Configurations

This utility uses two configuration files

• App Config

• Run Config

App Config

The App Config file contains app level customisations including FHIR server and database server details;

FHIR Server Configuration

The following FHIR server connection details needs to be updated in the configuration file to perfrm CRUD operations on the FHIR resources. An outline of the configuration for specifying the FHIR server is given below;

fhir_server_base_url: '<FHIR Server Base URL>'

Note

There are multiple test servers avaialble freely online to get started with. These servers are listed in this link: https://confluence.hl7.org/display/FHIR/Public+Test+Servers. You can use one of these servers if you do not have access for your own FHIR server.

An example configuration using one of the public FHIR server is given below;

fhir_server_base_url: 'https://hapi.fhir.org/baseR5/'

Here in this case, I have selected a public HAPI-FHIR R5 server.

Database Server Configuration

The following database server connection details needs to be updated in the configuration file to perform CRUD operations on the OMOP-CDM standard schema;

# database connection details
db_details = {
    "sql_host_name": '<Host Name>',
    "sql_port_number": '<Port Number>',
    "sql_user_name": '<User Name>',
    "sql_password": '<Password>',
    "sql_db_name": '<DB Name>',
}

Run Config

The Run Config file contains step-by-step instructions on how to run this application.

It can perform 4 different functionalities;

• OMOP-to-FHIR

• FHIR-to-OMOP

• GTF-to-FHIR

• FASTA-to-FHIR