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Suganya MS
Jul 30, 2025, 10:43:03 PMJul 30
to cBioPortal for Cancer Genomics Discussion Group
I have deployed cBioportal in our env and enable SAML using OKTA while trying accessing public dataset i am getting below
{"req":{"method":"POST","url":"https://cbioportal-dev.oneexample.com/api/session/custom_data/fetch","data":["paac_jhu_2014"],"headers":{"content-type":"application/json"}},"xhr":{},"text":"{\"timestamp\":1753894837440,\"status\":500,\"error\":\"Internal Server Error\",\"path\":\"/api/session/custom_data/fetch\"}","statusText":"","statusCode":500,"status":500,"statusType":5,"info":false,"ok":false,"redirect":false,"clientError":false,"serverError":true,"error":{"status":500,"method":"POST","url":"https://cbioportal-dev.oneexample.com/api/session/custom_data/fetch"},"created":false,"accepted":false,"noContent":false,"badRequest":false,"unauthorized":false,"notAcceptable":false,"forbidden":false,"notFound":false,"unprocessableEntity":false,"headers":{"cache-control":"no-cache, no-store, max-age=0, must-revalidate","content-encoding":"gzip","content-type":"application/json","date":"Wed, 30 Jul 2025 17:00:37 GMT","expires":"0","pragma":"no-cache","strict-transport-security":"max-age=31536000 ; includeSubDomains","vary":"origin,access-control-request-method,access-control-request-headers,accept-encoding","x-content-type-options":"nosniff","x-frame-options":"DENY","x-xss-protection":"0"},"header":{"cache-control":"no-cache, no-store, max-age=0, must-revalidate","content-encoding":"gzip","content-type":"application/json","date":"Wed, 30 Jul 2025 17:00:37 GMT","expires":"0","pragma":"no-cache","strict-transport-security":"max-age=31536000 ; includeSubDomains","vary":"origin,access-control-request-method,access-control-request-headers,accept-encoding","x-content-type-options":"nosniff","x-frame-options":"DENY","x-xss-protection":"0"},"type":"application/json","links":{},"body":{"timestamp":1753894837440,"status":500,"error":"Internal Server Error","path":"/api/session/custom_data/fetch"},"url":"https://cbioportal-dev.oneexample.com/study/summary?id=paac_jhu_2014"}
2025-07-30T16:59:43.162Z ERROR 1 --- [io-8080-exec-10] o.c.web.SessionServiceController : Error occurred
org.springframework.web.client.HttpServerErrorException$ServiceUnavailable: 503 Service Unavailable: "<!DOCTYPE html><EOL><html><EOL> <head><EOL> <meta name="viewport" content="width=device-width, initial-scale=1"><EOL> <meta charset="utf-8"><EOL> <title>Application Error</title><EOL> <style media="screen"><EOL> html,body,iframe {<EOL> margin: 0;<EOL> padding: 0;<EOL> }<EOL><EOL> html,body {<EOL> height: 100%;<EOL> overflow: hidden;<EOL> }<EOL><EOL> iframe {<EOL> width: 100%;<EOL> height: 100%;<EOL> border: 0;<EOL> }<EOL> </style><EOL> </head><EOL> <body><EOL> <iframe src="https://www.herokucdn.com/error-pages/application-error.html"></iframe><EOL> </body><EOL></html>"
at org.springframework.web.client.HttpServerErrorException.create(HttpServerErrorException.java:111) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:186) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:137) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.client.ResponseErrorHandler.handleError(ResponseErrorHandler.java:63) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.client.RestTemplate.handleResponse(RestTemplate.java:915) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.client.RestTemplate.doExecute(RestTemplate.java:864) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.client.RestTemplate.execute(RestTemplate.java:764) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.client.RestTemplate.exchange(RestTemplate.java:675) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.cbioportal.web.SessionServiceController.getRecentlyUpdatePageSettings(SessionServiceController.java:112) ~[classes!/:6.0.17]
at org.cbioportal.web.SessionServiceController.getPageSettings(SessionServiceController.java:464) ~[classes!/:6.0.17]
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) ~[na:na]
at java.base/java.lang.reflect.Method.invoke(Method.java:580) ~[na:na]
at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:150) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:118) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:884) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:797) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1081) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:974) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1011) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:914) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at jakarta.servlet.http.HttpServlet.service(HttpServlet.java:590) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:885) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:205) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51) ~[tomcat-embed-websocket-10.1.13.jar!/:na]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.cbioportal.web.util.RequestBodyGZipFilter.doFilter(RequestBodyGZipFilter.java:72) ~[classes!/:6.0.17]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.cbioportal.web.util.ResettableHttpServletRequestFilter.doFilter(ResettableHttpServletRequestFilter.java:33) ~[classes!/:6.0.17]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.springframework.security.web.FilterChainProxy.lambda$doFilterInternal$3(FilterChainProxy.java:231) ~[spring-security-web-6.1.4.jar!/:6.1.4]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:365) ~[spring-security-web-6.1.4.jar!/:6.1.4]
at org.springframework.security.web.access.intercept.AuthorizationFilter.doFilter(AuthorizationFilter.java:100) ~[spring-security-web-6.1.4.jar!/:6.1.4]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374) ~[spring-security-web-6.1.4.jar!/:6.1.4]
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:126) ~[spring-security-web-6.1.4.jar!/:6.1.4]
{"req":{"method":"POST","url":"https://cbioportal-dev.oneexample.com/api/session/custom_data/fetch","data":["paac_jhu_2014"],"headers":{"content-type":"application/json"}},"xhr":{},"text":"{\"timestamp\":1753894837440,\"status\":500,\"error\":\"Internal Server Error\",\"path\":\"/api/session/custom_data/fetch\"}","statusText":"","statusCode":500,"status":500,"statusType":5,"info":false,"ok":false,"redirect":false,"clientError":false,"serverError":true,"error":{"status":500,"method":"POST","url":"https://cbioportal-dev.oneexample.com/api/session/custom_data/fetch"},"created":false,"accepted":false,"noContent":false,"badRequest":false,"unauthorized":false,"notAcceptable":false,"forbidden":false,"notFound":false,"unprocessableEntity":false,"headers":{"cache-control":"no-cache, no-store, max-age=0, must-revalidate","content-encoding":"gzip","content-type":"application/json","date":"Wed, 30 Jul 2025 17:00:37 GMT","expires":"0","pragma":"no-cache","strict-transport-security":"max-age=31536000 ; includeSubDomains","vary":"origin,access-control-request-method,access-control-request-headers,accept-encoding","x-content-type-options":"nosniff","x-frame-options":"DENY","x-xss-protection":"0"},"header":{"cache-control":"no-cache, no-store, max-age=0, must-revalidate","content-encoding":"gzip","content-type":"application/json","date":"Wed, 30 Jul 2025 17:00:37 GMT","expires":"0","pragma":"no-cache","strict-transport-security":"max-age=31536000 ; includeSubDomains","vary":"origin,access-control-request-method,access-control-request-headers,accept-encoding","x-content-type-options":"nosniff","x-frame-options":"DENY","x-xss-protection":"0"},"type":"application/json","links":{},"body":{"timestamp":1753894837440,"status":500,"error":"Internal Server Error","path":"/api/session/custom_data/fetch"},"url":"https://cbioportal-dev.oneexample.com/study/summary?id=paac_jhu_2014"}
2025-07-30T16:59:43.162Z ERROR 1 --- [io-8080-exec-10] o.c.web.SessionServiceController : Error occurred
org.springframework.web.client.HttpServerErrorException$ServiceUnavailable: 503 Service Unavailable: "<!DOCTYPE html><EOL><html><EOL> <head><EOL> <meta name="viewport" content="width=device-width, initial-scale=1"><EOL> <meta charset="utf-8"><EOL> <title>Application Error</title><EOL> <style media="screen"><EOL> html,body,iframe {<EOL> margin: 0;<EOL> padding: 0;<EOL> }<EOL><EOL> html,body {<EOL> height: 100%;<EOL> overflow: hidden;<EOL> }<EOL><EOL> iframe {<EOL> width: 100%;<EOL> height: 100%;<EOL> border: 0;<EOL> }<EOL> </style><EOL> </head><EOL> <body><EOL> <iframe src="https://www.herokucdn.com/error-pages/application-error.html"></iframe><EOL> </body><EOL></html>"
at org.springframework.web.client.HttpServerErrorException.create(HttpServerErrorException.java:111) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:186) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:137) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.client.ResponseErrorHandler.handleError(ResponseErrorHandler.java:63) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.client.RestTemplate.handleResponse(RestTemplate.java:915) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.client.RestTemplate.doExecute(RestTemplate.java:864) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.client.RestTemplate.execute(RestTemplate.java:764) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.client.RestTemplate.exchange(RestTemplate.java:675) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.cbioportal.web.SessionServiceController.getRecentlyUpdatePageSettings(SessionServiceController.java:112) ~[classes!/:6.0.17]
at org.cbioportal.web.SessionServiceController.getPageSettings(SessionServiceController.java:464) ~[classes!/:6.0.17]
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) ~[na:na]
at java.base/java.lang.reflect.Method.invoke(Method.java:580) ~[na:na]
at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:150) ~[spring-web-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:118) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:884) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:797) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1081) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:974) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1011) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:914) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at jakarta.servlet.http.HttpServlet.service(HttpServlet.java:590) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:885) ~[spring-webmvc-6.0.12.jar!/:6.0.12]
at jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:205) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51) ~[tomcat-embed-websocket-10.1.13.jar!/:na]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.cbioportal.web.util.RequestBodyGZipFilter.doFilter(RequestBodyGZipFilter.java:72) ~[classes!/:6.0.17]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.cbioportal.web.util.ResettableHttpServletRequestFilter.doFilter(ResettableHttpServletRequestFilter.java:33) ~[classes!/:6.0.17]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149) ~[tomcat-embed-core-10.1.13.jar!/:na]
at org.springframework.security.web.FilterChainProxy.lambda$doFilterInternal$3(FilterChainProxy.java:231) ~[spring-security-web-6.1.4.jar!/:6.1.4]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:365) ~[spring-security-web-6.1.4.jar!/:6.1.4]
at org.springframework.security.web.access.intercept.AuthorizationFilter.doFilter(AuthorizationFilter.java:100) ~[spring-security-web-6.1.4.jar!/:6.1.4]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374) ~[spring-security-web-6.1.4.jar!/:6.1.4]
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:126) ~[spring-security-web-6.1.4.jar!/:6.1.4]
Prasanna Jagannathan
Jul 31, 2025, 10:03:35 AMJul 31
to Suganya MS, cBioPortal for Cancer Genomics Discussion Group
Hi Suganya
Can you check if the study got imported successfully when OKTA is disabled? The study page and query page should be working fine without the OKTA security.
Once the study is successfully imported, then you can turn on OKTA.
It seems that the Session service is not running properly based on the error messages.
thanks
Jag
cBioPortal Team, UHN
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