@inflexa-ai/harness 0.18.0 → 0.19.1

package/dist/tools/sandbox/list-available-refs.d.ts

@@ -14,7 +14,11 @@
  * it at — read where it lives, render where the caller will open it. Reading it
  * host-side is what lets a planner ask what reference data exists before any
  * sandbox is created; a step agent asking mid-run sees the same store, because
- * the mount and this path are the same bytes.
+ * the mount and this path are the same bytes. An omitted `refStorePath` falls
+ * back to that same container path — where a host that mounts the store into its
+ * own process (a K8s pod holding the ref-store PVC) already sees it. The fallback
+ * is stat-verified like any other root, so a host with nothing mounted there
+ * still reports the store as unavailable.
  *
  * The scan reports paths; meaning is joined on afterwards from the install
  * receipt and the catalog it names (organism, format, and each file's internal

package/dist/tools/sandbox/list-available-refs.js

@@ -14,7 +14,11 @@
  * it at — read where it lives, render where the caller will open it. Reading it
  * host-side is what lets a planner ask what reference data exists before any
  * sandbox is created; a step agent asking mid-run sees the same store, because
- * the mount and this path are the same bytes.
+ * the mount and this path are the same bytes. An omitted `refStorePath` falls
+ * back to that same container path — where a host that mounts the store into its
+ * own process (a K8s pod holding the ref-store PVC) already sees it. The fallback
+ * is stat-verified like any other root, so a host with nothing mounted there
+ * still reports the store as unavailable.
  *
  * The scan reports paths; meaning is joined on afterwards from the install
  * receipt and the catalog it names (organism, format, and each file's internal
@@ -30,9 +34,13 @@ import { z } from "zod";
 import { capCodePoints, DETAIL_MAX_LENGTH, DETAIL_NEEDLE_MAX_LENGTH } from "../../loop/tool-detail.js";
 import { REFERENCE_DATA_CATALOG } from "../../reference-data/catalog.js";
 import { parseReferenceInstallReceipt } from "../../reference-data/receipt.js";
+import { REFS_CONTAINER_PATH } from "../../sandbox/mount-plan.js";
 import { defineTool } from "../define-tool.js";
-/** Container path the ref store is mounted at; every reported path is rendered under it. */
-const REFS_ROOT = "/mnt/refs";
+/**
+ * Container path the ref store is mounted at: every reported path is rendered
+ * under it, and it is the read root when the embedder supplies none.
+ */
+const REFS_ROOT = REFS_CONTAINER_PATH;
 const MAX_ENTRIES = 200;
 const MAX_SCANNED_ENTRIES = 2_000;
 const MAX_PATH_BYTES = 40_000;
@@ -283,8 +291,6 @@ async function collectFiles(directory, relative, budget) {
  */
 async function scanStore(root, relative, recursive = false) {
     const empty = () => ({ entries: [], scannedEntries: 0, truncated: false });
-    if (!root)
-        return { state: "unavailable", ...empty() };
     try {
         if (!(await lstat(root)).isDirectory())
             return { state: "unavailable", ...empty() };
@@ -494,6 +500,7 @@ function renderContent(path, scan, entries) {
 }
 /** Create reference discovery over the host-visible reference store. */
 export function createListAvailableRefsTool(deps) {
+    const storeRoot = deps.refStorePath ?? REFS_ROOT;
     return defineTool({
         id: "list_available_refs",
         description: "Resolve reference data you need into a real path. Reports the reference data provisioned for this environment right now — the only reference data an analysis script can open. " +
@@ -570,7 +577,7 @@ export function createListAvailableRefsTool(deps) {
             // recursive pass a search from the store root only ever sees directories,
             // which carry no dataset labels, so "find me a regulon network" finds nothing.
             const needleGiven = (query?.trim() ?? "") !== "";
-            const raw = await scanStore(deps.refStorePath, posixPath.relative(REFS_ROOT, requested.path) || ".", needleGiven);
+            const raw = await scanStore(storeRoot, posixPath.relative(REFS_ROOT, requested.path) || ".", needleGiven);
             const enriched = enrichEntries(raw.entries, raw);
             const categories = collectCategories(enriched);
             const needle = query?.trim().toLowerCase();

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@inflexa-ai/harness",
-    "version": "0.18.0",
+    "version": "0.19.1",
     "description": "Host-agnostic bioinformatics agent harness \u2014 hand-rolled agent loop, DBOS-durable workflows, sandboxed compute.",
     "license": "Apache-2.0",
     "type": "module",
@@ -44,11 +44,12 @@
         "typecheck": "tsc --noEmit"
     },
     "dependencies": {
-        "@ai-sdk/anthropic": "^4.0.20",
-        "@ai-sdk/openai-compatible": "^3.0.10",
-        "@ai-sdk/provider": "^4.0.3",
-        "@ai-sdk/provider-utils": "5.0.10",
-        "@anthropic-ai/sdk": "^0.107.0",
+        "@ai-sdk/anthropic": "^4.0.38",
+        "@ai-sdk/openai": "^4.0.39",
+        "@ai-sdk/openai-compatible": "^3.0.30",
+        "@ai-sdk/provider": "^4.0.7",
+        "@ai-sdk/provider-utils": "5.0.27",
+        "@anthropic-ai/sdk": "^0.116.0",
         "@dbos-inc/dbos-sdk": "^4.23.6",
         "@kubernetes/client-node": "^1.4.0",
         "@opentelemetry/api": "^1.9.1",
@@ -60,17 +61,18 @@
         "@opentelemetry/sdk-trace-base": "^2.9.0",
         "@opentelemetry/sdk-trace-node": "^2.9.0",
         "@opentelemetry/semantic-conventions": "^1.43.0",
-        "ai": "^7.0.28",
+        "ai": "^7.0.61",
         "cheerio": "^1.2.0",
         "dockerode": "^4.0.12",
         "fast-xml-parser": "^5.10.0",
         "hono": "^4.12.30",
+        "hyparquet": "^1.28.1",
         "js-tiktoken": "^1.0.21",
         "mime": "^4.1.0",
         "nanoid": "^5.1.16",
         "neverthrow": "^8.2.0",
         "nunjucks": "^3.2.4",
-        "openai": "^4.104.0",
+        "openai": "^7.4.0",
         "p-queue": "^9.3.3",
         "pdf-parse": "^2.4.5",
         "pg": "^8.22.0",