diff --git a/extensions/ql-vscode/gulpfile.ts/appInsights.ts b/extensions/ql-vscode/gulpfile.ts/appInsights.ts
index 86d36aae4fe..c0589459f8c 100644
--- a/extensions/ql-vscode/gulpfile.ts/appInsights.ts
+++ b/extensions/ql-vscode/gulpfile.ts/appInsights.ts
@@ -1,18 +1,21 @@
-import { src, dest } from "gulp";
-import replace from "gulp-replace";
+import { readFile, writeFile } from "fs/promises";
 
 /** Inject the application insights key into the telemetry file */
-export function injectAppInsightsKey() {
+export async function injectAppInsightsKey() {
   if (!process.env.APP_INSIGHTS_KEY) {
     // noop
     console.log(
       "APP_INSIGHTS_KEY environment variable is not set. So, cannot inject it into the application.",
     );
-    return Promise.resolve();
+    return;
   }
 
   // replace the key
-  return src(["out/extension.js"])
-    .pipe(replace(/REPLACE-APP-INSIGHTS-KEY/, process.env.APP_INSIGHTS_KEY))
-    .pipe(dest("out/"));
+  const filePath = "out/extension.js";
+  const content = await readFile(filePath, "utf8");
+  await writeFile(
+    filePath,
+    content.replace(/REPLACE-APP-INSIGHTS-KEY/, process.env.APP_INSIGHTS_KEY),
+    "utf8",
+  );
 }
diff --git a/extensions/ql-vscode/gulpfile.ts/textmate.ts b/extensions/ql-vscode/gulpfile.ts/textmate.ts
index 3666722f6fe..7927d4f1ca4 100644
--- a/extensions/ql-vscode/gulpfile.ts/textmate.ts
+++ b/extensions/ql-vscode/gulpfile.ts/textmate.ts
@@ -1,6 +1,7 @@
 import { dest, src } from "gulp";
 import { load } from "js-yaml";
-import { objectTransform } from "through2";
+import type { TransformCallback } from "stream";
+import { Transform } from "stream";
 import PluginError from "plugin-error";
 import type Vinyl from "vinyl";
 import type {
@@ -247,12 +248,13 @@ function transformFile(yaml: ExtendedTextmateGrammar<ExtendedMatchType>) {
 }
 
 export function transpileTextMateGrammar() {
-  return objectTransform(
-    (
+  return new Transform({
+    objectMode: true,
+    transform(
       file: Vinyl,
-      _encoding: string,
-      callback: (err?: Error | null, file?: Vinyl) => void,
-    ): void => {
+      _encoding: BufferEncoding,
+      callback: TransformCallback,
+    ): void {
       if (file.isNull()) {
         callback(null, file);
       } else if (file.isBuffer()) {
@@ -270,7 +272,7 @@ export function transpileTextMateGrammar() {
         );
       }
     },
-  );
+  });
 }
 
 export function compileTextMateGrammar() {
diff --git a/extensions/ql-vscode/gulpfile.ts/typescript.ts b/extensions/ql-vscode/gulpfile.ts/typescript.ts
index d050205a4b0..a735e6ebbea 100644
--- a/extensions/ql-vscode/gulpfile.ts/typescript.ts
+++ b/extensions/ql-vscode/gulpfile.ts/typescript.ts
@@ -1,18 +1,19 @@
-import { gray, red } from "ansi-colors";
+import { styleText } from "util";
 import { dest, parallel, src, watch } from "gulp";
 import esbuild from "gulp-esbuild";
 import type { reporter } from "gulp-typescript";
 import { createProject } from "gulp-typescript";
-import del from "del";
 import { pipeline } from "stream/promises";
-import { mkdir } from "fs/promises";
+import { mkdir, rm } from "fs/promises";
+import { join } from "path";
 
 export function goodReporter(): reporter.Reporter {
   return {
     error: (error, typescript) => {
       if (error.tsFile) {
         console.log(
-          `[${gray("gulp-typescript")}] ${red(
+          `[${styleText("gray", "gulp-typescript")}] ${styleText(
+            "red",
             `${error.fullFilename}(${error.startPosition!.line + 1},${
               error.startPosition!.character
             }): `,
@@ -32,10 +33,13 @@ export function goodReporter(): reporter.Reporter {
 
 const tsProject = createProject("tsconfig.json");
 
-export function cleanOutput() {
-  return tsProject.projectDirectory
-    ? del(`${tsProject.projectDirectory}/out/*`)
-    : Promise.resolve();
+export async function cleanOutput() {
+  if (tsProject.projectDirectory) {
+    await rm(join(tsProject.projectDirectory, "out"), {
+      recursive: true,
+      force: true,
+    });
+  }
 }
 
 export function compileEsbuild() {
diff --git a/extensions/ql-vscode/package-lock.json b/extensions/ql-vscode/package-lock.json
index 63b6e47f7ba..1711aa6ce04 100644
--- a/extensions/ql-vscode/package-lock.json
+++ b/extensions/ql-vscode/package-lock.json
@@ -21,13 +21,11 @@
         "@vscode/debugprotocol": "^1.68.0",
         "ajv": "^8.18.0",
         "chokidar": "^5.0.0",
-        "d3": "^7.9.0",
         "d3-graphviz": "^5.6.0",
         "fs-extra": "^11.1.1",
         "js-yaml": "^5.2.3",
         "koffi": "^3.3.2",
         "msw": "^2.15.0",
-        "nanoid": "^6.0.1",
         "p-queue": "^8.0.1",
         "proper-lockfile": "^4.1.2",
         "react": "^19.3.0",
@@ -37,7 +35,6 @@
         "source-map-support": "^0.5.21",
         "stream-json": "^3.5.0",
         "styled-components": "^6.5.3",
-        "tmp": "^0.2.7",
         "tmp-promise": "^3.0.2",
         "tree-kill": "^1.2.2",
         "vscode-extension-telemetry": "^0.1.6",
@@ -69,7 +66,6 @@
         "@testing-library/react": "^16.3.3",
         "@testing-library/user-event": "^14.6.7",
         "@types/cross-spawn": "^6.0.6",
-        "@types/d3": "^7.4.0",
         "@types/d3-graphviz": "^3.1.0",
         "@types/fs-extra": "^11.0.1",
         "@types/gulp": "^4.0.18",
@@ -79,7 +75,6 @@
         "@types/proper-lockfile": "^4.1.4",
         "@types/react": "^19.3.0",
         "@types/react-dom": "^19.3.0",
-        "@types/readable-stream": "^4.0.24",
         "@types/sarif": "^2.1.2",
         "@types/semver": "^7.7.1",
         "@types/tar-stream": "^3.1.4",
@@ -89,12 +84,10 @@
         "@typescript-eslint/parser": "^8.71.0",
         "@vscode/test-electron": "^3.1.0",
         "@vscode/vsce": "^4.0.0",
-        "ansi-colors": "^4.1.1",
         "applicationinsights": "^2.9.8",
         "babel-jest": "30.2.0",
         "cross-env": "^10.1.0",
         "cross-spawn": "^7.0.6",
-        "del": "^6.0.0",
         "eslint": "^9.28.0",
         "eslint-config-prettier": "^10.1.8",
         "eslint-import-resolver-typescript": "^4.4.5",
@@ -107,7 +100,6 @@
         "glob": "^13.0.6",
         "gulp": "^5.0.1",
         "gulp-esbuild": "^0.14.1",
-        "gulp-replace": "^1.1.3",
         "gulp-typescript": "^5.0.1",
         "husky": "^9.1.7",
         "jest": "^30.2.0",
@@ -121,7 +113,6 @@
         "prettier": "^3.9.3",
         "storybook": "^10.6.1",
         "tar-stream": "^3.2.0",
-        "through2": "^5.0.11",
         "ts-jest": "^29.4.14",
         "ts-json-schema-generator": "^2.3.0",
         "ts-node": "^10.9.2",
@@ -12877,153 +12868,6 @@
         "@types/node": "*"
       }
     },
-    "node_modules/@types/d3": {
-      "version": "7.4.3",
-      "resolved": "https://registry.npmjs.org/@types/d3/-/d3-7.4.3.tgz",
-      "integrity": "sha512-lZXZ9ckh5R8uiFVt8ogUNf+pIrK4EsWrx2Np75WvF/eTpJ0FMHNhjXk8CKEx/+gpHbNQyJWehbFaTvqmHWB3ww==",
-      "dev": true,
-      "dependencies": {
-        "@types/d3-array": "*",
-        "@types/d3-axis": "*",
-        "@types/d3-brush": "*",
-        "@types/d3-chord": "*",
-        "@types/d3-color": "*",
-        "@types/d3-contour": "*",
-        "@types/d3-delaunay": "*",
-        "@types/d3-dispatch": "*",
-        "@types/d3-drag": "*",
-        "@types/d3-dsv": "*",
-        "@types/d3-ease": "*",
-        "@types/d3-fetch": "*",
-        "@types/d3-force": "*",
-        "@types/d3-format": "*",
-        "@types/d3-geo": "*",
-        "@types/d3-hierarchy": "*",
-        "@types/d3-interpolate": "*",
-        "@types/d3-path": "*",
-        "@types/d3-polygon": "*",
-        "@types/d3-quadtree": "*",
-        "@types/d3-random": "*",
-        "@types/d3-scale": "*",
-        "@types/d3-scale-chromatic": "*",
-        "@types/d3-selection": "*",
-        "@types/d3-shape": "*",
-        "@types/d3-time": "*",
-        "@types/d3-time-format": "*",
-        "@types/d3-timer": "*",
-        "@types/d3-transition": "*",
-        "@types/d3-zoom": "*"
-      }
-    },
-    "node_modules/@types/d3-array": {
-      "version": "3.2.1",
-      "resolved": "https://registry.npmjs.org/@types/d3-array/-/d3-array-3.2.1.tgz",
-      "integrity": "sha512-Y2Jn2idRrLzUfAKV2LyRImR+y4oa2AntrgID95SHJxuMUrkNXmanDSed71sRNZysveJVt1hLLemQZIady0FpEg==",
-      "dev": true
-    },
-    "node_modules/@types/d3-axis": {
-      "version": "3.0.6",
-      "resolved": "https://registry.npmjs.org/@types/d3-axis/-/d3-axis-3.0.6.tgz",
-      "integrity": "sha512-pYeijfZuBd87T0hGn0FO1vQ/cgLk6E1ALJjfkC0oJ8cbwkZl3TpgS8bVBLZN+2jjGgg38epgxb2zmoGtSfvgMw==",
-      "dev": true,
-      "dependencies": {
-        "@types/d3-selection": "*"
-      }
-    },
-    "node_modules/@types/d3-brush": {
-      "version": "3.0.6",
-      "resolved": "https://registry.npmjs.org/@types/d3-brush/-/d3-brush-3.0.6.tgz",
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-      "dev": true,
-      "dependencies": {
-        "@types/d3-selection": "*"
-      }
-    },
-    "node_modules/@types/d3-chord": {
-      "version": "3.0.6",
-      "resolved": "https://registry.npmjs.org/@types/d3-chord/-/d3-chord-3.0.6.tgz",
-      "integrity": "sha512-LFYWWd8nwfwEmTZG9PfQxd17HbNPksHBiJHaKuY1XeqscXacsS2tyoo6OdRsjf+NQYeB6XrNL3a25E3gH69lcg==",
-      "dev": true
-    },
-    "node_modules/@types/d3-color": {
-      "version": "3.1.3",
-      "resolved": "https://registry.npmjs.org/@types/d3-color/-/d3-color-3.1.3.tgz",
-      "integrity": "sha512-iO90scth9WAbmgv7ogoq57O9YpKmFBbmoEoCHDB2xMBY0+/KVrqAaCDyCE16dUspeOvIxFFRI+0sEtqDqy2b4A==",
-      "dev": true
-    },
-    "node_modules/@types/d3-contour": {
-      "version": "3.0.6",
-      "resolved": "https://registry.npmjs.org/@types/d3-contour/-/d3-contour-3.0.6.tgz",
-      "integrity": "sha512-BjzLgXGnCWjUSYGfH1cpdo41/hgdWETu4YxpezoztawmqsvCeep+8QGfiY6YbDvfgHz/DkjeIkkZVJavB4a3rg==",
-      "dev": true,
-      "dependencies": {
-        "@types/d3-array": "*",
-        "@types/geojson": "*"
-      }
-    },
-    "node_modules/@types/d3-delaunay": {
-      "version": "6.0.4",
-      "resolved": "https://registry.npmjs.org/@types/d3-delaunay/-/d3-delaunay-6.0.4.tgz",
-      "integrity": "sha512-ZMaSKu4THYCU6sV64Lhg6qjf1orxBthaC161plr5KuPHo3CNm8DTHiLw/5Eq2b6TsNP0W0iJrUOFscY6Q450Hw==",
-      "dev": true
-    },
-    "node_modules/@types/d3-dispatch": {
-      "version": "3.0.6",
-      "resolved": "https://registry.npmjs.org/@types/d3-dispatch/-/d3-dispatch-3.0.6.tgz",
-      "integrity": "sha512-4fvZhzMeeuBJYZXRXrRIQnvUYfyXwYmLsdiN7XXmVNQKKw1cM8a5WdID0g1hVFZDqT9ZqZEY5pD44p24VS7iZQ==",
-      "dev": true
-    },
-    "node_modules/@types/d3-drag": {
-      "version": "3.0.7",
-      "resolved": "https://registry.npmjs.org/@types/d3-drag/-/d3-drag-3.0.7.tgz",
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-      "dev": true,
-      "dependencies": {
-        "@types/d3-selection": "*"
-      }
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-    "node_modules/@types/d3-dsv": {
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-      "resolved": "https://registry.npmjs.org/@types/d3-dsv/-/d3-dsv-3.0.7.tgz",
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-      "dev": true
-    },
-    "node_modules/@types/d3-ease": {
-      "version": "3.0.2",
-      "resolved": "https://registry.npmjs.org/@types/d3-ease/-/d3-ease-3.0.2.tgz",
-      "integrity": "sha512-NcV1JjO5oDzoK26oMzbILE6HW7uVXOHLQvHshBUW4UMdZGfiY6v5BeQwh9a9tCzv+CeefZQHJt5SRgK154RtiA==",
-      "dev": true
-    },
-    "node_modules/@types/d3-fetch": {
-      "version": "3.0.7",
-      "resolved": "https://registry.npmjs.org/@types/d3-fetch/-/d3-fetch-3.0.7.tgz",
-      "integrity": "sha512-fTAfNmxSb9SOWNB9IoG5c8Hg6R+AzUHDRlsXsDZsNp6sxAEOP0tkP3gKkNSO/qmHPoBFTxNrjDprVHDQDvo5aA==",
-      "dev": true,
-      "dependencies": {
-        "@types/d3-dsv": "*"
-      }
-    },
-    "node_modules/@types/d3-force": {
-      "version": "3.0.9",
-      "resolved": "https://registry.npmjs.org/@types/d3-force/-/d3-force-3.0.9.tgz",
-      "integrity": "sha512-IKtvyFdb4Q0LWna6ymywQsEYjK/94SGhPrMfEr1TIc5OBeziTi+1jcCvttts8e0UWZIxpasjnQk9MNk/3iS+kA==",
-      "dev": true
-    },
-    "node_modules/@types/d3-format": {
-      "version": "3.0.4",
-      "resolved": "https://registry.npmjs.org/@types/d3-format/-/d3-format-3.0.4.tgz",
-      "integrity": "sha512-fALi2aI6shfg7vM5KiR1wNJnZ7r6UuggVqtDA+xiEdPZQwy/trcQaHnwShLuLdta2rTymCNpxYTiMZX/e09F4g==",
-      "dev": true
-    },
-    "node_modules/@types/d3-geo": {
-      "version": "3.1.0",
-      "resolved": "https://registry.npmjs.org/@types/d3-geo/-/d3-geo-3.1.0.tgz",
-      "integrity": "sha512-856sckF0oP/diXtS4jNsiQw/UuK5fQG8l/a9VVLeSouf1/PPbBE1i1W852zVwKwYCBkFJJB7nCFTbk6UMEXBOQ==",
-      "dev": true,
-      "dependencies": {
-        "@types/geojson": "*"
-      }
-    },
     "node_modules/@types/d3-graphviz": {
       "version": "3.1.0",
       "resolved": "https://registry.npmjs.org/@types/d3-graphviz/-/d3-graphviz-3.1.0.tgz",
@@ -13076,112 +12920,6 @@
         "@types/d3-selection": "^1"
       }
     },
-    "node_modules/@types/d3-hierarchy": {
-      "version": "3.1.6",
-      "resolved": "https://registry.npmjs.org/@types/d3-hierarchy/-/d3-hierarchy-3.1.6.tgz",
-      "integrity": "sha512-qlmD/8aMk5xGorUvTUWHCiumvgaUXYldYjNVOWtYoTYY/L+WwIEAmJxUmTgr9LoGNG0PPAOmqMDJVDPc7DOpPw==",
-      "dev": true
-    },
-    "node_modules/@types/d3-interpolate": {
-      "version": "3.0.4",
-      "resolved": "https://registry.npmjs.org/@types/d3-interpolate/-/d3-interpolate-3.0.4.tgz",
-      "integrity": "sha512-mgLPETlrpVV1YRJIglr4Ez47g7Yxjl1lj7YKsiMCb27VJH9W8NVM6Bb9d8kkpG/uAQS5AmbA48q2IAolKKo1MA==",
-      "dev": true,
-      "dependencies": {
-        "@types/d3-color": "*"
-      }
-    },
-    "node_modules/@types/d3-path": {
-      "version": "3.0.2",
-      "resolved": "https://registry.npmjs.org/@types/d3-path/-/d3-path-3.0.2.tgz",
-      "integrity": "sha512-WAIEVlOCdd/NKRYTsqCpOMHQHemKBEINf8YXMYOtXH0GA7SY0dqMB78P3Uhgfy+4X+/Mlw2wDtlETkN6kQUCMA==",
-      "dev": true
-    },
-    "node_modules/@types/d3-polygon": {
-      "version": "3.0.2",
-      "resolved": "https://registry.npmjs.org/@types/d3-polygon/-/d3-polygon-3.0.2.tgz",
-      "integrity": "sha512-ZuWOtMaHCkN9xoeEMr1ubW2nGWsp4nIql+OPQRstu4ypeZ+zk3YKqQT0CXVe/PYqrKpZAi+J9mTs05TKwjXSRA==",
-      "dev": true
-    },
-    "node_modules/@types/d3-quadtree": {
-      "version": "3.0.6",
-      "resolved": "https://registry.npmjs.org/@types/d3-quadtree/-/d3-quadtree-3.0.6.tgz",
-      "integrity": "sha512-oUzyO1/Zm6rsxKRHA1vH0NEDG58HrT5icx/azi9MF1TWdtttWl0UIUsjEQBBh+SIkrpd21ZjEv7ptxWys1ncsg==",
-      "dev": true
-    },
-    "node_modules/@types/d3-random": {
-      "version": "3.0.3",
-      "resolved": "https://registry.npmjs.org/@types/d3-random/-/d3-random-3.0.3.tgz",
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-      "dependencies": {
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-      }
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-      "version": "3.0.3",
-      "resolved": "https://registry.npmjs.org/@types/d3-scale-chromatic/-/d3-scale-chromatic-3.0.3.tgz",
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-      "dev": true
-    },
-    "node_modules/@types/d3-selection": {
-      "version": "3.0.10",
-      "resolved": "https://registry.npmjs.org/@types/d3-selection/-/d3-selection-3.0.10.tgz",
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diff --git a/extensions/ql-vscode/package.json b/extensions/ql-vscode/package.json
index e69cfa20ed8..88060034fa4 100644
--- a/extensions/ql-vscode/package.json
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     "@types/tar-stream": "^3.1.4",
@@ -2147,12 +2142,10 @@
     "@typescript-eslint/parser": "^8.71.0",
     "@vscode/test-electron": "^3.1.0",
     "@vscode/vsce": "^4.0.0",
-    "ansi-colors": "^4.1.1",
     "applicationinsights": "^2.9.8",
     "babel-jest": "30.2.0",
     "cross-env": "^10.1.0",
     "cross-spawn": "^7.0.6",
-    "del": "^6.0.0",
     "eslint": "^9.28.0",
     "eslint-config-prettier": "^10.1.8",
     "eslint-import-resolver-typescript": "^4.4.5",
@@ -2165,7 +2158,6 @@
     "glob": "^13.0.6",
     "gulp": "^5.0.1",
     "gulp-esbuild": "^0.14.1",
-    "gulp-replace": "^1.1.3",
     "gulp-typescript": "^5.0.1",
     "husky": "^9.1.7",
     "jest": "^30.2.0",
@@ -2179,7 +2171,6 @@
     "prettier": "^3.9.3",
     "storybook": "^10.6.1",
     "tar-stream": "^3.2.0",
-    "through2": "^5.0.11",
     "ts-jest": "^29.4.14",
     "ts-json-schema-generator": "^2.3.0",
     "ts-node": "^10.9.2",
diff --git a/extensions/ql-vscode/src/compare/compare-view.ts b/extensions/ql-vscode/src/compare/compare-view.ts
index 4ab42794d33..87483ffecbd 100644
--- a/extensions/ql-vscode/src/compare/compare-view.ts
+++ b/extensions/ql-vscode/src/compare/compare-view.ts
@@ -38,7 +38,7 @@ import {
   getResultSetNames,
 } from "./result-set-names";
 import { isCanary } from "../config";
-import { nanoid } from "nanoid";
+import { randomUUID } from "crypto";
 
 interface ComparePair {
   from: CompletedLocalQueryInfo;
@@ -243,7 +243,7 @@ export class CompareView extends AbstractWebview<
       return;
     }
 
-    const id = nanoid();
+    const id = randomUUID();
 
     // Streaming itself is implemented like this:
     // - 1 setup message which contains the first 1,000 results
diff --git a/extensions/ql-vscode/src/databases/database-fetcher.ts b/extensions/ql-vscode/src/databases/database-fetcher.ts
index c3240f6095c..6518dd52ca0 100644
--- a/extensions/ql-vscode/src/databases/database-fetcher.ts
+++ b/extensions/ql-vscode/src/databases/database-fetcher.ts
@@ -11,7 +11,7 @@ import {
 } from "fs-extra";
 import { basename, join } from "path";
 import type { Octokit } from "@octokit/rest";
-import { nanoid } from "nanoid";
+import { randomUUID } from "crypto";
 
 import type { DatabaseManager, DatabaseItem } from "./local-databases";
 import { tmpDir } from "../tmp-dir";
@@ -39,7 +39,7 @@ import { convertGithubNwoToDatabaseUrl } from "./github-databases/api";
 import { ensureZippedSourceLocation } from "./local-databases/database-contents";
 
 // The number of tries to use when generating a unique filename before
-// giving up and using a nanoid.
+// giving up and using a random UUID.
 const DUPLICATE_FILENAMES_TRIES = 10_000;
 
 export class DatabaseFetcher {
@@ -429,7 +429,7 @@ export class DatabaseFetcher {
       } else if (counter <= DUPLICATE_FILENAMES_TRIES + 5) {
         // If there are more than 10,000 similarly named databases,
         // give up on using a counter and use a random string instead.
-        folderName = `${lastName}-${nanoid()}`;
+        folderName = `${lastName}-${randomUUID()}`;
       } else {
         // This should almost never happen, but just in case, we don't want to
         // get stuck in an infinite loop.
diff --git a/extensions/ql-vscode/src/model-editor/extensions-workspace-folder.ts b/extensions/ql-vscode/src/model-editor/extensions-workspace-folder.ts
index f3736748805..2756f4d280a 100644
--- a/extensions/ql-vscode/src/model-editor/extensions-workspace-folder.ts
+++ b/extensions/ql-vscode/src/model-editor/extensions-workspace-folder.ts
@@ -5,7 +5,7 @@ import { containsPath, tmpdir } from "../common/files";
 import type { NotificationLogger } from "../common/logging";
 import { showAndLogErrorMessage } from "../common/logging";
 import { isAbsolute, normalize, resolve } from "path";
-import { nanoid } from "nanoid";
+import { randomUUID } from "crypto";
 import type { ModelConfig } from "../config";
 
 /**
@@ -245,11 +245,11 @@ export async function ensurePackLocationIsInWorkspaceFolder(
   const otherPackLocations = await Promise.all(
     Array.from({ length: 3 }).map(() =>
       packLocationToAbsolute(
-        modelConfig.getPackLocation(nanoid(), {
-          database: nanoid(),
-          language: nanoid(),
-          name: nanoid(),
-          owner: nanoid(),
+        modelConfig.getPackLocation(randomUUID(), {
+          database: randomUUID(),
+          language: randomUUID(),
+          name: randomUUID(),
+          owner: randomUUID(),
         }),
         logger,
       ),
diff --git a/extensions/ql-vscode/src/query-server/query-runner.ts b/extensions/ql-vscode/src/query-server/query-runner.ts
index 5d42e6056d7..78bdbdd3b07 100644
--- a/extensions/ql-vscode/src/query-server/query-runner.ts
+++ b/extensions/ql-vscode/src/query-server/query-runner.ts
@@ -24,7 +24,7 @@ import {
 } from "./messages";
 import type { BaseLogger, Logger } from "../common/logging";
 import { join } from "path";
-import { nanoid } from "nanoid";
+import { randomUUID } from "crypto";
 import type { QueryServerClient } from "./query-server-client";
 import { getOnDiskWorkspaceFolders } from "../common/vscode/workspace-folders";
 import { compileAndRunQueryAgainstDatabaseCore } from "./run-queries";
@@ -259,7 +259,7 @@ export class QueryRunner {
     queryBasename: string,
     templates: Record<string, string> | undefined,
   ): CoreQueryRun {
-    const id = `${queryBasename}-${nanoid()}`;
+    const id = `${queryBasename}-${randomUUID()}`;
     const outputDir = new QueryOutputDir(join(queryStorageDir, id));
 
     return {
diff --git a/extensions/ql-vscode/src/run-queries-shared.ts b/extensions/ql-vscode/src/run-queries-shared.ts
index b8e6a711c59..89025e0c865 100644
--- a/extensions/ql-vscode/src/run-queries-shared.ts
+++ b/extensions/ql-vscode/src/run-queries-shared.ts
@@ -16,7 +16,6 @@ import {
 import type { InitialQueryInfo } from "./query-results";
 import { ensureMetadataIsComplete } from "./query-results";
 import { isQuickQueryPath } from "./local-queries/quick-query";
-import { nanoid } from "nanoid";
 import type { CodeQLCliServer } from "./codeql-cli/cli";
 import { SELECT_QUERY_NAME } from "./language-support";
 import type { DatabaseManager } from "./databases/local-databases";
@@ -28,7 +27,7 @@ import type { BaseLogger } from "./common/logging";
 import { showAndLogWarningMessage } from "./common/logging";
 import { extLogger } from "./common/logging/vscode";
 import { getErrorMessage } from "./common/helpers-pure";
-import { createHash } from "crypto";
+import { createHash, randomUUID } from "crypto";
 import { QueryOutputDir } from "./local-queries/query-output-dir";
 import { progressUpdate } from "./common/vscode/progress";
 import type { ProgressCallback } from "./common/vscode/progress";
@@ -526,7 +525,7 @@ export async function createInitialQueryInfo(
     isQuickEvalCount,
     isQuickQuery: isQuickQueryPath(selectedQuery.queryPath),
     databaseInfo,
-    id: `${basename(selectedQuery.queryPath)}-${nanoid()}`,
+    id: `${basename(selectedQuery.queryPath)}-${randomUUID()}`,
     start: new Date(),
     ...(selectedQuery.quickEval !== undefined
       ? {
diff --git a/extensions/ql-vscode/src/stories/variant-analysis/VariantAnalysisAnalyzedRepos.stories.tsx b/extensions/ql-vscode/src/stories/variant-analysis/VariantAnalysisAnalyzedRepos.stories.tsx
index 7b8f08878e0..16836cae1c6 100644
--- a/extensions/ql-vscode/src/stories/variant-analysis/VariantAnalysisAnalyzedRepos.stories.tsx
+++ b/extensions/ql-vscode/src/stories/variant-analysis/VariantAnalysisAnalyzedRepos.stories.tsx
@@ -1,7 +1,6 @@
 import type { Meta, StoryFn } from "@storybook/react";
 
 import { faker } from "@faker-js/faker";
-import { customAlphabet } from "nanoid";
 
 import { VariantAnalysisContainer } from "../../view/variant-analysis/VariantAnalysisContainer";
 import { VariantAnalysisAnalyzedRepos } from "../../view/variant-analysis/VariantAnalysisAnalyzedRepos";
@@ -129,7 +128,6 @@ faker.seed(42);
 
 const manyScannedRepos = Array.from({ length: 1000 }, (_, i) => {
   const mockedScannedRepo = createMockScannedRepo();
-  const nanoid = customAlphabet("123456789");
   return {
     ...mockedScannedRepo,
     analysisStatus: VariantAnalysisRepoStatus.Succeeded,
@@ -137,8 +135,8 @@ const manyScannedRepos = Array.from({ length: 1000 }, (_, i) => {
     repository: {
       ...mockedScannedRepo.repository,
       // We need to ensure the ID is unique for React keys
-      id: parseInt(nanoid()),
-      fullName: `octodemo/${nanoid()}`,
+      id: faker.number.int(),
+      fullName: `octodemo/${faker.string.numeric({ length: 21, allowLeadingZeros: false })}`,
     },
   };
 });
diff --git a/extensions/ql-vscode/src/variant-analysis/run-remote-query.ts b/extensions/ql-vscode/src/variant-analysis/run-remote-query.ts
index f2670d914ae..0ab0e3eb2f9 100644
--- a/extensions/ql-vscode/src/variant-analysis/run-remote-query.ts
+++ b/extensions/ql-vscode/src/variant-analysis/run-remote-query.ts
@@ -3,7 +3,7 @@ import { window } from "vscode";
 import { join, basename, relative } from "path";
 import { dump } from "js-yaml";
 import { copy, writeFile, readFile, mkdirp, remove } from "fs-extra";
-import { nanoid } from "nanoid";
+import { randomUUID } from "crypto";
 import { tmpDir } from "../tmp-dir";
 import { getOnDiskWorkspaceFolders } from "../common/vscode/workspace-folders";
 import type { Credentials } from "../common/authentication";
@@ -167,7 +167,7 @@ async function createRemoteQueriesTempDirectory(): Promise<RemoteQueryTempDir> {
   // archive if the pack path contains any 8.3 components.
   const tmpDirPath = await expandShortPaths(tmpDir.name, extLogger);
 
-  const remoteQueryDir = join(tmpDirPath, `remote-query-${nanoid()}`);
+  const remoteQueryDir = join(tmpDirPath, `remote-query-${randomUUID()}`);
   await mkdirp(remoteQueryDir);
 
   const queryPackDir = join(remoteQueryDir, "query-pack");
@@ -175,7 +175,10 @@ async function createRemoteQueriesTempDirectory(): Promise<RemoteQueryTempDir> {
 
   const compiledPackDir = join(remoteQueryDir, "compiled-pack");
 
-  const bundleFile = join(remoteQueryDir, `qlpack-${nanoid()}-generated.tgz`);
+  const bundleFile = join(
+    remoteQueryDir,
+    `qlpack-${randomUUID()}-generated.tgz`,
+  );
 
   return { remoteQueryDir, queryPackDir, compiledPackDir, bundleFile };
 }
diff --git a/extensions/ql-vscode/src/view/results/Graph.tsx b/extensions/ql-vscode/src/view/results/Graph.tsx
index 0c82e41c008..c2bc9503ad8 100644
--- a/extensions/ql-vscode/src/view/results/Graph.tsx
+++ b/extensions/ql-vscode/src/view/results/Graph.tsx
@@ -1,4 +1,3 @@
-import { select } from "d3";
 import { jumpToLocation } from "./result-table-utils";
 import type { GraphvizOptions } from "d3-graphviz";
 import { graphviz } from "d3-graphviz";
@@ -48,10 +47,12 @@ export function Graph({ graphData, databaseUri }: GraphProps) {
             d.attributes["xlink:href"] = "#";
             d.attributes["href"] = "#";
             loc.uri = `file://${loc.uri}`;
-            select(this).on("click", (event: Event) => {
-              jumpToLocation(loc, databaseUri);
-              event.preventDefault(); // Avoid resetting scroll position
-            });
+            if (this && "addEventListener" in this) {
+              this.addEventListener("click", (event: Event) => {
+                jumpToLocation(loc, databaseUri);
+                event.preventDefault(); // Avoid resetting scroll position
+              });
+            }
           }
         }
         if ("fill" in d.attributes) {
diff --git a/extensions/ql-vscode/test/common/logging/output-channel-logger.test.ts b/extensions/ql-vscode/test/common/logging/output-channel-logger.test.ts
index ad835dda77e..19bd1995910 100644
--- a/extensions/ql-vscode/test/common/logging/output-channel-logger.test.ts
+++ b/extensions/ql-vscode/test/common/logging/output-channel-logger.test.ts
@@ -1,7 +1,7 @@
 import { readdirSync, readFileSync } from "fs-extra";
 import { join } from "path";
 import type { DirResult } from "tmp";
-import { dirSync } from "tmp";
+import { dirSync } from "tmp-promise";
 import type { BaseLogger, Logger } from "../../../src/common/logging";
 import { TeeLogger } from "../../../src/common/logging";
 import { OutputChannelLogger } from "../../../src/common/logging/vscode";
diff --git a/extensions/ql-vscode/test/jest-config.ts b/extensions/ql-vscode/test/jest-config.ts
index 2d9b3f1a397..4528dd0f886 100644
--- a/extensions/ql-vscode/test/jest-config.ts
+++ b/extensions/ql-vscode/test/jest-config.ts
@@ -13,7 +13,6 @@ const transformScopes = [
 const transformPackages = [
   "before-after-hook",
   "chokidar",
-  "d3",
   "data-uri-to-buffer",
   "delaunator",
   "exenv-es6",
@@ -21,7 +20,6 @@ const transformPackages = [
   "formdata-polyfill",
   "internmap",
   "lit",
-  "nanoid",
   "p-queue",
   "p-timeout",
   "readdirp",
diff --git a/extensions/ql-vscode/test/unit-tests/common/files.test.ts b/extensions/ql-vscode/test/unit-tests/common/files.test.ts
index b9b90136ee9..9434c826076 100644
--- a/extensions/ql-vscode/test/unit-tests/common/files.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/common/files.test.ts
@@ -11,7 +11,7 @@ import {
   walkDirectory,
 } from "../../../src/common/files";
 import type { DirResult } from "tmp";
-import { dirSync } from "tmp";
+import { dirSync } from "tmp-promise";
 import {
   createFileSync,
   ensureDirSync,
diff --git a/extensions/ql-vscode/test/unit-tests/databases/local-databases/db-contents-heuristics.test.ts b/extensions/ql-vscode/test/unit-tests/databases/local-databases/db-contents-heuristics.test.ts
index 771b55058fa..8c66bf8335e 100644
--- a/extensions/ql-vscode/test/unit-tests/databases/local-databases/db-contents-heuristics.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/databases/local-databases/db-contents-heuristics.test.ts
@@ -1,5 +1,5 @@
 import type { DirResult } from "tmp";
-import { dirSync } from "tmp";
+import { dirSync } from "tmp-promise";
 import { join } from "path";
 import { mkdirSync, writeFileSync } from "fs-extra";
 import {
diff --git a/extensions/ql-vscode/test/unit-tests/local-queries/query-contents.test.ts b/extensions/ql-vscode/test/unit-tests/local-queries/query-contents.test.ts
index 11d9d80e04e..c5aa79facbb 100644
--- a/extensions/ql-vscode/test/unit-tests/local-queries/query-contents.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/local-queries/query-contents.test.ts
@@ -1,5 +1,5 @@
 import type { DirResult } from "tmp";
-import { dirSync } from "tmp";
+import { dirSync } from "tmp-promise";
 import { dump } from "js-yaml";
 import { writeFileSync } from "fs-extra";
 import { join } from "path";
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts
index 4e5c9489869..701b84cbaf4 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts
@@ -5,7 +5,7 @@ import {
 } from "../../../../src/local-queries/skeleton-query-wizard";
 import { mockedObject, mockedQuickPickItem } from "../../utils/mocking.helpers";
 import type { DirResult } from "tmp";
-import { dirSync } from "tmp";
+import { dirSync } from "tmp-promise";
 import type { MessageItem, TextDocument, WorkspaceFolder } from "vscode";
 import { Uri, window, workspace } from "vscode";
 import { QlPackGenerator } from "../../../../src/local-queries/qlpack-generator";
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/model-editor/modeled-method-fs.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/model-editor/modeled-method-fs.test.ts
index 78bf3c11375..5180a85f498 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/model-editor/modeled-method-fs.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/model-editor/modeled-method-fs.test.ts
@@ -11,7 +11,7 @@ import { join } from "path";
 import { extLogger } from "../../../../src/common/logging/vscode";
 import { homedir, tmpdir } from "os";
 import { mkdir, rm } from "fs-extra";
-import { nanoid } from "nanoid";
+import { randomUUID } from "crypto";
 import { QueryLanguage } from "../../../../src/common/query-language";
 
 const dummyExtensionPackContents = `
@@ -68,7 +68,10 @@ describe("modeled-method-fs", () => {
       process.platform === "win32"
         ? join(homedir(), "AppData", "Local", "Temp")
         : tmpdir();
-    tmpDir = join(systemTmpDir, `codeql-vscode-test-${nanoid(8)}`);
+    tmpDir = join(
+      systemTmpDir,
+      `codeql-vscode-test-${randomUUID().slice(0, 8)}`,
+    );
     await mkdir(tmpDir, { recursive: true });
     tmpDirRemoveCallback = async () => {
       await rm(tmpDir, { recursive: true });
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/query-server/query-server-client.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/query-server/query-server-client.test.ts
index 655e30acc31..760d1ca614d 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/query-server/query-server-client.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/query-server/query-server-client.test.ts
@@ -1,5 +1,5 @@
 import { join, basename } from "path";
-import { dirSync } from "tmp";
+import { dirSync } from "tmp-promise";
 import { CancellationTokenSource } from "vscode-jsonrpc";
 import type { RunQueryParams } from "../../../../src/query-server/messages";
 import {
diff --git a/extensions/ql-vscode/test/vscode-tests/jest.activated-extension.setup.ts b/extensions/ql-vscode/test/vscode-tests/jest.activated-extension.setup.ts
index dc47c409111..e53cba38c31 100644
--- a/extensions/ql-vscode/test/vscode-tests/jest.activated-extension.setup.ts
+++ b/extensions/ql-vscode/test/vscode-tests/jest.activated-extension.setup.ts
@@ -1,7 +1,7 @@
 import { env } from "vscode";
 import { beforeEachAction as testConfigBeforeEachAction } from "./test-config";
 import type { DirResult } from "tmp";
-import { dirSync } from "tmp";
+import { dirSync } from "tmp-promise";
 import { realpathSync } from "fs-extra";
 import {
   getActivatedExtension,
diff --git a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/common/vscode/file-path-discovery.test.ts b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/common/vscode/file-path-discovery.test.ts
index 99dadc0cd85..55a5f0d0d3a 100644
--- a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/common/vscode/file-path-discovery.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/common/vscode/file-path-discovery.test.ts
@@ -8,7 +8,7 @@ import { FilePathDiscovery } from "../../../../../src/common/vscode/file-path-di
 import { basename, dirname, join } from "path";
 import { mkdirSync, readFileSync, rmSync, writeFileSync } from "fs";
 import { rm } from "fs/promises";
-import { dirSync } from "tmp";
+import { dirSync } from "tmp-promise";
 import { normalizePath } from "../../../../../src/common/files";
 import { extLogger } from "../../../../../src/common/logging/vscode/loggers";
 import { getErrorMessage } from "../../../../../src/common/helpers-pure";
diff --git a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-queries/local-databases.test.ts b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-queries/local-databases.test.ts
index 517373bd3fd..dd68ab52bc7 100644
--- a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-queries/local-databases.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-queries/local-databases.test.ts
@@ -1,5 +1,5 @@
 import type { DirResult } from "tmp";
-import { dirSync } from "tmp";
+import { dirSync } from "tmp-promise";
 import { ensureDir, ensureFile, pathExists, writeFile } from "fs-extra";
 import { join } from "path";
 import type { ExtensionContext } from "vscode";
diff --git a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/qlpack-generator.test.ts b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/qlpack-generator.test.ts
index f9a538250b3..cfbf7361052 100644
--- a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/qlpack-generator.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/qlpack-generator.test.ts
@@ -6,7 +6,7 @@ import type { CodeQLCliServer } from "../../../src/codeql-cli/cli";
 import { Uri, workspace } from "vscode";
 import { getErrorMessage } from "../../../src/common/helpers-pure";
 import type { DirResult } from "tmp";
-import { dirSync } from "tmp";
+import { dirSync } from "tmp-promise";
 import { mockedObject } from "../utils/mocking.helpers";
 import { ensureDir, readFile } from "fs-extra";
 import { load } from "js-yaml";
diff --git a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/queries-panel/query-discovery.test.ts b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/queries-panel/query-discovery.test.ts
index dbde79ef81e..969f1ef57df 100644
--- a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/queries-panel/query-discovery.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/queries-panel/query-discovery.test.ts
@@ -3,7 +3,7 @@ import type { QueryPackDiscoverer } from "../../../../src/queries-panel/query-di
 import { QueryDiscovery } from "../../../../src/queries-panel/query-discovery";
 import { createMockApp } from "../../../__mocks__/appMock";
 import { basename, dirname, join } from "path";
-import { dirSync } from "tmp";
+import { dirSync } from "tmp-promise";
 import { rm } from "fs/promises";
 import {
   FileTreeDirectory,
diff --git a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/queries-panel/query-pack-discovery.test.ts b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/queries-panel/query-pack-discovery.test.ts
index 326c4e5813e..ec32a93b20d 100644
--- a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/queries-panel/query-pack-discovery.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/queries-panel/query-pack-discovery.test.ts
@@ -1,6 +1,6 @@
 import { Uri, workspace } from "vscode";
 import { QueryPackDiscovery } from "../../../../src/queries-panel/query-pack-discovery";
-import { dirSync } from "tmp";
+import { dirSync } from "tmp-promise";
 import { rm } from "fs/promises";
 import { dirname, join } from "path";
 import { ensureDir, writeJSON } from "fs-extra";
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/code-tour/code-tour.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/code-tour/code-tour.test.ts
index 645da748bf0..edbe8f9ce1b 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/code-tour/code-tour.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/code-tour/code-tour.test.ts
@@ -1,7 +1,7 @@
 import type { WorkspaceFolder } from "vscode";
 import { Uri, window, workspace } from "vscode";
 import type { DirResult } from "tmp";
-import { dirSync } from "tmp";
+import { dirSync } from "tmp-promise";
 import { join } from "path";
 import { mkdir, writeFile } from "fs-extra";
 
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/databases/local-databases-ui.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/databases/local-databases-ui.test.ts
index abe3b22111b..5321b212890 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/databases/local-databases-ui.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/databases/local-databases-ui.test.ts
@@ -1,4 +1,4 @@
-import { dirSync, fileSync } from "tmp";
+import { dirSync, fileSync } from "tmp-promise";
 import { dirname, join } from "path";
 import {
   mkdirs,
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/local-queries/webview.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/local-queries/webview.test.ts
index 18556ab7aad..20694692847 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/local-queries/webview.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/local-queries/webview.test.ts
@@ -2,7 +2,7 @@ import type { WebviewPanel } from "vscode";
 import { Uri, ViewColumn, window } from "vscode";
 import { basename } from "path";
 import type { FileResult } from "tmp";
-import { fileSync } from "tmp";
+import { fileSync } from "tmp-promise";
 import { fileUriToWebviewUri } from "../../../../src/local-queries/webview";
 import { getDefaultResultSetName } from "../../../../src/common/interface-types";
 
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts
index e8ae5a82975..c0428ec2963 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts
@@ -14,7 +14,7 @@ import { CancellationTokenSource, Uri } from "vscode";
 import { tmpDir } from "../../../../../src/tmp-dir";
 import type { QueryHistoryInfo } from "../../../../../src/query-history/query-history-info";
 import { createMockVariantAnalysisHistoryItem } from "../../../../factories/query-history/variant-analysis-history-item";
-import { nanoid } from "nanoid";
+import { randomUUID } from "crypto";
 import type {
   QueryHistoryDto,
   QueryHistoryItemDto,
@@ -144,7 +144,7 @@ describe("write and read", () => {
           t: "remote",
           status: "InProgress",
           completed: false,
-          queryId: nanoid(),
+          queryId: randomUUID(),
           remoteQuery: {
             queryName: "query-name",
             queryFilePath: "query-file.ql",
@@ -163,7 +163,7 @@ describe("write and read", () => {
           t: "remote",
           status: "Completed",
           completed: true,
-          queryId: nanoid(),
+          queryId: randomUUID(),
           remoteQuery: {
             queryName: "query-name",
             queryFilePath: "query-file.ql",