[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 duckdb, which is not installed.
chromadb 0.3.26 requires hnswlib, which is not installed.
chromadb 0.3.26 has requirement numpy>=1.21.6, but you have numpy 1.21.3.

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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.

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[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 by addressing three identified vulnerabilities within its Python dependencies. The changes involve updating an existing package and introducing a new dependency to resolve these security concerns.

Highlights

• Dependency Upgrade: The pypdf dependency has been upgraded from version 3.11.0 to 6.6.0 to address identified vulnerabilities.
• New Dependency Added: The pyasn1 dependency has been added to requirements.txt with a minimum version of 0.6.2. This addition was made by Snyk to mitigate a specific vulnerability.

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[gemini-code-assist]

Code Review

This pull request, automatically generated by Snyk, addresses three security vulnerabilities by upgrading pypdf to version 6.6.0 and pinning pyasn1 to version 0.6.2 or higher.

While these security fixes are important, the project's dependencies are in a problematic state. The requirements.txt file contains numerous issues that are likely to break the build, including unresolved dependency conflicts, duplicated packages, and the use of two conflicting PDF libraries (pypdf and PyPDF2).

I've added a detailed comment in requirements.txt outlining these critical issues. It is strongly recommended to address all dependency problems in a separate, dedicated effort to ensure the project's stability and maintainability before or immediately after merging this security fix.

[gemini-code-assist]

While updating pypdf is necessary for security, this requirements.txt file has several critical issues that will likely cause the build to fail. These should be addressed before merging.

1. Unresolved Dependency Conflicts:
The PR description itself lists multiple conflicts. The following seem to be critical and will break the installation:

• transformers and chromadb require tokenizers, which is not installed.
• llama-index requires langchain, which is not installed.
• llama-index has a version conflict with its dependency fsspec.
• python-docx requires typing-extensions>=4.9.0, but version 4.5.0 is specified.
• chromadb requires duckdb and hnswlib, which are not installed.

2. Duplicate Dependencies:
There are several duplicated packages in this file, which should be cleaned up: tiktoken, psycopg2, pytest, Pillow.

3. Conflicting PDF Libraries:
The project depends on both PyPDF2 and pypdf (this line). Since pypdf is a fork of PyPDF2, having both can lead to conflicts. It's recommended to standardize on one, preferably pypdf as it is more actively maintained, and update the code accordingly.

Addressing these issues is crucial for project stability.