MalformedInputException when comparing branches
Platform Notice: Data Center Only - This article only applies to Atlassian products on the Data Center platform.
Note that this KB was created for the Data Center version of the product. Data Center KBs for non-Data-Center-specific features may also work for Server versions of the product, however they have not been tested. 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:
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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 omittedCause
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.
Updated on April 8, 2025
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