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Failing co-expression endpoint (related to refactoring of CoExpressionServiceImpl) #6391

Closed pvannierop closed 4 years ago

pvannierop commented 4 years ago

In release-3.1.0 branch localdb e2e-test show that co-expression functionality is broken when using gene/gene set cross comparisons. We suspect it is related to refactoring to introduce use of Iterable for MolecularDataService (done in commit a645fbec15).

The error is thrown from the getCoExpressions method. It appears that this is related to the use of Transactions in CoExpressionServiceImpl:

// transaction needs to be setup here in order to return Iterable from molecularDataService in fetchCoExpressions
    @Transactional(readOnly=true)
    public List<CoExpression> getCoExpressions(String geneticEntityId, CoExpression.GeneticEntityType geneticEntityType,
            String sampleListId, String molecularProfileIdA, String molecularProfileIdB, Double threshold)
            throws MolecularProfileNotFoundException, SampleListNotFoundException, GenesetNotFoundException,
            GeneNotFoundException {

The error is thrown from line 93 when the molecularDataService is being called:

} else {
            molecularDataListB = molecularDataService.getMolecularData(molecularProfileIdB, sampleListId, null,
                    "SUMMARY");
        }

The errors thrown are:

org.springframework.transaction.CannotCreateTransactionException: Could not create JDBC savepoint; nested exception is java.sql.SQLException: Connection is read-only. Queries leading to data modification are not allowed.
    org.springframework.jdbc.datasource.JdbcTransactionObjectSupport.createSavepoint(JdbcTransactionObjectSupport.java:112)
    org.springframework.transaction.support.AbstractTransactionStatus.createAndHoldSavepoint(AbstractTransactionStatus.java:144)
    org.springframework.transaction.support.AbstractPlatformTransactionManager.handleExistingTransaction(AbstractPlatformTransactionManager.java:458)
    org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:349)
    org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:461)
    org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:277)
    org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
    com.sun.proxy.$Proxy85.getGeneMolecularAlterations(Unknown Source)
    org.cbioportal.service.impl.MolecularDataServiceImpl.fetchMolecularData(MolecularDataServiceImpl.java:87)
    org.cbioportal.service.impl.MolecularDataServiceImpl.getMolecularData(MolecularDataServiceImpl.java:45)
    sun.reflect.GeneratedMethodAccessor389.invoke(Unknown Source)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    java.lang.reflect.Method.invoke(Method.java:498)
    org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
    org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    org.springframework.aop.framework.adapter.MethodBeforeAdviceInterceptor.invoke(MethodBeforeAdviceInterceptor.java:52)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.aspectj.AspectJAfterAdvice.invoke(AspectJAfterAdvice.java:47)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
    com.sun.proxy.$Proxy154.getMolecularData(Unknown Source)
    org.cbioportal.service.impl.CoExpressionServiceImpl.getCoExpressions(CoExpressionServiceImpl.java:93)
    sun.reflect.GeneratedMethodAccessor577.invoke(Unknown Source)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    java.lang.reflect.Method.invoke(Method.java:498)
    org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
    org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    org.springframework.aop.framework.adapter.MethodBeforeAdviceInterceptor.invoke(MethodBeforeAdviceInterceptor.java:52)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.aspectj.AspectJAfterAdvice.invoke(AspectJAfterAdvice.java:47)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
    org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
    org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
    com.sun.proxy.$Proxy163.getCoExpressions(Unknown Source)
    org.cbioportal.web.CoExpressionController.fetchCoExpressions(CoExpressionController.java:63)
    org.cbioportal.web.CoExpressionController$$FastClassBySpringCGLIB$$17a60ed.invoke(&lt;generated&gt;)
    org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
    org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:738)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    org.springframework.validation.beanvalidation.MethodValidationInterceptor.invoke(MethodValidationInterceptor.java:150)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.adapter.MethodBeforeAdviceInterceptor.invoke(MethodBeforeAdviceInterceptor.java:52)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.aspectj.AspectJAfterAdvice.invoke(AspectJAfterAdvice.java:47)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:673)
    org.cbioportal.web.CoExpressionController$$EnhancerBySpringCGLIB$$5366a02d.fetchCoExpressions(&lt;generated&gt;)
    sun.reflect.GeneratedMethodAccessor576.invoke(Unknown Source)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    java.lang.reflect.Method.invoke(Method.java:498)
    org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205)
    org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:133)
    org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:97)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:827)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:738)
    org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
    org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:967)
    org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:901)
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
    org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:872)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:661)
    org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
    org.mskcc.cbio.portal.util.XssFilter.doFilter(XssFilter.java:65)
    org.cbioportal.web.util.ResettableHttpServletRequestFilter.doFilter(ResettableHttpServletRequestFilter.java:26)
    org.apache.catalina.filters.HttpHeaderSecurityFilter.doFilter(HttpHeaderSecurityFilter.java:126)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:127)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:119)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:170)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:66)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215)
    org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178)
    org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:347)
    org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:263)
    com.vlkan.hrrs.servlet.HrrsFilter.doFilter(HrrsFilter.java:85)
    org.apache.catalina.filters.CorsFilter.handleNonCORS(CorsFilter.java:364)
    org.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:170)

and 

java.sql.SQLException: Connection is read-only. Queries leading to data modification are not allowed.
    com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
    com.mysql.jdbc.SQLError.createSQLException(SQLError.java:987)
    com.mysql.jdbc.SQLError.createSQLException(SQLError.java:982)
    com.mysql.jdbc.SQLError.createSQLException(SQLError.java:927)
    com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1650)
    com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1617)
    com.mysql.jdbc.ConnectionImpl.setSavepoint(ConnectionImpl.java:5169)
    com.mysql.jdbc.ConnectionImpl.setSavepoint(ConnectionImpl.java:5184)
    org.apache.commons.dbcp2.DelegatingConnection.setSavepoint(DelegatingConnection.java:687)
    org.apache.commons.dbcp2.DelegatingConnection.setSavepoint(DelegatingConnection.java:687)
    org.springframework.jdbc.datasource.ConnectionHolder.createSavepoint(ConnectionHolder.java:177)
    org.springframework.jdbc.datasource.JdbcTransactionObjectSupport.createSavepoint(JdbcTransactionObjectSupport.java:109)
    org.springframework.transaction.support.AbstractTransactionStatus.createAndHoldSavepoint(AbstractTransactionStatus.java:144)
    org.springframework.transaction.support.AbstractPlatformTransactionManager.handleExistingTransaction(AbstractPlatformTransactionManager.java:458)
    org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:349)
    org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:461)
    org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:277)
    org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
    com.sun.proxy.$Proxy85.getGeneMolecularAlterations(Unknown Source)
    org.cbioportal.service.impl.MolecularDataServiceImpl.fetchMolecularData(MolecularDataServiceImpl.java:87)
    org.cbioportal.service.impl.MolecularDataServiceImpl.getMolecularData(MolecularDataServiceImpl.java:45)
    sun.reflect.GeneratedMethodAccessor389.invoke(Unknown Source)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    java.lang.reflect.Method.invoke(Method.java:498)
    org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
    org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    org.springframework.aop.framework.adapter.MethodBeforeAdviceInterceptor.invoke(MethodBeforeAdviceInterceptor.java:52)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.aspectj.AspectJAfterAdvice.invoke(AspectJAfterAdvice.java:47)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
    com.sun.proxy.$Proxy154.getMolecularData(Unknown Source)
    org.cbioportal.service.impl.CoExpressionServiceImpl.getCoExpressions(CoExpressionServiceImpl.java:93)
    sun.reflect.GeneratedMethodAccessor577.invoke(Unknown Source)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    java.lang.reflect.Method.invoke(Method.java:498)
    org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
    org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    org.springframework.aop.framework.adapter.MethodBeforeAdviceInterceptor.invoke(MethodBeforeAdviceInterceptor.java:52)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.aspectj.AspectJAfterAdvice.invoke(AspectJAfterAdvice.java:47)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
    org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
    org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
    com.sun.proxy.$Proxy163.getCoExpressions(Unknown Source)
    org.cbioportal.web.CoExpressionController.fetchCoExpressions(CoExpressionController.java:63)
    org.cbioportal.web.CoExpressionController$$FastClassBySpringCGLIB$$17a60ed.invoke(&lt;generated&gt;)
    org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
    org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:738)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    org.springframework.validation.beanvalidation.MethodValidationInterceptor.invoke(MethodValidationInterceptor.java:150)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.adapter.MethodBeforeAdviceInterceptor.invoke(MethodBeforeAdviceInterceptor.java:52)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.aspectj.AspectJAfterAdvice.invoke(AspectJAfterAdvice.java:47)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:673)
    org.cbioportal.web.CoExpressionController$$EnhancerBySpringCGLIB$$5366a02d.fetchCoExpressions(&lt;generated&gt;)
    sun.reflect.GeneratedMethodAccessor576.invoke(Unknown Source)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    java.lang.reflect.Method.invoke(Method.java:498)
    org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205)
    org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:133)
    org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:97)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:827)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:738)
    org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
    org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:967)
    org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:901)
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
    org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:872)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:661)
    org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
    org.mskcc.cbio.portal.util.XssFilter.doFilter(XssFilter.java:65)
    org.cbioportal.web.util.ResettableHttpServletRequestFilter.doFilter(ResettableHttpServletRequestFilter.java:26)
    org.apache.catalina.filters.HttpHeaderSecurityFilter.doFilter(HttpHeaderSecurityFilter.java:126)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:127)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:119)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:170)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:66)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215)
    org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178)
    org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:347)
    org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:263)
    com.vlkan.hrrs.servlet.HrrsFilter.doFilter(HrrsFilter.java:85)
    org.apache.catalina.filters.CorsFilter.handleNonCORS(CorsFilter.java:364)
    org.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:170)
n1zea144 commented 4 years ago

@pvannierop Can you provide me the query that was being executed?

pvannierop commented 4 years ago

I do not know the SQL query that triggered the error. I do know that call

http://localhost:8081/api/molecular-profiles/co-expressions/fetch?molecularProfileIdA=study_es_0_gsva_scores&molecularProfileIdB=study_es_0_mrna&threshold=0

fails. When study_es_0 is loaded this call comes from the co-expression tab reached via URL: http://localhost:8081/results/coexpression?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=study_es_0&case_set_id=study_es_0_all&clinicallist=NUM_SAMPLES_PER_PATIENT%2CPROFILED_IN_study_es_0_gsva_scores%2CPROFILED_IN_study_es_0_mutations%2CPROFILED_IN_study_es_0_gistic%2CPROFILED_IN_study_es_0_mrna_median_Zscores&data_priority=0&gene_list=CREB3L1%2520RPS11%2520PNMA1%2520MMP2%2520ZHX3%2520ERCC5&geneset_list=GO_ATP_DEPENDENT_CHROMATIN_REMODELING&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=study_es_0_gistic&genetic_profile_ids_PROFILE_GENESET_SCORE=study_es_0_gsva_scores&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=study_es_0_mrna_median_Zscores&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=study_es_0_mutations&show_samples=false&tab_index=tab_visualize

n1zea144 commented 4 years ago

Just a quick update - I cannot get as far as you. I'm running into an exception from another call into the web service when the coexpression tab is selected:

ERROR org.cbioportal.web.util.InvolvedCancerStudyExtractorInterceptor - exception thrown during extraction o f genePanelSampleMolecularIdentifiers: com.fasterxml.jackson.databind.exc.MismatchedInputException: Cannot deserialize instance of org.cbioportal.web.parameter.SampleMolecularIdentifier[] out of START_OBJECT token

This is using a backend built from release-3.1.0. Working on figuring this out....

n1zea144 commented 4 years ago

@pvannierop I bypassed the jackson issue for the moment by rolling my own coexpression endpoint request. The following PR should address this issue: PR-6420

@oplantalech Is it possible for you to confirm fix while @pvannierop is on holiday?

n1zea144 commented 4 years ago

There was another issue with various executions paths leading to molecular data that is related to this issue. The following PR should be tested before closing this issue: PR-6450

stale[bot] commented 4 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

jjgao commented 4 years ago

since both #6420 and #6450 have been merged, I am closing this. Please feel free to reopen if the problem is still there.