Batch export FHIR resources to BigQuery

This page describes how to batch export FHIR resources to BigQuery for exploration and analysis. The export operation creates one BigQuery table for each FHIR resource type in your FHIR store.

To improve query performance and reduce costs, consider exporting FHIR resources to partitioned tables. For instructions, see Export FHIR resources to partitioned tables.

If you export FHIR resources on a schedule, consider exporting your data incrementally. For instructions, see Incremental exports.

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.

Understand export behavior

The behavior of the export operation depends on the following:

Whether the destination table exists.
Whether you set the force field.
Whether you specify an enum in WriteDisposition. If you specify an enum, don't set the force field.

The behavior in each case is as follows:

The destination table exists and force is set to true: the export operation overwrites the existing table
The destination table exists and force is set to false: an error occurs
The destination table doesn't exist: the export operation creates a new table, regardless of whether you specify the force field
The destination table exists and you set WriteDisposition to WRITE_TRUNCATE or WRITE_APPEND: the export operation succeeds instead of returning an error

Note: In the destination table, WRITE_TRUNCATE deletes existing data and WRITE_APPEND appends data.

The operation outputs one BigQuery table for each resource type in the FHIR store.

Batch export FHIR resources

The following samples show how to export FHIR resources to a BigQuery table.

When specifying the BigQuery destination, use the fully qualified URI:

bq://PROJECT_ID.BIGQUERY_DATASET_ID.BIGQUERY_TABLE_ID

Console

To export FHIR resources to BigQuery using the Google Cloud console, complete the following steps:

In the Google Cloud console, go to the Datasets page.

Go to Datasets
Click the dataset that has the FHIR store with the data you're exporting.
In the same row as the FHIR store, open the Actions list and select Export.
On the Export FHIR resources page that appears, find the Select a destination section. Select BigQuery table.
In the Destination table write disposition section, select one of the following options to determine the behavior of the export operation:
- Only export data if the destination tables are empty: this is equivalent to selecting the WRITE_EMPTY enum in WriteDisposition.
- Append data to the destination tables: this is equivalent to selecting the WRITE_APPEND enum in WriteDisposition.
- Erase all existing data in destination tables before writing the FHIR resources: this is equivalent to selecting the WRITE_TRUNCATE enum in WriteDisposition.
In the FHIR export configuration section, click Browse to select the BigQuery project and dataset.
In the Schema type dropdown, select the output schema for the BigQuery table. The following schemas are available:
- Analytics. A schema based on the SQL on FHIR document. Because BigQuery only allows for 10,000 columns per table, schemas are not generated for the Parameters.parameter.resource, Bundle.entry.resource, and Bundle.entry.response.outcome fields.
- Analytics V2. A schema similar to the Analytics schema, with added support for the following:
  - Extensions with multiple values for the same url
  - Contained FHIR resources
  The Analytics V2 schema uses more space in the destination table than the Analytics schema.
Select a depth level in the Recursive Structure Depth slider to set the depth for all recursive structures in the output schema. By default, the recursive value is 2.

For more information, see recursiveStructureDepth.
Click Export to export FHIR resources to BigQuery.
To track the status of the operation, click the Operations tab. After the operation completes, the following indications appear:
- The Long-running operation status section has a green check mark under the OK heading.
- The Overview section has a green check mark and an OK indicator in the same row as the operation ID.
If you encounter any errors, click Actions, and then click View details in Cloud Logging.

gcloud

To export FHIR resources to BigQuery, run the gcloud healthcare fhir-stores export bq command.

Export the FHIR resources.

Before using any of the command data below, make the following replacements:
- PROJECT_ID: the ID of your Google Cloud project
- LOCATION: the dataset location
- DATASET_ID: the FHIR store's parent dataset
- FHIR_STORE_ID: the FHIR store ID
- BIGQUERY_DATASET_ID: the name of the existing BigQuery dataset where you're exporting FHIR resources
- SCHEMA_TYPE: a value for SchemaType. Use one of the following values:
  - analytics. A schema based on the SQL on FHIR document. Because BigQuery only allows for 10,000 columns per table, schemas are not generated for the Parameters.parameter.resource, Bundle.entry.resource, and Bundle.entry.response.outcome fields.
  - analytics_v2. A schema similar to analytics with added support for the following:
    - Extensions with repeated fields
    - Contained FHIR resources
    analytics-v2 uses more space in the destination table than analytics.
- WRITE_DISPOSITION: a value for WriteDisposition. Use one of the following values:
  - write-empty. Only export data if the destination BigQuery tables are empty.
  - write-truncate. Erase all existing data in the BigQuery tables before writing the FHIR resources.
  - write-append. Append data to the destination BigQuery tables.
- FHIR_RESOURCE_TYPE: an optional field. Specify one or more comma-delimited FHIR resource types to only export FHIR resources of those types.
- SINCE_TIMESTAMP: an optional field. Specify a value in the format YYYY-MM-DDThh:mm:ss.sss+zz:zz to only export FHIR resources updated after a specific time. Specify the time to the second and include a time zone. For example, 2015-02-07T13:28:17.239+02:00 and 2017-01-01T00:00:00Z are valid times.
Execute the following command:
Linux, macOS, or Cloud Shell

Note: Ensure you have initialized the Google Cloud CLI with authentication and a project by running either gcloud init; or gcloud auth login and gcloud config set project.
```
gcloud healthcare fhir-stores export bq FHIR_STORE_ID \
  --location=LOCATION \
  --dataset=DATASET_ID \
  --bq-dataset=bq://PROJECT_ID.BIGQUERY_DATASET_ID \
  --schema-type=SCHEMA_TYPE \
  --write-disposition=WRITE_DISPOSITION \
  --resource-type=FHIR_RESOURCE_TYPE \
  --since=SINCE_TIMESTAMP
```
Windows (PowerShell)

Note: Ensure you have initialized the Google Cloud CLI with authentication and a project by running either gcloud init; or gcloud auth login and gcloud config set project.
```
gcloud healthcare fhir-stores export bq FHIR_STORE_ID `
  --location=LOCATION `
  --dataset=DATASET_ID `
  --bq-dataset=bq://PROJECT_ID.BIGQUERY_DATASET_ID `
  --schema-type=SCHEMA_TYPE `
  --write-disposition=WRITE_DISPOSITION `
  --resource-type=FHIR_RESOURCE_TYPE `
  --since=SINCE_TIMESTAMP
```
Windows (cmd.exe)

Note: Ensure you have initialized the Google Cloud CLI with authentication and a project by running either gcloud init; or gcloud auth login and gcloud config set project.
```
gcloud healthcare fhir-stores export bq FHIR_STORE_ID ^
  --location=LOCATION ^
  --dataset=DATASET_ID ^
  --bq-dataset=bq://PROJECT_ID.BIGQUERY_DATASET_ID ^
  --schema-type=SCHEMA_TYPE ^
  --write-disposition=WRITE_DISPOSITION ^
  --resource-type=FHIR_RESOURCE_TYPE ^
  --since=SINCE_TIMESTAMP
```
The response is the following. The response contains an identifier for a long-running operation. Long-running operations are returned when method calls might take a substantial amount of time to complete. The command polls the long-running operation, then prints the name of the operation in the name field after the export finishes. Note the value of OPERATION_ID. You need this value in the next step.
Response
```
Request issued for: [FHIR_STORE_ID]
Waiting for operation [projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/operations/OPERATION_ID] to complete...⠏
name: projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/operations/OPERATION_ID
```

To view more details about the operation, run the gcloud healthcare operations describe and provide the OPERATION_ID from the response.

Before using any of the command data below, make the following replacements:

PROJECT_ID: the ID of your Google Cloud project
DATASET_ID: the dataset ID
LOCATION: the dataset location
OPERATION_ID: the ID returned from the long-running operation

Execute the following command:

Linux, macOS, or Cloud Shell

gcloud healthcare operations describe OPERATION_ID \
    --project=PROJECT_ID \
    --dataset=DATASET_ID \
    --location=LOCATION

Windows (PowerShell)

gcloud healthcare operations describe OPERATION_ID `
    --project=PROJECT_ID `
    --dataset=DATASET_ID `
    --location=LOCATION

Windows (cmd.exe)

gcloud healthcare operations describe OPERATION_ID ^
    --project=PROJECT_ID ^
    --dataset=DATASET_ID ^
    --location=LOCATION

You should receive a response similar to the following:

Response

done: true
// If there were any errors, an `error` field displays instead of a `response` field.
// See Troubleshooting long-running operations for a list of response codes.
error: ERROR
  code: ERROR_CODE
  message: DESCRIPTION
metadata:
  '@type': 'type.googleapis.com/google.cloud.healthcare.v1.OperationMetadata'
  apiMethodName: 'google.cloud.healthcare.v1.fhir.FhirStoreService.ExportResources_bq'
  counter:
    success: 'SUCCESS_COUNT'
    // If there were any failures, they display in the `failure` field.
    failure: 'FAILURE_COUNT'
  createTime: 'YYYY-MM-DDTHH:MM:SS+ZZ:ZZ'
  endTime: 'YYYY-MM-DDTHH:MM:SS+ZZ:ZZ'
  logsUrl: https://console.cloud.google.com/CLOUD_LOGGING_URL
name: projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/operations/OPERATION_ID
// The `response` field only displays if there were no errors.
response:
  '@type': 'type.googleapis.com/google.cloud.healthcare.v1.fhir.ExportResourcesResponse'

REST

To export FHIR resources to BigQuery, use the projects.locations.datasets.fhirStores.export method.

Export the FHIR resources:

Before using any of the request data, make the following replacements:
- PROJECT_ID: the ID of your Google Cloud project
- LOCATION: the dataset location
- DATASET_ID: the FHIR store's parent dataset
- FHIR_STORE_ID: the FHIR store ID
- BIGQUERY_DATASET_ID: the name of the existing BigQuery dataset where you're exporting FHIR resources
- SCHEMA_TYPE: a value for SchemaType. Use one of the following values:
  - ANALYTICS. A schema based on the SQL on FHIR document. Because BigQuery only allows for 10,000 columns per table, schemas are not generated for the Parameters.parameter.resource, Bundle.entry.resource, and Bundle.entry.response.outcome fields.
  - ANALYTICS_V2. A schema similar to ANALYTICS with added support for the following:
    - Extensions with multiple values for the same url
    - Contained FHIR resources
    ANALYTICS_V2 uses more space in the destination table than ANALYTICS
    .
- WRITE_DISPOSITION: a value for WriteDisposition. Use one of the following values:
  - WRITE_EMPTY. Only export data if the destination BigQuery tables are empty.
  - WRITE_TRUNCATE. Erase all existing data in the BigQuery tables before writing the FHIR resources.
  - WRITE_APPEND. Append data to the destination BigQuery tables.
- FHIR_RESOURCE_TYPE: an optional field. Specify one or more comma-delimited FHIR resource types to only export FHIR resources of those types.
- SINCE_TIMESTAMP: an optional field. Specify a value in the format YYYY-MM-DDThh:mm:ss.sss+zz:zz to only export FHIR resources updated after a specific time. Specify the time to the second and include a time zone. For example, 2015-02-07T13:28:17.239+02:00 and 2017-01-01T00:00:00Z are valid times.
Request JSON body:
```
{
  "bigqueryDestination": {
    "datasetUri": "bq://PROJECT_ID.BIGQUERY_DATASET_ID",
    "schemaConfig": {
      "schemaType": "SCHEMA_TYPE",
    },
    "writeDisposition": "WRITE_DISPOSITION"
  },
  "_type": "FHIR_RESOURCE_TYPE",
  "_since": "SINCE_TIMESTAMP"
}
```
To send your request, choose one of these options:
curl

Note: The following command assumes that you have logged in to the gcloud CLI with your user account by running gcloud init or gcloud auth login , or by using Cloud Shell, which automatically logs you into the gcloud CLI . You can check the currently active account by running gcloud auth list.

Save the request body in a file named request.json. Run the following command in the terminal to create or overwrite this file in the current directory:
```
cat > request.json << 'EOF'
{
  "bigqueryDestination": {
    "datasetUri": "bq://PROJECT_ID.BIGQUERY_DATASET_ID",
    "schemaConfig": {
      "schemaType": "SCHEMA_TYPE",
    },
    "writeDisposition": "WRITE_DISPOSITION"
  },
  "_type": "FHIR_RESOURCE_TYPE",
  "_since": "SINCE_TIMESTAMP"
}
EOF
```
Then execute the following command to send your REST request:
curl -X POST \
-H "Authorization: Bearer $(gcloud auth print-access-token)" \
-H "Content-Type: application/json; charset=utf-8" \
-d @request.json \
"https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID:export"
PowerShell

Note: The following command assumes that you have logged in to the gcloud CLI with your user account by running gcloud init or gcloud auth login . You can check the currently active account by running gcloud auth list.

Save the request body in a file named request.json. Run the following command in the terminal to create or overwrite this file in the current directory:
```
@'
{
  "bigqueryDestination": {
    "datasetUri": "bq://PROJECT_ID.BIGQUERY_DATASET_ID",
    "schemaConfig": {
      "schemaType": "SCHEMA_TYPE",
    },
    "writeDisposition": "WRITE_DISPOSITION"
  },
  "_type": "FHIR_RESOURCE_TYPE",
  "_since": "SINCE_TIMESTAMP"
}
'@  | Out-File -FilePath request.json -Encoding utf8
```
Then execute the following command to send your REST request:
$cred = gcloud auth print-access-token
$headers = @{ "Authorization" = "Bearer $cred" }

Invoke-WebRequest `
-Method POST `
-Headers $headers `
-ContentType: "application/json; charset=utf-8" `
-InFile request.json `
-Uri "https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID:export" | Select-Object -Expand Content
APIs Explorer

Copy the request body and open the method reference page. The APIs Explorer panel opens on the right side of the page. You can interact with this tool to send requests. Paste the request body in this tool, complete any other required fields, and click Execute.
The output is the following. The response contains an identifier for a long-running operation (LRO). Long-running operations are returned when method calls might take additional time to complete. Note the value of OPERATION_ID. You need this value in the next step.
Response
```
{
  "name": "projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/operations/OPERATION_ID"
}
```

Use the projects.locations.datasets.operations.get method to get the status of the long-running operation.

Before using any of the request data, make the following replacements:

PROJECT_ID: the ID of your Google Cloud project
DATASET_ID: the dataset ID
LOCATION: the dataset location
OPERATION_ID: the ID returned from the long-running operation

To send your request, choose one of these options:

curl

Note: The following command assumes that you have logged in to the gcloud CLI with your user account by running gcloud init or gcloud auth login , or by using Cloud Shell, which automatically logs you into the gcloud CLI . You can check the currently active account by running gcloud auth list.

Execute the following command:

curl -X GET \
     -H "Authorization: Bearer $(gcloud auth print-access-token)" \
     "https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/operations/OPERATION_ID"

PowerShell

Note: The following command assumes that you have logged in to the gcloud CLI with your user account by running gcloud init or gcloud auth login . You can check the currently active account by running gcloud auth list.

Execute the following command:

$cred = gcloud auth print-access-token
$headers = @{ "Authorization" = "Bearer $cred" }

Invoke-WebRequest `
    -Method GET `
    -Headers $headers `
    -Uri "https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/operations/OPERATION_ID" | Select-Object -Expand Content

APIs Explorer

Open the method reference page. The APIs Explorer panel opens on the right side of the page. You can interact with this tool to send requests. Complete any required fields and click Execute.

The output is the following. When the response contains "done": true, the long-running operation has finished.

Response

{
  "name": "projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/operations/OPERATION_ID",
  "metadata": {
    "@type": "type.googleapis.com/google.cloud.healthcare.v1.OperationMetadata",
    "apiMethodName": "google.cloud.healthcare.v1.fhir.FhirStoreService.ExportResources_bq",
    "createTime": "YYYY-MM-DDTHH:MM:SS+ZZ:ZZ",
    "endTime": "YYYY-MM-DDTHH:MM:SS+ZZ:ZZ",
    "logsUrl": "https://console.cloud.google.com/CLOUD_LOGGING_URL"
    "counter": {
      "success": "SUCCESS_COUNT",
      // If there were any failures, they display in the `failure` field.
      "failure": "FAILURE_COUNT"
    }
  },
  "done": true,
  // The `response` field only displays if there were no errors.
  "response": {
    "@type": "type.googleapis.com/google.cloud.healthcare.v1.fhir.ExportResourcesResponse",
    
  },
  // If there were any errors, an `error` field displays instead of a `response` field.
  // See Troubleshooting long-running operations for a list of response codes.
  "error": {
    "code": ERROR_CODE,
    "message": "DESCRIPTION",
    "details": [
      {
        "@type": "...",
        FIELD1: ...,
        ...
      }
    ]
  }
}

Export FHIR resources to partitioned tables

To export FHIR resources to BigQuery partitioned tables, set the TimePartitioning enum in the lastUpdatedPartitionConfig field in your FHIR store.

The partitioned tables work like BigQuery time-unit partitioned tables. Partitioned tables have an added column named lastUpdated, which is a duplicate of the meta.lastUpdated column which is generated from the meta.lastUpdated field in a FHIR resource. BigQuery uses the lastUpdated column to partition tables by hour, day, month, or year.

See Select daily, hourly, monthly, or yearly partitioning for recommendations on how to select a partition granularity.

You can't convert existing, non-partitioned BigQuery tables into partitioned tables. If you export Patient resource changes to a non-partitioned Patients table, and later create a new FHIR store with table partitioning that exports to the same BigQuery dataset, the Cloud Healthcare API still exports data to the non-partitioned Patients table. To start using a partitioned table, delete the existing Patients table or use a different BigQuery dataset.

If you add partitioning to an existing FHIR store configuration, you can still export to existing non-partitioned tables. However, partitioning will only take effect on new tables.

The following samples show how to export FHIR resources to BigQuery partitioned tables.

Console

The Google Cloud console and the gcloud CLI don't support this action. Instead, use curl, PowerShell, or your preferred language.

gcloud

The Google Cloud console and the gcloud CLI don't support this action. Instead, use curl, PowerShell, or your preferred language.

REST

To export FHIR resources to BigQuery partitioned tables, use the projects.locations.datasets.fhirStores.export method.

Export the FHIR resources:

Before using any of the request data, make the following replacements:
- PROJECT_ID: the ID of your Google Cloud project
- LOCATION: the dataset location
- DATASET_ID: the FHIR store's parent dataset
- FHIR_STORE_ID: the FHIR store ID
- BIGQUERY_DATASET_ID: the name of the existing BigQuery dataset where you're exporting FHIR resources
- SCHEMA_TYPE: a value for SchemaType. Use one of the following values:
  - ANALYTICS. A schema based on the SQL on FHIR document. Because BigQuery only allows for 10,000 columns per table, schemas are not generated for the Parameters.parameter.resource, Bundle.entry.resource, and Bundle.entry.response.outcome fields.
  - ANALYTICS_V2. A schema similar to ANALYTICS with added support for the following:
    - Extensions with multiple values for the same url
    - Contained FHIR resources
    ANALYTICS_V2 uses more space in the destination table than ANALYTICS
    .
- TIME_PARTITION_TYPE: the granularity at which to partition exported FHIR resources. Use one of the following values:
  - HOUR: partition data by hour
  - DAY: partition data by day
  - MONTH: partition data by month
  - YEAR: partition data by year
- WRITE_DISPOSITION: a value for WriteDisposition. Use one of the following values:
  - WRITE_EMPTY: only export data if the BigQuery table is empty.
  - WRITE_TRUNCATE: erase all existing data in the BigQuery table before writing the DICOM instances.
  - WRITE_APPEND: append data to the BigQuery table.
Request JSON body:
```
{
  "bigqueryDestination": {
    "datasetUri": "bq://PROJECT_ID.BIGQUERY_DATASET_ID",
    "schemaConfig": {
      "schemaType": "SCHEMA_TYPE",
      "lastUpdatedPartitionConfig": {
        "type": "TIME_PARTITION_TYPE"
      }
    },
    "writeDisposition": "WRITE_DISPOSITION"
  }
}
```
To send your request, choose one of these options:
curl

Note: The following command assumes that you have logged in to the gcloud CLI with your user account by running gcloud init or gcloud auth login , or by using Cloud Shell, which automatically logs you into the gcloud CLI . You can check the currently active account by running gcloud auth list.

Save the request body in a file named request.json. Run the following command in the terminal to create or overwrite this file in the current directory:
```
cat > request.json << 'EOF'
{
  "bigqueryDestination": {
    "datasetUri": "bq://PROJECT_ID.BIGQUERY_DATASET_ID",
    "schemaConfig": {
      "schemaType": "SCHEMA_TYPE",
      "lastUpdatedPartitionConfig": {
        "type": "TIME_PARTITION_TYPE"
      }
    },
    "writeDisposition": "WRITE_DISPOSITION"
  }
}
EOF
```
Then execute the following command to send your REST request:
curl -X POST \
-H "Authorization: Bearer $(gcloud auth print-access-token)" \
-H "Content-Type: application/json; charset=utf-8" \
-d @request.json \
"https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID:export"
PowerShell

Note: The following command assumes that you have logged in to the gcloud CLI with your user account by running gcloud init or gcloud auth login . You can check the currently active account by running gcloud auth list.

Save the request body in a file named request.json. Run the following command in the terminal to create or overwrite this file in the current directory:
```
@'
{
  "bigqueryDestination": {
    "datasetUri": "bq://PROJECT_ID.BIGQUERY_DATASET_ID",
    "schemaConfig": {
      "schemaType": "SCHEMA_TYPE",
      "lastUpdatedPartitionConfig": {
        "type": "TIME_PARTITION_TYPE"
      }
    },
    "writeDisposition": "WRITE_DISPOSITION"
  }
}
'@  | Out-File -FilePath request.json -Encoding utf8
```
Then execute the following command to send your REST request:
$cred = gcloud auth print-access-token
$headers = @{ "Authorization" = "Bearer $cred" }

Invoke-WebRequest `
-Method POST `
-Headers $headers `
-ContentType: "application/json; charset=utf-8" `
-InFile request.json `
-Uri "https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID:export" | Select-Object -Expand Content
APIs Explorer

Copy the request body and open the method reference page. The APIs Explorer panel opens on the right side of the page. You can interact with this tool to send requests. Paste the request body in this tool, complete any other required fields, and click Execute.
You should receive a JSON response similar to the following:
Response
```
{
  "name": "projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID",
  "version": "FHIR_STORE_VERSION",
  "bigqueryDestination": {
    "datasetUri": "bq://PROJECT_ID.BIGQUERY_DATASET_ID",
    "schemaConfig": {
      "schemaType": "SCHEMA_TYPE",
      "lastUpdatedPartitionConfig": {
        "type": "TIME_PARTITION_TYPE"
      }
    },
    "writeDisposition": "WRITE_DISPOSITION"
  }
}
```

Use the projects.locations.datasets.operations.get method to get the status of the long-running operation.

Before using any of the request data, make the following replacements:

PROJECT_ID: the ID of your Google Cloud project
DATASET_ID: the dataset ID
LOCATION: the dataset location
OPERATION_ID: the ID returned from the long-running operation

To send your request, choose one of these options:

curl

Execute the following command:

curl -X GET \
     -H "Authorization: Bearer $(gcloud auth print-access-token)" \
     "https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/operations/OPERATION_ID"

PowerShell

Execute the following command:

$cred = gcloud auth print-access-token
$headers = @{ "Authorization" = "Bearer $cred" }

Invoke-WebRequest `
    -Method GET `
    -Headers $headers `
    -Uri "https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/operations/OPERATION_ID" | Select-Object -Expand Content

APIs Explorer

Open the method reference page. The APIs Explorer panel opens on the right side of the page. You can interact with this tool to send requests. Complete any required fields and click Execute.

The output is the following. When the response contains "done": true, the long-running operation has finished.

Response

{
  "name": "projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/operations/OPERATION_ID",
  "metadata": {
    "@type": "type.googleapis.com/google.cloud.healthcare.v1.OperationMetadata",
    "apiMethodName": "google.cloud.healthcare.v1.fhir.FhirStoreService.ExportResources_bq",
    "createTime": "YYYY-MM-DDTHH:MM:SS+ZZ:ZZ",
    "endTime": "YYYY-MM-DDTHH:MM:SS+ZZ:ZZ",
    "logsUrl": "https://console.cloud.google.com/CLOUD_LOGGING_URL"
    "counter": {
      "success": "SUCCESS_COUNT",
      // If there were any failures, they display in the `failure` field.
      "failure": "FAILURE_COUNT"
    }
  },
  "done": true,
  // The `response` field only displays if there were no errors.
  "response": {
    "@type": "type.googleapis.com/google.cloud.healthcare.v1.fhir.ExportResourcesResponse",
    
  },
  // If there were any errors, an `error` field displays instead of a `response` field.
  // See Troubleshooting long-running operations for a list of response codes.
  "error": {
    "code": ERROR_CODE,
    "message": "DESCRIPTION",
    "details": [
      {
        "@type": "...",
        FIELD1: ...,
        ...
      }
    ]
  }
}

Query a partitioned table

To reduce query costs when querying partitioned tables, use the WHERE clause to filter by time units.

For example, suppose that you set the PartitionType enum to DAY. To query a Patients table for Patient resources that were updated on a specific date, run the following query:

SELECT * FROM `PROJECT_ID.BIGQUERY_DATASET.Patients`
  WHERE DATE(lastUpdated) = 'YYYY-MM-DD'

Incremental exports

You can specify a timestamp to only export FHIR resources added to your FHIR store since a previous successful export. This improves performance and avoids the cost of re-exporting the entire FHIR store, while also ensuring your exported data is always up-to-date.

When calling fhirStores.export, specify the timestamp in the _since field.

Querying and analyzing FHIR data in BigQuery

After exporting the FHIR resources to BigQuery, see the Analyzing FHIR data in BigQuery solution for information on how to query and analyze the exported data. The solution uses the Synthea™ Generated Synthetic Data in FHIR public dataset, which hosts over 1 million synthetic patient records generated in the Synthea™ and FHIR formats.

Troubleshooting FHIR export requests

If errors occur during a FHIR export request, the errors are logged to Cloud Logging. For more information, see Viewing error logs in Cloud Logging.

If the entire operation returns an error, see Troubleshooting long-running operations.

Cannot convert column from NULLABLE to REPEATED

This error is caused by a repeated extension. To resolve this error, use the ANALYTICS_V2 schema type. If you're using ANALYTICS_V2, you might have a conflict between two extensions, or a conflict between an extension and another field.

Column names are generated from the text after the last / character in extension URLs. If an extension URL ends with a value like /resource_field name, a conflict can occur. \

To prevent this error from occurring again, don't use extensions if their field names are the same as the resource fields you're populating.

What's next

To learn more about data governance and security in BigQuery, see Overview of data security and governance.