Container unresponsive

Hello,

I have an error on the proxyshiny, and i don’t realy know what is going on.

My docker work perfectly when i run it without shinyproxy.

But when I use the shinyproxy the container is uresponsive.

I use the last two version of shinyproxy (2.3.0 and 2.3.1), and the response is the same.

This is the application.yml file :

proxy:
  port: 8080
  authentication: none
  specs:
  - id: padle
    display-name: PADLE
    description: Profiling Anaysis of DifferentiaL Expression
    container-cmd: ["R", "--vanilla", "-e", "options('shiny.port'=3838, shiny.host='0.0.0.0', golem.app.prod = T); RNASeqDE::run_app()"]
    container-image: padle
    container-volumes: ["/data/result:/data/result"]
    port: 3838

  - id: 01_hello
    container-cmd: ["R", "-e", "shinyproxy::run_01_hello()"]
    container-image: openanalytics/shinyproxy-demo


logging:
  file:
    shinyproxy.log

When I take the 01_hello image in the shinyproxy interface it’s working perfectly. But when i try with my image (padle), it don’t work at all.

This is what the things that the console log when I choose the PADLE application :

2020-07-02 15:15:00.248  INFO 43717 --- [  XNIO-2 task-3] c.s.docker.client.DefaultDockerClient    : Starting container with Id: 817480e695e761cedf174cacde84d6f881aa9e0ff239200e2c71b3c7e808d496
2020-07-02 15:15:03.314  WARN 43717 --- [  XNIO-2 task-3] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (2/10): http://817480e695e7:3838
2020-07-02 15:15:05.317  WARN 43717 --- [  XNIO-2 task-3] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (3/10): http://817480e695e7:3838
2020-07-02 15:15:07.321  WARN 43717 --- [  XNIO-2 task-3] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (4/10): http://817480e695e7:3838
2020-07-02 15:15:09.323  WARN 43717 --- [  XNIO-2 task-3] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (5/10): http://817480e695e7:3838
2020-07-02 15:15:11.327  WARN 43717 --- [  XNIO-2 task-3] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (6/10): http://817480e695e7:3838
2020-07-02 15:15:13.329  WARN 43717 --- [  XNIO-2 task-3] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (7/10): http://817480e695e7:3838
2020-07-02 15:15:15.331  WARN 43717 --- [  XNIO-2 task-3] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (8/10): http://817480e695e7:3838
2020-07-02 15:15:17.333  WARN 43717 --- [  XNIO-2 task-3] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (9/10): http://817480e695e7:3838
2020-07-02 15:15:19.334  WARN 43717 --- [  XNIO-2 task-3] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (10/10): http://817480e695e7:3838
2020-07-02 15:15:21.394 ERROR 43717 --- [  XNIO-2 task-3] io.undertow.request                      : UT005023: Exception handling request to /app/padle

org.springframework.web.util.NestedServletException: Request processing failed; nested exception is eu.openanalytics.containerproxy.ContainerProxyException: Container did not respond in time
        at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:986) ~[spring-webmvc-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:881) ~[spring-webmvc-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:707) ~[javax.servlet-api-3.1.0.jar!/:3.1.0]
        at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:855) ~[spring-webmvc-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) ~[javax.servlet-api-3.1.0.jar!/:3.1.0]
        at io.undertow.servlet.handlers.ServletHandler.handleRequest(ServletHandler.java:74) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:129) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:119) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:170) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.csrf.CsrfFilter.doFilterInternal(CsrfFilter.java:100) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) ~[spring-web-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:66) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) ~[spring-web-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) ~[spring-web-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178) ~[spring-security-web-5.0.3.RELEASE.jar!/:5.0.3.RELEASE]
        at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:357) ~[spring-web-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:270) ~[spring-web-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:99) ~[spring-web-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) ~[spring-web-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:200) ~[spring-web-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) ~[spring-web-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.FilterHandler.handleRequest(FilterHandler.java:84) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.security.ServletSecurityRoleHandler.handleRequest(ServletSecurityRoleHandler.java:62) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.ServletChain$1.handleRequest(ServletChain.java:64) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.ServletDispatchingHandler.handleRequest(ServletDispatchingHandler.java:36) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.server.handlers.PathHandler.handleRequest(PathHandler.java:94) ~[undertow-core-1.4.22.Final.jar!/:1.4.22.Final]
        at eu.openanalytics.containerproxy.util.ProxyMappingManager$ProxyPathHandler.handleRequest(ProxyMappingManager.java:159) ~[containerproxy-0.8.4.jar!/:0.8.4]
        at io.undertow.servlet.handlers.security.SSLInformationAssociationHandler.handleRequest(SSLInformationAssociationHandler.java:131) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.security.ServletAuthenticationCallHandler.handleRequest(ServletAuthenticationCallHandler.java:57) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) ~[undertow-core-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.security.handlers.AbstractConfidentialityHandler.handleRequest(AbstractConfidentialityHandler.java:46) ~[undertow-core-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.security.ServletConfidentialityConstraintHandler.handleRequest(ServletConfidentialityConstraintHandler.java:64) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.security.handlers.AuthenticationMechanismsHandler.handleRequest(AuthenticationMechanismsHandler.java:60) ~[undertow-core-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.security.CachedAuthenticatedSessionHandler.handleRequest(CachedAuthenticatedSessionHandler.java:77) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.security.handlers.AbstractSecurityContextAssociationHandler.handleRequest(AbstractSecurityContextAssociationHandler.java:43) ~[undertow-core-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) ~[undertow-core-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) ~[undertow-core-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.ServletInitialHandler.handleFirstRequest(ServletInitialHandler.java:292) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.ServletInitialHandler.access$100(ServletInitialHandler.java:81) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.ServletInitialHandler$2.call(ServletInitialHandler.java:138) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.ServletInitialHandler$2.call(ServletInitialHandler.java:135) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.core.ServletRequestContextThreadSetupAction$1.call(ServletRequestContextThreadSetupAction.java:48) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.core.ContextClassLoaderSetupAction$1.call(ContextClassLoaderSetupAction.java:43) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.ServletInitialHandler.dispatchRequest(ServletInitialHandler.java:272) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.ServletInitialHandler.access$000(ServletInitialHandler.java:81) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.servlet.handlers.ServletInitialHandler$1.handleRequest(ServletInitialHandler.java:104) ~[undertow-servlet-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.server.Connectors.executeRootHandler(Connectors.java:336) ~[undertow-core-1.4.22.Final.jar!/:1.4.22.Final]
        at io.undertow.server.HttpServerExchange$1.run(HttpServerExchange.java:830) ~[undertow-core-1.4.22.Final.jar!/:1.4.22.Final]
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) ~[na:na]
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) ~[na:na]
        at java.base/java.lang.Thread.run(Thread.java:834) ~[na:na]
Caused by: eu.openanalytics.containerproxy.ContainerProxyException: Container did not respond in time
        at eu.openanalytics.containerproxy.backend.AbstractContainerBackend.startProxy(AbstractContainerBackend.java:118) ~[containerproxy-0.8.4.jar!/:0.8.4]
        at eu.openanalytics.containerproxy.service.ProxyService.startProxy(ProxyService.java:213) ~[containerproxy-0.8.4.jar!/:0.8.4]
        at eu.openanalytics.shinyproxy.controllers.AppController.getOrStart(AppController.java:107) ~[classes!/:2.3.1]
        at eu.openanalytics.shinyproxy.controllers.AppController.startApp(AppController.java:64) ~[classes!/:2.3.1]
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:na]
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:na]
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
        at java.base/java.lang.reflect.Method.invoke(Method.java:566) ~[na:na]
        at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:209) ~[spring-web-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136) ~[spring-web-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:102) ~[spring-webmvc-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:870) ~[spring-webmvc-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:776) ~[spring-webmvc-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87) ~[spring-webmvc-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:991) ~[spring-webmvc-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:925) ~[spring-webmvc-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:978) ~[spring-webmvc-5.0.4.RELEASE.jar!/:5.0.4.RELEASE]
        ... 74 common frames omitted

And the page when I choose my application this word is show : undefined.

Please help me,
Thank you,
Arthur

2 Likes

I have the exact same problem. I have been able to rebuild and deploy continuously with no issues for a couple of months. Last successful rebuild/deploy was this Monday. Now, I can’t get it to work as the containers are unresponsive. Feel like I have tried everything to no avail.

1 Like

Same thing here. While the standalone docker image produces a viable app, when running it through shinyproxy, it timeouts.