Welcome to OMOPonFHIR Github Repository
This repository is an installable server deployment package that locks down the version of included components (using submodules). Please use the following step to compile and deploy the server. You may need to customize some of the environment variables.
Note: If you want to see current snapshots of OMOPonFHIR components or other versions of FHIR and OMOP, please visit the OMOPonFHIR GitHub organization at https://github.com/omoponfhir/
This package is tested with Google Big Query instance. And, the server supports mapping for FHIR R4 and OMOP v5.3. Please see omopv5_3_setup/ folder for some help on ddls for extra tables/views. Database ddls are also included.
**Note:** This repository contains submodules of anoter repositories that are needed. If you want to participate in
development and contribute, please use the repositories directly as this submodule points to a certain commit point.
Refer the follow repositories and use the latest to work on the code.
- path = omoponfhir-omopv5-sql
- url = https://github.com/omoponfhir/omoponfhir-omopv5-sql.git
- branch = 5.3.1
- path = omoponfhir-omopv5-r4-mapping
- url = https://github.com/omoponfhir/omoponfhir-omopv5-r4-mapping.git
- branch = sqlRender
- path = omoponfhir-r4-server
- url = https://github.com/omoponfhir/omoponfhir-r4-server.git
- branch = sqlRender
Download the package
git clone --recurse https://github.com/omoponfhir/omoponfhir-main-r4-sql.git
cd omoponfhir-main-r4-sql/
mvn clean install
cd omoponfhir-r4-server/target/
scp omoponfhir-r4-server.war <vm url>:omoponfhir-r4-server.war
Deploy to tomcat
cp omoponfhir-r4-server.war <tomcat_directory>/webapps/
cd <tomcat_directory>/bin
vi setenv.sh
Deploy using Docker
sudo docker build -t omoponfhir .
sudo docker run --name omoponfhir -p 8080:8080 -d omoponfhir:latest
Configuration of webapp
In setenv.sh file, add the following environment variables. Change the values for your environment
export JDBC_URL="jdbc:postgresql://url"
export JDBC_USERNAME="<your username of JDBC DB instance>"
export JDBC_PASSWORD="<your password of JDBC DB instance>"
export JDBC_DRIVER="<DB driver class>"
export SMART_INTROSPECTURL="<your_omoponfhir_root_server_NOT_a_fhir_url_base, eg: localhost:8080/omoponfhir-dstu2-server/>/smart/introspect"
export SMART_AUTHSERVERURL="<your_omoponfhir_root_server_NOT_a_fhir_url_base>/smart/authorize"
export SMART_TOKENSERVERURL="<your_omoponfhir_root_server_NOT_a_fhir_url_base>/smart/token"
export AUTH_BEARER="<any value>"
export AUTH_BASIC="<username_you_want>:<password_you_want>"
export FHIR_READONLY="<True or False>"
export SERVERBASE_URL="<your fhir base url, eg: http://localhost:8080/omoponfhir-dstu2-server/fhir/>"
export LOCAL_CODEMAPPING_FILE_PATH="<whatever the path you want to put your local mapping file. eg: /temp/my_local_code or none>"
export MEDICATION_TYPE="code"
export TARGETDATABASE="<SqlRenderTargetDialect value such as bigquery or postgresql. If you leave this empty, it will be postgresql. Use string from sqlRender>"
export OMOPONFHIR_NAME="OMOP v5.3.1 on FHIR R4"
export BIGQUERYDATASET="<BigQuery Dataset Name. It will be ignored if TARGETDATABASE is not bigquery>"
export BIGQUERYPROJECT="<BigQuery Project Name. It will be ignored if TARGETDATABASE is not bigquery>"
Docker deployment
This is not yet tested and validated. The same environment variables are applied here. The environment variable must be defined either using Dockerfile or docker command line when the docker image is instantiated to start running.