Error with survival analysis

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Irina Leonardi

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Nov 14, 2022, 4:33:52 AM11/14/22
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Hello, I receive an error message when I attempt a comparison/survival analysis of my gene of interest.

I select the samples of interest (Unaltered + altered). Then click on Survival.

Best,
Irina

See error below

{"req":{"method":"POST","url":"//www.cbioportal.org/api/alteration-enrichments/fetch?enrichmentType=SAMPLE","data":{},"headers":{"accept":"application/json","content-type":"application/json","content-encoding":"gzip"}},"xhr":{"_url":"//www.cbioportal.org/api/alteration-enrichments/fetch?enrichmentType=SAMPLE"},"text":"<!doctype html><html lang=\"en\"><head><title>HTTP Status 500 – Internal Server Error</title><style type=\"text/css\">body {font-family:Tahoma,Arial,sans-serif;} h1, h2, h3, b {color:white;background-color:#525D76;} h1 {font-size:22px;} h2 {font-size:16px;} h3 {font-size:14px;} p {font-size:12px;} a {color:black;} .line {height:1px;background-color:#525D76;border:none;}</style></head><body><h1>HTTP Status 500 – Internal Server Error</h1><hr class=\"line\" /><p><b>Type</b> Exception Report</p><p><b>Message</b> Request processing failed; nested exception is java.lang.NullPointerException: element cannot be mapped to a null key</p><p><b>Description</b> The server encountered an unexpected condition that prevented it from fulfilling the request.</p><p><b>Exception</b></p><pre>org.springframework.web.util.NestedServletException: Request processing failed; nested exception is java.lang.NullPointerException: element cannot be mapped to a null key\n\torg.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1014)\n\torg.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:909)\n\tjavax.servlet.http.HttpServlet.service(HttpServlet.java:652)\n\torg.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883)\n\tjavax.servlet.http.HttpServlet.service(HttpServlet.java:733)\n\torg.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)\n\torg.mskcc.cbio.portal.util.XssFilter.doFilter(XssFilter.java:65)\n\torg.cbioportal.web.util.ResettableHttpServletRequestFilter.doFilter(ResettableHttpServletRequestFilter.java:29)\n\torg.apache.catalina.filters.HttpHeaderSecurityFilter.doFilter(HttpHeaderSecurityFilter.java:126)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320)\n\torg.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:126)\n\torg.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:90)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:118)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:158)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:200)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.header.HeaderWriterFilter.doHeadersAfter(HeaderWriterFilter.java:92)\n\torg.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:77)\n\torg.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56)\n\torg.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215)\n\torg.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178)\n\torg.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:358)\n\torg.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:271)\n\tcom.vlkan.hrrs.servlet.HrrsFilter.doFilter(HrrsFilter.java:85)\n\torg.apache.catalina.filters.CorsFilter.handleNonCORS(CorsFilter.java:364)\n\torg.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:170)\n\torg.mskcc.cbio.portal.util.UrlParamFilter.doFilter(UrlParamFilter.java:29)\n\torg.mskcc.cbio.portal.util.RequestBodyGZipFilter.doFilter(RequestBodyGZipFilter.java:72)\n\torg.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:358)\n\torg.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:271)\n</pre><p><b>Root Cause</b></p><pre>java.lang.NullPointerException: element cannot be mapped to a null key\n\tjava.base&#47;java.util.Objects.requireNonNull(Objects.java:246)\n\tjava.base&#47;java.util.stream.Collectors.lambda$groupingBy$53(Collectors.java:1134)\n\tjava.base&#47;java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169)\n\tjava.base&#47;java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1655)\n\tjava.base&#47;java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)\n\tjava.base&#47;java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)\n\tjava.base&#47;java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:913)\n\tjava.base&#47;java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)\n\tjava.base&#47;java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:578)\n\torg.cbioportal.persistence.mybatis.AlterationMyBatisRepository.getSampleAlterationCounts(AlterationMyBatisRepository.java:52)\n\tjava.base&#47;jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\n\tjava.base&#47;jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)\n\tjava.base&#47;jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tjava.base&#47;java.lang.reflect.Method.invoke(Method.java:566)\n\torg.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)\n\torg.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)\n\torg.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)\n\torg.springframework.cache.interceptor.CacheInterceptor.lambda$invoke$0(CacheInterceptor.java:53)\n\torg.springframework.cache.interceptor.CacheAspectSupport.invokeOperation(CacheAspectSupport.java:366)\n\torg.springframework.cache.interceptor.CacheAspectSupport.execute(CacheAspectSupport.java:421)\n\torg.springframework.cache.interceptor.CacheAspectSupport.execute(CacheAspectSupport.java:346)\n\torg.springframework.cache.interceptor.CacheInterceptor.invoke(CacheInterceptor.java:61)\n\torg.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)\n\torg.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)\n\tcom.sun.proxy.$Proxy83.getSampleAlterationCounts(Unknown Source)\n\torg.cbioportal.service.impl.AlterationCountServiceImpl.lambda$getSampleAlterationCounts$0(AlterationCountServiceImpl.java:43)\n\torg.cbioportal.service.impl.AlterationCountServiceImpl.lambda$getAlterationCounts$15(AlterationCountServiceImpl.java:240)\n\tjava.base&#47;java.util.HashMap$Values.forEach(HashMap.java:977)\n\torg.cbioportal.service.impl.AlterationCountServiceImpl.getAlterationCounts(AlterationCountServiceImpl.java:239)\n\torg.cbioportal.service.impl.AlterationCountServiceImpl.getSampleAlterationCounts(AlterationCountServiceImpl.java:50)\n\torg.cbioportal.service.impl.AlterationEnrichmentServiceImpl.lambda$getAlterationCountsbyEntrezGeneIdAndGroup$1(AlterationEnrichmentServiceImpl.java:49)\n\tjava.base&#47;java.util.stream.Collectors.lambda$uniqKeysMapAccumulator$1(Collectors.java:178)\n\tjava.base&#47;java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169)\n\tjava.base&#47;java.util.HashMap$EntrySpliterator.forEachRemaining(HashMap.java:1764)\n\tjava.base&#47;java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)\n\tjava.base&#47;java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)\n\tjava.base&#47;java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:913)\n\tjava.base&#47;java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)\n\tjava.base&#47;java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:578)\n\torg.cbioportal.service.impl.AlterationEnrichmentServiceImpl.getAlterationCountsbyEntrezGeneIdAndGroup(AlterationEnrichmentServiceImpl.java:43)\n\torg.cbioportal.service.impl.AlterationEnrichmentServiceImpl.getAlterationEnrichments(AlterationEnrichmentServiceImpl.java:30)\n\torg.cbioportal.web.AlterationEnrichmentController.fetchAlterationEnrichments(AlterationEnrichmentController.java:55)\n\torg.cbioportal.web.AlterationEnrichmentController$$FastClassBySpringCGLIB$$838882b.invoke(&lt;generated&gt;)\n\torg.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218)\n\torg.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:783)\n\torg.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)\n\torg.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:753)\n\torg.springframework.validation.beanvalidation.MethodValidationInterceptor.invoke(MethodValidationInterceptor.java:119)\n\torg.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)\n\torg.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:753)\n\torg.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:698)\n\torg.cbioportal.web.AlterationEnrichmentController$$EnhancerBySpringCGLIB$$ba9c723f.fetchAlterationEnrichments(&lt;generated&gt;)\n\tjava.base&#47;jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\n\tjava.base&#47;jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)\n\tjava.base&#47;jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tjava.base&#47;java.lang.reflect.Method.invoke(Method.java:566)\n\torg.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:190)\n\torg.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:138)\n\torg.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:105)\n\torg.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:878)\n\torg.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:792)\n\torg.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)\n\torg.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1043)\n\torg.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:943)\n\torg.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006)\n\torg.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:909)\n\tjavax.servlet.http.HttpServlet.service(HttpServlet.java:652)\n\torg.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883)\n\tjavax.servlet.http.HttpServlet.service(HttpServlet.java:733)\n\torg.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)\n\torg.mskcc.cbio.portal.util.XssFilter.doFilter(XssFilter.java:65)\n\torg.cbioportal.web.util.ResettableHttpServletRequestFilter.doFilter(ResettableHttpServletRequestFilter.java:29)\n\torg.apache.catalina.filters.HttpHeaderSecurityFilter.doFilter(HttpHeaderSecurityFilter.java:126)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320)\n\torg.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:126)\n\torg.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:90)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:118)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:158)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:200)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.header.HeaderWriterFilter.doHeadersAfter(HeaderWriterFilter.java:92)\n\torg.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:77)\n\torg.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56)\n\torg.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)\n\torg.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215)\n\torg.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178)\n\torg.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:358)\n\torg.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:271)\n\tcom.vlkan.hrrs.servlet.HrrsFilter.doFilter(HrrsFilter.java:85)\n\torg.apache.catalina.filters.CorsFilter.handleNonCORS(CorsFilter.java:364)\n\torg.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:170)\n\torg.mskcc.cbio.portal.util.UrlParamFilter.doFilter(UrlParamFilter.java:29)\n\torg.mskcc.cbio.portal.util.RequestBodyGZipFilter.doFilter(RequestBodyGZipFilter.java:72)\n\torg.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:358)\n\torg.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:271)\n</pre><p><b>Note</b> The full stack trace of the root cause is available in the server logs.</p><hr class=\"line\" /><h3>Apache Tomcat/8.5.61</h3></body></html>","statusText":"","statusCode":500,"status":500,"statusType":5,"info":false,"ok":false,"redirect":false,"clientError":false,"serverError":true,"error":{"status":500,"method":"POST","url":"//www.cbioportal.org/api/alteration-enrichments/fetch?enrichmentType=SAMPLE"},"created":false,"accepted":false,"noContent":false,"badRequest":false,"unauthorized":false,"notAcceptable":false,"forbidden":false,"notFound":false,"unprocessableEntity":false,"headers":{"access-control-allow-origin":"*","access-control-expose-headers":"total-count,sample-count","cache-control":"no-cache, no-store, max-age=0, must-revalidate","content-encoding":"gzip","content-language":"en","content-type":"text/html;charset=utf-8","date":"Fri, 11 Nov 2022 17:55:09 GMT","expires":"0","pragma":"no-cache","server":"nginx/1.13.12","strict-transport-security":"max-age=15724800; includeSubDomains","vary":"accept-encoding","x-content-type-options":"nosniff","x-frame-options":"SAMEORIGIN","x-xss-protection":"1; mode=block"},"header":{"access-control-allow-origin":"*","access-control-expose-headers":"total-count,sample-count","cache-control":"no-cache, no-store, max-age=0, must-revalidate","content-encoding":"gzip","content-language":"en","content-type":"text/html;charset=utf-8","date":"Fri, 11 Nov 2022 17:55:09 GMT","expires":"0","pragma":"no-cache","server":"nginx/1.13.12","strict-transport-security":"max-age=15724800; includeSubDomains","vary":"accept-encoding","x-content-type-options":"nosniff","x-frame-options":"SAMEORIGIN","x-xss-protection":"1; mode=block"},"type":"text/html","charset":"utf-8","links":{},"body":null,"url":"https://www.cbioportal.org/results/comparison?case_set_id=all&gene_list=GPR171&cancer_study_list=5c8a7d55e4b046111fee2296&comparison_subtab=alterations"}

debr...@mskcc.org

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Nov 18, 2022, 6:37:24 PM11/18/22
to irina.l...@gmail.com, cbiop...@googlegroups.com

Hi Irina,

 

Thanks for reaching out!

 

Is it still crashing for you? The query is working for me now:

 

https://www.cbioportal.org/results/comparison?case_set_id=all&gene_list=GPR171&cancer_study_list=5c8a7d55e4b046111fee2296&comparison_subtab=alterations

 

Thanks!

Ino

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