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OHDSI / WebAPI

OHDSI WebAPI contains all OHDSI services that can be called from OHDSI applications
Apache License 2.0
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Search - RC/DRC counts give 'timeout' in BigQuery #2270

Closed konstjar closed 1 year ago

konstjar commented 1 year ago

Expected behavior

RC/DRC records are shown in ATLAS

Actual behavior

RC/DRC records give 'timeout'. The problem is in BigQuery maximum number of GoogleSQL query parameters. BigQuery maximum value is 10,000 while WebAPI sends 30,000.

Steps to reproduce behavior

  1. Get BigQuery dataset connected to ATLAS
  2. Search for some generic like 'aspirin'

Log from WebAPI:

Caused by: java.sql.SQLException: [Simba][BigQueryJDBCDriver](100032) Error executing query job. Message: 400 Bad Request
{
  "code" : 400,
  "errors" : [ {
    "domain" : "global",
    "message" : "Too many query parameters: 30000 exceeds limit of 10000.",
    "reason" : "invalid"
  } ],
  "message" : "Too many query parameters: 30000 exceeds limit of 10000.",
  "status" : "INVALID_ARGUMENT"
}
    at com.simba.googlebigquery.googlebigquery.client.BQClient.throwExecException(Unknown Source)
    at com.simba.googlebigquery.googlebigquery.client.BQClient.insertJob(Unknown Source)
    at com.simba.googlebigquery.googlebigquery.client.BQClient.executeQuery(Unknown Source)
    at com.simba.googlebigquery.googlebigquery.dataengine.BQAbstractExecutor.execute(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:745)
    at org.ohdsi.webapi.cdmresults.service.CDMCacheService.loadCache(CDMCacheService.java:172)
    at org.ohdsi.webapi.cdmresults.service.CDMCacheService.cacheRecordsById(CDMCacheService.java:146)
    at org.ohdsi.webapi.cdmresults.service.CDMCacheService.findAndCache(CDMCacheService.java:90)
    at org.ohdsi.webapi.service.CDMResultsService.getConceptRecordCount(CDMResultsService.java:187)
    at org.ohdsi.webapi.service.CDMResultsService$$FastClassBySpringCGLIB$$f65c71c1.invoke(<generated>)
    at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
    at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:736)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:671)
    at org.ohdsi.webapi.service.CDMResultsService$$EnhancerBySpringCGLIB$$1859a5e0.getConceptRecordCount(<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)
Caused by: com.simba.googlebigquery.support.exceptions.GeneralException: [Simba][BigQueryJDBCDriver](100032) Error executing query job. Message: 400 Bad Request
chrisknoll commented 1 year ago

I believe that there is a param about max param size in the codebase somewhere, I feel like I've seen dialect-specific checks for that. I'm sorry I can't do the search right away but I think this has a solution in the codebase, we may just have missed it for bigquery, or it is a application.properties config.

konstjar commented 1 year ago

I believe it's configurable. Thank you for suggestion. I will update the ticket after research.