How to load FHIR data into Elasticsearch via Logstash

Elasticsearch is a popular distributed full-text search engine. By centrally storing data, you can perform ultra-fast searches, fine-tuning relevance, and powerful analytics with ease. Elasticsearch has a pipeline tool for loading data called "Logstash". You can use CData JDBC Drivers to easily import data from any data source into Elasticsearch for search and analysis.

This article explains how to use the CData JDBC Driver for FHIR to load data from FHIR into Elasticsearch via Logstash.

Using CData JDBC Driver for FHIR with Elasticsearch Logstash

• Install the CData JDBC Driver for FHIR on the machine where Logstash is running.
• The JDBC Driver will be installed at the following path (the year part, e.g. 20XX, will vary depending on the product version you are using). You will use this path later. Place this .jar file (and the .lic file if it's a licensed version) in Logstash.
  C:\Program Files\CData\CData JDBC Driver for FHIR 20XX\lib\cdata.jdbc.fhir.jar
  
• Next, install the JDBC Input Plugin, which connects Logstash to the CData JDBC driver. The JDBC Plugin comes by default with the latest version of Logstash, but depending on the version, you may need to add it.
  https://www.elastic.co/guide/en/logstash/5.4/plugins-inputs-jdbc.html
• Move the CData JDBC Driver’s .jar file and .lic file to Logstash's "/logstash-core/lib/jars/".

Sending FHIR data to Elasticsearch with Logstash

Now, let's create a configuration file for Logstash to transfer FHIR data to Elasticsearch.

• Write the process to retrieve FHIR data in the logstash.conf file, which defines data processing in Logstash. The input will be JDBC, and the output will be Elasticsearch. The data loading job is set to run at 30-second intervals.
• Set the CData JDBC Driver's .jar file as the JDBC driver library, configure the class name, and set the connection properties to FHIR in the form of a JDBC URL. The JDBC URL allows detailed configuration, so please refer to the product documentation for more specifics.

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.

Executing data movement with Logstash

Now let's run Logstash using the created "logstash.conf" file.

 logstash-7.8.0\bin\logstash -f logstash.conf

A log indicating success will appear. This means the FHIR data has been loaded into Elasticsearch.

For example, let's view the data transferred to Elasticsearch in Kibana.

 GET fhir_table/_search
 {
 "query": {
 "match_all": {}
 }
 }

We have confirmed that the data is stored in Elasticsearch.

By using the CData JDBC Driver for FHIR with Logstash, it functions as a FHIR connector, making it easy to load data into Elasticsearch. Please try the 30-day free trial.