eMastercard Upgrade Automation

A set of tools to ease upgrade of emastercard 3.* to the new emastercard.

Configure the application

1. Change the root database password in docker-compose.yml and docker-compose-build.yml NOTE: The database password defaults to password which is highly insecure.

2. Copy the example configuration files for the api and the migration scripts.

     cp api/api-config.yml.example api/api-config.yml
     cp api/migration-config.yml.example api/migration-config.yml

   Please use new configurations going forward.

3. Edit the two configuration files created in the previous step setting the database passwords for the API and the old eMastercard application.

   NOTE: In the migration-config.yml, the api is under section emr and the old emastercard is under the emastercard section. The site_prefix in the migration-config.yml has to be set for the migration to run at all. That prefix is used to create patient identifiers in the migrated database. For more information on what the various fields in the migration configuration file mean, see the configuration section of the following: eMastercard2Nart.

Build and installation

NOTE: The installation requires an internet connection through out the installation process.

1. The following comand builds and installs the application:

     ./setup.py

   A service file that automatically starts the application is created thus the status of application can be queried like so:

     sudo systemctl status emastercard

2. The setup above simply creates the application with an empty database. To initialize the database execute the following:

     sudo docker-compose exec api initialize_database.sh

• WARNING: This command truncates all tables and loads the base metadata to the database.

3. Migrating data from the old emastercard to the new one, requires that both the old emastercard and new emastercard be running. To start the migration do the following:

     sudo docker-compose exec api migration.sh

   At the end of the migration, a number of reports are dumped into the tmp folder. The reports are: migration-errors.yml, outcomes-report.csv.

Offline installations

It's possible to use a pre-existing installation to create installers that can be used for offline installations. For information on how this can be done, please refer to the Offline installation document.

Updating the application

  git pull -f origin master && ./setup.py

Database mantainance

• To backup the database run the following command in the emastercard-upgrade-automation directory:

    sudo docker-compose exec api backup_database.sh > backup.sql

• To restore the database run the following command in the emastercard-upgrade-automation directory.

    sudo docker-compose exec -T api restore_database.sh < backup.sql

• To change the database password do the following:

    sudo docker-compose exec api change_database_password.sh

Troubleshooting the application

Below are basic instructions for troubleshooting issues with the application. For more detailed information on troubleshooting please visit the troubleshooting page.

• Manually start the application by running the following and checking for errors in the output:

    sudo docker-compose up

  In some cases you may notice that the application is still pulling the nginx and mysql containers. These are usually pulled when the application first starts up thus why an internet connection is needed through out the installation process.

• Restart the application if the configuration file(s) where changed as follows:

    sudo systemctl restart emastercard

• Rebuild the containers as follows:

    sudo docker-compose -f docker-compose-build.yml build
  
    sudo systemctl restart emastercard

• Look at past logs to see what was going wrong:

    sudo journalctl -u emastercard

  NOTE: If the log file gets too big and you are having problems reading the log, you can trim it down like so (this leaves 7 days worth of log files):

    sudo journalctl --vacuum-time=7d

• In some cases you may need to run the latest updates for the application, run the following command:

    git pull -f && ./setup.py --no-follow-tags

• In some cases the setup my crush and continue to show you errors. In such scenarios you can use this script to remove docker completely and do a fresh install:

    ./removedocker.sh

For developers

To update the frontend's static files do the following:

  $ ./setup.py --rebuild-frontend
  $ git add web/static/*
  $ git commit -m 'Some commit message'
  $ git push

Automation Scripts

Update viral load results bearing =1 to =LDL

• The script migrates all HIV viral load results =1 to =LDL. to run the script, please type the following command

sh vl_ldl_fix.sh