bulk_fhir_tools

README

Bulk FHIR Tools

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This repository contains bulk_fhir_fetch, an ingestion tool that connects to FHIR Bulk Data APIs and saves the FHIR to local disk or GCP's FHIR Store and BigQuery. bulk_fhir_fetch is feature rich with support for scheduling and incremental data pulls, integrations to GCP logging/metrics, fetching binary data referenced by FHIR DocumentReferences, rectifying invalid FHIR and more. Popular FHIR Bulk Data APIs bulk_fhir_fetch can ingest data from include:

• Medicare's Beneficiary Claims Data API (BCDA)
• The Cures Act §170.315(g)(10) regulation requires all US EHRs serve USCDI through a FHIR Bulk Data API

This is not an official Google product. If using these tools with protected health information (PHI), please be sure to follow your organization's policies with respect to PHI.

Overview

• cmd/bulk_fhir_fetch/: A program for fetching FHIR data from a FHIR Bulk Data API, and optionally saving to disk or sending to your FHIR Store. The tool is highly configurable via flags, and can support pulling incremental data only, among other features. See bulk_fhir_fetch configuration examples for details on how to use this program.
• bulkfhir/: A generic client package for interacting with FHIR Bulk Data APIs.
• analytics/: A folder with some analytics notebooks and examples.
• fhirstore/: A go helper package for uploading to FHIR store.
• fhir/: A go package with some helpful utilities for working with FHIR.

Set up bulk_fhir_fetch on GCP

The bulk_fhir_fetch command line program uses the bulkfhir/ client library to fetch FHIR data from a FHIR Bulk Data API.

There are three high level ways to set up this tool:

• On a GCP VM. This option is recommended for initial testing and exploration.
• With our Orchestration tooling that deploys on Cloud Batch using Cloud workflows, Cloud Scheduler, and Cloud Secret Manager. This is the recommended setup for production.
• Locally on your machine by following the Build instructions below.

By default logs and metrics will be written to STDOUT, but we documented how to send logs and set up dashboards in GCP.

bulk_fhir_fetch Configuration Examples

This section will detail common usage patterns for the bulk_fhir_fetch command line program using the BCDA Sandbox as an example. If you want to try this out without using real credentials, you can use the synthetic data sandbox credentials (client_id and client_secret) from the options listed here. You can check all of the various flag details by running ./bulk_fhir_fetch --help.

If using these tools with protected health information (PHI), please be sure to follow your organization's policies with respect to PHI.

• Fetch all BCDA data for your ACO to local NDJSON files:

  ./bulk_fhir_fetch \
    -client_id=YOUR_CLIENT_ID \
    -client_secret=YOUR_SECRET \
    -fhir_server_base_url="https://sandbox.bcda.cms.gov/api/v2" \
    -fhir_auth_url="https://sandbox.bcda.cms.gov/auth/token" \
    -output_dir="/path/to/store/output/data" \
  

• Rectify the data to pass R4 Validation. By default, the FHIR R4 Data returned by BCDA sandbox does not satisfy the default FHIR R4 profile at the time of this software release. bulk_fhir_fetch provides an option to tag the expected missing fields that BCDA does not map with an extension (if they are indeed missing) that will allow the data to pass R4 profile validation (and be uploaded to FHIR store, or other R4 FHIR servers). To do this, simply pass the following flag:

  -rectify=true
  

• Fetch all FHIR since some timestamp. This is useful if, for example, you only wish to fetch new FHIR since yesterday (or some other time). Simply pass a FHIR instant timestamp to the -since flag.

  -since="2021-12-09T11:00:00.123+00:00"
  

  Note that every time fetch is run, it will log the BCDA transaction time, which can be used in future runs of fetch to only get data since the last run. If you will be using fetch in this mode frequently, consider the since file option below which automates this behavior.

• Automatically fetch new FHIR since last successful run. The program provides a -since_file option, which the program uses to store and read BCDA timestamps from successful runs. When using this option, the fetch program will automatically read the latest timestamp from the since_file and use that to only fetch FHIR since that time. When completed successfully, it will write a new timestamp back out to that file, so that the next time fetch is run, only FHIR since that time will be fetched. The first time the program is run with -since_file it will fetch all historical FHIR from BCDA and initialize the since_file with the first timestamp.

  -since_file="path/to/some/file"
  

Do not run concurrent instances of fetch that use the same since file.

• Upload FHIR to a GCP FHIR Store:

  ./bulk_fhir_fetch \
    -client_id=YOUR_CLIENT_ID \
    -client_secret=YOUR_SECRET \
    -fhir_server_base_url="https://sandbox.bcda.cms.gov/api/v2" \
    -fhir_auth_url="https://sandbox.bcda.cms.gov/auth/token" \
    -output_dir="/path/to/store/output/data/" \
    -rectify=true \
    -enable_fhir_store=true \
    -fhir_store_gcp_project="your_project" \
    -fhir_store_gcp_location="us-east4" \
    -fhir_store_gcp_dataset_id="your_gcp_dataset_id" \
    -fhir_store_id="your_fhir_store_id"
  

  Note: If -enable_fhir_store=true specifying -output_dir is optional. If -output_dir is not specified, no NDJSON output will be written to local disk and the only output will be to FHIR store. If you are using an older version of the tool, use -output_prefix instead of -output_dir.

To set up the bulk_fhir_fetch program to run periodically on a GCP VM, take a look at the documentation. For a discussion on the different FHIR Store upload options see the performance and cost documentation.

Cloning at a pinned version

If cloning the repo for production use, we recommend cloning the repository at the latest released version, which can be found in the releases tab. For example for version v0.1.5:

git clone --branch v0.1.5 https://github.com/google/bulk_fhir_tools.git

Build

To build the program from source run the following from the root of the repository (note you must have Go installed):

go build cmd/bulk_fhir_fetch/bulk_fhir_fetch.go

This will build the bulk_fhir_fetch binary and write it out in your current directory.

Example Analytics

This repository also contains example analysis notebooks using synthetic data that showcase query patterns once the data is in FHIR Store and BigQuery.

Trademark

FHIR® is the registered trademark of HL7 and is used with the permission of HL7.