molgenis / molgenis

MOLGENIS - for scientific data: management, exploration, integration and analysis.
https://molgenis.org
GNU Lesser General Public License v3.0
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chore: bump to latest parent pom #9362

Closed sidohaakma closed 2 years ago

sidohaakma commented 2 years ago

Checklist

tommydeboer commented 2 years ago

I ran the commander's integration tests and it seems that this PR fixes the logo upload. Confirmed on the preview server and locally:

org.springframework.security.access.AccessDeniedException: Access is denied
    at org.springframework.security.access.vote.AffirmativeBased.decide(AffirmativeBased.java:73)
    at org.springframework.security.access.intercept.AbstractSecurityInterceptor.attemptAuthorization(AbstractSecurityInterceptor.java:238)
    at org.springframework.security.access.intercept.AbstractSecurityInterceptor.beforeInvocation(AbstractSecurityInterceptor.java:208)
    at org.springframework.security.access.intercept.aopalliance.MethodSecurityInterceptor.invoke(MethodSecurityInterceptor.java:58)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:753)
    at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:388)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:753)
    at org.springframework.aop.aspectj.MethodInvocationProceedingJoinPoint.proceed(MethodInvocationProceedingJoinPoint.java:89)
    at org.molgenis.security.core.runas.RunAsSystemAspect.runAsSystem(RunAsSystemAspect.java:49)
    at org.molgenis.security.core.runas.RunAsSystemAspect.aroundAdvice(RunAsSystemAspect.java:28)
    at jdk.internal.reflect.GeneratedMethodAccessor106.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at org.springframework.aop.aspectj.AbstractAspectJAdvice.invokeAdviceMethodWithGivenArgs(AbstractAspectJAdvice.java:634)
    at org.springframework.aop.aspectj.AbstractAspectJAdvice.invokeAdviceMethod(AbstractAspectJAdvice.java:624)
    at org.springframework.aop.aspectj.AspectJAroundAdvice.invoke(AspectJAroundAdvice.java:72)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:175)
    at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:753)
    at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:97)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:753)
    at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:698)
    at org.molgenis.core.ui.menumanager.MenuManagerServiceImpl$$EnhancerBySpringCGLIB$$56a11193.getPlugins(<generated>)
    at org.molgenis.core.ui.menumanager.MenuManagerController.init(MenuManagerController.java:60)
    at org.molgenis.core.ui.menumanager.MenuManagerController.uploadLogo(MenuManagerController.java:97)
    at org.molgenis.core.ui.menumanager.MenuManagerController$$FastClassBySpringCGLIB$$b866318b.invoke(<generated>)
    at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218)
    at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:783)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
    at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:753)
    at org.springframework.security.access.intercept.aopalliance.MethodSecurityInterceptor.invoke(MethodSecurityInterceptor.java:61)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:753)
    at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:698)
    at org.molgenis.core.ui.menumanager.MenuManagerController$$EnhancerBySpringCGLIB$$eb37519e.uploadLogo(<generated>)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    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:681)
    at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:764)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:227)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
    at org.springframework.web.filter.ShallowEtagHeaderFilter.doFilterInternal(ShallowEtagHeaderFilter.java:106)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
    at org.molgenis.core.ui.browserdetection.BrowserDetectionFilter.doFilter(BrowserDetectionFilter.java:52)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:327)
    at org.molgenis.security.twofactor.auth.TwoFactorAuthenticationFilter.doFilterInternal(TwoFactorAuthenticationFilter.java:54)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
    at org.molgenis.security.MolgenisChangePasswordFilter.doFilter(MolgenisChangePasswordFilter.java:52)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:115)
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:81)
    at org.springframework.security.web.FilterChainProxy$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$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
    at org.molgenis.security.token.TokenAuthenticationFilter.doFilter(TokenAuthenticationFilter.java:52)
    at org.springframework.security.web.FilterChainProxy$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 org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:149)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
    at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:218)
    at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:212)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
    at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:218)
    at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:212)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
    at org.springframework.security.oauth2.client.web.OAuth2AuthorizationRequestRedirectFilter.doFilterInternal(OAuth2AuthorizationRequestRedirectFilter.java:178)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
    at org.springframework.security.web.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$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
    at org.springframework.web.filter.CorsFilter.doFilterInternal(CorsFilter.java:91)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
    at org.springframework.security.web.FilterChainProxy$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$VirtualFilterChain.doFilter(FilterChainProxy.java:336)
    at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:211)
    at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:183)
    at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:354)
    at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:267)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
    at org.springframework.web.filter.ForwardedHeaderFilter.doFilterInternal(ForwardedHeaderFilter.java:156)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:197)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:540)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:135)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)
    at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:687)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:357)
    at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:382)
    at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65)
    at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:893)
    at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1726)
    at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
    at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191)
    at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.base/java.lang.Thread.run(Thread.java:833)
tommydeboer commented 2 years ago

Did some more digging and it's broken since 2.5.7

tommydeboer commented 2 years ago

The whole menu manager is unaccessible

tommydeboer commented 2 years ago

Upgrade spring parent POM (log4j fix)

tommydeboer commented 2 years ago

23 december: Update spring boot pom to 2.5.8 in molgenis/molgenis

sonarcloud[bot] commented 2 years ago

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication