Add comment and warning for MySQL repeatable read

ci/configurations/alpine-temurin21-mysql.compose.yml

@@ -22,7 +22,7 @@ services:
         condition: service_healthy
     environment:
       DATABASE: mysql
-      DATABASE_URL: jdbc:mysql://db:3306/mirthdb
+      DATABASE_URL: jdbc:mysql://db:3306/mirthdb?sessionVariables=transaction_isolation='READ-COMMITTED'
       DATABASE_USERNAME: mirthdb
       DATABASE_PASSWORD: mirthdb
       DATABASE_MAX_CONNECTIONS: 20

donkey/src/main/java/com/mirth/connect/donkey/server/data/jdbc/JdbcDaoFactory.java

@@ -159,6 +159,11 @@ public JdbcDao getDao(SerializerProvider serializerProvider) {
         return getDao(donkey, connection, querySource, statementSource, serializerProvider, encryptMessageContent, encryptAttachments, encryptCustomMetaData, decryptData, statisticsUpdater, channelController.getStatistics(), channelController.getTotalStatistics(), statsServerId);
     }
 
+    /** Assert a brand new database and server is acceptable */
+    public void checkNewDatabase(Connection connection) {
+        // By default, all new databases are considered acceptable.
+    }
+
     protected JdbcDao getDao(Donkey donkey, Connection connection, QuerySource querySource, PreparedStatementSource statementSource, SerializerProvider serializerProvider, boolean encryptMessageContent, boolean encryptAttachments, boolean encryptCustomMetaData, boolean decryptData, StatisticsUpdater statisticsUpdater, Statistics currentStats, Statistics totalStats, String statsServerId) {
         return new JdbcDao(donkey, connection, querySource, statementSource, serializerProvider, encryptMessageContent, encryptAttachments, encryptCustomMetaData, decryptData, statisticsUpdater, currentStats, totalStats, statsServerId);
     }

donkey/src/main/java/com/mirth/connect/donkey/server/data/jdbc/MysqlDaoFactory.java

@@ -9,13 +9,55 @@
 
 package com.mirth.connect.donkey.server.data.jdbc;
 
+import java.sql.Connection;
+import java.sql.SQLException;
+import java.util.concurrent.atomic.AtomicBoolean;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import com.mirth.connect.donkey.server.data.DonkeyDaoException;
 import com.mirth.connect.donkey.util.SerializerProvider;
 
 public class MysqlDaoFactory extends JdbcDaoFactory {
+    private static final Logger logger = LogManager.getLogger(MysqlDaoFactory.class);
+    private final AtomicBoolean hasCheckedTransactionIsolation = new AtomicBoolean(false);
+
     @Override
     public JdbcDao getDao(SerializerProvider serializerProvider) {
         JdbcDao dao = super.getDao(serializerProvider);
         dao.setQuoteChar('`');
+        checkTransactionIsolation(dao);
         return dao;
     }
+
+    @Override
+    public void checkNewDatabase(Connection connection) {
+        try {
+            if (connection.getTransactionIsolation() == Connection.TRANSACTION_REPEATABLE_READ) {
+                throw new DonkeyDaoException("Creating a new database with REPEATABLE-READ transaction " 
+                    + "isolation is not allowed.  Set the transaction isolation level in the database "
+                    + "URL or the database server to READ-COMMITTED.");
+            }
+        } catch (SQLException e) {
+            throw new DonkeyDaoException("Failed to check the transaction isolation level for this MySQL connection.", e);
+        }
+    }
+
+    /**
+     * Warns once if the connection is using the default REPEATABLE-READ transaction isolation level.
+     */
+    private void checkTransactionIsolation(JdbcDao dao) {
+        if (!hasCheckedTransactionIsolation.compareAndSet(false, true)) {
+            return;
+        }
+
+        try {
+            if (dao.getConnection().getTransactionIsolation() == Connection.TRANSACTION_REPEATABLE_READ) {
+                logger.error("This MySQL connection is using the REPEATABLE-READ transaction isolation level.  The MySQL REPEATABLE-READ will cause intermittent issues.  Set the transaction isolation level in the database URL or the database server to READ-COMMITTED to avoid these problems.");
+            }
+        } catch (SQLException e) {
+            logger.error("Failed to check the transaction isolation level for this MySQL connection.", e);
+        }
+    }
 }

server/conf/mirth.properties

@@ -80,7 +80,7 @@ database = derby
 # examples:
 #   Derby                       jdbc:derby:${dir.appdata}/mirthdb;create=true
 #   PostgreSQL                  jdbc:postgresql://localhost:5432/mirthdb
-#   MySQL                       jdbc:mysql://localhost:3306/mirthdb
+#   MySQL                       jdbc:mysql://localhost:3306/mirthdb?sessionVariables=transaction_isolation='READ-COMMITTED'
 #   Oracle                      jdbc:oracle:thin:@localhost:1521:DB
 #   SQL Server/Sybase (jTDS)    jdbc:jtds:sqlserver://localhost:1433/mirthdb
 #   Microsoft SQL Server        jdbc:sqlserver://localhost:1433;databaseName=mirthdb

server/src/main/java/com/mirth/connect/server/migration/ServerMigrator.java

@@ -33,6 +33,8 @@
 
 import com.mirth.connect.client.core.PropertiesConfigurationUtil;
 import com.mirth.connect.client.core.Version;
+import com.mirth.connect.donkey.server.data.DonkeyDaoException;
+import com.mirth.connect.donkey.server.data.jdbc.JdbcDaoFactory;
 import com.mirth.connect.model.Channel;
 import com.mirth.connect.model.ExportClearable;
 import com.mirth.connect.model.alert.AlertModel;
@@ -258,6 +260,14 @@ private Migrator getMigrator(Version version) {
     private void initDatabase(Connection connection) throws MigrationException {
         // If missing this table we can assume that they don't have the schema installed
         if (!DatabaseUtil.tableExists(connection, "CONFIGURATION")) {
+            // Since we are creating a new database, let the database-specific DAO 
+            // factory check if it is acceptable.
+            try {
+                JdbcDaoFactory.getInstance(getDatabaseType()).checkNewDatabase(connection);
+            } catch (DonkeyDaoException e) {
+                throw new MigrationException(e.getMessage(), e);
+            }
+
             executeScript("/" + getDatabaseType() + "/" + getDatabaseType() + "-database.sql");
 
             initializeAdminPassword();