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Converted JNDI name [java:comp/env/***] not found before reading the properties file

Good Mornig.
I have an application in tomcat 8, java 1.7, Spring 3.2.2 and primefaces 5.0. When the application starts, it shows the next debug message in console:
Looking up JNDI object with name [java:comp/env/etl.csv.token]
localhost-startStop-1: org.springframework.jndi.JndiLocatorDelegate
Converted JNDI name [java:comp/env/etl.csv.token] not found
But the key isn't in the JNDI context. It is in a properties file. The application works fine and takes the property from the properties file, but i can't understand why spring is trying to find the property in the JNDI context
The properties file is like this:
database.driverClassName=org.postgresql.Driver
database.initialSize=3
database.maxActive=15
database.maxIdle=10
database.minIdle=3
database.maxWait=10000
etl.csv.token=,
And its properties are used like this:
<bean id="dataSource" class="org.apache.tomcat.jdbc.pool.DataSource">
<property name="driverClassName" value="${database.driverClassName}" />
<property name="url" value="${database.url}" />
<property name="username" value="${database.username}" />
<property name="password" value="${database.password}" />
<property name="initialSize" value="${database.initialSize}" />
<property name="maxActive" value="${database.maxActive}" />
<property name="maxIdle" value="${database.maxIdle}" />
<property name="maxWait" value="${database.maxWait}" />
<property name="minIdle" value="${database.minIdle}" />
<property name="testOnBorrow" value="true" />
<property name="validationQuery" value="SELECT CURRENT_TIMESTAMP" />
<property name="removeAbandoned" value="true" />
</bean>
For all properties, the behaviour is the same. I would like that message does not appear
Sorry for the english, is not my native language
Any help will be apreciated.

ERROR: Communications link failure in MYSQL using JPA and Hibernate

I am developing an application where persistence is done via JPA and Hibernate 4.2.3. everything is working normally the first moment.
However when you spend a certain time (in my case one day) application aprensenta the following error.
ERROR: Communications link failure
The last packet successfully received from the server was 259.217.434 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
Abaixo deixo meu persistence.xml...
<persistence-unit name="amh_sys" transaction-type="RESOURCE_LOCAL">
<provider>org.hibernate.ejb.HibernatePersistence</provider>
<properties>
<property name="hibernate.dialect" value="org.hibernate.dialect.MySQL5InnoDBDialect" />
<property name="javax.persistence.jdbc.driver" value="com.mysql.jdbc.Driver" />
<property name="javax.persistence.jdbc.url" value="jdbc:mysql://localhost:3306/amh_sys" />
<property name="javax.persistence.jdbc.user" value="root"/>
<property name="javax.persistence.jdbc.password" value="root"/>
<property name="hibernate.show_sql" value="false" />
<property name="hibernate.format_sql" value="false" />
<property name="hibernate.use_sql_comments" value="false" />
<property name="hibernate.jdbc.wrap_result_sets" value="false" />
<property name="hibernate.hibernate.cache.use_query_cache" value="true" />
<property name="hibernate.c3p0.validate" value="true" />
</properties>
</persistence-unit>
I tried to configure using C3P0 connection pool, however had the same error ... Below configuration of C3P0.
<!-- Important -->
<property name="hibernate.connection.provider_class" value="org.hibernate.connection.C3P0ConnectionProvider" />
<property name="hibernate.c3p0.max_size" value="100" />
<property name="hibernate.c3p0.min_size" value="0" />
<property name="hibernate.c3p0.acquire_increment" value="1" />
<property name="hibernate.c3p0.idle_test_period" value="300" />
<property name="hibernate.c3p0.max_statements" value="0" />
<property name="hibernate.c3p0.timeout" value="100" />
I can force the error by changing the date on your computer, because MySQL gets the same date as a reference. I can not solve this problem, I hope someone here had the same problem trying to share your solution applied.
Felipe.

The MySQL server will timeout the connect if it has been idle for too long. http://dev.mysql.com/doc/refman/5.0/en/gone-away.html You can do use a scheduled query within the timeout to keep the connect active or re-establish the connection by closing and re-creating the EntityManager

Spring + Websphere 8.5: Unable to lookup JNDI name [java:comp/websphere/ExtendedJTATransaction]

There is a Websphere AS 8.5 where runs XA Datasource. Also there is a Spring application which must work in this environment and connect to the datasource. An application context is loaded by a servlet and the application uses RmiExporters to provide RMI access to some services (which are shared in the separate thread) and all DAOs' methods are marked with #Transactional.
If I try to write something to the database from the main thread (e.g. during initialization of any class), it works properly. But if I try to write (or read with HQL SELECT-query) something via RMI invokation I see an exception:
org.hibernate.service.jndi.JndiException: Unable to lookup JNDI name [java:comp/websphere/ExtendedJTATransaction]
at org.hibernate.service.jndi.internal.JndiServiceImpl.locate(JndiServiceImpl.java:68)
at org.hibernate.service.jta.platform.internal.WebSphereExtendedJtaPlatform$TransactionManagerAdapter$TransactionAdapter.<init>(WebSphereExtendedJtaPlatform.java:156)
at org.hibernate.service.jta.platform.internal.WebSphereExtendedJtaPlatform$TransactionManagerAdapter$TransactionAdapter.<init>(WebSphereExtendedJtaPlatform.java:152)
at org.hibernate.service.jta.platform.internal.WebSphereExtendedJtaPlatform$TransactionManagerAdapter.getTransaction(WebSphereExtendedJtaPlatform.java:124)
at org.hibernate.service.jta.platform.internal.WebSphereExtendedJtaPlatform$TransactionManagerAdapter.getStatus(WebSphereExtendedJtaPlatform.java:119)
at org.hibernate.engine.transaction.internal.jta.JtaStatusHelper.getStatus(JtaStatusHelper.java:73)
at org.hibernate.engine.transaction.internal.jta.JtaStatusHelper.isActive(JtaStatusHelper.java:115)
at org.hibernate.service.jta.platform.internal.TransactionManagerBasedSynchronizationStrategy.canRegisterSynchronization(TransactionManagerBasedSynchronizationStrategy.java:56)
at org.hibernate.service.jta.platform.internal.AbstractJtaPlatform.canRegisterSynchronization(AbstractJtaPlatform.java:148)
at org.hibernate.engine.transaction.internal.TransactionCoordinatorImpl.attemptToRegisterJtaSync(TransactionCoordinatorImpl.java:240)
at org.hibernate.engine.transaction.internal.TransactionCoordinatorImpl.pulse(TransactionCoordinatorImpl.java:268)
at org.hibernate.ejb.AbstractEntityManagerImpl.joinTransaction(AbstractEntityManagerImpl.java:1202)
at org.hibernate.ejb.AbstractEntityManagerImpl.postInit(AbstractEntityManagerImpl.java:178)
at org.hibernate.ejb.EntityManagerImpl.<init>(EntityManagerImpl.java:89)
at org.hibernate.ejb.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:179)
at org.hibernate.ejb.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:174)
at com.ibm.ws.jpa.management.JPAEMFactory.createEntityManager(JPAEMFactory.java:297)
at org.springframework.orm.jpa.EntityManagerFactoryUtils.doGetTransactionalEntityManager(EntityManagerFactoryUtils.java:202)
at org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler.invoke(SharedEntityManagerCreator.java:211)
at com.sun.proxy.$Proxy414.persist(Unknown Source)
Actual configuration is the following:
persistence unit in the persistence.xml:
<provider>org.hibernate.ejb.HibernatePersistence</provider>
<jta-data-source>jdbc/oracledatasource</jta-data-source>
<properties>
<property name="hibernate.dialect" value="org.hibernate.dialect.Oracle10gDialect" />
<property name="hibernate.archive.autodetection" value="class" />
<property name="hibernate.show_sql" value="false" />
<property name="hibernate.format_sql" value="true" />
<property name="connection.pool.size" value="5" />
<property name="current_session_context_class" value="managed" />
<property name="hibernate.cache.region.factory_class" value="org.hibernate.cache.ehcache.EhCacheRegionFactory" />
<property name="hibernate.transaction.factory_class" value="org.hibernate.transaction.CMTTransactionFactory" />
<property name="hibernate.transaction.manager_lookup_class" value="org.hibernate.transaction.WebSphereExtendedJTATransactionLookup" />
<property name="hibernate.cache.use_second_level_cache" value="false" />
<property name="hibernate.cache.use_query_cache" value="false" />
<property name="hibernate.generate_statistics" value="true" />
<property name="hibernate.enable_lazy_load_no_trans" value="true" />
</properties>
Spring configuration looks like this:
<tx:jta-transaction-manager />
<tx:annotation-driven />
<bean id="transactionManager" class="org.springframework.transaction.jta.WebSphereUowTransactionManager" />
<bean class="org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor">
<property name="persistenceUnits">
<map>
<entry key="pu1" value="persistence/pu1" />
</map>
</property>
</bean>
<jee:jndi-lookup id="entityManagerFactory" jndi-name="persistence/pu1"/>
What can I try to fix this problem?

The actual solution was to use JPATransactionManager of Spring with LOCAL_RESOURCE persistence unit.

JDBC connection to Microsoft SQL Server doesn't reconnect

I have a database that is connected through an unreliable network connection to an application server, so occasionally the connections break down. Each time this happens, all database connections in the AP pool will need to reconnect - which they don't unfortunately.
I went through different setups of c3p0, dbcp and bonecp as pools and used JTDS as well as the SQL Server V3 driver, (I even ditched pooling atogether to try out whether the regular DataSource would be able to create a new unpooled connection - which it didn't) but all configuration variants don't seem able to recover after network failure.
To clarify, none of the DataSources were able to get a new Connection. Is there some inherent Problem with the MS Sql Server regarding reconnects? Am I missing something fundamental here?
I realize this might not be of big help, but just as an example this is the dbcp configuration
<bean id="dataSource" class="com.jolbox.bonecp.BoneCPDataSource" destroy-method="close">
<property name="driverClass" value="${jdbc.driverClassName}" />
<property name="jdbcUrl" value="${jdbc.databaseurl}" />
<property name="username" value="${jdbc.username}" />
<property name="password" value="${jdbc.password}" />
<property name="idleConnectionTestPeriodInMinutes" value="1" />
<property name="idleMaxAgeInMinutes" value="1" />
<property name="maxConnectionsPerPartition" value="3" />
<property name="minConnectionsPerPartition" value="1" />
<property name="partitionCount" value="1" />
<property name="acquireIncrement" value="5" />
<property name="acquireRetryAttempts" value="50" />
<property name="acquireRetryDelayInMs" value="1000" />
<property name="queryExecuteTimeLimitInMs" value="5000" />
<property name="connectionTestStatement" value="SELECT count(*) FROM dbo.sysobjects" />
<property name="closeConnectionWatch" value="true" />
<property name="lazyInit" value="false" />
<property name="statementsCacheSize" value="100" />
<property name="releaseHelperThreads" value="3" />
</bean>

Hibernate > CLOB > Oracle :(

I am trying to write to an Oracle clob field a value over 4000 characters. This seams to be a common issue but non of the solutions seem to work. So I pray for help from here.
Down and dirty info:
Using Oracle 9.2.0.8.0
Hibernate3 implementing pojo's with annotations
Tomcat 6.0.16
Oracle 10.2.x drivers
C3P0 connction pool provider
In my persistence.xml I have:
<persistence-unit name="DWEB" transaction-type="RESOURCE_LOCAL">
<provider>org.hibernate.ejb.HibernatePersistence</provider>
<properties>
<property name="hibernate.archive.autodetection" value="class"/>
<property name="hibernate.connection.password" value="###" />
<property name="hibernate.connection.username" value="###" />
<property name="hibernate.default_schema" value="schema" />
<property name="hibernate.dialect" value="org.hibernate.dialect.Oracle10gDialect" />
<property name="hibernate.c3p0.min_size" value="5" />
<property name="hibernate.c3p0.max_size" value="20" />
<property name="hibernate.c3p0.timeout" value="300" />
<property name="hibernate.c3p0.max_statements" value="50" />
<property name="hibernate.c3p0.idle_test_period" value="3000" />
<property name="show_sql" value="true" />
<property name="format_sql" value="true" />
<property name="use_sql_comments" value="true" />
<property name="SetBigStringTryClob" value="true"/>
<property name="hibernate.jdbc.batch_size" value="0"/>
<property name="hibernate.connection.url" value="jdbc:oracle:thin:#server.ss.com:1521:DDD"/>
<property name="hibernate.connection.driver_class" value="oracle.jdbc.driver.OracleDriver"/>
</properties>
</persistence-unit>
The getter and setter looks like:
#Lob
#Column(name="COMMENT_DOC")
public String getDocument(){
return get("Document");
}
public void setDocument(String s){
put("Document",s);
}
The exception I am getting is:
SEVERE: Servlet.service() for servlet SW threw exception
java.sql.SQLException: Io exception: Software caused connection abort: socket write error
at oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:134)
at oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:179)
at oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:334)
at oracle.jdbc.ttc7.TTC7Protocol.handleIOException(TTC7Protocol.java:3678)
at oracle.jdbc.ttc7.TTC7Protocol.doOall7(TTC7Protocol.java:1999)
at oracle.jdbc.ttc7.TTC7Protocol.parseExecuteFetch(TTC7Protocol.java:1144)
at oracle.jdbc.driver.OracleStatement.executeNonQuery(OracleStatement.java:2152)
at oracle.jdbc.driver.OracleStatement.doExecuteOther(OracleStatement.java:2035)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:2876)
at oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePreparedStatement.java:609)
at org.hibernate.jdbc.NonBatchingBatcher.addToBatch(NonBatchingBatcher.java:46)
at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2275)
at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2688)
at org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:79)
at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:263)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:167)
at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:321)
at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1027)
at org.hibernate.ejb.AbstractEntityManagerImpl.flush(AbstractEntityManagerImpl.java:304)
at org.sw.website.actions.content.AddComment.performAction(AddComment.java:60)
...
If I need to give more info pleas ask. Everything works until the dreaded limit is exceeded.

Thanks to non sequitor for all the help. I have this working and figure I will put all the pieces here for future reference. Regardless of all the claims about upgrading the drivers and everything would work, non of that worked for me. In the end I had to implement a 'org.hibernate.usertype.UserType' I named it the same as all the examples on the web StringClobType. Save for some imports I used the example from Using Clobs/Blobs with Oracle and Hibernate. As far as I am concerned ignore the "beware" claim.
There was one change I had to make to get merges to work. Some of the methods were not implemented in the provided code sample. Eclipse fixed it for me by stubbing them out. Cool, but the replace method needs to be actually implemented or all merges will overwrite the data with a null. Here is my implementation:
public Object replace(Object newValue, Object existingValue, Object arg2)throws HibernateException {
return newValue;
}
I will not duplicate the class implementation here go to the above link to see it. I used the code in the third gray box. Then at the top of the pojo class I wanted to use it in I added the following after the imports
...
import org.hibernate.annotations.Type;
import org.hibernate.annotations.TypeDefs;
import org.hibernate.annotations.TypeDef;
#TypeDefs({
#TypeDef(
name="clob",
typeClass = foo.StringClobType.class
)
})
#Entity
#Table(name="EA_COMMENTS")
public class Comment extends SWDataObject implements JSONString, Serializable {
...
}
Then to use the new UserType I added the annotation to my getter:
#Type(type="clob")
#Column(name="COMMENT_DOC")
public String getDocument(){
return get("Document");
}
I did not need the #Lob annotation.
In my persistence.xml the persistence-unit declaration ended looking like:
<persistence-unit name="###" transaction-type="RESOURCE_LOCAL">
<provider>org.hibernate.ejb.HibernatePersistence</provider>
<properties>
<property name="hibernate.archive.autodetection" value="class"/>
<property name="hibernate.connection.password" value="###" />
<property name="hibernate.connection.username" value="###" />
<property name="hibernate.connection.url" value="jdbc:oracle:thin:#server.something.com:1521:###"/>
<property name="hibernate.connection.driver_class" value="oracle.jdbc.OracleDriver"/>
<property name="hibernate.default_schema" value="###" />
<property name="hibernate.dialect" value="org.hibernate.dialect.Oracle9iDialect" />
<property name="hibernate.c3p0.min_size" value="5" />
<property name="hibernate.c3p0.max_size" value="100" />
<property name="hibernate.c3p0.timeout" value="300" />
<property name="hibernate.c3p0.max_statements" value="50" />
<property name="hibernate.c3p0.idle_test period" value="3000" />
<property name="hibernate.c3p0.idle_connection_test_period" value="300" />
<property name="show_sql" value="false" />
<property name="format_sql" value="false" />
<property name="use_sql_comments" value="false" />
<property name="hibernate.jdbc.batch_size" value="0"/>
</properties>
</persistence-unit>
The SetBigStringTryClob never worked for me and was not needed for this final implementation.
My lesson learned is in the end it is probably better to join then to fight. It would of saved me three days.

I think your problem might be that you are using Oracle 9i but Hibernate dialect is 10g. Make sure your driver,db version and dialect are all in sync because there is a 9i dialect as well org.hibernate.dialect.Oracle9iDialect

It should be:
<property name="hibernate.connection.SetBigStringTryClob">true</property>
<property name="hibernate.jdbc.batch_size">0</property>
And not:
<property name="SetBigStringTryClob">true</property>
And use the right dialect for your database (org.hibernate.dialect.Oracle9iDialect).
Also make sure that you are using the latest Oracle 10g Release 2 thin driver (10.2.0.4) or later.

We had a similar problem in the past, with LONG columns instead of CLOBs. The problem was the JDBC driver, the one we use now and works fine is