This page is part of the FHIR Bulk Data Access (Flat FHIR) (v2.0.0: STU 2) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions

Bulk Data Export

Audience and Scope

This implementation guide is intended to be used by developers of backend services (clients) and FHIR Resource Servers (e.g., EHR systems, data warehouses, and other clinical and administrative systems) that aim to interoperate by sharing large FHIR datasets. The guide defines the application programming interfaces (APIs) through which an authenticated and authorized client may request a Bulk Data Export from a server, receive status information regarding progress in the generation of the requested files, and retrieve these files. It also includes recommendations regarding the FHIR resources that might be exposed through the export interface.

The scope of this document does NOT include:

• A legal framework for sharing data between partners, such as Business Associate Agreements, Service Level Agreements, and Data Use Agreements, though these may be required for some use cases.
• Real-time data exchange
• Data transformations that may be required by the client
• Patient matching (although identifiers may be included in the exported FHIR resources)
• Management of FHIR groups (although some Bulk Data operations require a FHIR Group id, this guide does not specify how Group resources are created and maintained within a system)

Underlying Standards

• HL7 FHIR
• Newline-delimited JSON
• RFC5246, Transport Layer Security (TLS) Protocol Version 1.2
• RFC6749, The OAuth 2.0 Authorization Framework
• RFC6750, The OAuth 2.0 Authorization Framework: Bearer Token Usage
• RFC7159, The JavaScript Object Notation (JSON) Data Interchange Format
• RFC7240, Prefer Header for HTTP

Terminology

This profile inherits terminology from the standards referenced above. The key words “REQUIRED”, “SHALL”, “SHALL NOT”, “SHOULD”, “SHOULD NOT”, “RECOMMENDED”, “MAY”, and “OPTIONAL” in this specification are to be interpreted as described in RFC2119.

Privacy and Security Considerations

All exchanges described herein between a client and a server SHALL be secured using Transport Layer Security (TLS) Protocol Version 1.2 (RFC5246) or a more recent version of TLS. Use of mutual TLS is OPTIONAL.

With each of the requests described herein, implementers SHOULD implement OAuth 2.0 access management in accordance with the SMART Backend Services Authorization Profile. When SMART Backend Services Authorization is used, Bulk Data Status Request and Bulk Data Output File Requests with requiresAccessToken=true SHALL be protected the same way the Bulk Data Kick-off Request, including an access token with scopes that cover all resources being exported. A server MAY additionally restrict Bulk Data Status Request and Bulk Data Output File Requests by limiting them to the client that originated the export. Implementations MAY include endpoints that use authorization schemes other than OAuth 2.0, such as mutual-TLS or signed URLs.

This implementation guide does not address protection of a server from potential compromise. An adversary who successfully captures administrative rights to the server will have full control over that server and can use those rights to undermine the server’s security protections. In the Bulk Data Export workflow, the file server will be a particularly attractive target, as it holds highly sensitive and valued PHI. An adversary who successfully takes control of a file server may choose to continue to deliver files in response to client requests, so that neither the client nor the FHIR server is aware of the take-over. Meanwhile, the adversary is able to put the PHI to use for its own malicious purposes.

Healthcare organizations have an imperative to protect PHI persisted in file servers in both cloud and data-center environments. A range of existing and emerging approaches can be used to accomplish this, not all of which would be visible at the API level. This specification does not dictate a particular approach at this time, though it does support the use of an Expires header to limit the time period a file will be available for client download (removal of the file from the server is left up to the server implementer). A server SHOULD NOT delete files from a Bulk Data response that a client is actively in the process of downloading regardless of the pre-specified expiration time.

Data access control obligations can be met with a combination of in-band restrictions (e.g., OAuth scopes), and out-of-band restrictions, where the server limits the data returned to a specific client in accordance with local considerations (e.g. policies or regulations). The FHIR server SHALL limit the data returned to only those FHIR resources for which the client is authorized. Implementers SHOULD incorporate technology that preserves and respects an individual’s wishes to share their data with desired privacy protections. For example, some clients are authorized to access sensitive mental health information and some aren’t; this authorization is defined out-of-band, but when a client requests a full data set, filtering is automatically applied by the server, restricting the data that the client receives.

Bulk Data Export can be a resource-intensive operation. Server developers SHOULD consider and mitigate the risk of intentional or inadvertent denial-of-service attacks though the details are beyond the scope of this specification. For example, transactional systems may wish to provide Bulk Data access to a read-only mirror of the database or may distribute processing over time to avoid loads that could impact clinical operations.

Bulk Data Export Operation Request Flow

This implementation guide builds on the FHIR Asynchronous Request Pattern, and in some places may extend the pattern.

Roles

There are two primary roles involved in a Bulk Data transaction:

1. Bulk Data Provider - consists of:

   a. FHIR Authorization Server - server that issues access tokens in response to valid token requests from client.

   b. FHIR Resource Server - server that accepts kick-off request and provides job status and completion manifest.

   c. Output File Server - server that returns FHIR Bulk Data files and attachments in response to urls in the completion manifest. This may be built into the FHIR Server, or may be independently hosted.

2. Bulk Data Client - system that requests and receives access tokens and Bulk Data files

Sequence Overview

Bulk Data Kick-off Request

The Bulk Data Export Operation initiates the asynchronous generation of a requested export dataset - whether that be data for all patients, data for a subset (defined group) of patients, or all FHIR data in the server.

As discussed in See Privacy and Security Considerations above, a server SHALL limit the data returned to only those FHIR resources for which the client is authorized.

The Resource FHIR server SHALL support invocation of this operation using the FHIR Asynchronous Request Pattern. A server SHALL support GET requests and MAY support POST requests that supply parameters using the FHIR Parameters Resource.

A client MAY repeat kick-off parameters that accept comma delimited values multiple times in a kick-off request. The server SHALL treat the values provided as if they were comma delimited values within a single instance of the parameter. Note that we will be soliciting feedback on the use of comma delimited values within parameters, and depending on the response may consider deprecating this input approach in favor of repeating parameters in a future version of this IG.

For Patient-level requests and Group-level requests associated with groups of patients, the Patient Compartment SHOULD be used as a point of reference for recommended resources to be returned and, where applicable, Patient resources SHOULD be returned. Other resources outside of the patient compartment that are helpful in interpreting the patient data (such as Organization and Practitioner) MAY also be returned.

Binary Resources whose content is associated with an individual patient SHALL be serialized as DocumentReference Resources with the content.attachment element populated as described in the Attachments section below. Binary Resources not associated with an individual patient MAY be included in a System Level export.

References in the resources returned MAY be relative URLs with the format <resource type>/<id>, or MAY be absolute URLs with the same structure rooted in the base URL for the server from which the export was performed.

Endpoint - All Patients

[fhir base]/Patient/$export

View table of parameters for Patient Export

FHIR Operation to obtain a detailed set of FHIR resources of diverse resource types pertaining to all patients.

Endpoint - Group of Patients

[fhir base]/Group/[id]/$export

View table of parameters for Group Export

FHIR Operation to obtain a detailed set of FHIR resources of diverse resource types pertaining to all members of a specified Group.

If a FHIR server supports Group-level data export, it SHOULD support reading and searching for Group resource. This enables clients to discover available groups based on stable characteristics such as Group.identifier.

Note: How these Groups are defined is specific to each FHIR system’s implementation. For example, a payer may send a healthcare institution a roster file that can be imported into their EHR to create or update a FHIR group. Group membership could be based upon explicit attributes of the patient, such as age, sex or a particular condition such as PTSD or Chronic Opioid use, or on more complex attributes, such as a recent inpatient discharge or membership in the population used to calculate a quality measure. FHIR-based group management is out of scope for the current version of this implementation guide.

Endpoint - System Level Export

[fhir base]/$export

View table of parameters for Export

Export data from a FHIR server, whether or not it is associated with a patient. This supports use cases like backing up a server, or exporting terminology data by restricting the resources returned using the _type parameter.

Headers

• Accept (string)

  Specifies the format of the optional FHIR OperationOutcome resource response to the kick-off request. Currently, only application/fhir+json is supported. A client SHOULD provide this header. If omitted, the server MAY return an error or MAY process the request as if application/fhir+json was supplied.

• Prefer (string)

  Specifies whether the response is immediate or asynchronous. Currently, only a value of respond-async is supported. A client SHOULD provide this header. If omitted, the server MAY return an error or MAY process the request as if respond-async was supplied.

Query Parameters

Note: Implementations MAY limit the resources returned to specific subsets of FHIR, such as those defined in the US Core Implementation Guide. If the client explicitly asks for export of resources that the Bulk Data server doesn’t support, the server SHOULD return details via a FHIR OperationOutcome resource in an error response to the request.

If an includeAssociatedValue value relevant to provenance is not specified, or if this parameter is not supported by a server, the server SHALL include all available Provenance resources whose Provenance.target is a resource in the Patient compartment in a patient level export request, and all available Provenance resources in a system level export request unless a specific resource set is specified using the _type parameter and this set does not include Provenance.

Group Membership Request Pattern

To obtain new and updated resources for patients in a group, as well as all data for patients who have joined the group since a prior query, a client can use following pattern:

• Initial Query (e.g., on January 1, 2020):

  • Client submits a group export request:

    [baseurl]/Group/[id]/$export

  • Client retrieves response data
  • Client retains a list of the patient ids returned
  • Client retains the transactionTime value from the response

• Subsequent Queries (e.g., on February 1, 2020):

  • Client submits a group export request to obtain a patient list:

    [baseurl]/Group/[id]/$export?_type=Patient&_elements=id

  • Client retains a list of patient ids returned
  • Client compares response to patient ids from first query request and identifies new patient ids

  • Client submits a group export request via POST for patients who are new members of the group:

    POST [baseurl]/Group/[id]/$export
        
    {"resourceType" : "Parameters",
      "parameter" : [{
        "name" : "patient",
        "valueReference" : {reference: "Patient/123"}
      },{
        "name" : "patient",
        "valueReference" : {reference: "Patient/456"}
      ...
      }]
    }
    

  • Client submits a group export request for updated group data:

    [baseurl]/Group/[id]/$export?_since=[initial transaction time]

    Note that data returned from this request may overlap with that returned from the prior step.

  • Client retains the transactionTime value from the response.

_typeFilter Experimental Query Parameter

The community has identified use cases for finer-grained, client-specified filtering. For example, some clients may want to retrieve only active prescriptions rather than historical prescriptions or only laboratory observations rather than all observations.

To request finer-grained filtering, a client MAY supply a _typeFilter parameter alongside the _type parameter. The value of the _typeFilter parameter is a comma-separated list of FHIR REST API queries that restrict the results of the export. FHIR search response parameters such as _include and _sort SHALL NOT be used. Since support for _typeFilter is OPTIONAL for a FHIR server, clients SHOULD be robust to servers that ignore _typeFilter. A client MAY repeat the _typeFilter parameter multiple times in a kick-off request. When repeated, the server SHALL treat the repeated values as if they were comma delimited values within a single _typeFilter parameter.

Example Request

The following is an export request for MedicationRequest resources and Condition resources, where the client would further like to restrict MedicationRequests to requests that are active, or else completed after July 1, 2018. This can be accomplished with two subqueries joined together with a comma for a logical “or”:

• MedicationRequest?status=active
• MedicationRequest?status=completed&date=gt2018-07-01T00:00:00Z

To create a _typeFilter parameter, a client should URL encode these two subqueries and join them with ,. Newlines and spaces have been added for clarity, and would not be included in a real request:

$export?
  _type=
    MedicationRequest,
    Condition&
  _typeFilter=
    MedicationRequest%3Fstatus%3Dactive,
    MedicationRequest%3Fstatus%3Dcompleted%26date%3Dgt2018-07-01T00%3A00%3A00Z

Note: The Condition resource is included in _type but omitted from _typeFilter because the client intends to request all Condition resources without any filters.

Response - Success

• HTTP Status Code of 202 Accepted
• Content-Location header with the absolute URL of an endpoint for subsequent status requests (polling location)
• Optionally, a FHIR OperationOutcome resource in the body in JSON format

Response - Error (e.g., unsupported search parameter)

• HTTP Status Code of 4XX or 5XX
• The body SHALL be a FHIR OperationOutcome resource in JSON format

If a server wants to prevent a client from beginning a new export before an in-progress export is completed, it SHOULD respond with a 429 Too Many Requests status and a Retry-After header, following the rate-limiting advice for “Bulk Data Status Request” below.

Bulk Data Delete Request

After a Bulk Data request has been started, a client MAY send a DELETE request to the URL provided in the Content-Location header to cancel the request as described in the FHIR Asynchronous Request Pattern. If the request has been completed, a server MAY use the request as a signal that a client is done retrieving files and that it is safe for the sever to remove those from storage. Following the delete request, when subsequent requests are made to the polling location, the server SHALL return a 404 Not Found error and an associated FHIR OperationOutcome in JSON format.

Endpoint

DELETE [polling content location]

Response - Success

• HTTP Status Code of 202 Accepted
• Optionally a FHIR OperationOutcome resource in the body in JSON format

Response - Error Status

• HTTP status code of 4XX or 5XX
• The body SHALL be a FHIR OperationOutcome resource in JSON format

Bulk Data Status Request

After a Bulk Data request has been started, the client MAY poll the status URL provided in the Content-Location header as described in the FHIR Asynchronous Request Pattern.

Clients SHOULD follow an exponential backoff approach when polling for status. A server SHOULD supply a Retry-After header with a with a delay time in seconds (e.g., 120 to represent two minutes) or a http-date (e.g., Fri, 31 Dec 1999 23:59:59 GMT). When provided, clients SHOULD use this information to inform the timing of future polling requests. The server SHOULD keep an accounting of status queries received from a given client, and if a client is polling too frequently, the server SHOULD respond with a 429 Too Many Requests status code in addition to a Retry-After header, and optionally a FHIR OperationOutcome resource with further explanation. If excessively frequent status queries persist, the server MAY return a 429 Too Many Requests status code and terminate the session. Other standard HTTP 4XX as well as 5XX status codes may be used to identify errors as mentioned.

When requesting status, the client SHOULD use an Accept header indicating a content type of application/json. In the case that errors prevent the export from completing, the server SHOULD respond with a FHIR OperationOutcome resource in JSON format.

Endpoint

GET [polling content location]

Responses

Status: 202 Accepted
X-Progress: “50% complete”
Retry-After: 120

Status: 500 Internal Server Error
Content-Type: application/fhir+json

{
 "resourceType": "OperationOutcome",
 "id": "1",
 "issue": [
  {
   "severity": "error",
   "code": "processing",
   "details": {
    "text": "An internal timeout has occurred"
   }
  }
 ]
}

Status: 200 OK
Expires: Mon, 22 Jul 2019 23:59:59 GMT
Content-Type: application/json

{
 "transactionTime": "2021-01-01T00:00:00Z",
 "request" : "https://example.com/fhir/Patient/$export?_type=Patient,Observation",
 "requiresAccessToken" : true,
 "output" : [{
  "type" : "Patient",
  "url" : "https://example.com/output/patient_file_1.ndjson"
 },{
  "type" : "Patient",
  "url" : "https://example.com/output/patient_file_2.ndjson"
 },{
  "type" : "Observation",
  "url" : "https://example.com/output/observation_file_1.ndjson"
 }],
 "deleted" : [{
  "type" : "Bundle",
  "url" : "https://example.com/output/del_file_1.ndjson"
 }],
 "error" : [{
  "type" : "OperationOutcome",
  "url" : "https://example.com/output/err_file_1.ndjson"
 }],
 "extension":{"https://example.com/extra-property": true}
}

Response - In-Progress Status

• HTTP Status Code of 202 Accepted
• Optionally, the server MAY return an X-Progress header with a text description of the status of the request that is less than 100 characters. The format of this description is at the server’s discretion and MAY be a percentage complete value, or MAY be a more general status such as “in progress”. The client MAY parse the description, display it to the user, or log it.

Response - Error Status

• HTTP status code of 4XX or 5XX
• Content-Type header of application/fhir+json when body is a FHIR OperationOutcome resource
• The body of the response SHOULD be a FHIR OperationOutcome resource in JSON format. If this is not possible (for example, the infrastructure layer returning the error is not FHIR aware), the server MAY return an error message in another format and include a corresponding value for the Content-Type header.

In the case of a polling failure that does not indicate failure of the export job, a server SHOULD use a transient code from the IssueType valueset when populating the FHIR OperationOutcome resource’s issue.code element to indicate to the client that it should retry the request at a later time.

Note: Even if some of the requested resources cannot successfully be exported, the overall export operation MAY still succeed. In this case, the Response.error array of the completion response body SHALL be populated with one or more files in ndjson format containing FHIR OperationOutcome resources to indicate what went wrong (see below). In the case of a partial success, the server SHALL use a 200 status code instead of 4XX or 5XX. The choice of when to determine that an export job has failed in its entirety (error status) vs. returning a partial success (complete status) is left up to the server implementer.

Response - Complete Status

• HTTP status of 200 OK
• Content-Type header of application/json
• The server SHOULD return an Expires header indicating when the files listed will no longer be available for access.
• A body containing a JSON object providing metadata, and links to the generated Bulk Data files. The files SHALL be accessible to the client at the URLs advertised. These URLs MAY be served by file servers other than a FHIR-specific server.

Required Fields:

{
 "resourceType": "Bundle",
 "id": "bundle-transaction",
 "meta": {"lastUpdated: "2020-04-27T02:56:00Z},
 "type": "transaction",
 "entry":[{
  "request": {"method": "DELETE", "url": "Patient/123"}
  ...
 }]
}

Example response body:

  {
    "transactionTime": "2021-01-01T00:00:00Z",
    "request" : "https://example.com/fhir/Patient/$export?_type=Patient,Observation",
    "requiresAccessToken" : true,
    "output" : [{
      "type" : "Patient",
      "url" : "https://example.com/output/patient_file_1.ndjson"
    },{
      "type" : "Patient",
      "url" : "https://example.com/output/patient_file_2.ndjson"
    },{
      "type" : "Observation",
      "url" : "https://example.com/output/observation_file_1.ndjson"
    }],
    "deleted": [{
      "type" : "Bundle",
      "url" : "https://example.com/output/del_file_1.ndjson"      
    }],
    "error" : [{
      "type" : "OperationOutcome",
      "url" : "https://example.com/output/err_file_1.ndjson"
    }],
    "extension":{"https://example.com/extra-property": true}
  }

Bulk Data Output File Request

Using the URLs supplied by the FHIR server in the Complete Status response body, a client MAY download the generated Bulk Data files (one or more per resource type) within the time period specified in the Expires header (if present). If the requiresAccessToken field in the Complete Status body is set to true, the request SHALL include a valid access token. See Privacy and Security Considerations above.

The exported data SHALL include only the most recent version of any exported resources unless the client explicitly requests different behavior in a fashion supported by the server (e.g., via a new query parameter yet to be defined). Inclusion of the Resource.meta information in the resources is at the discretion of the server (as it is for all FHIR interactions).

Example NDJSON output file:

{"id":"5c41cecf-cf81-434f-9da7-e24e5a99dbc2","name":[{"given":["Brenda"],"family":["Jackson"]}],"gender":"female","birthDate":"1956-10-14T00:00:00.000Z","resourceType":"Patient"}
{"id":"3fabcb98-0995-447d-a03f-314d202b32f4","name":[{"given":["Bram"],"family":["Sandeep"]}],"gender":"male","birthDate":"1994-11-01T00:00:00.000Z","resourceType":"Patient"}
{"id":"945e5c7f-504b-43bd-9562-a2ef82c244b2","name":[{"given":["Sandy"],"family":["Hamlin"]}],"gender":"female","birthDate":"1988-01-24T00:00:00.000Z","resourceType":"Patient"}

Endpoint

GET [url from status request output field]

Headers

• Accept (optional, defaults to application/fhir+ndjson)

Specifies the format of the file being requested.

Response - Success

• HTTP status of 200 OK
• Content-Type header that matches the file format being delivered. For files in ndjson format, SHALL be application/fhir+ndjson
• Body of FHIR resources in newline delimited json - ndjson or other requested format

Response - Error

• HTTP Status Code of 4XX or 5XX

Attachments

If resources in an output file contain elements of the type Attachment, the server SHOULD populate the Attachment.contentType code as well as either the data element or the url element. When populated, the url element SHALL be an absolute url that can be de-referenced to the attachment’s content.

When the url element is populated with an absolute URL and the requiresAccessToken field in the Complete Status body is set to true, the url location must be accessible by a client with a valid access token, and SHALL NOT require the use of additional authentication credentials. When the url element is populated and the requiresAccessToken field in the Complete Status body is set to false, the url location must be accessible by a client without an access token.

Note that if a server copies files to the Bulk Data output endpoint or proxies requests to facilitate access from this endpoint, it may need to modify the Attachment.url element when generating the Bulk Data output files.

Server Capability Documentation

This implementation guide is structured to support a wide variety of Bulk Data Export use cases and server architectures. To provide clarity to developers on which capabilities are implemented in a particular server, server providers SHOULD ensure that their Capability Statement accurately reflects the implemented Bulk Data Operations and that their documentation addresses the topics below. Future versions of this IG may define a computable format for this information as well.

• Does the server restrict responses to a specific profile like the US Core Implementation Guide or the Blue Button Implementation Guide?
• What approach does the server take to divide datasets into multiple files (e.g., single file per the resource type, limit file size to 100MB, limit number of resources per file to 100,000)?
• Are additional supporting resources such as Practitioner or Organization included in the export and under what circumstances?
• Does the server support system-wide (or all-patients, or Group-level) export? What parameters are supported for each request type? Note that this should also be captured in the server’s CapabilityStatement.
• What outputFormat values does this server support?
• In the case of a Group level export, does the _since parameter return additional resources modified prior to the supplied time if the resources belong to the patient compartment of a patient added to the Group after the supplied time?
• What includeAssociatedData values does this server support?