DB Connection with MySQL via Hibernate on Embedded Glassfish

Question

Hi! I have a problem to connect my MySQL Database via Hibernate/ JPA2 on a Embedded Glassfish.

My Environment:

• Maven 2
• Embedded Glassfish (integrated via Maven Plugin)
• Eclipse + M2Plugin
• Hibernate 3.5.6
• MySQL (@localhost) (runs and can be connected without container via Hibernate Sessionfactory)

Here is my Exception Stacktrace during Embedded Glassfish bootstrap

27.10.2010 16:22:14 com.sun.enterprise.v3.server.AppServerStartup run
INFO: GlassFish v3 (74.2) startup time : Embedded(229ms) startup services(154ms) total(383ms)
27.10.2010 16:22:14 com.sun.enterprise.transaction.JavaEETransactionManagerSimplified initDelegates
INFO: Using com.sun.enterprise.transaction.jts.JavaEETransactionManagerJTSDelegate as the delegate
27.10.2010 16:22:14 org.glassfish.admin.mbeanserver.JMXStartupService$JMXConnectorsStarterThread run
INFO: JMXStartupService: JMXConnector system is disabled, skipping.
27.10.2010 16:22:14 AppServerStartup run
INFO: [Thread[GlassFish Kernel Main Thread,5,main]] started
27.10.2010 16:22:14 org.hibernate.validator.util.Version 
INFO: Hibernate Validator null
27.10.2010 16:22:14 org.hibernate.validator.engine.resolver.DefaultTraversableResolver detectJPA
INFO: Instantiated an instance of org.hibernate.validator.engine.resolver.JPATraversableResolver.
27.10.2010 16:22:14 com.sun.enterprise.v3.services.impl.GrizzlyProxy$2$1 onReady
INFO: Grizzly Framework 1.9.18-k started in: 62ms listening on port 8090
27.10.2010 16:22:17 com.sun.enterprise.security.SecurityLifecycle 
INFO: security.secmgroff
27.10.2010 16:22:17 com.sun.enterprise.security.ssl.SSLUtils checkCertificateDates
SCHWERWIEGEND: java_security.expired_certificate
27.10.2010 16:22:17 com.sun.enterprise.security.SecurityLifecycle onInitialization
INFO: Security startup service called
27.10.2010 16:22:17 com.sun.enterprise.security.PolicyLoader loadPolicy
INFO: policy.loading
27.10.2010 16:22:17 com.sun.enterprise.security.auth.realm.Realm doInstantiate
INFO: Realm admin-realm of classtype com.sun.enterprise.security.auth.realm.file.FileRealm successfully created.
27.10.2010 16:22:17 com.sun.enterprise.security.auth.realm.Realm doInstantiate
INFO: Realm file of classtype com.sun.enterprise.security.auth.realm.file.FileRealm successfully created.
27.10.2010 16:22:17 com.sun.enterprise.security.auth.realm.Realm doInstantiate
INFO: Realm certificate of classtype com.sun.enterprise.security.auth.realm.certificate.CertificateRealm successfully created.
27.10.2010 16:22:17 com.sun.enterprise.security.SecurityLifecycle onInitialization
INFO: Security service(s) started successfully....
27.10.2010 16:22:18 com.sun.common.util.logging.LoggingConfigImpl openPropFile
INFO: Cannot read logging.properties file. 
27.10.2010 16:22:18 com.sun.enterprise.web.WebContainer createHttpListener
INFO: Created HTTP listener embedded-listener on port 8090
27.10.2010 16:22:18 com.sun.enterprise.web.WebContainer createHosts
INFO: Created virtual server server
27.10.2010 16:22:18 com.sun.enterprise.web.WebContainer loadSystemDefaultWebModules
INFO: Virtual server server loaded system default web module
27.10.2010 16:22:20 org.hibernate.validator.engine.resolver.DefaultTraversableResolver detectJPA
INFO: Instantiated an instance of org.hibernate.validator.engine.resolver.JPATraversableResolver.
27.10.2010 16:22:20 org.hibernate.cfg.annotations.Version 
INFO: Hibernate Annotations 3.5.6-Final
27.10.2010 16:22:20 org.hibernate.cfg.Environment 
INFO: Hibernate 3.5.6-Final
27.10.2010 16:22:20 org.hibernate.cfg.Environment 
INFO: hibernate.properties not found
27.10.2010 16:22:20 org.hibernate.cfg.Environment buildBytecodeProvider
INFO: Bytecode provider name : javassist
27.10.2010 16:22:20 org.hibernate.cfg.Environment 
INFO: using JDK 1.4 java.sql.Timestamp handling
27.10.2010 16:22:20 org.hibernate.annotations.common.Version 
INFO: Hibernate Commons Annotations 3.2.0.Final
27.10.2010 16:22:20 org.hibernate.ejb.Version 
INFO: Hibernate EntityManager 3.5.6-Final
27.10.2010 16:22:20 org.hibernate.ejb.Ejb3Configuration configure
INFO: Processing PersistenceUnitInfo [
    name: workbench
    ...]
27.10.2010 16:22:21 org.hibernate.ejb.Ejb3Configuration prepareProperties
WARNUNG: Defining hibernate.transaction.flush_before_completion=true ignored in HEM
27.10.2010 16:22:21 org.hibernate.cfg.AnnotationBinder bindClass
INFO: Binding entity from annotated class: com.pentasys.workbench.db.model.User
27.10.2010 16:22:21 org.hibernate.cfg.annotations.EntityBinder bindTable
INFO: Bind entity com.pentasys.workbench.db.model.User on table User
27.10.2010 16:22:21 org.hibernate.cfg.AnnotationBinder bindClass
INFO: Binding entity from annotated class: com.pentasys.workbench.db.model.base.ATask
27.10.2010 16:22:21 org.hibernate.cfg.annotations.EntityBinder bindTable
INFO: Bind entity com.pentasys.workbench.db.model.base.ATask on table JOB
27.10.2010 16:22:21 org.hibernate.cfg.AnnotationBinder bindClass
INFO: Binding entity from annotated class: com.pentasys.workbench.db.model.Job
27.10.2010 16:22:21 org.hibernate.cfg.AnnotationBinder bindClass
INFO: Binding entity from annotated class: com.pentasys.workbench.db.model.Comment
27.10.2010 16:22:21 org.hibernate.cfg.annotations.EntityBinder bindTable
INFO: Bind entity com.pentasys.workbench.db.model.Comment on table COMMENT
27.10.2010 16:22:21 org.hibernate.cfg.AnnotationBinder bindClass
INFO: Binding entity from annotated class: com.pentasys.workbench.db.model.Workflow
27.10.2010 16:22:21 org.hibernate.cfg.annotations.CollectionBinder bindOneToManySecondPass
INFO: Mapping collection: com.pentasys.workbench.db.model.base.ATask.childTasks -> JOB
27.10.2010 16:22:21 org.hibernate.cfg.AnnotationConfiguration applyHibernateValidatorLegacyConstraintsOnDDL
INFO: Hibernate Validator not found: ignoring
27.10.2010 16:22:21 org.hibernate.validator.engine.resolver.DefaultTraversableResolver detectJPA
INFO: Instantiated an instance of org.hibernate.validator.engine.resolver.JPATraversableResolver.
27.10.2010 16:22:21 org.hibernate.validator.engine.resolver.DefaultTraversableResolver detectJPA
INFO: Instantiated an instance of org.hibernate.validator.engine.resolver.JPATraversableResolver.
27.10.2010 16:22:21 org.hibernate.cfg.search.HibernateSearchEventListenerRegister enableHibernateSearch
INFO: Unable to find org.hibernate.search.event.FullTextIndexEventListener on the classpath. Hibernate Search is not enabled.
27.10.2010 16:22:21 org.hibernate.validator.engine.resolver.DefaultTraversableResolver detectJPA
INFO: Instantiated an instance of org.hibernate.validator.engine.resolver.JPATraversableResolver.
27.10.2010 16:22:21 org.hibernate.connection.ConnectionProviderFactory initializeConnectionProviderFromConfig
INFO: Initializing connection provider: org.hibernate.ejb.connection.InjectedDataSourceConnectionProvider
27.10.2010 16:22:21 org.hibernate.ejb.connection.InjectedDataSourceConnectionProvider configure
INFO: Using provided datasource
27.10.2010 16:22:21 com.sun.enterprise.resource.allocator.LocalTxConnectorAllocator createResource
WARNUNG: poolmgr.create_resource_error
27.10.2010 16:22:21 com.sun.enterprise.connectors.ConnectionManagerImpl internalGetConnection
WARNUNG: poolmgr.get_connection_failure
27.10.2010 16:22:21 com.sun.gjc.spi.base.DataSource getConnection
WARNUNG: jdbc.exc_get_conn
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
WARNUNG: Could not obtain connection to query metadata
java.sql.SQLException: Error in allocating a connection. Cause: Connection could not be allocated because: Unknown database 'workbench'
    at com.sun.gjc.spi.base.DataSource.getConnection(DataSource.java:133)
    at org.hibernate.ejb.connection.InjectedDataSourceConnectionProvider.getConnection(InjectedDataSourceConnectionProvider.java:68)
    at org.hibernate.cfg.SettingsFactory.buildSettings(SettingsFactory.java:114)
    at org.hibernate.cfg.Configuration.buildSettingsInternal(Configuration.java:2163)
    at org.hibernate.cfg.Configuration.buildSettings(Configuration.java:2159)
    at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1383)
    at org.hibernate.cfg.AnnotationConfiguration.buildSessionFactory(AnnotationConfiguration.java:954)
    at org.hibernate.ejb.Ejb3Configuration.buildEntityManagerFactory(Ejb3Configuration.java:892)
    at org.hibernate.ejb.HibernatePersistence.createContainerEntityManagerFactory(HibernatePersistence.java:74)
    at org.glassfish.persistence.jpa.PersistenceUnitLoader.loadPU(PersistenceUnitLoader.java:181)
    at org.glassfish.persistence.jpa.PersistenceUnitLoader.(PersistenceUnitLoader.java:96)
    at org.glassfish.persistence.jpa.JPADeployer.prepare(JPADeployer.java:121)
    at com.sun.enterprise.v3.server.ApplicationLifecycle.prepareModule(ApplicationLifecycle.java:644)
    at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:296)
    at org.glassfish.kernel.embedded.EmbeddedDeployerImpl.deploy(EmbeddedDeployerImpl.java:214)
    at org.glassfish.kernel.embedded.EmbeddedDeployerImpl.deploy(EmbeddedDeployerImpl.java:144)
    at org.glassfish.maven.RunMojo.execute(RunMojo.java:105)
    at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:490)
    at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:694)
    at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeStandaloneGoal(DefaultLifecycleExecutor.java:569)
    at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:539)
    at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:387)
    at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:348)
    at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:180)
    at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:328)
    at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:138)
    at org.apache.maven.cli.MavenCli.main(MavenCli.java:362)
    at org.apache.maven.cli.compat.CompatibleMain.main(CompatibleMain.java:60)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315)
    at org.codehaus.classworlds.Launcher.launch(Launcher.java:255)
    at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430)
    at org.codehaus.classworlds.Launcher.main(Launcher.java:375)
27.10.2010 16:22:21 org.hibernate.dialect.Dialect 
INFO: Using dialect: org.hibernate.dialect.MySQLDialect
27.10.2010 16:22:21 org.hibernate.engine.jdbc.JdbcSupportLoader useContextualLobCreation
INFO: Disabling contextual LOB creation as connection was null
27.10.2010 16:22:21 org.hibernate.transaction.TransactionFactoryFactory buildTransactionFactory
INFO: Transaction strategy: org.hibernate.ejb.transaction.JoinableCMTTransactionFactory
27.10.2010 16:22:21 org.hibernate.transaction.TransactionManagerLookupFactory getTransactionManagerLookup
INFO: instantiating TransactionManagerLookup: org.hibernate.transaction.SunONETransactionManagerLookup
27.10.2010 16:22:21 org.hibernate.transaction.TransactionManagerLookupFactory getTransactionManagerLookup
INFO: instantiated TransactionManagerLookup
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Automatic flush during beforeCompletion(): disabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Automatic session close at end of transaction: disabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Scrollable result sets: disabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: JDBC3 getGeneratedKeys(): disabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Connection release mode: auto
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Maximum outer join fetch depth: 2
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Default batch fetch size: 1
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Generate SQL with comments: disabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Order SQL updates by primary key: disabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Order SQL inserts for batching: disabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory createQueryTranslatorFactory
INFO: Query translator: org.hibernate.hql.ast.ASTQueryTranslatorFactory
27.10.2010 16:22:21 org.hibernate.hql.ast.ASTQueryTranslatorFactory 
INFO: Using ASTQueryTranslatorFactory
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Query language substitutions: {}
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: JPA-QL strict compliance: enabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Second-level cache: enabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Query cache: disabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory createRegionFactory
INFO: Cache region factory : org.hibernate.cache.impl.bridge.RegionFactoryCacheProviderBridge
27.10.2010 16:22:21 org.hibernate.cache.impl.bridge.RegionFactoryCacheProviderBridge 
INFO: Cache provider: org.hibernate.cache.HashtableCacheProvider
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Optimize cache for minimal puts: disabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Structured second-level cache entries: disabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Echoing all SQL to stdout
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Statistics: disabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Deleted entity synthetic identifier rollback: disabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Default entity-mode: pojo
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Named query checking : enabled
27.10.2010 16:22:21 org.hibernate.cfg.SettingsFactory buildSettings
INFO: Check Nullability in Core (should be disabled when Bean Validation is on): disabled
27.10.2010 16:22:21 org.hibernate.impl.SessionFactoryImpl 
INFO: building session factory

my persistence.xml

[...]
<persistence-unit name="workbench" >
  <provider>org.hibernate.ejb.HibernatePersistence</provider>
  <jta-data-source>jdbc/__default</jta-data-source>

    <class>com.pentasys.workbench.db.model.User</class>
    <class>com.pentasys.workbench.db.model.Job</class>
    <class>com.pentasys.workbench.db.model.Comment</class>
    <class>com.pentasys.workbench.db.model.Workflow</class>
    <class>com.pentasys.workbench.db.model.base.ATask</class>

  <properties>
     <property name="hibernate.hbm2ddl.auto" value="create-drop"/>
     <property name="hibernate.show_sql" value="true"/>
     <property name="hibernate.transaction.flush_before_completion" value="true"/>
     <property name="hibernate.cache.provider_class" value="org.hibernate.cache.HashtableCacheProvider"/>
     <property name="hibernate.dialect" value="org.hibernate.dialect.MySQLDialect"/>

    <property name="hibernate.connection.driver_class" value="com.mysql.jdbc.Driver"/>
    <property name="hibernate.connection.url" value="jdbc:mysql://localhost:3306/workbench"/>
    <property name="hibernate.connection.username" value="root"/>
    <property name="hibernate.connection.password" value="cannabis"/>

    <property name="hibernate.show_sql" value="true"/>


    <property name="hibernate.hbm2ddl.auto" value="alter"/>
  </properties>
</persistence-unit>

pom.xml - maven-plugin config (embedded glassfish)

[...]
    <plugin>
        <groupId>org.glassfish</groupId>
        <artifactId>maven-embedded-glassfish-plugin</artifactId>
        <version>3.0</version>
        <configuration>
            <goalPrefix>glassfish</goalPrefix>
            <app>${project.build.directory}/${project.build.finalName}.war</app>
            <port>8090</port>
            <contextRoot>workbench</contextRoot>
            <instanceRoot>${project.build.directory}/gfe-${maven.build.timestamp}</instanceRoot>            
            <autoDelete>true</autoDelete>
            <configFile>${basedir}/domain.xml</configFile>
        </configuration>
        <executions>
            <execution>
                <phase>install</phase>
                <goals>
                    <goal>run</goal>
                </goals>
            </execution>
        </executions>

domain.xml - configuration of embedded glassfish

[...]
<resources>
    <jdbc-resource pool-name="__TimerPool" jndi-name="jdbc/__TimerPool" object-type="system-admin" />
    <jdbc-resource pool-name="MYSQLPool" jndi-name="jdbc/__default" />
    <jdbc-resource pool-name="H2TestPool" jndi-name="${testDatabaseDataSourceName}" />
    <jdbc-connection-pool name="__TimerPool" datasource-classname="org.apache.derby.jdbc.EmbeddedXADataSource" res-type="javax.sql.XADataSource">
      <property value="${com.sun.aas.instanceRoot}/lib/databases/ejbtimer" name="databaseName" />
      <property value=";create=true" name="connectionAttributes" />
    </jdbc-connection-pool>
    <jdbc-connection-pool is-isolation-level-guaranteed="false" name="MYSQLPool" datasource-classname="com.mysql.jdbc.jdbc2.optional.MysqlDataSource" res-type="javax.sql.DataSource">
      <property value="3306" name="port" />
      <property value="test" name="password" />
      <property value="root" name="user" />
      <property value="localhost" name="hostName" />
      <property value="workbench" name="databaseName" />
      <property value="jdbc:mysql://localhost:3306/workbench" name="url" />
      <property value=";alter=true" name="connectionAttributes" />
    </jdbc-connection-pool>
[...]

thank you for advice!

Answer 1

I can't spot any obvious mistake in your GlassFish settings. FWIW, here is a similar configuration I use to connect to MySQL that is working:

<domain>
  ...
  <resources>
    ...
    <jdbc-resource pool-name="PetcatalogPool" jndi-name="jdbc/petcatalog"/>
    <jdbc-connection-pool datasource-classname="com.mysql.jdbc.jdbc2.optional.MysqlDataSource" res-type="javax.sql.DataSource" name="PetcatalogPool">
      <property name="DatabaseName" value="petcatalog"/>
      <property name="Password" value="petcatalog"/>
      <property name="Url" value="jdbc:mysql://localhost:3306/petcatalog"/>
      <property name="User" value="petcatalog"/>
    </jdbc-connection-pool>
    ...
  </resources>
  ...
</domain>

I'm not sure this will help though. If it doesn't:

• make sure that you can connect to the workbench database using a JDBC client (Eclipse, SquirelSQL)
• make sure that the pool is working fine under GlassFish first i.e. make sure that you can "ping" the pool from the admin console (activate GlassFish logging if required to debug).
• then throw Hibernate into the mix.