Cohort Sample fails for BigQuery Datasets #2427
Description
Steps to reproduce:
- Create Cohort Definition
- Generate on BigQuery datasource
- Create Sample for the datasource
Issue:
ATLAS will show error popup
WebAPI throws this stack trace:
2025-02-12 09:15:56.557 INFO http-nio-8080-exec-278 org.ohdsi.webapi.audittrail.AuditTrailServiceImpl - [] - <110>1 2025-02-12T09:15:56.544Z 48469e132e3c Atlas - - - myuser 172.18.0.1 b253f21d-3dcd-4a1f-91bc-1f3db3cce670 - http://atlas/#/cohortdefinition/2260/samples/SYNPUF_110K_BQ - POST /WebAPI/cohortsample/2260/SYNPUF_110K_BQ - FAILURE (see application log for details)
2025-02-12 09:15:56.558 ERROR http-nio-8080-exec-278 org.ohdsi.webapi.util.GenericExceptionMapper - [] - java.lang.NoClassDefFoundError: com/google/cloud/bigquery/storage/v1/BigQueryReadGrpc
at com.google.cloud.bigquery.storage.v1.stub.EnhancedBigQueryReadStub.readRowsCallable(EnhancedBigQueryReadStub.java:124)
at com.google.cloud.bigquery.storage.v1.BigQueryReadClient.readRowsCallable(BigQueryReadClient.java:290)
at com.simba.googlebigquery.googlebigquery.dataengine.BQBufferManager$StreamReader.call(Unknown Source)
at com.simba.googlebigquery.googlebigquery.dataengine.BQBufferManager.initStream(Unknown Source)
at com.simba.googlebigquery.googlebigquery.dataengine.BQBufferManager.startReadingWithHTAPI(Unknown Source)
at com.simba.googlebigquery.googlebigquery.dataengine.BQBufferManager.processTheFirstPage(Unknown Source)
at com.simba.googlebigquery.googlebigquery.dataengine.BQBufferManager.<init>(Unknown Source)
at com.simba.googlebigquery.googlebigquery.dataengine.BQResultSet.<init>(Unknown Source)
at com.simba.googlebigquery.googlebigquery.dataengine.BQSQLExecutor.execute(Unknown Source)
at com.simba.googlebigquery.jdbc.common.SPreparedStatement.executeWithParams(Unknown Source)
at com.simba.googlebigquery.jdbc.common.SPreparedStatement.executeQuery(Unknown Source)
at org.springframework.jdbc.core.JdbcTemplate$1.doInPreparedStatement(JdbcTemplate.java:696)
at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:638)
at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:688)
at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:720)
at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:730)
at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:780)
at org.ohdsi.webapi.cohortsample.CohortSamplingService.sampleElements(CohortSamplingService.java:434)
at org.ohdsi.webapi.cohortsample.CohortSamplingService.createSample(CohortSamplingService.java:176)
at org.ohdsi.webapi.service.CohortSampleService.createCohortSample(CohortSampleService.java:183)
at org.ohdsi.webapi.service.CohortSampleService$$FastClassBySpringCGLIB$$5c2766cc.invoke(<generated>)
at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:736)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.aop.aspectj.MethodInvocationProceedingJoinPoint.proceed(MethodInvocationProceedingJoinPoint.java:84)
at org.ohdsi.webapi.audittrail.AuditTrailAspect.auditLog(AuditTrailAspect.java:92)
at sun.reflect.GeneratedMethodAccessor277.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.aspectj.AbstractAspectJAdvice.invokeAdviceMethodWithGivenArgs(AbstractAspectJAdvice.java:627)
at org.springframework.aop.aspectj.AbstractAspectJAdvice.invokeAdviceMethod(AbstractAspectJAdvice.java:616)
at org.springframework.aop.aspectj.AspectJAroundAdvice.invoke(AspectJAroundAdvice.java:70)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:168)
at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:671)
at org.ohdsi.webapi.service.CohortSampleService$$EnhancerBySpringCGLIB$$cb3af01d.createCohortSample(<generated>)
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:498)
at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:144)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:161)
at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$TypeOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:205)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:99)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:389)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:347)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:102)
at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:326)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:305)
at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1154)
at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:473)
at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:427)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:388)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:341)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:228)
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.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61)
at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
at org.ohdsi.webapi.shiro.filters.ResponseNoCacheFilter.doFilter(ResponseNoCacheFilter.java:26)
at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:147)
at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:458)
at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:373)
at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:387)
at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:370)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.ohdsi.webapi.shiro.filters.CacheFilter.doFilter(CacheFilter.java:35)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.ohdsi.webapi.shiro.filters.ExceptionHandlerFilter.doFilter(ExceptionHandlerFilter.java:28)
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.RequestContextFilter.doFilterInternal(RequestContextFilter.java:99)
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.springframework.web.filter.HttpPutFormContentFilter.doFilterInternal(HttpPutFormContentFilter.java:109)
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.springframework.web.filter.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:93)
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.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.springframework.boot.web.support.ErrorPageFilter.doFilter(ErrorPageFilter.java:128)
at org.springframework.boot.web.support.ErrorPageFilter.access$000(ErrorPageFilter.java:66)
at org.springframework.boot.web.support.ErrorPageFilter$1.doFilterInternal(ErrorPageFilter.java:103)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.boot.web.support.ErrorPageFilter.doFilter(ErrorPageFilter.java:121)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:197)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:543)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:135)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:698)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:367)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:639)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:882)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1693)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191)
at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:750)
Caused by: java.lang.ClassNotFoundException: com.google.cloud.bigquery.storage.v1.BigQueryReadGrpc
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1420)
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1228)
... 153 more
It looks like it's some how related to JDBC Driver.