flask:2024-08-27

[iwmstjp]

Summary by Sourcery

Refactor the Flask application to improve security by using a random secret key, enhance error handling with a defaultdict for errors, and update the email notification system to support multiple recipients. Add a README.md file with setup instructions.

New Features:

• Introduce a new email notification system that sends emails to multiple recipients when a file is uploaded, with improved error handling for email sending.

Enhancements:

• Replace the use of a fixed secret key with a randomly generated one for improved security.
• Refactor error handling in form data processing to use a defaultdict for errors, improving the clarity and management of error messages.
• Enhance validation logic to ensure the uniqueness of the combination of SampleID, run_directory, and barcode.

Documentation:

• Add a README.md file with instructions on how to set up and run the application, including optional steps for saving files to a remote server.

[sourcery-ai[bot]]

Reviewer's Guide by Sourcery

This pull request implements several important changes to improve the security, error handling, and functionality of the Flask application. Key modifications include updating the secret key generation, implementing environment variable checks, refactoring error handling, enhancing email notifications, and improving data validation.

File-Level Changes

Change	Details	Files
Improved secret key generation and environment variable handling	Replaced static secret key with dynamically generated one using os.urandom() Added checks for required environment variables (META_REMOTE_PATH and META_KEY_PATH) Implemented a function to check for RECIPIENT_EMAIL environment variable	flask-version/metagenomongo/app.py
Refactored error handling and reporting	Replaced 'results' list with a defaultdict called 'errors' for more structured error handling Updated error reporting in various functions to use the new 'errors' structure Modified templates to display errors based on the new structure	flask-version/metagenomongo/app.py flask-version/metagenomongo/module/validation.py flask-version/metagenomongo/templates/index_with_table.html flask-version/metagenomongo/templates/index.html
Enhanced email notification system	Updated email sending function to accept file name and remote path as parameters Implemented support for multiple recipients Added more detailed email content including file name and upload location	flask-version/metagenomongo/module/email.py flask-version/metagenomongo/app.py
Improved data validation	Added validation for unique combinations of sampleID, run_directory, and barcode Updated error reporting in validation functions to use the new 'errors' structure	flask-version/metagenomongo/module/validation.py
Added README.md with setup and usage instructions	Included steps for cloning the repository, installing dependencies, setting environment variables, and running the application Added optional instructions for using the remote server file saving function	flask-version/metagenomongo/README.md

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