[Snyk] Security upgrade pypdf from 4.3.1 to 6.1.3

[arthrod]

Snyk has created this PR to fix 2 vulnerabilities in the pip dependencies of this project.

Snyk changed the following file(s):

• backend/requirements.txt

⚠️ Warning

openai 1.53.1 requires jiter, which is not installed.
openai 1.53.1 has requirement typing-extensions<5,>=4.11, but you have typing-extensions 4.7.1.
onnxruntime 1.14.1 has requirement numpy>=1.21.6, but you have numpy 1.21.3.
fake-useragent 1.5.1 has requirement importlib-metadata~=4.0; python_version < "3.8", but you have importlib-metadata 6.7.0.
extract-msg 0.39.2 has requirement tzlocal==4.2, but you have tzlocal 5.1.
anthropic 0.38.0 requires tokenizers, which is not installed.
anthropic 0.38.0 requires jiter, which is not installed.

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• Some vulnerabilities couldn't be fully fixed and so Snyk will still find them when the project is tested again. This may be because the vulnerability existed within more than one direct dependency, but not all of the affected dependencies could be upgraded.

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[gemini-code-assist]

Summary of Changes

Hello @arthrod, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request focuses on enhancing the security posture of the project by performing an automated upgrade of the pypdf dependency. The upgrade targets specific vulnerabilities, ensuring that the backend components relying on this library are more secure against known exploits. While the PR introduces a critical security fix, it also notes potential dependency conflicts with other packages that may require further attention.

Highlights

• Dependency Upgrade: The pypdf library has been upgraded from version 4.3.1 to 6.1.3 to address two identified security vulnerabilities.
• Automated Security Fix: This pull request was automatically generated by Snyk to remediate security issues within the project's dependencies.

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✨ Finishing touches

🧪 Generate unit tests (beta)

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• Commit unit tests in branch snyk-fix-89dede50af56e313899031f3b753b2b7

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[gemini-code-assist]

Code Review

This pull request updates the pypdf dependency in backend/requirements.txt from version 4.3.1 to 6.1.3 to address two vulnerabilities. I have reviewed the change and found one issue related to the usage of uv for installing dependencies in the Dockerfile, which could potentially lead to inconsistencies if not handled carefully.

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Update uv.lock to keep pypdf version consistent

This file now pins pypdf==6.1.3, but uv.lock still locks the dependency at 4.3.1. Any installation path that uses the lock file (for example, uv pip sync or uv pip install --resolution locked) will continue to pull 4.3.1, so the security fix never lands and environments end up out of sync with the requirements. Regenerate the lock file so both dependency manifests agree.

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[openhands-ai]

Looks like there are a few issues preventing this PR from being merged!

• GitHub Actions are failing:
  • Integration Test

If you'd like me to help, just leave a comment, like

@OpenHands please fix the failing actions on PR #85 at branch `snyk-fix-89dede50af56e313899031f3b753b2b7`

Feel free to include any additional details that might help me get this PR into a better state.

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