"HTTP Status 500 – Internal Server Error" on public dataset "all_phase2_target_2018_pub"

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Marc Deloger

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Jul 23, 2021, 9:38:18 AMJul 23
to cBioPortal for Cancer Genomics Discussion Group

Hi,

here is the error I have whatever public study I import in our internal cbioportal instance (during the "Rendering" step) :

{"portalVersion":"3.6.19-dirty-SNAPSHOT","dbVersion":"2.12.8","gitBranch":"11f1579f156a2762af9120effdaa26518a0e1da5","gitCommitId":"11f1579f156a2762af9120effdaa26518a0e1da5","gitCommitIdDescribe":"v3.6.19-dirty","gitCommitIdDescribeShort":"v3.6.19-dirty","gitCommitMessageFull":"use new frontend commit of v3.6.19","gitCommitMessageShort":"use new frontend commit of v3.6.19","gitCommitMessageUserEmail":"i...@ino.bio","gitCommitMessageUserName":"Ino de Bruijn","gitDirty":true}

Hereafter you will find the error obtained with the public dataset downloaded here : https://cbioportal-datahub.s3.amazonaws.com/all_phase2_target_2018_pub.tar.gz

Thank you in advance for your help

{"req":{"method":"POST","url":"http://31.10.14.160:8081/api/session/custom_data/fetch","data":["all_phase2_target_2018_pub"],"headers":{"content-type":"application/json"}},"xhr":{},"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$InternalServerError: 500 : [{&quot;timestamp&quot;:&quot;2021-07-23T13:35:33.620+00:00&quot;,&quot;status&quot;:500,&quot;error&quot;:&quot;Internal Server Error&quot;,&quot;message&quot;:&quot;&quot;,&quot;path&quot;:&quot;&#47;api&#47;sessions&#47;my_portal&#47;custom_data&#47;query&#47;fetch&quot;}]</p><p><b>Description</b> The server encountered an unexpected condition that prevented it from fulfilling the request.</p><p><b>Exception</b></p><pre>org.springframework.web.util.NestedServletException: Request processing failed; nested exception is org.springframework.web.client.HttpServerErrorException$InternalServerError: 500 : [{&quot;timestamp&quot;:&quot;2021-07-23T13:35:33.620+00:00&quot;,&quot;status&quot;:500,&quot;error&quot;:&quot;Internal Server Error&quot;,&quot;message&quot;:&quot;&quot;,&quot;path&quot;:&quot;&#47;api&#47;sessions&#47;my_portal&#47;custom_data&#47;query&#47;fetch&quot;}]\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$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137)\n\torg.springframework.security.web.FilterChainProxy$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.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 : [{&quot;timestamp&quot;:&quot;2021-07-23T13:35:33.620+00:00&quot;,&quot;status&quot;:500,&quot;error&quot;:&quot;Internal Server Error&quot;,&quot;message&quot;:&quot;&quot;,&quot;path&quot;:&quot;&#47;api&#47;sessions&#47;my_portal&#47;custom_data&#47;query&#47;fetch&quot;}]\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:674)\n\torg.springframework.web.client.RestTemplate.exchange(RestTemplate.java:612)\n\torg.cbioportal.web.SessionServiceController.fetchCustomProperties(SessionServiceController.java:472)\n\torg.cbioportal.web.SessionServiceController$$FastClassBySpringCGLIB$$6b4f2f08.invoke(&lt;generated&gt;)\n\torg.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218)\n\torg.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:771)\n\torg.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)\n\torg.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:749)\n\torg.springframework.aop.framework.adapter.MethodBeforeAdviceInterceptor.invoke(MethodBeforeAdviceInterceptor.java:56)\n\torg.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)\n\torg.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:749)\n\torg.springframework.aop.aspectj.AspectJAfterAdvice.invoke(AspectJAfterAdvice.java:47)\n\torg.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)\n\torg.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:749)\n\torg.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:95)\n\torg.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)\n\torg.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:749)\n\torg.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:691)\n\torg.cbioportal.web.SessionServiceController$$EnhancerBySpringCGLIB$$1af4f98d.fetchCustomProperties(&lt;generated&gt;)\n\tjava.base&#47;jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\n\tjava.base&#47;jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)\n\tjava.base&#47;jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)\n\tjava.base&#47;java.lang.reflect.Method.invoke(Unknown Source)\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.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$VirtualFilterChain.doFilter(FilterChainProxy.java:334)\n\torg.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137)\n\torg.springframework.security.web.FilterChainProxy$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.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":"POST","url":"http://31.10.14.160:8081/api/session/custom_data/fetch"},"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","connection":"close","content-language":"en","content-type":"text/html;charset=utf-8","date":"Fri, 23 Jul 2021 13:35:33 GMT","expires":"0","pragma":"no-cache","transfer-encoding":"chunked","x-content-type-options":"nosniff","x-frame-options":"DENY","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","connection":"close","content-language":"en","content-type":"text/html;charset=utf-8","date":"Fri, 23 Jul 2021 13:35:33 GMT","expires":"0","pragma":"no-cache","transfer-encoding":"chunked","x-content-type-options":"nosniff","x-frame-options":"DENY","x-xss-protection":"1; mode=block"},"type":"text/html","charset":"utf-8","links":{},"body":null,"url":"http://31.10.14.160:8081/study/summary?id=all_phase2_target_2018_pub"}

Marc Deloger

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Jul 23, 2021, 10:48:53 AMJul 23
to cBioPortal for Cancer Genomics Discussion Group
Just an other hint, I tried to start the cbioportal-container in "-Dauthenticate=false" instead of "-Dauthenticate=saml" and it works.
So it seems that keycloak permits me to login, to see the list of studies even to query by gene but not to explore studies.

Has anyone already encountered this kind of scenario ?

Best

John Reber

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Jul 23, 2021, 10:58:53 AMJul 23
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We had something similar and it was our session-services version.  We had v0.2.0 version.  Changed it too v0.2.0 and all was well. This was in docker-compose containers.

John Reber

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Jul 23, 2021, 11:01:23 AMJul 23
to cBioPortal for Cancer Genomics Discussion Group

Sorry, that should have been upgraded session-service to v0.4.0

Marc Deloger

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Jul 23, 2021, 11:13:39 AMJul 23
to cBioPortal for Cancer Genomics Discussion Group
Hi John, thank you for the answer but it seems we already have the latest version :

docker.io/cbioportal/session-service   latest              68905ee88fef        5 months ago        305 MB

You downgraded to 0.2.0 or you updated from 0.2.0 to 0.4.0 to solve ?

Marc Deloger

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Jul 23, 2021, 11:16:05 AMJul 23
to cBioPortal for Cancer Genomics Discussion Group
CONTAINER ID        IMAGE                               COMMAND                  CREATED             STATUS              PORTS                    NAMES
a8a165ec72f5        cbioportal/cbioportal:latest        "docker-entrypoint..."   30 minutes ago      Up 30 minutes       0.0.0.0:8081->8080/tcp   cbioportal-container
e78cd3a03811        jboss/keycloak:4.8.3.Final          "/opt/jboss/tools/..."   2 weeks ago         Up About an hour    0.0.0.0:8180->8080/tcp   cbiokc
ba424642e9c1        mysql:5.7                           "docker-entrypoint..."   2 weeks ago         Up 2 weeks          3306/tcp, 33060/tcp      kcdb
ede5e22d78c9        cbioportal/session-service:latest   "/bin/sh -c 'java ..."   2 weeks ago         Up About an hour                             cbio-session-service
f5ee1205c47a        mongo:3.6.6                         "docker-entrypoint..."   2 weeks ago         Up 39 minutes       27017/tcp                mongoDB
eaaa7b678de0        mysql:5.7                           "docker-entrypoint..."   2 weeks ago         Up 39 minutes       3306/tcp, 33060/tcp      cbioDB

John Reber

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Jul 23, 2021, 11:20:07 AMJul 23
to cBioPortal for Cancer Genomics Discussion Group
Sorry, upgraded to v0.4.0 (though I think the actual fix was v.0.3.0)

Just to confirm the version being used, what does the command "docker-compose images" show (ours is below)?

[cportal@cbioportal cbioportal-docker-compose]$ docker-compose images
              Container                         Repository            Tag      Image Id       Size  
----------------------------------------------------------------------------------------------------
cbioportal-container                    cbioportal/cbioportal        3.6.7   15f21bb00e0f   1.097 GB
cbioportal-database-container           mysql                        5.7     2c9028880e58   447 MB  
cbioportal-session-container            cbioportal/session-service   0.4.0   251e4cc83a12   305.5 MB
cbioportal-session-database-container   mongo                        3.7.9   3db1239d511b   365.3 MB
[cportal@cbioportal cbioportal-docker-compose]$

Marc Deloger

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Jul 23, 2021, 11:22:14 AMJul 23
to cBioPortal for Cancer Genomics Discussion Group
REPOSITORY                             TAG                 IMAGE ID            CREATED             SIZE
docker.io/cbioportal/cbioportal        latest              05da5a36d083        3 weeks ago         1.1 GB
docker.io/mysql                        5.7                 09361feeb475        4 weeks ago         447 MB

docker.io/cbioportal/session-service   latest              68905ee88fef        5 months ago        305 MB
docker.io/jboss/keycloak               4.8.3.Final         0ad4869e7fb5        2 years ago         822 MB
docker.io/mongo                        3.6.6               6c798900c232        2 years ago         368 MB

John Reber

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Jul 23, 2021, 11:29:17 AMJul 23
to cBioPortal for Cancer Genomics Discussion Group
Hi Marc,

Sorry, wish I could be of more help.  New to docker myself and I would think 'latest', as you have it, would pick the latest and greatest.

John

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