@barivia/barmesh-mcp 0.3.0 → 0.4.0

package/README.md

@@ -13,7 +13,14 @@ form on a shared self-organizing map (SOM)**:
 - **`barmesh_mesh_convergence`** — trains one SOM on all meshes (joint-normalized), projects
   each mesh to a volume-weighted fingerprint, and computes **symmetric KL** and
   **Wasserstein-1 (EMD)** distances stepwise and against a reference mesh, with publication
-  figures and an advisory convergence reading.
+  figures and an advisory convergence reading. The SOM features are preprocessed by the
+  same staged pipeline as barsom training, so any dataset (small or large, CSV/gzip/Parquet)
+  is handled out-of-core by default; optional `transforms`, `normalize`,
+  `normalization_methods`, and `row_range` give the same preprocessing controls. Submit
+  enqueues **`prepare_training_matrix`** on worker-io when the dataset is staged; the proxy
+  auto-polls `prepare_job_id` before the mesh job runs. Default **`defer_figures=true`** →
+  **`cfd_finalize`** on worker-io; **`barmesh_jobs(status)`** auto-polls **`finalize_job_id`**
+  when figures are deferred.
 - **`barmesh_richardson`** — classical three-level Richardson extrapolation / Grid
   Convergence Index (GCI) on scalar quantities of interest.
 
@@ -48,7 +55,7 @@ API key; otherwise the analysis calls return HTTP 403. Contact Barivia to enable
 | `barmesh_datasets` | Upload / preview / list the mesh CSV. |
 | `barmesh_mesh_convergence` | SOM fingerprint distances (async job). |
 | `barmesh_richardson` | Richardson/GCI on scalar QoIs (async job). |
-| `barmesh_jobs` | Poll job status / list jobs. |
+| `barmesh_jobs` | Poll job status / list jobs (auto-polls CFD prepare + finalize when applicable). |
 | `barmesh_results` | Distances, convergence reading, and figures. |
 | `barmesh_send_feedback` | Send a short note or bug report to the Barivia team. |
 

package/dist/cfd_finalize.js

@@ -0,0 +1,23 @@
+import { apiCall, pollUntilComplete } from "./shared.js";
+/**
+ * When CFD compute finishes with defer_figures, cfd_finalize may still be rendering on worker-io.
+ */
+export async function pollCfdFinalizeIfPresent(jobId, data, timeoutMs = 600_000) {
+    const finalizeJobId = data.finalize_job_id;
+    if (!finalizeJobId)
+        return { finalizeJobId: null, note: null };
+    const poll = await pollUntilComplete(finalizeJobId, timeoutMs);
+    if (poll.status === "failed") {
+        throw new Error(`CFD job ${jobId}: cfd_finalize ${finalizeJobId} failed: ${poll.error ?? "unknown error"}`);
+    }
+    if (poll.status !== "completed") {
+        throw new Error(`CFD job ${jobId}: cfd_finalize ${finalizeJobId} did not complete (status=${poll.status})`);
+    }
+    return {
+        finalizeJobId,
+        note: `Finalize job ${finalizeJobId} completed (figures uploaded).`,
+    };
+}
+export async function refreshJobAfterFinalize(jobId) {
+    return (await apiCall("GET", `/v1/jobs/${jobId}`));
+}

package/dist/cfd_prepare.js

@@ -0,0 +1,19 @@
+import { pollUntilComplete } from "./shared.js";
+/**
+ * Mesh-convergence on a staged dataset enqueues a preprocessing job
+ * (prepare_training_matrix) first; the submit response carries its id as
+ * `prepare_job_id`. Poll it to completion before the mesh job runs.
+ */
+export async function pollCfdPrepareIfPresent(data, label, timeoutMs = 600_000) {
+    const prepareJobId = data.prepare_job_id;
+    if (!prepareJobId)
+        return null;
+    const poll = await pollUntilComplete(prepareJobId, timeoutMs);
+    if (poll.status === "failed") {
+        throw new Error(`${label}: data preparation job ${prepareJobId} failed: ${poll.error ?? "unknown error"}`);
+    }
+    if (poll.status !== "completed") {
+        throw new Error(`${label}: data preparation job ${prepareJobId} did not complete (status=${poll.status})`);
+    }
+    return prepareJobId;
+}

package/dist/shared.js

@@ -20,7 +20,7 @@ export const FETCH_TIMEOUT_MS = parseInt(process.env.BARIVIA_FETCH_TIMEOUT_MS ??
 export const MAX_RETRIES = 2;
 export const RETRYABLE_STATUS = new Set([502, 503, 504]);
 /** Single source of truth for the proxy version. Keep in sync with package.json on bump. */
-export const CLIENT_VERSION = "0.3.0";
+export const CLIENT_VERSION = "0.4.0";
 export const PUBLIC_SITE_ORIGIN = "https://barivia.se";
 /** Large per-cell CSV uploads may exceed the default fetch timeout. */
 export const UPLOAD_DATASET_TIMEOUT_MS = 180_000;

package/dist/tools/cfd.js

@@ -1,6 +1,7 @@
 import { z } from "zod";
 import { registerAuditedTool } from "../audit.js";
 import { apiCall, textResult } from "../shared.js";
+import { pollCfdPrepareIfPresent } from "../cfd_prepare.js";
 export function registerCfdTools(server) {
     registerAuditedTool(server, "barmesh_mesh_convergence", `Run SOM-based mesh-convergence analysis on an uploaded combined per-cell CSV.
 
@@ -26,6 +27,10 @@ COMMON MISTAKES: omitting feature_columns (required); choosing a reference_mesh
         emd_method: z.enum(["exact", "sinkhorn"]).optional().describe("EMD solver: exact LP (default) or sinkhorn (fast approximation for large grids)"),
         component_planes_physical: z.boolean().optional().describe("Physical-scale component-plane colorbars (default true)"),
         figures: z.boolean().optional().describe("Generate publication figures (default true)"),
+        transforms: z.record(z.enum(["log", "log1p", "log10", "sqrt", "square", "abs", "invert", "none"])).optional().describe("Per-feature transform applied before normalization (e.g. log1p to compress k/epsilon/omega). Same preprocessing engine as barsom training."),
+        normalize: z.union([z.enum(["all", "auto", "mad", "sigmoidal", "sepd"]), z.array(z.string())]).optional().describe("Normalization mode for SOM features (default auto = joint z-score of non-cyclic features). Use mad for heavy-tailed channels."),
+        normalization_methods: z.record(z.enum(["zscore", "mad", "sigmoidal", "sepd", "none"])).optional().describe("Per-feature normalization override; keys must be in feature_columns."),
+        row_range: z.tuple([z.number().int().min(1), z.number().int().min(1)]).optional().describe("1-based inclusive [start, end] row slice applied during preprocessing (and to mesh labels / cell volumes)."),
         label: z.string().optional().describe("Optional job label"),
     }, async (args) => {
         const { dataset_id, label, ...rest } = args;
@@ -38,9 +43,12 @@ COMMON MISTAKES: omitting feature_columns (required); choosing a reference_mesh
         if (typeof label === "string" && label.length > 0)
             body.label = label;
         const data = (await apiCall("POST", "/v1/cfd/mesh-convergence", body));
+        await pollCfdPrepareIfPresent(data, "barmesh_mesh_convergence");
         const id = data.id;
-        if (id != null)
-            data.suggested_next_step = `Poll barmesh_jobs(action=status, job_id=${id}); on completion call barmesh_results(action=get, job_id=${id}).`;
+        if (id != null) {
+            const prep = data.prepare_job_id != null ? " (dataset prepare complete)" : "";
+            data.suggested_next_step = `Poll barmesh_jobs(action=status, job_id=${id})${prep}; on completion call barmesh_results(action=get, job_id=${id}).`;
+        }
         return textResult(data);
     });
     registerAuditedTool(server, "barmesh_richardson", `Run classical Richardson extrapolation / Grid Convergence Index (GCI) on scalar quantities of interest.

package/dist/tools/jobs.js

@@ -1,6 +1,7 @@
 import { z } from "zod";
 import { registerAuditedTool } from "../audit.js";
 import { apiCall, textResult } from "../shared.js";
+import { pollCfdFinalizeIfPresent, refreshJobAfterFinalize } from "../cfd_finalize.js";
 export function registerJobsTool(server) {
     registerAuditedTool(server, "barmesh_jobs", `Check job status or list jobs.
 
@@ -14,7 +15,20 @@ ESCALATION: status=failed returns an error message and (when available) a failur
         if (action === "status") {
             if (!job_id)
                 throw new Error("barmesh_jobs(status) requires job_id.");
-            const data = await apiCall("GET", `/v1/jobs/${job_id}`);
+            let data = (await apiCall("GET", `/v1/jobs/${job_id}`));
+            const status = String(data.status ?? "");
+            if (status === "completed" && data.finalize_job_id) {
+                const { note } = await pollCfdFinalizeIfPresent(job_id, data);
+                data = await refreshJobAfterFinalize(job_id);
+                const lines = [
+                    `Job ${job_id}: ${String(data.status ?? "unknown")}`,
+                    data.label != null ? `Label: ${String(data.label)}` : null,
+                    data.progress != null ? `Progress: ${String(data.progress)}` : null,
+                    data.result_ref != null ? `Results: ${String(data.result_ref)}` : null,
+                    note,
+                ].filter(Boolean);
+                return textResult({ ...data, status_text: lines.join("\n") });
+            }
             return textResult(data);
         }
         const data = await apiCall("GET", "/v1/jobs");

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@barivia/barmesh-mcp",
-  "version": "0.3.0",
+  "version": "0.4.0",
   "description": "barmesh MCP proxy — SOM-based CFD mesh-convergence and Richardson/GCI analysis on the Barivia cloud API",
   "keywords": [
     "mcp",