Cleanup database migrations

src/main/java/org/ohdsi/webapi/FlywayBaselineCallback.java

@@ -0,0 +1,112 @@
+package org.ohdsi.webapi;
+
+import org.flywaydb.core.api.callback.Callback;
+import org.flywaydb.core.api.callback.Context;
+import org.flywaydb.core.api.callback.Event;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+
+/**
+ * Flyway callback that handles baseline migration logic for fresh databases.
+ *
+ * For fresh databases (empty schema_version), this marks all V2.x migrations
+ * as applied so that only V3.0.0.0 baseline and later migrations run.
+ *
+ * For existing databases, this does nothing - the V2.15.0.20251214000000 migration
+ * handles marking the V3.0.0.0 baseline as applied.
+ */
+public class FlywayBaselineCallback implements Callback {
+
+    private static final Logger log = LoggerFactory.getLogger(FlywayBaselineCallback.class);
+
+    // Version threshold - migrations below this are skipped for fresh installs
+    private static final String BASELINE_VERSION = "3.0.0.0";
+
+    @Override
+    public boolean supports(Event event, Context context) {
+        return event == Event.BEFORE_MIGRATE;
+    }
+
+    @Override
+    public boolean canHandleInTransaction(Event event, Context context) {
+        return true;
+    }
+
+    @Override
+    public void handle(Event event, Context context) {
+        if (event != Event.BEFORE_MIGRATE) {
+            return;
+        }
+
+        try {
+            // Don't close the connection - Flyway manages it
+            Connection conn = context.getConnection();
+            if (isFreshDatabase(conn, context)) {
+                log.info("Fresh database detected - marking V2.x migrations as applied to use V3.0.0.0 baseline");
+                markOldMigrationsAsApplied(conn, context);
+            }
+        } catch (SQLException e) {
+            log.warn("Error checking database state for baseline: {}", e.getMessage());
+        }
+    }
+
+    private boolean isFreshDatabase(Connection conn, Context context) throws SQLException {
+        String schema = context.getConfiguration().getDefaultSchema();
+        String table = context.getConfiguration().getTable();
+        String fullTableName = schema != null ? schema + "." + table : table;
+
+        // Check if schema_version table exists and has any entries
+        String sql = "SELECT COUNT(*) FROM " + fullTableName;
+        try (PreparedStatement stmt = conn.prepareStatement(sql);
+             ResultSet rs = stmt.executeQuery()) {
+            if (rs.next()) {
+                return rs.getInt(1) == 0;
+            }
+        } catch (SQLException e) {
+            // Table doesn't exist yet - this is a fresh database
+            return true;
+        }
+        return false;
+    }
+
+    private void markOldMigrationsAsApplied(Connection conn, Context context) throws SQLException {
+        String schema = context.getConfiguration().getDefaultSchema();
+        String table = context.getConfiguration().getTable();
+        String fullTableName = schema != null ? schema + "." + table : table;
+
+        // Ensure schema_version table exists
+        try {
+            conn.prepareStatement("SELECT 1 FROM " + fullTableName + " LIMIT 1").executeQuery();
+        } catch (SQLException e) {
+            // Table doesn't exist - Flyway will create it, we'll handle this in afterMigrate if needed
+            log.debug("Schema version table doesn't exist yet, Flyway will create it");
+            return;
+        }
+
+        // Insert a baseline marker that tells Flyway to skip V2.x migrations
+        // We insert a synthetic "baseline" entry at version 2.15.0.20251214000000
+        String insertSql = "INSERT INTO " + fullTableName +
+            " (installed_rank, version, description, type, script, checksum, installed_by, installed_on, execution_time, success) " +
+            "SELECT COALESCE(MAX(installed_rank), 0) + 1, '2.15.0.20251214000000', " +
+            "'<< Flyway Baseline for V3.0.0.0 >>', 'BASELINE', '<< Baseline >>', NULL, 'WebAPI', NOW(), 0, true " +
+            "FROM " + fullTableName + " " +
+            "WHERE NOT EXISTS (SELECT 1 FROM " + fullTableName + " WHERE type = 'BASELINE')";
+
+        try (PreparedStatement stmt = conn.prepareStatement(insertSql)) {
+            int rows = stmt.executeUpdate();
+            if (rows > 0) {
+                log.info("Inserted baseline marker at version 2.15.0.20251214000000 - V2.x migrations will be skipped");
+            }
+        }
+    }
+
+    @Override
+    public String getCallbackName() {
+        return "BaselineCallback";
+    }
+}

src/main/java/org/ohdsi/webapi/FlywayConfig.java

@@ -4,6 +4,7 @@
 
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
+import org.springframework.boot.autoconfigure.flyway.FlywayConfigurationCustomizer;
 import org.springframework.boot.autoconfigure.flyway.FlywayDataSource;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
@@ -79,4 +80,13 @@ public ApplicationContextHolder applicationContextHolder(ApplicationContext appl
         return new ApplicationContextHolder();
     }
 
+    /**
+     * Register baseline callback to handle fresh database installations.
+     * For fresh databases, marks V2.x migrations as applied so V3.0.0.0 baseline runs.
+     */
+    @Bean
+    public FlywayConfigurationCustomizer flywayBaselineCustomizer() {
+        return configuration -> configuration.callbacks(new FlywayBaselineCallback());
+    }
+
 }