[Snyk] Fix for 3 vulnerabilities

[q1blue]

Snyk has created this PR to fix 3 vulnerabilities in the pip dependencies of this project.

Snyk changed the following file(s):

• requirements.txt

⚠️ Warning

transformers 4.30.2 requires tokenizers, which is not installed.
qdrant-client 1.3.1 has requirement numpy<1.21; python_version < "3.8", but you have numpy 1.21.3.
python-docx 1.1.2 has requirement typing-extensions>=4.9.0, but you have typing-extensions 4.5.0.
platformdirs 4.0.0 has requirement typing-extensions>=4.7.1; python_version < "3.8", but you have typing-extensions 4.5.0.
onnxruntime 1.14.1 has requirement numpy>=1.21.6, but you have numpy 1.21.3.
llama-index 0.6.35 requires tiktoken, which is not installed.
llama-index 0.6.35 requires langchain, which is not installed.
llama-index 0.6.35 has requirement fsspec>=2023.5.0, but you have fsspec 2023.1.0.
fake-useragent 1.1.3 has requirement importlib-metadata~=4.0; python_version < "3.8", but you have importlib-metadata 6.6.0.
chromadb 0.3.26 requires tokenizers, which is not installed.
chromadb 0.3.26 requires hnswlib, which is not installed.
chromadb 0.3.26 requires duckdb, which is not installed.
chromadb 0.3.26 has requirement numpy>=1.21.6, but you have numpy 1.21.3.

---

Important

• Check the changes in this PR to ensure they won't cause issues with your project.
• Max score is 1000. Note that the real score may have changed since the PR was raised.
• This PR was automatically created by Snyk using the credentials of a real user.
• 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.

---

Note: You are seeing this because you or someone else with access to this repository has authorized Snyk to open fix PRs.

For more information:
🧐 View latest project report
📜 Customise PR templates
🛠 Adjust project settings
📚 Read about Snyk's upgrade logic

---

Learn how to fix vulnerabilities with free interactive lessons:

🦉 Allocation of Resources Without Limits or Throttling
🦉 Regular Expression Denial of Service (ReDoS)

[gemini-code-assist]

Summary of Changes

Hello @q1blue, 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, automatically generated by Snyk, aims to enhance the project's security posture by resolving three identified vulnerabilities within its Python dependencies. The changes involve updating an existing dependency, pypdf, to a more secure version and introducing a new dependency, pyasn1, to address specific security concerns, ensuring the project's dependencies are up-to-date and more robust against known exploits.

Highlights

• Dependency Upgrade: The pypdf package has been upgraded from version 3.11.0 to 6.6.0 to address two identified security vulnerabilities (SNYK-PYTHON-PYPDF-14912439 and SNYK-PYTHON-PYPDF-14912440).
• New Dependency Added: The pyasn1 package has been added to the requirements.txt file with a minimum version of 0.6.2 to mitigate a security vulnerability (SNYK-PYTHON-PYASN1-15032639).

Using Gemini Code Assist

The full guide for Gemini Code Assist can be found on our documentation page, here are some quick tips.

Invoking Gemini

You can request assistance from Gemini at any point by creating a comment using either /gemini <command> or @gemini-code-assist <command>. Below is a summary of the supported commands on the current page.

Feature	Command	Description
Code Review	/gemini review	Performs a code review for the current pull request in its current state.
Pull Request Summary	/gemini summary	Provides a summary of the current pull request in its current state.
Comment	@gemini-code-assist	Responds in comments when explicitly tagged, both in pull request comments and review comments.
Help	/gemini help	Displays a list of available commands.

Customization

To customize Gemini Code Assist for GitHub experience, repository maintainers can create a configuration file and/or provide a custom code review style guide (such as PEP-8 for Python) by creating and adding files to a .gemini/ folder in the base of the repository. Detailed instructions can be found here.

Limitations & Feedback

Gemini Code Assist may make mistakes. Please leave feedback on any instances where its feedback is incorrect or counter productive. You can react with 👍 and 👎 on @gemini-code-assist comments. If you're interested in giving your feedback about your experience with Gemini Code Assist for Github and other Google products, sign up here.

You can also get AI-powered code generation, chat, as well as code reviews directly in the IDE at no cost with the Gemini Code Assist IDE Extension.

Footnotes

1. Review the Privacy Notices, Generative AI Prohibited Use Policy, Terms of Service, and learn how to configure Gemini Code Assist in GitHub here. Gemini can make mistakes, so double check it and use code with caution. ↩

[gemini-code-assist]

Code Review

This pull request, automatically generated by Snyk, addresses security vulnerabilities by upgrading pypdf and pinning pyasn1. While security is paramount, this change introduces significant risks. The upgrade of pypdf from 3.11.0 to 6.6.0 is a major version jump that could introduce breaking changes. More critically, the project depends on both pypdf and its predecessor PyPDF2, which is a practice that can lead to conflicts and should be resolved by standardizing on a single library. Additionally, the numerous dependency conflicts listed in the pull request description remain unaddressed, indicating a fragile dependency environment that needs attention to ensure stability. I recommend a thorough review of dependencies and extensive testing before merging.

[gemini-code-assist]

This upgrade of pypdf from 3.11.0 to 6.6.0 is a major version change and may introduce breaking API changes. It's important to test functionality that relies on PDF processing.

Furthermore, this file also includes PyPDF2==3.0.1 (line 96). Since pypdf is a fork of PyPDF2, having both in the same project is redundant and can cause conflicts. It is strongly recommended to consolidate to a single PDF library, migrate any code as needed, and remove the other dependency.

[gemini-code-assist]

While pinning pyasn1 is a good practice, this requirements.txt file appears to have several duplicate entries which can make dependency management confusing. For example:

• Pillow==9.5.0 (lines 89 and 153)
• psycopg2==2.9.6 (lines 92 and 143)
• pytest==7.3.2 (lines 99 and 145)
• tiktoken==0.4.0 (lines 125 and 142)

It would be beneficial to clean up these duplicates. Sorting the file alphabetically can also help in maintaining it and spotting such issues in the future.

[snyk-io]

✅ Snyk checks have passed. No issues have been found so far.

Status	Scanner	Critical	High	Medium	Low	Total (0)
✅	Open Source Security	0	0	0	0	0 issues

💻 Catch issues earlier using the plugins for VS Code, JetBrains IDEs, Visual Studio, and Eclipse.