nexus-public
nexus-public copied to clipboard
Published
20 hours ago •
sonatype
sonatype
Repository Merge is failing and leaving temp files behind
We have noticed that our sonatype-work tmp directory with primary and other xml gzips. This causes disk space to grow relatively quickly as files are left behind on error. We basically need to go in and manually clear these files out. As far as we know there is not a configurable job to clean these files out. As far as we have been able to tell, these files are related to repository groups.
System: CentOS: 7.9 Nexus OSS: 3.57.0
Log Messages:
2023-07-28 11:32:22,153+0000 INFO [qtp1900489922-4973] *UNKNOWN org.sonatype.nexus.repository.yum.orient.internal.group.OrientYumGroupFacetImpl - Creating latest metadata by merging metadata of group members for repository yum-centos-7.9.2009
2023-07-28 11:32:22,155+0000 INFO [qtp1900489922-4973] *UNKNOWN org.sonatype.nexus.repository.yum.internal.group.YumGroupMergerImpl - Requesting repodata/34b37c9c34564540db06c489786c4202c3e8d59c9da4509c0c15328a2c25f24e-other.xml.gz from yum-centos-7.9.2009-mirror
2023-07-28 11:32:22,155+0000 INFO [qtp1900489922-4973] *UNKNOWN org.sonatype.nexus.repository.yum.internal.group.YumGroupMergerImpl - Merge of other.xml.gz starting
2023-07-28 11:32:22,342+0000 INFO [qtp1900489922-4973] *UNKNOWN org.sonatype.nexus.repository.yum.internal.group.YumGroupMergerImpl - Merge of other.xml.gz completed
2023-07-28 11:32:22,342+0000 INFO [qtp1900489922-4973] *UNKNOWN org.sonatype.nexus.repository.yum.internal.group.YumGroupMergerImpl - Requesting repodata/eb98f44060d1a5c7abeebaf88147525c2f893399f446158454050737f5433c21-primary.xml.gz from yum-centos-7.9.2009-mirror
2023-07-28 11:32:22,343+0000 INFO [qtp1900489922-4973] *UNKNOWN org.sonatype.nexus.repository.yum.internal.group.YumGroupMergerImpl - Merge of primary.xml.gz starting
2023-07-28 11:32:23,971+0000 WARN [qtp1900489922-4973] *UNKNOWN org.sonatype.nexus.repository.httpbridge.internal.ViewServlet - Failure servicing: GET /repository/yum-centos-7.9.2009/updates/x86_64/repodata/repomd.xml
java.lang.RuntimeException: Unable to copy when there is only one input stream
at org.sonatype.nexus.repository.yum.internal.mergerepo.YumMetadataMerger.copyOfInputStream(YumMetadataMerger.java:185)
at org.sonatype.nexus.repository.yum.internal.mergerepo.YumMetadataMerger.merge(YumMetadataMerger.java:132)
at org.sonatype.nexus.repository.yum.internal.mergerepo.YumMergeServiceImpl.generateMergedFile(YumMergeServiceImpl.java:78)
at org.sonatype.nexus.repository.yum.internal.mergerepo.YumMergeServiceImpl.merge(YumMergeServiceImpl.java:57)
at org.sonatype.nexus.repository.yum.internal.group.YumGroupMergerImpl.mergeResponses(YumGroupMergerImpl.java:118)
at org.sonatype.nexus.repository.yum.internal.group.YumGroupMergerImpl.lambda$2(YumGroupMergerImpl.java:71)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.HashMap$EntrySpliterator.forEachRemaining(HashMap.java:1723)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566)
at org.sonatype.nexus.repository.yum.internal.group.YumGroupMergerImpl.fetchAndMergeMetadata(YumGroupMergerImpl.java:73)
at org.sonatype.nexus.repository.yum.orient.internal.group.OrientYumGroupFacetImpl.buildMergedRepomd(OrientYumGroupFacetImpl.java:224)
at org.sonatype.nexus.repository.yum.orient.internal.group.OrientYumGroupFacetImpl.lambda$0(OrientYumGroupFacetImpl.java:187)
at org.sonatype.nexus.common.io.CooperatingFuture.performCall(CooperatingFuture.java:123)
at org.sonatype.nexus.common.io.CooperatingFuture.call(CooperatingFuture.java:65)
at org.sonatype.nexus.common.io.ScopedCooperationFactorySupport$ScopedCooperation.cooperate(ScopedCooperationFactorySupport.java:99)
at org.sonatype.nexus.repository.yum.orient.internal.group.OrientYumGroupFacetImpl.buildRepomd(OrientYumGroupFacetImpl.java:176)
at org.sonatype.nexus.repository.yum.internal.group.YumGroupFacet$buildRepomd$0.call(Unknown Source)
at org.sonatype.nexus.repository.yum.internal.group.YumAbstractGroupHandler.buildMergedRepomd(YumAbstractGroupHandler.groovy:131)
at sun.reflect.GeneratedMethodAccessor285.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:193)
at org.sonatype.nexus.repository.yum.internal.group.YumAbstractGroupHandler.buildMergedRepomd(YumAbstractGroupHandler.groovy:103)
at sun.reflect.GeneratedMethodAccessor277.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:177)
at org.sonatype.nexus.repository.yum.internal.group.YumAbstractGroupHandler.doGet(YumAbstractGroupHandler.groovy:64)
at org.sonatype.nexus.repository.group.GroupHandler.handle(GroupHandler.java:100)
at org.sonatype.nexus.repository.view.Context.proceed(Context.java:88)
at org.sonatype.nexus.repository.storage.LastDownloadedHandler.handle(LastDownloadedHandler.java:59)
at org.sonatype.nexus.repository.view.Context.proceed(Context.java:88)
at org.sonatype.nexus.repository.storage.UnitOfWorkHandler.handle(UnitOfWorkHandler.java:39)
at org.sonatype.nexus.repository.view.Context.proceed(Context.java:88)
at org.sonatype.nexus.repository.view.handlers.ContentHeadersHandler.handle(ContentHeadersHandler.java:46)
at org.sonatype.nexus.repository.view.Context.proceed(Context.java:88)
at org.sonatype.nexus.repository.view.handlers.ConditionalRequestHandler.handleConditional(ConditionalRequestHandler.java:80)
at org.sonatype.nexus.repository.view.handlers.ConditionalRequestHandler.handle(ConditionalRequestHandler.java:60)
at org.sonatype.nexus.repository.view.Context.proceed(Context.java:88)
at com.sonatype.nexus.clm.internal.orient.FirewallContributedHandler.handle(FirewallContributedHandler.java:105)
at org.sonatype.nexus.repository.view.Context.proceed(Context.java:88)
at org.sonatype.nexus.repository.view.handlers.HandlerContributor.handle(HandlerContributor.java:67)
at org.sonatype.nexus.repository.view.Context.proceed(Context.java:88)
at org.sonatype.nexus.repository.view.handlers.ExceptionHandler.handle(ExceptionHandler.java:42)
at org.sonatype.nexus.repository.view.Context.proceed(Context.java:88)
at org.sonatype.nexus.repository.security.SecurityHandler.handle(SecurityHandler.java:51)
at org.sonatype.nexus.repository.view.Context.proceed(Context.java:88)
at org.sonatype.nexus.repository.view.Context$proceed.call(Unknown Source)
at org.sonatype.nexus.repository.yum.orient.internal.OrientYumRecipeSupport$_closure1.doCall(OrientYumRecipeSupport.groovy:134)
at sun.reflect.GeneratedMethodAccessor261.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:98)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1099)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
at groovy.lang.Closure.call(Closure.java:420)
at org.codehaus.groovy.runtime.ConvertedClosure.invokeCustom(ConvertedClosure.java:54)
at org.codehaus.groovy.runtime.ConversionHandler.invoke(ConversionHandler.java:124)
at com.sun.proxy.$Proxy204.handle(Unknown Source)
at org.sonatype.nexus.repository.view.Context.proceed(Context.java:88)
at com.sonatype.analytics.internal.handler.AnalyticsMeteringHandler.handle(AnalyticsMeteringHandler.java:69)
at org.sonatype.nexus.repository.view.Context.proceed(Context.java:88)
at org.sonatype.nexus.repository.view.handlers.TimingHandler.handle(TimingHandler.java:58)
at org.sonatype.nexus.repository.view.Context.proceed(Context.java:88)
at org.sonatype.nexus.repository.view.Context.start(Context.java:179)
at org.sonatype.nexus.repository.view.Router.dispatch(Router.java:65)
at org.sonatype.nexus.repository.view.ConfigurableViewFacet.dispatch(ConfigurableViewFacet.java:52)
at org.sonatype.nexus.repository.view.ConfigurableViewFacet.dispatch(ConfigurableViewFacet.java:43)
at org.sonatype.nexus.repository.httpbridge.internal.ViewServlet.dispatchAndSend(ViewServlet.java:212)
at org.sonatype.nexus.repository.httpbridge.internal.ViewServlet.doService(ViewServlet.java:174)
at org.sonatype.nexus.repository.httpbridge.internal.ViewServlet.service(ViewServlet.java:126)
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.DynamicServletPipeline.service(DynamicServletPipeline.java:71)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:85)
at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61)
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.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
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.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
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.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
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.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:458)
at org.sonatype.nexus.security.SecurityFilter.executeChain(SecurityFilter.java:96)
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.sonatype.nexus.security.SecurityFilter.doFilterInternal(SecurityFilter.java:112)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at com.codahale.metrics.servlet.AbstractInstrumentedFilter.doFilter(AbstractInstrumentedFilter.java:112)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61)
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.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
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.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
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.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
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.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:458)
at org.sonatype.nexus.security.SecurityFilter.executeChain(SecurityFilter.java:96)
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.sonatype.nexus.security.SecurityFilter.doFilterInternal(SecurityFilter.java:112)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at org.sonatype.nexus.repository.httpbridge.internal.ExhaustRequestFilter.doFilter(ExhaustRequestFilter.java:80)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at com.sonatype.nexus.licensing.internal.LicensingRedirectFilter.doFilter(LicensingRedirectFilter.java:116)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at com.codahale.metrics.servlet.AbstractInstrumentedFilter.doFilter(AbstractInstrumentedFilter.java:112)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at org.sonatype.nexus.internal.web.ErrorPageFilter.doFilter(ErrorPageFilter.java:79)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at org.sonatype.nexus.internal.web.EnvironmentFilter.doFilter(EnvironmentFilter.java:101)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at org.sonatype.nexus.internal.web.HeaderPatternFilter.doFilter(HeaderPatternFilter.java:98)
at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:82)
at com.google.inject.servlet.DynamicFilterPipeline.dispatch(DynamicFilterPipeline.java:104)
at com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:133)
at org.sonatype.nexus.bootstrap.osgi.DelegatingFilter.doFilter(DelegatingFilter.java:73)
at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:201)
at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1626)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:552)
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:1440)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:505)
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:1355)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at com.codahale.metrics.jetty9.InstrumentedHandler.handle(InstrumentedHandler.java:239)
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$1(HttpChannel.java:487)
at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:732)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:479)
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:277)
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)
at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105)
at org.eclipse.jetty.io.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.lang.Thread.run(Thread.java:750)
Caused by: java.io.IOException: Gzip-compressed data is corrupt (CRC32 error)
at org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream.read(GzipCompressorInputStream.java:378)
at java.io.InputStream.read(InputStream.java:101)
at org.apache.commons.io.IOUtils.copyLarge(IOUtils.java:1309)
at org.apache.commons.io.IOUtils.copy(IOUtils.java:978)
at org.apache.commons.io.IOUtils.copyLarge(IOUtils.java:1282)
at org.apache.commons.io.IOUtils.copy(IOUtils.java:953)
at org.sonatype.nexus.repository.yum.internal.mergerepo.YumMetadataMerger.copyOfInputStream(YumMetadataMerger.java:182)
... 196 common frames omitted
Thanks for opening this @bmagistro - this could be a bug. We'll take a look and report back.
