Error when running application NoClassDef jakarta/persistance/EntityManager

[dgeiselmanMOO]

Running Grails 6.2.0, JDK 11, Springboot 2.7.18, Hibernate core 6.4.18, hibernate5 8.1.0, hikari is involved, Gradle 7.6.2

Got through an error with MVCC by upgrading to Hibernate core 6.4.18.Final and now I'm getting an error about jakarta/persistance/EntityManger is not found. What library or setting am I missing?

2024-05-02 15:47:43,927 [main] [] ERROR org.springframework.boot.SpringApplication | parent-span: | trace: | span: |: Application run failed
java.lang.IllegalStateException: Failed to introspect Class [org.grails.orm.hibernate.HibernateDatastore] from ClassLoader [jdk.internal.loader.ClassLoaders$AppClassLoader@5c29bfd]
at org.springframework.util.ReflectionUtils.getDeclaredMethods(ReflectionUtils.java:485)
at org.springframework.util.ReflectionUtils.doWithMethods(ReflectionUtils.java:361)
at org.springframework.util.ReflectionUtils.getUniqueDeclaredMethods(ReflectionUtils.java:418)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.lambda$getTypeForFactoryMethod$2(AbstractAutowireCapableBeanFactory.java:765)
at java.base/java.util.concurrent.ConcurrentHashMap.computeIfAbsent(ConcurrentHashMap.java:1705)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.getTypeForFactoryMethod(AbstractAutowireCapableBeanFactory.java:764)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.determineTargetType(AbstractAutowireCapableBeanFactory.java:703)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.predictBeanType(AbstractAutowireCapableBeanFactory.java:674)
at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:1685)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doGetBeanNamesForType(DefaultListableBeanFactory.java:570)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeanNamesForType(DefaultListableBeanFactory.java:542)
at org.springframework.context.support.PostProcessorRegistrationDelegate.invokeBeanFactoryPostProcessors(PostProcessorRegistrationDelegate.java:132)
at org.springframework.context.support.AbstractApplicationContext.invokeBeanFactoryPostProcessors(AbstractApplicationContext.java:756)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:573)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:147)
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:732)
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:409)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:308)
at grails.boot.GrailsApp.run(GrailsApp.groovy:99)
at grails.boot.GrailsApp.run(GrailsApp.groovy:458)
at grails.boot.GrailsApp.run(GrailsApp.groovy:445)
at qwr.Application.main(Application.groovy:11)
Caused by: java.lang.NoClassDefFoundError: jakarta/persistence/EntityManager
at java.base/java.lang.ClassLoader.defineClass1(Native Method)
at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1016)
at java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:174)
at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:800)
at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:698)
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:621)
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:579)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
at java.base/java.lang.Class.getDeclaredMethods0(Native Method)
at java.base/java.lang.Class.privateGetDeclaredMethods(Class.java:3166)
at java.base/java.lang.Class.getDeclaredMethods(Class.java:2309)
at org.springframework.util.ReflectionUtils.getDeclaredMethods(ReflectionUtils.java:467)
... 21 common frames omitted
Caused by: java.lang.ClassNotFoundException: jakarta.persistence.EntityManager
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
... 34 common frames omitted

[matrei]

Grails 6 is not compatible with Hibernate 6.

[dgeiselmanMOO]

Ok, how do I get around this error from hibernate 5.6.15.Final? This is what I was getting before Hibernate 6.4.18

2024-05-03 07:35:01,564 [main] [] ERROR org.apache.tomcat.jdbc.pool.ConnectionPool | parent-span: | trace: | span: |: Unable to create initial connections of pool.
org.h2.jdbc.JdbcSQLNonTransientConnectionException: Unsupported connection setting "MVCC" [90113-224]

[matrei]

Can you show your dataSource.url config? The MVCC connection parameter is no longer valid for H2 v2.

[dgeiselmanMOO]

jdbc:sqlserver://WN4747.corp.mutualofomaha.com;databaseName=QUALITY_WORK_REVIEW

[dgeiselmanMOO]

MVCC is not in my code at all.

[matrei]

Ok, but even if you say that "hikari is involved", you have a tomcat jdbc connection pool trying to create a H2 jdbc connection with the MVCC parameter. I cannot say why with the information you have given.

[dgeiselmanMOO]

Any of this help?

Here are the yaml settings

datasource:
    type: com.zaxxer.hikari.HikariDataSource
    driver-class-name: com.microsoft.sqlserver.jdbc.SQLServerDriver
    url: jdbc:sqlserver://WN4747.corp.mutualofomaha.com;databaseName=QUALITY_WORK_REVIEW
    username: user
    password: pass
    hikari:
        driver-class-name: com.microsoft.sqlserver.jdbc.SQLServerDriver
        data-source-class-name: com.microsoft.sqlserver.jdbc.SQLServerDataSource
        minimum-idle: 5
        idle-timeout: 600000
        maximum-pool-size: 10
        auto-commit: true
        pool-name: HikariCorePool
        max-lifetime: 1800000
        connection-timeout: 30000

hibernate:
default_schema: dbo
enable_lazy_load_no_trans: true
dialect: org.hibernate.dialect.SQLServerDialect
driverClassName: org.h2.Driver
cache:
use_second_level_cache: true
use_query_cache: false
region.factory_class: org.hibernate.cache.ehcache.EhCacheRegionFactory
legacy_limit_handler: true

gradle
configurations {
all*.with {
exclude group: 'log4j'
exclude module: 'xml-apis'
exclude module: 'bcprov-jdk15on'
exclude module: 'bcprov-jdk14'
}
all {
resolutionStrategy {
force 'com.h2database:h2:2.2.224'
force 'io.micronaut.sql:micronaut-sql-bom:5.6.0'
force 'io.micronaut:micronaut-bom:3.10.4'
force 'org.grails:grails-datastore-gorm-hibernate5:8.1.0'
force 'io.micronaut.spring:micronaut-spring-context:5.6.0'
force 'io.micronaut.cache:micronaut-cache-core:4.3.0'
force 'org.apache.tomcat:tomcat-jdbc:11.0.0-M19'

    }
}

}

dependencies {
runtimeOnly "com.bertramlabs.plugins:asset-pipeline-grails:4.3.0"
compileOnly "io.micronaut:micronaut-inject-groovy"
//developmentOnly("org.springframework.boot:spring-boot-devtools")
console "org.grails:grails-console"
implementation "com.mutualofomaha:enterprise-ldap-service-client:4.0.1"

// default dependencies for web app
implementation 'org.springframework.boot:spring-boot-starter'
implementation 'org.springframework.boot:spring-boot-starter-logging'
implementation 'org.springframework.boot:spring-boot-starter-actuator'
implementation 'org.springframework.boot:spring-boot-autoconfigure'
implementation 'org.springframework.boot:spring-boot-starter-data-jpa'
implementation 'org.springframework.boot:spring-boot-starter-web'
implementation "org.springframework.boot:spring-boot-starter-tomcat"

implementation "org.springframework.boot:spring-boot-starter-validation"
implementation 'org.springframework.ldap:spring-ldap-core'
implementation 'com.okta.spring:okta-spring-boot-starter:+'
api 'com.okta.spring:okta-spring-boot-starter:3.0.6'
implementation 'org.grails.plugins:spring-security-oauth2:2.0.0-RC1'
implementation 'com.okta.spring:okta-spring-security-oauth2:3.0.2'
implementation 'com.okta.sdk:okta-sdk-api:8.2.3'
runtimeOnly 'com.okta.sdk:okta-sdk-impl:8.2.3'
runtimeOnly 'com.okta.sdk:okta-sdk-httpclient:8.2.3'

implementation 'org.grails:grails-dependencies'
implementation 'org.grails:grails-web-boot'
implementation 'org.grails.plugins:spring-security-core:5.2.0'
implementation 'org.grails.plugins:spring-security-ldap:4.0.0.M1'
implementation "org.grails:grails-core"
implementation "org.grails:grails-logging"
implementation "org.grails.plugins:scaffolding"
implementation "org.grails.plugins:async"
implementation "org.grails:grails-plugin-rest"
implementation "org.grails:grails-plugin-datasource"
implementation "org.grails:grails-plugin-databinding"
implementation "org.grails:grails-plugin-i18n"
implementation "org.grails:grails-plugin-services"
implementation "org.grails:grails-plugin-url-mappings"
implementation 'org.grails:grails-datastore-gorm-hibernate5:8.1.0'
implementation "org.grails:grails-plugin-interceptors"
implementation ("org.grails.plugins:cache:5.0.1") {
    exclude group: "gradle.plugin.com.github.erdi.webdriver-binaries", module: "webdriver-binaries-gradle-plugin"
}
implementation "org.grails.plugins:export:2.0.0"
implementation "org.grails.plugins:wslite:0.7.2.0"
implementation "org.grails.plugins:events"
implementation "org.grails.plugins:gsp"
profile "org.grails.profiles:web"
testImplementation "org.grails:grails-gorm-testing-support"
testImplementation "org.grails.plugins:geb"
testImplementation "org.grails:grails-web-testing-support"
implementation "org.grails:grails-datastore-test-support:1.0.2-grails-2.4"
implementation "org.grails.plugins:underscore:1.5.2"
implementation "org.grails.plugins:remote-pagination:0.4.8"
implementation "org.grails.plugins:build-test-data:2.4.0"
implementation "org.grails.plugins:ckeditor:4.5.4.1"
implementation "org.grails.plugins:joda-time:1.5"
implementation "org.grails.plugins:quartz:1.0.2"
implementation "org.grails.plugins:csv:0.3.1"
implementation "org.grails.plugins:resources:1.2.14"
implementation "org.grails.plugins:twitter-bootstrap:3.3.5"
implementation "org.grails.plugins:jquery:1.11.1"
implementation "org.grails.plugins:fields:3.0.0.RC1"
implementation "org.grails.plugins:greenmail:1.3.4"
implementation "org.grails.plugins:mail:3.0.0"
implementation 'org.grails.plugins:filterpane:2.4.4'
implementation 'com.zaxxer:HikariCP:5.1.0'

implementation 'org.grails.plugins:hibernate5:8.1.0'
implementation 'org.hibernate:hibernate-core:5.6.15.Final'
implementation "org.hibernate:hibernate-ehcache:5.6.15.Final"
implementation "org.hibernate:hibernate-hikaricp:5.6.15.Final"

implementation "org.grails:gorm-hibernate5-spring-boot:8.1.0"
implementation 'com.github.javaparser:javaparser-core:3.25.2'

implementation 'org.xhtmlrenderer:flying-saucer-pdf:9.5.1'
implementation 'org.xhtmlrenderer:flying-saucer-core:9.5.1'
implementation 'org.grails.plugins:rendering:2.0.3'
implementation 'org.apache.commons:commons-lang3:3.14.0'

compileOnly 'org.springframework:spring-test:5.3.34'
runtimeOnly 'org.grails.plugins:ajax-tags:1.0.0'

testImplementation 'junit:junit:4.13.2'

implementation 'com.mutualofomaha:mutualofomahautilities:6.0.0'
implementation 'com.mutualofomaha.hrp:HRDataServiceClient:2.0.3'
implementation 'com.jscape:sftp:9.0.0'
implementation 'com.microsoft.sqlserver:mssql-jdbc:12.6.0.jre11'
runtimeOnly "com.h2database:h2"
runtimeOnly "org.apache.tomcat:tomcat-jdbc"
implementation group: 'com.googlecode.concurrentlinkedhashmap', name: 'concurrentlinkedhashmap-lru', version: '1.4.2'

implementation 'org.apache.directory.server:apacheds-core:1.5.4'
implementation 'org.apache.directory.server:apacheds-protocol-ldap:1.5.4'
implementation 'org.apache.directory.shared:shared-ldap:0.9.12'
implementation 'org.codehaus.groovy:groovy-dateutil:3.0.14'

implementation "org.apache.httpcomponents:httpclient:+"
implementation 'com.mutualofomaha.afi:cyberark-client:2.0.+'

testImplementation "io.micronaut:micronaut-inject-groovy"
testImplementation "org.seleniumhq.selenium:selenium-remote-driver"
testImplementation "org.seleniumhq.selenium:selenium-api"
testImplementation "org.seleniumhq.selenium:selenium-support"
testRuntimeOnly "org.seleniumhq.selenium:selenium-chrome-driver"
testRuntimeOnly "org.seleniumhq.selenium:selenium-firefox-driver"

}

[dgeiselmanMOO]

Commenting out runtimeOnly "org.apache.tomcat:tomcat-jdbc" gives this error

2024-05-03 09:40:03,409 [main] [] ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper | parent-span: | trace: | span: |: Unsupported connection setting "MVCC" [90113-224]
2024-05-03 09:40:07,884 [main] [] ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper | parent-span: | trace: | span: |: Unsupported connection setting "MVCC" [90113-224]
2024-05-03 09:40:07,885 [main] [] ERROR org.springframework.boot.web.embedded.tomcat.TomcatStarter | parent-span: | trace: | span: |: Error starting Tomcat context. Exception: org.springframework.beans.factory.BeanCreationException. Message: Error creating bean with name 'authenticationProcessingFilterDeregistrationBean': Cannot resolve reference to bean 'authenticationProcessingFilter' while setting bean property 'filter'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'authenticationProcessingFilter': Cannot resolve reference to bean 'authenticationManager' while setting bean property 'authenticationManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'authenticationManager': Cannot resolve reference to bean 'daoAuthenticationProvider' while setting constructor argument with key [0]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'daoAuthenticationProvider': Cannot resolve reference to bean 'userDetailsService' while setting bean property 'userDetailsService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'userDetailsService': Unsatisfied dependency expressed through method 'setTargetDatastore' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateDatastore': Bean instantiation via constructor failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.grails.orm.hibernate.HibernateDatastore]: Constructor threw exception; nested exception is org.hibernate.exception.JDBCConnectionException: Unable to check JDBC Connection auto-commit in preparation for DDL execution
2024-05-03 09:40:07,936 [main] [] WARN org.springframework.boot.web.servlet.context.AnnotationConfigServletWebServerApplicationContext | parent-span: | trace: | span: |: Exception encountered during context initialization - cancelling refresh attempt: org.springframework.context.ApplicationContextException: Unable to start web server; nested exception is org.springframework.boot.web.server.WebServerException: Unable to start embedded Tomcat
2024-05-03 09:40:08,017 [main] [] ERROR org.springframework.boot.SpringApplication | parent-span: | trace: | span: |: Application run failed

[matrei]

It looks like your using the Spring way to declare a datasource (not the Grails way).
Then you also configure hibernate with dialect: org.hibernate.dialect.SQLServerDialect and driverClassName: org.h2.Driver.

I would start with a new project and setup the database connection according to the Grails configuration docs to try and get it working. There is an example of using HikariCP there. Then map that over to your existing application.