Projects/docs/APIEndpoint.md

Legend
✅ = endpoint exists in backend (controllers or dynamic routes)
⚠️ = exists but path differs or only partial implementation
❌ = completely missing

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🔍 1. Authentication & User Management

Method	Endpoint	Frontend Usage	Status	Notes
POST	/api/login	useAuth	✅	AuthRoutes
POST	/api/login/2fa	useAuth (2FA step)	✅	AuthRoutes
POST	/api/logout	useAuth	✅	AuthRoutes
POST	/api/register	useRegister	✅	AuthRoutes
POST	/api/token/refresh	useAuth (token refresh)	✅	AuthRoutes
GET	/api/users/me	useAuth, useDashboard, useProfile	✅	UserRoutes
PUT	/api/users/me	useProfile, useSecuritySettings	✅	UserRoutes
PUT	/api/users/me/email	useProfile	✅	UserRoutes
PUT	/api/users/me/password	useSecuritySettings	✅	UserRoutes
DELETE	/api/users/me	useProfile (deactivate)	✅	UserRoutes
POST	/api/users/me/avatar	useProfile, useDashboard	✅	UserRoutes
GET	/api/users/{username}	usePublicProfile, useProfile	✅	UserRoutes
GET	/api/search/users	useSearchUsers, useContacts	✅	UserRoutes
GET	/api/users/me/security-question	useSecuritySettings	✅	UserRoutes
PUT	/api/users/me/security-question	useSecuritySettings	✅	UserRoutes
GET	/api/users/me/2fa/status	useSecuritySettings	✅	UserRoutes
POST	/api/users/me/2fa/enable	useSecuritySettings	✅	AuthRoutes
POST	/api/users/me/2fa/verify	useSecuritySettings	✅	AuthRoutes
POST	/api/users/me/2fa/disable	useSecuritySettings	✅	AuthRoutes
GET	/api/users/me/2fa/backup-codes	useSecuritySettings	✅	AuthRoutes
POST	/api/users/me/2fa/backup-codes/regenerate	useSecuritySettings	✅	AuthRoutes
POST	/api/forgot-password	usePasswordReset	✅	AuthRoutes
POST	/api/reset-password	usePasswordReset	✅	AuthRoutes

All user/auth endpoints present. ✅

---

🔍 2. Follow System

Method	Endpoint	Frontend Usage	Status
POST	/api/users/{username}/follow	useFollow, useArticle	✅
DELETE	/api/users/{username}/follow	useFollow	✅
GET	/api/users/{username}/followers	usePublicProfile	✅
GET	/api/users/{username}/following	usePublicProfile, useArticle	✅
GET	/api/users/me/contacts	useContacts	✅

All follow endpoints present. ✅

---

🔍 3. Articles

Method	Endpoint	Frontend Usage	Status
GET	/api/articles	useArticles, ArticlesPage	✅
GET	/api/articles/{id}	useArticle	✅
POST	/api/articles	useCreateArticle	✅
PUT	/api/articles/{id}	useArticle, useCreateArticle	✅
DELETE	/api/articles/{id}	useArticle, useDashboard	✅
GET	/api/articles/search	useSearch, ArticlesPage	✅
GET	/api/users/me/articles	useDashboard	✅
POST	/api/articles/{id}/like	useArticle	✅
GET	/api/articles/{id}/like	useArticle	✅
GET	/api/articles/{id}/comments	useArticle	✅
POST	/api/articles/{id}/comments	useArticle	✅
DELETE	/api/comments/{commentId}	useArticle	✅
GET	/api/articles/{id}/citation	useArticle	✅
GET	/api/users/me/analytics	useDashboard, useAnalytics	✅
POST	/api/articles/{id}/publish	useCreateArticle	✅
GET	/api/articles/trending	useRecommendations	✅
GET	/api/articles/featured	useRecommendations	✅
GET	/api/articles/{id}/graph-recommendations	useRecommendations (graph)	✅
POST	/api/articles/{id}/view	useArticle (view count)	✅
GET	/api/articles/{id}/analytics	usePaperAnalytics	✅
GET	/api/users/me/liked-articles	LikedArticlesPage	❌ Missing (backend has /users/{username}/liked-articles only)

Missing: GET /api/users/me/liked-articles – frontend uses this (see LikedArticlesPage). Backend has only public version for a given username. Add an alias to the same logic.

---

🔍 4. Messaging (Private & Group)

Method	Endpoint	Frontend Usage	Status	Notes
GET	/api/conversations	useMessaging	✅
DELETE	/api/conversations/{username}	useMessaging	✅
GET	/api/conversations/{username}/messages	useMessaging	✅
POST	/api/conversations/{username}/messages	useMessaging	✅
PUT	/api/conversations/{username}/messages/{messageId}	useMessaging	✅
DELETE	/api/conversations/{username}/messages/{messageId}	useMessaging	✅
POST	/api/conversations/{username}/messages/{messageId}/reactions	useMessaging	✅
POST	/api/conversations/{username}/typing	useMessaging	✅
GET	/api/conversations/{username}/typing	useMessaging	✅
POST	/api/conversations/{username}/read	useMessaging	✅
GET	/api/conversations/{username}/read-status	useMessaging	✅
GET	/api/conversations/{username}/last-read	useMessaging	❌	Missing – backend has /read-status but frontend calls /last-read separately. Add alias.
POST	/api/conversations/{username}/archive	useMessaging	✅
DELETE	/api/conversations/{username}/archive	useMessaging	✅
GET	/api/users/me/archived-conversations	useMessaging	✅
GET	/api/messages/{messageId}/edits	useEditHistory	✅
GET	/api/messages/{messageId}/thread	useMessaging (threads)	✅
POST	/api/messages/{messageId}/reply	useMessaging	✅
POST	/api/messages/{messageId}/forward	useMessaging	✅
POST	/api/groups/messages/{messageId}/forward-to-group	useMessaging	✅
POST	/api/conversations/{username}/schedule	useMessaging	✅
POST	/api/conversations/{username}/ephemeral	useMessaging	✅
GET	/api/messages/scheduled	useMessaging	✅
DELETE	/api/messages/scheduled/{messageId}	useMessaging	✅
POST	/api/media/upload	ChatArea	✅
GET	/api/media/{mediaId}	ChatArea	✅
DELETE	/api/media/{mediaId}	useMessaging	✅

Groups:

Method	Endpoint	Frontend Usage	Status
GET	/api/groups	useMessaging	✅
POST	/api/groups	useMessaging	✅
GET	/api/groups/{groupId}	useMessaging	✅
PUT	/api/groups/{groupId}	useMessaging	✅
DELETE	/api/groups/{groupId}	useMessaging	✅
GET	/api/groups/{groupId}/members	useMessaging	✅
POST	/api/groups/{groupId}/members	useMessaging	✅
DELETE	/api/groups/{groupId}/members/{memberId}	useMessaging	✅
POST	/api/groups/{groupId}/admins/{memberId}	useMessaging	✅
POST	/api/groups/{groupId}/members/{memberId}/demote	useMessaging	✅
POST	/api/groups/{groupId}/leave	useMessaging	✅
POST	/api/groups/{groupId}/invite	useMessaging	✅
GET	/api/join/{token}	useMessaging	✅
GET	/api/groups/{groupId}/messages	useMessaging	✅
POST	/api/groups/{groupId}/messages	useMessaging	✅
PUT	/api/groups/{groupId}/messages/{messageId}	useMessaging	✅
DELETE	/api/groups/{groupId}/messages/{messageId}	useMessaging	✅
GET	/api/groups/{groupId}/messages/since	useMessaging	✅
POST	/api/groups/{groupId}/read	useMessaging	✅
GET	/api/groups/{groupId}/read-status	useMessaging	✅
POST	/api/groups/{groupId}/mute	useMessaging	✅
DELETE	/api/groups/{groupId}/mute	useMessaging	✅
GET	/api/groups/{groupId}/pins	useMessaging (pinned list)	✅ (backend uses /pins)
GET	/api/groups/{groupId}/pinned	useMessaging (frontend uses /pinned)	❌ Missing – add alias to /pins.
POST	/api/groups/{groupId}/pin/{messageId}	useMessaging	✅
DELETE	/api/groups/{groupId}/pin/{messageId}	useMessaging	✅
POST	/api/groups/{groupId}/transfer/{newOwnerId}	useMessaging	✅
GET	/api/groups/{groupId}/meta	useMessaging	✅

Secret Chats (E2EE):

Method	Endpoint	Frontend Usage	Status
POST	/api/secret/prekeys	useSecretChat	✅
GET	/api/secret/prekeys/{username}	useSecretChat	✅
POST	/api/secret/prekeys/refresh	useSecretChat	✅
POST	/api/conversations/{username}/start-secret	useSecretChat	✅
POST	/api/conversations/{username}/accept-secret	useSecretChat (maybe not)	✅ (in SecretConversationRoutes)
GET	/api/conversations/{username}/keys	useSecretChat	❌ Missing – needed to fetch peer’s public keys.
POST	/api/secret/send	useSecretChat	✅
GET	/api/secret/messages/{conversationKey}	useSecretChat	✅
POST	/api/secret/ratchet	useSecretChat	✅

---

🔍 5. Notifications

Method	Endpoint	Frontend Usage	Status
GET	/api/notifications	useDashboard, useNotifications	✅
GET	/api/notifications/unread-count	useNotifications	✅
POST	/api/notifications/{id}/read	useDashboard	✅
POST	/api/notifications/read-all	useNotifications	✅
POST	/api/notifications/read-multiple	useNotifications	✅
DELETE	/api/notifications/{id}	useNotifications	✅
DELETE	/api/notifications	useNotifications	✅

All present. ✅

---

🔍 6. Recommendations & Discovery

Method	Endpoint	Frontend Usage	Status	Notes
GET	/api/recommendations/feed	useRecommendations, useRecommendationFeed	✅
GET	/api/recommendations/trending	useRecommendations	✅
GET	/api/recommendations/users	useRecommendations	✅
GET	/api/discovery/digest	useRecommendationFeed	❌	Missing (only POST exists)
POST	/api/discovery/digest	useRecommendationFeed	✅
GET	/api/discovery/recommendations	useRecommendationFeed	❌	Missing – frontend calls this; use /recommendations/feed instead.

Missing: GET /api/discovery/digest and GET /api/discovery/recommendations.

---

🔍 7. RAG Assistant (Research Assistant)

Method	Endpoint	Frontend Usage	Status
POST	/api/ai/rag-chat	useRagSystem	✅
POST	/api/ai/chat	useRagSystem	✅
POST	/api/ai/command-palette/predict	usePredictiveActions	✅
GET	/api/documents/rag-list	useRagSystem	✅
DELETE	/api/documents/{docId}/rag-delete	useRagSystem	✅
POST	/api/documents/{docId}/rag-index	useRagSystem	✅
GET	/api/documents/{docId}/rag-status	useRagSystem	✅
GET	/api/ai/conversation	useRagSystem	✅
DELETE	/api/ai/conversation	useRagSystem	✅

All present. ✅

---

🔍 8. Lab Inventory

All endpoints under /api/inventory/ (chemicals, alerts, scan, compatibility, stats) are fully present in LabInventoryRoutes. ✅

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🔍 9. Peer Review

All endpoints under /api/peer-review/ and /api/admin/peer-review/ are present. ✅

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🔍 10. Gap Analysis

All endpoints under /api/gap-analysis/ are present. ✅

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🔍 11. Projects & Tasks

All endpoints under /api/projects/ (CRUD, members, tasks, outputs) are present. ✅

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🔍 12. Data Hub (Research Objects, Protocols, Preregistrations)

All endpoints under /api/repository/, /api/protocols/, /api/preregistrations/ are present in DataHubRoutes. ✅

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🔍 13. Events

All endpoints under /api/events/ are present in EventRoutes. ✅

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🔍 14. Workspace (SmartGlass)

All endpoints under /api/workspace/ are present in WorkspaceRoutes. ✅

Missing alias: GET /api/groups/{groupId}/pinned (frontend uses /pinned, backend has /pins). Not critical but add for consistency.

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🔍 15. Voice Settings

All endpoints under /api/users/me/voice-settings, /api/voice/ are present. ✅

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🔍 16. Admin

All admin endpoints (/api/admin/*) are present (stats, users, articles, activity, search, rag, etc.). ✅

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🔍 17. Collections (Paper Collections) – COMPLETELY MISSING

The frontend usePaperCollections calls:

Method	Endpoint	Status
GET	/api/collections	❌
POST	/api/collections	❌
DELETE	/api/collections/{id}	❌
POST	/api/collections/{id}/papers	❌
DELETE	/api/collections/{id}/papers/{paperId}	❌

No backend implementation. You need to add these.

---

🔍 18. References / Bibliography Manager – MISSING

useReferenceManager calls:

Method	Endpoint	Status
GET	/api/documents/{docId}/references	❌
POST	/api/documents/{docId}/references	❌
PUT	/api/documents/{docId}/references/{refId}	❌
DELETE	/api/documents/{docId}/references/{refId}	❌
POST	/api/references/connect-zotero	❌
POST	/api/references/connect-mendeley	❌

No backend implementation. Add these.

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🔍 19. Preprint Submission – MISSING

Method	Endpoint	Status
POST	/api/preprints/screen	❌
POST	/api/preprints/submit	❌

No backend implementation.

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🔍 20. Provenance / Trust – MISSING

Method	Endpoint	Status
GET	/api/provenance/{entityType}/{entityId}	❌
POST	/api/provenance/{entityType}/{entityId}/verify	❌

No backend implementation.

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🔍 21. Unified Inbox – MISSING

Method	Endpoint	Status
GET	/api/unified-inbox	❌

Frontend uses useUnifiedInbox to fetch aggregated messages. Not present.

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🔍 22. Recent Items (Command Palette) – MISSING

Method	Endpoint	Status
GET	/api/recent-items	❌

App.tsx fetches recent papers and contacts. Add this endpoint.

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🔍 23. Export (Documents / Articles) – MISSING

Method	Endpoint	Status
POST	/api/ai/export	❌
POST	/api/documents/{docId}/export	❌

useSubmissionExport and useCollaborativeEditor call these to export PDF, DOCX, LaTeX, etc. Not present.

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🔍 24. Miscellaneous – MISSING / PARTIAL

• GET /api/health – ✅ present.
• GET /api/me – ✅ present.
• GET /api/popular-tags – ✅ present (in AnalyticsRoutes).
• GET /api/trending – ✅ present.
• POST /api/callback (inline keyboard) – ✅ present in MessagingRoutes.

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📋 Final Missing Endpoints Summary

#	Endpoint	Frontend Feature	Urgency
1	GET /api/recent-items	Command palette	High
2	GET /api/unified-inbox	Unified Inbox	High
3	POST /api/preprints/screen	Preprint screening	Medium
4	POST /api/preprints/submit	Preprint submission	Medium
5	GET /api/discovery/digest	Discovery digest preference	Low
6	GET /api/discovery/recommendations	Discovery feed	Low (can alias to /recommendations/feed)
7-11	All /api/collections/*	Paper collections	High
12-17	All /api/documents/{docId}/references/* & /api/references/*	Reference manager	High
18	POST /api/ai/export	Document export	High
19	POST /api/documents/{docId}/export	Export (alternative)	High
20-21	/api/provenance/*	Trust / provenance	Low
22	GET /api/users/me/liked-articles	User liked articles	Medium (can be aliased)
23	GET /api/conversations/{username}/last-read	Messaging	Low (use /read-status)
24	GET /api/conversations/{username}/keys	Secret chat	High
25	GET /api/groups/{groupId}/pinned	Group pinned messages	Low (alias for /pins)

Total missing endpoints: 25 distinct URLs (some are groups).

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✅ Recommended Next Steps

1. Implement the “high” urgency endpoints first:

   • GET /api/recent-items
   • GET /api/unified-inbox
   • Collections CRUD
   • Reference manager endpoints
   • Export endpoints
   • Secret chat key retrieval

2. For low urgency, add simple aliases or use existing endpoints:

   • /groups/{groupId}/pinned → forward to /groups/{groupId}/pins
   • /conversations/{username}/last-read → forward to /read-status and extract the field

3. For missing discovery endpoints, you can either implement them or modify the frontend to use existing /recommendations/feed and /recommendations/trending.