flask:2024-08-26

[iwmstjp]

Summary by Sourcery

Enhance data validation by ensuring unique combinations of SampleID, run_directory, and barcode. Improve error handling in the Flask app for environment variables and file operations. Update the HTML template to display validation results. Add a README.md with setup and usage instructions.

New Features:

• Add validation for unique combinations of SampleID, run_directory, and barcode in the data validation process.

Enhancements:

• Improve error handling for missing environment variables and file operations in the Flask application.
• Enhance the HTML template to display error and data messages from the validation results.

Documentation:

• Add a README.md file with instructions on cloning the repository, installing dependencies, running the application, and optional features like email and remote server file saving.

[sourcery-ai[bot]]

Reviewer's Guide by Sourcery

This pull request implements several changes to improve data validation, error handling, and user experience in a Flask-based web application for metagenomics data processing. The changes include enhancing the validation process for sample IDs, adding new fields for validation, improving error handling for file uploads and environment variables, and updating the UI to display results.

File-Level Changes

Change	Details	Files
Enhanced data validation for sample identification	Replaced single sampleID validation with a combination of sampleID, run_directory, and barcode Added checks for empty values in sampleID, run_directory, and barcode fields Implemented uniqueness check for the combination of sampleID, run_directory, and barcode	flask-version/metagenomongo/module/validation.py
Improved error handling and environment variable management	Added try-except block for retrieving the FLASK_SK environment variable Implemented checks for META_KEY_PATH environment variable Updated file transfer process with better error handling and logging	flask-version/metagenomongo/app.py
Enhanced user interface for displaying results	Added a new div element to display error messages and data results Implemented Jinja2 template logic to iterate through and display results	flask-version/metagenomongo/templates/index.html
Added README file with setup and usage instructions	Included steps for cloning the repository Listed required Python libraries and their versions Provided instructions for running the application and accessing it Added optional setup information for email and remote server file saving functions	flask-version/metagenomongo/README.md

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