"Exception in thread "main" java.util.zip.ZipException: zip file is empty" while starting Bitbucket Datacenter container
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
Summary
Bitbucket container fails to start with the message "Exception in thread "main" java.util.zip.ZipException: zip file is empty"
Environment
Tested on Bitbucket 8.14 and 8.18
Docker
Diagnosis
While running the docker-compose up command, you'll see the below messages on the terminal:
Click here to see the full output on the terminal
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bitbucket | WARNING:root:######################################################################
bitbucket | WARNING:root:Starting Bitbucket with embedded search service. Note that this is
bitbucket | not a recommended configuration and is known to have issues with
bitbucket | clean shutdown. Ideally OpenSearch (previously Elasticsearch) should
bitbucket | be started in a separate container/pod.
bitbucket | WARNING:root:######################################################################
bitbucket | INFO:root:User is currently root. Will downgrade run user to bitbucket
bitbucket | INFO:root:Running Bitbucket with command '/opt/atlassian/bitbucket/bin/start-bitbucket.sh', arguments ['/opt/atlassian/bitbucket/bin/start-bitbucket.sh', '-fg']
bitbucket | Starting Atlassian Bitbucket as the current user
bitbucket |
bitbucket | Starting the bundled search server
bitbucket | Hint: Run start-bitbucket.sh --no-search to skip starting the bundled search server
bitbucket | Bundled search server started successfully
bitbucket |
bitbucket | Bitbucket is being run with a umask that contains potentially unsafe settings.
bitbucket | The following issues were found with the mask "u=rwx,g=rx,o=rx" (0022):
bitbucket | - Access is allowed to 'others'. It is recommended that 'others' be denied
bitbucket | all access for security reasons.
bitbucket | The recommended umask for Bitbucket is "u=,g=w,o=rwx" (0027) and can be
bitbucket | configured in _start-webapp.sh
bitbucket |
bitbucket | Starting Bitbucket webapp at http://localhost:7990
bitbucket | Exception in thread "main" java.util.zip.ZipException: zip file is empty
bitbucket | at java.base/java.util.zip.ZipFile$Source.zerror(ZipFile.java:1762)
bitbucket | at java.base/java.util.zip.ZipFile$Source.findEND(ZipFile.java:1546)
bitbucket | at java.base/java.util.zip.ZipFile$Source.initCEN(ZipFile.java:1641)
bitbucket | at java.base/java.util.zip.ZipFile$Source.<init>(ZipFile.java:1479)
bitbucket | at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1441)
bitbucket | at java.base/java.util.zip.ZipFile$CleanableResource.<init>(ZipFile.java:718)
bitbucket | at java.base/java.util.zip.ZipFile.<init>(ZipFile.java:252)
bitbucket | at java.base/java.util.zip.ZipFile.<init>(ZipFile.java:181)
bitbucket | at java.base/java.util.jar.JarFile.<init>(JarFile.java:346)
bitbucket | at java.base/java.util.jar.JarFile.<init>(JarFile.java:317)
bitbucket | at java.base/java.util.jar.JarFile.<init>(JarFile.java:283)
bitbucket | at org.springframework.boot.loader.jar.AbstractJarFile.<init>(AbstractJarFile.java:39)
bitbucket | at org.springframework.boot.loader.jar.JarFile.<init>(JarFile.java:130)
bitbucket | at org.springframework.boot.loader.jar.JarFile.<init>(JarFile.java:125)
bitbucket | at org.springframework.boot.loader.jar.JarFile.<init>(JarFile.java:111)
bitbucket | at org.springframework.boot.loader.jar.JarFile.<init>(JarFile.java:102)
bitbucket | at org.springframework.boot.loader.archive.JarFileArchive.<init>(JarFileArchive.java:73)
bitbucket | at org.springframework.boot.loader.archive.JarFileArchive.<init>(JarFileArchive.java:69)
bitbucket | at com.atlassian.bitbucket.internal.launcher.BitbucketServerLauncher.postProcessClassPathArchives(BitbucketServerLauncher.java:146)
bitbucket | at org.springframework.boot.loader.ExecutableArchiveLauncher.applyClassPathArchivePostProcessing(ExecutableArchiveLauncher.java:142)
bitbucket | at org.springframework.boot.loader.ExecutableArchiveLauncher.getClassPathArchivesIterator(ExecutableArchiveLauncher.java:125)
bitbucket | at com.atlassian.bitbucket.internal.launcher.BitbucketServerLauncher.start(BitbucketServerLauncher.java:156)
bitbucket | at com.atlassian.bitbucket.internal.launcher.BitbucketServerLauncher.main(BitbucketServerLauncher.java:99)
bitbucket | WARNING: A terminally deprecated method in java.lang.System has been called
bitbucket | WARNING: System::setSecurityManager has been called by org.opensearch.bootstrap.OpenSearch (file:/opt/atlassian/bitbucket/opensearch/lib/opensearch-1.3.14.jar)
bitbucket | WARNING: Please consider reporting this to the maintainers of org.opensearch.bootstrap.OpenSearch
bitbucket | WARNING: System::setSecurityManager will be removed in a future release
bitbucket |
bitbucket | No process was found for PID 209, or the current user cannot signal itCause
While attempting to migrate from MySQL to say Postgres, you remove the volume mapping of the MySQL driver, by removing something similar to the below from the docker-compose.yaml file:
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- /local/app/bitbucket/mysql-connector-j-8.0.32.jar:/var/atlassian/application-data/bitbucket/lib/mysql-connector-j-8.0.32.jar
The above could've been done after successful Database migration, stopping Bitbucket and validating that there is no reference to the MySQL database in both Docker environment variables and the bitbucket.properties configuration file.
This can cause the “Exception in thread "main" java.util.zip.ZipException: zip file is empty” error because Bitbucket still tries to access the MySQL driver after migration, even though there is no configuration reference to MySQL.
Solution
Solution 1
Before running the "docker-compose up"command while using thedocker-compose.ymlfile, go to the/local/data/bitbucket/libpath (which is the volume mapping) and rename the.jarfile.
The above path applies if your docker-compose.yaml file has the below:
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volumes:
- /local/data/bitbucket:/var/atlassian/application-data/bitbucketThe contents of this path would look something like this:
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username@ubuntu lib % ls
mysql-connector-j-8.0.32.jar_bkup nativeSolution 2
There could be a zero-byte file remaining of the MySQL driver in the <Bitbucket-HOME>/lib folder from the time the container was stopped and not mapped with the docker-compose file. Removing the zero-byte file should resolve the issue.
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