Jira or confluence upgrade causes all subfolders to get deleted

I am in the process of moving our existing instances of jira and confluence over to a 64-bit RHEL server, due to the issue with confluence version upgrades only being 64-bit going forward. Currently we have version 7.2 of jira running on the 64-bit server. Today I tried to do an upgrade to version 7.4 and it ended up deleting ALL of the subfolders below the jira folder on the server. Last week I tried the same thing on this server; going from version 5 to 6 of confluence and the upgrade deleted ALL of the subfolders below the confluence directory. I have only been working with Atlassian products for a little over 5 years but I have NEVER seen anything like this happen on an upgrade. Any thoughts out there? This is way bizarre!

1 answer

John - are you talking about the DATA directory or the SYSTEM directory? Usually the DATA directory should not be changed during the install, the SYSTEM directory is deleted and reinstalled. How are you doing the upgrade/which commands are you using?



Christoph thanks for the quick reply. What I'm saying is that when I performed the upgrade for jira or confluence either one, the upgrade wiped out everything below the jira or confluence directory; all of the folders below the jira or confluence folder itself. This is the folder that has the bin and config subfolders below it. Fortunately I had copied that entire folder structure over to my laptop before I started the upgrade each time. The way I did the upgrade is the same way that I have always done upgrades for jira or confluence; download the bin file and then run it, choosing option # 3 for "Upgrade". Hope this helps,

John Ellis

Here is a screenshot of what I'm talking about. These are all the subfolders in the jira directory before I tried to do the upgrade.

John - "Delete the contents of the existing JIRA Installation Directory" - https://confluence.atlassian.com/adminjiraserver071/upgrading-jira-applications-using-a-rapid-upgrade-method-802592264.html

Is this what you are talking about? 



Yes this screenshot shows the steps that I go through to do an upgrade of either jira or confluence but in the past this has always worked fine. This time the upgrade physically deleted all the folders below the jira or confluence folder, as I indicated previuosly.

Christoph, any ideas?

For me reading the docs it still sounds like default behavior, sorry... 

No, it is NOT normal behaviour because the upgrade is WIPING OUT the entire jira folder structure. After I try to perform this upgrade jira DOES NOT WORK AT ALL. This is what I am saying. I have to copy all of the jira folders back over from my laptop, where I copied them to before I did the upgrade, in order to get jira to run again. How can this be normal behaviour? The same thing happened when I tried to upgrade the version of confluence; the upgrade attempt wiped out the entire confluence folder structure. I had to copy it back over from my laptop to get confluence to run again. I have been doing jira/confluence upgrades for over 5 years now and I have never ever seen an upgrade do this.

Okay one last question - do you have one directory for your data and one for the application? The application directory gets deleted and repopulated by the installer, the data directory should stay untouched. If you have separate directories please try a different version to install to see if the installer is somehow broken. 

Yes there is another directory for the data, under /var/atlassian/application-data/jira and the jira application is under /opt/atlassian/jira

Okay and the application directory gets deleted during the installation and doesn't get repopulated? Sounds like the installer is having an issue - is there any log available? Also you are writing something about migrating to another server - could this have an impact on the installation? To be honest - I can't fix this without having it to fix myself so only guesses... 

Yes the application directory and everything below is getting deleted by the upgrade so there are no log files to check as the log directories get deleted as well. I will try another version and see what happens.

OK I just tried the jira upgrade again, using version 7.4.0 rather than 7.4.1 which showed to be the latest versionfor  download. The upgrade failed again in the same way, deleting all the folders within the jira application folder. Here are screenshots of the error log that was created-

64-bit jira upgrade issue_4.png64-bit jira upgrade issue_5.png


Is the installer deleting itself or is this a known IO error? Have you tried to make a clean install in another folder? From which version are you upgrading by the way? 

I believe that the installer does delete the existing directory but it is supposed to replace it with the new one and it appears that the errors are causing that part of the install to fail. Currently we are running version 7.2.6 of jira and have been trying to upgrade to the latest; version 7.4.1 

I will try running the install from a different folder and if that fails as well I think I will just do a clean install of jira with thev latest version and then see if I can import a backup from our existing version, unless you have any other ideas?

Sounds like a plan - would do the same. Only thing I am wondering is if you really need to import a backup then or can just connect the new installation to the database (be sure to backup the database before anyway!)... 

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