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hapifhir / hapi-fhir

🔥 HAPI FHIR - Java API for HL7 FHIR Clients and Servers
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Incorrect SQL syntax exception when using $expunge #2013

Closed seanmcilvenna closed 3 years ago

seanmcilvenna commented 4 years ago

Describe the bug When trying to permanently delete/$expunge a resource, I received the following exception:

Caused by: java.sql.SQLSyntaxErrorException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ')' at line 1
        at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:118)
        at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:95)
        at com.mysql.cj.jdbc.exceptions.SQLExceptionsMapping.translateException(SQLExceptionsMapping.java:122)
        at com.mysql.cj.jdbc.ClientPreparedStatement.executeInternal(ClientPreparedStatement.java:960)
        at com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdateInternal(ClientPreparedStatement.java:1116)
        at com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdateInternal(ClientPreparedStatement.java:1066)
        at com.mysql.cj.jdbc.ClientPreparedStatement.executeLargeUpdate(ClientPreparedStatement.java:1396)
        at com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdate(ClientPreparedStatement.java:1051)
        at org.apache.commons.dbcp2.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:136)
        at org.apache.commons.dbcp2.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:136)
        at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:197)
        ... 100 common frames omitted
2020-08-05 01:31:38.560 [http-nio-8080-exec-218] ERROR c.u.f.r.s.i.ExceptionHandlingInterceptor [ExceptionHandlingInterceptor.java:140] Failure during REST processing
ca.uhn.fhir.rest.server.exceptions.InternalErrorException: could not execute statement; SQL [n/a]; nested exception is org.hibernate.exception.SQLGrammarException: could not execute statement
        at ca.uhn.fhir.jpa.dao.expunge.PartitionRunner.runInPartitionedThreads(PartitionRunner.java:64)
        at ca.uhn.fhir.jpa.dao.expunge.ExpungeOperation.deleteHistoricalVersions(ExpungeOperation.java:124)
        at ca.uhn.fhir.jpa.dao.expunge.ExpungeOperation.expungeDeletedResources(ExpungeOperation.java:87)
        at ca.uhn.fhir.jpa.dao.expunge.ExpungeOperation.call(ExpungeOperation.java:68)
        at ca.uhn.fhir.jpa.dao.expunge.ExpungeService.expunge(ExpungeService.java:63)
        at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.forceExpungeInExistingTransaction(BaseHapiFhirResourceDao.java:617)
        at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.expunge(BaseHapiFhirResourceDao.java:594)
        at jdk.internal.reflect.GeneratedMethodAccessor726.invoke(Unknown Source)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
        at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:139)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:366)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:99)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
        at com.sun.proxy.$Proxy201.expunge(Unknown Source)
        at ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider.doExpunge(BaseJpaResourceProvider.java:63)
        at ca.uhn.fhir.jpa.provider.r4.JpaResourceProviderR4.expunge(JpaResourceProviderR4.java:89)
        at jdk.internal.reflect.GeneratedMethodAccessor725.invoke(Unknown Source)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at ca.uhn.fhir.rest.server.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:239)
        at ca.uhn.fhir.rest.server.method.OperationMethodBinding.invokeServer(OperationMethodBinding.java:329)
        at ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding.doInvokeServer(BaseResourceReturningMethodBinding.java:247)
        at ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding.invokeServer(BaseResourceReturningMethodBinding.java:384

        at ca.uhn.fhir.rest.server.method.OperationMethodBinding.invokeServer(OperationMethodBinding.java:304)
        at ca.uhn.fhir.rest.server.RestfulServer.handleRequest(RestfulServer.java:991)
        at ca.uhn.fhir.rest.server.RestfulServer.doPost(RestfulServer.java:346)
        at ca.uhn.fhir.rest.server.RestfulServer.service(RestfulServer.java:1681)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:741)
        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:53)
        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:200)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:490)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:139)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)
        at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:678)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343)
        at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:408)
        at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
        at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:836)
        at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1839)
        at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: org.springframework.dao.InvalidDataAccessResourceUsageException: could not execute statement; SQL [n/a]; nested exception is org.hibernate.exception.SQLGrammarException: could not execute statement
        at org.springframework.orm.jpa.vendor.HibernateJpaDialect.convertHibernateAccessException(HibernateJpaDialect.java:281)
        at ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.convertHibernateAccessException(HapiFhirHibernateJpaDialect.java:105)
        at ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.convertHibernateAccessException(HapiFhirHibernateJpaDialect.java:62)
        at org.springframework.orm.jpa.vendor.HibernateJpaDialect.translateExceptionIfPossible(HibernateJpaDialect.java:255)
        at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.translateExceptionIfPossible(AbstractEntityManagerFactoryBean.java:528)
        at org.springframework.dao.support.ChainedPersistenceExceptionTranslator.translateExceptionIfPossible(ChainedPersistenceExceptionTranslator.java:61)
        at org.springframework.dao.support.DataAccessUtils.translateIfNecessary(DataAccessUtils.java:242)
        at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:153)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
        at org.springframework.data.jpa.repository.support.CrudMethodMetadataPostProcessor$CrudMethodMetadataPopulatingMethodInterceptor.invoke(CrudMethodMetadataPostProcessor.java:149)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
        at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:93)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
        at com.sun.proxy.$Proxy185.deleteByPid(Unknown Source)
        at ca.uhn.fhir.jpa.dao.expunge.ResourceExpungeService.expungeHistoricalVersion(ResourceExpungeService.java:154)
        at ca.uhn.fhir.jpa.dao.expunge.ResourceExpungeService.expungeHistoricalVersionsOfId(ResourceExpungeService.java:250)
        at ca.uhn.fhir.jpa.dao.expunge.ResourceExpungeService.expungeHistoricalVersionsOfIds(ResourceExpungeService.java:181)
        at jdk.internal.reflect.GeneratedMethodAccessor747.invoke(Unknown Source)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:366)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:99)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
        at com.sun.proxy.$Proxy187.expungeHistoricalVersionsOfIds(Unknown Source)
        at ca.uhn.fhir.jpa.dao.expunge.ExpungeOperation.lambda$deleteHistoricalVersions$2(ExpungeOperation.java:124)
        at ca.uhn.fhir.jpa.dao.expunge.PartitionRunner.lambda$buildCallableTasks$0(PartitionRunner.java:94)
        at ca.uhn.fhir.jpa.dao.expunge.PartitionRunner.runInPartitionedThreads(PartitionRunner.java:60)
        ... 55 common frames omitted

To Reproduce Steps to reproduce the behavior:

  1. Delete resource
  2. $expunge resource with all options = true

Unfortunately, I'm not sure what makes this $expunge fail... Other $expunge calls that I've made have worked fine.

Environment (please complete the following information):

seanmcilvenna commented 3 years ago

I believe this is the same #2015