labgate 0.5.39 → 0.5.42

package/dist/mcp-bundles/results-mcp.bundle.mjs

@@ -2979,7 +2979,7 @@ var require_compile = __commonJS({
       const schOrFunc = root.refs[ref];
       if (schOrFunc)
         return schOrFunc;
-      let _sch = resolve2.call(this, root, ref);
+      let _sch = resolve3.call(this, root, ref);
       if (_sch === void 0) {
         const schema = (_a2 = root.localRefs) === null || _a2 === void 0 ? void 0 : _a2[ref];
         const { schemaId } = this.opts;
@@ -3006,7 +3006,7 @@ var require_compile = __commonJS({
     function sameSchemaEnv(s1, s2) {
       return s1.schema === s2.schema && s1.root === s2.root && s1.baseId === s2.baseId;
     }
-    function resolve2(root, ref) {
+    function resolve3(root, ref) {
       let sch;
       while (typeof (sch = this.refs[ref]) == "string")
         ref = sch;
@@ -3581,7 +3581,7 @@ var require_fast_uri = __commonJS({
       }
       return uri;
     }
-    function resolve2(baseURI, relativeURI, options) {
+    function resolve3(baseURI, relativeURI, options) {
       const schemelessOptions = options ? Object.assign({ scheme: "null" }, options) : { scheme: "null" };
       const resolved = resolveComponent(parse3(baseURI, schemelessOptions), parse3(relativeURI, schemelessOptions), schemelessOptions, true);
       schemelessOptions.skipEscape = true;
@@ -3808,7 +3808,7 @@ var require_fast_uri = __commonJS({
     var fastUri = {
       SCHEMES,
       normalize,
-      resolve: resolve2,
+      resolve: resolve3,
       resolveComponent,
       equal,
       serialize,
@@ -27964,7 +27964,7 @@ var Protocol = class {
           return;
         }
         const pollInterval = task2.pollInterval ?? this._options?.defaultTaskPollInterval ?? 1e3;
-        await new Promise((resolve2) => setTimeout(resolve2, pollInterval));
+        await new Promise((resolve3) => setTimeout(resolve3, pollInterval));
         options?.signal?.throwIfAborted();
       }
     } catch (error48) {
@@ -27981,7 +27981,7 @@ var Protocol = class {
    */
   request(request, resultSchema, options) {
     const { relatedRequestId, resumptionToken, onresumptiontoken, task, relatedTask } = options ?? {};
-    return new Promise((resolve2, reject) => {
+    return new Promise((resolve3, reject) => {
       const earlyReject = (error48) => {
         reject(error48);
       };
@@ -28059,7 +28059,7 @@ var Protocol = class {
           if (!parseResult.success) {
             reject(parseResult.error);
           } else {
-            resolve2(parseResult.data);
+            resolve3(parseResult.data);
           }
         } catch (error48) {
           reject(error48);
@@ -28320,12 +28320,12 @@ var Protocol = class {
       }
     } catch {
     }
-    return new Promise((resolve2, reject) => {
+    return new Promise((resolve3, reject) => {
       if (signal.aborted) {
         reject(new McpError(ErrorCode.InvalidRequest, "Request cancelled"));
         return;
       }
-      const timeoutId = setTimeout(resolve2, interval);
+      const timeoutId = setTimeout(resolve3, interval);
       signal.addEventListener("abort", () => {
         clearTimeout(timeoutId);
         reject(new McpError(ErrorCode.InvalidRequest, "Request cancelled"));
@@ -29284,7 +29284,7 @@ var McpServer = class {
     let task = createTaskResult.task;
     const pollInterval = task.pollInterval ?? 5e3;
     while (task.status !== "completed" && task.status !== "failed" && task.status !== "cancelled") {
-      await new Promise((resolve2) => setTimeout(resolve2, pollInterval));
+      await new Promise((resolve3) => setTimeout(resolve3, pollInterval));
       const updatedTask = await extra.taskStore.getTask(taskId);
       if (!updatedTask) {
         throw new McpError(ErrorCode.InternalError, `Task ${taskId} not found during polling`);
@@ -29927,35 +29927,36 @@ var StdioServerTransport = class {
     this.onclose?.();
   }
   send(message) {
-    return new Promise((resolve2) => {
+    return new Promise((resolve3) => {
       const json2 = serializeMessage(message);
       if (this._stdout.write(json2)) {
-        resolve2();
+        resolve3();
       } else {
-        this._stdout.once("drain", resolve2);
+        this._stdout.once("drain", resolve3);
       }
     });
   }
 };
 
 // src/lib/results-mcp.ts
-import { chmodSync as chmodSync2, existsSync as existsSync3, mkdirSync as mkdirSync2, readFileSync as readFileSync3, writeFileSync as writeFileSync2 } from "fs";
-import { dirname as dirname2, isAbsolute, relative, resolve } from "path";
+import { chmodSync as chmodSync2, existsSync as existsSync3, mkdirSync as mkdirSync2, readFileSync as readFileSync3, writeFileSync as writeFileSync3 } from "fs";
+import { dirname as dirname3, isAbsolute, relative, resolve as resolve2 } from "path";
 import { createHash } from "crypto";
 import { execFile } from "child_process";
 import { promisify } from "util";
 
 // src/lib/results-store.ts
 import { randomUUID } from "crypto";
-import { existsSync as existsSync2, readFileSync as readFileSync2, renameSync, unlinkSync, writeFileSync } from "fs";
-import { dirname, join as join2 } from "path";
+import { existsSync as existsSync2, readFileSync as readFileSync2, renameSync, unlinkSync, writeFileSync as writeFileSync2 } from "fs";
+import { dirname as dirname2, join as join2 } from "path";
 
 // src/lib/config.ts
-import { readFileSync, existsSync, chmodSync, mkdirSync } from "fs";
-import { join } from "path";
+import { readFileSync, existsSync, chmodSync, mkdirSync, writeFileSync } from "fs";
+import { dirname, join, resolve } from "path";
 import { homedir } from "os";
 var DEFAULT_CONFIG = {
   runtime: "auto",
+  images_dir: "",
   // Default sandbox image: includes python3 + basic build tools (git/make/g++).
   // Note: pip/venv are not included by default in Debian; users may still need a
   // custom image for richer Python workflows.
@@ -29988,7 +29989,8 @@ var DEFAULT_CONFIG = {
       "mkfs",
       "reboot",
       "shutdown"
-    ]
+    ],
+    ensure_commands: ["git"]
   },
   network: {
     mode: "host",
@@ -30014,13 +30016,9 @@ var DEFAULT_CONFIG = {
   },
   plugins: {
     files: true,
+    activity: true,
     datasets: false,
     results: false,
-    charting: true,
-    molecular: true,
-    genomics: true,
-    phylogenetics: true,
-    network: true,
     slurm: true,
     explorer: true,
     automation: false
@@ -30041,7 +30039,7 @@ var DEFAULT_CONFIG = {
     max_tokens: 1024
   },
   headless: {
-    claude_run_with_allowed_permissions: true,
+    claude_run_with_allowed_permissions: false,
     continuation_in_other_terminals: true,
     git_integration: false
   }
@@ -30594,9 +30592,9 @@ var ResultsStore = class {
       }
     }
     try {
-      ensurePrivateDir(dirname(this.dbPath));
+      ensurePrivateDir(dirname2(this.dbPath));
       const normalizedRaw = legacyRaw.trimEnd();
-      writeFileSync(
+      writeFileSync2(
         this.dbPath,
         (normalizedRaw || JSON.stringify({ version: 1, results: [] }, null, 2)) + "\n",
         {
@@ -30609,10 +30607,10 @@ var ResultsStore = class {
     }
   }
   ensureFile() {
-    ensurePrivateDir(dirname(this.dbPath));
+    ensurePrivateDir(dirname2(this.dbPath));
     if (!existsSync2(this.dbPath)) {
       const initial = { version: 1, results: [] };
-      writeFileSync(this.dbPath, JSON.stringify(initial, null, 2) + "\n", {
+      writeFileSync2(this.dbPath, JSON.stringify(initial, null, 2) + "\n", {
         encoding: "utf-8",
         mode: PRIVATE_FILE_MODE
       });
@@ -30666,8 +30664,8 @@ var ResultsStore = class {
   }
   writeFile(next) {
     const payload = JSON.stringify(next, null, 2) + "\n";
-    const tmpPath = join2(dirname(this.dbPath), `.${Date.now()}.${process.pid}.${randomUUID()}.results.tmp`);
-    writeFileSync(tmpPath, payload, {
+    const tmpPath = join2(dirname2(this.dbPath), `.${Date.now()}.${process.pid}.${randomUUID()}.results.tmp`);
+    writeFileSync2(tmpPath, payload, {
       encoding: "utf-8",
       mode: PRIVATE_FILE_MODE
     });
@@ -30682,7 +30680,7 @@ var ResultsStore = class {
         throw err;
       }
       try {
-        writeFileSync(this.dbPath, payload, {
+        writeFileSync2(this.dbPath, payload, {
           encoding: "utf-8",
           mode: PRIVATE_FILE_MODE
         });
@@ -30759,9 +30757,9 @@ function isPathInside(rootPath, targetPath) {
 }
 function buildAllowedRoots(input) {
   const roots = [
-    input.executionWorkdir ? resolve(input.executionWorkdir) : "",
-    input.workdir ? resolve(input.workdir) : "",
-    resolve(process.cwd())
+    input.executionWorkdir ? resolve2(input.executionWorkdir) : "",
+    input.workdir ? resolve2(input.workdir) : "",
+    resolve2(process.cwd())
   ].filter(Boolean);
   return [...new Set(roots)];
 }
@@ -30773,16 +30771,16 @@ function ensurePathAllowed(path, allowedRoots) {
   );
 }
 function ensureScriptOnDisk(scriptPath, allowedRoots, scriptContent) {
-  const resolvedPath = resolve(String(scriptPath || "").trim());
+  const resolvedPath = resolve2(String(scriptPath || "").trim());
   if (!resolvedPath) {
     throw new Error("reproducibility.script_path is required.");
   }
   ensurePathAllowed(resolvedPath, allowedRoots);
   if (typeof scriptContent === "string") {
-    mkdirSync2(dirname2(resolvedPath), { recursive: true });
+    mkdirSync2(dirname3(resolvedPath), { recursive: true });
     const normalized = scriptContent.endsWith("\n") ? scriptContent : `${scriptContent}
 `;
-    writeFileSync2(resolvedPath, normalized, "utf-8");
+    writeFileSync3(resolvedPath, normalized, "utf-8");
     try {
       chmodSync2(resolvedPath, 493);
     } catch {
@@ -30807,7 +30805,7 @@ function makeDefaultExecution(strategy, runNow) {
   return { status: "not_run" };
 }
 async function executeLocalReproScript(input) {
-  const cwd = input.workdir ? resolve(input.workdir) : dirname2(input.scriptPath);
+  const cwd = input.workdir ? resolve2(input.workdir) : dirname3(input.scriptPath);
   const timeoutMs = clampInt2(input.timeoutSeconds, DEFAULT_REPRO_TIMEOUT_SECONDS, 10, 86400) * 1e3;
   const start = Date.now();
   const scriptKind = String(input.scriptKind || "").toLowerCase();
@@ -30883,7 +30881,7 @@ async function executeLocalReproScript(input) {
   }
 }
 async function executeSlurmReproScript(input) {
-  const cwd = input.workdir ? resolve(input.workdir) : dirname2(input.scriptPath);
+  const cwd = input.workdir ? resolve2(input.workdir) : dirname3(input.scriptPath);
   const timeoutMs = clampInt2(input.timeoutSeconds, DEFAULT_REPRO_TIMEOUT_SECONDS, 10, 86400) * 1e3;
   const start = Date.now();
   const useCustomCommand = typeof input.commandOverride === "string" && input.commandOverride.trim().length > 0;

package/dist/mcp-bundles/slurm-mcp.bundle.mjs

@@ -2985,7 +2985,7 @@ var require_compile = __commonJS({
       const schOrFunc = root.refs[ref];
       if (schOrFunc)
         return schOrFunc;
-      let _sch = resolve.call(this, root, ref);
+      let _sch = resolve2.call(this, root, ref);
       if (_sch === void 0) {
         const schema = (_a2 = root.localRefs) === null || _a2 === void 0 ? void 0 : _a2[ref];
         const { schemaId } = this.opts;
@@ -3012,7 +3012,7 @@ var require_compile = __commonJS({
     function sameSchemaEnv(s1, s2) {
       return s1.schema === s2.schema && s1.root === s2.root && s1.baseId === s2.baseId;
     }
-    function resolve(root, ref) {
+    function resolve2(root, ref) {
       let sch;
       while (typeof (sch = this.refs[ref]) == "string")
         ref = sch;
@@ -3587,7 +3587,7 @@ var require_fast_uri = __commonJS({
       }
       return uri;
     }
-    function resolve(baseURI, relativeURI, options) {
+    function resolve2(baseURI, relativeURI, options) {
       const schemelessOptions = options ? Object.assign({ scheme: "null" }, options) : { scheme: "null" };
       const resolved = resolveComponent(parse3(baseURI, schemelessOptions), parse3(relativeURI, schemelessOptions), schemelessOptions, true);
       schemelessOptions.skipEscape = true;
@@ -3814,7 +3814,7 @@ var require_fast_uri = __commonJS({
     var fastUri = {
       SCHEMES,
       normalize,
-      resolve,
+      resolve: resolve2,
       resolveComponent,
       equal,
       serialize,
@@ -27970,7 +27970,7 @@ var Protocol = class {
           return;
         }
         const pollInterval = task2.pollInterval ?? this._options?.defaultTaskPollInterval ?? 1e3;
-        await new Promise((resolve) => setTimeout(resolve, pollInterval));
+        await new Promise((resolve2) => setTimeout(resolve2, pollInterval));
         options?.signal?.throwIfAborted();
       }
     } catch (error48) {
@@ -27987,7 +27987,7 @@ var Protocol = class {
    */
   request(request, resultSchema, options) {
     const { relatedRequestId, resumptionToken, onresumptiontoken, task, relatedTask } = options ?? {};
-    return new Promise((resolve, reject) => {
+    return new Promise((resolve2, reject) => {
       const earlyReject = (error48) => {
         reject(error48);
       };
@@ -28065,7 +28065,7 @@ var Protocol = class {
           if (!parseResult.success) {
             reject(parseResult.error);
           } else {
-            resolve(parseResult.data);
+            resolve2(parseResult.data);
           }
         } catch (error48) {
           reject(error48);
@@ -28326,12 +28326,12 @@ var Protocol = class {
       }
     } catch {
     }
-    return new Promise((resolve, reject) => {
+    return new Promise((resolve2, reject) => {
       if (signal.aborted) {
         reject(new McpError(ErrorCode.InvalidRequest, "Request cancelled"));
         return;
       }
-      const timeoutId = setTimeout(resolve, interval);
+      const timeoutId = setTimeout(resolve2, interval);
       signal.addEventListener("abort", () => {
         clearTimeout(timeoutId);
         reject(new McpError(ErrorCode.InvalidRequest, "Request cancelled"));
@@ -29290,7 +29290,7 @@ var McpServer = class {
     let task = createTaskResult.task;
     const pollInterval = task.pollInterval ?? 5e3;
     while (task.status !== "completed" && task.status !== "failed" && task.status !== "cancelled") {
-      await new Promise((resolve) => setTimeout(resolve, pollInterval));
+      await new Promise((resolve2) => setTimeout(resolve2, pollInterval));
       const updatedTask = await extra.taskStore.getTask(taskId);
       if (!updatedTask) {
         throw new McpError(ErrorCode.InternalError, `Task ${taskId} not found during polling`);
@@ -29933,12 +29933,12 @@ var StdioServerTransport = class {
     this.onclose?.();
   }
   send(message) {
-    return new Promise((resolve) => {
+    return new Promise((resolve2) => {
       const json2 = serializeMessage(message);
       if (this._stdout.write(json2)) {
-        resolve();
+        resolve2();
       } else {
-        this._stdout.once("drain", resolve);
+        this._stdout.once("drain", resolve2);
       }
     });
   }
@@ -30312,10 +30312,11 @@ var SlurmJobDB = class {
 };
 
 // src/lib/config.ts
-import { join } from "path";
+import { dirname as dirname2, join, resolve } from "path";
 import { homedir } from "os";
 var DEFAULT_CONFIG = {
   runtime: "auto",
+  images_dir: "",
   // Default sandbox image: includes python3 + basic build tools (git/make/g++).
   // Note: pip/venv are not included by default in Debian; users may still need a
   // custom image for richer Python workflows.
@@ -30348,7 +30349,8 @@ var DEFAULT_CONFIG = {
       "mkfs",
       "reboot",
       "shutdown"
-    ]
+    ],
+    ensure_commands: ["git"]
   },
   network: {
     mode: "host",
@@ -30374,13 +30376,9 @@ var DEFAULT_CONFIG = {
   },
   plugins: {
     files: true,
+    activity: true,
     datasets: false,
     results: false,
-    charting: true,
-    molecular: true,
-    genomics: true,
-    phylogenetics: true,
-    network: true,
     slurm: true,
     explorer: true,
     automation: false
@@ -30401,7 +30399,7 @@ var DEFAULT_CONFIG = {
     max_tokens: 1024
   },
   headless: {
-    claude_run_with_allowed_permissions: true,
+    claude_run_with_allowed_permissions: false,
     continuation_in_other_terminals: true,
     git_integration: false
   }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "labgate",
-  "version": "0.5.39",
+  "version": "0.5.42",
   "description": "Secure HPC wrapper for AI coding agents (Claude-first): policy controls, Apptainer sandboxes, and SLURM workflows — https://labgate.dev",
   "homepage": "https://labgate.dev",
   "keywords": [