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Get the Report →How to create FHIR federated tables in MySQL
Use the SQL Gateway and the ODBC Driver to set up federated tables for FHIR data in MySQL .
You can use the SQL Gateway to configure a MySQL remoting service and set up federated tables for FHIR data. The service is a daemon process that provides a MySQL interface to the CData ODBC Driver for FHIR: After you have started the service, you can create a server and tables using the FEDERATED Storage Engine in MySQL. You can then work with FHIR data just as you would local MySQL tables.
Connect to FHIR Data
If you have not already done so, provide values for the required connection properties in the data source name (DSN). You can use the built-in Microsoft ODBC Data Source Administrator to configure the DSN. This is also the last step of the driver installation. See the "Getting Started" chapter in the help documentation for a guide to using the Microsoft ODBC Data Source Administrator to create and configure a DSN.
Set URL to the Service Base URL of the FHIR server. This is the address where the resources are defined in the FHIR server you would like to connect to. Set ConnectionType to a supported connection type. Set ContentType to the format of your documents. Set AuthScheme based on the authentication requirements for your FHIR server.
Generic, Azure-based, AWS-based, and Google-based FHIR server implementations are supported.
Sample Service Base URLs
- Generic: http://my_fhir_server/r4b/
- Azure: https://MY_AZURE_FHIR.azurehealthcareapis.com/
- AWS: https://healthlake.REGION.amazonaws.com/datastore/DATASTORE_ID/r4/
- Google: https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID/fhir/
Generic FHIR Instances
The product supports connections to custom instances of FHIR. Authentication to custom FHIR servers is handled via OAuth (read more about OAuth in the Help documentation. Before you can connect to custom FHIR instances, you must set ConnectionType to Generic.
Configure the SQL Gateway
See the SQL Gateway Overview to set up connectivity to FHIR data as a virtual MySQL database. You will configure a MySQL remoting service that listens for MySQL requests from clients. The service can be configured in the SQL Gateway UI.
Create a FEDERATED Server and Tables for FHIR Data
After you have configured and started the service, create a FEDERATED server to simplify the process of creating FEDERATED tables:
Create a FEDERATED Server
The following statement will create a FEDERATED server based on the ODBC Driver for FHIR. Note that the username and password of the FEDERATED server must match a user account you defined on the Users tab of the SQL Gateway.
CREATE SERVER fedFHIR FOREIGN DATA WRAPPER mysql OPTIONS (USER 'sql_gateway_user', PASSWORD 'sql_gateway_passwd', HOST 'sql_gateway_host', PORT ####, DATABASE 'CData FHIR Sys');
Create a FEDERATED Table
To create a FEDERATED table using our newly created server, use the CONNECTION keyword and pass the name of the FEDERATED server and the remote table (Patient). Refer to the following template for the statement to create a FEDERATED table:
CREATE TABLE fed_patient ( ..., id TYPE(LEN), [name-use] TYPE(LEN), ..., ) ENGINE=FEDERATED DEFAULT CHARSET=latin1 CONNECTION='fedFHIR/patient';
NOTE: The table schema for the FEDERATED table must match the remote table schema exactly. You can always connect directly to the MySQL remoting service using any MySQL client and run a SHOW CREATE TABLE query to get the table schema.
Execute Queries
You can now execute queries to the FHIR FEDERATED tables from any tool that can connect to MySQL, which is particularly useful if you need to JOIN data from a local table with data from FHIR. Refer to the following example:
SELECT fed_patient.id, local_table.custom_field FROM local_table JOIN fed_patient ON local_table.foreign_id = fed_patient.id;