the pack file might be corrupt. Caught 1 consecutive errors while trying to read this pack. about scm-manager

[eheimbuch]

Hey @nikossakellariou,

after some research we assume it could be related to not enough memory during the compression of large files.

Maybe this could help you?
https://stackoverflow.com/a/66246671

Edit: Please try to scan your repository for corrupt files with git fsck --full. Unfortunately we cannot reproduce this error yet.

[christophloose]

Thank you @nikossakellariou we will have a look at it

[pfeuffer]

Hi @nikossakellariou , we have not noticed such errors outside of our integration tests before. Can you tell us a bit more about your usage and your setup?

Roughly

• how many users,
• how many repositories,
• do you access your repositories often using the browser or mostly by the normal git client,
• how many requests,
• what does your general setup look like,
• how often does this error occur
• do you have "GC Cron Expression" configured in the global git configuration?

Additionally, could you post some more of the stack trace that follows the line java.io.EOFException: Short compressed stream at 4,815? This could tell us, where exactly the error occurs.

Tanks for your support!

[nikossakellariou]

Thanks for the reply!

1. how many users
   30-40
2. how many repositories,
   200-250
3. do you access your repositories often using the browser or mostly by the normal git client,
   Both
4. how many requests,
   same as users
5. what does your general setup look like,
   installed on debian 11 behind nginx reverse proxy
6. how often does this error occur
   approximately onces a month
7. do you have "GC Cron Expression" configured in the global git configuration?
   No

Full log example:
2023-10-03 16:06:44.003 [qtp1975358023-5316] [DMTrd14HxAvb] ERROR org.eclipse.jgit.internal.storage.file.PackDirectory - Exception caught while accessing pack file /my/repositoy/location/data/objects/pack/pack-5857461d013db1fa74e0105a1be2ef92ce32f083.pack, the pack file might be corrupt. Caught 1 consecutive errors while trying to read this pack.
java.io.EOFException: Short compressed stream at 1,721,592
at org.eclipse.jgit.internal.storage.file.Pack.decompress(Pack.java:370)
at org.eclipse.jgit.internal.storage.file.Pack.load(Pack.java:803)
at org.eclipse.jgit.internal.storage.file.Pack.get(Pack.java:273)
at org.eclipse.jgit.internal.storage.file.PackDirectory.open(PackDirectory.java:212)
at org.eclipse.jgit.internal.storage.file.ObjectDirectory.openPackedObject(ObjectDirectory.java:404)
at org.eclipse.jgit.internal.storage.file.ObjectDirectory.openPackedFromSelfOrAlternate(ObjectDirectory.java:368)
at org.eclipse.jgit.internal.storage.file.ObjectDirectory.openObjectWithoutRestoring(ObjectDirectory.java:359)
at org.eclipse.jgit.internal.storage.file.ObjectDirectory.openObject(ObjectDirectory.java:344)
at org.eclipse.jgit.internal.storage.file.WindowCursor.open(WindowCursor.java:132)
at org.eclipse.jgit.treewalk.CanonicalTreeParser.reset(CanonicalTreeParser.java:191)
at org.eclipse.jgit.treewalk.TreeWalk.parserFor(TreeWalk.java:1442)
at org.eclipse.jgit.treewalk.TreeWalk.addTree(TreeWalk.java:820)
at sonia.scm.repository.spi.GitBrowseCommand.getEntry(GitBrowseCommand.java:227)
at sonia.scm.repository.spi.GitBrowseCommand.getBrowserResult(GitBrowseCommand.java:138)
at sonia.scm.repository.api.BrowseCommandBuilder.computeBrowserResult(BrowseCommandBuilder.java:178)
at sonia.scm.repository.api.BrowseCommandBuilder.getBrowserResult(BrowseCommandBuilder.java:156)
at sonia.scm.api.v2.resources.SourceRootResource.getSource(SourceRootResource.java:93)
at sonia.scm.api.v2.resources.SourceRootResource.getAll(SourceRootResource.java:72)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.jboss.resteasy.core.MethodInjectorImpl.invoke(MethodInjectorImpl.java:170)
at org.jboss.resteasy.core.MethodInjectorImpl.invoke(MethodInjectorImpl.java:130)
at org.jboss.resteasy.core.ResourceMethodInvoker.internalInvokeOnTarget(ResourceMethodInvoker.java:660)
at org.jboss.resteasy.core.ResourceMethodInvoker.invokeOnTargetAfterFilter(ResourceMethodInvoker.java:524)
at org.jboss.resteasy.core.ResourceMethodInvoker.lambda$invokeOnTarget$2(ResourceMethodInvoker.java:474)
at org.jboss.resteasy.core.interception.jaxrs.PreMatchContainerRequestContext.filter(PreMatchContainerRequestContext.java:364)
at org.jboss.resteasy.core.ResourceMethodInvoker.invokeOnTarget(ResourceMethodInvoker.java:476)
at org.jboss.resteasy.core.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:434)
at org.jboss.resteasy.core.ResourceLocatorInvoker.invokeOnTargetObject(ResourceLocatorInvoker.java:192)
at org.jboss.resteasy.core.ResourceLocatorInvoker.invoke(ResourceLocatorInvoker.java:152)
at org.jboss.resteasy.core.ResourceLocatorInvoker.invokeOnTargetObject(ResourceLocatorInvoker.java:183)
at org.jboss.resteasy.core.ResourceLocatorInvoker.invoke(ResourceLocatorInvoker.java:141)
at org.jboss.resteasy.core.ResourceLocatorInvoker.invoke(ResourceLocatorInvoker.java:32)
at org.jboss.resteasy.core.SynchronousDispatcher.invoke(SynchronousDispatcher.java:492)
at org.jboss.resteasy.core.SynchronousDispatcher.lambda$invoke$4(SynchronousDispatcher.java:261)
at org.jboss.resteasy.core.SynchronousDispatcher.lambda$preprocess$0(SynchronousDispatcher.java:161)
at org.jboss.resteasy.core.interception.jaxrs.PreMatchContainerRequestContext.filter(PreMatchContainerRequestContext.java:364)
at org.jboss.resteasy.core.SynchronousDispatcher.preprocess(SynchronousDispatcher.java:164)
at org.jboss.resteasy.core.SynchronousDispatcher.invoke(SynchronousDispatcher.java:247)
at org.jboss.resteasy.plugins.server.servlet.ServletContainerDispatcher.service(ServletContainerDispatcher.java:249)
at org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(HttpServletDispatcher.java:60)
at org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(HttpServletDispatcher.java:55)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at com.google.inject.servlet.ServletDefinition.doServiceImpl(ServletDefinition.java:290)
at com.google.inject.servlet.ServletDefinition.doService(ServletDefinition.java:280)
at com.google.inject.servlet.ServletDefinition.service(ServletDefinition.java:184)
at com.google.inject.servlet.ManagedServletPipeline.service(ManagedServletPipeline.java:89)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:85)
at sonia.scm.legacy.RepositoryLegacyProtocolRedirectFilter$Worker.noRedirect(RepositoryLegacyProtocolRedirectFilter.java:127)
at sonia.scm.legacy.RepositoryLegacyProtocolRedirectFilter$Worker.checkPathElements(RepositoryLegacyProtocolRedirectFilter.java:100)
at sonia.scm.legacy.RepositoryLegacyProtocolRedirectFilter$Worker.doFilter(RepositoryLegacyProtocolRedirectFilter.java:89)
at sonia.scm.legacy.RepositoryLegacyProtocolRedirectFilter.doFilter(RepositoryLegacyProtocolRedirectFilter.java:71)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.web.security.TokenRefreshFilter.doFilter(TokenRefreshFilter.java:83)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.filter.MDCFilter.doFilter(MDCFilter.java:103)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.web.filter.AuthenticationFilter.processChain(AuthenticationFilter.java:266)
at sonia.scm.web.filter.AuthenticationFilter.handleAuthentication(AuthenticationFilter.java:225)
at sonia.scm.web.filter.AuthenticationFilter.doFilter(AuthenticationFilter.java:109)
at sonia.scm.web.security.ApiAuthenticationFilter.doFilter(ApiAuthenticationFilter.java:99)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.security.TokenExpiredFilter.doFilter(TokenExpiredFilter.java:66)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.filter.BaseUrlFilter.doFilter(BaseUrlFilter.java:73)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.metrics.HttpMetricsFilter.doFilter(HttpMetricsFilter.java:68)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at org.apache.shiro.guice.web.SimpleFilterChain.doFilter(SimpleFilterChain.java:44)
at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at org.apache.shiro.guice.web.SimpleFilterChain.doFilter(SimpleFilterChain.java:41)
at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at org.apache.shiro.guice.web.SimpleFilterChain.doFilter(SimpleFilterChain.java:41)
at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:458)
at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:373)
at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:387)
at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:370)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:121)
at com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:133)
at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:201)
at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:548)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:600)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1624)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1434)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:501)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1594)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1349)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:146)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at org.eclipse.jetty.server.Server.handle(Server.java:516)
at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:400)
at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:645)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:392)
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:277)
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)
at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105)
at org.eclipse.jetty.io.ssl.SslConnection$DecryptedEndPoint.onFillable(SslConnection.java:555)
at org.eclipse.jetty.io.ssl.SslConnection.onFillable(SslConnection.java:410)
at org.eclipse.jetty.io.ssl.SslConnection$2.succeeded(SslConnection.java:164)
at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105)
at org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:338)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:315)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:173)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:409)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:883)
at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1034)
at java.base/java.lang.Thread.run(Thread.java:829)
2023-10-03 16:06:44.006 [qtp1975358023-5316] [DMTrd14HxAvb] WARN sonia.scm.api.FallbackExceptionMapper - mapping unexpected org.eclipse.jgit.errors.MissingObjectException to status code 500
org.eclipse.jgit.errors.MissingObjectException: Missing tree 14a4efd4863ac6880c9dfb673fe44632d5163cd8
at org.eclipse.jgit.internal.storage.file.WindowCursor.open(WindowCursor.java:137)
at org.eclipse.jgit.treewalk.CanonicalTreeParser.reset(CanonicalTreeParser.java:191)
at org.eclipse.jgit.treewalk.TreeWalk.parserFor(TreeWalk.java:1442)
at org.eclipse.jgit.treewalk.TreeWalk.addTree(TreeWalk.java:820)
at sonia.scm.repository.spi.GitBrowseCommand.getEntry(GitBrowseCommand.java:227)
at sonia.scm.repository.spi.GitBrowseCommand.getBrowserResult(GitBrowseCommand.java:138)
at sonia.scm.repository.api.BrowseCommandBuilder.computeBrowserResult(BrowseCommandBuilder.java:178)
at sonia.scm.repository.api.BrowseCommandBuilder.getBrowserResult(BrowseCommandBuilder.java:156)
at sonia.scm.api.v2.resources.SourceRootResource.getSource(SourceRootResource.java:93)
at sonia.scm.api.v2.resources.SourceRootResource.getAll(SourceRootResource.java:72)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.jboss.resteasy.core.MethodInjectorImpl.invoke(MethodInjectorImpl.java:170)
at org.jboss.resteasy.core.MethodInjectorImpl.invoke(MethodInjectorImpl.java:130)
at org.jboss.resteasy.core.ResourceMethodInvoker.internalInvokeOnTarget(ResourceMethodInvoker.java:660)
at org.jboss.resteasy.core.ResourceMethodInvoker.invokeOnTargetAfterFilter(ResourceMethodInvoker.java:524)
at org.jboss.resteasy.core.ResourceMethodInvoker.lambda$invokeOnTarget$2(ResourceMethodInvoker.java:474)
at org.jboss.resteasy.core.interception.jaxrs.PreMatchContainerRequestContext.filter(PreMatchContainerRequestContext.java:364)
at org.jboss.resteasy.core.ResourceMethodInvoker.invokeOnTarget(ResourceMethodInvoker.java:476)
at org.jboss.resteasy.core.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:434)
at org.jboss.resteasy.core.ResourceLocatorInvoker.invokeOnTargetObject(ResourceLocatorInvoker.java:192)
at org.jboss.resteasy.core.ResourceLocatorInvoker.invoke(ResourceLocatorInvoker.java:152)
at org.jboss.resteasy.core.ResourceLocatorInvoker.invokeOnTargetObject(ResourceLocatorInvoker.java:183)
at org.jboss.resteasy.core.ResourceLocatorInvoker.invoke(ResourceLocatorInvoker.java:141)
at org.jboss.resteasy.core.ResourceLocatorInvoker.invoke(ResourceLocatorInvoker.java:32)
at org.jboss.resteasy.core.SynchronousDispatcher.invoke(SynchronousDispatcher.java:492)
at org.jboss.resteasy.core.SynchronousDispatcher.lambda$invoke$4(SynchronousDispatcher.java:261)
at org.jboss.resteasy.core.SynchronousDispatcher.lambda$preprocess$0(SynchronousDispatcher.java:161)
at org.jboss.resteasy.core.interception.jaxrs.PreMatchContainerRequestContext.filter(PreMatchContainerRequestContext.java:364)
at org.jboss.resteasy.core.SynchronousDispatcher.preprocess(SynchronousDispatcher.java:164)
at org.jboss.resteasy.core.SynchronousDispatcher.invoke(SynchronousDispatcher.java:247)
at org.jboss.resteasy.plugins.server.servlet.ServletContainerDispatcher.service(ServletContainerDispatcher.java:249)
at org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(HttpServletDispatcher.java:60)
at org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(HttpServletDispatcher.java:55)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at com.google.inject.servlet.ServletDefinition.doServiceImpl(ServletDefinition.java:290)
at com.google.inject.servlet.ServletDefinition.doService(ServletDefinition.java:280)
at com.google.inject.servlet.ServletDefinition.service(ServletDefinition.java:184)
at com.google.inject.servlet.ManagedServletPipeline.service(ManagedServletPipeline.java:89)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:85)
at sonia.scm.legacy.RepositoryLegacyProtocolRedirectFilter$Worker.noRedirect(RepositoryLegacyProtocolRedirectFilter.java:127)
at sonia.scm.legacy.RepositoryLegacyProtocolRedirectFilter$Worker.checkPathElements(RepositoryLegacyProtocolRedirectFilter.java:100)
at sonia.scm.legacy.RepositoryLegacyProtocolRedirectFilter$Worker.doFilter(RepositoryLegacyProtocolRedirectFilter.java:89)
at sonia.scm.legacy.RepositoryLegacyProtocolRedirectFilter.doFilter(RepositoryLegacyProtocolRedirectFilter.java:71)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.web.security.TokenRefreshFilter.doFilter(TokenRefreshFilter.java:83)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.filter.MDCFilter.doFilter(MDCFilter.java:103)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.web.filter.AuthenticationFilter.processChain(AuthenticationFilter.java:266)
at sonia.scm.web.filter.AuthenticationFilter.handleAuthentication(AuthenticationFilter.java:225)
at sonia.scm.web.filter.AuthenticationFilter.doFilter(AuthenticationFilter.java:109)
at sonia.scm.web.security.ApiAuthenticationFilter.doFilter(ApiAuthenticationFilter.java:99)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.security.TokenExpiredFilter.doFilter(TokenExpiredFilter.java:66)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.filter.BaseUrlFilter.doFilter(BaseUrlFilter.java:73)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.metrics.HttpMetricsFilter.doFilter(HttpMetricsFilter.java:68)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at org.apache.shiro.guice.web.SimpleFilterChain.doFilter(SimpleFilterChain.java:44)
at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at org.apache.shiro.guice.web.SimpleFilterChain.doFilter(SimpleFilterChain.java:41)
at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at org.apache.shiro.guice.web.SimpleFilterChain.doFilter(SimpleFilterChain.java:41)
at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:458)
at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:373)
at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:387)
at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:370)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:121)
at com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:133)
at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:201)
at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:548)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:600)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1624)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1434)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:501)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1594)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1349)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:146)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at org.eclipse.jetty.server.Server.handle(Server.java:516)
at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:400)
at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:645)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:392)
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:277)
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)
at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105)
at org.eclipse.jetty.io.ssl.SslConnection$DecryptedEndPoint.onFillable(SslConnection.java:555)
at org.eclipse.jetty.io.ssl.SslConnection.onFillable(SslConnection.java:410)
at org.eclipse.jetty.io.ssl.SslConnection$2.succeeded(SslConnection.java:164)
at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105)
at org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:338)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:315)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:173)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:409)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:883)
at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1034)
at java.base/java.lang.Thread.run(Thread.java:829)

[nikossakellariou]

Today this error occurred fisrt:
ERROR sonia.scm.repository.spi.GitHookChangesetCollector - could not collect changesets
and then all repos started failling with ERROR org.eclipse.jgit.internal.storage.file.PackDirectory - Exception caught while accessing pack file
Log:
2023-10-04 11:25:07.450 [ScmEventBus-1-2] [ ] ERROR sonia.scm.repository.spi.GitHookChangesetCollector - could not collect changesets
java.lang.NullPointerException: null
at org.eclipse.jgit.internal.storage.file.WindowCursor.inflate(WindowCursor.java:286)
at org.eclipse.jgit.internal.storage.file.Pack.decompress(Pack.java:369)
at org.eclipse.jgit.internal.storage.file.Pack.load(Pack.java:803)
at org.eclipse.jgit.internal.storage.file.Pack.get(Pack.java:273)
at org.eclipse.jgit.internal.storage.file.PackDirectory.open(PackDirectory.java:212)
at org.eclipse.jgit.internal.storage.file.ObjectDirectory.openPackedObject(ObjectDirectory.java:404)
at org.eclipse.jgit.internal.storage.file.ObjectDirectory.openPackedFromSelfOrAlternate(ObjectDirectory.java:368)
at org.eclipse.jgit.internal.storage.file.ObjectDirectory.openObjectWithoutRestoring(ObjectDirectory.java:359)
at org.eclipse.jgit.internal.storage.file.ObjectDirectory.openObject(ObjectDirectory.java:344)
at org.eclipse.jgit.internal.storage.file.WindowCursor.open(WindowCursor.java:132)
at org.eclipse.jgit.lib.ObjectReader.open(ObjectReader.java:214)
at org.eclipse.jgit.revwalk.RevWalk.parseAny(RevWalk.java:1086)
at org.eclipse.jgit.revwalk.RevWalk.parseCommit(RevWalk.java:996)
at sonia.scm.repository.GitUtil.getCommit(GitUtil.java:334)
at sonia.scm.repository.GitUtil.createTagMap(GitUtil.java:137)
at sonia.scm.repository.GitChangesetConverter.(GitChangesetConverter.java:64)
at sonia.scm.repository.GitChangesetConverterFactory$Builder.create(GitChangesetConverterFactory.java:90)
at sonia.scm.repository.GitChangesetConverterFactory.create(GitChangesetConverterFactory.java:52)
at sonia.scm.repository.spi.GitHookChangesetCollector.collectChangesets(GitHookChangesetCollector.java:99)
at sonia.scm.repository.spi.GitHookChangesetCollector.collectChangesets(GitHookChangesetCollector.java:90)
at sonia.scm.repository.spi.GitHookChangesetCollector.collectChangesets(GitHookChangesetCollector.java:84)
at sonia.scm.repository.spi.GitHookChangesetProvider.handleRequest(GitHookChangesetProvider.java:55)
at sonia.scm.repository.api.HookChangesetBuilder.getChangesets(HookChangesetBuilder.java:106)
at sonia.scm.issuetracker.internal.ChangesetSubscriber.handle(ChangesetSubscriber.java:63)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at com.github.legman.InvocationContext.invoke(InvocationContext.java:108)
at com.github.legman.InvocationContext.proceed(InvocationContext.java:101)
at com.github.legman.micrometer.MicrometerInvocationInterceptor.invoke(MicrometerInvocationInterceptor.java:47)
at com.github.legman.InvocationContext.proceed(InvocationContext.java:99)
at com.github.legman.EventHandler.handleEvent(EventHandler.java:103)
at com.github.legman.SynchronizedEventHandler.handleEvent(SynchronizedEventHandler.java:52)
at com.github.legman.EventBus.dispatchSynchronous(EventBus.java:452)
at com.github.legman.EventBus.lambda$dispatch$1(EventBus.java:444)
at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120)
at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
2023-10-04 11:25:07.451 [ScmEventBus-1-2] [ ] WARN org.eclipse.jgit.lib.Repository - close() called when useCnt is already zero for Repository[/repository/location/data]
2023-10-04 11:25:31.729 [qtp1975358023-19] [ ] INFO sonia.scm.user.DefaultUserManager - modify user xxxx of type null
2023-10-04 11:25:40.454 [qtp1975358023-17] [ ] INFO sonia.scm.user.DefaultUserManager - modify user xxxxxxx of type null
2023-10-04 11:25:43.810 [qtp1975358023-19] [COTrhiqmRMl] ERROR org.eclipse.jgit.internal.storage.file.PackDirectory - Exception caught while accessing pack file /repository/location/data/objects/pack/pack-d10ca0a4ef5002f1c8cc1587de07e050cc0363c5.pack, the pack file might be corrupt. Caught 1 consecutive errors while trying to read this pack.
java.io.EOFException: Short compressed stream at 14
at org.eclipse.jgit.internal.storage.file.Pack.decompress(Pack.java:370)
at org.eclipse.jgit.internal.storage.file.Pack.load(Pack.java:803)
at org.eclipse.jgit.internal.storage.file.Pack.get(Pack.java:273)
at org.eclipse.jgit.internal.storage.file.PackDirectory.open(PackDirectory.java:212)
at org.eclipse.jgit.internal.storage.file.ObjectDirectory.openPackedObject(ObjectDirectory.java:404)
at org.eclipse.jgit.internal.storage.file.ObjectDirectory.openPackedFromSelfOrAlternate(ObjectDirectory.java:368)
at org.eclipse.jgit.internal.storage.file.ObjectDirectory.openObjectWithoutRestoring(ObjectDirectory.java:359)
at org.eclipse.jgit.internal.storage.file.ObjectDirectory.openObject(ObjectDirectory.java:344)
at org.eclipse.jgit.internal.storage.file.WindowCursor.open(WindowCursor.java:132)
at org.eclipse.jgit.lib.ObjectReader.open(ObjectReader.java:214)
at org.eclipse.jgit.revwalk.RevWalk.parseAny(RevWalk.java:1086)
at org.eclipse.jgit.internal.storage.file.RefDirectory.doPeel(RefDirectory.java:530)
at org.eclipse.jgit.internal.storage.file.RefDirectory.peel(RefDirectory.java:510)
at org.eclipse.jgit.transport.RefAdvertiser.send(RefAdvertiser.java:298)
at org.eclipse.jgit.transport.UploadPack.lsRefsV2(UploadPack.java:1122)
at org.eclipse.jgit.transport.UploadPack.serveOneCommandV2(UploadPack.java:1336)
at org.eclipse.jgit.transport.UploadPack.serviceV2(UploadPack.java:1394)
at org.eclipse.jgit.transport.UploadPack.uploadWithExceptionPropagation(UploadPack.java:841)
at org.eclipse.jgit.http.server.UploadPackServlet.lambda$1(UploadPackServlet.java:197)
at org.eclipse.jgit.http.server.UploadPackServlet.defaultUploadPackHandler(UploadPackServlet.java:220)
at org.eclipse.jgit.http.server.UploadPackServlet.doPost(UploadPackServlet.java:214)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.eclipse.jgit.http.server.glue.UrlPipeline$Chain.doFilter(UrlPipeline.java:212)
at org.eclipse.jgit.http.server.UploadPackServlet$Factory.doFilter(UploadPackServlet.java:139)
at org.eclipse.jgit.http.server.glue.UrlPipeline$Chain.doFilter(UrlPipeline.java:210)
at org.eclipse.jgit.http.server.RepositoryFilter.doFilter(RepositoryFilter.java:112)
at org.eclipse.jgit.http.server.glue.UrlPipeline$Chain.doFilter(UrlPipeline.java:210)
at org.eclipse.jgit.http.server.NoCacheFilter.doFilter(NoCacheFilter.java:53)
at org.eclipse.jgit.http.server.glue.UrlPipeline$Chain.doFilter(UrlPipeline.java:210)
at org.eclipse.jgit.http.server.glue.UrlPipeline.service(UrlPipeline.java:189)
at org.eclipse.jgit.http.server.glue.SuffixPipeline.service(SuffixPipeline.java:70)
at org.eclipse.jgit.http.server.glue.MetaFilter.doFilter(MetaFilter.java:151)
at org.eclipse.jgit.http.server.glue.MetaServlet.service(MetaServlet.java:109)
at sonia.scm.web.ScmGitServlet.handleRegularGitRequest(ScmGitServlet.java:166)
at sonia.scm.web.ScmGitServlet.service(ScmGitServlet.java:121)
at sonia.scm.repository.spi.ScmProviderHttpServletDecorator.service(ScmProviderHttpServletDecorator.java:45)
at sonia.scm.web.filter.PermissionFilter.service(PermissionFilter.java:98)
at sonia.scm.repository.spi.InitializingHttpScmProtocolWrapper$ProtocolWrapper.serve(InitializingHttpScmProtocolWrapper.java:148)
at sonia.scm.repository.spi.HttpScmProtocol.serve(HttpScmProtocol.java:59)
at sonia.scm.web.protocol.HttpProtocolServlet.service(HttpProtocolServlet.java:111)
at sonia.scm.web.protocol.HttpProtocolServlet.service(HttpProtocolServlet.java:92)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at com.google.inject.servlet.ServletDefinition.doServiceImpl(ServletDefinition.java:290)
at com.google.inject.servlet.ServletDefinition.doService(ServletDefinition.java:280)
at com.google.inject.servlet.ServletDefinition.service(ServletDefinition.java:184)
at com.google.inject.servlet.ManagedServletPipeline.service(ManagedServletPipeline.java:89)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:85)
at sonia.scm.legacy.RepositoryLegacyProtocolRedirectFilter$Worker.noRedirect(RepositoryLegacyProtocolRedirectFilter.java:127)
at sonia.scm.legacy.RepositoryLegacyProtocolRedirectFilter$Worker.checkPathElements(RepositoryLegacyProtocolRedirectFilter.java:100)
at sonia.scm.legacy.RepositoryLegacyProtocolRedirectFilter$Worker.doFilter(RepositoryLegacyProtocolRedirectFilter.java:89)
at sonia.scm.legacy.RepositoryLegacyProtocolRedirectFilter.doFilter(RepositoryLegacyProtocolRedirectFilter.java:71)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.filter.MDCFilter.doFilter(MDCFilter.java:103)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.web.filter.AuthenticationFilter.processChain(AuthenticationFilter.java:266)
at sonia.scm.web.filter.AuthenticationFilter.handleAuthentication(AuthenticationFilter.java:225)
at sonia.scm.web.filter.AuthenticationFilter.doFilter(AuthenticationFilter.java:109)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.security.TokenExpiredFilter.doFilter(TokenExpiredFilter.java:66)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.filter.BaseUrlFilter.doFilter(BaseUrlFilter.java:73)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at sonia.scm.metrics.HttpMetricsFilter.doFilter(HttpMetricsFilter.java:68)
at sonia.scm.web.filter.HttpFilter.doFilter(HttpFilter.java:93)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at org.apache.shiro.guice.web.SimpleFilterChain.doFilter(SimpleFilterChain.java:44)
at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at org.apache.shiro.guice.web.SimpleFilterChain.doFilter(SimpleFilterChain.java:41)
at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at org.apache.shiro.guice.web.SimpleFilterChain.doFilter(SimpleFilterChain.java:41)
at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:458)
at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:373)
at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:387)
at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:370)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:121)
at com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:133)
at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:201)
at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:548)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:600)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1624)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1434)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:501)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1594)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1349)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:146)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at org.eclipse.jetty.server.Server.handle(Server.java:516)
at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:400)
at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:645)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:392)
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:277)
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)
at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105)
at org.eclipse.jetty.io.ssl.SslConnection$DecryptedEndPoint.onFillable(SslConnection.java:555)
at org.eclipse.jetty.io.ssl.SslConnection.onFillable(SslConnection.java:410)
at org.eclipse.jetty.io.ssl.SslConnection$2.succeeded(SslConnection.java:164)
at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105)
at org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:338)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:315)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:173)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:409)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:883)
at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1034)
at java.base/java.lang.Thread.run(Thread.java:829)