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GeoLatte / geolatte-geom

A geometry model that conforms to the OGC Simple Features for SQL specification.
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Hibernate deserialization error #160

Closed bigalnz closed 10 months ago

bigalnz commented 10 months ago

I have a Spring Boot 3.2 project which requires me to store WGS84 point data in MySql8 but I am getting a cannot deserialize error from Hibernate when I try to recall from the database a entity with point data attached.

public class Timer {
    @Id
    @GeneratedValue(strategy = SEQUENCE, generator = "ct_seq")
    private Long id;

    @JsonSerialize(using = GeometrySerializer.class)
    @JsonDeserialize(using = GeometryDeserializer.class)
    private Point<G2D> location;

I am inserting a test record into the database with SQL:

INSERT INTO TIMER (id, location, otherfields)
VALUES (6, ST_GeomFromText('POINT(-36.5 174.5)'), otherfields);

But then when I try to findAll(); on this repo I get the hibernate deserialization error.

What is wrong here?

maesenka commented 10 months ago

Can you post the stack trace?

bigalnz commented 10 months ago

Sure.

PS: I think it is something to do with the way I am sending my test data to the DB. If I write:

Point pnt=point(WGS84,g(4.33,53.21)); HealthCheck hc = healthCheckRepository.findById(5L).orElse(null); hc.setLocation(pnt); healthCheckRepository.save(hc);

THEN I cant retrieve hc from the database without the deserialization exception.

java.lang.IllegalStateException: Failed to execute CommandLineRunner at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:774) ~[spring-boot-3.1.2.jar:3.1.2] at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:755) ~[spring-boot-3.1.2.jar:3.1.2] at org.springframework.boot.SpringApplication.run(SpringApplication.java:319) ~[spring-boot-3.1.2.jar:3.1.2] at org.springframework.boot.SpringApplication.run(SpringApplication.java:1306) ~[spring-boot-3.1.2.jar:3.1.2] at org.springframework.boot.SpringApplication.run(SpringApplication.java:1295) ~[spring-boot-3.1.2.jar:3.1.2] at com.nz.kiwi.KiwiApplication.main(KiwiApplication.java:50) ~[main/:na] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104) ~[na:na] at java.base/java.lang.reflect.Method.invoke(Method.java:577) ~[na:na] at org.springframework.boot.devtools.restart.RestartLauncher.run(RestartLauncher.java:50) ~[spring-boot-devtools-3.1.2.jar:3.1.2] Caused by: org.springframework.orm.jpa.JpaSystemException: could not deserialize at org.springframework.orm.jpa.vendor.HibernateJpaDialect.convertHibernateAccessException(HibernateJpaDialect.java:320) ~[spring-orm-6.0.11.jar:6.0.11] at org.springframework.orm.jpa.vendor.HibernateJpaDialect.translateExceptionIfPossible(HibernateJpaDialect.java:229) ~[spring-orm-6.0.11.jar:6.0.11] at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.translateExceptionIfPossible(AbstractEntityManagerFactoryBean.java:550) ~[spring-orm-6.0.11.jar:6.0.11] at org.springframework.dao.support.ChainedPersistenceExceptionTranslator.translateExceptionIfPossible(ChainedPersistenceExceptionTranslator.java:61) ~[spring-tx-6.0.11.jar:6.0.11] at org.springframework.dao.support.DataAccessUtils.translateIfNecessary(DataAccessUtils.java:242) ~[spring-tx-6.0.11.jar:6.0.11] at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:152) ~[spring-tx-6.0.11.jar:6.0.11] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184) ~[spring-aop-6.0.11.jar:6.0.11] at com.blazebit.persistence.spring.data.base.repository.EntityViewAwareCrudMethodMetadataPostProcessor$CrudMethodMetadataPopulatingMethodInterceptor.invoke(EntityViewAwareCrudMethodMetadataPostProcessor.java:143) ~[blaze-persistence-integration-spring-data-base-3.1-1.6.9.jar:1.6.9] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:97) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.data.repository.core.support.SurroundingTransactionDetectorMethodInterceptor.invoke(SurroundingTransactionDetectorMethodInterceptor.java:57) ~[spring-data-commons-3.1.2.jar:3.1.2] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:244) ~[spring-aop-6.0.11.jar:6.0.11] at jdk.proxy4/jdk.proxy4.$Proxy143.findAll(Unknown Source) ~[na:na] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104) ~[na:na] at java.base/java.lang.reflect.Method.invoke(Method.java:577) ~[na:na] at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:196) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:137) ~[spring-tx-6.0.11.jar:6.0.11] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:244) ~[spring-aop-6.0.11.jar:6.0.11] at jdk.proxy4/jdk.proxy4.$Proxy143.findAll(Unknown Source) ~[na:na] at com.nz.kiwi.implementation.ChickTimerServiceImpl.findAll(ChickTimerServiceImpl.java:32) ~[main/:na] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104) ~[na:na] at java.base/java.lang.reflect.Method.invoke(Method.java:577) ~[na:na] at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:196) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:756) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123) ~[spring-tx-6.0.11.jar:6.0.11] at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:391) ~[spring-tx-6.0.11.jar:6.0.11] at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119) ~[spring-tx-6.0.11.jar:6.0.11] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:756) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:708) ~[spring-aop-6.0.11.jar:6.0.11] at com.nz.kiwi.implementation.ChickTimerServiceImpl$$SpringCGLIB$$0.findAll() ~[main/:na] at com.nz.kiwi.KiwiApplication.run(KiwiApplication.java:65) ~[main/:na] at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:771) ~[spring-boot-3.1.2.jar:3.1.2] ... 8 common frames omitted Caused by: org.hibernate.type.SerializationException: could not deserialize at org.hibernate.internal.util.SerializationHelper.doDeserialize(SerializationHelper.java:242) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.internal.util.SerializationHelper.deserialize(SerializationHelper.java:286) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.type.descriptor.java.SerializableJavaType.fromBytes(SerializableJavaType.java:152) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.type.descriptor.java.SerializableJavaType.wrap(SerializableJavaType.java:127) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.type.descriptor.java.SerializableJavaType.wrap(SerializableJavaType.java:32) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.type.descriptor.jdbc.VarbinaryJdbcType$2.doExtract(VarbinaryJdbcType.java:115) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.type.descriptor.jdbc.BasicExtractor.extract(BasicExtractor.java:44) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.sql.results.jdbc.internal.JdbcValuesResultSetImpl.readCurrentRowValues(JdbcValuesResultSetImpl.java:314) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.sql.results.jdbc.internal.JdbcValuesResultSetImpl.advance(JdbcValuesResultSetImpl.java:293) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.sql.results.jdbc.internal.JdbcValuesResultSetImpl.processNext(JdbcValuesResultSetImpl.java:134) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.sql.results.jdbc.internal.AbstractJdbcValues.next(AbstractJdbcValues.java:19) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.sql.results.internal.RowProcessingStateStandardImpl.next(RowProcessingStateStandardImpl.java:66) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.sql.results.spi.ListResultsConsumer.consume(ListResultsConsumer.java:198) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.sql.results.spi.ListResultsConsumer.consume(ListResultsConsumer.java:33) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.sql.exec.internal.JdbcSelectExecutorStandardImpl.doExecuteQuery(JdbcSelectExecutorStandardImpl.java:361) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.sql.exec.internal.JdbcSelectExecutorStandardImpl.executeQuery(JdbcSelectExecutorStandardImpl.java:168) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.sql.exec.internal.JdbcSelectExecutorStandardImpl.list(JdbcSelectExecutorStandardImpl.java:93) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.sql.exec.spi.JdbcSelectExecutor.list(JdbcSelectExecutor.java:31) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.query.sqm.internal.ConcreteSqmSelectQueryPlan.lambda$new$0(ConcreteSqmSelectQueryPlan.java:110) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.query.sqm.internal.ConcreteSqmSelectQueryPlan.withCacheableSqmInterpretation(ConcreteSqmSelectQueryPlan.java:303) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.query.sqm.internal.ConcreteSqmSelectQueryPlan.performList(ConcreteSqmSelectQueryPlan.java:244) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.query.sqm.internal.QuerySqmImpl.doList(QuerySqmImpl.java:518) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.query.spi.AbstractSelectionQuery.list(AbstractSelectionQuery.java:367) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.query.Query.getResultList(Query.java:119) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at com.blazebit.persistence.spring.data.base.repository.AbstractEntityViewAwareRepository.findAll(AbstractEntityViewAwareRepository.java:528) ~[blaze-persistence-integration-spring-data-base-3.1-1.6.9.jar:1.6.9] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104) ~[na:na] at java.base/java.lang.reflect.Method.invoke(Method.java:577) ~[na:na] at org.springframework.data.repository.core.support.RepositoryMethodInvoker$RepositoryFragmentMethodInvoker.lambda$new$0(RepositoryMethodInvoker.java:288) ~[spring-data-commons-3.1.2.jar:3.1.2] at org.springframework.data.repository.core.support.RepositoryMethodInvoker.doInvoke(RepositoryMethodInvoker.java:136) ~[spring-data-commons-3.1.2.jar:3.1.2] at org.springframework.data.repository.core.support.RepositoryMethodInvoker.invoke(RepositoryMethodInvoker.java:120) ~[spring-data-commons-3.1.2.jar:3.1.2] at org.springframework.data.repository.core.support.RepositoryComposition$RepositoryFragments.invoke(RepositoryComposition.java:516) ~[spring-data-commons-3.1.2.jar:3.1.2] at org.springframework.data.repository.core.support.RepositoryComposition.invoke(RepositoryComposition.java:285) ~[spring-data-commons-3.1.2.jar:3.1.2] at org.springframework.data.repository.core.support.RepositoryFactorySupport$ImplementationMethodExecutionInterceptor.invoke(RepositoryFactorySupport.java:628) ~[spring-data-commons-3.1.2.jar:3.1.2] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.data.repository.core.support.QueryExecutorMethodInterceptor.doInvoke(QueryExecutorMethodInterceptor.java:168) ~[spring-data-commons-3.1.2.jar:3.1.2] at org.springframework.data.repository.core.support.QueryExecutorMethodInterceptor.invoke(QueryExecutorMethodInterceptor.java:143) ~[spring-data-commons-3.1.2.jar:3.1.2] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.data.projection.DefaultMethodInvokingMethodInterceptor.invoke(DefaultMethodInvokingMethodInterceptor.java:72) ~[spring-data-commons-3.1.2.jar:3.1.2] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184) ~[spring-aop-6.0.11.jar:6.0.11] at com.blazebit.persistence.spring.data.repository.EntityViewReplacingMethodInterceptor.invoke(EntityViewReplacingMethodInterceptor.java:52) ~[blaze-persistence-integration-spring-data-base-3.1-1.6.9.jar:1.6.9] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123) ~[spring-tx-6.0.11.jar:6.0.11] at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:391) ~[spring-tx-6.0.11.jar:6.0.11] at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119) ~[spring-tx-6.0.11.jar:6.0.11] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184) ~[spring-aop-6.0.11.jar:6.0.11] at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:137) ~[spring-tx-6.0.11.jar:6.0.11] ... 42 common frames omitted Caused by: java.io.StreamCorruptedException: invalid stream header: 00000000 at java.base/java.io.ObjectInputStream.readStreamHeader(ObjectInputStream.java:987) ~[na:na] at java.base/java.io.ObjectInputStream.(ObjectInputStream.java:414) ~[na:na] at org.hibernate.internal.util.SerializationHelper$CustomObjectInputStream.(SerializationHelper.java:308) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] at org.hibernate.internal.util.SerializationHelper.doDeserialize(SerializationHelper.java:217) ~[hibernate-core-6.2.6.Final.jar:6.2.6.Final] ... 87 common frames omitted

On Sun, Aug 27, 2023 at 9:58 PM Karel Maesen @.***> wrote:

Can you post the stack trace?

— Reply to this email directly, view it on GitHub https://github.com/GeoLatte/geolatte-geom/issues/160#issuecomment-1694624076, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACSLKRDFZYASX5VGOJPRKLTXXMK2XANCNFSM6AAAAAA4AFPCWQ . You are receiving this because you authored the thread.Message ID: @.***>

-- "Beat it punk!"

bigalnz commented 10 months ago

Do I need the to string method on the entity?

On Sun, Aug 27, 2023 at 9:58 PM Karel Maesen @.***> wrote:

Can you post the stack trace?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

-- "Beat it punk!"

maesenka commented 10 months ago

The stacktrace tells me that Hibernate tries to use object deserialisation when reading the value, which means Hibernate doesn't recognize it as a Geometry type. Most often this is due to a configuration problem. Are you sure that Hibernate Spatial is used? You should see an INFO log message to that effect when Hibernate is initializing.

maesenka commented 10 months ago

We're discussing this further on the Hibernate-User Zulip channel