fix(security): update dependencies to fix security vulnerabilities#5936
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…directly depends on it.
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* fix: Use newer ONNX version and load without errors * Only changes to enable SAM again * fix(seg hydration): auto-hydrate RT struct on second load with disableConfirmationPrompts (#5875) * chore(version): Update package versions to 3.13.0-beta.34 [skip ci] * fix(Threshold tool): Threshold tool no longer becomes deselected when the Dynamic option is selected (#5884) fix(Threshold tool): Added 'ThresholdCircularBrushDynamic' to the toolNames array so the evaluator correctly recognizes it as an active state for the Threshold button when Dynamic mode is selected. * chore(version): Update package versions to 3.13.0-beta.35 [skip ci] * fix: Modalities in study list should select starts with as primary (#5886) * chore(version): Update package versions to 3.13.0-beta.36 [skip ci] * fix(security): Bump tar version to address CVE-2026-31802. (#5893) * chore(version): Update package versions to 3.13.0-beta.37 [skip ci] * fix(segmentation): Display "No description S:{series number} {modality}" for segmentations with no label. (#5874) * Bump CS3D dependency to get the fallbackLabel field additions. * chore(version): Update package versions to 3.13.0-beta.38 [skip ci] * fix(window level): The window level value is not displayed by default on all the viewports when selecting common/custom layout and TMTV. (#5865) * fix(window level): Set up listener for viewport availability such that the initial window level can be read and displayed. * PR feedback. * PR feedback. --------- Co-authored-by: Bill Wallace <wayfarer3130@gmail.com> * chore(version): Update package versions to 3.13.0-beta.39 [skip ci] * fix(security): Bump flattened version to address CVE-2026-32141. (#5897) * chore(version): Update package versions to 3.13.0-beta.40 [skip ci] * fix(sr-hydration): enable hydration and arrow navigation for 3D SR measurements (#5887) Joe is away, so approving based on the code having the requested change, and otherwise looking good/passing tests. * fix(sr-hydration): enable hydration and arrows navigation for 3D SR measurements * test: add automated test for SR measurement navigation with arrows after hydration * add cross-study warning in the 3D branch * test: address reviewer feedback for the test * fix: support 3D and 2D annotations for SR hydration * test: improve navigation to first image --------- Co-authored-by: Bill Wallace <wayfarer3130@gmail.com> * chore(version): Update package versions to 3.13.0-beta.41 [skip ci] * feat: Add combined build (#5895) * Add combined build * Link script location update * Security and validation fixes * Allow specifying target path in PR description * fix: Version match * Fix build detection issue * fix: Playwright deploy * Separate out the branch merge guard * Update docs and link info * test: Update the layout change to wait for network idle * Move audit late so the rest of the build can be worked on * Add text with network check to ensure we see this change is updated * Attempt to fix the mpr loading on ohif-downstream * PR review comments * Update docs * Update to CS3D 4.20.0 * PR comments * Add log on ohif-integration builds * Update build test * Removed unused space to kickoff build * chore(version): Update package versions to 3.13.0-beta.42 [skip ci] * fix(SR): Added support for spline and live wire SR items. (#5870) * fix(SR): Added support for spline and live wire SR items. * Apply suggestion from @greptile-apps[bot] Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Add a script to checkout a worktree for test builds * fix: Allow download for testing sr validator * Remove script that wasn't intended to be included * Bump CS3D version. * PR comments - simplify code and use single codepath for download * Allow both download and save buttons for SEG and RTSTRUCT --------- Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> Co-authored-by: Bill Wallace <wayfarer3130@gmail.com> * chore(version): Update package versions to 3.13.0-beta.43 [skip ci] * chore(tests): contour segment interactions e2e tests - rename and togglevisibility (#5891) * chore(version): Update package versions to 3.13.0-beta.44 [skip ci] * chore(refactor): use public appConfig getter instead of private _appConfig field (#5923) * chore(version): Update package versions to 3.13.0-beta.45 [skip ci] * refactor(tests): update viewport page object usage to async and update all effected tests (#5927) * chore(version): Update package versions to 3.13.0-beta.46 [skip ci] * fix: prevent black viewport when navigating series with client-created segmentation (#5919) * chore(version): Update package versions to 3.13.0-beta.47 [skip ci] * fix(measurement): Restore viewport interactivity when deleting in-progress Spline or Livewire measurement (#5905) * chore(version): Update package versions to 3.13.0-beta.48 [skip ci] * fix(segmentation): restrict overlay segmentation menu to same frame of reference as viewport background display set (#5900) - Add FrameOfReferenceUID to SEG and RTSTRUCT displaySet in SOP Class Handlers so the FOR is available for filtering - Sync optimisticOverlayDisplaySets when background display set changes so the overlay menu reflects the correct state after a background switch - Add FOR matching guard to the hydrate segmentation synchronizer to prevent the hydration synchronizer from blindly mirroring segmentations from a source viewport to a target viewport if their primary Frames of Reference do not align. - fix segmentation overlay order reversal on viewport re-render * chore(version): Update package versions to 3.13.0-beta.49 [skip ci] * fix(security): update dependencies to fix security vulnerabilities (#5936) * chore(version): Update package versions to 3.13.0-beta.50 [skip ci] * fix(security): Update yarn.lock that was missed in PR #5936. (#5940) * chore(version): Update package versions to 3.13.0-beta.51 [skip ci] * feat(component): Adds SmartScrollbar to ui-next - OHIF-2558 (#5924) Co-authored-by: Joe Boccanfuso <joe.boccanfuso@radicalimaging.com> * fix(defaultRouteInit): pass sorted display sets to hanging protocol for deterministic viewport order (#5933) fix: pass sorted display sets to hanging protocol for deterministic viewport order The `applyHangingProtocol` function already sorts display sets by modality priority and series number into `sortedDisplaySets`, but the unsorted `displaySets` array was being passed to `hangingProtocolService.run()`. This caused non-deterministic viewport ordering across page loads because `displaySetService.getActiveDisplaySets()` returns display sets in creation order, which depends on asynchronous network responses. Made-with: Cursor * chore(version): Update package versions to 3.13.0-beta.52 [skip ci] * revert: rename DisplaySet.frameOfReferenceUID back to FrameOfReferenceUID (#5943) * chore(version): Update package versions to 3.13.0-beta.53 [skip ci] * fix(cornerstone): read FrameOfReferenceUID from display set in viewport service (#5950) * chore(version): Update package versions to 3.13.0-beta.54 [skip ci] * fix: ignore auth in git (#5955) * chore(version): Update package versions to 3.13.0-beta.55 [skip ci] * ONNX latest version * chore(version): Update package versions to 3.13.0-beta.56 [skip ci] * bun lock * fix high sev mathjs issue * Revert onnx changes * Update to recent CS3D version * Undo unneeded change * Add null check * Undo unneeded change --------- Co-authored-by: Ghadeer Albattarni <165973963+GhadeerAlbattarni@users.noreply.github.com> Co-authored-by: ohif-bot <danny.ri.brown+ohif-bot@gmail.com> Co-authored-by: Joe Boccanfuso <109477394+jbocce@users.noreply.github.com> Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> Co-authored-by: diattamo <mmddiatta@gmail.com> Co-authored-by: Pedro Köhler <pedrokohlerbh@gmail.com> Co-authored-by: Dan Rukas <dan.rukas@gmail.com> Co-authored-by: Joe Boccanfuso <joe.boccanfuso@radicalimaging.com> Co-authored-by: Alireza <ar.sedghi@gmail.com>
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Context
Address various security bulletins...
GHSA-r5fr-rjxr-66jc
GHSA-677m-j7p3-52f9
GHSA-rf6f-7fwh-wjgh
GHSA-2328-f5f3-gj25
GHSA-q67f-28xg-22rw
GHSA-5m6q-g25r-mvwx
GHSA-ppp5-5v6c-4jwp
GHSA-2w6w-674q-4c4q
GHSA-9cx6-37pm-9jff
GHSA-xhpv-hc6g-r9c6
GHSA-xjpj-3mr7-gcpf
GHSA-3mfm-83xf-c92r
GHSA-37ch-88jc-xwx2
GHSA-c2c7-rcm5-vvqj
Changes & Results
Patched some versions. Ignored dev only vulnerability.
Testing
Run automated tests.
Checklist
PR
semantic-release format and guidelines.
Code
etc.)
Public Documentation Updates
additions or removals.
Greptile Summary
This PR addresses 14 security advisories by bumping several direct and transitive dependency overrides in
package.json, and updating the correspondingyarn.lockandbun.lockfiles. A new advisory forpicomatch(GHSA-c2c7-rcm5-vvqj) is intentionally ignored in CI, with the justification that it is only used in build/CI contexts.Confidence Score: 5/5
Safe to merge — all security fixes are correctly reflected in yarn.lock; the only finding is a P2 cosmetic gap in bun.lock that does not affect runtime behavior.
All updated packages (path-to-regexp, node-forge, lodash, lodash-es, flatted, handlebars, socket.io-parser) are properly resolved with correct versions and integrity hashes in yarn.lock, which is the primary package manager. The single finding (missing bun.lock package entry for socket.io-parser) is a P2 style issue that does not affect how packages are actually installed or used at runtime.
bun.lock — socket.io-parser override lacks a resolved package entry
Important Files Changed
Flowchart
%%{init: {'theme': 'neutral'}}%% flowchart TD A[Security Advisories Identified] --> B[Bump direct resolutions in package.json] B --> C{Package type} C -->|Bumped version| D[path-to-regexp 0.1.12 → 0.1.13] C -->|Bumped version| E[node-forge 1.3.2 → 1.4.0] C -->|Bumped version| F[lodash / lodash-es 4.17.23 → 4.18.1] C -->|Bumped version| G[flatted 3.4.0 → 3.4.2] C -->|Bumped version| H[handlebars 4.7.8 → 4.7.9] C -->|New override| I[socket.io-parser 4.2.6 added] C -->|Ignored - dev only| J[picomatch GHSA-c2c7-rcm5-vvqj] D & E & F & G & H --> K[yarn.lock + bun.lock updated] I --> L[yarn.lock fully resolved] I --> M[bun.lock overrides only - no package entry] J --> N[CI ignore list + bun audit --ignore flag]Reviews (1): Last reviewed commit: "fix(security): update dependencies to fi..." | Re-trigger Greptile