Receiving a CommunicationsException using Spring Data JPA and mysql database - mysql

Question

on a project i am importing data from an oracle database into a mysql database.
The import is working fine.
I user hibernate envers to track changes on a specific field of an entity.
However, if i try to request the stored data via a rest endpoint (controller -> service -> repository) i receive a exception.
If i call the endpoint on a daily basis, the application works fine. But if the the endpoint is not triggered e.g. over the weekend, then the application fails.
Following the dependencies i am using in the project:
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.0.1.RELEASE</version>
<relativePath/>
</parent>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>com.oracle.jdbc</groupId>
<artifactId>ojdbc8</artifactId>
<version>${oracle.version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-java8</artifactId>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-envers</artifactId>
</dependency>
<dependency>
<groupId>org.liquibase</groupId>
<artifactId>liquibase-core</artifactId>
</dependency>
The application properties for the mysql database connection:
spring:
datasource:
url: jdbc:mysql://servername:3306/schema
username: username
password: password
initialize-mode: never
jpa:
open-in-view: false
database-platform: org.hibernate.dialect.MySQL5Dialect
liquibase:
change-log: classpath:/db/changelog/changelog-master.xml
The configuration of the primary database, I am using the default hikari connection pool.
#SpringBootApplication
#EnableScheduling
public class MyApplication {
public static void main(String[] args) {
SpringApplication.run(MyApplication.class, args);
}
#Bean
#Primary
#ConfigurationProperties("spring.datasource")
public DataSourceProperties primaryDataSourceProperties() {
return new DataSourceProperties();
}
#Bean
#Primary
public DataSource primaryDataSource() {
return primaryDataSourceProperties()
.initializeDataSourceBuilder()
.build();
}
#Bean
#Primary
public JdbcTemplate primaryJdbcTemplate() {
return new JdbcTemplate(primaryDataSource());
}
}
The following exception do i receive, if the application was not called over a longer period:
2018-09-17T11:50:11.639708697Z com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 271,547,086 milliseconds ago. The last packet sent successfully to the server was 271,547,087 milliseconds ago. is longer than the server configured value of 'wait_timeout'. You should consider either expiring and/or testing connection validity before use in your application, increasing the server configured values for client timeouts, or using the Connector/J connection property 'autoReconnect=true' to avoid this problem.
2018-09-17T11:50:11.639718269Z at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_181]
2018-09-17T11:50:11.639724140Z at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:1.8.0_181]
2018-09-17T11:50:11.639729703Z at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.8.0_181]
2018-09-17T11:50:11.639735197Z at java.lang.reflect.Constructor.newInstance(Constructor.java:423) ~[na:1.8.0_181]
2018-09-17T11:50:11.639740378Z at com.mysql.jdbc.Util.handleNewInstance(Util.java:425) ~[mysql-connector-java-5.1.46.jar!/:5.1.46]
2018-09-17T11:50:11.639745633Z at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:990) ~[mysql-connector-java-5.1.46.jar!/:5.1.46]
2018-09-17T11:50:11.639751054Z at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3749) ~[mysql-connector-java-5.1.46.jar!/:5.1.46]
2018-09-17T11:50:11.639756342Z at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2512) ~[mysql-connector-java-5.1.46.jar!/:5.1.46]
2018-09-17T11:50:11.639772891Z at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2683) ~[mysql-connector-java-5.1.46.jar!/:5.1.46]
2018-09-17T11:50:11.639778495Z at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2486) ~[mysql-connector-java-5.1.46.jar!/:5.1.46]
2018-09-17T11:50:11.639783448Z at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1858) ~[mysql-connector-java-5.1.46.jar!/:5.1.46]
2018-09-17T11:50:11.639789900Z at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1966) ~[mysql-connector-java-5.1.46.jar!/:5.1.46]
2018-09-17T11:50:11.639795247Z at com.zaxxer.hikari.pool.ProxyPreparedStatement.executeQuery(ProxyPreparedStatement.java:52) ~[HikariCP-2.7.8.jar!/:na]
2018-09-17T11:50:11.639800145Z at com.zaxxer.hikari.pool.HikariProxyPreparedStatement.executeQuery(HikariProxyPreparedStatement.java) [HikariCP-2.7.8.jar!/:na]
2018-09-17T11:50:11.639805182Z at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.extract(ResultSetReturnImpl.java:60) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639810237Z at org.hibernate.loader.Loader.getResultSet(Loader.java:2168) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639815102Z at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1931) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639819990Z at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1893) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639824896Z at org.hibernate.loader.Loader.doQuery(Loader.java:938) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639829655Z at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:341) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639834611Z at org.hibernate.loader.Loader.doList(Loader.java:2692) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639839395Z at org.hibernate.loader.Loader.doList(Loader.java:2675) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639844167Z at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2507) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639849073Z at org.hibernate.loader.Loader.list(Loader.java:2502) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639853943Z at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:502) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639858773Z at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:392) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639863765Z at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:216) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639868646Z at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1489) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639874051Z at org.hibernate.query.internal.AbstractProducedQuery.doList(AbstractProducedQuery.java:1445) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639882957Z at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1414) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639888299Z at org.hibernate.query.internal.AbstractProducedQuery.uniqueResult(AbstractProducedQuery.java:1457) [hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T11:50:11.639893354Z at org.hibernate.envers.internal.reader.AuditReaderImpl.getRevisionNumberForDate(AuditReaderImpl.java:195) [hibernate-envers-5.2.16.Final.jar!/:5.2.16.Final]
.....(common frames ommitted)
2018-09-17T11:50:11.640471778Z Caused by: java.net.SocketException: Broken pipe (Write failed)
2018-09-17T11:50:11.640476371Z at java.net.SocketOutputStream.socketWrite0(Native Method) ~[na:1.8.0_181]
2018-09-17T11:50:11.640481083Z at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:111) ~[na:1.8.0_181]
2018-09-17T11:50:11.640485818Z at java.net.SocketOutputStream.write(SocketOutputStream.java:155) ~[na:1.8.0_181]
2018-09-17T11:50:11.640490460Z at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82) ~[na:1.8.0_181]
2018-09-17T11:50:11.640495069Z at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140) ~[na:1.8.0_181]
2018-09-17T11:50:11.640499775Z at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3731) ~[mysql-connector-java-5.1.46.jar!/:5.1.46]
2018-09-17T11:50:11.640504540Z ... 124 common frames omitted
2018-09-17T11:50:11.640508983Z
2018-09-17T11:50:11.640513301Z 2018-09-17 11:50:11.639 WARN 1 --- [ XNIO-2 task-5] o.h.engine.jdbc.spi.SqlExceptionHelper : SQL Error: 0, SQLState: 08S01
The next time i call the application rest endpoint i receive the following exception:
2018-09-17 12:01:59.571 WARN 1 --- [ XNIO-2 task-6] o.h.engine.jdbc.spi.SqlExceptionHelper : SQL Error: 0, SQLState: null
2018-09-17 12:01:59.571 ERROR 1 --- [ XNIO-2 task-6] o.h.engine.jdbc.spi.SqlExceptionHelper : Connection is closed
2018-09-17 12:01:59.577 ERROR 1 --- [ XNIO-2 task-6] io.undertow.request : UT005023: Exception handling request to /userdata/changed/1
2018-09-17T12:01:59.578946831Z
2018-09-17T12:01:59.578952545Z org.springframework.web.util.NestedServletException: Request processing failed; nested exception is javax.persistence.PersistenceException: org.hibernate.exception.GenericJDBCException: could not prepare statement
2018-09-17T12:01:59.579639175Z Caused by: java.sql.SQLException: Connection is closed
2018-09-17T12:01:59.579643612Z at com.zaxxer.hikari.pool.ProxyConnection$ClosedConnection.lambda$getClosedConnection$0(ProxyConnection.java:490) ~[HikariCP-2.7.8.jar!/:na]
2018-09-17T12:01:59.579648391Z at com.sun.proxy.$Proxy75.prepareStatement(Unknown Source) ~[na:na]
2018-09-17T12:01:59.579652972Z at com.zaxxer.hikari.pool.ProxyConnection.prepareStatement(ProxyConnection.java:318) ~[HikariCP-2.7.8.jar!/:na]
2018-09-17T12:01:59.579657687Z at com.zaxxer.hikari.pool.HikariProxyConnection.prepareStatement(HikariProxyConnection.java) ~[HikariCP-2.7.8.jar!/:na]
2018-09-17T12:01:59.579662500Z at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$5.doPrepare(StatementPreparerImpl.java:145) ~[hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T12:01:59.579667400Z at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:171) ~[hibernate-core-5.2.16.Final.jar!/:5.2.16.Final]
2018-09-17T12:01:59.579672405Z ... 117 common frames omitted
Maybe someone has any idea, why the connection to the database gets invalid.
Here are the settings of the hikari
Driver class com.mysql.jdbc.Driver found in Thread context class loader sun.misc.Launcher$AppClassLoader#18b4aac2
HikariPool-1 - configuration:
allowPoolSuspension.............false
autoCommit......................true
catalog.........................none
connectionInitSql...............none
connectionTestQuery.............none
connectionTimeout...............30000
dataSource......................none
dataSourceClassName.............none
dataSourceJNDI..................none
dataSourceProperties............{password=<masked>}
driverClassName................."com.mysql.jdbc.Driver"
healthCheckProperties...........{}
healthCheckRegistry.............none
idleTimeout.....................600000
initializationFailFast..........true
initializationFailTimeout.......1
isolateInternalQueries..........false
jdbc4ConnectionTest.............false
jdbcUrl.........................jdbc:mysql://server:3306/schema
leakDetectionThreshold..........0
maxLifetime.....................1800000
maximumPoolSize.................10
metricRegistry..................none
metricsTrackerFactory...........none
minimumIdle.....................10
password........................<masked>
poolName........................"HikariPool-1"
readOnly........................false
registerMbeans..................false
scheduledExecutor...............none
scheduledExecutorService........internal
schema..........................none
threadFactory...................internal
transactionIsolation............default
username........................"user"
validationTimeout...............5000

Answer 1

i expected the issue at the wrong part of my application. I configured the envers AuditReader as spring bean and injected a entity manager. The entity manager holds a database connection that breaks when the database is closing the connection after the configured timeout.
#Configuration
#RequiredArgsConstructor
public class AuditConfiguration {
private final EntityManagerFactory entityManagerFactory;
#Bean
public AuditReader auditReader() {
return AuditReaderFactory.get(entityManagerFactory.createEntityManager());
}
}
So i removed this configuration and create a entity manager for every request to the audit reader.
#Component
#RequiredArgsConstructor
public class AuditService {
private final EntityManagerFactory entityManagerFactory;
public int getLatestRevision() {
return AuditReaderFactory.get(entityManagerFactory.createEntityManager())
.getRevisionNumberForDate(from(now()))
.intValue();
}
}
With this setup hikari is handling the database connections correct and the exception does not occur anymore.

Answer 2

Use jdbc url as below , while making connection:
url: jdbc:mysql://servername:3306/schema?autoReconnect=true