$export
FHIR Bulk Data Export
Last updated
FHIR Bulk Data Export
Last updated
The feature allows to export FHIR resources in ndjson format.
Aidbox supports patient-level and group-level export. When the export request is submitted the server returns URL to check the export status. When export is finished, status endpoint returns URLs to download resources.
Only one export process can be run at the same time. If you try to submit an export request while there is active export, you get 429 Too Many Requests error.
Aidbox can export data to GCP or AWS cloud. Export results will be in <datetime>_<uuid> folder on the bucket.
and that has read and write access to the bucket.
in Aidbox. Example:
Set the following environment variables:
box_bulk__storage_backend=gcp — backend for export
box_bulk__storage_gcp_service__account — id of the GcpServiceAccount resource
box_bulk__storage_gcp_bucket — bucket name
Create AzureAccount resource in Aidbox.
Create AzureContainer resource in Aidbox.
Set the following environment variables:
box_bulk__storage_backend=azure — backend for export
box_bulk__storage_azure_container=smartboxexporttestcontainer — id of the AzureContainer resource
Set the following environment variables:
box_bulk__storage_backend=aws — backend for export
box_bulk__storage_aws_account — id of the AwsAccount resource
box_bulk__storage_aws_bucket — bucket name
To start export make a request to /fhir/Patient/$export:
Rest console
Make a request to the export status endpoint to check the status:
Rest console
Delete request on the export status endpoint cancels export.
Rest console
To start export make a request to /fhir/Group/<group-id>/$export:
Rest console
Make a request to the export status endpoint to check the status:
Rest console
Delete request on the export status endpoint cancels export.
Rest console
System-level export exports data from a FHIR server, whether or not it is associated with a patient. You may restrict the resources returned using the _type parameter.
Limitation: export operation will work for standard FHIR resources only, not for custom resources.
Delete request on the export status endpoint cancels export.
Rest console
$export operation expects you setup external storage, Aidbox exports data into. In most cases issues with $exoprt are the consequence of incorrect Adbox configuration. In order to exclude this run the following rpc:
Normally, you should see something like this in response body:
This means, that integration between Aidbox and your storage setup correctly.
What other responses you may see
Storage-type not specified error means, box_bulk__storage_backend env variable wasn't setup. Valid values are aws and gcp.
unsupported storage-type error means, box_bulk__storage_backend env variable has invalid value. Valid values are aws and gcp.
This error means account is not specified
box_bulk__storage_gcp_service__account for GCP
box_bulk__storage_aws_account for AWS
This means there is no account for aws or gcp
This error means, bucket is not specified.
Specify box_bulk__storage_gcp_bucket for GCP.
Specify box_bulk__storage_aws_bucket for AWS.
and .
Create and that has read and write access to the bucket.
in Aidbox. Example:
| Parameter | Description |
|---|
Patient-level export exports all Patient resources and resources associated with them. This association is defined by .
Group-level export exports all Patient resources that belong to the specified group and resources associated with them. Characteristics of the group are not exported. This association is defined by .
Create or , depending on your config.
| Specifies format in which the server generates files. The following formats are supported:
|
| Includes only the specified types. This list is comma-separated. |
| Includes only resources changed after the specified time. |
| Export data that belongs only to listed patient. Format: comma-separated list of patient ids. Available only for patient-level export. |