MalformedInputException when comparing branches

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Platform notice: Server and Data Center only. This article only applies to Atlassian products on the Server and Data Center platforms.

Support for Server* products ended on February 15th 2024. If you are running a Server product, you can visit the Atlassian Server end of support announcement to review your migration options.

*Except Fisheye and Crucible

Problem

If you try to diff two branches you get an error in the UI "Something went wrong while trying to serve your request."

The following appears in the <BitbucketHome>/log/atlassian-bitbucket.log  file:

2017-05-23 11:11:39,589 ERROR [http-nio-7990-exec-4] Andrei.Lipovchenko @97OJNBx671x35x1 oemzlu 10.0.0.1,10.0.0.2 "GET /projects/PROJ/repos/repo/commits HTTP/1.1" c.a.s.i.w.HandlerExceptionResolverImpl Could not read loose ref
com.atlassian.stash.internal.scm.git.ref.InvalidRefException: Could not read loose ref
	at com.atlassian.stash.internal.scm.git.ref.LooseRefDb.retryingRead(LooseRefDb.java:143)
	at com.atlassian.stash.internal.scm.git.ref.LooseRefDb.readRef(LooseRefDb.java:363)
	at com.atlassian.stash.internal.scm.git.ref.LooseRefDb.internalResolveSha1(LooseRefDb.java:326)
	at com.atlassian.stash.internal.scm.git.ref.LooseRefDb.internalResolve(LooseRefDb.java:265)
	at com.atlassian.stash.internal.scm.git.ref.LooseRefDb.resolve(LooseRefDb.java:115)
	at com.atlassian.stash.internal.scm.git.ref.CompositeGitRefDb.resolve(CompositeGitRefDb.java:109)
	at com.atlassian.stash.internal.scm.git.command.refdb.ResolveGitRefDbCommand.internalCall(ResolveGitRefDbCommand.java:54)
	at com.atlassian.stash.internal.scm.git.command.refdb.ResolveGitRefDbCommand.internalCall(ResolveGitRefDbCommand.java:23)
	at com.atlassian.stash.internal.scm.git.command.refdb.AbstractGitRefDbCommand.call(AbstractGitRefDbCommand.java:49)
	at com.atlassian.stash.internal.scm.git.command.refdb.ResolveGitRefDbCommand.call(ResolveGitRefDbCommand.java:43)
	at com.atlassian.stash.internal.scm.git.command.refdb.ResolveGitRefDbCommand.call(ResolveGitRefDbCommand.java:23)
	at com.atlassian.stash.internal.scm.git.command.TransformedGitCommand.call(TransformedGitCommand.java:45)
	at com.atlassian.stash.internal.repository.DefaultRefService.resolveRef(DefaultRefService.java:248)
	at com.atlassian.stash.internal.web.repos.RepositoryController.findViewRef(RepositoryController.java:599)
	at com.atlassian.stash.internal.web.repos.RepositoryController.getCommits(RepositoryController.java:159)
	at com.atlassian.stash.internal.web.repos.RepositoryController.getCommitListContents(RepositoryController.java:228)
	at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:24)
	at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:24)
	at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:24)
	at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:24)
	at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:24)
	at com.atlassian.bitbucket.internal.importer.web.RepositoryImportFilter.doFilter(RepositoryImportFilter.java:68)
	at com.atlassian.stash.internal.spring.lifecycle.LifecycleJohnsonServletFilterModuleContainerFilter.doFilter(LifecycleJohnsonServletFilterModuleContainerFilter.java:42)
	at com.atlassian.stash.internal.spring.lifecycle.LifecycleJohnsonServletFilterModuleContainerFilter.doFilter(LifecycleJohnsonServletFilterModuleContainerFilter.java:42)
	at com.atlassian.stash.internal.spring.security.StashAuthenticationFilter.doFilter(StashAuthenticationFilter.java:88)
	at com.atlassian.stash.internal.web.auth.BeforeLoginPluginAuthenticationFilter.doInsideSpringSecurityChain(BeforeLoginPluginAuthenticationFilter.java:112)
	at com.atlassian.stash.internal.web.auth.BeforeLoginPluginAuthenticationFilter.doFilter(BeforeLoginPluginAuthenticationFilter.java:75)
	at com.atlassian.security.auth.trustedapps.filter.TrustedApplicationsFilter.doFilter(TrustedApplicationsFilter.java:94)
	at com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.doFilter(OAuthFilter.java:67)
	at com.atlassian.stash.internal.spring.lifecycle.LifecycleJohnsonServletFilterModuleContainerFilter.doFilter(LifecycleJohnsonServletFilterModuleContainerFilter.java:42)
	at com.atlassian.stash.internal.spring.lifecycle.LifecycleJohnsonServletFilterModuleContainerFilter.doFilter(LifecycleJohnsonServletFilterModuleContainerFilter.java:42)
	at com.atlassian.security.auth.trustedapps.filter.TrustedApplicationsFilter.doFilter(TrustedApplicationsFilter.java:94)
	at com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.doFilter(OAuthFilter.java:67)
	at com.atlassian.core.filters.ServletContextThreadLocalFilter.doFilter(ServletContextThreadLocalFilter.java:21)
	at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
	at com.atlassian.stash.internal.spring.lifecycle.LifecycleJohnsonServletFilterModuleContainerFilter.doFilter(LifecycleJohnsonServletFilterModuleContainerFilter.java:42)
	at com.atlassian.plugin.connect.plugin.auth.user.ThreeLeggedAuthFilter.doFilter(ThreeLeggedAuthFilter.java:109)
	at com.atlassian.jwt.internal.servlet.JwtAuthFilter.doFilter(JwtAuthFilter.java:32)
	at com.atlassian.analytics.client.filter.DefaultAnalyticsFilter.doFilter(DefaultAnalyticsFilter.java:38)
	at com.atlassian.analytics.client.filter.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:39)
	at com.atlassian.stash.internal.spring.lifecycle.LifecycleJohnsonServletFilterModuleContainerFilter.doFilter(LifecycleJohnsonServletFilterModuleContainerFilter.java:42)
	at com.atlassian.stash.internal.web.auth.BeforeLoginPluginAuthenticationFilter.doBeforeBeforeLoginFilters(BeforeLoginPluginAuthenticationFilter.java:90)
	at com.atlassian.stash.internal.web.auth.BeforeLoginPluginAuthenticationFilter.doFilter(BeforeLoginPluginAuthenticationFilter.java:73)
	at com.atlassian.stash.internal.request.DefaultRequestManager.doAsRequest(DefaultRequestManager.java:83)
	at com.atlassian.stash.internal.hazelcast.ConfigurableWebFilter.doFilter(ConfigurableWebFilter.java:38)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.lang.Thread.run(Thread.java:745)
	... 294 frames trimmed
Caused by: java.nio.charset.MalformedInputException: Input length = 1
	at java.nio.charset.CoderResult.throwException(CoderResult.java:281)
	at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:339)
	at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
	at java.io.InputStreamReader.read(InputStreamReader.java:184)
	at java.io.BufferedReader.fill(BufferedReader.java:161)
	at java.io.BufferedReader.readLine(BufferedReader.java:324)
	at java.io.BufferedReader.readLine(BufferedReader.java:389)
	at com.atlassian.stash.internal.scm.git.ref.LooseRefDb.readFirstLine(LooseRefDb.java:357)
	at com.atlassian.stash.internal.scm.git.ref.LooseRefDb.lambda$readRef$16(LooseRefDb.java:364)
	at com.atlassian.stash.internal.scm.git.ref.LooseRefDb.retryingRead(LooseRefDb.java:138)
	... 47 common frames omitted

Cause

Someone used an editor to manually edit refs in BitbucketHome/shared/data/repositories/<id>/refs  and then did not clean up the swap files (*.swp)created by the editor.

Resolution

Stop Bitbucket Server, and remove the swap files (*.swp) in the repository directory to resolve the issue.


Last modified on Jul 6, 2022

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