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Export your FHIR data

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By using the bulk $export operation in the FHIR® service, you can export data as described in the HL7 FHIR Bulk Data Access specification.

Before you attempt to use $export, make sure that your FHIR service is configured to connect with an Azure Data Lake Storage Gen2 account. To configure export settings and create a Data Lake Storage Gen2 account, refer to Configure settings for export.

Call the $export endpoint

After you set up the FHIR service to connect with a Data Lake Storage Gen2 account, you can call the $export endpoint, and the FHIR service will export data into an Azure Blob Storage container inside the storage account. The following example request exports all resources into a container, which is specified by name ({{containerName}}). Note: You must create the container in the Data Lake Storage Gen2 account before hand if you want to specify the {{containerName}} in the request.

GET {{fhirurl}}/$export?_container={{containerName}}

If you don't specify a container name in the request (for example, by calling GET {{fhirurl}}/$export), a new container with an autogenerated name will be created for the exported data.

For general information about the FHIR $export API spec, see the HL7 FHIR Export Request Flow documentation.

The FHIR service supports $export at the following levels:

  • System: GET {{fhirurl}}/$export
  • Patient: GET {{fhirurl}}/Patient/$export
  • Group of patients*: GET {{fhirurl}}/Group/[ID]/$export
    *The FHIR service exports all referenced resources but doesn't export the characteristics of the group resource itself.

Data is exported in multiple files. Each file contains resources of only one type. The number of resources in an individual file is. The maximum number of resources is based on system performance. It's currently set to 5,000, but can change. The result is that you might get multiple files for a resource type. The file names follow the format <resourceName>-<number>-<number>.ndjson. The order of the files isn't guaranteed to correspond to any ordering of the resources in the database.

Note

Patient/$export and Group/[ID]/$export can export duplicate resources if a resource is in multiple groups or in a compartment of more than one resource.

In addition to checking the presence of exported files in your storage account, you can check your $export operation status through the URL in the Content-Location header that's returned in the FHIR service response. For more information, see the Bulk Data Status Request documentation from HL7.

Export your FHIR data to Data Lake Storage Gen2

Currently, the FHIR service supports $export to Data Lake Storage Gen2 accounts, with the following limitations:

  • Data Lake Storage Gen2 provides hierarchical namespaces, yet there isn't a way to target $export operations to a specific subdirectory within a container. The FHIR service can specify only the destination container for the export, where a new folder for each $export operation is created.
  • After an $export operation is complete and all data has been written inside a folder, the FHIR service doesn't export anything to that folder again. Subsequent exports to the same container will be inside a newly created folder.

To export data to a storage account behind a firewall, see Configure settings for export.

Settings and parameters

Headers

Two required header parameters must be set for $export jobs. The values are set according to the current HL7 $export specification.

  • Accept: application/fhir+json
  • Prefer: respond-async

Query parameters

The FHIR service supports the following query parameters for filtering exported data. All these parameters are optional.

Query parameter Defined by the FHIR specification? Description
_outputFormat Yes Currently supports three values to align to the FHIR specification: application/fhir+ndjson, application/ndjson, or just ndjson. All export jobs return .ndjson files and the passed value has no effect on code behavior.
_since Yes Allows you to export only resources that have been modified since the specified time.
_type Yes Allows you to specify which types of resources to be included. For example, _type=Patient would return only patient resources.
_typeFilter Yes To request finer-grained filtering, you can use _typeFilter along with the _type parameter. The value of the _typeFilter parameter is a comma-separated list of FHIR queries that further limit the results.
_container No Specifies the name of the container in the configured storage account where the data should be exported. If a container is specified, the data is exported into a folder in that container. If the container isn't specified, the data is exported to a new container with an autogenerated name.
_till No Allows you to export resources that have been modified up to the specified time. This parameter is applicable only with System-Level export. In this case, if historical versions haven't been disabled or purged, export guarantees a true snapshot view.
includeAssociatedData No Allows you to export history and soft deleted resources. This filter doesn't work with '_typeFilter' query parameter. Include value as '_history' to export history/non-latest versioned resources. Include value as '_deleted' to export soft deleted resources.

Note

Only storage accounts in the same subscription as the FHIR service are allowed to be registered as the destination for $export operations.

Troubleshoot

The following information can help you resolve problems with exporting FHIR data.

Jobs stuck in a bad state

In some situations, there's a potential for a job to be stuck in a bad state while the FHIR service is attempting to export data. This can occur especially if the Data Lake Storage Gen2 account permissions haven't been set up correctly.

One way to check the status of your $export operation is to go to your storage account's storage browser and see whether any .ndjson files are present in the export container. If the files aren't present and no other $export jobs are running, it's possible that the current job is stuck in a bad state. In this case, you can cancel the $export job by sending a DELETE request to the URL provided in the Content-Location header to cancel the request

Note

In the FHIR service, the default time for an $export operation to idle in a bad state is 10 minutes before the service stops the operation and moves to a new job.

Next steps

In this article, you've learned about exporting FHIR resources by using the $export operation. For information about how to set up and use other options for export, see:

Export de-identified data

Copy data from the FHIR service to Azure Synapse Analytics

Note

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