Standardize API Response Format Across All Backend Endpoints

[androemeda]

Summary

This PR introduces a standardized API response format across all backend endpoints to improve consistency, debugging, and frontend integration. All responses now follow a uniform structure that includes a success flag, timestamp, optional message, and metadata when relevant.

Implementation

ResponseFormatter Utility

• Added a centralized ResponseFormatter utility with:
  • success_response()
  • error_response()
• Ensures consistent structure for all API responses.

Controller Updates

• Updated all backend controllers to use the new response format:
  • LLM Controller
  • VCell Database Controller
  • Knowledge Base Controller

Error Handling

• Simplified error responses while preserving correct HTTP status codes.
• Ensures predictable error structures for frontend handling and debugging.

Backward Compatibility

• Updated the frontend ChatBox component to support both old and new response formats during the transition phase.
• Prevents breaking changes while the system migrates to the standardized format.

Response Format

Before (Inconsistent formats)

// LLM endpoint
{"response": "...", "bmkeys": [...]}

// VCell endpoint
{"data": [...], "models_count": 50}

// Knowledge Base endpoint
{"files": [...]}

After (Standardized format)

Success Response

{
  "success": true,
  "data": {...},
  "message": "Request completed successfully",
  "timestamp": "2026-03-12T10:30:45.123Z",
  "meta": {
    "bmkeys": [...]
  } // Included only when relevant
}

Error Response

{
  "success": false,
  "data": null,
  "message": "Failed to fetch biomodels from VCell API",
  "timestamp": "2026-03-12T10:30:45.123Z"
}

Testing

• Syntax Validation: All controller files pass Python compilation checks.
• Frontend Integration: Updated ChatBox component works with the new response structure.
• Error Handling: Existing error conditions preserved with improved consistency.
• Backward Compatibility: No breaking changes introduced to existing API contracts.