89 read from postgres db drizzle

.gitignore

@@ -40,6 +40,7 @@ yarn-error.log*
 # data folder
 /data
 
+
 # random files
 **/*.pdf
 **/*.json

package.json

@@ -1,6 +1,6 @@
 {
 	"name": "consort-frontend",
-	"version": "0.15.0",
+	"version": "0.17.0",
 	"description": "",
 	"engines": {
 		"npm": ">=10",
@@ -25,11 +25,13 @@
 		"lint:fix": "npm run lint -- --fix",
 		"codegen": "./node_modules/.bin/openapi -i https://consort.clowderframework.org/clowder/swagger -o src/openapi/v1",
 		"codegen:dev": "./node_modules/.bin/openapi -i {CLOWDER_REMOTE_HOSTNAME}/swagger -o src/openapi/v1",
-		"docs": "typedoc"
+		"docs": "typedoc",
+		"rctdb:examples": "babel-node src/utils/rctdb-client-example.js"
 	},
 	"author": "NCSA",
 	"dependencies": {
 		"@allenai/pdf-components": "^1.0.1",
+		"axios": "^1.6.0",
 		"@emotion/react": "^11.7.1",
 		"@emotion/styled": "^11.6.0",
 		"@material-ui/core": "^4.12.3",

server/.templateenv

@@ -1,7 +1,18 @@
+# Database Configuration
+PGSERVER='localhost'
+PGPORT=5432
+PGUSER=postgres
+PGPASSWORD=postgres
+PGDATABASE=consort
+PGSSL=false
+
+# Authentication Configuration
 CILOGON_CLIENT_ID=
 CILOGON_CLIENT_SECRET=
 CILOGON_CALLBACK_URL=''
 UI_URL=
+
+# Clowder Configuration
 CLOWDER_PREFIX=''
 CLOWDER_REMOTE_HOSTNAME=
 APIKEY=

server/README.md

@@ -0,0 +1,166 @@
+# CONSORT Server with Drizzle ORM
+
+This server uses Drizzle ORM with PostgreSQL to manage the CONSORT database schema.
+
+## Setup
+
+### 1. Environment Configuration
+
+Copy the template environment file and configure your database settings:
+
+```bash
+cp .templateenv .env
+```
+
+Update the database configuration in `.env`:
+
+```env
+# Database Configuration
+PGSERVER='localhost'
+PGPORT=5432
+PGUSER=postgres
+PGPASSWORD=strong_password_here
+PGDATABASE=consort
+PGSSL=false
+```
+
+### 2. Database Setup
+
+Make sure you have PostgreSQL running and create the database:
+
+```sql
+CREATE DATABASE consort;
+```
+
+### 3. Install Dependencies
+
+If you need drizzle-kit for advanced features:
+
+```bash
+npm install drizzle-kit
+```
+
+### 4. Run Database Migration
+
+Initialize the database with the schema:
+
+```bash
+npm run db:migrate
+```
+
+### 5. Test Database Connection
+
+```bash
+npm run db:test
+```
+
+### 6. Check Database Health
+
+```bash
+npm run db:health
+```
+
+## Usage
+
+### Starting the Server
+
+```bash
+npm start
+```
+
+### Running Examples
+
+To see the database operations in action:
+
+```bash
+npm run db:examples
+```
+
+### API Endpoints
+
+The server provides the following API endpoints:
+
+#### Users
+- `GET /api/users` - Get all users
+- `POST /api/users` - Create a new user
+- `GET /api/users/:uuid` - Get user by UUID
+
+#### Publications
+- `GET /api/publications` - Get all publications with user info
+- `POST /api/publications` - Create a new publication
+- `GET /api/publications/:uuid` - Get publication by UUID
+- `GET /api/publications/:uuid/annotations` - Get annotations for a publication
+
+#### Annotations
+- `POST /api/annotations` - Create a new annotation
+- `PUT /api/annotations/:uuid` - Update an annotation
+
+#### Feedback
+- `POST /api/feedback` - Create feedback for an annotation
+- `GET /api/annotations/:uuid/feedback` - Get feedback for an annotation
+
+#### Health Check
+- `GET /api/health` - Check database connection status
+
+## Database Schema
+
+The database schema includes the following tables:
+
+- **users** - User information
+- **publication** - Research publications/papers
+- **section** - Document sections
+- **sentence** - Individual sentences with coordinates
+- **annotation** - ML annotations for sentences
+- **annotationfeedback** - User feedback on annotations
+- **statement_section** - CONSORT/SPIRIT statement sections
+- **statement_topic** - CONSORT/SPIRIT statement topics
+
+## File Structure
+
+```
+server/
+├── db/
+│   ├── schema.js         # Drizzle ORM schema definitions
+│   ├── connection.js     # Database connection setup
+│   ├── queries.js        # Common database queries
+│   ├── migrate.js        # Database migration script
+│   └── examples.js       # Usage examples
+├── routes/
+│   ├── api.js           # API routes using Drizzle ORM
+│   ├── auth.js          # Authentication routes
+│   └── index.js         # Main routes
+├── drizzle.config.js    # Drizzle configuration
+```
+
+## Development
+
+### Query Operations
+
+Use the pre-built query functions from `db/queries.js`:
+
+```javascript
+const { userQueries, publicationQueries } = require('./db/queries');
+
+// Create a user
+const user = await userQueries.createUser({
+  name: 'John Doe',
+  email: 'john@example.com',
+  role: 'researcher'
+});
+
+// Get publications by user
+const publications = await publicationQueries.getPublicationsByUser(userUuid);
+```
+
+### Direct Database Access
+
+For custom queries, use the database instance:
+
+```javascript
+const { db } = require('./db/connection');
+const { users } = require('./db/schema');
+const { eq } = require('drizzle-orm');
+
+const result = await db.select().from(users).where(eq(users.email, 'test@example.com'));
+```
+

server/app.js

@@ -19,9 +19,39 @@ var SQLiteStore = require('connect-sqlite3')(session);
 
 var indexRouter = require('./routes/index');
 var authRouter = require('./routes/auth');
+var rctdbRouter = require('./routes/rctdb');
+
+// Import database connection and migration functions
+var { rctdbTestConnection } = require('./rctdb/connection');
+var { rctdbMigrate } = require('./rctdb/migrate');
 
 var app = express();
 
+// Database initialization function
+async function initializeDatabase() {
+  try {
+    console.log('🔍 Testing database connection...');
+    const isConnected = await rctdbTestConnection();
+
+    if (!isConnected) {
+      throw new Error('Database connection failed');
+    }
+
+    console.log('🚀 Running database migrations...');
+    await rctdbMigrate();
+    console.log('✅ Database initialized successfully');
+
+  } catch (error) {
+    console.error('❌ Database initialization failed:', error.message);
+    console.error('Application will continue but database features may not work properly');
+    // Don't exit the process - let the app start even if DB fails
+    // This allows for graceful degradation
+  }
+}
+
+// Initialize database on startup
+initializeDatabase();
+
 // view engine setup
 app.set('views', path.join(__dirname, 'views'));
 app.set('view engine', 'ejs');
@@ -39,7 +69,13 @@ app.use(session({
   saveUninitialized: false, // don't create session until something stored
   store: new SQLiteStore({ db: 'sessions.db', dir: './var/db' })
 }));
-app.use(csrf());
+// Apply CSRF protection to all routes except API routes
+app.use((req, res, next) => {
+  if (req.path.startsWith('/api/rctdb')) {
+    return next();
+  }
+  return csrf()(req, res, next);
+});
 app.use(passport.authenticate('session'));
 app.use(function(req, res, next) {
   var msgs = req.session.messages || [];
@@ -49,13 +85,17 @@ app.use(function(req, res, next) {
   next();
 });
 app.use(function(req, res, next) {
+  if (req.path.startsWith('/api/rctdb')) {
+    return next();
+  }
   res.locals.csrfToken = req.csrfToken();
   next();
 });
 
 //const baseUrl = process.env.BASE_URL;
 app.use('/', indexRouter);
 app.use('/', authRouter);
+app.use('/api/rctdb', rctdbRouter);
 
 // redirect any other route back to home route /
 // app.use((req,res,next)=>{

server/drizzle.config.js

@@ -0,0 +1,19 @@
+require('dotenv').config();
+
+module.exports = {
+  schema: './rctdb/schema.js',
+  out: './drizzle',
+  dialect: 'postgresql',
+  dbCredentials: {
+    host: process.env.PGSERVER || 'localhost',
+    port: process.env.PGPORT || 5432,
+    user: process.env.PGUSER || 'postgres',
+    password: process.env.PGPASSWORD,
+    database: process.env.PGDATABASE || 'consort',
+    ssl: process.env.PGSSL === 'true' ? { rejectUnauthorized: false } : false,
+  },
+  migrations: {
+    table: 'drizzle_migrations',
+    schema: 'public'
+  }
+};