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Load FHIR Data to a Database Using Embulk


Use CData JDBC drivers with the open source ETL/ELT tool Embulk to load FHIR data to a database.

Embulk is an open source bulk data loader. When paired with the CData JDBC Driver for FHIR, Embulk easily loads data from FHIR to any supported destination. In this article, we explain how to use the CData JDBC Driver for FHIR in Embulk to load FHIR data to a MySQL dtabase.

With built-in optimized data processing, the CData JDBC Driver offers unmatched performance for interacting with live FHIR data. When you issue complex SQL queries to FHIR, the driver pushes supported SQL operations, like filters and aggregations, directly to FHIR and utilizes the embedded SQL engine to process unsupported operations client-side (often SQL functions and JOIN operations).

Configure a JDBC Connection to FHIR Data

Before creating a bulk load job in Embulk, note the installation location for the JAR file for the JDBC Driver (typically C:\Program Files\CData\CData JDBC Driver for FHIR\lib).

Embulk supports JDBC connectivity, so you can easily connect to FHIR and execute SQL queries. Before creating a bulk load job, create a JDBC URL for authenticating with FHIR.

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.

Built-in Connection String Designer

For assistance in constructing the JDBC URL, use the connection string designer built into the FHIR JDBC Driver. Either double-click the JAR file or execute the jar file from the command-line.

java -jar cdata.jdbc.fhir.jar

Fill in the connection properties and copy the connection string to the clipboard.

Below is a typical JDBC connection string for FHIR:

jdbc:fhir:URL=http://test.fhir.org/r4b/;ConnectionType=Generic;ContentType=JSON;AuthScheme=None;

Load FHIR Data in Embulk

After installing the CData JDBC Driver and creating a JDBC connection string, install the required Embulk plugins.

Install Embulk Input & Output Plugins

  1. Install the JDBC Input Plugin in Embulk.
    https://github.com/embulk/embulk-input-jdbc/tree/master/embulk-input-jdbc
    2. embulk gem install embulk-input-jdbc
  2. In this article, we use MySQL as the destination database. You can also choose SQL Server, PostgreSQL, or Google BigQuery as the destination using the output Plugins.
    https://github.com/embulk/embulk-output-jdbc/tree/master/embulk-output-mysql embulk gem install embulk-output-mysql

With the input and output plugins installed, we are ready to load FHIR data into MySQL using Embulk.

Create a Job to Load FHIR Data

Start by creating a config file in Embulk, using a name like fhir-mysql.yml.

  1. For the input plugin options, use the CData JDBC Driver for FHIR, including the path to the driver JAR file, the driver class (e.g. cdata.jdbc.fhir.FHIRDriver), and the JDBC URL from above
  2. For the output plugin options, use the values and credentials for the MySQL database

Sample Config File (fhir-mysql.yml)

in: type: jdbc driver_path: C:\Program Files\CData[product_name] 20xx\lib\cdata.jdbc.fhir.jar driver_class: cdata.jdbc.fhir.FHIRDriver url: jdbc:fhir:URL=http://test.fhir.org/r4b/;ConnectionType=Generic;ContentType=JSON;AuthScheme=None; table: "Patient" out: type: mysql host: localhost database: DatabaseName user: UserId password: UserPassword table: "Patient" mode: insert

After creating the file, run the Embulk job.

embulk run fhir-mysql.yml

After running the the Embulk job, find the Salesforce data in the MySQL table.

Load Filtered FHIR Data

In addition to loading data directly from a table, you can use a custom SQL query to have more granular control of the data loaded. You can also perform increment loads by setting a last updated column in a SQL WHERE clause in the query field.

in: type: jdbc driver_path: C:\Program Files\CData[product_name] 20xx\lib\cdata.jdbc.fhir.jar driver_class: cdata.jdbc.fhir.FHIRDriver url: jdbc:fhir:URL=http://test.fhir.org/r4b/;ConnectionType=Generic;ContentType=JSON;AuthScheme=None; query: "SELECT Id, [name-use] FROM Patient WHERE [RecordId] = 1" out: type: mysql host: localhost database: DatabaseName user: UserId password: UserPassword table: "Patient" mode: insert

More Information & Free Trial

By using CData JDBC Driver for FHIR as a connector, Embulk can integrate FHIR data into your data load jobs. And with drivers for more than 200+ other enterprise sources, you can integrate any enterprise SaaS, big data, or NoSQL source as well. Download a 30-day free trial and get started today.