search

openanalytics / shinyproxy-config-examples

Configuration examples for ShinyProxy
https://www.shinyproxy.io
147 stars 110 forks source link

Getting Shiny Proxy working on Mac 02-containerized-docker-engine #30

Closed russellkemmit closed 1 year ago

russellkemmit commented 2 years ago

Below is my docker container 

FROM openanalytics/shinyproxy:2.6.1
COPY application.yml /opt/shinyproxy/application.yml

Below is the yaml file

proxy:
  title: Open Analytics Shiny Proxy
  logo-url: https://www.openanalytics.eu/shinyproxy/logo.png
  port: 8080
  authentication: none
  admin-groups: admins
  users:
  - name: jack
    password: password
    groups: admins
  - name: jeff
    password: password
  docker:
      url: http://localhost:2375
      internal-networking: true
  specs:
  - id: 01_hello
    display-name: Hello Application
    description: Application which demonstrates the basics of a Shiny app
    container-cmd: ["R", "-e", "shinyproxy::run_01_hello()"]
    container-image: openanalytics/shinyproxy-demo
    container-network: sp-example-net
  - id: 06_tabsets
    container-cmd: ["R", "-e", "shinyproxy::run_06_tabsets()"]
    container-image: openanalytics/shinyproxy-demo
    container-network: sp-example-net

logging:
  file:
    shinyproxy.log

I am able to start and run the container successfully, with command 

sudo docker run -v /var/run/docker.sock:/var/run/docker.sock:ro --net sp-example-net -p 8080:8080 shinyproxy-example

NOTE that I am unable to run the full command as the --group-add $(getent group docker | cut -d: -f3) portion below does not work on Mac

sudo docker run -v /var/run/docker.sock:/var/run/docker.sock:ro --group-add $(getent group docker | cut -d: -f3) --net sp-example-net -p 8080:8080 shinyproxy-example

I am able to get to the home screen, but when I click on one of the example apps I get this stack trace

Status code: 500

Message: Container failed to start

Stack Trace:
eu.openanalytics.containerproxy.ContainerProxyException: Container failed to start
at eu.openanalytics.containerproxy.service.ProxyService.startProxy(ProxyService.java:283)
at eu.openanalytics.shinyproxy.controllers.AppController.getOrStart(AppController.java:150)
at eu.openanalytics.shinyproxy.controllers.AppController.startApp(AppController.java:91)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205)
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:150)
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:117)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:895)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:808)
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1067)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:963)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006)
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:909)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:517)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:584)
at io.undertow.servlet.handlers.ServletHandler.handleRequest(ServletHandler.java:74)
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:129)
at eu.openanalytics.containerproxy.util.AppRecoveryFilter.doFilter(AppRecoveryFilter.java:63)
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61)
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:327)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:115)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:81)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:121)
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:115)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:126)
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:81)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:105)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:149)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
at eu.openanalytics.containerproxy.util.AppRecoveryFilter.doFilter(AppRecoveryFilter.java:63)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:103)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:89)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
at org.springframework.security.web.csrf.CsrfFilter.doFilterInternal(CsrfFilter.java:117)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
at org.springframework.security.web.header.HeaderWriterFilter.doHeadersAfter(HeaderWriterFilter.java:90)
at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:75)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:110)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:80)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:55)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:211)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:183)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:354)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:267)
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61)
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131)
at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:100)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61)
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131)
at org.springframework.boot.actuate.metrics.web.servlet.WebMvcMetricsFilter.doFilterInternal(WebMvcMetricsFilter.java:96)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61)
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131)
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61)
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131)
at io.undertow.servlet.handlers.FilterHandler.handleRequest(FilterHandler.java:84)
at io.undertow.servlet.handlers.security.ServletSecurityRoleHandler.handleRequest(ServletSecurityRoleHandler.java:62)
at io.undertow.servlet.handlers.ServletChain$1.handleRequest(ServletChain.java:68)
at io.undertow.servlet.handlers.ServletDispatchingHandler.handleRequest(ServletDispatchingHandler.java:36)
at io.undertow.server.handlers.PathHandler.handleRequest(PathHandler.java:104)
at eu.openanalytics.containerproxy.util.ProxyMappingManager$ProxyPathHandler.handleRequest(ProxyMappingManager.java:160)
at io.undertow.servlet.handlers.RedirectDirHandler.handleRequest(RedirectDirHandler.java:68)
at io.undertow.servlet.handlers.security.SSLInformationAssociationHandler.handleRequest(SSLInformationAssociationHandler.java:117)
at io.undertow.servlet.handlers.security.ServletAuthenticationCallHandler.handleRequest(ServletAuthenticationCallHandler.java:57)
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43)
at io.undertow.security.handlers.AbstractConfidentialityHandler.handleRequest(AbstractConfidentialityHandler.java:46)
at io.undertow.servlet.handlers.security.ServletConfidentialityConstraintHandler.handleRequest(ServletConfidentialityConstraintHandler.java:64)
at io.undertow.security.handlers.AuthenticationMechanismsHandler.handleRequest(AuthenticationMechanismsHandler.java:60)
at io.undertow.servlet.handlers.security.CachedAuthenticatedSessionHandler.handleRequest(CachedAuthenticatedSessionHandler.java:77)
at io.undertow.security.handlers.AbstractSecurityContextAssociationHandler.handleRequest(AbstractSecurityContextAssociationHandler.java:43)
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43)
at io.undertow.server.handlers.SameSiteCookieHandler.handleRequest(SameSiteCookieHandler.java:97)
at io.undertow.servlet.handlers.SendErrorPageHandler.handleRequest(SendErrorPageHandler.java:52)
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43)
at io.undertow.servlet.handlers.ServletInitialHandler.handleFirstRequest(ServletInitialHandler.java:269)
at io.undertow.servlet.handlers.ServletInitialHandler.access$100(ServletInitialHandler.java:78)
at io.undertow.servlet.handlers.ServletInitialHandler$2.call(ServletInitialHandler.java:133)
at io.undertow.servlet.handlers.ServletInitialHandler$2.call(ServletInitialHandler.java:130)
at io.undertow.servlet.core.ServletRequestContextThreadSetupAction$1.call(ServletRequestContextThreadSetupAction.java:48)
at io.undertow.servlet.core.ContextClassLoaderSetupAction$1.call(ContextClassLoaderSetupAction.java:43)
at io.undertow.servlet.handlers.ServletInitialHandler.dispatchRequest(ServletInitialHandler.java:249)
at io.undertow.servlet.handlers.ServletInitialHandler.access$000(ServletInitialHandler.java:78)
at io.undertow.servlet.handlers.ServletInitialHandler$1.handleRequest(ServletInitialHandler.java:99)
at io.undertow.server.Connectors.executeRootHandler(Connectors.java:387)
at io.undertow.server.HttpServerExchange$1.run(HttpServerExchange.java:841)
at org.jboss.threads.ContextClassLoaderSavingRunnable.run(ContextClassLoaderSavingRunnable.java:35)
at org.jboss.threads.EnhancedQueueExecutor.safeRun(EnhancedQueueExecutor.java:2019)
at org.jboss.threads.EnhancedQueueExecutor$ThreadBody.doRunTask(EnhancedQueueExecutor.java:1558)
at org.jboss.threads.EnhancedQueueExecutor$ThreadBody.run(EnhancedQueueExecutor.java:1449)
at org.xnio.XnioWorker$WorkerThreadFactory$1$1.run(XnioWorker.java:1280)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: com.spotify.docker.client.exceptions.DockerException: java.util.concurrent.ExecutionException: javax.ws.rs.ProcessingException: java.io.IOException: Permission denied
at com.spotify.docker.client.DefaultDockerClient.propagate(DefaultDockerClient.java:2848)
at com.spotify.docker.client.DefaultDockerClient.request(DefaultDockerClient.java:2723)
at com.spotify.docker.client.DefaultDockerClient.createContainer(DefaultDockerClient.java:742)
at com.spotify.docker.client.DefaultDockerClient.createContainer(DefaultDockerClient.java:724)
at eu.openanalytics.containerproxy.backend.docker.DockerEngineBackend.startContainer(DockerEngineBackend.java:99)
at eu.openanalytics.containerproxy.backend.AbstractContainerBackend.doStartProxy(AbstractContainerBackend.java:163)
at eu.openanalytics.containerproxy.backend.AbstractContainerBackend.startProxy(AbstractContainerBackend.java:129)
at eu.openanalytics.containerproxy.service.ProxyService.startProxy(ProxyService.java:279)
... 112 more
Caused by: java.util.concurrent.ExecutionException: javax.ws.rs.ProcessingException: java.io.IOException: Permission denied
at java.base/java.util.concurrent.CompletableFuture.reportGet(Unknown Source)
at java.base/java.util.concurrent.CompletableFuture.get(Unknown Source)
at com.spotify.docker.client.DefaultDockerClient.request(DefaultDockerClient.java:2721)
... 118 more
Caused by: javax.ws.rs.ProcessingException: java.io.IOException: Permission denied
at org.glassfish.jersey.apache.connector.ApacheConnector.apply(ApacheConnector.java:531)
at org.glassfish.jersey.apache.connector.ApacheConnector.apply(ApacheConnector.java:538)
at org.glassfish.jersey.client.ClientRuntime.lambda$null$6(ClientRuntime.java:182)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244)
at org.glassfish.jersey.internal.Errors.process(Errors.java:292)
at org.glassfish.jersey.internal.Errors.process(Errors.java:274)
at org.glassfish.jersey.internal.Errors.process(Errors.java:244)
at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:288)
at org.glassfish.jersey.client.ClientRuntime.lambda$createRunnableForAsyncProcessing$7(ClientRuntime.java:156)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
... 1 more
Caused by: java.io.IOException: Permission denied
at jnr.unixsocket.UnixSocketChannel.doConnect(UnixSocketChannel.java:127)
at jnr.unixsocket.UnixSocketChannel.connect(UnixSocketChannel.java:136)
at jnr.unixsocket.UnixSocketChannel.connect(UnixSocketChannel.java:223)
at com.spotify.docker.client.UnixConnectionSocketFactory.connectSocket(UnixConnectionSocketFactory.java:85)
at org.apache.http.impl.conn.DefaultHttpClientConnectionOperator.connect(DefaultHttpClientConnectionOperator.java:142)
at org.apache.http.impl.conn.PoolingHttpClientConnectionManager.connect(PoolingHttpClientConnectionManager.java:376)
at org.apache.http.impl.execchain.MainClientExec.establishRoute(MainClientExec.java:393)
at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:236)
at org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:186)
at org.apache.http.impl.execchain.RetryExec.execute(RetryExec.java:89)
at org.apache.http.impl.execchain.RedirectExec.execute(RedirectExec.java:110)
at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:185)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:72)
at org.glassfish.jersey.apache.connector.ApacheConnector.apply(ApacheConnector.java:483)
... 14 more
russellkemmit commented 2 years ago

I believe this has to do with the user not having access to the docker daemon?? I found that a workaround for this is adding the user to the docker group, but the docker group no longer exists on Mac. Any help would be greatly appreciated.

LEDfan commented 1 year ago

Hi

I think on Macos passing the docker socket as a volume will not work. You can use the HTTP API of Docker instead. See this link for information on how to make the API accessible, https://stackoverflow.com/questions/39411126/access-docker-daemon-remote-api-on-docker-for-mac . Next you have to change the proxy.docker.url setting to http://[host IP address]:2375

Kastakin commented 5 months ago

I did not have any luck in making this work. I probably missed something but in the end I gave up spinning a dev environment for our application on my local machine. It would probably be a good idea adding a small guide or at least a notice to the Faqs on the website.