feat: upgrade to Java 25 and replace OrientDB with H2

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ jobs:
 
     strategy:
       matrix:
-        java-version: [21]
+        java-version: [25]
 
     steps:
       - name: Checkout repository

.gitignore

@@ -18,3 +18,4 @@ opal-gwt-client/war/org.obiba.opal.web.gwt.*
 *.lck
 opal_home
 opal_home.*/
+/.claude/settings.local.json

.mvn/wrapper/maven-wrapper.properties

@@ -0,0 +1,3 @@
+wrapperVersion=3.3.4
+distributionType=only-script
+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.9/apache-maven-3.9.9-bin.zip

CLAUDE.md

@@ -0,0 +1,121 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+Opal is OBiBa's core database application for biobanks and epidemiological studies. 
+It provides data storage, management, and harmonization capabilities with R integration for statistical analysis and DataSHIELD support for federated analysis.
+
+## Technology Stack
+
+- **Backend**: Java 25, Spring Framework 6.x, Maven multi-module project
+- **Frontend**: Vue 3 + TypeScript with Quasar Framework (in `opal-ui/`)
+- **Databases**: MongoDB, MySQL/MariaDB, PostgreSQL, OrientDB (configuration store)
+- **Security**: Apache Shiro with OIDC support
+- **REST API**: RESTEasy (JAX-RS)
+- **R Integration**: Rserve for R server communication
+- **Search**: Apache Lucene 9.x
+
+## Build Commands
+
+```bash
+# Full build (clean, compile, package)
+make all
+
+# Compile only
+make compile
+
+# Faster compile (skip GWT - legacy)
+mvn install -Dgwt.compiler.skip=true
+
+# Clean
+make clean
+
+# Prepare local development environment (run once)
+make prepare
+
+# Run Opal server
+make run
+
+# Run in debug mode (remote debugging enabled)
+make debug
+```
+
+## Frontend Development (opal-ui)
+
+```bash
+cd opal-ui
+
+# Install dependencies
+npm install
+
+# Development server with hot reload (runs on localhost:9000)
+npm run dev
+
+# Lint
+npm run lint
+
+# Format code
+npm run format
+
+# Production build
+npm run build
+```
+
+**CORS for development**: Add `cors.allowed=http://localhost:9000` to `OPAL_HOME/conf/opal-config.properties`.
+
+## Running Tests
+
+```bash
+# Run all tests
+mvn test
+
+# Run tests for a specific module
+cd opal-core && mvn test
+
+# Skip tests during build
+mvn install -DskipTests
+```
+
+## Module Architecture
+
+| Module | Purpose |
+|--------|---------|
+| `opal-core-api` | Core domain interfaces and DTOs |
+| `opal-core` | Core business logic implementation |
+| `opal-core-ws` | Core REST web services |
+| `opal-ws` | Additional REST endpoints |
+| `opal-spi` | Service Provider Interface for plugins |
+| `opal-spi-r` | R-specific SPI |
+| `opal-r` | R server integration (Rserve) |
+| `opal-datashield` | DataSHIELD federated analysis support |
+| `opal-search` | Lucene-based search functionality |
+| `opal-fs` | File system management (VFS) |
+| `opal-shell` | Command-line shell interface |
+| `opal-sql` | SQL parsing (ANTLR-based) |
+| `opal-httpd` | HTTP server (Jetty) configuration |
+| `opal-server` | Server assembly and startup |
+| `opal-rest-client` | Java REST client library |
+| `opal-web-model` | Protobuf message definitions |
+| `opal-upgrade` | Database migration scripts |
+| `opal-ui` | Vue.js admin web application |
+
+## Key External Dependencies
+
+- **Magma**: OBiBa's data abstraction layer (`org.obiba.magma:*`) - handles data sources, variables, and values
+- **obiba-commons**: Shared OBiBa utilities including security, OIDC, and Git integration
+
+## Development Setup
+
+1. Ensure Java 25 and Maven 3+ are installed
+2. Have MongoDB or MySQL/MariaDB running locally
+3. Run `make all` to build
+4. Run `make prepare` to initialize `opal_home` directory (first time only)
+5. Run `make debug` to start server with remote debugging on port 8000
+6. Access at http://localhost:8080 (credentials: administrator/password)
+
+## Environment
+
+- `OPAL_HOME`: Configuration directory (defaults to `./opal_home`)
+- Default ports: HTTP 8080, HTTPS 8443, SSH 8022

Makefile

@@ -22,7 +22,7 @@ else
 endif
 
 skipTests=false
-mvn_exec=mvn -Dmaven.test.skip=${skipTests}
+mvn_exec=./mvnw -Dmaven.test.skip=${skipTests}
 orientdb_version=3.2.27
 hsqldb_version=2.7.1
 

README.md

@@ -11,7 +11,7 @@ Opal is OBiBa’s core database application for biobanks or epidemiological stud
 
 Set up a development environment:
 
-* Make sure Java8 is available.
+* Make sure Java 25 is available.
 * Make sure you have a MongoDB, MySQL or MariaDB database running.
 * Compile with `make all`
 * Get the [obiba-home](https://github.com/obiba/obiba-home) repository to have some seeding material.