Upgrading the OS is a pretty dangerous operation.

• Open the port 1022 on ufw
• Enable the extra SSH port on 1022 when offered on the installer.
• Do this upgrade first in staging. Make sure all the services are correctly working.
• Make sure there's someone on call to help you in case things go wrong.
• Do a manual backup of any required data.
• Try to not do upgrades on Fridays or over the weekend

• Sites-available should have only *.conf files

root@gw116:/etc/apache2# ls -l sites-available/
total 20
-rw-r--r-- 1 root root 1348 Feb 10 02:54 000-default.conf
-rw-r--r-- 1 root root 6338 Apr  5  2016 default-ssl.conf
-rw-r--r-- 1 root root 2741 Feb 10 03:55 id.openmrs.org.conf
-rw-r--r-- 1 root root 1977 Feb 10 04:34 issues.openmrs.org.conf

• Sites-enabled should only have links, and *.conf only

root@gw116:/etc/apache2# ls -l sites-enabled/
total 0
lrwxrwxrwx 1 root root 35 Feb 10 02:51 000-default.conf -> ../sites-available/000-default.conf
lrwxrwxrwx 1 root root 38 Feb 10 03:38 id.openmrs.org.conf -> ../sites-available/id.openmrs.org.conf
lrwxrwxrwx 1 root root 42 Feb 10 03:39 issues.openmrs.org.conf -> ../sites-available/issues.openmrs.org.conf

• Make sure ssl_module, proxy_module, proxy_ajp_module and proxy_http_module are installed and enabled:

$ apachectl -M

• Confirm that all files in conf-enabled and mod-enabled are symlinks.

• Change the path to rotatelogs in sites-available config from /usr/sbin/ to /usr/bin:

CustomLog "|/usr/bin/rotatelogs /opt/www/logs/id.openmrs.org-access.log 86400" common

• Check for updated files in apache config, and check for inconsistences:

$ find /etc/apache2/ -name "*.back"

• Verify that

Order deny,allow
Deny from all

is now:

Require all granted

https://httpd.apache.org/docs/2.4/upgrading.html

• Verify that ServerName is the first item on every configuration file
• Verify that NameServer is not available anymore

Error logs can be found in:

$ journalctl -u apache2
$ cat /var/log/apache2/error.log

OpenJDK 6 and 7 were removed. JDK 7 is still available in PPA.

$ apt-get install software-properties-common
$ add-apt-repository ppa:openjdk-r/ppa

So, before uploading any machine, verify if there's any process using the system java, and verify if they can be upgraded to JDK 8, or at least JDK 7.