@barivia/barsom-mcp 0.23.5 → 0.23.9

package/README.md

@@ -32,7 +32,7 @@ MCP clients typically run it with **`npx`** (downloads on first use):
 1. **Get an API key** — Sign up at [barivia.se/dashboard](https://barivia.se/dashboard) (self-serve) or ask your admin for a `bv_…` key.
 2. **Add the MCP server** — Paste the JSON block above into your client’s MCP config (`mcp.json` in Cursor). Set `BARIVIA_API_KEY` and keep `BARIVIA_API_URL=https://api.barivia.se`.
 3. **Orient** — In chat, invoke **`guide_barsom_workflow`** (no parameters). It returns your plan-scoped tool map and async rules.
-4. **Upload data** — `datasets(action=upload, file_path="your.csv")` → note `dataset_id` (and `stage_job_id` if staging is enqueued; poll until complete).
+4. **Upload data** — `datasets(action=upload, file_path="your.csv")` → note `dataset_id`. The proxy waits for staging on upload; confirm with `datasets(action=get)` → `train_ready=yes` before train if you bypass the proxy wait.
 5. **Train** — `train(action=map, dataset_id=…, preset=quick)` → returns `job_id`. Poll with `jobs(action=status, job_id=…)` every 60–120s, or use **`training_monitor(job_id=…)`** for live curves.
 6. **Results** — When status is `completed`, `results(action=get, job_id=…)` for metrics + headline figure; **`results_explorer(job_id=…)`** to browse all figures.
 
@@ -53,10 +53,11 @@ MCP clients typically run it with **`npx`** (downloads on first use):
 | `BARIVIA_API_KEY` | Yes | -- | API key (starts with `bv_`) |
 | `BARIVIA_API_URL` | No | `https://api.barivia.se` | API base URL |
 | `BARIVIA_WORKSPACE_ROOT` | No | `process.cwd()` or `PWD` | Directory for relative `file_path` and `save_to_disk`. In Cursor MCP, `process.cwd()` is often the MCP install dir — add `BARIVIA_WORKSPACE_ROOT` to your MCP config `env` with your project path (e.g. `/home/user/myproject`). Absolute paths and `file://` URIs work without it. |
+| `BARIVIA_WORKSPACE_EXTRA_ROOTS` | No | (empty) | Comma- or colon-separated absolute directories whose **realpath** targets are also allowed for uploads when the sandbox is on. Use for shared fixture trees reached via symlinks under the case workspace (e.g. `…/barivia-testing/data`). Does not weaken the default sandbox for paths outside these roots. |
 | `BARIVIA_FETCH_TIMEOUT_MS` | No | `60000` | Per-request HTTP timeout (ms) to the API. Increase (e.g. `120000`) on slow networks or when the API does long-running work. Large dataset uploads use a separate longer timeout internally, and `datasets(analyze)` runs asynchronously (auto-polled) so it is not bound by this. A timeout is not auto-retried (re-firing slow work would only multiply load / risk duplicates). |
 | `BARIVIA_VIZ_PORT` | No | OS-assigned | Local viz server on `127.0.0.1`. Port is **per MCP session** unless pinned — standalone `…/viz/…` URLs go stale after proxy restart. Set a fixed port for stable bookmark URLs. Diagnostic: `GET http://127.0.0.1:<port>/api/health?job_id=<id>`. |
 | `BARIVIA_UI_DELIVERY` | No | `auto` | Client-capability override for App tools: `auto` \| `apps` \| `localhost` \| `inline`. Tool responses always lead with a standalone localhost URL (hosts may list `ui://` without mounting widgets) and include a structured `ui_delivery` block. `account(status)` reports detected Apps support, viz port, and active tier. |
-| `BARIVIA_ENFORCE_WORKSPACE_SANDBOX` | No | `1` (enabled) | File uploads are constrained to the MCP workspace root by default. Set to `0` or `false` to allow absolute paths anywhere on the machine (high trust). **Changed in v0.x:** previously defaulted to off; now on for security. If uploads fail with "paths outside the workspace are disabled", either set `BARIVIA_WORKSPACE_ROOT` to cover your data directory, or opt out with `BARIVIA_ENFORCE_WORKSPACE_SANDBOX=0`. |
+| `BARIVIA_ENFORCE_WORKSPACE_SANDBOX` | No | `1` (enabled) | File uploads are constrained to the MCP workspace root (and optional `BARIVIA_WORKSPACE_EXTRA_ROOTS`) by default. Set to `0` or `false` to allow absolute paths anywhere on the machine (high trust). If uploads fail with "symlink resolves outside workspace", either point `BARIVIA_WORKSPACE_ROOT` / `BARIVIA_WORKSPACE_EXTRA_ROOTS` at the real data dir, copy the file into the workspace, or opt out with `BARIVIA_ENFORCE_WORKSPACE_SANDBOX=0`. |
 
 Legacy `BARSOM_API_KEY` / `BARSOM_API_URL` / `BARSOM_WORKSPACE_ROOT` are also accepted as fallbacks.
 
@@ -102,7 +103,7 @@ Call at the **start of mapping work** (or when the user asks what the MCP can do
 | `preview` | Before training — inspect columns, stats, cyclic/datetime hints |
 | `analyze` | Pre-training recommendations (correlation, columns to consider dropping, etc.) |
 | `list` | Finding dataset IDs |
-| `get` | One dataset by id — status, staging fields, `stage_job_id`, ingest errors |
+| `get` | One dataset by id — status, **`train_ready`**, staging fields, `stage_job_id`, ingest errors |
 | `subset` | Creating a filtered/sliced copy (row_range, filter, `sample_n`) — **only when the user asks**; agents must not auto-downsample before train/analyze |
 | `add_expression` | Add a derived column from an expression (formula → new column on the dataset) |
 | `reduce_spectral` | Pre-training reducer for long ordered numeric blocks (spectra, time series, sensor fingerprints, gene panels). Methods: **pca** (top-k principal components), **log_sample** (k columns at log-spaced indices — scattering, audio bands), **uniform_sample** (k columns at evenly-spaced indices — regularly-sampled time series), **stats** (6 fixed per-row summary columns). All produce one feature vector per row; appends derived columns to the dataset. |

package/dist/job_monitor.js

@@ -34,14 +34,30 @@ function tailOrderingErrors(data, n = 4) {
 export function snapshotFromJob(data, elapsedSec, note) {
     const status = String(data.status ?? "unknown");
     const progress_pct = (data.progress ?? 0) * 100;
+    const kernelComplete = data.kernel_complete === true;
+    const awaitingFinalize = kernelComplete &&
+        status !== "completed" &&
+        status !== "failed" &&
+        status !== "cancelled";
     const snap = {
         elapsed_sec: elapsedSec,
         status,
-        progress_pct: Math.round(progress_pct * 10) / 10,
+        // Kernel progress can hit 100% before finalize; do not present as job-done.
+        progress_pct: awaitingFinalize
+            ? Math.min(Math.round(progress_pct * 10) / 10, 99.0)
+            : Math.round(progress_pct * 10) / 10,
     };
-    const phase = str(data, "progress_phase");
-    if (phase)
+    const phaseRaw = str(data, "progress_phase");
+    const phase = phaseRaw && phaseRaw !== "missing" ? phaseRaw : undefined;
+    if (awaitingFinalize) {
+        snap.phase = phase && phase !== "complete" ? `${phase}+awaiting_finalize` : "awaiting_finalize";
+    }
+    else if (phase) {
         snap.phase = phase;
+    }
+    else if (str(data, "prepare_job_id") && String(data.status ?? "") !== "completed") {
+        snap.phase = "waiting_for_prepare";
+    }
     const epoch = num(data, "epoch");
     const total = num(data, "total_epochs");
     if (epoch != null)
@@ -57,7 +73,7 @@ export function snapshotFromJob(data, elapsedSec, note) {
     const panelTe = num(data, "panel_topographic_error");
     if (panelTe != null)
         snap.panel_te = Math.round(panelTe * 10_000) / 10_000;
-    if (data.kernel_complete === true)
+    if (kernelComplete)
         snap.kernel_complete = true;
     const failureStage = str(data, "failure_stage");
     if (failureStage)
@@ -68,8 +84,12 @@ export function snapshotFromJob(data, elapsedSec, note) {
     const tail = tailOrderingErrors(data);
     if (tail && tail.length > 0)
         snap.ordering_errors_tail = tail;
-    if (note)
+    if (note) {
         snap.note = note;
+    }
+    else if (awaitingFinalize) {
+        snap.note = "kernel complete — awaiting finalize (not fully done)";
+    }
     return snap;
 }
 /** True when a new snapshot is worth recording (phase/epoch/progress/status change). */
@@ -95,7 +115,10 @@ export function shouldRecordSnapshot(prev, next) {
     return false;
 }
 export function formatSnapshotLine(s) {
-    const parts = [`[+${s.elapsed_sec}s] ${s.status} ${s.progress_pct.toFixed(1)}%`];
+    const progressLabel = s.kernel_complete && s.status !== "completed" && s.status !== "failed" && s.status !== "cancelled"
+        ? `kernel ${s.progress_pct.toFixed(1)}% (awaiting finalize)`
+        : `${s.progress_pct.toFixed(1)}%`;
+    const parts = [`[+${s.elapsed_sec}s] ${s.status} ${progressLabel}`];
     if (s.phase)
         parts.push(`phase ${s.phase}`);
     if (s.epoch != null && s.total_epochs != null)
@@ -106,8 +129,9 @@ export function formatSnapshotLine(s) {
         parts.push(`Epoch TE ${s.te.toFixed(4)}`);
     if (s.panel_te != null)
         parts.push(`Panel TE ${s.panel_te.toFixed(4)}`);
-    if (s.kernel_complete)
+    if (s.kernel_complete && (s.status === "completed" || s.status === "failed" || s.status === "cancelled")) {
         parts.push("kernel complete");
+    }
     if (s.failure_stage)
         parts.push(`failure_stage ${s.failure_stage}`);
     if (s.eta_sec != null)

package/dist/job_status_format.js

@@ -36,22 +36,41 @@ export function formatJobStatusText(job_id, data) {
     const progress = (data.progress ?? 0) * 100;
     const label = data.label != null && data.label !== "" ? String(data.label) : null;
     const jobDesc = label ? `Job ${label} (id: ${job_id})` : `Job ${job_id}`;
-    const parts = [`${jobDesc}: ${status} (${progress.toFixed(1)}%)`];
+    const kernelComplete = data.kernel_complete === true;
+    const awaitingFinalize = kernelComplete && status !== "completed" && status !== "failed" && status !== "cancelled";
+    const progressBit = awaitingFinalize
+        ? `kernel ${Math.min(progress, 99).toFixed(1)}% — awaiting finalize`
+        : `${progress.toFixed(1)}%`;
+    const parts = [`${jobDesc}: ${status} (${progressBit})`];
     const attempt = data.attempt != null ? Number(data.attempt) : null;
     if (attempt != null && attempt > 1) {
         parts.push(`attempt ${attempt} (job was requeued after worker timeout — not stuck from scratch)`);
     }
-    const phase = data.progress_phase != null && String(data.progress_phase) !== ""
+    const rawPhase = data.progress_phase != null && String(data.progress_phase) !== ""
         ? String(data.progress_phase)
         : null;
-    if (status === "running") {
+    // API historically serialized SQL NULL as the literal "missing" (Julia missing).
+    const phase = rawPhase && rawPhase !== "missing" ? rawPhase : null;
+    const prepareJobId = data.prepare_job_id != null && String(data.prepare_job_id) !== ""
+        ? String(data.prepare_job_id)
+        : null;
+    if (status === "pending" && prepareJobId) {
+        parts.push(`phase: waiting_for_prepare (prepare_job_id=${prepareJobId})`);
+    }
+    else if (status === "running") {
         if (phase) {
             parts.push(`phase: ${phase}`);
         }
+        else if (prepareJobId) {
+            parts.push(`phase: waiting_for_prepare (prepare_job_id=${prepareJobId})`);
+        }
         else {
             parts.push(`phase: preprocessing (not set yet — often download/parse before first progress tick)`);
         }
     }
+    else if (prepareJobId && (status === "completed" || status === "failed")) {
+        parts.push(`prepare_job_id: ${prepareJobId}`);
+    }
     const startedAt = data.started_at != null ? String(data.started_at) : null;
     if (startedAt) {
         parts.push(`started_at: ${startedAt}`);
@@ -78,7 +97,10 @@ export function formatJobStatusText(job_id, data) {
         if (panelTe != null) {
             parts.push(`panel_te: ${panelTe.toFixed(4)}`);
         }
-        if (data.kernel_complete === true) {
+        if (awaitingFinalize) {
+            parts.push("kernel_complete — figures/finalize still pending (not fully done)");
+        }
+        else if (kernelComplete) {
             parts.push("kernel_complete");
         }
     }

package/dist/shared.js

@@ -39,7 +39,7 @@ function newRequestId() {
  * X-Barsom-Client-Version so the server can annotate tool guidance with the
  * wrapper version each action requires. Keep in sync with package.json on bump.
  */
-export const CLIENT_VERSION = "0.23.5";
+export const CLIENT_VERSION = "0.23.9";
 /** User-facing links; keep aligned with barivia.se / api.barivia.se. */
 export const PUBLIC_SITE_ORIGIN = "https://barivia.se";
 /** Self-serve account dashboard (manage plan, billing, and API keys). */
@@ -77,6 +77,97 @@ export const LARGE_UPLOAD_BYTES = 64 * 1024 * 1024; // 64 MB
 export const PRESIGNED_PUT_TIMEOUT_MS = 30 * 60_000; // 30 min
 /** Poll window for the async stage_dataset job (large files take minutes). */
 export const POLL_STAGE_MAX_MS = 30 * 60_000; // 30 min
+/** Normalize upload JSON after staging completes — never leave staging:true with train_ready. */
+export function finalizeStagedUploadResponse(data, ready) {
+    const merged = ready
+        ? { ...data, ...ready }
+        : { ...data };
+    const trainReady = merged.train_ready === true || String(merged.status ?? "") === "ready";
+    if (trainReady) {
+        merged.status = ready?.status ?? merged.status ?? "ready";
+        merged.train_ready = true;
+        merged.staging = false;
+        // stage_job_id is only useful while staging is pending
+        if (ready?.stage_job_id == null)
+            delete merged.stage_job_id;
+    }
+    return merged;
+}
+/**
+ * After a small POST /v1/datasets upload, poll stage_job_id until the dataset is
+ * train-ready (mirrors the large-upload finalize path).
+ */
+export async function awaitDatasetStageIfNeeded(data) {
+    const stageJobId = data.stage_job_id != null ? String(data.stage_job_id) : "";
+    if (!stageJobId) {
+        if (data.train_ready === true || data.status === "ready") {
+            return finalizeStagedUploadResponse(data);
+        }
+        return data;
+    }
+    if (data.train_ready === true || data.status === "ready") {
+        return finalizeStagedUploadResponse(data);
+    }
+    const poll = await pollUntilComplete(stageJobId, POLL_STAGE_MAX_MS);
+    if (poll.status === "failed") {
+        throw new Error(`Dataset staging failed (stage_job_id=${stageJobId}): ${poll.error ?? "unknown error"}`);
+    }
+    if (poll.status === "timeout") {
+        throw new Error(`Dataset staging timed out after ${POLL_STAGE_MAX_MS / 60000} min (stage_job_id=${stageJobId}). Poll jobs(action=status, job_id="${stageJobId}").`);
+    }
+    const datasetId = String(data.id ?? data.dataset_id ?? "");
+    if (datasetId) {
+        try {
+            const ready = (await apiCall("GET", `/v1/datasets/${datasetId}`));
+            return finalizeStagedUploadResponse(data, ready);
+        }
+        catch {
+            /* fall through */
+        }
+    }
+    return finalizeStagedUploadResponse({ ...data, status: "ready", train_ready: true });
+}
+/**
+ * Before train / CFD submit: ensure the dataset has finished staging.
+ * Prefer train_ready from GET; otherwise poll stage_job_id.
+ */
+export async function ensureDatasetTrainReady(datasetId) {
+    const ds = (await apiCall("GET", `/v1/datasets/${datasetId}`));
+    if (ds.train_ready === true)
+        return;
+    if (String(ds.status) === "failed") {
+        const err = ds.ingest_error != null ? String(ds.ingest_error) : "staging failed";
+        throw new Error(`Dataset ${datasetId} staging failed: ${err}`);
+    }
+    const stageJobId = ds.stage_job_id != null ? String(ds.stage_job_id) : "";
+    if (stageJobId) {
+        const poll = await pollUntilComplete(stageJobId, POLL_STAGE_MAX_MS);
+        if (poll.status === "failed") {
+            throw new Error(`Dataset staging failed (stage_job_id=${stageJobId}): ${poll.error ?? "unknown error"}`);
+        }
+        if (poll.status === "timeout") {
+            throw new Error(`Dataset staging timed out (stage_job_id=${stageJobId}). Poll jobs(action=status, job_id="${stageJobId}").`);
+        }
+        return;
+    }
+    // No stage job listed — brief poll on GET for race windows
+    const deadline = Date.now() + 60_000;
+    while (Date.now() < deadline) {
+        await new Promise((r) => setTimeout(r, 1000));
+        const again = (await apiCall("GET", `/v1/datasets/${datasetId}`));
+        if (again.train_ready === true)
+            return;
+        if (String(again.status) === "failed") {
+            const err = again.ingest_error != null ? String(again.ingest_error) : "staging failed";
+            throw new Error(`Dataset ${datasetId} staging failed: ${err}`);
+        }
+        if (again.stage_job_id != null) {
+            await ensureDatasetTrainReady(datasetId);
+            return;
+        }
+    }
+    throw new Error(`Dataset ${datasetId} is not train_ready (status=${ds.status ?? "?"}). Wait for staging or poll datasets(action=get).`);
+}
 export const BARSOM_VIZ_VIEWS = {
     trainingMonitor: "training-monitor",
     resultsExplorer: "results-explorer",
@@ -288,11 +379,51 @@ function enforceWorkspaceSandboxUpload() {
         return false;
     return true;
 }
+/** Extra realpath roots allowed for uploads (comma- or colon-separated absolute paths). */
+export function getWorkspaceExtraRoots() {
+    const raw = process.env.BARIVIA_WORKSPACE_EXTRA_ROOTS ?? "";
+    if (!raw.trim())
+        return [];
+    return raw
+        .split(/[,:]/)
+        .map((s) => s.trim())
+        .filter(Boolean)
+        .map((s) => path.resolve(s));
+}
+async function realpathIfExists(p) {
+    try {
+        return await fs.realpath(p);
+    }
+    catch {
+        return null;
+    }
+}
+/** True when `realPath` is under workspace root or any BARIVIA_WORKSPACE_EXTRA_ROOTS entry. */
+export async function isPathUnderSandboxRoots(realPath, workspaceRoot) {
+    const candidates = [workspaceRoot, ...getWorkspaceExtraRoots()];
+    for (const root of candidates) {
+        const realRoot = await realpathIfExists(root);
+        if (!realRoot)
+            continue;
+        if (realPath === realRoot || realPath.startsWith(realRoot + path.sep))
+            return true;
+    }
+    return false;
+}
+function sandboxEscapeError(realPath, workspaceRoot) {
+    const extras = getWorkspaceExtraRoots();
+    const extraHint = extras.length > 0
+        ? ` Also checked BARIVIA_WORKSPACE_EXTRA_ROOTS (${extras.join(", ")}).`
+        : " Set BARIVIA_WORKSPACE_EXTRA_ROOTS to allow shared fixture dirs (e.g. a data/ sibling), or copy the file into the workspace.";
+    return new Error(`Resolved path escapes workspace — symlink resolves outside BARIVIA_WORKSPACE_ROOT` +
+        ` (${workspaceRoot}). Target: ${realPath}.${extraHint}`);
+}
 /**
  * Resolves file_path for dataset upload. Security: auth before read, generic errors, reject "..".
  * Accepts: absolute paths, file:// URIs, relative paths (resolved against workspace root).
  * Pre-security-patch behavior: absolute paths worked without BARIVIA_WORKSPACE_ROOT.
- * Set BARIVIA_ENFORCE_WORKSPACE_SANDBOX=1 to require absolute paths to lie under the resolved workspace root.
+ * Set BARIVIA_ENFORCE_WORKSPACE_SANDBOX=1 to require absolute paths to lie under the resolved workspace root
+ * or an entry in BARIVIA_WORKSPACE_EXTRA_ROOTS (after realpath, so symlinks are allowed when the target is under an allowed root).
  */
 export async function resolveFilePathForUpload(filePath, mcpServer) {
     const trimmed = filePath.trim();
@@ -309,9 +440,8 @@ export async function resolveFilePathForUpload(filePath, mcpServer) {
             if (enforceWorkspaceSandboxUpload()) {
                 const root = await getWorkspaceRootAsync(mcpServer);
                 const real = await fs.realpath(p);
-                const realRoot = await fs.realpath(root);
-                if (real !== realRoot && !real.startsWith(realRoot + path.sep)) {
-                    throw new Error(`file:// paths outside the workspace are disabled (BARIVIA_ENFORCE_WORKSPACE_SANDBOX). Workspace: ${realRoot}`);
+                if (!(await isPathUnderSandboxRoots(real, root))) {
+                    throw sandboxEscapeError(real, root);
                 }
                 const stat = await fs.stat(real);
                 if (!stat.isFile()) {
@@ -324,7 +454,7 @@ export async function resolveFilePathForUpload(filePath, mcpServer) {
         catch (err) {
             if (err instanceof Error && err.message.includes("remote hosts"))
                 throw err;
-            if (err instanceof Error && err.message.includes("BARIVIA_ENFORCE_WORKSPACE_SANDBOX"))
+            if (err instanceof Error && err.message.includes("symlink resolves outside"))
                 throw err;
             if (err instanceof Error && err.message.includes("regular file"))
                 throw err;
@@ -339,11 +469,10 @@ export async function resolveFilePathForUpload(filePath, mcpServer) {
                 real = await fs.realpath(trimmed);
             }
             catch {
-                throw new Error(`File not accessible at absolute path. With BARIVIA_ENFORCE_WORKSPACE_SANDBOX, use a path under the workspace root (${root}).`);
+                throw new Error(`File not accessible at absolute path. With BARIVIA_ENFORCE_WORKSPACE_SANDBOX, use a path under the workspace root (${root}) or BARIVIA_WORKSPACE_EXTRA_ROOTS.`);
             }
-            const realRoot = await fs.realpath(root);
-            if (real !== realRoot && !real.startsWith(realRoot + path.sep)) {
-                throw new Error(`Absolute paths outside the workspace are disabled (BARIVIA_ENFORCE_WORKSPACE_SANDBOX). Workspace root: ${realRoot}`);
+            if (!(await isPathUnderSandboxRoots(real, root))) {
+                throw sandboxEscapeError(real, root);
             }
             const stat = await fs.stat(real);
             if (!stat.isFile()) {
@@ -355,14 +484,14 @@ export async function resolveFilePathForUpload(filePath, mcpServer) {
     }
     const root = await getWorkspaceRootAsync(mcpServer);
     const resolved = path.resolve(root, trimmed);
+    // Lexical check against workspace root only (relative paths must stay under the case workspace).
     if (resolved !== root && !resolved.startsWith(root + path.sep)) {
         throw new Error("Path must be within the workspace directory.");
     }
     try {
         const real = await fs.realpath(resolved);
-        const realRoot = await fs.realpath(root);
-        if (real !== realRoot && !real.startsWith(realRoot + path.sep)) {
-            throw new Error("Resolved path escapes workspace (e.g. symlink).");
+        if (!(await isPathUnderSandboxRoots(real, root))) {
+            throw sandboxEscapeError(real, root);
         }
         const stat = await fs.stat(real);
         if (!stat.isFile()) {
@@ -371,7 +500,8 @@ export async function resolveFilePathForUpload(filePath, mcpServer) {
         return real;
     }
     catch (err) {
-        if (err instanceof Error && (err.message.includes("escapes") || err.message.includes("regular file"))) {
+        if (err instanceof Error &&
+            (err.message.includes("symlink resolves outside") || err.message.includes("regular file"))) {
             throw err;
         }
         throw new Error(`File not accessible. Easiest fix: pass an ABSOLUTE path (e.g. "/home/you/project/data.csv" or ` +
@@ -444,7 +574,15 @@ export function classifyApiError(status, bodyText, requestId) {
     }
     else if (status === 409) {
         cause = "client";
-        hint = "The job may not be in the expected state.";
+        if (apiCode === "staging_not_ready") {
+            const stageId = parsed?.stage_job_id != null ? String(parsed.stage_job_id) : "";
+            hint = stageId
+                ? `Wait for stage_dataset to finish: jobs(action=monitor, job_id="${stageId}"), then retry train. Prefer datasets(action=get) train_ready=true.`
+                : "Wait for dataset staging (status=ready with staged_prefix / train_ready=true), then retry train.";
+        }
+        else {
+            hint = "The job may not be in the expected state.";
+        }
         retryable = false;
     }
     else if (status === 429) {
@@ -824,15 +962,30 @@ export function structuredTextResult(structuredContent, text, content) {
 }
 export async function pollUntilComplete(jobId, maxWaitMs = 30_000, intervalMs = 1000) {
     const start = Date.now();
+    /** Brief 404s happen when finalize_job_id is visible before the child row is readable. */
+    let notFoundStreak = 0;
+    const maxNotFoundRetries = 5;
     while (Date.now() - start < maxWaitMs) {
-        const data = (await apiCall("GET", `/v1/jobs/${jobId}`));
-        const status = data.status;
-        if (status === "completed" || status === "failed" || status === "cancelled") {
-            return {
-                status,
-                result_ref: data.result_ref,
-                error: data.error,
-            };
+        try {
+            const data = (await apiCall("GET", `/v1/jobs/${jobId}`));
+            notFoundStreak = 0;
+            const status = data.status;
+            if (status === "completed" || status === "failed" || status === "cancelled") {
+                return {
+                    status,
+                    result_ref: data.result_ref,
+                    error: data.error,
+                };
+            }
+        }
+        catch (err) {
+            const status = err?.httpStatus;
+            if (status === 404 && notFoundStreak < maxNotFoundRetries) {
+                notFoundStreak += 1;
+                await new Promise((r) => setTimeout(r, intervalMs));
+                continue;
+            }
+            throw err;
         }
         await new Promise((r) => setTimeout(r, intervalMs));
     }
@@ -986,6 +1139,43 @@ export function inlineAttachBytesUsed() {
 export function shouldFetchAllRemainingFigures(figures) {
     return figures === "all" || figures === "images";
 }
+/** Enum tokens accepted by results(figures). Prefer string "all"/"none"; arrays are for names/filenames. */
+const RESULTS_FIGURE_ENUMS = new Set([
+    "default",
+    "combined_only",
+    "all",
+    "images",
+    "none",
+]);
+/**
+ * Coerce host-stringified figures args (e.g. `'["all"]'`) and singleton enum arrays
+ * (`["all"]` → `"all"`) before Zod validation. Real filename arrays stay arrays.
+ */
+export function coerceFiguresArg(v) {
+    if (v === undefined || v === null)
+        return v;
+    let val = v;
+    if (typeof val === "string") {
+        const trimmed = val.trim();
+        if ((trimmed.startsWith("[") && trimmed.endsWith("]")) ||
+            (trimmed.startsWith('"') && trimmed.endsWith('"'))) {
+            try {
+                val = JSON.parse(trimmed);
+            }
+            catch {
+                return v;
+            }
+        }
+    }
+    if (Array.isArray(val)) {
+        const asStrings = val.map((x) => String(x));
+        if (asStrings.length === 1 && RESULTS_FIGURE_ENUMS.has(asStrings[0])) {
+            return asStrings[0];
+        }
+        return asStrings;
+    }
+    return val;
+}
 /** Attach result figures with captions; tracks inlined names for dedup. */
 export async function attachResultsImages(content, jobId, jobType, summary, figures, includeIndividual, inlinedImages) {
     for (const name of getResultsImagesToFetch(jobType, summary, figures, includeIndividual)) {

package/dist/tools/account.js

@@ -38,7 +38,7 @@ export function registerAccountTool(server) {
 | Action | Use when |
 |--------|----------|
 | status | Before large jobs — see plan tier, GPU availability, queue depth, training time estimates, credit balance. When the API is down, returns calm \`{ok:false, retry_after_sec}\` instead of HTML. |
-| history | Viewing recent compute usage and credit spend |
+| history | Viewing recent compute usage and credit spend (gateway-only; local/direct API soft-degrades to "unavailable" — use inventory/jobs list) |
 | inventory | Rebuild a durable markdown overview of datasets + recent jobs (agent-friendly org catalog) |
 | add_funds | Getting instructions to add credits |
 | health | Diagnose API reachability during outages — GET /health + /ready; does **not** probe R2/object storage |
@@ -157,11 +157,32 @@ NOT FOR: Training itself — use train(action=map). This tool only manages the a
             return { content: [{ type: "text", text: lines.join("\n") }] };
         }
         if (action === "history") {
-            const data = await apiCall("GET", `/v1/compute/history?limit=${limit || 10}`);
-            const history = data.history.map((h) => `- ${h.started_at} | ${h.tier} | ${h.duration_minutes} min | $${(h.credits_charged / 100).toFixed(2)}`).join("\n");
-            return {
-                content: [{ type: "text", text: `Credit Balance: $${(data.credit_balance_cents / 100).toFixed(2)}\n\nRecent Usage:\n${history}` }]
-            };
+            // Gateway serves /v1/compute/history (D1 leases). Local direct API has no handler → 404.
+            try {
+                const data = await apiCall("GET", `/v1/compute/history?limit=${limit || 10}`);
+                const rows = Array.isArray(data?.history) ? data.history : [];
+                const history = rows.length === 0
+                    ? "(none)"
+                    : rows.map((h) => `- ${h.started_at} | ${h.tier} | ${h.duration_minutes} min | $${(h.credits_charged / 100).toFixed(2)}`).join("\n");
+                const bal = data?.credit_balance_cents != null
+                    ? `Credit Balance: $${(Number(data.credit_balance_cents) / 100).toFixed(2)}\n\n`
+                    : "";
+                return {
+                    content: [{ type: "text", text: `${bal}Recent Usage:\n${history}` }]
+                };
+            }
+            catch (e) {
+                const status = e?.httpStatus;
+                if (status === 404 || status === 410) {
+                    return {
+                        content: [{
+                                type: "text",
+                                text: "Usage history unavailable on this API endpoint (compute-lease history is gateway-only). Use account(action=inventory) or jobs(action=list) for recent job activity.",
+                            }]
+                    };
+                }
+                throw e;
+            }
         }
         if (action === "inventory") {
             const jobLimit = limit && limit > 0 ? Math.min(Math.floor(limit), 100) : 50;

package/dist/tools/datasets.js

@@ -4,10 +4,14 @@ import { gzipSync } from "node:zlib";
 import { createHash } from "node:crypto";
 import { z } from "zod";
 import { registerAuditedTool } from "../audit.js";
-import { apiCall, getWorkspaceRootAsync, resolveFilePathForUpload, textResult, structuredTextResult, pollUntilComplete, POLL_DERIVE_MAX_MS, POLL_ANALYZE_MAX_MS, UPLOAD_DATASET_TIMEOUT_MS, LARGE_UPLOAD_BYTES, PRESIGNED_PUT_TIMEOUT_MS, POLL_STAGE_MAX_MS, streamFileSha256, putPresignedStream, resolveUploadContentType, suggestDatasetPreview, } from "../shared.js";
+import { apiCall, getWorkspaceRootAsync, resolveFilePathForUpload, textResult, structuredTextResult, pollUntilComplete, POLL_DERIVE_MAX_MS, POLL_ANALYZE_MAX_MS, UPLOAD_DATASET_TIMEOUT_MS, LARGE_UPLOAD_BYTES, PRESIGNED_PUT_TIMEOUT_MS, POLL_STAGE_MAX_MS, awaitDatasetStageIfNeeded, streamFileSha256, putPresignedStream, resolveUploadContentType, suggestDatasetPreview, } from "../shared.js";
 import { GZIP_UPLOAD_HINT } from "../job_status_format.js";
 import { formatDatasetInventoryLine, formatTags } from "../inventory_format.js";
 import { PERIODICITY_ROW_ORDER_NOTE, SMALL_N_SOFT, buildCpuScaleGuidanceLines, buildSmallNGuardrailLines, } from "../training_scale_guidance.js";
+/** Percent-encode header values so Node fetch accepts Unicode (ByteString limit). */
+function encodeHeaderValue(s) {
+    return encodeURIComponent(s);
+}
 /**
  * Normalize a nullable string field from the API. Returns "" for absent values,
  * empty strings, and the literal SQL/serialization sentinels "missing"/"null"
@@ -165,7 +169,7 @@ Step 1 (after upload): always datasets(action=preview) to verify column types an
 action=preview: Show columns, stats, sample rows, cyclic/datetime detections. ALWAYS preview before train(action=map) on an unfamiliar dataset.
 action=analyze: Pre-training analysis on numeric columns — Pearson correlation, autocorrelation periodicity scores, and column recommendations (train, consider_dropping, project_later, low_variance). Use to choose which columns to include in training and which to project onto the map after training.
 action=list: List all datasets belonging to the organisation with id, name, rows, cols, created_at, description, tags (use tags/description or id to distinguish datasets with the same name).
-action=get: Fetch one dataset by dataset_id — returns status, staged_prefix, staged_version, ingest_error, description/tags, and stage_job_id when staging is pending.
+action=get: Fetch one dataset by dataset_id — returns status, train_ready (true only when status=ready AND staged_prefix is set), staged_prefix, staged_version, ingest_error, description/tags, and stage_job_id when staging is pending. Train only when train_ready=true (do not treat bare status=ready as enough).
 action=update: PATCH name/description/tags on an existing dataset.
 action=upload: Optional description and tags help later inventory (also settable via update).
 DO NOT AUTO-SUBSET: Call action=subset only when the user explicitly requests a filter, slice, or random sample. Default path is upload → preview/analyze → train on the full dataset_id (GPU handles scale). Never downsample to "save time" or "be helpful".
@@ -230,7 +234,7 @@ ESCALATION: If upload fails with column errors, open the file locally and verify
         })
             .optional()
             .describe("Deprecated — use filters instead. Single filter condition."),
-        expression: z.string().optional().describe("action=add_expression: math expression referencing column names (e.g. revenue/cost, log(price), rolling_mean(vol, 20))"),
+        expression: z.string().optional().describe("action=add_expression: math expression referencing column names (e.g. revenue/cost, log(price), rolling_mean(vol, 20)). Awkward names (spaces/parens): quote with backticks, e.g. `P1 (bar)` / 2"),
         options: z
             .object({
             missing: z.enum(["skip", "zero", "interpolate"]).optional(),
@@ -368,16 +372,16 @@ ESCALATION: If upload fails with column errors, open the file locally and verify
                 if (isGzipInput) {
                     const gzBytes = await fs.readFile(resolved);
                     const gzHeaders = {
-                        "X-Dataset-Name": name,
+                        "X-Dataset-Name": encodeHeaderValue(name),
                         "Content-Type": uploadContentType,
                         "Content-Encoding": "gzip",
                         "Idempotency-Key": createHash("sha256").update(`${name}\n`).update(gzBytes).digest("hex"),
                     };
                     if (description !== undefined)
-                        gzHeaders["X-Dataset-Description"] = description;
+                        gzHeaders["X-Dataset-Description"] = encodeHeaderValue(description);
                     if (tags !== undefined)
-                        gzHeaders["X-Dataset-Tags"] = JSON.stringify(tags);
-                    const data = (await apiCall("POST", "/v1/datasets", gzBytes, gzHeaders, UPLOAD_DATASET_TIMEOUT_MS));
+                        gzHeaders["X-Dataset-Tags"] = encodeHeaderValue(JSON.stringify(tags));
+                    const data = await awaitDatasetStageIfNeeded((await apiCall("POST", "/v1/datasets", gzBytes, gzHeaders, UPLOAD_DATASET_TIMEOUT_MS)));
                     const gid = data.id ?? data.dataset_id;
                     if (gid != null)
                         data.suggested_next_step = `${suggestDatasetPreview(String(gid))} to inspect columns before training.`;
@@ -395,22 +399,22 @@ ESCALATION: If upload fails with column errors, open the file locally and verify
             // cap) small; the API transparently decompresses. Small bodies stay plain.
             const GZIP_THRESHOLD = 1024 * 1024; // 1 MB
             const uploadHeaders = {
-                "X-Dataset-Name": name,
+                "X-Dataset-Name": encodeHeaderValue(name),
                 "Content-Type": uploadContentType,
                 // Deterministic key so a timed-out retry of the SAME upload reconciles to
                 // the original dataset server-side instead of creating a duplicate.
                 "Idempotency-Key": createHash("sha256").update(`${name}\n`).update(body).digest("hex"),
             };
             if (description !== undefined)
-                uploadHeaders["X-Dataset-Description"] = description;
+                uploadHeaders["X-Dataset-Description"] = encodeHeaderValue(description);
             if (tags !== undefined)
-                uploadHeaders["X-Dataset-Tags"] = JSON.stringify(tags);
+                uploadHeaders["X-Dataset-Tags"] = encodeHeaderValue(JSON.stringify(tags));
             let uploadBody = body;
             if (Buffer.byteLength(body, "utf-8") > GZIP_THRESHOLD) {
                 uploadBody = gzipSync(Buffer.from(body, "utf-8"));
                 uploadHeaders["Content-Encoding"] = "gzip";
             }
-            const data = (await apiCall("POST", "/v1/datasets", uploadBody, uploadHeaders, UPLOAD_DATASET_TIMEOUT_MS));
+            const data = await awaitDatasetStageIfNeeded((await apiCall("POST", "/v1/datasets", uploadBody, uploadHeaders, UPLOAD_DATASET_TIMEOUT_MS)));
             const id = data.id ?? data.dataset_id;
             if (id != null)
                 data.suggested_next_step = `${suggestDatasetPreview(String(id))} to inspect columns before training.`;
@@ -732,16 +736,20 @@ ESCALATION: If upload fails with column errors, open the file locally and verify
                 throw new Error("datasets(get) requires dataset_id");
             const ds = (await apiCall("GET", `/v1/datasets/${dataset_id}`));
             const tagStr = formatTags(ds.tags);
+            const trainReady = ds.train_ready === true;
             const lines = [
                 `Dataset: ${ds.name ?? "?"} (${ds.id ?? dataset_id})`,
-                `Status: ${ds.status ?? "ready"}`,
+                `Status: ${ds.status ?? "unknown"}`,
+                `Train ready: ${trainReady ? "yes" : "no"}`,
                 `Rows × cols: ${ds.rows ?? "?"} × ${ds.cols ?? "?"}`,
                 ds.size_bytes != null ? `Size: ${Number(ds.size_bytes).toLocaleString()} bytes` : "",
                 ds.description != null && String(ds.description).trim() !== "" ? `Description: ${String(ds.description)}` : "",
                 tagStr ? `Tags: ${tagStr}` : "",
                 ds.staged_prefix != null ? `Staged prefix: ${String(ds.staged_prefix)}` : "",
                 ds.staged_version != null ? `Staged version: ${String(ds.staged_version)}` : "",
-                ds.stage_job_id != null ? `Stage job: ${String(ds.stage_job_id)} (poll jobs(action=status))` : "",
+                !trainReady && ds.stage_job_id != null
+                    ? `Stage job: ${String(ds.stage_job_id)} (poll jobs(action=status) until train_ready)`
+                    : "",
                 cleanNullable(ds.ingest_error) ? `Ingest error: ${cleanNullable(ds.ingest_error)}` : "",
                 ds.created_at != null ? `Created: ${String(ds.created_at)}` : "",
             ].filter(Boolean);

package/dist/tools/inference.js

@@ -79,7 +79,7 @@ action=predict: Score rows against the trained map.
     - "compact"   → predictions.csv (row_id, bmu_x, bmu_y, bmu_node_index, cluster_id [, quantization_error, potential_anomaly]).
     - "annotated" → annotated.csv (full source CSV with bmu_x, bmu_y, bmu_node_index, cluster_id appended). Requires a dataset (no inline rows).
   Regime (auto): if the resolved dataset is the parent training dataset, regime="training" and QE / qe_p95 / potential_anomaly are omitted (QE on training data is fitting error, not generalisation — use a held-out dataset for quality). Otherwise regime="new" and full QE columns are returned.
-  Schema rules: dataset / batch rows must match the trained feature set including cyclic-expanded columns (e.g. key_cos, key_sin, not raw key). For a single inline row, the proxy uses the stateless model endpoint — raw categorical strings are allowed for baseline categorical_features models, and raw cyclic inputs are expanded from training config.
+  Schema rules: prefer dataset_id for scoring. Inline rows may use raw cyclic keys (e.g. hour) — the API/worker expands them from training config to hour_cos/hour_sin; pre-expanded cos/sin columns also work. For a single inline row, the proxy uses the stateless model endpoint (same cyclic expansion). Raw categorical strings are allowed for baseline categorical_features models on that single-row path.
   Routing: prefer dataset_id for many rows or whenever the map uses irregular SIOM / GeneralTopology layouts — the async worker path is the supported batch scorer. Single-row rows take a fast stateless path that may return invalid_inference_input on some topologies; if so, retry with dataset_id (a one-row dataset is fine). FLooP-SIOM: use dataset_id predict first.
   When the scored set has at most ${PREDICT_PREVIEW_ROW_CAP} rows, completed responses include a short per-line preview in the tool text for chat agents.
 
@@ -348,32 +348,64 @@ action=report: Returns a report manifest for the given job_id (job must be compl
         const download_urls = (results.download_urls ?? {});
         const figure_manifest = (results.figure_manifest ?? []);
         const cluster_summary = results.cluster_summary;
+        const summary = (results.summary ?? {});
         const expires_in = results.expires_in ?? 900;
+        const downloadKeys = Object.keys(download_urls);
+        const clusterSnippet = Array.isArray(cluster_summary) && cluster_summary.length > 0
+            ? cluster_summary.slice(0, 3).map((c) => {
+                const id = c.cluster_id ?? c.id ?? "?";
+                const n = c.n_nodes ?? c.size ?? "?";
+                return { cluster_id: id, n_nodes: n };
+            })
+            : [];
         const lines = [
             `Report manifest — job: ${job_id}`,
             `Use these artifacts to build your own report (Quarto, Jupyter, script). URLs expire in ${expires_in}s.`,
             "",
             "Figures (figure_manifest → download_urls):",
-            ...figure_manifest.slice(0, 12).map((e) => `  ${e.logical_name} → ${e.filename}`),
+            ...(figure_manifest.length
+                ? figure_manifest.slice(0, 12).map((e) => `  ${e.logical_name} → ${e.filename}`)
+                : ["  (none listed — small grids may omit PNGs; use cluster_summary / summary metrics below)"]),
             figure_manifest.length > 12 ? `  ... and ${figure_manifest.length - 12} more` : "",
             "",
             "Key download URLs (use get_result_image or download_urls from results(action=get)):",
-            ...Object.keys(download_urls)
-                .filter((k) => !k.endsWith(".json") || k === "cluster_summary.json")
-                .slice(0, 8)
-                .map((k) => `  ${k}: ${download_urls[k]?.slice(0, 60)}...`),
+            ...(downloadKeys.length
+                ? downloadKeys
+                    .filter((k) => !k.endsWith(".json") || k === "cluster_summary.json")
+                    .slice(0, 8)
+                    .map((k) => `  ${k}: ${download_urls[k]?.slice(0, 60)}...`)
+                : ["  (no presigned URLs — artifacts may still be in summary / cluster_summary inline)"]),
             "",
             cluster_summary?.length
-                ? `Cluster summary: ${cluster_summary.length} clusters (in response or GET .../cluster_summary).`
+                ? `Cluster summary: ${cluster_summary.length} clusters (inline snippet below; full via GET .../cluster_summary or download_urls.cluster_summary.json).`
                 : "Cluster summary: not available for this job (train with current worker to get it).",
+            ...(clusterSnippet.length
+                ? ["Inline cluster_summary (first 3):", ...clusterSnippet.map((c) => `  cluster ${c.cluster_id}: n_nodes=${c.n_nodes}`)]
+                : []),
             "",
             "Metrics: in summary (quantization_error, topographic_error, explained_variance, silhouette, etc.) or GET .../quality-report.",
+            summary.quantization_error != null ? `  QE=${summary.quantization_error}` : "",
+            summary.topographic_error != null ? `  TE=${summary.topographic_error}` : "",
         ];
         const manifestText = lines.filter(Boolean).join("\n");
         return {
             content: [
                 { type: "text", text: manifestText },
-                { type: "text", text: "Structured manifest (for automation): " + JSON.stringify({ job_id, figure_manifest, has_cluster_summary: !!cluster_summary?.length, download_url_keys: Object.keys(download_urls) }) },
+                {
+                    type: "text",
+                    text: "Structured manifest (for automation): " +
+                        JSON.stringify({
+                            job_id,
+                            figure_manifest,
+                            has_cluster_summary: !!cluster_summary?.length,
+                            cluster_summary_snippet: clusterSnippet,
+                            download_url_keys: downloadKeys,
+                            summary_metrics: {
+                                quantization_error: summary.quantization_error ?? null,
+                                topographic_error: summary.topographic_error ?? null,
+                            },
+                        }),
+                },
             ],
         };
     });

package/dist/tools/results.js

@@ -2,7 +2,7 @@ import path from "node:path";
 import fs from "node:fs/promises";
 import { z } from "zod";
 import { registerAuditedTool } from "../audit.js";
-import { apiCall, apiRawCall, getWorkspaceRootAsync, sandboxPath, pollUntilComplete, tryAttachImage, resetInlineAttachBudget, attachResultsImages, resolveOutputDpi, POLL_RECOLOR_MAX_MS, fmtDensityDiffNode, getCaptionForImage, shouldFetchAllRemainingFigures, mimeForFilename, structuredTextResult, } from "../shared.js";
+import { apiCall, apiRawCall, getWorkspaceRootAsync, sandboxPath, pollUntilComplete, tryAttachImage, resetInlineAttachBudget, attachResultsImages, resolveOutputDpi, POLL_RECOLOR_MAX_MS, fmtDensityDiffNode, getCaptionForImage, shouldFetchAllRemainingFigures, mimeForFilename, structuredTextResult, coerceFiguresArg, } from "../shared.js";
 export function registerResultsTool(server) {
     registerAuditedTool(server, "results", `Retrieve, recolor, download, or export figures and metrics for a completed map job. Presentation and artifact access only — operations on the frozen map (predict, compare, project, impute_column, transition_flow) live in **inference**.
 
@@ -20,21 +20,21 @@ ONLY call this after jobs(action=status) returns "completed".
 ESCALATION: If job not found, verify job_id. If "job not complete", poll with jobs(action=status).
 
 action=get: Returns text summary with quality metrics and inline images.
-  - figures: omit = combined only. "all" = all published plots (excludes unpublished cyclic cos/sin expansions unless train used viz_upload_cyclic_components=true). "none" = metrics text only, no images (recommended for sweeps and LLM clients to keep tool payloads small). Array = specific logical names (combined, umatrix, hit_histogram, learning_curve, correlation, divergence_kl, component_1..N). Request unpublished cyclic planes via results(recolor, figures=[component_N, ...]).
+  - figures: omit = combined only. Prefer string "all" / "none" (not an array). "all" = all published plots (excludes unpublished cyclic cos/sin expansions unless train used viz_upload_cyclic_components=true). "none" = metrics text only, no images (recommended for sweeps and LLM clients to keep tool payloads small). Array = specific logical names (combined, umatrix, hit_histogram, learning_curve, correlation, divergence_kl, component_1..N) or download filenames. Hosts that stringify arrays are coerced. Request unpublished cyclic planes via results(recolor, figures=[component_N, ...]).
   - include_individual: if true (and figures omitted), inlines every component plane.
   - After recolor or project, use the job_id returned by that operation to get the new artifacts, not the original training job_id.
   - After showing results, guide the user: QE interpretation, whether to retrain, which features to explore.
   - METRIC INTERPRETATION: QE lower=better (<1.5 good) | TE<0.1 good | Explained variance>0.7 good | Silhouette higher=better | Davies-Bouldin lower=better.
 
-action=export: Structured data exports. Use export_type= to choose what to export.
-  - export_type=training_log: learning curve sparklines + plot. Diagnose convergence/plateau/divergence.
+action=export: Structured data exports (not the same as download). Use export_type= to choose what to export.
+  - export_type=training_log: learning curve sparklines + plot. Diagnose convergence/plateau/divergence. Prefer this over download for the training log.
   - export_type=weights: full weight matrix + normalization stats. For external analysis or custom viz.
   - export_type=nodes: per-node hit count + feature stats. Profile clusters and operating modes.
 
-action=download: Save figures to disk. Use so user can open, share, or version files locally.
+action=download: Save figures/artifacts to disk (deduped file list). Use so user can open, share, or version files locally.
   - folder: e.g. "." or "./results". Relative to the client's working directory (or MCP workspace). Each job lands in a dedicated subfolder under folder: {job_type}_{label} when label was set at train time, otherwise {job_type}_{job_id_prefix} — so parallel downloads never overwrite summary.json or figure names.
-  - figures: "all" (default) or array of filenames.
-  - include_json: when true, also saves summary.json (and adds it to the download list if figures omitted).
+  - figures: "all" (default) downloads published image files; OR a string array of exact artifact filenames from the job (e.g. ["predictions.csv"], ["combined.png","umatrix.png"]). Enum tokens like "none" are for action=get, not download.
+  - include_json: when true, also saves summary.json and other JSON artifacts (use this when you need CSVs listed in summary.files without naming each figure).
 
 action=recolor: Change colormap or output format — no retraining. Returns a new job_id; auto-polls 60s.
   AFTER: use results(action=get, job_id=NEW_JOB_ID).
@@ -47,10 +47,10 @@ NOT FOR: Jobs that haven't completed (use jobs(action=status) first), or tempora
             .enum(["get", "recolor", "download", "export", "feature_divergences"])
             .describe("get: inline results + metrics; recolor: new colormap/format (async); download: save to disk; export: structured data; feature_divergences: KL/W1 on component planes (async)."),
         job_id: z.string().describe("Job ID of a completed job"),
-        figures: z
+        figures: z.preprocess(coerceFiguresArg, z
             .union([z.enum(["default", "combined_only", "all", "images", "none"]), z.array(z.string())])
             .optional()
-            .describe("action=get: omit=combined only; 'all'=all plots; 'none'=metrics text only (no images, ideal for sweeps and LLM clients); array=specific (combined,umatrix,hit_histogram,learning_curve,correlation,divergence_kl,component_1..N). action=download: 'all'=all image files; array=specific filenames."),
+            .describe("Prefer string 'all'/'none'. action=get: omit=combined only; 'all'=all plots; 'none'=metrics text only; array=logical names (combined,umatrix,…). action=download: 'all'=image files; array=exact filenames (e.g. combined.png). Stringified JSON arrays from hosts are accepted.")),
         include_individual: z
             .boolean()
             .optional()
@@ -631,6 +631,7 @@ NOT FOR: Jobs that haven't completed (use jobs(action=status) first), or tempora
             else {
                 toDownload = files.filter(isImage);
             }
+            toDownload = [...new Set(toDownload)];
             let resolvedDir = sandboxPath(folder, await getWorkspaceRootAsync(server));
             // Always namespace each job's files into its own subfolder so that
             // downloading multiple jobs (or job types) into the same folder never

package/dist/tools/train.js

@@ -1,6 +1,6 @@
 import { z } from "zod";
 import { registerAuditedTool } from "../audit.js";
-import { apiCall } from "../shared.js";
+import { apiCall, ensureDatasetTrainReady } from "../shared.js";
 import { buildTrainSubmitExtras } from "../train_submit_message.js";
 import { TRAINING_MONITOR_URI, buildTrainingMonitorResult, } from "./training_monitor.js";
 import { TRAINING_INPUT_SCHEMA, buildTrainMapParams, buildFloopParams, fetchTrainingPresets, assertValidNormalizationArgs, } from "./training_core.js";
@@ -52,6 +52,7 @@ function assertImputeTrainingArgs(args) {
 }
 /** Shared POST /v1/jobs + train submit message extras (map/siom/impute and floop). */
 async function submitTrainJob(opts) {
+    await ensureDatasetTrainReady(opts.dataset_id);
     const submitBody = { dataset_id: opts.dataset_id, params: opts.params };
     if (opts.label && opts.label.trim() !== "")
         submitBody.label = opts.label;

package/dist/train_submit_message.js

@@ -2,9 +2,10 @@ import { buildVizStandaloneUrl } from "./viz_links.js";
 export function buildTrainSubmitExtras(opts) {
     const { newJobId, totalRows, hasTransforms, prepareJobId, variantPrefix, paramSummary, impute, resultsHint } = opts;
     const monitorUrl = buildVizStandaloneUrl("training-monitor", newJobId);
+    const prepareKind = impute ? "prepare_impute_matrix" : "prepare_training_matrix";
     let msg = `Job submitted (${variantPrefix}, ${paramSummary}). `;
     if (prepareJobId) {
-        msg += `Preprocessing job prepare_training_matrix (${prepareJobId}) runs on worker-io first; train job ${newJobId} starts after it completes. Poll jobs(action=status, job_id="${prepareJobId}") until completed, then poll the train job. `;
+        msg += `Preprocessing job ${prepareKind} (${prepareJobId}) runs on worker-io first; train job ${newJobId} starts after it completes. Poll jobs(action=status, job_id="${prepareJobId}") or jobs(action=status, job_id="${newJobId}") (shows prepare_job_id + waiting_for_prepare) until prepare completes, then poll the train job. `;
     }
     msg += `Training monitor opened for job ${newJobId}`;
     if (monitorUrl)

package/dist/training_monitor_curve.js

@@ -25,7 +25,8 @@ export function teCurveLabel(base) {
  * epochs=[N,0], so convergence_errors is empty while ordering has many batch points.
  */
 export function isFloopJob(data) {
-    const phase = String(data.training_progress_phase ?? data.progress_phase ?? "").toLowerCase();
+    const rawPhase = String(data.training_progress_phase ?? data.progress_phase ?? "").toLowerCase();
+    const phase = rawPhase === "missing" ? "" : rawPhase;
     if (phase === "floop")
         return true;
     const jt = String(data.job_type ?? "").toLowerCase();

package/dist/views/src/views/training-monitor/index.html

@@ -139,7 +139,7 @@ for compatibility with Zod schema generation. Both are functionally equivalent f
 - "app": Tool callable by the app from this server only`)});v.object({mimeTypes:v.array(v.string()).optional().describe('Array of supported MIME types for UI resources.\nMust include `"text/html;profile=mcp-app"` for MCP Apps support.')});v.object({method:v.literal("ui/message"),params:v.object({role:v.literal("user").describe('Message role, currently only "user" is supported.'),content:v.array(fo).describe("Message content blocks (text, image, etc.).")})});v.object({method:v.literal("ui/notifications/sandbox-resource-ready"),params:v.object({html:v.string().describe("HTML content to load into the inner iframe."),sandbox:v.string().optional().describe("Optional override for the inner iframe's sandbox attribute."),csp:fd.optional().describe("CSP configuration from resource metadata."),permissions:md.optional().describe("Sandbox permissions from resource metadata.")})});var TT=v.object({method:v.literal("ui/notifications/tool-result"),params:Na.describe("Standard MCP tool execution result.")}),h$=v.object({toolInfo:v.object({id:oo.optional().describe("JSON-RPC id of the tools/call request."),tool:gu.describe("Tool definition including name, inputSchema, etc.")}).optional().describe("Metadata of the tool call that instantiated this App."),theme:mT.optional().describe("Current color theme preference."),styles:kT.optional().describe("Style configuration for theming the app."),displayMode:Qr.optional().describe("How the UI is currently displayed."),availableDisplayModes:v.array(Qr).optional().describe("Display modes the host supports."),containerDimensions:v.union([v.object({height:v.number().describe("Fixed container height in pixels.")}),v.object({maxHeight:v.union([v.number(),v.undefined()]).optional().describe("Maximum container height in pixels.")})]).and(v.union([v.object({width:v.number().describe("Fixed container width in pixels.")}),v.object({maxWidth:v.union([v.number(),v.undefined()]).optional().describe("Maximum container width in pixels.")})])).optional().describe(`Container dimensions. Represents the dimensions of the iframe or other
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@barivia/barsom-mcp",
-  "version": "0.23.5",
+  "version": "0.23.9",
   "description": "barSOM MCP proxy — connect any MCP client to the barSOM cloud API for Self-Organizing Map analytics",
   "keywords": [
     "mcp",