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Mappings and Serialized Object Pipeline

Warning

  • First start with your local instance before attempting to update the live server.
  • When configuring the live server, please make sure that no one is using the system when doing Step 1 and 2 Removing and Creating New Container.
  • Backup live server database before doing any of these steps.
  • It has been noticed that some of the backup services have some technical issues and therefore you are advised to double check the file size after restarting the backup service before removing and stopping the container. The other option you can manually backup facility database by yourself.

Our automated deployment for mappings and serialized object comprises 5 steps:

0. Preparatory Steps
  • SSH into the server with ssh openmrs@_SERVER_IP_ADDRESS
  • First check to see if your server has internet connectivity with ping github.com
  • If not try to check contents of resolv.conf in /etc/ by running the following command: cat /etc/resolv.conf.Normally you should see google.com nameserver pointing to its ip 8.8.8.8.Edit the file if name server is not configured in the file.

  • Nameserver(all in lowercase) 8.8.8.8.Ping 8.8.8.8 or google.com.After you may ping github.com just to make sure you are able to get packets from github.com

  • Then download all of the files need with git clone https://github.com/eRegister/docs.git

  • The command above will create a folder called docs in /home/openmrs if you didn't change to another directory. All of files that need to be transfered to the server are in docs/scripts/mappingsscripts:

    • concepts_restore.sh
    • gitpull_bahmniapps.sh
    • gitpull_concepts.sh
    • gitpull_mappings.sh
    • gitpull_serial.sh
    • gitpullbahmniapps.service
    • gitpullconcepts.service
    • gitpullmappings.service
    • gitpullserializedobject.service
    • serializedboject_restore.sh

  • Go to /development/ and create the following directories openmrs_reporting_release and openmrs_concepts_release and grant openmrs user permissions to own the files.

  • Move the following files to /usr/local/bin/ and make them executable: concept_restore.sh,serializedobject_restore.

  • Move gitpull_concepts.sh to /development/openmrs_concepts_release and gitpull_serial.sh to /development/openmrs_reporting_release/, make them executable.

Note

Files are already on the server

Caution

PLEASE ENSURE THAT YOU HAVE BACKED UP THE DB BEFORE EXECUTING THE STEPS BELOW!!!

1. Removing Current Container
  • check the running container: docker ps
  • Stop the container: docker stop openmrseregister
  • Check that the container has stopped run docker ps and you should see an empty table
  • Create a new image from the stopped container: docker commit openmrseregister omrsregrepo/bahmni_base:09082020 [tag should be date at time of creating image]
  • you can check the newly created image with docker images
  • Remove the container: docker container rm openmrseregister
2. Creating a Volumes and enabling services
  • Now it's time to create a new container from the image we created earlier with: docker run -e container_name=openmrseregister -it -d --restart always -p 443:443 -p 80:80 -p 8069:8069 -p 8000:8000 --privileged --name openmrseregister -v /development/bahmni_config_release:/development/bahmni_config_release -v /development/dhisconnector_mappings:/development/dhisconnector_mappings -v /development/bahmniapps_release:/development/bahmniapps_release omrsregrepo/bahmni_base:06082020 /bin/bash
  • Go to /development/ and grant openmrs user permissions to files in /development/dhisconnector_mappings and /development/bahmniapps_release
  • Move gitpull_bahmniapps.sh to /development/bahmniapps_release and gitpull_mappings.sh to /development/dhisconnector_mappings, make them executable.

  • Create local repo's in all directories in /development except /development/bahmni_config_release, with the following commands: git init , git remote add git origin https://github.com:/eRegister/repo_name

  • test that you are able to fetch files from remote repo's by git fetch --all

  • move all services gitpullmappings.service,gitpullconcepts.serivce, gitpullbahmniapps.service and gitpullserializedobject.service.

  • Nagivate into /etc/system/system/ and type the following commands to enable gitpull_mappings.service, gitpullconcepts.service, gitpullbahmniapps.service,gitpullserializedobject.service

    sudo chmod 664 service_name
    sudo systemctl daemon-reload
    sudo systemctl enable service_name

Note

when the service has been registered successfully you should see created sym link in /etc/systemd/system/default.target.wants/.

3. Configuring cronjob
  • configure the cronjob to trigger the services everyday 7 am if our servers universal time is at UTC.
  • to edit the cronjob do: sudo crontab -e if it's first time running the this command it'll probably ask you to choose the default text editor, please be kind enough to choose Nano as it's the easiest editor for most administrators.
  • configure the script as shown below and then when the updates have been pulled successfully change the script to trigger services at 7:05,7:10,7:15,7:25 respectively. Do not change the command that trigger serialized object script
    */3 * * * * systemctl restart gitpullmappings.service >> /var/log gitpull_mappings.log
    */4 * * * * systemctl restart gitpullserializedobject.service >> /var/log/gitpull_serial.log
    */5 * * * * systemctl restart gitpullconcepts.service >> /var/log/gitpull_concepts.log
    */6 * * * * sudo bash /usr/local/bin/concepts_restore.sh >> /var/log/concept_restore.log
    20 7 * * * sudo bash /usr/local/bin/serializedobject_restore.sh >> /var/log/serial_restore.log
  • Wait for a while for cron job to execute the commands and check directories in development have updates from GitHub. For failed services refer to Automated Deployment Exit Codes to troubleshoot.
  • Go to into a container and start mysql service.
  • Connect to database server using no password mysql -uroot -p
  • Initialise openmrs database and users by sourcing openmsq.sql file in container root directory, source openmrs.sql;
  • Wait a moment for databases to be created and once the script is done quit or exit the database server and restart mysql.
  • Restore facility database using the command mysql -uroot -ppassword openmrs;
  • Go to /opt/openmrs/dhisconnector
  • Remove mappings folder and create soft link to /development/dhisconnector_mappings/dhisconnector_mappings/mappings
    command:
    sudo ln -s /development/dhisconnector_mappings/dhisconnector_mappings/mappings/ mappings
  • Exit the container and go to /usr/local/bin and run serializedobject_restore.sh
  • Restart other services and openmrs the broswer to access openmrs admin page.
  • Go to reporting you should see total of 36 openmrs period indicator reports. Refer to staging server to see example eRegister Staging server
Last update: March 1, 2021