Enhance document and DB interaction, add new functionality and improv…

[glrs]

This pull request includes several significant updates to the lib/couchdb module, focusing on improving logging, enhancing sample and project status management, and adding new utility methods. Below are the most important changes:

Logging Enhancements:

• Added a custom logger to lib/couchdb/document.py for improved logging capabilities.
• Added logging for error handling and warnings in lib/couchdb/manager.py to provide better insights into document processing and status updates. [1] [2]

Sample and Project Status Management:

• Enhanced the add_sample method to include an optional flowcell_ids_processed_for parameter, allowing for better tracking of sample processing.
• Updated the update_sample_status method to log an error if the sample is not found and to refine the status update logic for different processing states.
• Introduced the update_project_status method to handle project status updates and ensure proper end date management.

Utility Methods:

• Added get_sample_status and get_project_status methods to lib/couchdb/manager.py for retrieving the status of specific samples and projects, respectively.

Document Handling:

• Modified the save_document method to handle existing documents by preserving the _rev field to avoid update conflicts.
• Refactored the update_sample_status method in lib/couchdb/manager.py to use the from_dict method for creating YggdrasilDocument instances from dictionaries.…e existing code