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Running Bahmni Lite with DB backup from cloud (Docker)

Running Bahmni Lite with DB backup from cloud (Docker)

Owned by Ramkumar G
Last updated: Aug 28, 2023 by Gurpreet Luthra
3 min read

This page documents how to take a DB Backup of your OpenMRS / EMR DB from Kubernetes environment (running on cloud), build a docker image with this DB, and then run Bahmni docker compose with the restored database.

WARNING: If you are working with production data, please be very careful how you handle it, who has access to it, and where you share/keep it. It is illegal to make private patient data available to people without authorisation in most countries!

Repositories

🔸 Bahmni Lite

🔸 Bahmni Lite - India based with ABDM integration

🔸 Bahmni Scripts - to build DB for openMRS

Setup

🔹 Git clone the respective Bahmni Lite repository

🔹 Git clone the Bahmni Scripts repository

🔹 Install Docker

DB backup from Kubernetes/AWS

We ran Bahmni Lite on AWS/Kubernetes. So the following setup will extract DB dump based on Kubernetes commands.

  1. Get into the openMRS kubernetes pod

kubectl exec -it openmrs<POD_ID> -n <namespace> -- bash

 

2. Navigate to the openmrs/data folder and zip the configuration_checksum folder (which is used by Initializer module to determine if an initializer entry has run or not run).

# install zip yum install zip # Navigate to openmrs/data directory cd /openmrs/data # Zip the checksums folder zip -r configuration_checksums.zip configuration_checksums

 

3. Backup the DB as a SQL dump

# Install mysql cli yum install mysql # Export the current live DB as a sql dump to the pod mysql -u username -p database_name > omrsdb.sql # Provide password and press Enter # Exit Mysql Exit

4. Note down the Database details

# Open the runtime properties cat openmrs-runtime.properties # Exit the openMRS pod Exit

Keep a note of the above DB details and maintain them securely until the setup is completed successfully

5. Copy the files to local machine

# Copy the checksums zip to the local kubectl cp performance/openmrs-<POD_ID>:/openmrs/data/configuration_checksums.zip configuration_checksums.zip # Copy the sql dump to the local kubectl cp performance/openmrs-<POD_ID>:/openmrs/data/omrsdb.sql omrsdb.sql

Build the DB in Docker

We used mysql 5.7 for our setup, if you use mysql 5.6 kindly change it wherever applicable.

  1. Navigate to ~/bahmni-scripts/demo/db-backups/1.0.0-lite/mysql5.7/resources

2. Delete the files present in this directory

3. Copy and paste the files exported from the pod i.e configuration_checksums.zip and omrsdb.sql to this directory

4. Navigate back to the mysql5.7 directory and replace the Dockerfile contents with the following code:

Apple M1 Chip (Mac)

ARG arch FROM --platform=linux/amd64 mysql:5.7 #Install the required tools RUN yum update -y && \    yum install -y \    unzip #Set the mysql root password ENV MYSQL_ROOT_PASSWORD=<ROOTPASSWORD> #Copy configuration_checksums & DB Backup COPY demo/db-backups/1.0.0-lite/mysql5.7/resources/*.zip  . COPY demo/db-backups/1.0.0-lite/mysql5.7/resources/*.sql  /docker-entrypoint-initdb.d/omrs_db_backup.sql RUN unzip configuration_checksums.zip && \    rm configuration_checksums.zip

Others (Linux)

FROM mysql:5.7 #Install the required tools RUN yum update -y && \    yum install -y \    unzip #Set the mysql root password ENV MYSQL_ROOT_PASSWORD=<ROOTPASSWORD> #Copy configuration_checksums & DB Backup COPY demo/db-backups/1.0.0-lite/mysql5.7/resources/*.zip  . COPY demo/db-backups/1.0.0-lite/mysql5.7/resources/*.sql  /docker-entrypoint-initdb.d/omrs_db_backup.sql RUN unzip configuration_checksums.zip && \    rm configuration_checksums.zip

5. Navigate to bahmni-scripts root directory and execute the following docker command (note the TAGNAME should be set to some specific value. e.g my-build-1):

docker build --no-cache -t bahmni/openmrs-db:<TAGNAME> -f demo/db-backups/1.0.0-lite/mysql5.7/Dockerfile .

Config the environment and docker compose

  1. Navigate to the bahmni-docker/bahmni-lite or bahmni-india-package directory where the docker- compose.yml is present

If using Apple M1 chip, add platform: linux/amd64 to each service present under the docker compose file.

2. Add the openMRS DB details captured earlier in DB backup extraction to the .env file and save it. Ensure the OPENMRS_DB_IMAGE_NAME is pointing to the newly created docker image (as generated in the previous step).

# OpenMRS Environment Variables OPENMRS_IMAGE_TAG=latest OPENMRS_DB_IMAGE_NAME=bahmni/openmrs-db:<TAGNAME> OPENMRS_DB_NAME=<DBNAME> OPENMRS_DB_HOST=openmrsdb OPENMRS_DB_USERNAME=<DBUSERNAME> OPENMRS_DB_PASSWORD=<DBPASSWORD> OPENMRS_DB_CREATE_TABLES='false' OPENMRS_DB_AUTO_UPDATE='true' OPENMRS_MODULE_WEB_ADMIN='true' MYSQL_ROOT_USERNAME=root # OMRS_DEV_DEBUG_PORT= OMRS_JAVA_SERVER_OPTS='' OMRS_JAVA_MEMORY_OPTS='' OPENMRS_UPLOAD_FILES_PATH=./openmrs-uploads BAHMNI_OPENMRS_MODULES_PATH= MYSQL_ROOT_PASSWORD=<ROOTPASSWORD> OPENMRS_DB_TYPE=mysql OPENMRS_DOCKER_ENV='true'

Invoke Bahmni Lite

  1. Bring up Bahmni through Docker compose

docker-compose up -d --build

2. Wait for openmrs to load with all the required indexes

3. Enter “http://localhost/openmrs” in browser and verify openMRS is up

4. Navigate to “http://localhost/” and start using Bahmni (this should now run with the new DB)

 

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