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Alan Herbert

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Aug 2, 2021, 10:46:37 AMAug 2
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{"req":{"method":"GET","url":"https://www.cbioportal.org/proxy/oncokb/utils/cancerGeneList","headers":{"accept":"application/json","content-type":"application/json"}},"xhr":{"_url":"https://www.cbioportal.org/proxy/oncokb/utils/cancerGeneList"},"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 org.springframework.web.client.HttpServerErrorException$InternalServerError: 500 Internal Server Error: [{&quot;type&quot;:&quot;https:&#47;&#47;www.oncokb.org&#47;problem&#47;problem-with-message&quot;,&quot;title&quot;:&quot;Internal Server Error&quot;,&quot;status&quot;:500,&quot;detail&quot;:&quot;500 Internal Server Error: [&lt;!DOCTYPE html&gt;&lt;html&gt;&lt;head&gt;&lt;title&gt;Apache Tomcat&#47;8.0.30 ... (431 bytes)]</p><p><b>Description</b> The server encountered an unexpected condition that prevented it from fulfilling the request.</p><p><b>Exception</b></p><pre>org.springframework.web.util.NestedServletException: Request processing failed; nested exception is org.springframework.web.client.HttpServerErrorException$InternalServerError: 500 Internal Server Error: [{&quot;type&quot;:&quot;https:&#47;&#47;www.oncokb.org&#47;problem&#47;problem-with-message&quot;,&quot;title&quot;:&quot;Internal Server Error&quot;,&quot;status&quot;:500,&quot;detail&quot;:&quot;500 Internal Server Error: [&lt;!DOCTYPE html&gt;&lt;html&gt;&lt;head&gt;&lt;title&gt;Apache Tomcat&#47;8.0.30 ... (431 bytes)]\n\torg.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1014)\n\torg.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:898)\n\tjavax.servlet.http.HttpServlet.service(HttpServlet.java:626)\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.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$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215)\n\torg.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178)\n\torg.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:358)\n\torg.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:271)\n\tcom.vlkan.hrrs.servlet.HrrsFilter.doFilter(HrrsFilter.java:85)\n\torg.apache.catalina.filters.CorsFilter.handleNonCORS(CorsFilter.java:364)\n\torg.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:170)\n\torg.mskcc.cbio.portal.util.RequestBodyGZipFilter.doFilter(RequestBodyGZipFilter.java:72)\n\torg.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:358)\n\torg.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:271)\n</pre><p><b>Root Cause</b></p><pre>org.springframework.web.client.HttpServerErrorException$InternalServerError: 500 Internal Server Error: [{&quot;type&quot;:&quot;https:&#47;&#47;www.oncokb.org&#47;problem&#47;problem-with-message&quot;,&quot;title&quot;:&quot;Internal Server Error&quot;,&quot;status&quot;:500,&quot;detail&quot;:&quot;500 Internal Server Error: [&lt;!DOCTYPE html&gt;&lt;html&gt;&lt;head&gt;&lt;title&gt;Apache Tomcat&#47;8.0.30 ... (431 bytes)]\n\torg.springframework.web.client.HttpServerErrorException.create(HttpServerErrorException.java:100)\n\torg.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:172)\n\torg.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:112)\n\torg.springframework.web.client.ResponseErrorHandler.handleError(ResponseErrorHandler.java:63)\n\torg.springframework.web.client.RestTemplate.handleResponse(RestTemplate.java:782)\n\torg.springframework.web.client.RestTemplate.doExecute(RestTemplate.java:740)\n\torg.springframework.web.client.RestTemplate.execute(RestTemplate.java:714)\n\torg.springframework.web.client.RestTemplate.exchange(RestTemplate.java:602)\n\torg.cbioportal.proxy.ProxyController.exchangeData(ProxyController.java:95)\n\torg.cbioportal.proxy.ProxyController.proxyOncokb(ProxyController.java:66)\n\tjdk.internal.reflect.GeneratedMethodAccessor634.invoke(Unknown Source)\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:879)\n\torg.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:793)\n\torg.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)\n\torg.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1040)\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.doGet(FrameworkServlet.java:898)\n\tjavax.servlet.http.HttpServlet.service(HttpServlet.java:626)\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.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.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":"GET","url":"https://www.cbioportal.org/proxy/oncokb/utils/cancerGeneList"},"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":"Sun, 01 Aug 2021 14:38:32 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":"Sun, 01 Aug 2021 14:38:32 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/oncoprint?cancer_study_list=sarc_tcga_pan_can_atlas_2018&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cfusion%2Cgistic&case_set_id=sarc_tcga_pan_can_atlas_2018_cnaseq&gene_list=TNFRSF1A%250ATNFRSF1B%250AZBP1%250ARIPK3%250AMAP4K4%250AIRF1%250AMLKL%250AIRF3%250AIRF5%250AIRF7%250ABIRC2%250ABIRC3%250ARIPK1%250AFCGR3A%250ACD163%250ACD248%250AHMMR&geneset_list=%20&tab_index=tab_visualize&Action=Submit"}

Ino de Bruijn

unread,
Aug 2, 2021, 12:41:43 PMAug 2
to Alan Herbert, cBioPortal for Cancer Genomics Discussion Group
Hi Alan,

Thanks for reaching out!

We had some server issues this weekend. My apologies for the inconvenience. It seems to work for me now. Does it work for you?

Best wishes,
Ino

On Mon, Aug 2, 2021 at 10:46 AM Alan Herbert <dr.alan...@gmail.com> wrote:
{"req":{"method":"GET","url":"https://www.cbioportal.org/proxy/oncokb/utils/cancerGeneList","headers":{"accept":"application/json","content-type":"application/json"}},"xhr":{"_url":"https://www.cbioportal.org/proxy/oncokb/utils/cancerGeneList"},"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 org.springframework.web.client.HttpServerErrorException$InternalServerError: 500 Internal Server Error: [{&quot;type&quot;:&quot;https:&#47;&#47;www.oncokb.org&#47;problem&#47;problem-with-message&quot;,&quot;title&quot;:&quot;Internal Server Error&quot;,&quot;status&quot;:500,&quot;detail&quot;:&quot;500 Internal Server Error: [&lt;!DOCTYPE html&gt;&lt;html&gt;&lt;head&gt;&lt;title&gt;Apache Tomcat&#47;8.0.30 ... (431 bytes)]</p><p><b>Description</b> The server encountered an unexpected condition that prevented it from fulfilling the request.</p><p><b>Exception</b></p><pre>org.springframework.web.util.NestedServletException: Request processing failed; nested exception is org.springframework.web.client.HttpServerErrorException$InternalServerError: 500 Internal Server Error: [{&quot;type&quot;:&quot;https:&#47;&#47;www.oncokb.org&#47;problem&#47;problem-with-message&quot;,&quot;title&quot;:&quot;Internal Server Error&quot;,&quot;status&quot;:500,&quot;detail&quot;:&quot;500 Internal Server Error: [&lt;!DOCTYPE html&gt;&lt;html&gt;&lt;head&gt;&lt;title&gt;Apache Tomcat&#47;8.0.30 ... (431 bytes)]\n\torg.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1014)\n\torg.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:898)\n\tjavax.servlet.http.HttpServlet.service(HttpServlet.java:626)\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.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$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215)\n\torg.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178)\n\torg.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:358)\n\torg.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:271)\n\tcom.vlkan.hrrs.servlet.HrrsFilter.doFilter(HrrsFilter.java:85)\n\torg.apache.catalina.filters.CorsFilter.handleNonCORS(CorsFilter.java:364)\n\torg.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:170)\n\torg.mskcc.cbio.portal.util.RequestBodyGZipFilter.doFilter(RequestBodyGZipFilter.java:72)\n\torg.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:358)\n\torg.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:271)\n</pre><p><b>Root Cause</b></p><pre>org.springframework.web.client.HttpServerErrorException$InternalServerError: 500 Internal Server Error: [{&quot;type&quot;:&quot;https:&#47;&#47;www.oncokb.org&#47;problem&#47;problem-with-message&quot;,&quot;title&quot;:&quot;Internal Server Error&quot;,&quot;status&quot;:500,&quot;detail&quot;:&quot;500 Internal Server Error: [&lt;!DOCTYPE html&gt;&lt;html&gt;&lt;head&gt;&lt;title&gt;Apache Tomcat&#47;8.0.30 ... (431 bytes)]\n\torg.springframework.web.client.HttpServerErrorException.create(HttpServerErrorException.java:100)\n\torg.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:172)\n\torg.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:112)\n\torg.springframework.web.client.ResponseErrorHandler.handleError(ResponseErrorHandler.java:63)\n\torg.springframework.web.client.RestTemplate.handleResponse(RestTemplate.java:782)\n\torg.springframework.web.client.RestTemplate.doExecute(RestTemplate.java:740)\n\torg.springframework.web.client.RestTemplate.execute(RestTemplate.java:714)\n\torg.springframework.web.client.RestTemplate.exchange(RestTemplate.java:602)\n\torg.cbioportal.proxy.ProxyController.exchangeData(ProxyController.java:95)\n\torg.cbioportal.proxy.ProxyController.proxyOncokb(ProxyController.java:66)\n\tjdk.internal.reflect.GeneratedMethodAccessor634.invoke(Unknown Source)\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:879)\n\torg.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:793)\n\torg.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)\n\torg.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1040)\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.doGet(FrameworkServlet.java:898)\n\tjavax.servlet.http.HttpServlet.service(HttpServlet.java:626)\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.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.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":"GET","url":"https://www.cbioportal.org/proxy/oncokb/utils/cancerGeneList"},"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":"Sun, 01 Aug 2021 14:38:32 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":"Sun, 01 Aug 2021 14:38:32 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/oncoprint?cancer_study_list=sarc_tcga_pan_can_atlas_2018&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cfusion%2Cgistic&case_set_id=sarc_tcga_pan_can_atlas_2018_cnaseq&gene_list=TNFRSF1A%250ATNFRSF1B%250AZBP1%250ARIPK3%250AMAP4K4%250AIRF1%250AMLKL%250AIRF3%250AIRF5%250AIRF7%250ABIRC2%250ABIRC3%250ARIPK1%250AFCGR3A%250ACD163%250ACD248%250AHMMR&geneset_list=%20&tab_index=tab_visualize&Action=Submit"}

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Ino de Bruijn

unread,
Aug 3, 2021, 4:17:54 PMAug 3
to Alan Herbert, cBioPortal for Cancer Genomics Discussion Group
Hi Alan,

Sorry to hear that - could you clarify what was working until today?

The URL you shared above seems to work now:


> A limit of 20 genes?

Are you referring to the query limit? We limit it by the product of number of samples x genes. The limit of this product is 1 million. Depending on your cohort size, you should be able to query many more genes than 20.

> No RNA-Seq available?

Where do you see this data missing? If you are trying to show RNASeq profiling in the oncoprint, make sure to select it by clicking the modify query button. Here is your query with the expression included for instance:


You can find several other datasets with rna seq data by exploring the data sets page:


> What problem are you solving?

Hope I was able to help address the error message you shared in the first email. Don't hesitate to reach out if you are still experiencing issues

Best wishes,
Ino





On Mon, Aug 2, 2021 at 10:09 PM Alan Herbert <dr.alan...@gmail.com> wrote:
Hi Ino,

It  worked until today.

Why have you now restricted the portal?


A limit of 20 genes?


No RNA-Seq available?


Is this what you intended to do?


What problem are you solving?



Best,


Alan




Ino de Bruijn

unread,
Aug 3, 2021, 7:46:36 PMAug 3
to Alan Herbert, cBioPortal for Cancer Genomics Discussion Group
Thanks so much for the kind words!

Best wishes
Ino

On Tue, Aug 3, 2021, 5:05 PM Alan Herbert <dr.alan...@gmail.com> wrote:
Thanks Ino for all the work you put into the site and for the clarifications on how the limits work. I have found the site to be immensely useful and appreciate all the effort that went into it.



Best,


Alan
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