Add PostgreSQL persistence layer for Record class

pom.xml

@@ -100,6 +100,23 @@
             <artifactId>log4j-core</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.postgresql</groupId>
+            <artifactId>postgresql</artifactId>
+            <version>42.7.4</version>
+        </dependency>
+        <dependency>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>postgresql</artifactId>
+            <version>1.20.4</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>junit-jupiter</artifactId>
+            <version>1.20.4</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <dependencyManagement>

src/main/java/massbank/db/DatabaseConnection.java

@@ -0,0 +1,92 @@
+/*******************************************************************************
+ * Copyright (C) 2025 MassBank consortium
+ * 
+ * This file is part of MassBank.
+ * 
+ * MassBank is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+ * 
+ ******************************************************************************/
+package massbank.db;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.SQLException;
+import java.sql.Statement;
+import java.util.stream.Collectors;
+
+/**
+ * Utility class for managing database connections.
+ */
+public class DatabaseConnection {
+    private static final Logger logger = LogManager.getLogger(DatabaseConnection.class);
+
+    /**
+     * Creates a connection to a PostgreSQL database.
+     * 
+     * @param url The JDBC URL
+     * @param username The database username
+     * @param password The database password
+     * @return A Connection object
+     * @throws SQLException if a database access error occurs
+     */
+    public static Connection getConnection(String url, String username, String password) throws SQLException {
+        logger.info("Connecting to database: {}", url);
+        return DriverManager.getConnection(url, username, password);
+    }
+
+    /**
+     * Initializes the database schema from the schema.sql file.
+     * 
+     * @param connection The database connection
+     * @throws SQLException if a database error occurs
+     * @throws IOException if the schema file cannot be read
+     */
+    public static void initializeSchema(Connection connection) throws SQLException, IOException {
+        logger.info("Initializing database schema");
+
+        String schemaScript = loadResourceAsString("/db/schema.sql");
+
+        try (Statement stmt = connection.createStatement()) {
+            stmt.execute(schemaScript);
+        }
+
+        logger.info("Database schema initialized successfully");
+    }
+
+    /**
+     * Loads a resource file as a String.
+     * 
+     * @param resourcePath The path to the resource
+     * @return The contents of the resource as a String
+     * @throws IOException if the resource cannot be read
+     */
+    private static String loadResourceAsString(String resourcePath) throws IOException {
+        try (InputStream is = DatabaseConnection.class.getResourceAsStream(resourcePath)) {
+            if (is == null) {
+                throw new IOException("Resource not found: " + resourcePath);
+            }
+            try (BufferedReader reader = new BufferedReader(new InputStreamReader(is))) {
+                return reader.lines().collect(Collectors.joining("\n"));
+            }
+        }
+    }
+}

src/main/java/massbank/db/README.md

@@ -0,0 +1,120 @@
+# PostgreSQL Database Support for MassBank Records
+
+This package provides PostgreSQL database support for storing and retrieving MassBank `Record` objects.
+
+## Features
+
+- Store and retrieve MassBank records in PostgreSQL database
+- JSONB support for complex data structures
+- Full CRUD operations (Create, Read, Update, Delete)
+- Upsert support (automatic update on conflict)
+- Comprehensive unit tests with TestContainers
+
+## Usage
+
+### 1. Initialize Database Connection
+
+```java
+import massbank.db.DatabaseConnection;
+import massbank.db.RecordRepository;
+import java.sql.Connection;
+
+// Create connection
+Connection connection = DatabaseConnection.getConnection(
+    "jdbc:postgresql://localhost:5432/massbank",
+    "username",
+    "password"
+);
+
+// Initialize schema (first time only)
+DatabaseConnection.initializeSchema(connection);
+
+// Create repository
+RecordRepository repository = new RecordRepository(connection);
+```
+
+### 2. Store a Record
+
+```java
+import massbank.Record;
+
+Record record = new Record();
+// ... populate record fields ...
+
+repository.store(record);
+```
+
+### 3. Retrieve a Record
+
+```java
+// Retrieve by accession ID
+Record record = repository.retrieve("MSBNK-TEST-00001");
+
+// Retrieve all records
+List<Record> allRecords = repository.retrieveAll();
+```
+
+### 4. Update a Record
+
+```java
+// Store with same accession ID to update
+record.AUTHORS("Updated Author");
+repository.store(record);
+```
+
+### 5. Delete a Record
+
+```java
+boolean deleted = repository.delete("MSBNK-TEST-00001");
+```
+
+### 6. Check if Record Exists
+
+```java
+boolean exists = repository.exists("MSBNK-TEST-00001");
+```
+
+## Database Schema
+
+The schema is automatically created by the `DatabaseConnection.initializeSchema()` method.
+
+Key features:
+- Primary key on `accession` field
+- JSONB columns for complex structures (lists, maps)
+- GIN indexes on JSONB columns for efficient queries
+- Timestamps for created_at and updated_at
+
+## Dependencies
+
+Add these dependencies to your `pom.xml`:
+
+```xml
+<dependency>
+    <groupId>org.postgresql</groupId>
+    <artifactId>postgresql</artifactId>
+    <version>42.7.4</version>
+</dependency>
+```
+
+## Testing
+
+The package includes comprehensive unit tests using TestContainers:
+
+```bash
+mvn test
+```
+
+Tests cover:
+- Basic CRUD operations
+- Complex record with all fields
+- Deprecated records
+- Peak data storage
+- Annotation data storage
+- Update operations
+
+## Notes
+
+- JSONB is used for complex data structures to maintain flexibility
+- The repository uses prepared statements to prevent SQL injection
+- All operations are logged using log4j
+- Connection management is left to the caller (not auto-closed)