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.

---

## 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.

---

## 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`.

---

## 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.

---

## 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.

---

## 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 |

---

## ✅ 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?