.role === "user")) return prev;
-      return createInitialMessages(startMessage);
-    });
+    setLocalSeedMessages(createInitialMessages(startMessage));
   }, [startMessage, isInitialLoading, boundConversationId]);
 
   const handleQuickAction = (action: QuickAction) => {