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Error during specs scan - GitCommandException

Rafael Neris
Rafael Neris September 28, 2022

Error during specs scan for Bamboo version 8.2.3 and Git 2.37.3 :

Error during specs scan:
com.atlassian.bamboo.plugins.stash.repository.StashRepositoryException: com.atlassian.bamboo.plugins.git.GitCommandException: command [/usr/local/bin/git remote set-url origin file:///data/atlassian-bamboo-8.2.4/local-working-dir/_git-repositories-cache/6dc9b77d8e89ef31d4172c3f3d4ed5f214a6a191] failed with code 128. Working directory was [/data/atlassian-bamboo-8.2.4/local-working-dir/serverSide/REPOSITORY_STORED_SPECS/repository-82673736-master/checkout]., stderr:
fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
	at com.atlassian.bamboo.plugins.stash.v2.BitbucketServerWorkingCopyManager.updateToLatestRevision(BitbucketServerWorkingCopyManager.java:150)
	at com.atlassian.bamboo.configuration.external.RepositoryStoredSpecsServiceImpl.lambda$runBambooSpecs$0(RepositoryStoredSpecsServiceImpl.java:164)
	at com.atlassian.bamboo.variable.CustomVariableContextImpl.withVariableSubstitutor(CustomVariableContextImpl.java:140)
	at com.atlassian.bamboo.configuration.external.RepositoryStoredSpecsServiceImpl.lambda$runBambooSpecs$1(RepositoryStoredSpecsServiceImpl.java:169)
	at com.atlassian.bamboo.util.CacheAwareness.withValuesOlderThanTimestampReloaded(CacheAwareness.java:126)
	at com.atlassian.bamboo.configuration.external.RepositoryStoredSpecsServiceImpl.runBambooSpecs(RepositoryStoredSpecsServiceImpl.java:167)
	at com.atlassian.bamboo.configuration.external.RssDetectionServiceImpl.runRssDetection(RssDetectionServiceImpl.java:374)
	at com.atlassian.bamboo.configuration.external.detection.RssDetectionRunnable.run(RssDetectionRunnable.java:42)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at com.atlassian.bamboo.utils.BambooRunnables$1.run(BambooRunnables.java:48)
	at com.atlassian.bamboo.security.ImpersonationHelper.runWith(ImpersonationHelper.java:26)
	at com.atlassian.bamboo.security.ImpersonationHelper.runWithSystemAuthority(ImpersonationHelper.java:17)
	at com.atlassian.bamboo.security.ImpersonationHelper$1.run(ImpersonationHelper.java:41)
	at java.lang.Thread.run(Thread.java:748)
Caused by: com.atlassian.bamboo.plugins.git.GitCommandException: command [/usr/local/bin/git remote set-url origin file:///data/atlassian-bamboo-8.2.4/local-working-dir/_git-repositories-cache/6dc9b77d8e89ef31d4172c3f3d4ed5f214a6a191] failed with code 128. Working directory was [/data/atlassian-bamboo-8.2.4/local-working-dir/serverSide/REPOSITORY_STORED_SPECS/repository-82673736-master/checkout]., stderr:
fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
	at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCommand(GitCommandProcessor.java:773)
	at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCommand(GitCommandProcessor.java:702)
	at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCommand(GitCommandProcessor.java:693)
	at com.atlassian.bamboo.plugins.git.GitCommandProcessor.setOrigin(GitCommandProcessor.java:597)
	at com.atlassian.bamboo.plugins.git.GitCommandProcessor.setOriginToLocalDirectory(GitCommandProcessor.java:654)
	at com.atlassian.bamboo.plugins.git.NativeGitOperationHelper.checkout(NativeGitOperationHelper.java:505)
	at com.atlassian.bamboo.plugins.git.v2.GitWorkingCopyManager.lambda$checkout$1(GitWorkingCopyManager.java:246)
	at io.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:293)
	at com.atlassian.bamboo.plugins.git.GitCacheDirectory$LoggingManagedLock.withLock(GitCacheDirectory.java:44)
	at com.atlassian.bamboo.plugins.git.v2.GitWorkingCopyManager.checkout(GitWorkingCopyManager.java:234)
	at com.atlassian.bamboo.plugins.git.v2.GitWorkingCopyManager.updateToLatestRevision(GitWorkingCopyManager.java:136)
	at com.atlassian.bamboo.plugins.stash.v2.BitbucketServerWorkingCopyManager.updateToLatestRevision(BitbucketServerWorkingCopyManager.java:146)
	... 16 more

 

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Eduardo Alvarenga
Eduardo Alvarenga
Atlassian Team
Atlassian Team members are employees working across the company in a wide variety of roles.
September 28, 2022

Hello @Rafael Neris

It appears that the local Git cache on the Bamboo Server is corrupted. Please follow the instructions below:

  1. Bamboo Administration >> Overview >> Repository settings
  2. Locate 6dc9b77d8e89ef31d4172c3f3d4ed5f214a6a191 >> Delete

Wait some minutes so Bamboo can run the deletion tasks and try the Specs scan again.

Best regards,

Eduardo Alvarenga
Atlassian Support APAC

--please don't forget to Accept the answer if the reply is helpful-- 

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Rafael Neris
Rafael Neris September 29, 2022

Hi @Eduardo Alvarenga !

Thanks for the help, but the problem persisted. There is something else we can do, here is the updated log:

Error during specs scan:
com.atlassian.bamboo.plugins.stash.repository.StashRepositoryException: com.atlassian.bamboo.plugins.git.GitCommandException: command [/usr/local/bin/git remote set-url origin file:///data/atlassian-bamboo-8.2.4/local-working-dir/_git-repositories-cache/6dc9b77d8e89ef31d4172c3f3d4ed5f214a6a191] failed with code 128. Working directory was [/data/atlassian-bamboo-8.2.4/local-working-dir/serverSide/REPOSITORY_STORED_SPECS/repository-82673736-master/checkout]., stderr:
fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
 at com.atlassian.bamboo.plugins.stash.v2.BitbucketServerWorkingCopyManager.updateToLatestRevision(BitbucketServerWorkingCopyManager.java:150)
 at com.atlassian.bamboo.configuration.external.RepositoryStoredSpecsServiceImpl.lambda$runBambooSpecs$0(RepositoryStoredSpecsServiceImpl.java:164)
 at com.atlassian.bamboo.variable.CustomVariableContextImpl.withVariableSubstitutor(CustomVariableContextImpl.java:140)
 at com.atlassian.bamboo.configuration.external.RepositoryStoredSpecsServiceImpl.lambda$runBambooSpecs$1(RepositoryStoredSpecsServiceImpl.java:169)
 at com.atlassian.bamboo.util.CacheAwareness.withValuesOlderThanTimestampReloaded(CacheAwareness.java:126)
 at com.atlassian.bamboo.configuration.external.RepositoryStoredSpecsServiceImpl.runBambooSpecs(RepositoryStoredSpecsServiceImpl.java:167)
 at com.atlassian.bamboo.configuration.external.RssDetectionServiceImpl.runRssDetection(RssDetectionServiceImpl.java:374)
 at com.atlassian.bamboo.configuration.external.detection.RssDetectionRunnable.run(RssDetectionRunnable.java:42)
 at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
 at java.util.concurrent.FutureTask.run(FutureTask.java:266)
 at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
 at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
 at com.atlassian.bamboo.utils.BambooRunnables$1.run(BambooRunnables.java:48)
 at com.atlassian.bamboo.security.ImpersonationHelper.runWith(ImpersonationHelper.java:26)
 at com.atlassian.bamboo.security.ImpersonationHelper.runWithSystemAuthority(ImpersonationHelper.java:17)
 at com.atlassian.bamboo.security.ImpersonationHelper$1.run(ImpersonationHelper.java:41)
 at java.lang.Thread.run(Thread.java:748)
Caused by: com.atlassian.bamboo.plugins.git.GitCommandException: command [/usr/local/bin/git remote set-url origin file:///data/atlassian-bamboo-8.2.4/local-working-dir/_git-repositories-cache/6dc9b77d8e89ef31d4172c3f3d4ed5f214a6a191] failed with code 128. Working directory was [/data/atlassian-bamboo-8.2.4/local-working-dir/serverSide/REPOSITORY_STORED_SPECS/repository-82673736-master/checkout]., stderr:
fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
 at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCommand(GitCommandProcessor.java:773)
 at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCommand(GitCommandProcessor.java:702)
 at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCommand(GitCommandProcessor.java:693)
 at com.atlassian.bamboo.plugins.git.GitCommandProcessor.setOrigin(GitCommandProcessor.java:597)
 at com.atlassian.bamboo.plugins.git.GitCommandProcessor.setOriginToLocalDirectory(GitCommandProcessor.java:654)
 at com.atlassian.bamboo.plugins.git.NativeGitOperationHelper.checkout(NativeGitOperationHelper.java:505)
 at com.atlassian.bamboo.plugins.git.v2.GitWorkingCopyManager.lambda$checkout$1(GitWorkingCopyManager.java:246)
 at io.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:293)
 at com.atlassian.bamboo.plugins.git.GitCacheDirectory$LoggingManagedLock.withLock(GitCacheDirectory.java:44)
 at com.atlassian.bamboo.plugins.git.v2.GitWorkingCopyManager.checkout(GitWorkingCopyManager.java:234)
 at com.atlassian.bamboo.plugins.git.v2.GitWorkingCopyManager.updateToLatestRevision(GitWorkingCopyManager.java:136)
 at com.atlassian.bamboo.plugins.stash.v2.BitbucketServerWorkingCopyManager.updateToLatestRevision(BitbucketServerWorkingCopyManager.java:146)
 ... 16 more
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Eduardo Alvarenga
Eduardo Alvarenga
Atlassian Team
Atlassian Team members are employees working across the company in a wide variety of roles.
September 29, 2022

Hello @Rafael Neris

As the git cache folder was not the issue, you can try:

  • Remove the /data/atlassian-bamboo-8.2.4/local-working-dir/serverSide/REPOSITORY_STORED_SPECS/repository-82673736-master folder
  • Check if you are not running out of disk space
  • Is this Repository using submodules? You may have come into a bug BAM-21880

If you still have issues, please raise a ticket with Atlassian at https://support.atlassian.com/contact and we'll be happy to assist.

Cheers,

Eduardo Alvarenga
Atlassian Support APAC

--please don't forget to Accept the answer if the reply is helpful-- 

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