refactor(sources/mongodb): move source implementation in Invoke() function into Source

[Yuan325]

Move source-related queries from Invoke() function into Source.

This is an effort to generalizing tools to work with any Source that implements a specific interface. This will provide a better segregation of the roles for Tools vs Source.

Tool's role will be limited to the following:

• Resolve any pre-implementation steps or parameters (e.g. template parameters)
• Retrieving Source
• Calling the source's implementation

[gemini-code-assist]

Summary of Changes

Hello @Yuan325, 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 significantly refactors the MongoDB integration by centralizing all database interaction logic within the Source implementation. This change aims to establish a clearer separation of responsibilities, where individual tools are primarily concerned with parameter resolution and invoking the appropriate Source method, rather than directly handling MongoDB queries and data processing. This architectural improvement enhances modularity and prepares the system for more generalized source interactions.

Highlights

• Refactored MongoDB Source Implementation: Moved all MongoDB query and data manipulation logic from individual tool Invoke() functions into new methods on the Source struct within internal/sources/mongodb/mongodb.go.
• Centralized Database Operations: Introduced dedicated methods on the Source struct, such as Aggregate, Find, FindOne, InsertMany, InsertOne, UpdateMany, UpdateOne, DeleteMany, and DeleteOne, to encapsulate all MongoDB interactions.
• Simplified Tool Invoke() Functions: The Invoke() functions in various MongoDB tools (e.g., mongodbaggregate, mongodbfind) have been significantly simplified to delegate directly to the corresponding new Source methods, reducing their complexity and improving readability.
• Updated Interfaces and Dependencies: The compatibleSource interfaces in each tool have been updated to reflect the new methods available on the Source. Additionally, direct bson and json imports were removed from tool files, as data marshalling/unmarshalling is now handled internally by the Source.

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[gemini-code-assist]

Code Review

This pull request effectively refactors the MongoDB tools by centralizing the database interaction logic within the mongodb.Source type. This is a solid architectural improvement that enhances separation of concerns and will make the tools more generic and maintainable. The changes across the various tool packages are clean and consistent with the refactoring goal. My review focuses on the new implementation in mongodb.go and includes suggestions to improve error handling, code clarity, and behavioral consistency, particularly around BSON/JSON conversions and delete operations. Overall, this is a valuable refactoring, and addressing the feedback will further strengthen the implementation.