Hapi 3.4.0 Spring Boot Issue:No EntityManager with actual transaction available for current thread

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contac...@gmail.com

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Aug 6, 2018, 1:18:31 PM8/6/18
to HAPI FHIR
Hi,

We have the SpringBoot Application version of HAPI FHIR and for some reason the 3.4.0 build is giving issues when we try posting ValueSet resource. We have not seen any such issues in the previous builds and I tried many configurations but nothing seem to work .

I have uploaded our basic Spring Boot version which throws the error into GIT https://github.com/contactkuchi/Hapi3.4.0Issue.git

You can run this project with LOCAL profile and try to post any ValueSet resource @ http://localhost:8598/STU3/fhirapi/ValueSet to bring up the issue. (You would need to add the headers  “fhir-user-name” = XXX, “fhir-app-name” = XXX, “fhir-user-id” = XXX)


I tried many ways to resolve this but nothing seems to work, the problem looks like in the JpaTransactionManager and EntityManagerFactoryBean definitions but I have followed the same approach from the sample project which works for other bean definitions. 


If anyone has already faced this issue or if you have a springboot configuration that work for 3.4.0 version please share so we can move on.


Thanks

Ravi Kuchi 

contac...@gmail.com

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Aug 6, 2018, 1:33:45 PM8/6/18
to HAPI FHIR
This is the error we get :

13:31:33.784 INFO  com.fmcna.fhir.Application Started Application in 56.493 seconds (JVM running for 58.892)

13:33:00.074 INFO  o.h.f.d.h.v.DefaultProfileValidationSupport Loading structure definitions from classpath: /org/hl7/fhir/dstu3/model/profile/profiles-resources.xml

13:33:00.630 INFO  o.h.f.d.h.v.DefaultProfileValidationSupport Loading structure definitions from classpath: /org/hl7/fhir/dstu3/model/profile/profiles-types.xml

13:33:00.673 INFO  o.h.f.d.h.v.DefaultProfileValidationSupport Loading structure definitions from classpath: /org/hl7/fhir/dstu3/model/profile/profiles-others.xml

13:33:00.841 INFO  o.h.f.d.h.v.DefaultProfileValidationSupport Loading structure definitions from classpath: /org/hl7/fhir/dstu3/model/extension/extension-definitions.xml

13:33:01.213 ERROR c.u.f.r.s.i.ExceptionHandlingInterceptor Failure during REST processing

ca.uhn.fhir.rest.server.exceptions.InternalErrorException: Failed to call access method: org.springframework.dao.InvalidDataAccessApiUsageException: No EntityManager with actual transaction available for current thread - cannot reliably process 'persist' call; nested exception is javax.persistence.TransactionRequiredException: No EntityManager with actual transaction available for current thread - cannot reliably process 'persist' call

at ca.uhn.fhir.rest.server.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:261)

at ca.uhn.fhir.rest.server.method.BaseOutcomeReturningMethodBinding.invokeServer(BaseOutcomeReturningMethodBinding.java:156)

at ca.uhn.fhir.rest.server.method.CreateMethodBinding.invokeServer(CreateMethodBinding.java:39)

at ca.uhn.fhir.rest.server.RestfulServer.handleRequest(RestfulServer.java:921)

at ca.uhn.fhir.rest.server.RestfulServer.doPost(RestfulServer.java:345)

at ca.uhn.fhir.rest.server.RestfulServer.service(RestfulServer.java:1500)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:197)

at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)

at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)

at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)

at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)

at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)

at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)

at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)

at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800)

at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)

at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:800)

at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1471)

at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)

at java.lang.Thread.run(Thread.java:745)

Caused by: java.lang.reflect.InvocationTargetException: null

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:497)

at ca.uhn.fhir.rest.server.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:256)

... 31 common frames omitted

Caused by: org.springframework.dao.InvalidDataAccessApiUsageException: No EntityManager with actual transaction available for current thread - cannot reliably process 'persist' call; nested exception is javax.persistence.TransactionRequiredException: No EntityManager with actual transaction available for current thread - cannot reliably process 'persist' call

at org.springframework.orm.jpa.EntityManagerFactoryUtils.convertJpaAccessExceptionIfPossible(EntityManagerFactoryUtils.java:413)

at org.springframework.orm.jpa.vendor.HibernateJpaDialect.translateExceptionIfPossible(HibernateJpaDialect.java:246)

at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.translateExceptionIfPossible(AbstractEntityManagerFactoryBean.java:525)

at org.springframework.dao.support.ChainedPersistenceExceptionTranslator.translateExceptionIfPossible(ChainedPersistenceExceptionTranslator.java:59)

at org.springframework.dao.support.DataAccessUtils.translateIfNecessary(DataAccessUtils.java:209)

at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:147)

at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)

at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:671)

at ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoValueSetDstu3$$EnhancerBySpringCGLIB$$4c5cadff.create(<generated>)

at ca.uhn.fhir.jpa.provider.dstu3.JpaResourceProviderDstu3.create(JpaResourceProviderDstu3.java:62)

... 36 common frames omitted

Caused by: javax.persistence.TransactionRequiredException: No EntityManager with actual transaction available for current thread - cannot reliably process 'persist' call

at org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler.invoke(SharedEntityManagerCreator.java:284)

at com.sun.proxy.$Proxy116.persist(Unknown Source)

at ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.updateEntity(BaseHapiFhirDao.java:1980)

at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.doCreate(BaseHapiFhirResourceDao.java:426)

at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.create(BaseHapiFhirResourceDao.java:156)

at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.create(BaseHapiFhirResourceDao.java:132)

at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao$$FastClassBySpringCGLIB$$5578fb67.invoke(<generated>)

at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)

at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:736)

at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)

at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:136)

... 40 common frames omitted

13:33:01.229 INFO  c.u.f.n.BaseThymeleafNarrativeGenerator Initializing narrative generator

James Agnew

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Aug 7, 2018, 5:17:25 PM8/7/18
to Kuchi Ravi, HAPI FHIR
Just to further this in case anyone on the list has any ideas: I had some discussion with Ravi about this, and I was able to reproduce the issue.

This definitely appears to be a Spring Boot thing- In "normal spring" the @Transactional annotation is being honoured on HAPI FHIR's DAOs, but in Boot it is not.

I don't know a lot about Boot, so I am at a loss beyond that (although I was able to find a workaround..)

Cheers,
James

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O. K.

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Aug 8, 2018, 10:39:45 AM8/8/18
to HAPI FHIR
I have the same problem. What kind of workaround did you make?

contac...@gmail.com

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Aug 9, 2018, 1:52:58 PM8/9/18
to HAPI FHIR
James suggested to add the below as a workaround in the fhirserverconfig file:

@Bean(name="myValueSetDaoDstu3", autowire=Autowire.BY_NAME)

   @Lazy

   public

   IFhirResourceDaoValueSet<org.hl7.fhir.dstu3.model.ValueSet, org.hl7.fhir.dstu3.model.Coding, org.hl7.fhir.dstu3.model.CodeableConcept> daoValueSetDstu3() {

      MyFhirResourceDaoValueSetDstu3 retVal = new MyFhirResourceDaoValueSetDstu3();

      retVal.setResourceType(org.hl7.fhir.dstu3.model.ValueSet.class);

      retVal.setContext(fhirContextDstu3());

      return retVal;

   }


   public static class MyFhirResourceDaoValueSetDstu3 extends FhirResourceDaoValueSetDstu3

   {


      @Autowired

      private PlatformTransactionManager myTxManager;


      @Override

      public DaoMethodOutcome create(ValueSet theResource, RequestDetails theRequestDetails) {

         return new TransactionTemplate(myTxManager).execute(t->{

            return super.create(theResource, theRequestDetails);

         });

      }


      @Override

      public DaoMethodOutcome create(ValueSet theResource, String theIfNoneExist, RequestDetails theRequestDetails) {

         return new TransactionTemplate(myTxManager).execute(t-> {

            return super.create(theResource, theIfNoneExist, theRequestDetails);

         });

O. K.

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Aug 10, 2018, 3:50:01 AM8/10/18
to HAPI FHIR
Thank you!! I will try this later today.
Message has been deleted

O. K.

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Aug 13, 2018, 5:44:31 AM8/13/18
to HAPI FHIR
It did not work. The server starts and returns ValueSet resources with a search. However, read (e.g. ValueSet/50) throws an exception.

This is what I get with Postgres 9.6:

org.springframework.orm.jpa.JpaSystemException: org.hibernate.HibernateException: Unable to access lob stream; nested exception is javax.persistence.PersistenceException: org.hibernate.HibernateException: Unable to access lob stream
    at org.springframework.orm.jpa.
EntityManagerFactoryUtils.convertJpaAccessExceptionIfPossible(EntityManagerFactoryUtils.java:418) ~[spring-orm-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.translateExceptionIfPossible(AbstractEntityManagerFactoryBean.java:526) ~[spring-orm-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.dao.support.ChainedPersistenceExceptionTranslator.translateExceptionIfPossible(ChainedPersistenceExceptionTranslator.java:59) ~[spring-tx-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.dao.support.DataAccessUtils.translateIfNecessary(DataAccessUtils.java:209) ~[spring-tx-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:147) ~[spring-tx-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.data.jpa.repository.support.CrudMethodMetadataPostProcessor$CrudMethodMetadataPopulatingMethodInterceptor.invoke(CrudMethodMetadataPostProcessor.java:133) ~[spring-data-jpa-1.11.13.RELEASE.jar:na]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.data.repository.core.support.SurroundingTransactionDetectorMethodInterceptor.invoke(SurroundingTransactionDetectorMethodInterceptor.java:57) ~[spring-data-commons-1.13.13.RELEASE.jar:na]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at com.sun.proxy.$Proxy165.findForIdAndVersion(Unknown Source) ~[na:na]
    at ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.toResource(BaseHapiFhirDao.java:1598) ~[hapi-fhir-jpaserver-base-3.4.0.jar:na]
    at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.read(BaseHapiFhirResourceDao.java:857) ~[hapi-fhir-jpaserver-base-3.4.0.jar:na]
    at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao$$FastClassBySpringCGLIB$$5578fb67.invoke(<generated>) ~[hapi-fhir-jpaserver-base-3.4.0.jar:na]
    at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204) ~[spring-core-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:736) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:136) ~[spring-tx-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:671) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at fi.oda.phr.config.ServerConfig$MyFhirResourceDaoValueSetDstu3$$EnhancerBySpringCGLIB$$ab705ec5.read(<generated>) ~[main/:na]
    at ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider.read(BaseJpaResourceProvider.java:131) ~[hapi-fhir-jpaserver-base-3.4.0.jar:na]
    ... 54 common frames omitted
Caused by: javax.persistence.PersistenceException: org.hibernate.HibernateException: Unable to access lob stream
    at org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:149) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:157) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1423) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.query.internal.AbstractProducedQuery.getSingleResult(AbstractProducedQuery.java:1463) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_102]
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[na:1.8.0_102]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[na:1.8.0_102]
    at java.lang.reflect.Method.invoke(Unknown Source) ~[na:1.8.0_102]
    at org.springframework.orm.jpa.SharedEntityManagerCreator$DeferredQueryInvocationHandler.invoke(SharedEntityManagerCreator.java:374) ~[spring-orm-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at com.sun.proxy.$Proxy237.getSingleResult(Unknown Source) ~[na:na]
    at org.springframework.data.jpa.repository.query.JpaQueryExecution$SingleEntityExecution.doExecute(JpaQueryExecution.java:210) ~[spring-data-jpa-1.11.13.RELEASE.jar:na]
    at org.springframework.data.jpa.repository.query.JpaQueryExecution.execute(JpaQueryExecution.java:89) ~[spring-data-jpa-1.11.13.RELEASE.jar:na]
    at org.springframework.data.jpa.repository.query.AbstractJpaQuery.doExecute(AbstractJpaQuery.java:128) ~[spring-data-jpa-1.11.13.RELEASE.jar:na]
    at org.springframework.data.jpa.repository.query.AbstractJpaQuery.execute(AbstractJpaQuery.java:118) ~[spring-data-jpa-1.11.13.RELEASE.jar:na]
    at org.springframework.data.repository.core.support.RepositoryFactorySupport$QueryExecutorMethodInterceptor.doInvoke(RepositoryFactorySupport.java:494) ~[spring-data-commons-1.13.13.RELEASE.jar:na]
    at org.springframework.data.repository.core.support.RepositoryFactorySupport$QueryExecutorMethodInterceptor.invoke(RepositoryFactorySupport.java:477) ~[spring-data-commons-1.13.13.RELEASE.jar:na]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.data.projection.DefaultMethodInvokingMethodInterceptor.invoke(DefaultMethodInvokingMethodInterceptor.java:56) ~[spring-data-commons-1.13.13.RELEASE.jar:na]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) ~[spring-tx-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282) ~[spring-tx-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) ~[spring-tx-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:136) ~[spring-tx-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    ... 74 common frames omitted
Caused by: org.hibernate.HibernateException: Unable to access lob stream
    at org.hibernate.type.descriptor.java.PrimitiveByteArrayTypeDescriptor.wrap(PrimitiveByteArrayTypeDescriptor.java:123) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.type.descriptor.java.PrimitiveByteArrayTypeDescriptor.wrap(PrimitiveByteArrayTypeDescriptor.java:26) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.type.descriptor.sql.BlobTypeDescriptor$1.doExtract(BlobTypeDescriptor.java:48) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.type.descriptor.sql.BasicExtractor.extract(BasicExtractor.java:47) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.type.AbstractStandardBasicType.nullSafeGet(AbstractStandardBasicType.java:261) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.type.AbstractStandardBasicType.nullSafeGet(AbstractStandardBasicType.java:257) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.type.AbstractStandardBasicType.nullSafeGet(AbstractStandardBasicType.java:247) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.type.AbstractStandardBasicType.hydrate(AbstractStandardBasicType.java:333) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.persister.entity.AbstractEntityPersister.hydrate(AbstractEntityPersister.java:2854) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.loader.Loader.loadFromResultSet(Loader.java:1747) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.loader.Loader.instanceNotYetLoaded(Loader.java:1673) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.loader.Loader.getRow(Loader.java:1562) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:732) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.loader.Loader.processResultSet(Loader.java:991) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.loader.Loader.doQuery(Loader.java:949) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:341) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.loader.Loader.doList(Loader.java:2692) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.loader.Loader.doList(Loader.java:2675) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2507) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.loader.Loader.list(Loader.java:2502) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:502) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:392) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:216) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1489) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.query.internal.AbstractProducedQuery.doList(AbstractProducedQuery.java:1445) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1414) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    ... 95 common frames omitted
Caused by: org.postgresql.util.PSQLException: Large Objects may not be used in auto-commit mode.
    at org.postgresql.largeobject.LargeObjectManager.open(LargeObjectManager.java:262) ~[postgresql-42.2.2.jar:42.2.2]
    at org.postgresql.largeobject.LargeObjectManager.open(LargeObjectManager.java:248) ~[postgresql-42.2.2.jar:42.2.2]
    at org.postgresql.jdbc.AbstractBlobClob.getLo(AbstractBlobClob.java:272) ~[postgresql-42.2.2.jar:42.2.2]
    at org.postgresql.jdbc.AbstractBlobClob.getBinaryStream(AbstractBlobClob.java:116) ~[postgresql-42.2.2.jar:42.2.2]
    at org.hibernate.type.descriptor.java.PrimitiveByteArrayTypeDescriptor.wrap(PrimitiveByteArrayTypeDescriptor.java:120) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    ... 120 common frames omitted

O. K.

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Aug 13, 2018, 5:45:54 AM8/13/18
to HAPI FHIR
With in-memory hsqldb I get this:


ca.uhn.fhir.rest.server.exceptions.InternalErrorException: Failed to call access method: org.springframework.orm.jpa.JpaSystemException: failed to lazily initialize a collection of role: ca.uhn.fhir.jpa.entity.ResourceTable.myTags, could not initialize proxy - no Session; nested exception is org.hibernate.LazyInitializationException: failed to lazily initialize a collection of role: ca.uhn.fhir.jpa.entity.ResourceTable.myTags, could not initialize proxy - no Session
    at ca.uhn.fhir.rest.server.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:261) ~[hapi-fhir-server-3.4.0.jar:na]
    at ca.uhn.fhir.rest.server.method.ReadMethodBinding.invokeServer(ReadMethodBinding.java:149) ~[hapi-fhir-server-3.4.0.jar:na]
    at ca.uhn.fhir.rest.server.method.ReadMethodBinding.invokeServer(ReadMethodBinding.java:47) ~[hapi-fhir-server-3.4.0.jar:na]
    at ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding.doInvokeServer(BaseResourceReturningMethodBinding.java:237) ~[hapi-fhir-server-3.4.0.jar:na]
    at ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding.invokeServer(BaseResourceReturningMethodBinding.java:371) ~[hapi-fhir-server-3.4.0.jar:na]
    at ca.uhn.fhir.rest.server.RestfulServer.handleRequest(RestfulServer.java:921) [hapi-fhir-server-3.4.0.jar:na]
    at ca.uhn.fhir.rest.server.RestfulServer.doGet(RestfulServer.java:335) [hapi-fhir-server-3.4.0.jar:na]
    at ca.uhn.fhir.rest.server.RestfulServer.service(RestfulServer.java:1494) [hapi-fhir-server-3.4.0.jar:na]
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:742) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat-embed-websocket-8.5.31.jar:8.5.31]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.springframework.boot.web.filter.ApplicationContextHeaderFilter.doFilterInternal(ApplicationContextHeaderFilter.java:55) [spring-boot-1.5.14.RELEASE.jar:1.5.14.RELEASE]
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:101) [spring-web-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.springframework.boot.actuate.trace.WebRequestTraceFilter.doFilterInternal(WebRequestTraceFilter.java:111) [spring-boot-actuator-1.5.14.RELEASE.jar:1.5.14.RELEASE]
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:197) [spring-web-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.springframework.boot.actuate.autoconfigure.MetricsFilter.doFilterInternal(MetricsFilter.java:106) [spring-boot-actuator-1.5.14.RELEASE.jar:1.5.14.RELEASE]
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:496) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:677) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:803) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:790) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1468) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.8.0_102]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.8.0_102]
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-embed-core-8.5.31.jar:8.5.31]
    at java.lang.Thread.run(Unknown Source) [na:1.8.0_102]
Caused by: java.lang.reflect.InvocationTargetException: null

    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_102]
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[na:1.8.0_102]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[na:1.8.0_102]
    at java.lang.reflect.Method.invoke(Unknown Source) ~[na:1.8.0_102]
    at ca.uhn.fhir.rest.server.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:256) ~[hapi-fhir-server-3.4.0.jar:na]
    ... 49 common frames omitted
Caused by: org.springframework.orm.jpa.JpaSystemException: failed to lazily initialize a collection of role: ca.uhn.fhir.jpa.entity.ResourceTable.myTags, could not initialize proxy - no Session; nested exception is org.hibernate.LazyInitializationException: failed to lazily initialize a collection of role: ca.uhn.fhir.jpa.entity.ResourceTable.myTags, could not initialize proxy - no Session
    at org.springframework.orm.jpa.EntityManagerFactoryUtils.convertJpaAccessExceptionIfPossible(EntityManagerFactoryUtils.java:418) ~[spring-orm-4.3.18.RELEASE.jar:4.3.18.RELEASE]

    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.translateExceptionIfPossible(AbstractEntityManagerFactoryBean.java:526) ~[spring-orm-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.dao.support.ChainedPersistenceExceptionTranslator.translateExceptionIfPossible(ChainedPersistenceExceptionTranslator.java:59) ~[spring-tx-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.dao.support.DataAccessUtils.translateIfNecessary(DataAccessUtils.java:209) ~[spring-tx-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:147) ~[spring-tx-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:671) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at fi.oda.phr.config.ServerConfig$MyFhirResourceDaoValueSetDstu3$$EnhancerBySpringCGLIB$$315245b5.read(<generated>) ~[main/:na]

    at ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider.read(BaseJpaResourceProvider.java:131) ~[hapi-fhir-jpaserver-base-3.4.0.jar:na]
    ... 54 common frames omitted
Caused by: org.hibernate.LazyInitializationException: failed to lazily initialize a collection of role: ca.uhn.fhir.jpa.entity.ResourceTable.myTags, could not initialize proxy - no Session
    at org.hibernate.collection.internal.AbstractPersistentCollection.throwLazyInitializationException(AbstractPersistentCollection.java:582) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.collection.internal.AbstractPersistentCollection.withTemporarySessionIfNeeded(AbstractPersistentCollection.java:201) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.collection.internal.AbstractPersistentCollection.initialize(AbstractPersistentCollection.java:561) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.collection.internal.AbstractPersistentCollection.read(AbstractPersistentCollection.java:132) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at org.hibernate.collection.internal.PersistentSet.iterator(PersistentSet.java:163) ~[hibernate-core-5.2.15.Final.jar:5.2.15.Final]
    at ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.populateResourceMetadataRi(BaseHapiFhirDao.java:1442) ~[hapi-fhir-jpaserver-base-3.4.0.jar:na]

    at ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.toResource(BaseHapiFhirDao.java:1679) ~[hapi-fhir-jpaserver-base-3.4.0.jar:na]
    at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.read(BaseHapiFhirResourceDao.java:857) ~[hapi-fhir-jpaserver-base-3.4.0.jar:na]
    at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao$$FastClassBySpringCGLIB$$5578fb67.invoke(<generated>) ~[hapi-fhir-jpaserver-base-3.4.0.jar:na]
    at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204) ~[spring-core-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:736) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) ~[spring-aop-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:136) ~[spring-tx-4.3.18.RELEASE.jar:4.3.18.RELEASE]
    ... 58 common frames omitted

O. K.

unread,
Aug 13, 2018, 5:51:10 AM8/13/18
to HAPI FHIR
The validator is also broken in 3.4.0 (possibly already in 3.3.0). I will start a new thread about it.

ja...@interopion.com

unread,
Dec 12, 2018, 12:30:56 PM12/12/18
to HAPI FHIR
Hey guys,
Will there be a fix for this in future versions of HAPI? It seems to still be broken in HAPI 3.6.0.

Thanks,
Jacob
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