How to integrate FHIR with Apache Airflow

Apache Airflow supports the creation, scheduling, and monitoring of data engineering workflows. When paired with the CData JDBC Driver for FHIR, Airflow can work with live FHIR data. This article describes how to connect to and query FHIR data from an Apache Airflow instance and store the results in a CSV file.

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). Its built-in dynamic metadata querying allows you to work with and analyze FHIR data using native data types.

Configuring the Connection to FHIR

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.

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.

👁 Using the built-in connection string designer to generate a JDBC URL (fhir is shown.)

To host the JDBC driver in clustered environments or in the cloud, you will need a license (full or trial) and a Runtime Key (RTK). For more information on obtaining this license (or a trial), contact our sales team.

The following are essential properties needed for our JDBC connection.

Establishing a JDBC Connection within Airflow

1. Log into your Apache Airflow instance.
2. On the navbar of your Airflow instance, hover over Admin and then click Connections. 👁 Clicking connections
   
3. Next, click the + sign on the following screen to create a new connection.
4. In the Add Connection form, fill out the required connection properties:
   • Connection Id: Name the connection, i.e.: fhir_jdbc
   • Connection Type: JDBC Connection
   • Connection URL: The JDBC connection URL from above, i.e.: jdbc:fhir:RTK=5246...;URL=http://test.fhir.org/r4b/;ConnectionType=Generic;ContentType=JSON;AuthScheme=None;)
   • Driver Class: cdata.jdbc.fhir.FHIRDriver
   • Driver Path: PATH/TO/cdata.jdbc.fhir.jar
   👁 Add JDBC connection form
   
5. Test your new connection by clicking the Test button at the bottom of the form.
6. After saving the new connection, on a new screen, you should see a green banner saying that a new row was added to the list of connections: 👁 New connection added
   

Creating a DAG

A DAG in Airflow is an entity that stores the processes for a workflow and can be triggered to run this workflow. Our workflow is to simply run a SQL query against FHIR data and store the results in a CSV file.

1. To get started, in the Home directory, there should be an "airflow" folder. Within there, we can create a new directory and title it "dags". In here, we store Python files that convert into Airflow DAGs shown on the UI.
2. Next, create a new Python file and title it fhir_hook.py. Insert the following code inside of this new file:

   	import time
   	from datetime import datetime
   	from airflow.decorators import dag, task
   	from airflow.providers.jdbc.hooks.jdbc import JdbcHook
   	import pandas as pd
   
   	# Declare Dag
   	@dag(dag_id="fhir_hook", schedule_interval="0 10 * * *", start_date=datetime(2022,2,15), catchup=False, tags=['load_csv'])
   	
   	# Define Dag Function
   	def extract_and_load():
   	# Define tasks
   		@task()
   		def jdbc_extract():
   			try:
   				hook = JdbcHook(jdbc_conn_id="jdbc")
   				sql = """ select * from Account """
   				df = hook.get_pandas_df(sql)
   				df.to_csv("/{some_file_path}/{name_of_csv}.csv",header=False, index=False, quoting=1)
   				# print(df.head())
   				print(df)
   				tbl_dict = df.to_dict('dict')
   				return tbl_dict
   			except Exception as e:
   				print("Data extract error: " + str(e))
    
   		jdbc_extract()
    
   	sf_extract_and_load = extract_and_load()
   

3. Save this file and refresh your Airflow instance. Within the list of DAGs, you should see a new DAG titled "fhir_hook". 👁 New DAG added
   
4. Click on this DAG and, on the new screen, click on the unpause switch to make it turn blue, and then click the trigger (i.e. play) button to run the DAG. This executes the SQL query in our fhir_hook.py file and export the results as a CSV to whichever file path we designated in our code. 👁 Run the DAG
   
5. After triggering our new DAG, we check the Downloads folder (or wherever you chose within your Python script), and see that the CSV file has been created - in this case, account.csv. 👁 CSV created
   
6. Open the CSV file to see that your FHIR data is now available for use in CSV format thanks to Apache Airflow. 👁 CSV file with FHIR data.
   

More Information & Free Trial

Download a free, 30-day trial of the CData JDBC Driver for FHIR and start working with your live FHIR data in Apache Airflow. Reach out to our Support Team if you have any questions.