Problem/NullpointerException when upgrading Jira standalone from 7.4.2 to 7.13.9 on Linux 64-Bit

[Fencer]

Hi all,

I'm trying to upgrade a jira standalone installation on a Linux system from 7.4.2 to 7.13.9. I followed the instructions in the guides and release/upgrade notes.

First of all I have to state that the jira installation directory of the instance seems to be '/opt', which is quite strange indeed, but the contents of '/opt' are:

drwxr-xr-x 6 root root 4096 Oct 18 00:39 ./
drwxr-xr-x 23 root root 4096 Oct 18 00:28 ../
drwx------ 17 jira 500 4096 Aug 3 2017 atlassian-jira/
-rwxrw-r-- 1 jira jira 350614470 Oct 14 17:20 atlassian-jira-software-7.13.9-x64.bin*
drwxr-xr-x 2 500 500 4096 Jan 24 2018 collaboraoffice5.3/
-rw-r--r-- 1 root root 1856091 Jul 5 2017 httpclienttest-1.0.2.jar
drwx------ 12 jira 500 4096 Oct 17 23:33 jira-7.4.2/

Anyway the installer does not accept the subdirectory 'jira-7.4.2' as installation directory and from the documentation I know that the installation directory is defined as the directory containing the subdirectory 'atlassian-jira' and a directory lile 'jira-x.x.x', so it seems pretty sure that '/opt' indeed is the installation directory.

That said, the installer indeed starts when choosing '/opt' as installation directory, but it complaints about 2Problems reading the installation directory". This can be ignored and the installation process continues. Though this might be the reason why it later aborts:

jira@srv:opt$ sudo ./atlassian-jira-software-7.13.9-x64.bin
Unpacking JRE ...
Starting Installer ...

This will install JIRA Software 7.13.9 on your computer.
OK [o, Enter], Cancel [c]
o
Choose the appropriate installation or upgrade option.
Please choose one of the following:
Express Install (use default settings) [1], Custom Install (recommended for advanced users) [2], Upgrade an existing JIRA installation [3, Enter]
3
Existing installation directory:
[/opt/jira-7.4.2]
/opt
Problems reading the installation directory.
Ignore [i, Enter], Retry [r], Quit [q]
i
Back up JIRA home directory
The upgrade process will automatically back up your JIRA installation
directory. You can also choose to back up your existing JIRA home directory.
Both directories are backed up as zip archive files in their respective
parent directory locations.

We strongly recommend choosing this option in the unlikely event that you
experience problems with the upgrade and may require these backups to
restore your existing JIRA installation.

If you have many attachments in your JIRA home directory, the zip archive of
this directory may consume a significant amount of disk space.
Back up JIRA home directory?
Yes [y, Enter], No [n]
y

Checking for local modifications.

Checking if your instance of JIRA Software is running
In action "Run script" (screen "Check if JIRA is running [Display progress]"), property "Script":
java.lang.NullPointerException
at I4jScript_Internal_344.eval(I4jScript_Internal_344.java:20)
at I4jScript_Internal_344.evaluate(I4jScript_Internal_344.java:28)
at com.install4j.runtime.installer.helper.Script.evaluate(Unknown Source)
at com.install4j.runtime.installer.ContextImpl.runScript(Unknown Source)
at com.install4j.runtime.installer.ContextImpl.runScript(Unknown Source)
at com.install4j.runtime.beans.actions.control.RunScriptAction.execute(Unknown Source)
at com.install4j.runtime.beans.actions.SystemInstallOrUninstallAction.install(Unknown Source)
at com.install4j.runtime.installer.InstallerContextImpl.performActionInt(Unknown Source)
at com.install4j.runtime.installer.ContextImpl.performAction(Unknown Source)
at com.install4j.runtime.installer.controller.Controller.executeActions(Unknown Source)
at com.install4j.runtime.installer.controller.Controller.handleCommand(Unknown Source)
at com.install4j.runtime.installer.controller.Controller.start(Unknown Source)
at com.install4j.runtime.installer.Installer.main(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)
at com.install4j.runtime.launcher.Launcher.main(Unknown Source)
Upgrade check list
Back up your external database
We strongly recommend you back up your JIRA Software database if you have
not already done so.

Please refer to the following URL for back up guidelines:
http://docs.atlassian.com/jira/jadm-docs-0713/Backing+up+data

Check plugin compatibility
Check that your non-bundled plugins are compatible with JIRA Software
7.13.9.

For more information see our documentation at the following URL:
http://docs.atlassian.com/jira/jadm-docs-0713/Upgrading+JIRA+applications

Please ensure you have read the above checklist before upgrading.
Your existing JIRA installation is about to be upgraded! Do you want to proceed?
Upgrade [u, Enter], Exit [e]
u

Your instance of JIRA is currently being upgraded.
Checking if JIRA has been shutdown...
In action "Check jira is shut [Run script]" (screen "Upgrade Actions [Display progress]"), property "Script":
java.lang.NullPointerException
at I4jScript_Internal_352.eval(I4jScript_Internal_352.java:20)
at I4jScript_Internal_352.evaluate(I4jScript_Internal_352.java:39)
at com.install4j.runtime.installer.helper.Script.evaluate(Unknown Source)
at com.install4j.runtime.installer.ContextImpl.runScript(Unknown Source)
at com.install4j.runtime.installer.ContextImpl.runScript(Unknown Source)
at com.install4j.runtime.beans.actions.control.RunScriptAction.execute(Unknown Source)
at com.install4j.runtime.beans.actions.SystemInstallOrUninstallAction.install(Unknown Source)
at com.install4j.runtime.installer.InstallerContextImpl.performActionInt(Unknown Source)
at com.install4j.runtime.installer.ContextImpl.performAction(Unknown Source)
at com.install4j.runtime.installer.controller.Controller.executeActions(Unknown Source)
at com.install4j.runtime.installer.controller.Controller.handleCommand(Unknown Source)
at com.install4j.runtime.installer.controller.Controller.start(Unknown Source)
at com.install4j.runtime.installer.Installer.main(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)
at com.install4j.runtime.launcher.Launcher.main(Unknown Source)
Rolling back changes ...

 Since I used sudo there should not be any problem reading the directory, right?

Any help with this will be highly appreciated.

P.S.: I did find the article about the Upgrade to JIRA 4.4,but though the output seems to be quite the same, the suggested solution did not solve my problem.

[Fencer · Accepted solution]

The issue seems in fact to be the messed up file structure. I reinstalled Jira 7.4.2 ins '/opt/jira' leaning all other things as they were. Despite from having to deal with the jira1-user-issue, that was quite easy and after that I can see, that in '/opt/jira' there are not only two parallel directories, but the content of the former subdirectory of '/opt' having had the name 'jira-7.4.2' is now in the installation directory itself and there is also the directory 'atlassian-jira'. The new installation directory looks like this:

drwxr-xr-x 15 root root 4096 Oct 18 16:19 ./
drwxr-xr-x 7 root root 4096 Oct 18 16:15 ../
drwxr-xr-x 18 root root 4096 Oct 18 16:15 atlassian-jira/
drwxr-xr-x 3 root root 4096 Oct 18 16:15 bin/
-rw-r--r-- 1 root root 20106 Oct 14 14:57 BUILDING.txt
drwxr-xr-x 2 root root 4096 Oct 18 16:15 conf/
-rw-r--r-- 1 root root 6237 Oct 14 14:57 CONTRIBUTING.md
drwxr-xr-x 2 root root 4096 Oct 18 16:15 external-source/
drwxr-xr-x 3 root root 4096 Oct 18 16:19 .install4j/
-rw-r--r-- 1 root root 97695 Oct 18 16:19 install.reg
drwxr-xr-x 4 root root 4096 Oct 18 16:15 jre/
drwxr-xr-x 2 root root 4096 Oct 18 16:16 lib/
drwxr-xr-x 2 root root 69632 Oct 18 16:15 licenses/
drwx------ 2 jira root 4096 Oct 18 16:19 logs/
-rw-r--r-- 1 root root 1777 Oct 14 14:57 NOTICE
-rw-r--r-- 1 root root 3835 Oct 14 14:57 README.html
-rw-r--r-- 1 root root 3334 Oct 14 14:57 README.md
-rw-r--r-- 1 root root 2097 Oct 14 14:57 README.txt
drwx------ 2 jira root 4096 Oct 18 16:15 temp/
drwxr-xr-x 2 root root 4096 Oct 18 16:15 tomcat-docs/
-rwx------ 1 root root 11201 Oct 14 14:58 uninstall*
drwxr-xr-x 2 root root 4096 Oct 14 14:58 webapps/
drwx------ 3 jira root 4096 Oct 18 16:19 work/

After the re-install-process I tried the upgrade again. The 'Problems reading the installation directory' are gone and the upgrade process completed successfully.

I do not know, why the file structure was the way it was and I also no not know if there is another quicker way to solve the issue. But the described way can be done in less than an hour.