OpenELIS-OpenCR-HIE-Setup

This integration aims to connect OpenELIS, a laboratory information system, with a FHIR-Based Open Client Registry which will allow users to search for patients within their local OpenELIS system, If the patient isn't found locally, search the client registry then Import patient information from the client registry to OpenELIS.

In simpler terms, this lets users find patients within their local system and if not found, search for them in a central database and bring their information back into the local system.

How-Tos

Pre-Requesites

• Git: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git
• Git Large File Storage: https://docs.github.com/en/repositories/working-with-files/managing-large-files/installing-git-large-file-storage
• Docker: https://docs.docker.com/engine/install/

Startup

•   git clone https://github.com/mherman22/OpenELIS-OpenCR-HIE-Setup
  

•   git lfs fetch
  

•  git lfs checkout
  

•   git lfs pull
  

In the file found at "./configs/opencr/config.json" change the installed flag under app to false to load configs for Opencr

"app": {
    "port": 3000,
    "installed": false
}

Resetting and Clearing OpenCR

•   docker stop opencr opencr-fhir es
  

•   docker system prune --volumes
  

Local setup

• cd esplugin/string-similarity
  

• unzip string-similarity-scoring-0.0.6-es7.9.1.zip
  

Spin up the services

•   docker compose -f openelis-opencr-hie-docker-compose.yml up -d
  

You should be able to acces the OpenELIS ,OpenHIM , OpenCR and Hapi-Fhir instances at the following urls

Instance	URL	credentials (user : password)
OpenHIM	http://localhost:9000	root@openhim.org : openhim
OpenCR	http://localhost:3000/crux	root@intrahealth.org : intrahealth
OpenELIS	https://localhost/login	admin : adminADMIN!

Restart the Streaming pipeline to work Properly

After spinning up the Sigdep3 , restart the Streaming pipeline to Stream all Changes to the SHR (Fixed by adding depends-on meta in compose file)

•   docker restart streaming-pipeline
  

Configure OpenHIM URL for client registry module of OpenMRS

Set the CLIENTREGISTRY_SERVERURL, CLIENTREGISTRY_USERNAME, CLIENTREGISTRY_PASSWORD, CLIENTREGISTRY_IDENTIFIERROOT in the .env file Note that the Openhim should be up before starting the OpenMRS service. Currently this is ensured on local setup with the depends-on meta in the compose file

Possible challenges

Ensure the .db folder at the root has permissions to allow docker to write files

Running on gitpod Change the env var of es to have only - xpack.security.enabled=false - discovery.type=single-node and change the ulimit as ulimits: nofile: soft: 65536 hard: 65536
Follow the blog here: https://www.gitpod.io/blog/local-app to enable localhost on your machine

Incase spark image is failing. Consider upgrading the docker engine. See here

Deploying with ansible to remote server

Install ansible on the host machine following steps here https://docs.ansible.com/ansible/latest/installation_guide/installation_distros.html
Ensure the public key is already added to the remote server
Update the path to your private key on the variable ansible_ssh_private_key_file
Update the inventory.ini file with the host addresses
Run the command below in the distribution
Enter password of the private key when prompted

•   cd deployment
    ansible-playbook -i inventory.ini deployment.yml

Run the following command in the test folder using newman to preload the client registry

•   npm install -g newman
  

•   newman run postman_collection.json -e postman_environment.json --iteration-data pims_rule_test_dataset.csv --insecure