This page explains how to export FHIR resources to BigQuery for exploration and analysis.
Setting BigQuery permissions
Before exporting FHIR resources to BigQuery, you must grant additional permissions to the Cloud Healthcare Service Agent service account. For more information, see FHIR store BigQuery permissions.
Exporting FHIR resources
The following samples show how to export FHIR resources to a
BigQuery table. For more information, see
projects.locations.datasets.fhirStores.export.
curl command
To export FHIR resources, make a POST request and provide the name of
the parent dataset, the name of the FHIR store, the name of an existing
BigQuery dataset, the name of the project that owns the
BigQuery dataset, and an access token. The operation outputs
one BigQuery table for each resource type in the FHIR store.
The following sample shows a POST request using curl.
curl -X POST \
-H "Authorization: Bearer "$(gcloud auth print-access-token) \
-H "Content-Type: application/json; charset=utf-8" \
--data "{
'bigqueryDestination': {
'datasetUri': 'bq://PROJECT_ID .DATASET_ID '
}
}" "https://healthcare.googleapis.com/v1beta1/projects/PROJECT_ID /locations/REGION /datasets/DATASET_ID /fhirStores/FHIR_STORE_ID :export"
If the request is successful, the server returns a 200 OK HTTP status code
and the response in JSON format:
200 OK
{
"name": "projects/PROJECT_ID/locations/REGION/datasets/DATASET_ID/operations/OPERATION_NAME"
}
The response contains an operation name. You can use the
Operation get method
to track the status of the operation:
curl -X GET \
-H "Authorization: Bearer "$(gcloud auth print-access-token) \
"https://healthcare.googleapis.com/v1beta1/projects/PROJECT_ID /locations/REGION /datasets/DATASET_ID /operations/OPERATION_NAME "
If the request is successful, the server returns a 200 OK HTTP status code
and a response with the status of the operation in JSON format:
200 OK
{
"name": "projects/PROJECT_ID/locations/REGION/datasets/DATASET_ID/operations/OPERATION_NAME",
"metadata": {
"@type": "type.googleapis.com/google.cloud.healthcare.v1beta1.OperationMetadata",
"apiMethodName": "google.cloud.healthcare.v1beta1.fhir.FhirService.ExportResources",
"createTime": "2018-01-01T00:00:00Z",
"endTime": "2018-01-01T00:00:00Z"
},
"done": true,
"response": {
"@type": "type.googleapis.com/google.cloud.healthcare.v1beta1.fhir.rest.ExportResourcesResponse",
"name": "projects/PROJECT_ID/locations/REGION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID",
"resourceCount": "RESOURCE_COUNT"
}
}
PowerShell
To export FHIR resources, make a POST request and provide the name of
the parent dataset, the name of the FHIR store, the name of an existing
BigQuery dataset, the name of the project that owns the
BigQuery dataset, and an access token. The operation outputs
one BigQuery table for each resource type in the FHIR store.
The following sample shows a POST request using Windows PowerShell.
$cred = gcloud auth print-access-token
$headers = @{ Authorization = "Bearer $cred" }
Invoke-WebRequest `
-Method Post `
-Headers $headers `
-ContentType: "application/json; charset=utf-8" `
-Body "{
'bigqueryDestination': {
'datasetUri': 'bq://PROJECT_ID .DATASET_ID '
}
}" `
-Uri "https://healthcare.googleapis.com/v1beta1/projects/PROJECT_ID /locations/REGION /datasets/DATASET_ID /fhirStores/FHIR_STORE_ID :export" | Select-Object -Expand Content
If the request is successful, the server returns a 200 OK HTTP status code
and the response in JSON format:
200 OK
{
"name": "projects/PROJECT_ID/locations/REGION/datasets/DATASET_ID/operations/OPERATION_NAME"
}
The response contains an operation name. You can use the
Operation get method
to track the status of the operation:
$cred = gcloud auth print-access-token
$headers = @{ Authorization = "Bearer $cred" }
Invoke-WebRequest `
-Method Get `
-Headers $headers `
-Uri "https://healthcare.googleapis.com/v1beta1/projects/PROJECT_ID /locations/REGION /datasets/DATASET_ID /operations/OPERATION_NAME " | Select-Object -Expand Content
If the request is successful, the server returns a 200 OK HTTP status code
and a response with the status of the operation in JSON format:
200 OK
{
"name": "projects/PROJECT_ID/locations/REGION/datasets/DATASET_ID/operations/OPERATION_NAME",
"metadata": {
"@type": "type.googleapis.com/google.cloud.healthcare.v1beta1.OperationMetadata",
"apiMethodName": "google.cloud.healthcare.v1beta1.fhir.FhirService.ExportResources",
"createTime": "2018-01-01T00:00:00Z",
"endTime": "2018-01-01T00:00:00Z"
},
"done": true,
"response": {
"@type": "type.googleapis.com/google.cloud.healthcare.v1beta1.fhir.rest.ExportResourcesResponse",
"name": "projects/PROJECT_ID/locations/REGION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID",
"resourceCount": "RESOURCE_COUNT"
}
}
Troubleshooting FHIR export requests
If errors occur during a FHIR export request, the errors are logged to Stackdriver Logging. For more information, see Viewing error logs in Stackdriver Logging.
