chore(security): resolve pnpm audit vulnerabilities (1 critical, 3 moderate) by tkislan · Pull Request #387 · deepnote/deepnote

tkislan · 2026-06-03T11:13:01Z

Summary

Resolves all 4 vulnerabilities reported by pnpm audit (1 critical, 3 moderate). Each finding was researched independently to confirm the dependency could be updated, verify the patched version exists, and check for breaking changes. Following the convention established in #376, transitive deps are pinned via pnpm.overrides; directly-declared deps are bumped in place.

After these changes:

✅ pnpm audit → No known vulnerabilities found
✅ pnpm typecheck → passes
✅ pnpm test → 2200 tests / 127 files pass
✅ pnpm build → all packages build

Findings

Package	Severity	Advisory	Installed → Patched	Fix
`vitest`	🔴 Critical	GHSA-5xrq-8626-4rwp	4.0.5 → 4.1.8	direct devDep bump
`ws`	🟡 Moderate	GHSA-58qx-3vcg-4xpx	8.19.0 → 8.21.0	range bump + override
`qs`	🟡 Moderate	GHSA-q8mj-m7cp-5q26	6.14.2 → 6.15.2	new override
`brace-expansion`	🟡 Moderate	GHSA-jxxr-4gwj-5jf2	5.0.5 → 5.0.6	override bump

`vitest` 4.0.5 → 4.1.8 (critical)

Vitest UI server could read/execute arbitrary files when listening; fixed in >=4.1.0. vitest and @vitest/coverage-v8 are directly-declared, pinned devDependencies, so they are bumped in place (not via an override) and move in lockstep (coverage peer-requires the exact vitest version). 4.0 → 4.1 is an additive minor — the breaking restoreAllMocks/poolOptions changes landed in the 4.0.0 major, which the repo already runs. The bump also resolves a latent vite 8 peer mismatch (4.1.x widens the vite peer range to include ^8). This repo runs vitest run without --ui/--api, so real-world exposure was low, but the bump cleanly eliminates the advisory.

`ws` 8.19.0 → 8.21.0 (moderate)

Uninitialized memory disclosure in websocket.close() when passing a TypedArray reason; fixed in >=8.20.1. ws appears at two edges — runtime-core's direct dep and a transitive @jupyterlab/services > ws. The runtime-core declared range is bumped ^8.18.0 → ^8.20.1 (it's a published package, so this makes the security floor explicit downstream) and a ws: ">=8.20.1" override is added to unconditionally cover the transitive edge. No ws API is imported directly in source — it's the WebSocket impl consumed by @jupyterlab/services — so no behavior change.

`qs` 6.14.2 → 6.15.2 (moderate)

Remotely-triggerable DoS: qs.stringify crashes on null/undefined entries in comma-format arrays with encodeValuesOnly; fixed in >=6.15.2. Transitive via packages/mcp > @modelcontextprotocol/sdk > express > qs. express@5.2.1 is already the latest express and declares qs: ^6.14.0 (which 6.15.2 satisfies), so an override is the correct fix. 6.14 → 6.15 is a non-breaking minor (one opt-in strictMerge option + fixes).

`brace-expansion` 5.0.5 → 5.0.6 (moderate)

A large numeric range defeats the documented max DoS protection; fixed in >=5.0.6. Transitive via license-checker-rseidelsohn > … > minimatch. The existing override is bumped >=5.0.5 → >=5.0.6; the fix is an internal loop guard with no API change. The separate @isaacs/brace-expansion override is left unchanged — it's a different fork covered by a different, already-patched advisory (<=5.0.0, patched 5.0.1) and is not actually installed.

🤖 Generated with Claude Code

Summary by CodeRabbit

Chores
- Updated testing framework and code coverage analysis tooling to the latest stable versions to improve development workflow efficiency
- Updated WebSocket runtime library dependency to the latest compatible version for enhanced reliability
- Refined build infrastructure dependency constraints for better cross-environment compatibility

…derate) Resolve all 4 vulnerabilities reported by `pnpm audit`. After these changes `pnpm audit` reports no known vulnerabilities, and typecheck, the full test suite (2200 tests), and the package builds all pass. - vitest (CRITICAL, GHSA-5xrq-8626-4rwp): bump root devDependency vitest and @vitest/coverage-v8 4.0.5 -> 4.1.8. Vitest UI server could read/execute arbitrary files; fixed in >=4.1.0. These are directly declared (not transitive) so they are bumped in place rather than via an override, and must move in lockstep. 4.0->4.1 is an additive minor (the breaking restoreAllMocks/poolOptions changes landed in 4.0.0, already in use); the bump also resolves a latent vite 8 peer mismatch. - ws (MODERATE, GHSA-58qx-3vcg-4xpx): uninitialized memory disclosure in websocket.close(), fixed in >=8.20.1. Bump the runtime-core declared range ^8.18.0 -> ^8.20.1 (published package, makes the floor explicit) and add a `ws: ">=8.20.1"` override to also cover the transitive @jupyterlab/services > ws edge. Resolves to 8.21.0. - qs (MODERATE, GHSA-q8mj-m7cp-5q26): remotely triggerable DoS in qs.stringify, fixed in >=6.15.2. Add override `qs: ">=6.15.2"` (transitive via packages/mcp > @modelcontextprotocol/sdk > express). express@5.2.1 declares qs ^6.14.0, which 6.15.2 satisfies. Resolves to 6.15.2. - brace-expansion (MODERATE, GHSA-jxxr-4gwj-5jf2): large numeric range defeats the documented `max` DoS protection, fixed in >=5.0.6. Bump the existing override >=5.0.5 -> >=5.0.6 (transitive via license-checker-rseidelsohn). The separate @isaacs/brace-expansion override is left unchanged: it is a different fork covered by a different, already-patched advisory and is not installed. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

coderabbitai · 2026-06-03T11:13:11Z

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: ASSERTIVE

Plan: Pro

Run ID: cfbf5876-4992-4109-bec3-26b15907d1d0

📥 Commits

Reviewing files that changed from the base of the PR and between d6d6944 and f1529e9.

⛔ Files ignored due to path filters (1)

pnpm-lock.yaml is excluded by !**/pnpm-lock.yaml

📒 Files selected for processing (2)

package.json
packages/runtime-core/package.json

📝 Walkthrough

Walkthrough

Root package.json updates Vitest coverage tooling and related test infrastructure from 4.0.5 to 4.1.8, adjusts the pnpm override constraint for @isaacs/brace-expansion from >=5.0.5 to >=5.0.6, and maintains ws override alignment. Simultaneously, packages/runtime-core/package.json bumps the ws dependency from ^8.18.0 to ^8.20.1.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Suggested reviewers

saltenasl

🚥 Pre-merge checks | ✅ 5 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Updates Docs	❓ Inconclusive	Repository clone failed, so this custom check could not run with code access.	Retry the review run. If this persists, inspect pre-merge custom-check logs for infrastructure or agent runtime failures.

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title directly addresses the main change: resolving pnpm audit vulnerabilities with specific counts (1 critical, 3 moderate) that align with the PR objectives.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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codecov · 2026-06-03T11:15:40Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 83.35%. Comparing base (d6d6944) to head (f1529e9).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #387      +/-   ##
==========================================
+ Coverage   82.24%   83.35%   +1.10%     
==========================================
  Files         144      145       +1     
  Lines        5868     7988    +2120     
  Branches     1096     2158    +1062     
==========================================
+ Hits         4826     6658    +1832     
- Misses       1042     1329     +287     
- Partials        0        1       +1

☔ View full report in Codecov by Sentry.
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Resolve 4 moderate pnpm audit vulnerabilities in hono (transitive via packages/mcp > @modelcontextprotocol/sdk > hono), all fixed in 4.12.21: - GHSA-xrhx-7g5j-rcj5 (CVE-2026-47674, CVSS 5.3): ip-restriction middleware bypasses static deny rules for non-canonical IPv6. - GHSA-3hrh-pfw6-9m5x (CVE-2026-47675, CVSS 4.3): cookie helper does not sanitize sameSite and priority, allowing Set-Cookie injection. - GHSA-f577-qrjj-4474 (CVE-2026-47673, CVSS 4.8): jwt/jwk middleware accepts any Authorization scheme, not only Bearer. - GHSA-2gcr-mfcq-wcc3 (CVE-2026-47676, CVSS 5.3): app.mount() strips mount prefix using undecoded path, causing incorrect routing for percent-encoded paths. Bump the existing pnpm.overrides floor for hono >=4.12.18 -> >=4.12.21 following the established convention in this repo (see #387, #368, #307, #295, #292). pnpm install resolves hono to 4.12.23. After this change `pnpm audit` reports no known vulnerabilities. `pnpm typecheck`, `pnpm test` (2242 tests), and `pnpm prettier:check` all pass.

coderabbitai Bot approved these changes Jun 3, 2026

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tkislan marked this pull request as ready for review June 3, 2026 11:15

tkislan requested a review from a team as a code owner June 3, 2026 11:15

dinohamzic approved these changes Jun 3, 2026

View reviewed changes

tkislan merged commit ed2e587 into main Jun 3, 2026
21 checks passed

tkislan deleted the tk/resolve-vulnerabilities-2026-06-03 branch June 3, 2026 13:52

coderabbitai Bot mentioned this pull request Jun 4, 2026

chore(security): patch pnpm audit vulnerabilities via overrides #390

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tkislan mentioned this pull request Jun 5, 2026

fix(security): bump hono override to >=4.12.21 #393

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tkislan mentioned this pull request Jun 16, 2026

chore: bump package versions #406

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chore(security): resolve pnpm audit vulnerabilities (1 critical, 3 moderate)#387

chore(security): resolve pnpm audit vulnerabilities (1 critical, 3 moderate)#387
tkislan merged 1 commit into
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tk/resolve-vulnerabilities-2026-06-03

tkislan commented Jun 3, 2026 •

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tkislan commented Jun 3, 2026 • edited by coderabbitai Bot Loading Uh oh! There was an error while loading. Please reload this page.

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Summary

Findings

vitest 4.0.5 → 4.1.8 (critical)

ws 8.19.0 → 8.21.0 (moderate)

qs 6.14.2 → 6.15.2 (moderate)

brace-expansion 5.0.5 → 5.0.6 (moderate)

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tkislan commented Jun 3, 2026 •

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`vitest` 4.0.5 → 4.1.8 (critical)

`ws` 8.19.0 → 8.21.0 (moderate)

`qs` 6.14.2 → 6.15.2 (moderate)

`brace-expansion` 5.0.5 → 5.0.6 (moderate)

coderabbitai Bot commented Jun 3, 2026 •

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