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Known Issues & Developer Action Items

AI Agent & Developer Reference This document catalogs known UI bugs, API limitations, and developer action items.

Current Issues (March 2026)

🔴 CRITICAL: Model Submission Only Works on PATRIC Accounts

Severity: High
Affected: /plant page, model reconstruction jobs
Description: Users with RAST accounts cannot submit model reconstruction jobs. Only PATRIC accounts can create new models via the Build Model workflow. This is a backend/API limitation - RAST accounts lack the necessary workspace permissions for model creation.

Impact: RAST users can only view existing models, not create new ones.

Action Item: This is a backend authorization issue. RAST accounts need workspace write permissions to submit reconstruct jobs.

🟡 ACTIVE: Model Editing Not Fully Implemented

Severity: Medium
Affected: Model detail page, Edit tab
Description: Users can view model details and make local changes in the UI, but cannot save edits back to the workspace. The POST /api/models/edit endpoint may return 501 (not implemented).

Impact: Edit functionality is read-only. Users see "API unavailable" message when attempting to save changes.

Location: lib/api/modelseed.ts:editModelFromApi

Action Item: Backend needs to implement the model edit API endpoint.

🟡 ACTIVE: My Models/Media Not Consistent Across RAST and PATRIC

Severity: High
Affected: /my-models, /myMedia pages
Description: Models and media lists are NOT the same when logging in with RAST vs PATRIC credentials for the same user. This is because:

  • PATRIC and RAST maintain separate user workspaces
  • Each authentication system has its own independent data storage
  • Users may have created models/media in one system but not the other

Impact:

  • Users who use both RAST and PATRIC accounts see different data in each
  • Switching from RAST to PATRIC (or vice versa) shows different models/media
  • No unified view of user's complete data across authentication systems

Action Item: Document this limitation clearly in UI or consider implementing data migration/sync between systems.

🟡 ACTIVE: RAST MS FBA Not Working

Severity: High
Affected: /fba/* pages, FBA analysis
Description: Flux Balance Analysis (FBA) jobs submitted through RAST accounts fail to complete or return errors. This affects:

  • Running FBA on models owned by RAST users
  • Viewing FBA results for RAST-owned models

Impact: RAST users cannot perform metabolic modeling analysis through the UI.

Action Item: Backend investigation required - RAST MS FBA service may be unavailable or require different authentication.

🟡 ACTIVE: My Models Data Depends on Account Type

Severity: Medium
Affected: /my-models page
Description: The models visible to a user depend on their authentication method:

  • PATRIC accounts - Can view and create models in their workspace
  • RAST accounts - Limited visibility; some operations may fail

This is expected behavior based on how each system stores user data, but the UX could be clearer about account differences.

Impact: Users switching between RAST and PATRIC accounts see different model lists.

Action Item: Add UI messaging to explain account-type differences when applicable.

🟢 COMPLETED: My Media Consistent Across Account Types

Severity: Low
Status: ✅ Resolved
Description: Media data is stored in a shared location and remains accessible regardless of whether user is logged in via RAST or PATRIC. Users see the same media library when switching accounts.

Location: app/(user-data)/myMedia/page.tsx

🟡 ACTIVE: Workspace Write Operations Limited

Severity: High
Affected Operations:

  • workspaceCreate - Cannot create new workspace objects
  • workspaceDelete - Cannot delete workspace objects
  • workspaceCopy - Cannot copy workspace objects
  • workspaceMetadata - Cannot get object metadata
  • workspacePermissions - Cannot manage permissions
  • workspaceDownloadUrl - Cannot generate download URLs

Impact: Users cannot save edited models/media to workspace. Delete operations fail silently. Media editor shows "API unavailable" warning.

Location: lib/api/workspace.ts

Backend Required: Yes - Fix POST /api/workspace/create, /delete, /copy, /metadata, /permissions, /download-url endpoints in modelseed-api

🟡 ACTIVE: Public Media List Empty

Severity: Low
Affected: /list-media page
Description: The public media table renders but shows 0 rows. The API endpoint /api/media/public returns an empty array.

Impact: Users cannot browse available public media formulations.

Location: app/(reference-data)/list-media/page.tsx, lib/api/modelseed.ts:listPublicMediaFromApi

Backend Required: Yes - Populate the /api/media/public endpoint with media data

🟢 COMPLETED: Job Status Sync with Model Table

Severity: Low
Status: ✅ Resolved
Description: Previously, after a reconstruct job completed, the My Models table would not immediately show the new model. Now includes retry logic that polls for model appearance after job completion.

Location: app/(user-data)/my-models/page.tsx

Quick Reference

Issue Severity Status Account Affected
Model submission (PATRIC only) High 🔴 Active RAST
Model/Media list inconsistency (RAST vs PATRIC) High 🟡 Active Both
RAST MS FBA not working High 🔴 Active RAST
Model editing Medium 🟡 Active All
My Models account differences Medium 🟡 Active RAST
Workspace writes High 🟡 Active All
Public media list empty Low 🟡 Active All
Invalid model path timeout Low ✅ Fixed All
Media consistency Low ✅ Complete -
Job status sync Low ✅ Complete -

Legacy Issues (Resolved/Not Applicable)

The following issues from the previous tracking document are now marked complete:

  • W001: Workspace Write Operations → Superseded by ACTIVE issue above
  • W002: Model Edit API May Return 501 → Superseded by ACTIVE issue above
  • WS001: Workspace /get Returns 500 → Resolved
  • UI001: Chemical Equation Formatting → Low priority, deferred
  • MF001: Model Merge Workflow → Not yet implemented
  • MF005: Build Model Plant Workflow → Works on PATRIC accounts only

Last Updated: 2026-03-26 Maintained by: Development Team Document Version: 2.0