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Jenkinsfile Updated Jenkinsfile to define environment variables. Feb 18, 2019
README.md
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README.md

OMH-on-FHIR

Implementation of the OMH-on-FHIR application described here: https://healthedata1.github.io/mFHIR/#smart-app-workflow

Top Level Project Directories

omhclient           --> AngularJS project for the OMH on FHIR user interface
omhserver           --> Spring Boot project for the OMH on FHIR web service
docker-compose.yml  --> Docker Compose file to create the service stack for the application
Jenkinsfile         --> Jenkinsfile to tell Jenkins how to build the application
README.md           --> This file

Project Containers

The application uses Docker Compose to create a service stack for each component of the application. It creates the following containers:

Container Name in Docker Compose Description
Shimmer Resource Server resource-server The container running the Shimmer resource server which makes Shimmer API calls availble to other containers running in the Docker Compose service stack
Shimmer Database mongo The container running the Mongo database used by Shimmer
Shimmer Console console The container running the Shimmer console
OMH Server Database mdata-db The container running the Postgres database used by the OMH Web Service
OMH Web Service mdata-app The container running the webservice endpoints for Shimmer Authentication, DocumentReference, Binary, and Observation queries
OMH Client omh-on-fhir-client The container running the User Interface for the OMH on FHIR application

Environment Variables

The following environment variables need to be set for the containers

resource-server

Variable Description
OPENMHEALTH_SHIMMER_DATA_PROVIDER_REDIRECT_BASE_URL Base URL for Shimmer to use for OAuth redirects
OPENMHEALTH_SHIM_FITBIT_CLIENT_ID Client ID for Shimmer to use for FitBit Authentication
OPENMHEALTH_SHIM_FITBIT_CLIENT_SECRET Client Secret for Shimmer to use for FitBit authentication
OPENMHEALTH_SHIM_GOOGLEFIT_CLIENT_ID Client ID for Shimmer to use for Google Fit authentication
OPENMHEALTH_SHIM_GOOGLEFIT_CLIENT_SECRET Client secret for Shimmer to use for Google Fit authentication

For run time they can be set in the ./shimmer-resource-server.env file or explicitly in a Dockerfile or docker-compose.yml

mongo

none

console

none

mdata-db

Variable Description
POSTGRES_DB The name of the database to create/use
POSTGRES_USER The name of the database user
POSTGRES_PASSWORD The password for the database user

For run time they can be set in the ./omhserver/postgres.env file or explicitly in a Dockerfile or docker-compose.yml

mdata-app

Variable Description
SHIMMER_SERVER_URL The URL to the Shimmer resource server
SHIMMER_REDIRECT_URL The redirect URL to pass to the Shimmer API. It contains the URL to the mdata-app /authorize/fitbit/callback endpoint that handles successful user authentication. Shimmer only redirects to this URL after successful authentication.
OMH_ON_FHIR_CALLBACK The URL to the OMH on FHIR UI application to use after successful Shimmer authentication.
OMH_ON_FHIR_LOGIN The URL to the user interface that handles login to Fitbit and Google fit.

For run time they can be set in the ./omhserver/omh-server.env file or explicitly in a Dockerfile or docker-compose.yml

omh-on-fhir-client

none

To Run

Do the following to run the application:

  1. Create a ./shimmer-resource-server.env file with environment variable to configure the Shimmer server, https://github.com/openmhealth/shimmer/blob/e3fef06d4d7d5f93d2a45e7656a823889f247499/resource-server.env, Place the file in the root directory of the project.
  2. Create a ./omhserver/postgres.env file with environment variables to configure the Postgress database.
  3. Create a ./omhserver/omh-server.env file with environment variables to configure the OMH on Fhir web service.
  4. From the root directory of the project run docker-compose up -d

User Interface Constraints

  • DocumentReference search can only support two date parameters, one for the start date and one for the end date. If the start date uses a prefix it must be ge. If the end date uses a prefix it must be le. The application only searches for documents between the specified date ranges.

mdata-app web service API

Swagger is used to document the endpoints made available by the mdata-app. Use the following URLs to view details on the web service endpoints.

  • JSON - <server_dns_name>/mdata/v2/api-docs
  • UI - <server_dns_name>/mdata/swagger-ui.html#/

Reference Deployment

A reference deployment of the application can be found here: https://launch.smarthealthit.org/?auth_error=&fhir_version_1=r2&fhir_version_2=r3&iss=&launch_ehr=1&launch_url=https%3A%2F%2Fapps.hdap.gatech.edu%2Fomhonfhir%2Flaunch&patient=&prov_skip_auth=1&provider=&pt_skip_auth=1&pt_skip_login=0&public_key=&sb=&sde=&sim_ehr=1&token_lifetime=15&user_pt=undefined It uses the SMART Application Launcher to simulate an EHR launch.

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