PaperTrail: Collaborative Research Project Management Platform

PaperTrail is a centralized workspace designed for student research teams and faculty guides to collaborate throughout the research lifecycle. It addresses the fragmentation of information caused by managing papers, notes, progress reports, faculty feedback, and team discussions across separate channels such as Google Docs, Drive, WhatsApp, and email.

Key Features and Roles

Roles

• Leader: Create research projects, invite team members, invite faculty guides, and manage tasks.
• Member: Upload research papers, add reference notes, log project progress, and participate in discussions.
• Faculty Guide: Review team progress logs, add suggestions/comments, and comment on document submissions.

Core Workflow

1. Leader registers and creates a project.
2. Leader invites members and faculty guides via email.
3. Invitees accept the invitation to join the project workspace.
4. Team members upload relevant research papers, write notes, and log project progress.
5. Faculty guides review the progress logs and leave suggestions or comments.
6. The project dashboard visualizes the active timeline (activity feed), documents, progress log contributions, and project comments.

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Technology Stack

Frontend

• React
• Tailwind CSS
• React Router
• Lucide React Icons

Backend

• Node.js
• Express

Database

• MongoDB
• Mongoose ODM

Authentication & Services

• JWT (JSON Web Tokens) for session authorization
• bcryptjs for secure password hashing
• Nodemailer for email-based invitation flows
• Cloudinary for paper storage
• Multer for file upload handling
• CORS for cross-origin resource sharing

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System Architecture

The application uses an MVC (Model-View-Controller) architecture on the backend to decouple database schemas, application controllers, and route definitions. Source code is organized under a src/ subdirectory within server/.

Directory Structure

PaperTrail/
├── client/                     # Frontend React application
│   ├── src/
│   │   ├── components/         # Shared React components (PortalLayout, etc.)
│   │   ├── context/            # Auth and Theme React Contexts
│   │   ├── pages/              # Frontend pages (Dashboard, ProjectWorkspace, Login, etc.)
│   │   └── index.css
│   ├── package.json
│   └── vite.config.js
├── server/                     # Backend Node.js / Express application
│   ├── src/
│   │   ├── config/             # DB, Mailer, and Cloudinary configurations
│   │   ├── controllers/        # Business logic handlers
│   │   ├── middlewares/        # Auth & Upload middlewares
│   │   ├── models/             # Mongoose schemas (User, Project, Paper, Note, Comment, ProgressLog, Invitation)
│   │   └── routes/             # Express API route endpoints
│   ├── tests/                  # Integration tests and utility scripts
│   ├── server.js               # Backend entry point
│   ├── package.json
│   └── .env
├── vercel.json                 # Monorepo Vercel deployment configuration
└── README.md

Database Design

• User: name, email, password (hashed), role (LEADER, MEMBER, FACULTY)
• Project: title, description, leader (Ref: User), faculty (Ref: User), members (Ref: User Array)
• Paper: title, authors, year, keywords, projectId (Ref: Project), uploadedBy (Ref: User), pdfUrl
• Note: paperId (Ref: Paper), authorId (Ref: User), content
• Invitation: email, projectId (Ref: Project), role, token, status (PENDING, ACCEPTED, REJECTED)
• ProgressLog: projectId (Ref: Project), userId (Ref: User), description, date
• Comment: projectId (Ref: Project), authorId (Ref: User), content

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API Endpoints

Authentication (/api/auth)

Method	Route	Description	Auth Required
POST	/register	Register a new user	No
POST	/login	Login and receive JWT token	No
GET	/me	Get current user profile	Yes

Projects (/api/projects)

Method	Route	Description	Auth Required	Role Required
POST	/	Create a new project	Yes	LEADER
GET	/	Get all projects for current user	Yes	Any
GET	/:id	Get a specific project by ID	Yes	Any (member)
DELETE	/:projectId/members/:memberId	Remove a member from the project	Yes	LEADER/FACULTY

Invitations (/api/invitations)

Method	Route	Description	Auth Required	Role Required
POST	/	Send project invitation email	Yes	LEADER
POST	/accept	Accept project invitation	Yes	Any
GET	/verify/:token	Verify invitation token status	No	Any

Papers (/api/papers)

Method	Route	Description	Auth Required
POST	/	Upload a new PDF paper to project	Yes
GET	/project/:projectId	Fetch all papers for a project	Yes
DELETE	/:id	Delete a paper (and Cloudinary asset)	Yes

Paper Notes (/api/notes)

Method	Route	Description	Auth Required
POST	/	Add note to a paper	Yes
GET	/paper/:paperId	Get all notes for a specific paper	Yes
PUT	/:id	Update an existing note (author only)	Yes
DELETE	/:id	Delete a note (author or project lead)	Yes

Progress Logs (/api/progress)

Method	Route	Description	Auth Required
POST	/	Add a new progress log entry	Yes
GET	/project/:projectId	Fetch progress logs for a project	Yes

Project Comments (/api/comments)

Method	Route	Description	Auth Required
POST	/	Add a new project comment	Yes
GET	/project/:projectId	Fetch project comments	Yes

Activity Feed (/api/activity)

Method	Route	Description	Auth Required
GET	/project/:projectId	Fetch combined project activity feed	Yes

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Installation and Execution

Prerequisites

• Node.js (version 18 or above recommended)
• MongoDB database instance (local community server or MongoDB Atlas cluster)

Setup Instructions

1. Clone and navigate to the project directory:

   cd PaperTrail

2. Configure environment variables: Create a .env file in the server directory and configure the variables based on the template:

   PORT=5000
   MONGODB_URI=your_mongodb_connection_string
   JWT_SECRET=your_jwt_secret_key
   JWT_EXPIRES_IN=7d
   CLIENT_URL=http://localhost:3000
   
   EMAIL_USER=your_email_address
   EMAIL_PASSWORD=your_email_app_password
   
   CLOUDINARY_CLOUD_NAME=your_cloudinary_cloud_name
   CLOUDINARY_API_KEY=your_cloudinary_api_key
   CLOUDINARY_API_SECRET=your_cloudinary_api_secret

3. Install Dependencies:

   • Inside the server directory:

     cd server
     npm install

   • Inside the client directory:

     cd client
     npm install

4. Run the Application locally:

   • Start the backend server:

     cd server
     npm run dev

   • Start the frontend development server:

     cd client
     npm run dev

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Testing & DB Utilities

All integration tests are placed in the server/tests/ directory. They dynamically resolve server configurations using your .env variables.

• Run all integration tests: Ensure the server is running locally on port 5000, then execute:

  node tests/testProjects.js
  node tests/testInvitations.js
  node tests/testPapers.js
  node tests/testNotes.js
  node tests/testProgress.js
  node tests/testComment.js
  node tests/testActivity.js

• Reset/Clean Test Database: To purge all automated test projects, progress logs, comments, and temporary users while keeping base accounts intact:

  node tests/cleanDb.js