I upgrade the Chef Server to version 12.4.1, just follow the instructions from chef docs

Verify that the make command is available on the Chef server server. If it is not available, install the make command.

~# make

    _The program 'make' is currently not installed. You can install it by typing:_
    _apt-get install make_

~# apt-get install make

Run the following on all servers to make sure all services are in a sane state:

~# chef-server-ctl reconfigure
    Starting Chef Client, version 12.0.3
    resolving cookbooks for run list: ["private-chef::default"]


    Running handlers:
    Running handlers complete
    Chef Client finished, 32/390 resources updated in 51.240191762 seconds
    opscode Reconfigured!

Download the new version of Chef Server, get the link here chef downloads

~# wget https://packagecloud.io/chef/stable/packages/ubuntu/trusty/chef-server-core-<version>.deb/download -O chef-server-core-<version>.deb

Stop the server:

~# chef-server-ctl stop

    ok: down: bookshelf: 0s, normally up
    ok: down: ec_sync_client: 0s, normally up
    ok: down: ec_sync_server: 0s, normally up
    ok: down: nginx: 1s, normally up
    ok: down: oc_bifrost: 0s, normally up
    ok: down: oc_id: 1s, normally up
    ok: down: opscode-chef-mover: 2212s, normally up
    ok: down: opscode-erchef: 1s, normally up
    ok: down: opscode-expander: 0s, normally up
    ok: down: opscode-expander-reindexer: 0s, normally up
    ok: down: opscode-pushy-server: 1s, normally up
    ok: down: opscode-reporting: 0s, normally up
    ok: down: opscode-solr4: 1s, normally up
    ok: down: postgresql: 0s, normally up
    ok: down: rabbitmq: 1s, normally up
    ok: down: redis_lb: 0s, normally up

Run dpkg, the -D enables debugging and 10 creates output for each file processed in the upgrade

~# dpkg -D10 -i /path/to/chef-server-core-<version>.deb

Upgrade the server with this:

~# chef-server-ctl upgrade

    ok: down: opscode-chef-mover: 0s, normally up
    down: opscode-chef-mover: 2s, normally up; run: log: (pid 993) 8313s
    down: opscode-chef-mover: 4s, normally up; run: log: (pid 993) 8315s
    [private-chef-upgrade] - Sleeping for 10 seconds while services stop...
    [private-chef-upgrade] - Finished Migration 1.29 in 76.87 seconds
    Chef Server Upgraded!

Start Chef server 12:

~# chef-server-ctl start

    ok: run: bookshelf: (pid 17405) 1s
    ok: run: ec_sync_client: (pid 17446) 0s
    ok: run: ec_sync_server: (pid 17450) 0s
    ok: run: nginx: (pid 17480) 1s
    ok: run: oc_bifrost: (pid 16053) 1249s
    ok: run: oc_id: (pid 17487) 0s
    ok: run: opscode-chef-mover: (pid 17507) 1s
    ok: run: opscode-erchef: (pid 17540) 0s
    ok: run: opscode-expander: (pid 17545) 0s
    ok: run: opscode-expander-reindexer: (pid 17552) 0s
    ok: run: opscode-pushy-server: (pid 17557) 0s
    ok: run: opscode-reporting: (pid 17564) 1s
    ok: run: opscode-solr4: (pid 17617) 0s
    ok: run: postgresql: (pid 15930) 1296s
    ok: run: rabbitmq: (pid 17635) 0s
    ok: run: redis_lb: (pid 17645) 0s

After the upgrade is complete and everything verified to be working properly, clean up the server by removing all of the old data:

$ chef-server-ctl cleanup

    Starting Chef Client, version 12.7.0
    Chef Client finished, 2/113 resources updated in 04 seconds