Exception encountered during spring context initialization BeanCreationException: Error creating bean with name 'flywayInitializer'

Receiving the below error on running integration tests after migrating spring boot and it's related packages(including spring-boot-starter-test) from 2.2.4.RELEASE to 3.1.1.

Error creating bean with name flywayInitializer defined in class path resource
[com/freit/medicalservice/config/CustomFlywayConfiguration.class]

@Configuration
class CustomFlywayConfiguration extends FlywayAutoConfiguration.FlywayConfiguration {
    
    @DependsOn("springContext")
    public FlywayMigrationInitializer flywayInitializer(Flyway flyway) {
       return super.flywayInitializer(flyway, null);
    }
}

The error is occuring because SpringContext is null, which could be the result of some miss configuration of flyway or annotations being used in tests.

Flywayconfig in .properties file
spring.flyway.locations=classpath:db/migration,classpath:/db/test_data,classpath:/db_scripts,com/freit/medicalservice/common/migrations
spring.flyway.enabled=true
spring.flyway.baseline-on-migrate=true
spring.flyway.validate-on-migrate=true

Annotations being used in tests files:
@SpringBootTest
@AutoConfigureMockMvc
@Transactional
@ActiveProfileTest

<br>

12:33:50.412 [main] ERROR o.f.core.internal.command.DbMigrate - org.flywaydb.core.internal.logging.slf4j.Slf4jLog.error:45 - {  } - Migration of schema `medical_service` to version "1.1.13 - Rename Logo Files To Header Files" failed! Please restore backups and roll back database and code!
12:33:50.458 [main] WARN  o.s.w.c.s.GenericWebApplicationContext - org.springframework.context.support.AbstractApplicationContext.refresh:616 - {  } - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'flywayInitializer' defined in class path resource [com/freit/medicalservice/config/CustomFlywayConfiguration.class]: Migration failed !
12:33:50.459 [main] INFO  com.zaxxer.hikari.HikariDataSource - com.zaxxer.hikari.HikariDataSource.close:350 - {  } - HikariPool-1 - Shutdown initiated...
12:33:50.474 [main] INFO  com.zaxxer.hikari.HikariDataSource - com.zaxxer.hikari.HikariDataSource.close:352 - {  } - HikariPool-1 - Shutdown completed.
12:33:50.513 [main] INFO  o.s.b.a.l.ConditionEvaluationReportLogger - org.springframework.boot.autoconfigure.logging.ConditionEvaluationReportLogger.logMessage:82 - {  } - 
Error starting ApplicationContext. To display the condition evaluation report re-run your application with 'debug' enabled.
12:33:50.556 [main] ERROR o.s.boot.SpringApplication - org.springframework.boot.SpringApplication.reportFailure:824 - {  } - Application run failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'flywayInitializer' defined in class path resource [com/freit/medicalservice/config/CustomFlywayConfiguration.class]: Migration failed !
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1770)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:598)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:520)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:326)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:324)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:200)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:313)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:200)
at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1154)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:931)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:608)
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:734)
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:436)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:312)
at org.springframework.boot.test.context.SpringBootContextLoader.lambda$loadContext$3(SpringBootContextLoader.java:137)
at org.springframework.util.function.ThrowingSupplier.get(ThrowingSupplier.java:58)
at org.springframework.util.function.ThrowingSupplier.get(ThrowingSupplier.java:46)
at org.springframework.boot.SpringApplication.withHook(SpringApplication.java:1406)
at org.springframework.boot.test.context.SpringBootContextLoader$ContextLoaderHook.run(SpringBootContextLoader.java:545)
at org.springframework.boot.test.context.SpringBootContextLoader.loadContext(SpringBootContextLoader.java:137)
at org.springframework.boot.test.context.SpringBootContextLoader.loadContext(SpringBootContextLoader.java:108)
at org.springframework.test.context.cache.DefaultCacheAwareContextLoaderDelegate.loadContextInternal(DefaultCacheAwareContextLoaderDelegate.java:187)
at org.springframework.test.context.cache.DefaultCacheAwareContextLoaderDelegate.loadContext(DefaultCacheAwareContextLoaderDelegate.java:119)
at org.springframework.test.context.support.DefaultTestContext.getApplicationContext(DefaultTestContext.java:127)
at org.springframework.test.context.web.ServletTestExecutionListener.setUpRequestContextIfNecessary(ServletTestExecutionListener.java:191)
at org.springframework.test.context.web.ServletTestExecutionListener.prepareTestInstance(ServletTestExecutionListener.java:130)
at org.springframework.test.context.TestContextManager.prepareTestInstance(TestContextManager.java:241)
at org.springframework.test.context.junit.jupiter.SpringExtension.postProcessTestInstance(SpringExtension.java:138)
at org.junit.jupiter.engine.descriptor.ClassBasedTestDescriptor.lambda$invokeTestInstancePostProcessors$10(ClassBasedTestDescriptor.java:377)
at org.junit.jupiter.engine.descriptor.ClassBasedTestDescriptor.executeAndMaskThrowable(ClassBasedTestDescriptor.java:382)
at org.junit.jupiter.engine.descriptor.ClassBasedTestDescriptor.lambda$invokeTestInstancePostProcessors$11(ClassBasedTestDescriptor.java:377)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)
at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1625)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
at java.base/java.util.stream.StreamSpliterators$WrappingSpliterator.forEachRemaining(StreamSpliterators.java:310)
at java.base/java.util.stream.Streams$ConcatSpliterator.forEachRemaining(Streams.java:735)
at java.base/java.util.stream.Streams$ConcatSpliterator.forEachRemaining(Streams.java:734)
at java.base/java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:762)
at org.junit.jupiter.engine.descriptor.ClassBasedTestDescriptor.invokeTestInstancePostProcessors(ClassBasedTestDescriptor.java:376)
at org.junit.jupiter.engine.descriptor.ClassBasedTestDescriptor.lambda$instantiateAndPostProcessTestInstance$6(ClassBasedTestDescriptor.java:289)
at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
at org.junit.jupiter.engine.descriptor.ClassBasedTestDescriptor.instantiateAndPostProcessTestInstance(ClassBasedTestDescriptor.java:288)
at org.junit.jupiter.engine.descriptor.ClassBasedTestDescriptor.lambda$testInstancesProvider$4(ClassBasedTestDescriptor.java:278)
at java.base/java.util.Optional.orElseGet(Optional.java:364)
at org.junit.jupiter.engine.descriptor.ClassBasedTestDescriptor.lambda$testInstancesProvider$5(ClassBasedTestDescriptor.java:277)
at org.junit.jupiter.engine.execution.TestInstancesProvider.getTestInstances(TestInstancesProvider.java:31)
at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$prepare$0(TestMethodTestDescriptor.java:105)
at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.prepare(TestMethodTestDescriptor.java:104)
at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.prepare(TestMethodTestDescriptor.java:68)
at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$prepare$2(NodeTestTask.java:123)
at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
at org.junit.platform.engine.support.hierarchical.NodeTestTask.prepare(NodeTestTask.java:123)
at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:90)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41)
at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155)
at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141)
at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137)
at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139)
at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138)
at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41)
at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155)
at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141)
at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137)
at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139)
at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138)
at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95)
at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35)
at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57)
at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54)
at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:147)
at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:127)
at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:90)
at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:55)
at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:102)
at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:54)
at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:114)
at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:86)
at org.junit.platform.launcher.core.DefaultLauncherSession$DelegatingLauncher.execute(DefaultLauncherSession.java:86)
at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:53)
at com.intellij.junit5.JUnit5IdeaTestRunner.startRunnerWithArgs(JUnit5IdeaTestRunner.java:57)
at com.intellij.rt.junit.IdeaTestRunner$Repeater$1.execute(IdeaTestRunner.java:38)
at com.intellij.rt.execution.junit.TestsRepeater.repeat(TestsRepeater.java:11)
at com.intellij.rt.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:35)
at com.intellij.rt.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:232)
at com.intellij.rt.junit.JUnitStarter.main(JUnitStarter.java:55)
Caused by: org.flywaydb.core.internal.command.DbMigrate$FlywayMigrateException: Migration failed !
at org.flywaydb.core.internal.command.DbMigrate.doMigrateGroup(DbMigrate.java:384)
at org.flywaydb.core.internal.command.DbMigrate.lambda$applyMigrations$1(DbMigrate.java:274)
at org.flywaydb.core.internal.jdbc.TransactionalExecutionTemplate.execute(TransactionalExecutionTemplate.java:55)
at org.flywaydb.core.internal.command.DbMigrate.applyMigrations(DbMigrate.java:273)
at org.flywaydb.core.internal.command.DbMigrate.migrateGroup(DbMigrate.java:246)
at org.flywaydb.core.internal.command.DbMigrate.lambda$migrateAll$0(DbMigrate.java:141)
at org.flywaydb.database.mysql.MySQLNamedLockTemplate.execute(MySQLNamedLockTemplate.java:58)
at org.flywaydb.database.mysql.MySQLConnection.lock(MySQLConnection.java:152)
at org.flywaydb.core.internal.schemahistory.JdbcTableSchemaHistory.lock(JdbcTableSchemaHistory.java:143)
at org.flywaydb.core.internal.command.DbMigrate.migrateAll(DbMigrate.java:141)
at org.flywaydb.core.internal.command.DbMigrate.migrate(DbMigrate.java:98)
at org.flywaydb.core.Flyway.lambda$migrate$0(Flyway.java:176)
at org.flywaydb.core.FlywayExecutor.execute(FlywayExecutor.java:204)
at org.flywaydb.core.Flyway.migrate(Flyway.java:128)
at org.springframework.boot.autoconfigure.flyway.FlywayMigrationInitializer.afterPropertiesSet(FlywayMigrationInitializer.java:66)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1816)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1766)
... 95 common frames omitted
Caused by: org.flywaydb.core.api.FlywayException: Migration failed !
at org.flywaydb.core.internal.resolver.java.JavaMigrationExecutor.executeOnce(JavaMigrationExecutor.java:76)
at org.flywaydb.core.internal.resolver.java.JavaMigrationExecutor.lambda$execute$0(JavaMigrationExecutor.java:54)
at org.flywaydb.core.internal.database.DefaultExecutionStrategy.execute(DefaultExecutionStrategy.java:27)
at org.flywaydb.core.internal.resolver.java.JavaMigrationExecutor.execute(JavaMigrationExecutor.java:53)
at org.flywaydb.core.internal.command.DbMigrate.doMigrateGroup(DbMigrate.java:376)
... 111 common frames omitted
Caused by: java.lang.NullPointerException: Cannot invoke "org.springframework.context.ApplicationContext.getBean(java.lang.Class)" because "com.freit.medicalservice.config.SpringContext.context" is null
at com.freit.medicalservice.config.SpringContext.getBean(SpringContext.java:20)
at com.freit.medicalservice.common.migrations.V1_1_13__Rename_Logo_Files_To_Header_Files.migrate(V1_1_13__Rename_Logo_Files_To_Header_Files.java:30)
at org.flywaydb.core.internal.resolver.java.JavaMigrationExecutor.executeOnce(JavaMigrationExecutor.java:62)
... 115 common frames omitted
============================
CONDITIONS EVALUATION REPORT
============================
Positive matches:
-----------------
None
Negative matches:
-----------------
None
Exclusions:
-----------
None
Unconditional classes:
----------------------
None

I think you need to remove CustomFlywayConfiguration completely, because as far as I understand in declares dependency on com.freit.medicalservice.config.SpringContext which is your custom bean, but FlywayMigrationInitializer is an infrastructural one. Usually infrastructural beans mustn't depend on custom ones.

If you still need custom initialization order then pat attention, that the problem is about particular field com.freit.medicalservice.config.SpringContext.context and not about the bean itself. Maybe you have Objects.requireNonNull() in constructor of com.freit.medicalservice.config.SpringContext? Try to debug creation of bean com.freit.medicalservice.config.SpringContext.

Just added @Bean("flywayInitializer") over flywayInitializer() function;

@Configuration
class CustomFlywayConfiguration extends FlywayAutoConfiguration.FlywayConfiguration {
@DependsOn("springContext")
@Bean("flywayInitializer")
public FlywayMigrationInitializer flywayInitializer(Flyway flyway) {
return super.flywayInitializer(flyway, null);
}
}