leap-fhir-seed-data

This repository contains data load mechanisms for populating a new instance of LEAP HAPI-FHIR JPAServer version 4.1.0. It utilizes Postman version 8.10.0 to simplify the bulk loading of Organization, Practitioners, Questionnaires, and our test Patients clinical records. There are other freely available tools for performing this task. This is just one example we have setup for you.

Steps For Bulk Data Load

Step #1 Check out this repository:

> git clone https://github.com/sdhealthconnect/leap-fhir-seed-data.git

Step #2 Install Postman

• Download and install Postman desktop for your OS platform at postman.com. Postman.com provides a "Free" community addition plan for up to 3 team members.

Step #3 Setup Postman

• Create a workspace for this activity. Name it LEAP.

• Import Enviroment File {clone directory}/leap-fhir-seed-data/src/main/resources/fhir-seed-data-environment.postman_environment.json

• Modify Enviroment Variables for your working enviroment.
  You will need to change the values for you SEED_DATA_DIR and HAPI_FHIR_URL they are currently set as.

SEED_DATA_DIR=/Users/duanedecouteau/leap-fhir-seed-data/seed-data

HAPI_FHIR_URL=http://34.94.253.50:8080/hapi-fhir-jpaserver/fhir/

• Set Environment

To

• Modify your settings to allow you to process files outside of your LEAP workspace.

• Import FHIR Seed Data Postman Collection File {clone directory}/leap-fhir-seed-data/src/main/resources/postman-collection/fhir-seed-data-collection.postman_collection.json

Step #4 Run Postman Collection

• This will load base LEAP FHIR Resources and the generated clincial history of 10 test patients created using Synthea at https://synthea.mitre.org/downloads. This will take some time.

Steps for Loading Informed Consent Experimental Use Cases

Step #1 - Modify application-test.yaml with your HAPI FHIR endpoint. This file is located in the folder {clone directory}/src/test/resources/config.

hapi-fhir:
  url: ${HAPI_FHIR_URL:https://sdhc-hapi-fhir-leap-wafxyq4bza-uc.a.run.app/fhir/}

Step #2 - Run Load Tests

• These tests will load ResearchStudy for Pre-Diabetics, identify and create ResearchSubject as potential candiates, and load a MedicationRequest for all patients that requires informed consent.

> cd {clone directory}/leap-fhir-seed-data
> mvn test

Post Load Patient-User Provisioning

• Patient Users of the LEAP Consent UI require their accounts to be mapped to their FHIR patient resource on the consent repositiory. This is done for you as an automated function provided to admin user on our demonstration platform. For more info on this refer to https://github.com/sdhealthconnect/leap-consent-ui#readme.

Refreshing Data

If you wish to reload your hapi-fhir-jpaserver instance. Perform the following;

• 1 Shutdown your hapi fhir instance, if using docker the command would be similar to

> docker stop hapi-fhir-jpaserver

• 2 Log into your mysql instance, and drop hapi database, again if using docker and mysql the command would be similar to

>  docker exec -it {container id} bash
>  mysql -u root -ppassword

mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| hapi               |
| information_schema |
| mysql              |
| performance_schema |
| sys                |
+--------------------+
5 rows in set (0.00 sec)

mysql> drop database hapi;
mysql> exit
> exit

• 3 Restart hapi-fhir-jpaserver. Again if using docker the command would be similar to;

> docker start hapi-fhir-jpaserver

If your hapi-fhir-jpaserver is configured correctly it will automatically recreate the database and its tables on first request to base URL.

Redo Steps.

• Bulk Load - Step #4 Run Postman Collection
• Experimental Use Cases Load - Step #2 Run Load Tests