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Deadlock during measurement creation #1009

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Steffengreiner opened this issue Feb 10, 2025 · 1 comment
Open
1 task done

Deadlock during measurement creation #1009

Steffengreiner opened this issue Feb 10, 2025 · 1 comment
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@sven1103 @Shraddha0903
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bug Something isn't working high prio tasks that require urgent attention triage An issue that is in discussion to be either scheduled for implepmentation or denied

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@Steffengreiner
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What happened?

I wanted to see what would happen if i register multiple measurement templates at the same time.
Turns out, that the underlying data repo doesn't like that and this result in an exception possibly due to a deadlook during sample lookup

life.qbic.projectmanagement.infrastructure.sample.openbis.OpenbisConnector
Unexpected exception during openBIS operation.
life.qbic.projectmanagement.infrastructure.experiment.measurement.MeasurementRepositoryImplementation
Saving proteomics measurement in data repo failed

This can be reproduced on our Test instance Qpylon by registering the measurement files at least 6 times within the same upload.

Experiment

https://qpylon.qbic.uni-tuebingen.de/test/projects/2935224a-8190-4d9c-891e-b8747c6947d3/experiments/05e3d0b2-6484-458a-a5a6-469983a1b622/measurements

Measurement Files

ngs new.xlsx
protnew.xlsx

Possible solution
Update OpenBis to version 20.10.7.5 which addresses a deadlock situation within it's session manager in one of its commits:
https://sissource.ethz.ch/sispub/openbis/-/commits/20.10.7.5

What browsers are you seeing the problem on?

Firefox

Relevant log output

ERROR [async-10] l.q.p.i.s.openbis.OpenbisConnector: Unexpected exception during openBIS operation.
ch.systemsx.cisd.common.exceptions.UserFailureException: ERROR: deadlock detected
  Detail: Process 75288 waits for ShareLock on transaction 56260; blocked by process 75290.
Process 75290 waits for ShareLock on transaction 56261; blocked by process 75288.
  Hint: See server log for query details.
  Where: while locking tuple (98,20) in relation "samples_all" (Context: [])
	at ch.ethz.sis.openbis.generic.server.asapi.v3.utils.ExceptionUtils.create(ExceptionUtils.java:27)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.operation.OperationsExecutor.doExecute(OperationsExecutor.java:711)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.operation.OperationsExecutor.execute(OperationsExecutor.java:674)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.operation.SynchronousOperationExecutor.execute(SynchronousOperationExecutor.java:82)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.operation.ExecuteOperationExecutor.execute(ExecuteOperationExecutor.java:56)
	at jdk.internal.reflect.GeneratedMethodAccessor448.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:343)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:197)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:295)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
	at com.sun.proxy.$Proxy147.execute(Unknown Source)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.ApplicationServerApi.executeOperations(ApplicationServerApi.java:1672)
	at jdk.internal.reflect.GeneratedMethodAccessor546.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:197)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
	at ch.systemsx.cisd.openbis.generic.server.ServerExceptionTranslatingAdvisor$UserFailureExceptionTranslatingInterceptor.invoke(ServerExceptionTranslatingAdvisor.java:78)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:295)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at ch.systemsx.cisd.openbis.generic.server.OptimisticLockingRetryAdvisor$RetryInterceptor.invoke(OptimisticLockingRetryAdvisor.java:85)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at ch.systemsx.cisd.openbis.common.spring.LogInterceptor.invoke(LogInterceptor.java:115)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at ch.systemsx.cisd.openbis.common.pat.PersonalAccessTokenInterceptor$PersonalAccessTokenInvocation.proceedWithNewFirstArgument(PersonalAccessTokenInterceptor.java:82)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.ApplicationServerApiPersonalAccessTokenInvocationHandler.executeOperations(ApplicationServerApiPersonalAccessTokenInvocationHandler.java:1234)
	at jdk.internal.reflect.GeneratedMethodAccessor546.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 ch.systemsx.cisd.openbis.common.pat.PersonalAccessTokenInterceptor.invoke(PersonalAccessTokenInterceptor.java:41)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at ch.systemsx.cisd.openbis.generic.server.LongRunningThreadInterceptor.invoke(LongRunningThreadInterceptor.java:50)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
	at com.sun.proxy.$Proxy135.executeOperations(Unknown Source)
	at jdk.internal.reflect.GeneratedMethodAccessor546.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:197)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
	at org.springframework.aop.framework.adapter.ThrowsAdviceInterceptor.invoke(ThrowsAdviceInterceptor.java:112)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
	at com.sun.proxy.$Proxy185.executeOperations(Unknown Source)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	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.remoting.support.RemoteInvocation.invoke(RemoteInvocation.java:215)
	at org.springframework.remoting.support.DefaultRemoteInvocationExecutor.invoke(DefaultRemoteInvocationExecutor.java:39)
	at org.springframework.remoting.support.RemoteInvocationBasedExporter.invoke(RemoteInvocationBasedExporter.java:78)
	at org.springframework.remoting.support.RemoteInvocationBasedExporter.invokeAndCreateResult(RemoteInvocationBasedExporter.java:114)
	at org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter.handleRequest(HttpInvokerServiceExporter.java:79)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.ApplicationServerApiServer.handleRequest(ApplicationServerApiServer.java:55)
	at jdk.internal.reflect.GeneratedMethodAccessor262.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.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:209)
	at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136)
	at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:102)
	at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:871)
	at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:777)
	at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)
	at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:991)
	at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:925)
	at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:978)
	at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:881)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
	at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:855)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
	at org.eclipse.jetty.servlet.ServletHolder$NotAsync.service(ServletHolder.java:1459)
	at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:799)
	at org.eclipse.jetty.servlet.ServletHandler$ChainEnd.doFilter(ServletHandler.java:1631)
	at ch.systemsx.cisd.common.servlet.AbstractCrossOriginFilter.doFilter(AbstractCrossOriginFilter.java:130)
	at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
	at ch.systemsx.cisd.openbis.generic.server.CacheFilter.doFilter(CacheFilter.java:69)
	at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
	at ch.systemsx.cisd.common.servlet.HeaderFilter.doFilter(HeaderFilter.java:65)
	at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
	at ch.systemsx.cisd.common.servlet.MethodFilter.doFilter(MethodFilter.java:63)
	at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:201)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:548)
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:600)
	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
	at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235)
	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1624)
	at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233)
	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1434)
	at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)
	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:501)
	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1594)
	at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186)
	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1349)
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:191)
	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:146)
	at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:763)
	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
	at org.eclipse.jetty.server.Server.handle(Server.java:516)
	at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:400)
	at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:645)
	at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:392)
	at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:277)
	at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)
	at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105)
	at org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104)
	at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:338)
	at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:315)
	at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:173)
	at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
	at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:409)
	at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:883)
	at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1034)
	at java.base/java.lang.Thread.run(Thread.java:829)
	at org.springframework.remoting.support.RemoteInvocationUtils.fillInClientStackTraceIfPossible(RemoteInvocationUtils.java:45)
	at org.springframework.remoting.support.RemoteInvocationResult.recreate(RemoteInvocationResult.java:156)
	at org.springframework.remoting.support.RemoteInvocationBasedAccessor.recreateRemoteInvocationResult(RemoteInvocationBasedAccessor.java:85)
	at org.springframework.remoting.httpinvoker.HttpInvokerClientInterceptor.invoke(HttpInvokerClientInterceptor.java:162)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:223)
	at jdk.proxy2/jdk.proxy2.$Proxy225.executeOperations(Unknown Source)
	at life.qbic.projectmanagement.infrastructure.sample.openbis.OpenbisConnector.handleOperations(OpenbisConnector.java:661)
	at life.qbic.projectmanagement.infrastructure.sample.openbis.OpenbisConnector.createOpenbisSamples(OpenbisConnector.java:258)
	at life.qbic.projectmanagement.infrastructure.sample.openbis.OpenbisConnector.saveAllProteomics(OpenbisConnector.java:433)
	at life.qbic.projectmanagement.infrastructure.experiment.measurement.MeasurementRepositoryImplementation.saveAllProteomics(MeasurementRepositoryImplementation.java:208)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:355)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:196)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)
	at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:138)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)
	at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:720)
	at life.qbic.projectmanagement.infrastructure.experiment.measurement.MeasurementRepositoryImplementation$$SpringCGLIB$$0.saveAllProteomics(<generated>)
	at life.qbic.projectmanagement.domain.service.MeasurementDomainService.addProteomicsAll(MeasurementDomainService.java:47)
	at life.qbic.projectmanagement.application.measurement.MeasurementService.performRegistrationPxP(MeasurementService.java:296)
	at life.qbic.projectmanagement.application.measurement.MeasurementService.performRegistration(MeasurementService.java:230)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:355)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:196)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:379)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)
	at org.springframework.security.authorization.method.AuthorizationManagerBeforeMethodInterceptor.proceed(AuthorizationManagerBeforeMethodInterceptor.java:269)
	at org.springframework.security.authorization.method.AuthorizationManagerBeforeMethodInterceptor.attemptAuthorization(AuthorizationManagerBeforeMethodInterceptor.java:264)
	at org.springframework.security.authorization.method.AuthorizationManagerBeforeMethodInterceptor.invoke(AuthorizationManagerBeforeMethodInterceptor.java:197)
	at org.springframework.security.config.annotation.method.configuration.DeferringMethodInterceptor.invoke(DeferringMethodInterceptor.java:44)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)
	at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:720)
	at life.qbic.projectmanagement.application.measurement.MeasurementService$$SpringCGLIB$$0.performRegistration(<generated>)
	at life.qbic.projectmanagement.application.measurement.MeasurementService.registerAll(MeasurementService.java:203)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:355)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:196)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)
	at org.springframework.security.authorization.method.AuthorizationManagerBeforeMethodInterceptor.proceed(AuthorizationManagerBeforeMethodInterceptor.java:269)
	at org.springframework.security.authorization.method.AuthorizationManagerBeforeMethodInterceptor.attemptAuthorization(AuthorizationManagerBeforeMethodInterceptor.java:264)
	at org.springframework.security.authorization.method.AuthorizationManagerBeforeMethodInterceptor.invoke(AuthorizationManagerBeforeMethodInterceptor.java:197)
	at org.springframework.security.config.annotation.method.configuration.DeferringMethodInterceptor.invoke(DeferringMethodInterceptor.java:44)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)
	at org.springframework.aop.interceptor.AsyncExecutionInterceptor.lambda$invoke$0(AsyncExecutionInterceptor.java:113)
	at org.springframework.util.concurrent.FutureUtils.lambda$toSupplier$0(FutureUtils.java:74)
	at java.base/java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1768)
	at org.springframework.security.concurrent.DelegatingSecurityContextRunnable.run(DelegatingSecurityContextRunnable.java:94)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: ch.systemsx.cisd.common.exceptions.UserFailureException: ERROR: deadlock detected
  Detail: Process 75288 waits for ShareLock on transaction 56260; blocked by process 75290.
Process 75290 waits for ShareLock on transaction 56261; blocked by process 75288.
  Hint: See server log for query details.
  Where: while locking tuple (98,20) in relation "samples_all"
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.entity.AbstractCreateEntityExecutor.create(AbstractCreateEntityExecutor.java:99)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.sample.CreateSamplesOperationExecutor.doExecute(CreateSamplesOperationExecutor.java:51)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.sample.CreateSamplesOperationExecutor.doExecute(CreateSamplesOperationExecutor.java:34)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.common.OperationExecutor$2.execute(OperationExecutor.java:96)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.common.OperationExecutor$2.execute(OperationExecutor.java:88)
	at ch.systemsx.cisd.openbis.generic.server.ConcurrentOperationLimiter.executeLimited(ConcurrentOperationLimiter.java:108)
	at ch.systemsx.cisd.openbis.generic.server.ConcurrentOperationLimiter.executeLimitedWithTimeout(ConcurrentOperationLimiter.java:85)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.common.OperationExecutor.execute(OperationExecutor.java:87)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.operation.OperationsExecutor.executeCreations(OperationsExecutor.java:863)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.operation.OperationsExecutor.doExecute(OperationsExecutor.java:685)
	... 195 common frames omitted
Caused by: ch.systemsx.cisd.common.exceptions.MasqueradingException: ERROR: deadlock detected
  Detail: Process 75288 waits for ShareLock on transaction 56260; blocked by process 75290.
Process 75290 waits for ShareLock on transaction 56261; blocked by process 75288.
  Hint: See server log for query details.
  Where: while locking tuple (98,20) in relation "samples_all"
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2676)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2366)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:356)
	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:496)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:413)
	at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:190)
	at org.postgresql.jdbc.PgPreparedStatement.executeUpdate(PgPreparedStatement.java:152)
	at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:105)
	at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:105)
	at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:175)
	at org.hibernate.engine.jdbc.batch.internal.NonBatchingBatch.addToBatch(NonBatchingBatch.java:45)
	at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:3198)
	at org.hibernate.persister.entity.AbstractEntityPersister.updateOrInsert(AbstractEntityPersister.java:3077)
	at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:3457)
	at org.hibernate.action.internal.EntityUpdateAction.execute(EntityUpdateAction.java:145)
	at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:599)
	at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:473)
	at org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:337)
	at org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:39)
	at org.hibernate.internal.SessionImpl.doFlush(SessionImpl.java:1436)
	at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1422)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.entity.AbstractCreateEntityExecutor.create(AbstractCreateEntityExecutor.java:88)
	... 204 common frames omitted
2025-02-10 16:15:13,714 ERROR [async-10] l.q.p.i.e.m.MeasurementRepositoryImplementation: Saving proteomics measurement in data repo failed
life.qbic.application.commons.ApplicationException: Unexpected exception during openBIS operation.
	at life.qbic.projectmanagement.infrastructure.sample.openbis.OpenbisConnector.handleOperations(OpenbisConnector.java:664)
	at life.qbic.projectmanagement.infrastructure.sample.openbis.OpenbisConnector.createOpenbisSamples(OpenbisConnector.java:258)
	at life.qbic.projectmanagement.infrastructure.sample.openbis.OpenbisConnector.saveAllProteomics(OpenbisConnector.java:433)
	at life.qbic.projectmanagement.infrastructure.experiment.measurement.MeasurementRepositoryImplementation.saveAllProteomics(MeasurementRepositoryImplementation.java:208)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:355)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:196)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)
	at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:138)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)
	at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:720)
	at life.qbic.projectmanagement.infrastructure.experiment.measurement.MeasurementRepositoryImplementation$$SpringCGLIB$$0.saveAllProteomics(<generated>)
	at life.qbic.projectmanagement.domain.service.MeasurementDomainService.addProteomicsAll(MeasurementDomainService.java:47)
	at life.qbic.projectmanagement.application.measurement.MeasurementService.performRegistrationPxP(MeasurementService.java:296)
	at life.qbic.projectmanagement.application.measurement.MeasurementService.performRegistration(MeasurementService.java:230)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:355)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:196)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:379)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)
	at org.springframework.security.authorization.method.AuthorizationManagerBeforeMethodInterceptor.proceed(AuthorizationManagerBeforeMethodInterceptor.java:269)
	at org.springframework.security.authorization.method.AuthorizationManagerBeforeMethodInterceptor.attemptAuthorization(AuthorizationManagerBeforeMethodInterceptor.java:264)
	at org.springframework.security.authorization.method.AuthorizationManagerBeforeMethodInterceptor.invoke(AuthorizationManagerBeforeMethodInterceptor.java:197)
	at org.springframework.security.config.annotation.method.configuration.DeferringMethodInterceptor.invoke(DeferringMethodInterceptor.java:44)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)
	at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:720)
	at life.qbic.projectmanagement.application.measurement.MeasurementService$$SpringCGLIB$$0.performRegistration(<generated>)
	at life.qbic.projectmanagement.application.measurement.MeasurementService.registerAll(MeasurementService.java:203)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:355)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:196)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)
	at org.springframework.security.authorization.method.AuthorizationManagerBeforeMethodInterceptor.proceed(AuthorizationManagerBeforeMethodInterceptor.java:269)
	at org.springframework.security.authorization.method.AuthorizationManagerBeforeMethodInterceptor.attemptAuthorization(AuthorizationManagerBeforeMethodInterceptor.java:264)
	at org.springframework.security.authorization.method.AuthorizationManagerBeforeMethodInterceptor.invoke(AuthorizationManagerBeforeMethodInterceptor.java:197)
	at org.springframework.security.config.annotation.method.configuration.DeferringMethodInterceptor.invoke(DeferringMethodInterceptor.java:44)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)
	at org.springframework.aop.interceptor.AsyncExecutionInterceptor.lambda$invoke$0(AsyncExecutionInterceptor.java:113)
	at org.springframework.util.concurrent.FutureUtils.lambda$toSupplier$0(FutureUtils.java:74)
	at java.base/java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1768)
	at org.springframework.security.concurrent.DelegatingSecurityContextRunnable.run(DelegatingSecurityContextRunnable.java:94)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: ch.systemsx.cisd.common.exceptions.UserFailureException: ERROR: deadlock detected
  Detail: Process 75288 waits for ShareLock on transaction 56260; blocked by process 75290.
Process 75290 waits for ShareLock on transaction 56261; blocked by process 75288.
  Hint: See server log for query details.
  Where: while locking tuple (98,20) in relation "samples_all" (Context: [])
	at ch.ethz.sis.openbis.generic.server.asapi.v3.utils.ExceptionUtils.create(ExceptionUtils.java:27)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.operation.OperationsExecutor.doExecute(OperationsExecutor.java:711)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.operation.OperationsExecutor.execute(OperationsExecutor.java:674)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.operation.SynchronousOperationExecutor.execute(SynchronousOperationExecutor.java:82)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.operation.ExecuteOperationExecutor.execute(ExecuteOperationExecutor.java:56)
	at jdk.internal.reflect.GeneratedMethodAccessor448.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:343)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:197)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:295)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
	at com.sun.proxy.$Proxy147.execute(Unknown Source)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.ApplicationServerApi.executeOperations(ApplicationServerApi.java:1672)
	at jdk.internal.reflect.GeneratedMethodAccessor546.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:343)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:197)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
	at ch.systemsx.cisd.openbis.generic.server.ServerExceptionTranslatingAdvisor$UserFailureExceptionTranslatingInterceptor.invoke(ServerExceptionTranslatingAdvisor.java:78)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:295)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at ch.systemsx.cisd.openbis.generic.server.OptimisticLockingRetryAdvisor$RetryInterceptor.invoke(OptimisticLockingRetryAdvisor.java:85)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at ch.systemsx.cisd.openbis.common.spring.LogInterceptor.invoke(LogInterceptor.java:115)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at ch.systemsx.cisd.openbis.common.pat.PersonalAccessTokenInterceptor$PersonalAccessTokenInvocation.proceedWithNewFirstArgument(PersonalAccessTokenInterceptor.java:82)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.ApplicationServerApiPersonalAccessTokenInvocationHandler.executeOperations(ApplicationServerApiPersonalAccessTokenInvocationHandler.java:1234)
	at jdk.internal.reflect.GeneratedMethodAccessor546.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at ch.systemsx.cisd.openbis.common.pat.PersonalAccessTokenInterceptor.invoke(PersonalAccessTokenInterceptor.java:41)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at ch.systemsx.cisd.openbis.generic.server.LongRunningThreadInterceptor.invoke(LongRunningThreadInterceptor.java:50)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
	at com.sun.proxy.$Proxy135.executeOperations(Unknown Source)
	at jdk.internal.reflect.GeneratedMethodAccessor546.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:343)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:197)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
	at org.springframework.aop.framework.adapter.ThrowsAdviceInterceptor.invoke(ThrowsAdviceInterceptor.java:112)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
	at com.sun.proxy.$Proxy185.executeOperations(Unknown Source)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	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.remoting.support.RemoteInvocation.invoke(RemoteInvocation.java:215)
	at org.springframework.remoting.support.DefaultRemoteInvocationExecutor.invoke(DefaultRemoteInvocationExecutor.java:39)
	at org.springframework.remoting.support.RemoteInvocationBasedExporter.invoke(RemoteInvocationBasedExporter.java:78)
	at org.springframework.remoting.support.RemoteInvocationBasedExporter.invokeAndCreateResult(RemoteInvocationBasedExporter.java:114)
	at org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter.handleRequest(HttpInvokerServiceExporter.java:79)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.ApplicationServerApiServer.handleRequest(ApplicationServerApiServer.java:55)
	at jdk.internal.reflect.GeneratedMethodAccessor262.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.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:209)
	at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136)
	at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:102)
	at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:871)
	at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:777)
	at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)
	at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:991)
	at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:925)
	at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:978)
	at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:881)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
	at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:855)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
	at org.eclipse.jetty.servlet.ServletHolder$NotAsync.service(ServletHolder.java:1459)
	at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:799)
	at org.eclipse.jetty.servlet.ServletHandler$ChainEnd.doFilter(ServletHandler.java:1631)
	at ch.systemsx.cisd.common.servlet.AbstractCrossOriginFilter.doFilter(AbstractCrossOriginFilter.java:130)
	at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
	at ch.systemsx.cisd.openbis.generic.server.CacheFilter.doFilter(CacheFilter.java:69)
	at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
	at ch.systemsx.cisd.common.servlet.HeaderFilter.doFilter(HeaderFilter.java:65)
	at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
	at ch.systemsx.cisd.common.servlet.MethodFilter.doFilter(MethodFilter.java:63)
	at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:201)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:548)
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:600)
	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
	at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235)
	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1624)
	at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233)
	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1434)
	at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)
	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:501)
	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1594)
	at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186)
	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1349)
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:191)
	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:146)
	at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:763)
	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
	at org.eclipse.jetty.server.Server.handle(Server.java:516)
	at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:400)
	at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:645)
	at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:392)
	at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:277)
	at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)
	at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105)
	at org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104)
	at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:338)
	at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:315)
	at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:173)
	at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
	at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:409)
	at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:883)
	at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1034)
	at java.base/java.lang.Thread.run(Thread.java:829)
	at org.springframework.remoting.support.RemoteInvocationUtils.fillInClientStackTraceIfPossible(RemoteInvocationUtils.java:45)
	at org.springframework.remoting.support.RemoteInvocationResult.recreate(RemoteInvocationResult.java:156)
	at org.springframework.remoting.support.RemoteInvocationBasedAccessor.recreateRemoteInvocationResult(RemoteInvocationBasedAccessor.java:85)
	at org.springframework.remoting.httpinvoker.HttpInvokerClientInterceptor.invoke(HttpInvokerClientInterceptor.java:162)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:223)
	at jdk.proxy2/jdk.proxy2.$Proxy225.executeOperations(Unknown Source)
	at life.qbic.projectmanagement.infrastructure.sample.openbis.OpenbisConnector.handleOperations(OpenbisConnector.java:661)
	... 61 common frames omitted
Caused by: ch.systemsx.cisd.common.exceptions.UserFailureException: ERROR: deadlock detected
  Detail: Process 75288 waits for ShareLock on transaction 56260; blocked by process 75290.
Process 75290 waits for ShareLock on transaction 56261; blocked by process 75288.
  Hint: See server log for query details.
  Where: while locking tuple (98,20) in relation "samples_all"
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.entity.AbstractCreateEntityExecutor.create(AbstractCreateEntityExecutor.java:99)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.sample.CreateSamplesOperationExecutor.doExecute(CreateSamplesOperationExecutor.java:51)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.sample.CreateSamplesOperationExecutor.doExecute(CreateSamplesOperationExecutor.java:34)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.common.OperationExecutor$2.execute(OperationExecutor.java:96)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.common.OperationExecutor$2.execute(OperationExecutor.java:88)
	at ch.systemsx.cisd.openbis.generic.server.ConcurrentOperationLimiter.executeLimited(ConcurrentOperationLimiter.java:108)
	at ch.systemsx.cisd.openbis.generic.server.ConcurrentOperationLimiter.executeLimitedWithTimeout(ConcurrentOperationLimiter.java:85)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.common.OperationExecutor.execute(OperationExecutor.java:87)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.operation.OperationsExecutor.executeCreations(OperationsExecutor.java:863)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.operation.OperationsExecutor.doExecute(OperationsExecutor.java:685)
	... 195 common frames omitted
Caused by: ch.systemsx.cisd.common.exceptions.MasqueradingException: ERROR: deadlock detected
  Detail: Process 75288 waits for ShareLock on transaction 56260; blocked by process 75290.
Process 75290 waits for ShareLock on transaction 56261; blocked by process 75288.
  Hint: See server log for query details.
  Where: while locking tuple (98,20) in relation "samples_all"
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2676)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2366)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:356)
	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:496)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:413)
	at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:190)
	at org.postgresql.jdbc.PgPreparedStatement.executeUpdate(PgPreparedStatement.java:152)
	at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:105)
	at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:105)
	at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:175)
	at org.hibernate.engine.jdbc.batch.internal.NonBatchingBatch.addToBatch(NonBatchingBatch.java:45)
	at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:3198)
	at org.hibernate.persister.entity.AbstractEntityPersister.updateOrInsert(AbstractEntityPersister.java:3077)
	at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:3457)
	at org.hibernate.action.internal.EntityUpdateAction.execute(EntityUpdateAction.java:145)
	at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:599)
	at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:473)
	at org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:337)
	at org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:39)
	at org.hibernate.internal.SessionImpl.doFlush(SessionImpl.java:1436)
	at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1422)
	at ch.ethz.sis.openbis.generic.server.asapi.v3.executor.entity.AbstractCreateEntityExecutor.create(AbstractCreateEntityExecutor.java:88)
	... 204 common frames omitted
2025-02-10 16:15:13,779 ERROR [async-10] l.q.p.a.m.MeasurementService: Failed to register measurement
life.qbic.application.commons.ApplicationException: Unexpected exception during openBIS operation.
	at life.qbic.projectmanagement.infrastructure.sample.openbis.OpenbisConnector.handleOperations(OpenbisConnector.java:664)
	at life.qbic.projectmanagement.infrastructure.sample.openbis.OpenbisConnector.createOpenbisSamples(OpenbisConnector.java:258)
	at life.qbic.projectmanagement.infrastructure.sample.openbis.OpenbisConnector.saveAllProteomics(OpenbisConnector.java:433)
	at life.qbic.projectmanagement.infrastructure.experiment.measurement.MeasurementRepositoryImplementation.saveAllProteomics(MeasurementRepositoryImplementation.java:208)

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@Steffengreiner Steffengreiner added bug Something isn't working triage An issue that is in discussion to be either scheduled for implepmentation or denied labels Feb 10, 2025
@Steffengreiner Steffengreiner added the high prio tasks that require urgent attention label Feb 10, 2025
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There is no way for us to see if this issue is related to the work in #1005 , or if it has been there before as well.

Please note the commit for this issue, if it is not a release.

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