fix(ui): restore equation columns, add RAST genome preview with API endpoints

app/api/rast/genome/route.ts

@@ -0,0 +1,88 @@
+/**
+ * Server-side proxy for RAST genome data.
+ *
+ * Proxies GET /api/rast/genome from the configured modelseed-api backend.
+ * Runs server-side so it can access PATRIC_TOKEN and avoid CORS restrictions.
+ */
+import { NextRequest, NextResponse } from 'next/server';
+
+function buildUpstreamCandidates(params: string): string[] {
+    const configured = process.env.NEXT_PUBLIC_API_BASE_URL?.replace(/\/+$/, '');
+    const candidates = new Set<string>();
+    if (configured) {
+        candidates.add(`${configured}/api/rast/genome?${params}`);
+    }
+    candidates.add(`https://staging.modelseed.org/PMS/api/rast/genome?${params}`);
+    candidates.add(`https://modelseed.org/PMS/api/rast/genome?${params}`);
+    return Array.from(candidates);
+}
+
+export async function GET(request: NextRequest): Promise<NextResponse> {
+    const token =
+        request.headers.get('authorization') ||
+        process.env.PATRIC_TOKEN;
+
+    if (!token) {
+        return NextResponse.json(
+            { error: 'Authentication required' },
+            { status: 401 },
+        );
+    }
+
+    const { searchParams } = new URL(request.url);
+    const genomeId = searchParams.get('genome_id');
+    const jobId = searchParams.get('job_id');
+
+    if (!genomeId) {
+        return NextResponse.json(
+            { error: 'genome_id is required' },
+            { status: 400 },
+        );
+    }
+
+    const params = new URLSearchParams({ genome_id: genomeId });
+    if (jobId) params.set('job_id', jobId);
+
+    const headers: HeadersInit = {
+        Accept: 'application/json',
+        Authorization: token,
+    };
+
+    const upstreamCandidates = buildUpstreamCandidates(params.toString());
+    let lastStatus = 503;
+    let lastDetail: string | null = null;
+
+    for (const url of upstreamCandidates) {
+        try {
+            const res = await fetch(url, { headers, cache: 'no-store' });
+
+            if (res.ok) {
+                const data: unknown = await res.json();
+                return NextResponse.json(data);
+            }
+
+            lastStatus = res.status;
+            try {
+                const body = await res.json() as Record<string, unknown>;
+                lastDetail = typeof body.detail === 'string' ? body.detail : null;
+            } catch {
+                // ignore JSON parse failure
+            }
+
+            console.warn(`[rast/genome proxy] ${url} → HTTP ${res.status}${lastDetail ? ': ' + lastDetail : ''}`);
+        } catch (err) {
+            console.warn(
+                `[rast/genome proxy] ${url} unreachable:`,
+                err instanceof Error ? err.message : err,
+            );
+        }
+    }
+
+    return NextResponse.json(
+        {
+            error: 'RAST genome data service unavailable',
+            detail: lastDetail ?? 'All upstream endpoints failed',
+        },
+        { status: lastStatus },
+    );
+}

components/build-model/RastGenomePreviewDialog.tsx

@@ -32,6 +32,7 @@ export default function RastGenomePreviewDialog({ open, job, onProceed, onClose
         if (!open || !job) return;
 
         const genomeId = job.genome_id || job.id;
+        const jobId = job.id;
         if (!genomeId) return;
 
         let cancelled = false;
@@ -40,7 +41,7 @@ export default function RastGenomePreviewDialog({ open, job, onProceed, onClose
         setGenomeData(null);
         setError(null);
 
-        getRastGenomeData(genomeId)
+        getRastGenomeData(genomeId, jobId)
             .then((data) => {
                 if (cancelled) return;
                 setGenomeData(data);

lib/api/modelseed.ts

@@ -11,7 +11,7 @@
     MODELSEED_API_URL,
     MODELSEED_SUPPORT_URL,
     USE_MODELSEED_API,
     USE_NEW_PROXY,
     WORKSPACE_URL,
 } from './config';
 import { getStoredAuthUsername, withRawTokenAuth } from './requestAuth';
@@ -65,13 +65,36 @@
 /**
  * Fetch genome annotation data from RAST.
  *
- * Calls MSSeedSupportServer.get_rast_genome_data over JSON-RPC.
- * Returns genome metadata including taxonomy, domain, features, and contigs.
+ * Tries José's modelseed-api endpoint first (GET /api/rast/genome),
+ * then falls back to MSSS JSON-RPC (MSSeedSupportServer.getRastGenomeData).
  *
  * @param genomeId - RAST genome ID to fetch data for
+ * @param jobId - Optional RAST job ID (needed for the modelseed-api endpoint)
  * @returns Promise resolving to genome data record
  */
-export async function getRastGenomeData(genomeId: string): Promise<Record<string, unknown>> {
+export async function getRastGenomeData(genomeId: string, jobId?: string): Promise<Record<string, unknown>> {
+    // Try José's modelseed-api endpoint first
+    if (jobId) {
+        try {
+            const token = getStoredAuthUsername();
+            const headers: Record<string, string> = { Accept: 'application/json' };
+            if (token) {
+                headers['Authorization'] = token;
+            }
+            const params = new URLSearchParams({ genome_id: genomeId, job_id: jobId });
+            const res = await fetch(`/api/rast/genome?${params}`, { headers });
+            if (res.ok) {
+                const data: unknown = await res.json();
+                if (data && typeof data === 'object') {
+                    return data as Record<string, unknown>;
+                }
+            }
+        } catch {
+            // Fall through to MSSS
+        }
+    }
+
+    // Fallback: MSSS JSON-RPC
     const response = await fetch(MODELSEED_SUPPORT_URL, {
         method: 'POST',
         headers: withRawTokenAuth(
@@ -83,9 +106,9 @@
         ),
         body: JSON.stringify({
             version: '1.1',
-            method: 'MSSeedSupportServer.get_rast_genome_data',
+            method: 'MSSeedSupportServer.getRastGenomeData',
             id: 'get-rast-genome-data',
-            params: [{ genome_id: genomeId }],
+            params: [{ genome: genomeId }],
         }),
     });
 
@@ -850,7 +873,7 @@
     }
 }
 
 async function listMediaViaWorkspaceLs(path: string): Promise<ModelseedMediaSummary[]> {
     const response = await fetch(`${WORKSPACE_URL}/ls`, {
         method: 'POST',
         headers: withRawTokenAuth(