Projects/docs/Missing.md

Based on a thorough review of all frontend React code (hooks, pages, components) and the backend Java repositories and route files you provided, the following backend components are missing or incomplete. The repositories you have are excellent low‑level data access, but the service layer that orchestrates them and the route handlers that implement the actual endpoints are largely absent.

Below is the complete list of what you still need to implement to have a fully functioning backend.

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1. Missing Service Classes

These services contain business logic, call repositories, and are injected into route handlers. Your route files (e.g., ArticleRoutes, AuthRoutes, MessagingRoutes) reference them – they are not implemented yet.

Service	Purpose	Used By
ArticleService	CRUD, search, tags, likes, comments, analytics, graph recommendations	ArticleRoutes, AdminRoutes
UserService	User profiles, follow/unfollow, bookmarks, security (2FA, password reset), activity	UserRoutes, AuthRoutes
MessageService	Private messages, conversations, read status, threading, ephemeral, scheduled	MessagingRoutes
GroupService	Group chat, members, admins, pins, mute, messages, polls	MessagingRoutes
NotificationService	Create, list, mark read, delete notifications (also SSE broadcasting)	NotificationRoutes
AnalyticsService	User and article analytics (views over time, top articles, platform stats)	AnalyticsRoutes
GapAnalysisService	Graph nodes/edges CRUD, AI‑powered gap detection	GapAnalysisRoutes
GrantService	Grant deadlines, user grants, AI draft generation	GrantRoutes
ProjectService	Projects, members, tasks (Kanban), outputs	ProjectRoutes
DataHubService	Research objects, protocols, preregistrations (CRUD, fork, submit)	DataHubRoutes
PollService	Polls/quizzes, voting, results, templates, analytics	PollRoutes
EventService	Events (create, RSVP, reminders, iCal export, recurring)	EventRoutes
LabInventoryService	Chemicals, locations, alerts, compatibility, statistics	LabInventoryRoutes
PeerReviewService	Submissions, reviews, reviewer credentials, assignment	PeerReviewRoutes
WorkspaceService	SmartGlass panels, presets, sharing, backup, import/export	WorkspaceRoutes
VoiceSettingsService	Voice settings (profiles, language overrides, wake words)	VoiceSettingsRoutes
RagService	RAG chat, document indexing, AI predictions, conversation history	RagRoutes
PasswordResetService	Security question retrieval and password reset	PasswordResetRoutes
TwoFactorService	TOTP secret generation, QR code, verification, backup codes	AuthRoutes
SearchService	Advanced message search (full‑text)	MessagingRoutes
MediaService	Upload, retrieve, delete media attachments	MessagingRoutes
RateLimitService	Token‑bucket rate limiting (already has TokenBucket class but no service)	MessagingRoutes, AuthRoutes
ContentModeration	Censor profanity, detect offensive language	MessagingRoutes
CitationGraphService	Build citation graph, provide co‑citation and PageRank recommendations	ArticleRoutes
GNNRecommendationService	Graph Neural Network based recommendations (personalised feed)	GNNRecommendationRoutes
RecommendationService	Traditional collaborative filtering / content‑based feed	RecommendationRoutes
SseManager	Server‑Sent Events manager for real‑time notifications	SseRoutes, NotificationService

Note: You have many repositories (ArticleRepository, UserRepository, etc.). The services above would use them.

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2. Missing Route Handlers (Endpoints)

Even though you have many route files (e.g., ArticleRoutes, AuthRoutes), the following endpoints are not yet implemented (from our earlier frontend API audit):

Endpoint	Frontend Feature	Required Service
GET /api/recent-items	Command palette	UserService (or a dedicated RecentItemService)
GET /api/unified-inbox	Unified inbox	UnifiedInboxService (aggregate messages from multiple sources)
GET /api/discovery/digest	Discovery digest preference	NotificationService (or UserService)
GET /api/discovery/recommendations	Discovery feed (alias)	RecommendationService (can redirect to /recommendations/feed)
GET /api/users/me/liked-articles	Liked articles page	ArticleService
GET /api/conversations/{username}/last-read	Messaging last read ID	MessageService (alias to /read-status)
GET /api/conversations/{username}/keys	Secret chat key exchange	EncryptionKeyRepository (already has repo, but no endpoint)
GET /api/groups/{groupId}/pinned	Group pinned messages (alias)	GroupService (currently /pins exists)
Collections (all endpoints)	Paper collections	CollectionService + new CollectionRepository (not provided)
Reference Manager (all endpoints)	Citations, DOI/BibTeX import	ReferenceService + new ReferenceRepository
Preprint (all endpoints)	Preprint screening & submission	PreprintService + PreprintRepository
Provenance (all endpoints)	Trust / audit log	ProvenanceService + ProvenanceEventRepository
Export (POST /ai/export, POST /documents/{docId}/export)	Document export (PDF, DOCX, LaTeX)	ExportService (calls external converters)

Additionally, the following complete route groups are completely missing (no route files found):

• Paper collections – CRUD for collections and papers inside them.
• Reference manager – endpoints for /api/documents/{docId}/references and /api/references/connect-*.
• Preprint submission – /api/preprints/screen and /api/preprints/submit.
• Provenance – /api/provenance/{entityType}/{entityId} and /verify.

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3. Missing Model Classes (Already provided in previous answer)

You already received the missing model classes for:

• Paper collections (PaperCollection, CollectionPaper)
• Reference manager (ManagedReference, ReferenceGroup)
• Preprint (Preprint, ScreeningResult)
• Provenance (ProvenanceEvent)
• Unified inbox (UnifiedMessage, BroadcastChannel, BroadcastPost, PaperQuestion, PaperAnswer)
• Recent items (RecentItem)
• Workspace (WorkspacePanel, WorkspacePreset)
• Pre‑key encryption (PreKey, SignedPreKey)
• Notification settings (NotificationSettings)
• Export options (ExportOptions)

If you haven't created them yet, you must add those .java files.

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4. Missing Utility / Helper Classes

Class	Purpose	Where Used
JsonUtils	JSON serialisation (you have it in util package?)	Every route handler
TokenUtil	Extract JWT from Authorization header	AuthUtils
SessionManager	Manage user sessions, tokens, CSRF	AuthUtils, AuthRoutes
WebSocketManager	Push real‑time events to connected clients	MessagingRoutes, NotificationService
RateLimitService (wrapper for TokenBucket)	Apply rate limits per IP/user	MessagingRoutes
ContentModeration	Censor profanity (e.g., using external API)	MessagingRoutes
MailService	Send verification emails, password reset emails	UserService, AuthRoutes
FileStorageService	Save uploaded files (avatars, manuscripts, research objects)	UserService, PeerReviewService, DataHubService
CitationGenerator	Convert article metadata to APA/MLA/BibTeX	ArticleService
ExportConverter	Convert HTML to PDF/DOCX/LaTeX	ExportService

Many of these are referenced in your route files but not implemented.

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5. Summary of What You Must Build Now

Category	Items	Priority
Services	All 20+ services listed above	High
Route Handlers	Missing endpoints (collections, references, preprints, provenance, etc.)	High
Model Classes	Already provided – add to model package	Medium
Utility Classes	SessionManager, WebSocketManager, MailService, FileStorageService, etc.	Medium
Database Schema	Create tables matching all repository schemas (SQL scripts)	High
Authentication / Security	JWT generation, CSRF, password hashing (BCrypt)	High
Real‑time WebSocket	Implement WebSocketManager and integrate with MessageService, GroupService	Medium

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✅ Recommended Next Steps

1. Implement the core services first: UserService, ArticleService, MessageService, GroupService. These are used by many routes.
2. Add missing route handlers for the endpoints listed above (start with /api/recent-items, /api/unified-inbox, and collections).
3. Create the missing model classes (you already have the code).
4. Implement SessionManager and WebSocketManager to enable real‑time messaging.
5. Write the SQL schema for all repositories (tables for users, articles, messages, groups, etc.).

Once these are in place, the frontend will have zero missing API calls and the application will be fully functional.

Would you like me to provide Java skeleton code for any of these services or route handlers?