What causes the mutation data panel load to fail?

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John Reber

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Jan 28, 2019, 10:53:36 AM1/28/19
to cBioPortal for Cancer Genomics Discussion Group
What causes the mutation data panel load to fail and then load properly after a page refresh (sometimes several refreshes)?

We have a local cbioportal instance.  When we try to load to local studies, 1 a little over 11k samples, the second ~1.2k samples.

We are trying to track down what causes the failure to load.  Have increased memory from 32G to 64G, increased amount of memory available to tomcat and still we are having issues.  W'd like to correct this prior to rolling out to our users.


Pieter Lukasse

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Jan 29, 2019, 6:41:46 AM1/29/19
to John Reber, cBioPortal for Cancer Genomics Discussion Group
Hi John,

could you please share the tomcat log files and any errors you are seeing there? Please also set the log level to DEBUG to get more information (see also https://github.com/thehyve/cbioportal-docker/blob/master/log4j.properties)

Best,

Pieter Lukasse


E.   pie...@thehyve.nl

T.   +31(0)30 700 9713

W.  www.thehyve.nl


We empower scientists by building on open source software


Op ma 28 jan. 2019 om 16:53 schreef John Reber <John....@jefferson.edu>:
What causes the mutation data panel load to fail and then load properly after a page refresh (sometimes several refreshes)?

We have a local cbioportal instance.  When we try to load to local studies, 1 a little over 11k samples, the second ~1.2k samples.

We are trying to track down what causes the failure to load.  Have increased memory from 32G to 64G, increased amount of memory available to tomcat and still we are having issues.  W'd like to correct this prior to rolling out to our users.


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John Reber

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Jan 30, 2019, 11:01:48 AM1/30/19
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Have not set to DEBUG yet, will do this morning, but this is the exception that is thrown:

28-Jan-2019 13:27:40.955 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 23966 ms
Recaching...
Finished recaching...
28-Jan-2019 13:32:38.668 SEVERE [http-nio-8080-exec-3] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [MutationsJSON] in context with path [/cbioportal] threw exception
 java.lang.NullPointerException
    at org.mskcc.cbio.portal.util.InternalIdUtil.getStableSampleIds(InternalIdUtil.java:47)
    at org.mskcc.cbio.portal.servlet.MutationsJSON.processGetSmgRequest(MutationsJSON.java:250)
    at org.mskcc.cbio.portal.servlet.MutationsJSON.processRequest(MutationsJSON.java:144)
    at org.mskcc.cbio.portal.servlet.MutationsJSON.doPost(MutationsJSON.java:816)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:661)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.mskcc.cbio.portal.util.XssFilter.doFilter(XssFilter.java:65)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilter(BasicAuthenticationFilter.java:150)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:50)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
    at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
    at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:347)
    at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:263)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.apache.catalina.filters.CorsFilter.handleNonCORS(CorsFilter.java:438)
    at org.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:169)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
    at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
    at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800)
    at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
    at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:800)
    at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1471)
    at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1135)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.base/java.lang.Thread.run(Thread.java:844)

28-Jan-2019 13:32:52.962 SEVERE [http-nio-8080-exec-1] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [MutationsJSON] in context with path [/cbioportal] threw exception
 java.lang.NullPointerException
    at org.mskcc.cbio.portal.util.InternalIdUtil.getStableSampleIds(InternalIdUtil.java:47)
    at org.mskcc.cbio.portal.servlet.MutationsJSON.processGetSmgRequest(MutationsJSON.java:250)
    at org.mskcc.cbio.portal.servlet.MutationsJSON.processRequest(MutationsJSON.java:144)
    at org.mskcc.cbio.portal.servlet.MutationsJSON.doPost(MutationsJSON.java:816)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:661)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.mskcc.cbio.portal.util.XssFilter.doFilter(XssFilter.java:65)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilter(BasicAuthenticationFilter.java:150)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:50)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
    at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
    at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:347)
    at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:263)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.apache.catalina.filters.CorsFilter.handleNonCORS(CorsFilter.java:438)
    at org.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:169)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
    at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
    at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800)
    at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
    at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:800)
    at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1471)
    at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1135)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.base/java.lang.Thread.run(Thread.java:844)



John Reber

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Jan 30, 2019, 11:01:48 AM1/30/19
to cBioPortal for Cancer Genomics Discussion Group
Attached is the information from the cbioportal.log at the time of the null pointer exception in catalina.out.


On Tuesday, January 29, 2019 at 6:41:46 AM UTC-5, Pieter Lukasse wrote:
cbioportal_log.txt

Pieter Lukasse

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Feb 1, 2019, 9:00:55 AM2/1/19
to John Reber, cBioPortal for Cancer Genomics Discussion Group
Hi John,

this could be a limitation of an old version. Which version are you using? 

The scenario I see is: the processGetSmgRequest is maybe called via a GET request. If this is the case, there is a limitation on the number of parameters (so in this case samples) it can handle (because there is a limitation to the size of the URL). This limitation would explain why the NullPointerException occurs specifically     at org.mskcc.cbio.portal.util.InternalIdUtil.getStableSampleIds(InternalIdUtil.java:47): most likely the caseIds in the URL parameter is getting truncated, which causes one of the case ids (aka sample id) to be invalid and not found in the DB, making the line  Sample s = DaoSample.getSampleById(internalSampleId)  return null which will cause the subsequent line with s.getStableId() trigger a NullPointerException since s is null.

But again, I expect this to be very old and dead code by now. It looks like you are using an old version of cBioPortal, correct?

Best,


Pieter Lukasse


E.   pie...@thehyve.nl

T.   +31(0)30 700 9713

W.  www.thehyve.nl


We empower scientists by building on open source software


Op wo 30 jan. 2019 om 17:01 schreef John Reber <John....@jefferson.edu>:
To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/2ff700e0-a6b6-4190-80c7-a5d31c607f58%40googlegroups.com.

Pieter Lukasse

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Feb 1, 2019, 9:31:36 AM2/1/19
to John Reber, cBioPortal for Cancer Genomics Discussion Group, Christopher McNair
Thanks John. Let us know how that goes. 

Pieter Lukasse


E.   pie...@thehyve.nl

T.   +31(0)30 700 9713

W.  www.thehyve.nl


We empower scientists by building on open source software


Op vr 1 feb. 2019 om 15:04 schreef John Reber <John....@jefferson.edu>:

1.15.1-SNAPSHOT

 

It was downloaded by default when we first installed the portal a couple of months ago.  Will update our version to the latest and greatest.

 

Thanks,

John

From: Pieter Lukasse <pie...@thehyve.nl>
Date: Friday, February 1, 2019 at 9:01 AM
To: John Reber <John....@jefferson.edu>
Cc: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] What causes the mutation data panel load to fail?

 

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Hi John,

 

this could be a limitation of an old version. Which version are you using? 

 

The scenario I see is: the processGetSmgRequest is maybe called via a GET request. If this is the case, there is a limitation on the number of parameters (so in this case samples) it can handle (because there is a limitation to the size of the URL). This limitation would explain why the NullPointerException occurs specifically     at org.mskcc.cbio.portal.util.InternalIdUtil.getStableSampleIds(InternalIdUtil.java:47): most likely the caseIds in the URL parameter is getting truncated, which causes one of the case ids (aka sample id) to be invalid and not found in the DB, making the line  Sample s = DaoSample.getSampleById(internalSampleId)  return null which will cause the subsequent line with s.getStableId() trigger a NullPointerException since s is null.

 

But again, I expect this to be very old and dead code by now. It looks like you are using an old version of cBioPortal, correct?

 

Best,

 

 

Pieter Lukasse

 

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Best,

Pieter Lukasse

 

Image removed by sender.

E.   pie...@thehyve.nl

T.   +31(0)30 700 9713

W.  www.thehyve.nl

 

We empower scientists by building on open source software

 

Op ma 28 jan. 2019 om 16:53 schreef John Reber <John....@jefferson.edu>:

What causes the mutation data panel load to fail and then load properly after a page refresh (sometimes several refreshes)?

 

We have a local cbioportal instance.  When we try to load to local studies, 1 a little over 11k samples, the second ~1.2k samples.

 

We are trying to track down what causes the failure to load.  Have increased memory from 32G to 64G, increased amount of memory available to tomcat and still we are having issues.  W'd like to correct this prior to rolling out to our users.

 

 

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John Reber

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Feb 4, 2019, 12:35:45 PM2/4/19
to cBioPortal for Cancer Genomics Discussion Group
Having issues trying to upgrade.

java -version
NOTE: Picked up JDK_JAVA_OPTIONS: --add-modules java.xml.bind
openjdk version "10.0.2" 2018-07-17
OpenJDK Runtime Environment (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.4)
OpenJDK 64-Bit Server VM (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.4, mixed mode)

tomcat version apache-tomcat-8.5.32

Started with a clean directory /home/jreber/cBioPortal2.
cd cbioportal
git checkout master
edit portal.properties
mvn -DskipTests clean install
copy the newly created cbioportal.war file over to tomcat.
start tomcat

I get a login screen (which doesn't show the version information)
When I try logging in (using ldap) it takes me back to the login screen.

I see the following in cbioportal.log:
2019-02-04 11:26:43 [http-nio-8080-exec-2] DEBUG org.springframework.security.web.authentication.UsernamePasswordAuthenticationFilter - Request is to process authentication
2019-02-04 11:26:43 [http-nio-8080-exec-2] DEBUG org.springframework.security.authentication.ProviderManager - Authentication attempt using org.springframework.security.ldap.authentication.LdapAuthenticationProvider
2019-02-04 11:26:43 [http-nio-8080-exec-2] DEBUG org.springframework.security.ldap.authentication.LdapAuthenticationProvider - Processing authentication request for user:
2019-02-04 11:26:43 [http-nio-8080-exec-2] DEBUG org.springframework.beans.factory.support.DefaultListableBeanFactory - Returning cached instance of singleton bean 'sqlSessionFactory'
2019-02-04 11:26:43 [http-nio-8080-exec-2] DEBUG org.springframework.security.web.authentication.UsernamePasswordAuthenticationFilter - Authentication request failed: org.springframework.security.authentication.BadCredentialsException: Empty Username
org.springframework.security.authentication.BadCredentialsException: Empty Username
    at org.springframework.security.ldap.authentication.AbstractLdapAuthenticationProvider.authenticate(AbstractLdapAuthenticationProvider.java:73)
    at org.springframework.security.authentication.ProviderManager.authenticate(ProviderManager.java:174)
    at org.springframework.security.authentication.ProviderManager.authenticate(ProviderManager.java:199)
    at org.springframework.security.web.authentication.UsernamePasswordAuthenticationFilter.attemptAuthentication(UsernamePasswordAuthenticationFilter.java:94)
    at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:212)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:66)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
    at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215)
    at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178)
2019-02-04 11:26:43 [http-nio-8080-exec-2] DEBUG org.springframework.security.web.authentication.UsernamePasswordAuthenticationFilter - Updated SecurityContextHolder to contain null Authentication
2019-02-04 11:26:43 [http-nio-8080-exec-2] DEBUG org.springframework.security.web.authentication.UsernamePasswordAuthenticationFilter - Delegating to authentication failure handler org.springframework.security.web.authentication.SimpleUrlAuthenticationFailureHandler@4997ddbd
2019-02-04 11:26:43 [http-nio-8080-exec-2] DEBUG org.springframework.security.web.authentication.SimpleUrlAuthenticationFailureHandler - Redirecting to /login.jsp?error
2019-02-04 11:26:43 [http-nio-8080-exec-2] DEBUG org.springframework.security.web.DefaultRedirectStrategy - Redirecting to '/cbioportal/login.jsp?error'

To post to this group, send email to cbio...@googlegroups.com.

Pieter Lukasse

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Feb 6, 2019, 11:41:38 AM2/6/19
to John Reber, cBioPortal for Cancer Genomics Discussion Group
Hi John,

thanks for reporting. I have logged it here https://github.com/cBioPortal/cbioportal/issues/5695 . This might be an issue in the new release. 

Best,

Pieter Lukasse


E.   pie...@thehyve.nl

T.   +31(0)30 700 9713

W.  www.thehyve.nl


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Op ma 4 feb. 2019 om 18:35 schreef John Reber <John....@jefferson.edu>:
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