MINOR - Remove flyway (#23179)

* test

* test

* format

* pom

* pom

* format

* Handle migration

* Handle migration

* Handle migration

* fix merge

* bump main

* bump main

* undo unnecessary changes

* simplify checksum for migration

* format

* FIX

bootstrap/MIGRATION_SYSTEM.md

@@ -0,0 +1,163 @@
+# OpenMetadata Migration System
+
+This document describes the migration system architecture and execution order for OpenMetadata database schema and data migrations.
+
+## Migration System Overview
+
+OpenMetadata uses a hybrid migration system that combines:
+1. **Legacy Flyway migrations** (being phased out)
+2. **Native OpenMetadata migrations** (current system)
+3. **Extension migrations** (for custom/plugin functionality)
+
+## Migration Execution Order
+
+The migration system executes in a specific order to ensure database consistency:
+
+```
+1. Flyway Migrations (Legacy)
+   ├── v000__create_server_change_log.sql  (Creates migration tracking tables)
+   ├── v001__*.sql
+   ├── v002__*.sql
+   └── ...
+
+2. Native OpenMetadata Migrations
+   ├── 1.1.0/
+   ├── 1.1.1/
+   ├── 1.2.0/
+   └── ...
+
+3. Extension Migrations
+   ├── custom-extension-1.0.0/
+   └── ...
+```
+
+## Migration Tracking Tables
+
+### SERVER_CHANGE_LOG
+Primary table for tracking all migration executions:
+- `installed_rank`: Auto-increment sequence number
+- `version`: Migration version identifier (PRIMARY KEY)
+- `migrationFileName`: Path to the migration file
+- `checksum`: Hash of migration content for integrity validation
+- `installed_on`: Timestamp of migration execution
+- `metrics`: JSON/JSONB field for migration execution metrics
+
+### SERVER_MIGRATION_SQL_LOGS
+Detailed SQL execution logs:
+- `version`: Migration version identifier
+- `sqlStatement`: Individual SQL statement executed
+- `checksum`: Hash of the SQL statement (PRIMARY KEY)
+- `executedAt`: Timestamp of SQL execution
+
+## Migration Logic
+
+The migration workflow follows this decision tree:
+
+```
+IF native migrations are already executed:
+    └── Skip all Flyway migrations (they've already run)
+    └── Execute remaining native migrations
+    └── Execute extension migrations
+
+ELSE IF no native migrations executed:
+    ├── Execute Flyway migrations (creates SERVER_CHANGE_LOG tables)
+    ├── Execute native migrations  
+    └── Execute extension migrations
+```
+
+## File Structure
+
+```
+bootstrap/sql/migrations/
+├── flyway/
+│   ├── com.mysql.cj.jdbc.Driver/     # MySQL-specific Flyway migrations
+│   │   ├── v000__create_server_change_log.sql
+│   │   ├── v001__*.sql
+│   │   └── ...
+│   └── org.postgresql.Driver/        # PostgreSQL-specific Flyway migrations
+│       ├── v000__create_server_change_log.sql
+│       ├── v001__*.sql
+│       └── ...
+├── native/
+│   ├── 1.1.0/
+│   │   ├── mysql/schemaChanges.sql
+│   │   └── postgres/schemaChanges.sql
+│   ├── 1.1.1/
+│   └── ...
+└── extensions/                       # Custom extension migrations
+    └── [extension-name]/
+        ├── mysql/
+        └── postgres/
+```
+
+## Migration Implementation Classes
+
+- `MigrationWorkflow`: Orchestrates the entire migration process
+- `FlywayMigrationFile`: Adapter for legacy Flyway migrations
+- `MigrationFile`: Handler for native OpenMetadata migrations
+- `MigrationProcess`: Executes individual migration steps
+
+## SQL Statement Parsing
+
+**Important**: While OpenMetadata has removed Flyway as the migration framework, we still use **Flyway's SQL parsers** for reliable statement splitting:
+
+- **MySQL**: Uses `org.flywaydb.database.mysql.MySQLParser`
+- **PostgreSQL**: Uses `org.flywaydb.database.postgresql.PostgreSQLParser`
+
+This ensures proper handling of:
+- Complex SQL statements with string literals containing semicolons
+- Comments (both `--` and `/* */` style)
+- Escaped characters and quotes
+- Database-specific SQL syntax
+
+The parsers split SQL files into individual statements via `SqlStatementIterator`, which is far more reliable than simple string splitting.
+
+**Dependencies**: Requires `flyway-core` and `flyway-mysql` for SQL parsing only (not migration management).
+
+## Key Design Decisions
+
+1. **Hybrid Approach**: Custom migration management + Flyway SQL parsing for reliability
+2. **Backward Compatibility**: Flyway migrations continue to work during transition period
+3. **Single Source of Truth**: All migrations are tracked in `SERVER_CHANGE_LOG` regardless of type
+4. **Database Agnostic**: Separate migration files for MySQL and PostgreSQL
+5. **Execution Order**: Flyway → Native → Extensions ensures proper dependency resolution
+6. **Migration Tracking**: v000 Flyway migration creates the tracking infrastructure before any other migrations
+
+## Troubleshooting
+
+### Common Issues
+
+1. **Missing SERVER_CHANGE_LOG table**:
+   - Ensure v000 Flyway migration has executed
+   - Check database permissions
+
+2. **Migration version conflicts**:
+   - Verify no duplicate version numbers across migration types
+   - Check migration file naming conventions
+
+3. **Database-specific failures**:
+   - Ensure correct SQL syntax for target database (MySQL vs PostgreSQL)
+   - Validate database-specific features (JSON vs JSONB, AUTO_INCREMENT vs SERIAL)
+
+### Migration Recovery
+
+If migrations fail:
+1. Check `SERVER_CHANGE_LOG` table for last successful migration
+2. Review `SERVER_MIGRATION_SQL_LOGS` for failed SQL statements
+3. Fix underlying issues and restart migration process
+4. Use `--force` flag only if absolutely necessary
+
+## Configuration
+
+Migration paths are configured in `MigrationConfiguration`:
+- `nativePath`: Path to native OpenMetadata migrations
+- `flywayPath`: Path to legacy Flyway migrations  
+- `extensionPath`: Path to extension migrations
+
+Example:
+```yaml
+migrationConfiguration:
+  nativePath: "bootstrap/sql/migrations/native"
+  flywayPath: "bootstrap/sql/migrations/flyway"
+  extensionPath: "bootstrap/sql/migrations/extensions"
+```

bootstrap/sql/migrations/flyway/com.mysql.cj.jdbc.Driver/v000__create_server_change_log.sql

@@ -0,0 +1,20 @@
+-- Create tables for tracking server migrations
+-- This migration runs before all other migrations to ensure migration tracking tables exist
+
+CREATE TABLE IF NOT EXISTS SERVER_CHANGE_LOG (
+    installed_rank BIGINT UNSIGNED NOT NULL AUTO_INCREMENT,
+    version VARCHAR(256) NOT NULL,
+    migrationFileName VARCHAR(256) NOT NULL,
+    checksum VARCHAR(256) NOT NULL,
+    installed_on TIMESTAMP NULL DEFAULT CURRENT_TIMESTAMP,
+    metrics JSON,
+    PRIMARY KEY (version),
+    UNIQUE KEY installed_rank (installed_rank)
+);
+
+CREATE TABLE IF NOT EXISTS SERVER_MIGRATION_SQL_LOGS (
+    version VARCHAR(256) NOT NULL,
+    sqlStatement VARCHAR(10000) NOT NULL,
+    checksum VARCHAR(256) PRIMARY KEY,
+    executedAt TIMESTAMP DEFAULT CURRENT_TIMESTAMP
+);

bootstrap/sql/migrations/flyway/com.mysql.cj.jdbc.Driver/v015__update_server_change_log.sql

@@ -1 +1,2 @@
-ALTER TABLE SERVER_CHANGE_LOG ADD COLUMN metrics JSON;
+-- This column is already created in v000__create_server_change_log.sql
+-- ALTER TABLE SERVER_CHANGE_LOG ADD COLUMN metrics JSON;

bootstrap/sql/migrations/flyway/org.postgresql.Driver/v000__create_server_change_log.sql

@@ -0,0 +1,18 @@
+-- Create tables for tracking server migrations
+-- This migration runs before all other migrations to ensure migration tracking tables exist
+
+CREATE TABLE IF NOT EXISTS SERVER_CHANGE_LOG (
+    installed_rank SERIAL,
+    version VARCHAR(256) PRIMARY KEY,
+    migrationFileName VARCHAR(256) NOT NULL,
+    checksum VARCHAR(256) NOT NULL,
+    installed_on TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+    metrics JSONB
+);
+
+CREATE TABLE IF NOT EXISTS SERVER_MIGRATION_SQL_LOGS (
+    version VARCHAR(256) NOT NULL,
+    sqlStatement VARCHAR(10000) NOT NULL,
+    checksum VARCHAR(256) PRIMARY KEY,
+    executedAt TIMESTAMP DEFAULT CURRENT_TIMESTAMP
+);

bootstrap/sql/migrations/flyway/org.postgresql.Driver/v015__update_server_change_log.sql

@@ -1 +1,2 @@
-ALTER TABLE SERVER_CHANGE_LOG ADD COLUMN metrics jsonb;
+-- This column is already created in v000__create_server_change_log.sql
+-- ALTER TABLE SERVER_CHANGE_LOG ADD COLUMN metrics jsonb;

openmetadata-service/pom.xml

@@ -375,14 +375,6 @@
       <groupId>commons-cli</groupId>
       <artifactId>commons-cli</artifactId>
     </dependency>
-    <dependency>
-      <groupId>org.flywaydb</groupId>
-      <artifactId>flyway-maven-plugin</artifactId>
-    </dependency>
-    <dependency>
-      <groupId>org.flywaydb</groupId>
-      <artifactId>flyway-mysql</artifactId>
-    </dependency>
     <dependency>
       <groupId>io.github.classgraph</groupId>
       <artifactId>classgraph</artifactId>
@@ -498,6 +490,16 @@
       <scope>import</scope>
     </dependency>
 
+    <!-- Flyway dependencies - only for SQL parsing, not migration management -->
+    <dependency>
+      <groupId>org.flywaydb</groupId>
+      <artifactId>flyway-core</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.flywaydb</groupId>
+      <artifactId>flyway-mysql</artifactId>
+    </dependency>
+
     <!-- Micrometer Core -->
     <dependency>
       <groupId>io.micrometer</groupId>

openmetadata-service/src/main/java/org/openmetadata/service/OpenMetadataApplication.java

@@ -54,7 +54,6 @@ import java.security.NoSuchAlgorithmException;
 import java.security.cert.CertificateException;
 import java.util.EnumSet;
 import java.util.Objects;
-import java.util.Optional;
 import javax.naming.ConfigurationException;
 import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
@@ -103,7 +102,6 @@ import org.openmetadata.service.jobs.JobDAO;
 import org.openmetadata.service.jobs.JobHandlerRegistry;
 import org.openmetadata.service.limits.DefaultLimits;
 import org.openmetadata.service.limits.Limits;
-import org.openmetadata.service.migration.Migration;
 import org.openmetadata.service.migration.MigrationValidationClient;
 import org.openmetadata.service.migration.api.MigrationWorkflow;
 import org.openmetadata.service.monitoring.EventMonitor;
@@ -271,7 +269,7 @@ public class OpenMetadataApplication extends Application<OpenMetadataApplication
             .buildValidatorFactory()
             .getValidator());
 
-    // Validate flyway Migrations
+    // Validate native migrations
     validateMigrations(jdbi, catalogConfig);
 
     // Register Authorizer
@@ -579,21 +577,6 @@ public class OpenMetadataApplication extends Application<OpenMetadataApplication
 
   private void validateMigrations(Jdbi jdbi, OpenMetadataApplicationConfig conf)
       throws IOException {
-    LOG.info("Validating Flyway migrations");
-    Optional<String> lastMigrated = Migration.lastMigrated(jdbi);
-    String maxMigration = Migration.lastMigrationFile(conf.getMigrationConfiguration());
-    if (lastMigrated.isEmpty()) {
-      throw new IllegalStateException(
-          "Could not validate Flyway migrations in the database. Make sure you have run `./bootstrap/openmetadata-ops.sh migrate` at least once.");
-    }
-    if (lastMigrated.get().compareTo(maxMigration) < 0) {
-      throw new IllegalStateException(
-          "There are pending migrations to be run on the database."
-              + " Please backup your data and run `./bootstrap/openmetadata-ops.sh migrate`."
-              + " You can find more information on upgrading OpenMetadata at"
-              + " https://docs.open-metadata.org/deployment/upgrade ");
-    }
-
     LOG.info("Validating native migrations");
     ConnectionType connectionType =
         ConnectionType.from(conf.getDataSourceFactory().getDriverClass());
@@ -603,6 +586,7 @@ public class OpenMetadataApplication extends Application<OpenMetadataApplication
             conf.getMigrationConfiguration().getNativePath(),
             connectionType,
             conf.getMigrationConfiguration().getExtensionPath(),
+            conf.getMigrationConfiguration().getFlywayPath(),
             conf,
             false);
     migrationWorkflow.loadMigrations();

openmetadata-service/src/main/java/org/openmetadata/service/jdbi3/MigrationDAO.java

@@ -61,7 +61,7 @@ public interface MigrationDAO {
       connectionType = MYSQL)
   @ConnectionAwareSqlUpdate(
       value =
-          "INSERT INTO server_change_log (version, migrationFileName, checksum, metrics, installed_on)"
+          "INSERT INTO SERVER_CHANGE_LOG (version, migrationFileName, checksum, metrics, installed_on)"
               + "VALUES (:version, :migrationFileName, :checksum, (:metrics :: jsonb), current_timestamp) "
               + "ON CONFLICT (version) DO UPDATE SET "
               + "migrationFileName = EXCLUDED.migrationFileName, "
@@ -123,6 +123,15 @@ public interface MigrationDAO {
   @SqlQuery("SELECT version FROM SERVER_CHANGE_LOG")
   List<String> getMigrationVersions();
 
+  @SqlQuery(
+      "SELECT version FROM SERVER_CHANGE_LOG WHERE migrationFileName LIKE '%/migrations/flyway/%' ORDER BY version")
+  List<String> getFlywayMigrationVersions();
+
+  @SqlQuery(
+      "SELECT installed_rank, version, migrationFileName, checksum, installed_on, metrics FROM SERVER_CHANGE_LOG WHERE migrationFileName LIKE '%/migrations/flyway/%' ORDER BY version")
+  @RegisterRowMapper(FromServerChangeLogMapper.class)
+  List<ServerChangeLog> getFlywayMigrationRecords();
+
   @Getter
   @Setter
   class ServerMigrationSQLTable {

openmetadata-service/src/main/java/org/openmetadata/service/migration/Migration.java

@@ -1,60 +0,0 @@
-package org.openmetadata.service.migration;
-
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-import java.util.Optional;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-import lombok.extern.slf4j.Slf4j;
-import org.jdbi.v3.core.Jdbi;
-import org.jdbi.v3.core.statement.StatementException;
-import org.openmetadata.service.jdbi3.MigrationDAO;
-
-@Slf4j
-public final class Migration {
-  private Migration() {}
-
-  /**
-   * Run a query to MySQL to retrieve the last migrated Flyway version. If the Flyway table DATABASE_CHANGE_LOG does not
-   * exist, we will stop the Catalog App and inform users how to run Flyway.
-   */
-  public static Optional<String> lastMigrated(Jdbi jdbi) {
-    try {
-      return jdbi.withExtension(MigrationDAO.class, MigrationDAO::getMaxVersion);
-    } catch (StatementException e) {
-      throw new IllegalArgumentException(
-          "Exception encountered when trying to obtain last migrated Flyway version."
-              + " Make sure you have run `./bootstrap/openmetadata-ops.sh migrate` at least once.",
-          e);
-    }
-  }
-
-  public static String lastMigrationFile(MigrationConfiguration conf) throws IOException {
-    List<String> migrationFiles = getMigrationVersions(conf);
-    return Collections.max(migrationFiles);
-  }
-
-  /** Read the migrations path from the Catalog YAML config and return a list of all the files' versions. */
-  private static List<String> getMigrationVersions(MigrationConfiguration conf) throws IOException {
-    try (Stream<String> names =
-        Files.walk(Paths.get(conf.getFlywayPath()))
-            .filter(Files::isRegularFile)
-            .map(Path::toFile)
-            .map(File::getName)
-            .map(Migration::cleanName)) {
-
-      return names.collect(Collectors.toList());
-    }
-  }
-
-  /** Given a Flyway migration filename, e.g., v001__my_file.sql, return the version information "001". */
-  private static String cleanName(String name) {
-    return Arrays.asList(name.split("_")).get(0).replace("v", "");
-  }
-}

openmetadata-service/src/main/java/org/openmetadata/service/migration/MigrationConfiguration.java

@@ -5,7 +5,7 @@ import lombok.Getter;
 import lombok.Setter;
 
 public class MigrationConfiguration {
-  @NotEmpty @Getter @Setter private String flywayPath;
   @NotEmpty @Getter @Setter private String nativePath;
   @NotEmpty @Getter @Setter private String extensionPath;
+  @NotEmpty @Getter @Setter private String flywayPath;
 }

openmetadata-service/src/main/java/org/openmetadata/service/migration/MigrationValidationClient.java

@@ -45,16 +45,24 @@ public class MigrationValidationClient {
 
       List<String> availableOMNativeMigrations = getMigrationFilesFromPath(nativePath);
 
-      // If we only have OM migrations, return them
+      // Get Flyway versions from server_change_log (they have metrics = NULL)
+      List<String> expectedFlywayVersions = getExpectedFlywayVersions();
+
+      // If we only have OM and Flyway migrations, return them
       if (extensionPath == null || extensionPath.isEmpty()) {
-        return availableOMNativeMigrations;
+        return Stream.concat(expectedFlywayVersions.stream(), availableOMNativeMigrations.stream())
+            .sorted()
+            .toList();
       }
 
-      // Otherwise, fetch the extension migration and sort the results
+      // Otherwise, fetch the extension migration and sort all results
       List<String> availableOMExtensionMigrations = getMigrationFilesFromPath(extensionPath);
 
-      return Stream.concat(
+      return Stream.of(
-              availableOMNativeMigrations.stream(), availableOMExtensionMigrations.stream())
+              expectedFlywayVersions.stream(),
+              availableOMNativeMigrations.stream(),
+              availableOMExtensionMigrations.stream())
+          .flatMap(s -> s)
           .sorted()
           .toList();
     } catch (Exception e) {
@@ -69,4 +77,15 @@ public class MigrationValidationClient {
         .sorted()
         .toList();
   }
+
+  private List<String> getExpectedFlywayVersions() {
+    try {
+      // Query server_change_log for versions where migrationFileName contains 'flyway'
+      return migrationDAO.getFlywayMigrationVersions();
+    } catch (Exception e) {
+      // If there's an error (e.g., table doesn't exist yet), return empty list
+      LOG.debug("Could not fetch Flyway versions from SERVER_CHANGE_LOG: {}", e.getMessage());
+      return List.of();
+    }
+  }
 }

openmetadata-service/src/main/java/org/openmetadata/service/migration/api/MigrationProcess.java

@@ -8,10 +8,9 @@ import org.openmetadata.service.migration.QueryStatus;
 import org.openmetadata.service.migration.context.MigrationOps;
 
 /**
- * Migration framework interface that supports three implementation approaches:
+ * Migration framework interface that supports two implementation approaches:
- * 1. Flyway (deprecated, do not add new migrations here)
+ * 1. Native SQL migrations
- * 2. Native SQL migrations
+ * 2. Java-based migrations
- * 3. Java-based migrations
  *
  * <p><strong>Migration Execution Order:</strong>
  * Migrations are executed in a specific sequence that must be maintained:

openmetadata-service/src/main/java/org/openmetadata/service/migration/api/MigrationProcessImpl.java

@@ -118,10 +118,22 @@ public class MigrationProcessImpl implements MigrationProcess {
     if (!nullOrEmpty(queryList)) {
       for (String sql : queryList) {
         try {
-          String previouslyRanSql = migrationDAO.getSqlQuery(hash(sql), version);
+          String previouslyRanSql = null;
+          try {
+            previouslyRanSql = migrationDAO.getSqlQuery(hash(sql), version);
+          } catch (Exception dbException) {
+            // If SERVER_MIGRATION_SQL_LOGS table doesn't exist yet, assume query hasn't run
+            previouslyRanSql = null;
+          }
+
           if ((previouslyRanSql == null || previouslyRanSql.isEmpty())) {
             handle.execute(sql);
-            migrationDAO.upsertServerMigrationSQL(version, sql, hash(sql));
+            try {
+              migrationDAO.upsertServerMigrationSQL(version, sql, hash(sql));
+            } catch (Exception logException) {
+              // If logging fails (table doesn't exist yet), continue - the SQL was executed
+              // successfully
+            }
           }
           queryStatusMap.put(
               sql, new QueryStatus(QueryStatus.Status.SUCCESS, "Successfully Executed Query"));

openmetadata-service/src/main/java/org/openmetadata/service/migration/api/MigrationWorkflow.java

@@ -23,6 +23,7 @@ import org.openmetadata.service.jdbi3.locator.ConnectionType;
 import org.openmetadata.service.migration.QueryStatus;
 import org.openmetadata.service.migration.context.MigrationContext;
 import org.openmetadata.service.migration.context.MigrationWorkflowContext;
+import org.openmetadata.service.migration.utils.FlywayMigrationFile;
 import org.openmetadata.service.migration.utils.MigrationFile;
 import org.openmetadata.service.util.AsciiTable;
 
@@ -35,6 +36,7 @@ public class MigrationWorkflow {
   private final String nativeSQLScriptRootPath;
   private final ConnectionType connectionType;
   private final String extensionSQLScriptRootPath;
+  private final String flywayPath;
   @Getter private final OpenMetadataApplicationConfig openMetadataApplicationConfig;
   private final MigrationDAO migrationDAO;
   private final Jdbi jdbi;
@@ -47,6 +49,7 @@ public class MigrationWorkflow {
       String nativeSQLScriptRootPath,
       ConnectionType connectionType,
       String extensionSQLScriptRootPath,
+      String flywayPath,
       OpenMetadataApplicationConfig config,
       boolean forceMigrations) {
     this.jdbi = jdbi;
@@ -55,6 +58,7 @@ public class MigrationWorkflow {
     this.nativeSQLScriptRootPath = nativeSQLScriptRootPath;
     this.connectionType = connectionType;
     this.extensionSQLScriptRootPath = extensionSQLScriptRootPath;
+    this.flywayPath = flywayPath;
     this.openMetadataApplicationConfig = config;
   }
 
@@ -65,7 +69,8 @@ public class MigrationWorkflow {
             nativeSQLScriptRootPath,
             connectionType,
             openMetadataApplicationConfig,
-            extensionSQLScriptRootPath);
+            extensionSQLScriptRootPath,
+            flywayPath);
     // Filter Migrations to Be Run
     this.migrations = filterAndGetMigrationsToRun(availableMigrations);
   }
@@ -84,27 +89,35 @@ public class MigrationWorkflow {
       String nativeSQLScriptRootPath,
       ConnectionType connectionType,
       OpenMetadataApplicationConfig config,
-      String extensionSQLScriptRootPath) {
+      String extensionSQLScriptRootPath,
+      String flywayPath) {
     List<MigrationFile> availableOMNativeMigrations =
         getMigrationFilesFromPath(nativeSQLScriptRootPath, connectionType, config, false);
 
-    // If we only have OM migrations, return them
+    // Get Flyway migrations first (they should run before native migrations)
-    if (extensionSQLScriptRootPath == null || extensionSQLScriptRootPath.isEmpty()) {
+    List<FlywayMigrationFile> availableFlywayMigrations =
-      return availableOMNativeMigrations;
+        FlywayMigrationFile.getFlywayMigrationFiles(
+            flywayPath, connectionType, config, migrationDAO);
+
+    // Get extension migrations if available
+    List<MigrationFile> availableExtensionMigrations = new ArrayList<>();
+    if (extensionSQLScriptRootPath != null && !extensionSQLScriptRootPath.isEmpty()) {
+      availableExtensionMigrations =
+          getMigrationFilesFromPath(extensionSQLScriptRootPath, connectionType, config, true);
     }
 
-    // Otherwise, fetch the extension migrations and sort the executions
-    List<MigrationFile> availableExtensionMigrations =
-        getMigrationFilesFromPath(extensionSQLScriptRootPath, connectionType, config, true);
-
     /*
-     If we create migrations version as:
+     Combined execution order:
-       - OpenMetadata: 1.1.0, 1.1.1, 1.2.0
+       1. Flyway migrations (legacy SQL files from Flyway)
-       - Extension: 1.1.0-extension, 1.2.0-extension
+       2. OpenMetadata native migrations
-     The end result will be 1.1.0, 1.1.0-extension, 1.1.1, 1.2.0, 1.2.0-extension
+       3. Extension migrations
+     All sorted by version within their respective groups
     */
-    return Stream.concat(
+    return Stream.of(
-            availableOMNativeMigrations.stream(), availableExtensionMigrations.stream())
+            availableFlywayMigrations.stream().map(f -> (MigrationFile) f),
+            availableOMNativeMigrations.stream(),
+            availableExtensionMigrations.stream())
+        .flatMap(stream -> stream)
         .sorted()
         .toList();
   }
@@ -123,7 +136,14 @@ public class MigrationWorkflow {
   private List<MigrationProcess> filterAndGetMigrationsToRun(
       List<MigrationFile> availableMigrations) {
     LOG.debug("Filtering Server Migrations");
-    executedMigrations = migrationDAO.getMigrationVersions();
+    try {
+      executedMigrations = migrationDAO.getMigrationVersions();
+    } catch (Exception e) {
+      // SERVER_CHANGE_LOG table doesn't exist yet, run all migrations including Flyway
+      LOG.info(
+          "SERVER_CHANGE_LOG table doesn't exist yet, will run all migrations including Flyway");
+      executedMigrations = new ArrayList<>();
+    }
     currentMaxMigrationVersion =
         executedMigrations.stream().max(MigrationWorkflow::compareVersions);
     List<MigrationFile> applyMigrations;

openmetadata-service/src/main/java/org/openmetadata/service/migration/mysql/v1110/Migration.java

@@ -1,7 +1,9 @@
 package org.openmetadata.service.migration.mysql.v1110;
 
 import java.util.Map;
+import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
+import org.openmetadata.service.jdbi3.locator.ConnectionType;
 import org.openmetadata.service.migration.QueryStatus;
 import org.openmetadata.service.migration.api.MigrationProcessImpl;
 import org.openmetadata.service.migration.utils.MigrationFile;
@@ -13,7 +15,7 @@ public class Migration extends MigrationProcessImpl {
 
   public Migration(MigrationFile migrationFile) {
     super(migrationFile);
-    this.migrationUtil = new MigrationUtil(migrationFile);
+    this.migrationUtil = new MigrationUtil(ConnectionType.MYSQL, migrationFile);
   }
 
   @Override
@@ -28,4 +30,10 @@ public class Migration extends MigrationProcessImpl {
             isForceMigration));
     return result;
   }
+
+  @Override
+  @SneakyThrows
+  public void runDataMigration() {
+    this.migrationUtil.migrateFlywayHistory(handle);
+  }
 }

openmetadata-service/src/main/java/org/openmetadata/service/migration/postgres/v1110/Migration.java

@@ -1,7 +1,9 @@
 package org.openmetadata.service.migration.postgres.v1110;
 
 import java.util.Map;
+import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
+import org.openmetadata.service.jdbi3.locator.ConnectionType;
 import org.openmetadata.service.migration.QueryStatus;
 import org.openmetadata.service.migration.api.MigrationProcessImpl;
 import org.openmetadata.service.migration.utils.MigrationFile;
@@ -13,7 +15,7 @@ public class Migration extends MigrationProcessImpl {
 
   public Migration(MigrationFile migrationFile) {
     super(migrationFile);
-    this.migrationUtil = new MigrationUtil(migrationFile);
+    this.migrationUtil = new MigrationUtil(ConnectionType.POSTGRES, migrationFile);
   }
 
   @Override
@@ -28,4 +30,10 @@ public class Migration extends MigrationProcessImpl {
             isForceMigration));
     return result;
   }
+
+  @Override
+  @SneakyThrows
+  public void runDataMigration() {
+    this.migrationUtil.migrateFlywayHistory(handle);
+  }
 }

openmetadata-service/src/main/java/org/openmetadata/service/migration/utils/FlywayMigrationFile.java

@@ -0,0 +1,163 @@
+package org.openmetadata.service.migration.utils;
+
+import java.io.File;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import org.flywaydb.core.api.configuration.ClassicConfiguration;
+import org.flywaydb.core.api.configuration.Configuration;
+import org.flywaydb.core.internal.database.postgresql.PostgreSQLParser;
+import org.flywaydb.core.internal.parser.Parser;
+import org.flywaydb.core.internal.parser.ParsingContext;
+import org.flywaydb.core.internal.resource.filesystem.FileSystemResource;
+import org.flywaydb.core.internal.sqlscript.SqlStatementIterator;
+import org.flywaydb.database.mysql.MySQLParser;
+import org.jetbrains.annotations.Nullable;
+import org.openmetadata.service.OpenMetadataApplicationConfig;
+import org.openmetadata.service.jdbi3.MigrationDAO;
+import org.openmetadata.service.jdbi3.locator.ConnectionType;
+import org.openmetadata.service.util.EntityUtil;
+
+public class FlywayMigrationFile extends MigrationFile {
+  private static final Pattern FLYWAY_FILE_PATTERN =
+      Pattern.compile("^[vV](\\d+(?:\\.\\d+)*)__.*\\.sql$");
+
+  private final File sqlFile;
+
+  public FlywayMigrationFile(
+      File sqlFile,
+      MigrationDAO migrationDAO,
+      ConnectionType connectionType,
+      OpenMetadataApplicationConfig config) {
+    super(createFlywayVersionDir(sqlFile), migrationDAO, connectionType, config, false);
+    this.sqlFile = sqlFile;
+  }
+
+  private static File createFlywayVersionDir(File sqlFile) {
+    // Create a virtual directory with semantic version name that doesn't need to exist
+    String flywayVersion = extractVersionFromFilename(sqlFile.getName());
+    String semanticVersion = String.format("0.0.%d", Integer.parseInt(flywayVersion));
+    // Return a virtual directory - it doesn't need to exist since we override file methods
+    return new File(sqlFile.getParent(), semanticVersion);
+  }
+
+  private static String extractVersionFromFilename(String filename) {
+    Matcher matcher = FLYWAY_FILE_PATTERN.matcher(filename);
+    if (matcher.matches()) {
+      return matcher.group(1);
+    }
+    throw new IllegalArgumentException("Invalid Flyway migration filename: " + filename);
+  }
+
+  @Override
+  public void parseSQLFiles() {
+    if (sqlFile.exists() && sqlFile.isFile()) {
+      try {
+        final ParsingContext parsingContext = new ParsingContext();
+        Configuration configuration = new ClassicConfiguration();
+        Parser parser = new PostgreSQLParser(configuration, parsingContext);
+        if (connectionType == ConnectionType.MYSQL) {
+          parser = new MySQLParser(configuration, parsingContext);
+        }
+
+        try (SqlStatementIterator sqlIterator =
+            parser.parse(
+                new FileSystemResource(
+                    null, sqlFile.getAbsolutePath(), StandardCharsets.UTF_8, true))) {
+          while (sqlIterator.hasNext()) {
+            String sqlStatement = sqlIterator.next().getSql();
+            if (!checkIfQueryPreviouslyRan(sqlStatement)) {
+              schemaChanges.add(sqlStatement);
+            }
+          }
+        }
+      } catch (Exception e) {
+        throw new RuntimeException(
+            "Failed to parse Flyway migration file: " + sqlFile.getPath(), e);
+      }
+    }
+  }
+
+  @Override
+  public String getSchemaChangesFile() {
+    return sqlFile.getAbsolutePath();
+  }
+
+  @Override
+  public String getPostDDLScriptFile() {
+    // Flyway files don't have separate post DDL scripts
+    return "";
+  }
+
+  @Override
+  public String getMigrationsFilePath() {
+    return sqlFile.getAbsolutePath();
+  }
+
+  public static boolean isFlywayMigrationFile(File file) {
+    return file.isFile() && FLYWAY_FILE_PATTERN.matcher(file.getName()).matches();
+  }
+
+  public static List<FlywayMigrationFile> getFlywayMigrationFiles(
+      String flywayPath,
+      ConnectionType connectionType,
+      OpenMetadataApplicationConfig config,
+      MigrationDAO migrationDAO) {
+    List<FlywayMigrationFile> flywayMigrations = new ArrayList<>();
+
+    if (flywayPath == null || flywayPath.isEmpty()) {
+      return flywayMigrations;
+    }
+
+    File flywayDir = new File(flywayPath);
+    if (!flywayDir.exists() || !flywayDir.isDirectory()) {
+      return flywayMigrations;
+    }
+
+    // Get database-specific subdirectory using the actual directory names
+    File[] sqlFiles = getFiles(connectionType, flywayDir);
+
+    if (sqlFiles != null) {
+      Arrays.stream(sqlFiles)
+          .map(file -> new FlywayMigrationFile(file, migrationDAO, connectionType, config))
+          .sorted()
+          .forEach(flywayMigrations::add);
+    }
+
+    return flywayMigrations;
+  }
+
+  private static File @Nullable [] getFiles(ConnectionType connectionType, File flywayDir) {
+    String dbSubDir =
+        connectionType == ConnectionType.MYSQL
+            ? "com.mysql.cj.jdbc.Driver"
+            : "org.postgresql.Driver";
+    File dbSpecificDir = new File(flywayDir, dbSubDir);
+
+    if (!dbSpecificDir.exists() || !dbSpecificDir.isDirectory()) {
+      // Try legacy naming convention
+      String legacyDbSubDir = connectionType == ConnectionType.MYSQL ? "mysql" : "postgresql";
+      dbSpecificDir = new File(flywayDir, legacyDbSubDir);
+      if (!dbSpecificDir.exists() || !dbSpecificDir.isDirectory()) {
+        // Try the root flyway directory
+        dbSpecificDir = flywayDir;
+      }
+    }
+
+    return dbSpecificDir.listFiles((dir1, name) -> FLYWAY_FILE_PATTERN.matcher(name).matches());
+  }
+
+  private boolean checkIfQueryPreviouslyRan(String query) {
+    try {
+      String checksum = EntityUtil.hash(query);
+      String sqlStatement = migrationDAO.checkIfQueryPreviouslyRan(checksum);
+      return sqlStatement != null;
+    } catch (Exception e) {
+      // If SERVER_MIGRATION_SQL_LOGS table doesn't exist yet, assume query hasn't run
+      return false;
+    }
+  }
+}

openmetadata-service/src/main/java/org/openmetadata/service/migration/utils/MigrationFile.java

@@ -28,9 +28,9 @@ public class MigrationFile implements Comparable<MigrationFile> {
   public final Boolean isExtension;
   public final String dbPackageName;
 
-  private final MigrationDAO migrationDAO;
+  protected final MigrationDAO migrationDAO;
-  private final List<String> schemaChanges;
+  protected final List<String> schemaChanges;
-  private final List<String> postDDLScripts;
+  protected final List<String> postDDLScripts;
   public static final String DEFAULT_MIGRATION_PROCESS_CLASS =
       "org.openmetadata.service.migration.api.MigrationProcessImpl";
 
@@ -70,6 +70,7 @@ public class MigrationFile implements Comparable<MigrationFile> {
     if (connectionType == ConnectionType.MYSQL) {
       parser = new MySQLParser(configuration, parsingContext);
     }
+
     if (new File(getSchemaChangesFile()).isFile()) {
       try (SqlStatementIterator schemaChangesIterator =
           parser.parse(
@@ -80,18 +81,24 @@ public class MigrationFile implements Comparable<MigrationFile> {
             schemaChanges.add(sqlStatement);
           }
         }
+      } catch (Exception e) {
+        throw new RuntimeException(
+            "Failed to parse schema changes file: " + getSchemaChangesFile(), e);
       }
     }
     if (new File(getPostDDLScriptFile()).isFile()) {
-      try (SqlStatementIterator schemaChangesIterator =
+      try (SqlStatementIterator postDDLIterator =
           parser.parse(
               new FileSystemResource(null, getPostDDLScriptFile(), StandardCharsets.UTF_8, true))) {
-        while (schemaChangesIterator.hasNext()) {
+        while (postDDLIterator.hasNext()) {
-          String sqlStatement = schemaChangesIterator.next().getSql();
+          String sqlStatement = postDDLIterator.next().getSql();
           if (!checkIfQueryPreviouslyRan(sqlStatement)) {
             postDDLScripts.add(sqlStatement);
           }
         }
+      } catch (Exception e) {
+        throw new RuntimeException(
+            "Failed to parse post DDL script file: " + getPostDDLScriptFile(), e);
       }
     }
   }
@@ -188,8 +195,13 @@ public class MigrationFile implements Comparable<MigrationFile> {
   }
 
   private boolean checkIfQueryPreviouslyRan(String query) {
-    String checksum = EntityUtil.hash(query);
+    try {
-    String sqlStatement = migrationDAO.checkIfQueryPreviouslyRan(checksum);
+      String checksum = EntityUtil.hash(query);
-    return sqlStatement != null;
+      String sqlStatement = migrationDAO.checkIfQueryPreviouslyRan(checksum);
+      return sqlStatement != null;
+    } catch (Exception e) {
+      // If SERVER_MIGRATION_SQL_LOGS table doesn't exist yet, assume query hasn't run
+      return false;
+    }
   }
 }

openmetadata-service/src/main/java/org/openmetadata/service/migration/utils/v1110/MigrationUtil.java

@@ -15,6 +15,7 @@ import org.openmetadata.schema.type.Recognizer;
 import org.openmetadata.schema.utils.JsonUtils;
 import org.openmetadata.service.jdbi3.EntityRepository;
 import org.openmetadata.service.jdbi3.MigrationDAO;
+import org.openmetadata.service.jdbi3.locator.ConnectionType;
 import org.openmetadata.service.migration.QueryStatus;
 import org.openmetadata.service.migration.utils.MigrationFile;
 
@@ -26,7 +27,11 @@ public class MigrationUtil {
           "PII.NonSensitive", "data/tags/NonSensitive.json");
   private final MigrationFile migrationFile;
 
-  public MigrationUtil(MigrationFile migrationFile) {
+  private final ConnectionType connectionType;
+  public static final String FLYWAY_TABLE_NAME = "DATABASE_CHANGE_LOG";
+
+  public MigrationUtil(ConnectionType connectionType, MigrationFile migrationFile) {
+    this.connectionType = connectionType;
     this.migrationFile = migrationFile;
   }
 
@@ -96,4 +101,132 @@ public class MigrationUtil {
       }
     }
   }
+
+  public void migrateFlywayHistory(Handle handle) {
+    try {
+      LOG.info("Starting v1100 migration of Flyway history to SERVER_CHANGE_LOG");
+
+      // Check if DATABASE_CHANGE_LOG table exists
+      boolean tableExists = checkTableExists(handle, "DATABASE_CHANGE_LOG");
+
+      if (!tableExists) {
+        LOG.info("Flyway DATABASE_CHANGE_LOG table does not exist, skipping migration");
+        return;
+      }
+
+      // Check if Flyway records have already been migrated
+      if (hasFlywayDataAlreadyMigrated(handle)) {
+        LOG.info(
+            "Flyway records have already been migrated to SERVER_CHANGE_LOG, skipping migration");
+        return;
+      }
+
+      // Insert missing v000 baseline record if not present
+      insertV000RecordIfMissing(handle);
+
+      // Migrate Flyway migration records to SERVER_CHANGE_LOG
+      int migratedCount = migrateFlywayHistoryRecords(handle);
+
+      if (migratedCount > 0) {
+        LOG.info(
+            "Successfully migrated {} Flyway migration records to SERVER_CHANGE_LOG",
+            migratedCount);
+      } else {
+        LOG.info("No new Flyway migration records to migrate");
+      }
+
+    } catch (Exception e) {
+      LOG.error("Error during Flyway history migration", e);
+    }
+  }
+
+  public boolean checkTableExists(Handle handle, String tableName) {
+    String query =
+        switch (connectionType) {
+          case MYSQL -> "SELECT COUNT(*) FROM information_schema.tables "
+              + "WHERE table_schema = DATABASE() AND table_name = ?";
+          case POSTGRES -> "SELECT COUNT(*) FROM information_schema.tables "
+              + "WHERE table_schema = current_schema() AND table_name = ?";
+        };
+
+    Integer count = handle.createQuery(query).bind(0, tableName).mapTo(Integer.class).one();
+
+    return count > 0;
+  }
+
+  public boolean hasFlywayDataAlreadyMigrated(Handle handle) {
+    String countQuery =
+        switch (connectionType) {
+          case MYSQL -> """
+              SELECT COUNT(*) FROM SERVER_CHANGE_LOG scl
+              INNER JOIN DATABASE_CHANGE_LOG dcl ON CONCAT('0.0.', CAST(dcl.version AS UNSIGNED)) = scl.version
+              WHERE scl.migrationfilename LIKE '%flyway%'
+              """;
+          case POSTGRES -> """
+              SELECT COUNT(*) FROM SERVER_CHANGE_LOG scl
+              INNER JOIN "DATABASE_CHANGE_LOG" dcl ON '0.0.' || CAST(dcl.version AS INTEGER) = scl.version
+              WHERE scl.migrationfilename LIKE '%flyway%'
+              """;
+        };
+
+    Integer count = handle.createQuery(countQuery).mapTo(Integer.class).one();
+
+    return count > 0;
+  }
+
+  private void insertV000RecordIfMissing(Handle handle) {
+    String insertQuery =
+        switch (connectionType) {
+          case MYSQL -> """
+              INSERT IGNORE INTO SERVER_CHANGE_LOG (version, migrationfilename, checksum, installed_on, metrics)
+              VALUES ('0.0.0', 'bootstrap/sql/migrations/flyway/mysql/v000__create_db_connection_info.sql', '0', NOW(), NULL)
+              """;
+          case POSTGRES -> """
+              INSERT INTO SERVER_CHANGE_LOG (version, migrationfilename, checksum, installed_on, metrics)
+              VALUES ('0.0.0', 'bootstrap/sql/migrations/flyway/postgres/v000__create_db_connection_info.sql', '0', current_timestamp, NULL)
+              ON CONFLICT (version) DO NOTHING
+              """;
+        };
+
+    int inserted = handle.createUpdate(insertQuery).execute();
+    if (inserted > 0) {
+      LOG.info("Inserted missing v0.0.0 baseline record");
+    }
+  }
+
+  private int migrateFlywayHistoryRecords(Handle handle) {
+    String insertQuery =
+        switch (connectionType) {
+          case MYSQL -> """
+              INSERT INTO SERVER_CHANGE_LOG (version, migrationfilename, checksum, installed_on, metrics)
+              SELECT CONCAT('0.0.', CAST(version AS UNSIGNED)) as version,
+                     CASE
+                       WHEN script LIKE 'v%__.sql' THEN CONCAT('bootstrap/sql/migrations/flyway/mysql/', script)
+                       ELSE CONCAT('bootstrap/sql/migrations/flyway/mysql/v', version, '__', REPLACE(LOWER(description), ' ', '_'), '.sql')
+                     END as migrationfilename,
+                     '0' as checksum,
+                     installed_on,
+                     NULL as metrics
+              FROM DATABASE_CHANGE_LOG
+              WHERE CONCAT('0.0.', CAST(version AS UNSIGNED)) NOT IN (SELECT version FROM SERVER_CHANGE_LOG)
+              AND success = true
+              """;
+          case POSTGRES -> """
+              INSERT INTO SERVER_CHANGE_LOG (version, migrationfilename, checksum, installed_on, metrics)
+              SELECT '0.0.' || CAST(version AS INTEGER) as version,
+                     CASE
+                       WHEN script LIKE 'v%__.sql' THEN 'bootstrap/sql/migrations/flyway/postgres/' || script
+                       ELSE 'bootstrap/sql/migrations/flyway/postgres/v' || version || '__' || REPLACE(LOWER(description), ' ', '_') || '.sql'
+                     END as migrationfilename,
+                     '0' as checksum,
+                     installed_on,
+                     NULL as metrics
+              FROM "DATABASE_CHANGE_LOG"
+              WHERE '0.0.' || CAST(version AS INTEGER) NOT IN (SELECT version FROM SERVER_CHANGE_LOG)
+              AND success = true
+              """;
+        };
+
+    return handle.createUpdate(insertQuery).execute();
+  }
 }

openmetadata-service/src/main/java/org/openmetadata/service/util/OpenMetadataOperations.java

@@ -1,6 +1,5 @@
 package org.openmetadata.service.util;
 
-import static org.flywaydb.core.internal.info.MigrationInfoDumper.dumpToAsciiTable;
 import static org.openmetadata.common.utils.CommonUtil.nullOrEmpty;
 import static org.openmetadata.service.Entity.ADMIN_USER_NAME;
 import static org.openmetadata.service.Entity.FIELD_OWNERS;
@@ -25,7 +24,6 @@ import io.dropwizard.db.DataSourceFactory;
 import io.dropwizard.jackson.Jackson;
 import io.dropwizard.jersey.validation.Validators;
 import jakarta.validation.Validator;
-import java.io.File;
 import java.net.URI;
 import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
@@ -40,8 +38,7 @@ import java.util.Set;
 import java.util.concurrent.Callable;
 import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
-import org.flywaydb.core.Flyway;
+import org.jdbi.v3.core.Handle;
-import org.flywaydb.core.api.MigrationVersion;
 import org.jdbi.v3.core.Jdbi;
 import org.openmetadata.schema.EntityInterface;
 import org.openmetadata.schema.ServiceEntityInterface;
@@ -129,7 +126,6 @@ import picocli.CommandLine.Option;
 public class OpenMetadataOperations implements Callable<Integer> {
 
   private OpenMetadataApplicationConfig config;
-  private Flyway flyway;
   private Jdbi jdbi;
   private SearchRepository searchRepository;
   private String nativeSQLScriptRootPath;
@@ -158,54 +154,6 @@ public class OpenMetadataOperations implements Callable<Integer> {
     return 0;
   }
 
-  @Command(
-      name = "info",
-      description =
-          "Shows the list of migrations applied and the pending migration "
-              + "waiting to be applied on the target database")
-  public Integer info() {
-    try {
-      parseConfig();
-      LOG.info(dumpToAsciiTable(flyway.info().all()));
-      return 0;
-    } catch (Exception e) {
-      LOG.error("Failed due to ", e);
-      return 1;
-    }
-  }
-
-  @Command(
-      name = "validate",
-      description =
-          "Checks if the all the migrations haven been applied " + "on the target database.")
-  public Integer validate() {
-    try {
-      parseConfig();
-      flyway.validate();
-      return 0;
-    } catch (Exception e) {
-      LOG.error("Database migration validation failed due to ", e);
-      return 1;
-    }
-  }
-
-  @Command(
-      name = "repair",
-      description =
-          "Repairs the DATABASE_CHANGE_LOG table which is used to track"
-              + "all the migrations on the target database This involves removing entries for the failed migrations and update"
-              + "the checksum of migrations already applied on the target database")
-  public Integer repair() {
-    try {
-      parseConfig();
-      flyway.repair();
-      return 0;
-    } catch (Exception e) {
-      LOG.error("Repair of CHANGE_LOG failed due to ", e);
-      return 1;
-    }
-  }
-
   @Command(
       name = "setOpenMetadataUrl",
       description = "Set or update the OpenMetadata URL in the system repository")
@@ -561,7 +509,7 @@ public class OpenMetadataOperations implements Callable<Integer> {
   public Integer checkConnection() {
     try {
       parseConfig();
-      flyway.getConfiguration().getDataSource().getConnection();
+      jdbi.open().getConnection();
       return 0;
     } catch (Exception e) {
       LOG.error("Failed to check connection due to ", e);
@@ -579,9 +527,7 @@ public class OpenMetadataOperations implements Callable<Integer> {
       promptUserForDelete();
       parseConfig();
       LOG.info("Deleting all the OpenMetadata tables.");
-      flyway.clean();
+      dropAllTables();
-      LOG.info("Creating the OpenMetadata Schema.");
-      flyway.migrate();
       LOG.info("Running the Native Migrations.");
       validateAndRunSystemDataMigrations(true);
       LOG.info("OpenMetadata Database Schema is Updated.");
@@ -660,7 +606,6 @@ public class OpenMetadataOperations implements Callable<Integer> {
     try {
       LOG.info("Migrating the OpenMetadata Schema.");
       parseConfig();
-      flyway.migrate();
       validateAndRunSystemDataMigrations(force);
       LOG.info("Update Search Indexes.");
       searchRepository.updateIndexes();
@@ -1725,30 +1670,6 @@ public class OpenMetadataOperations implements Callable<Integer> {
               dataSourceFactory.setPassword(token);
             });
 
-    String jdbcUrl = dataSourceFactory.getUrl();
-    String user = dataSourceFactory.getUser();
-    String password = dataSourceFactory.getPassword();
-    assert user != null && password != null;
-    String flywayRootPath = config.getMigrationConfiguration().getFlywayPath();
-    String location =
-        "filesystem:"
-            + flywayRootPath
-            + File.separator
-            + config.getDataSourceFactory().getDriverClass();
-    flyway =
-        Flyway.configure()
-            .encoding(StandardCharsets.UTF_8)
-            .table("DATABASE_CHANGE_LOG")
-            .sqlMigrationPrefix("v")
-            .validateOnMigrate(false)
-            .outOfOrder(false)
-            .baselineOnMigrate(true)
-            .baselineVersion(MigrationVersion.fromVersion("000"))
-            .cleanOnValidationError(false)
-            .locations(location)
-            .dataSource(jdbcUrl, user, password)
-            .cleanDisabled(false)
-            .load();
     nativeSQLScriptRootPath = config.getMigrationConfiguration().getNativePath();
     extensionSQLScriptRootPath = config.getMigrationConfiguration().getExtensionPath();
 
@@ -1773,6 +1694,43 @@ public class OpenMetadataOperations implements Callable<Integer> {
     DatasourceConfig.initialize(connType.label);
   }
 
+  // This was before handled via flyway's clean command.
+  private void dropAllTables() {
+    try (Handle handle = jdbi.open()) {
+      ConnectionType connType = ConnectionType.from(config.getDataSourceFactory().getDriverClass());
+      if (connType == ConnectionType.MYSQL) {
+        handle.execute("SET FOREIGN_KEY_CHECKS = 0");
+        handle
+            .createQuery("SHOW TABLES")
+            .mapTo(String.class)
+            .list()
+            .forEach(
+                tableName -> {
+                  try {
+                    handle.execute("DROP TABLE IF EXISTS " + tableName);
+                  } catch (Exception e) {
+                    LOG.warn("Failed to drop table: " + tableName, e);
+                  }
+                });
+        handle.execute("SET FOREIGN_KEY_CHECKS = 1");
+      } else if (connType == ConnectionType.POSTGRES) {
+        handle
+            .createQuery(
+                "SELECT table_name FROM information_schema.tables WHERE table_schema = 'public'")
+            .mapTo(String.class)
+            .list()
+            .forEach(
+                tableName -> {
+                  try {
+                    handle.execute("DROP TABLE IF EXISTS \"" + tableName + "\" CASCADE");
+                  } catch (Exception e) {
+                    LOG.warn("Failed to drop table: " + tableName, e);
+                  }
+                });
+      }
+    }
+  }
+
   private void promptUserForDelete() {
     LOG.info(
         """
@@ -1797,7 +1755,13 @@ public class OpenMetadataOperations implements Callable<Integer> {
     DatasourceConfig.initialize(connType.label);
     MigrationWorkflow workflow =
         new MigrationWorkflow(
-            jdbi, nativeSQLScriptRootPath, connType, extensionSQLScriptRootPath, config, force);
+            jdbi,
+            nativeSQLScriptRootPath,
+            connType,
+            extensionSQLScriptRootPath,
+            config.getMigrationConfiguration().getFlywayPath(),
+            config,
+            force);
     workflow.loadMigrations();
     workflow.printMigrationInfo();
     workflow.runMigrationWorkflows(true);

openmetadata-service/src/test/java/org/openmetadata/service/JwtAuthOpenMetadataApplicationTest.java

@@ -273,6 +273,7 @@ public abstract class JwtAuthOpenMetadataApplicationTest {
             nativeMigrationSQLPath,
             connType,
             extensionSQLScriptRootPath,
+            "", // flywayPath - empty string as placeholder
             config,
             forceMigrations);
     // Initialize search repository

openmetadata-service/src/test/java/org/openmetadata/service/OpenMetadataApplicationTest.java

@@ -45,7 +45,6 @@ import org.apache.http.auth.UsernamePasswordCredentials;
 import org.apache.http.client.CredentialsProvider;
 import org.apache.http.impl.client.BasicCredentialsProvider;
 import org.eclipse.jetty.client.HttpClient;
-import org.flywaydb.core.Flyway;
 import org.glassfish.jersey.client.ClientConfig;
 import org.glassfish.jersey.client.ClientProperties;
 import org.glassfish.jersey.jetty.connector.JettyClientProperties;
@@ -176,9 +175,6 @@ public abstract class OpenMetadataApplicationTest {
     dataSourceFactory.setDriverClass(sqlContainer.getDriverClassName());
     config.setDataSourceFactory(dataSourceFactory);
 
-    final String flyWayMigrationScriptsLocation =
-        ResourceHelpers.resourceFilePath(
-            "db/sql/migrations/flyway/" + sqlContainer.getDriverClassName());
     final String nativeMigrationScriptsLocation =
         ResourceHelpers.resourceFilePath("db/sql/migrations/native/");
 
@@ -193,17 +189,6 @@ public abstract class OpenMetadataApplicationTest {
     } catch (Exception ex) {
       LOG.info("Extension migrations not found");
     }
-    Flyway flyway =
-        Flyway.configure()
-            .dataSource(
-                sqlContainer.getJdbcUrl(), sqlContainer.getUsername(), sqlContainer.getPassword())
-            .table("DATABASE_CHANGE_LOG")
-            .locations("filesystem:" + flyWayMigrationScriptsLocation)
-            .sqlMigrationPrefix("v")
-            .cleanDisabled(false)
-            .load();
-    flyway.clean();
-    flyway.migrate();
 
     ELASTIC_SEARCH_CONTAINER = new ElasticsearchContainer(elasticSearchContainerImage);
     ELASTIC_SEARCH_CONTAINER.withPassword("password");
@@ -227,8 +212,6 @@ public abstract class OpenMetadataApplicationTest {
     IndexMappingLoader.init(getEsConfig());
 
     // Migration overrides
-    configOverrides.add(
-        ConfigOverride.config("migrationConfiguration.flywayPath", flyWayMigrationScriptsLocation));
     configOverrides.add(
         ConfigOverride.config("migrationConfiguration.nativePath", nativeMigrationScriptsLocation));
 
@@ -274,6 +257,7 @@ public abstract class OpenMetadataApplicationTest {
             nativeMigrationSQLPath,
             connType,
             extensionSQLScriptRootPath,
+            config.getMigrationConfiguration().getFlywayPath(),
             config,
             forceMigrations);
     // Initialize search repository

openmetadata-service/src/test/java/org/openmetadata/service/migration/FlywayMigrationIntegrationTest.java

@@ -0,0 +1,167 @@
+/*
+ *  Copyright 2021 Collate
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *  http://www.apache.org/licenses/LICENSE-2.0
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+
+package org.openmetadata.service.migration;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.util.List;
+import org.jdbi.v3.core.Handle;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.TestInstance;
+import org.openmetadata.service.OpenMetadataApplicationTest;
+import org.openmetadata.service.jdbi3.MigrationDAO;
+import org.openmetadata.service.jdbi3.locator.ConnectionType;
+import org.openmetadata.service.migration.utils.v1110.MigrationUtil;
+
+@TestInstance(TestInstance.Lifecycle.PER_CLASS)
+public class FlywayMigrationIntegrationTest extends OpenMetadataApplicationTest {
+
+  private static MigrationDAO migrationDAO;
+  private static ConnectionType connectionType;
+  private static MigrationUtil migrationUtil;
+
+  @BeforeAll
+  public static void setup() {
+    migrationDAO = jdbi.onDemand(MigrationDAO.class);
+    connectionType =
+        ConnectionType.from(APP.getConfiguration().getDataSourceFactory().getDriverClass());
+    migrationUtil = new MigrationUtil(connectionType, null);
+  }
+
+  @Test
+  public void testFlywayMigrationVersionsQuery() {
+    List<String> flywayVersions = migrationDAO.getFlywayMigrationVersions();
+    assertNotNull(flywayVersions, "Flyway migration versions list should not be null");
+
+    // Verify that versions are ordered correctly
+    if (flywayVersions.size() > 1) {
+      for (int i = 1; i < flywayVersions.size(); i++) {
+        String previous = flywayVersions.get(i - 1);
+        String current = flywayVersions.get(i);
+        assertTrue(
+            previous.compareTo(current) <= 0,
+            String.format(
+                "Flyway versions should be ordered: %s should be <= %s", previous, current));
+      }
+    }
+  }
+
+  @Test
+  public void testServerChangeLogFlywayRecords() {
+    List<MigrationDAO.ServerChangeLog> flywayRecords = migrationDAO.getFlywayMigrationRecords();
+
+    for (MigrationDAO.ServerChangeLog record : flywayRecords) {
+      // Verify that the record has the expected Flyway characteristics
+      assertNotNull(record.getVersion(), "Version should not be null");
+      assertNotNull(record.getMigrationFileName(), "Migration file name should not be null");
+      assertTrue(
+          record.getMigrationFileName().contains("flyway"),
+          "Migration file name should contain 'flyway'");
+
+      // Verify version format for Flyway migrations (should be 0.0.X format)
+      if (record.getMigrationFileName().contains("flyway")) {
+        assertTrue(
+            record.getVersion().matches("^0\\.0\\.\\d+$"),
+            String.format(
+                "Flyway version should match 0.0.X format, but was: %s", record.getVersion()));
+      }
+
+      // Verify that the file name includes the full path for proper identification
+      assertTrue(
+          record.getMigrationFileName().contains("bootstrap/sql/migrations/flyway")
+              || record.getMigrationFileName().contains("v0")
+              || record.getMigrationFileName().endsWith(".sql"),
+          "Migration file name should contain proper path or be a valid SQL file");
+    }
+  }
+
+  @Test
+  public void testMigrationDAOFlywayVersionsConsistency() {
+    List<String> flywayVersions = migrationDAO.getFlywayMigrationVersions();
+    List<MigrationDAO.ServerChangeLog> flywayRecords = migrationDAO.getFlywayMigrationRecords();
+
+    assertEquals(
+        flywayRecords.size(),
+        flywayVersions.size(),
+        "Flyway versions and records should have same count");
+
+    // Verify that each version from getFlywayMigrationVersions has a corresponding record
+    for (int i = 0; i < flywayVersions.size(); i++) {
+      String version = flywayVersions.get(i);
+      MigrationDAO.ServerChangeLog record = flywayRecords.get(i);
+      assertEquals(version, record.getVersion(), "Version should match between methods");
+    }
+  }
+
+  @Test
+  public void testFlywayMigrationFilePathFormat() {
+    List<MigrationDAO.ServerChangeLog> flywayRecords = migrationDAO.getFlywayMigrationRecords();
+
+    for (MigrationDAO.ServerChangeLog record : flywayRecords) {
+      String filePath = record.getMigrationFileName();
+
+      assertFalse(
+          filePath.endsWith("org.postgresql.Driver")
+              || filePath.endsWith("com.mysql.cj.jdbc.Driver"),
+          String.format("File path should not end with driver name: %s", filePath));
+
+      // Should contain proper Flyway path structure
+      assertTrue(
+          filePath.contains("flyway") || filePath.startsWith("v0"),
+          String.format("File path should contain 'flyway' or be a versioned file: %s", filePath));
+    }
+  }
+
+  @Test
+  public void testMigrationUtilFlywayDataCheck() {
+    try (Handle handle = jdbi.open()) {
+      boolean flywayTableExists =
+          migrationUtil.checkTableExists(handle, MigrationUtil.FLYWAY_TABLE_NAME);
+      assertFalse(flywayTableExists, "Flyway schema history table should not exist for new runs");
+
+      boolean serverChangeLogExists = migrationUtil.checkTableExists(handle, "SERVER_CHANGE_LOG");
+      assertTrue(serverChangeLogExists, "SERVER_CHANGE_LOG table should exist after migrations");
+    }
+  }
+
+  @Test
+  public void testVersionFormatValidation() {
+    List<String> flywayVersions = migrationDAO.getFlywayMigrationVersions();
+
+    for (String version : flywayVersions) {
+      assertTrue(
+          version.matches("^\\d+\\.\\d+\\.\\d+.*$"),
+          String.format("Version should follow semantic versioning format: %s", version));
+
+      if (version.startsWith("0.0.")) {
+        String[] parts = version.split("\\.");
+        assertTrue(
+            parts.length >= 3,
+            String.format("0.0.X version should have at least 3 parts: %s", version));
+
+        try {
+          Integer.parseInt(parts[2]);
+        } catch (NumberFormatException e) {
+          assertTrue(
+              parts[2].matches("\\d+.*"),
+              String.format("Third version part should start with a number: %s", version));
+        }
+      }
+    }
+  }
+}

openmetadata-service/src/test/java/org/openmetadata/service/util/MigrationWorkflowTest.java

@@ -28,7 +28,13 @@ public class MigrationWorkflowTest extends OpenMetadataApplicationTest {
     migrationWorkflow =
         spy(
             new MigrationWorkflow(
-                jdbi, "nativePath", ConnectionType.MYSQL, "extensionPath", null, false));
+                jdbi,
+                "nativePath",
+                ConnectionType.MYSQL,
+                "extensionPath",
+                "flywayPath",
+                null,
+                false));
 
     omMigrationList =
         List.of(
@@ -83,7 +89,8 @@ public class MigrationWorkflowTest extends OpenMetadataApplicationTest {
             "nativePath",
             ConnectionType.MYSQL,
             migrationWorkflow.getOpenMetadataApplicationConfig(),
-            "extensionPath");
+            "extensionPath",
+            "flywayPath");
 
     assertEquals(
         List.of("1.1.0", "1.1.0-collate", "1.2.0", "1.2.1", "1.2.2-collate"),

pom.xml

@@ -101,7 +101,6 @@
     <jdbi3.version>3.37.1</jdbi3.version>
     <commons-cli.version>1.9.0</commons-cli.version>
     <commons-io.version>2.17.0</commons-io.version>
-    <flyway.version>9.22.3</flyway.version>
     <redshift-jdbc.version>2.1.0.30</redshift-jdbc.version>
     <gson.version>2.11.0</gson.version>
     <mysql.connector.version>9.3.0</mysql.connector.version>
@@ -161,6 +160,7 @@
     <jakarta-el.version>5.0.0-M1</jakarta-el.version>
     <mcp-sdk.version>0.11.2</mcp-sdk.version>
     <lettuce.version>6.7.1.RELEASE</lettuce.version>
+    <flyway.version>9.22.3</flyway.version>
     <angus-mail.version>2.0.4</angus-mail.version>
   </properties>
 
@@ -359,17 +359,6 @@
         <artifactId>commons-io</artifactId>
         <version>${commons-io.version}</version>
       </dependency>
-      <dependency>
-        <groupId>org.flywaydb</groupId>
-        <artifactId>flyway-maven-plugin</artifactId>
-        <version>${flyway.version}</version>
-        <exclusions>
-          <exclusion>
-            <groupId>org.codehaus.plexus</groupId>
-            <artifactId>plexus-utils</artifactId>
-          </exclusion>
-        </exclusions>
-      </dependency>
       <dependency>
         <groupId>com.mysql</groupId>
         <artifactId>mysql-connector-j</artifactId>
@@ -381,11 +370,6 @@
           </exclusion>
         </exclusions>
       </dependency>
-      <dependency>
-        <groupId>org.flywaydb</groupId>
-        <artifactId>flyway-mysql</artifactId>
-        <version>${flyway.version}</version>
-      </dependency>
       <dependency>
         <groupId>org.postgresql</groupId>
         <artifactId>postgresql</artifactId>
@@ -676,6 +660,29 @@
         <artifactId>lettuce-core</artifactId>
         <version>${lettuce.version}</version>
       </dependency>
+
+      <!-- Flyway dependencies - only for SQL parsing, not migration management -->
+      <dependency>
+        <groupId>org.flywaydb</groupId>
+        <artifactId>flyway-core</artifactId>
+        <version>${flyway.version}</version>
+      </dependency>
+      <dependency>
+        <groupId>org.flywaydb</groupId>
+        <artifactId>flyway-maven-plugin</artifactId>
+        <version>${flyway.version}</version>
+        <exclusions>
+          <exclusion>
+            <groupId>org.codehaus.plexus</groupId>
+            <artifactId>plexus-utils</artifactId>
+          </exclusion>
+        </exclusions>
+      </dependency>
+      <dependency>
+        <groupId>org.flywaydb</groupId>
+        <artifactId>flyway-mysql</artifactId>
+        <version>${flyway.version}</version>
+      </dependency>
     </dependencies>
   </dependencyManagement>