[Deprecated] Update MySQL in Cromwell on Azure

MySQL update for Cromwell on Azure

NOTE!!! As of 4.0.0 Cromwell on Azure has moved to PostgreSQL. These instructions are relevant for versions prior to 4.0.0

To update MySQL you need to complete the following steps:

• Stop CromwellOnAzure while leaving the VM up and running

• Start MySQL container using the previous version, let it process the logs and shut it down

• Start latest MySQL container, let it process the update and shut it down

• Start CoA

The detailed instructions are provided below:

1. Connect to Cromwell on Azure VM via SSH. Default CoA deployment creates Network security group with SSH port closed. To connect to a VM follow instructions Connect to a Linux VM.

2. Have 2 terminals with SSH connection open.

3. In terminal 1

• Stop Cromwell on Azure

  sudo systemctl stop cromwellazure

• List docker containers

  sudo docker container ls -a

• mysql:latest will be listed there, start it

  sudo docker run -e MYSQL_ROOT_PASSWORD=<Your MySQL root password> -e MYSQL_DATABASE=<Your MySQL database name> -v /data/mysql:/var/lib/mysql -v /data/cromwellazure/mysql-init:/mysql-init mysql:latest

  You can find values for MYSQL_ROOT_PASSWORD and MYSQL_DATABASE in Blob container configuration that is located in the deployed Storage account. Open file cromwell-application.conf and search for database section

  database {
     db.url = "jdbc:mysql://mysqldb/<Your MySQL database name>?<Properties>"
     db.user = <Your MySQL root user>
     db.password = <Your MySQL root password>
     ...
  }
  

• It is supposed to fail. If it keeps running, follow instructions in step 6 to stop the container, and return to terminal 1

• Find MySQL version that was used to create the log (see above in red), start this version, and let it process the log

  sudo docker run -e MYSQL_ROOT_PASSWORD=<Your MySQL root password> -e MYSQL_DATABASE=<Your MySQL database name> -v /data/mysql:/var/lib/mysql -v /data/cromwellazure/mysql-init:/mysql-init mysql:8.0.28

4. Switch to terminal 2

• List docker containers and find CONTAINER ID for MySQL version you just started

  sudo docker container ls -a

• Stop this container

  sudo docker container stop a235404427a5

5. Switch to terminal 1

• Check that MySQL shutdown complete

• Start the latest MySQL image and let it process the update

  sudo docker run -e MYSQL_ROOT_PASSWORD=<Your MySQL root password> -e MYSQL_DATABASE=<Your MySQL database name> -v /data/mysql:/var/lib/mysql -v /data/cromwellazure/mysql-init:/mysql-init mysql:latest

6. Switch to terminal 2

• List docker containers and find CONTAINER ID for latest MySQL you just started

  sudo docker container ls -a

• Stop this container

  sudo docker container stop 071ee4796cd0

7. Switch to terminal 1

• Check that MySQL shutdown complete

• Start Cromwell on Azure

  sudo systemctl start cromwellazure

8. Go to Network security group and close SSH port.