fhirBulkClient: fhirBulkClient
In FirelyTeam/RonFHIR: Read and Search Interface to the 'HL7 FHIR' REST API

Description Usage Arguments Details Examples

Bulk data client in R for FHIR STU 3.

bulkclient <- fhirBulkClient$new(endpoint, tokenURL = NULL, token = NULL)

bulkclient$patientExport(criteria = NULL)
bulkclient$groupExport(groupId, criteria = NULL)
bulkclient$wholeSystemExport(criteria = NULL)
bulkclient$getBulkStatus()
bulkclient$downloadBulk(requestNumber, returnType = "parsed" ,deleteFromQueue = TRUE)
bulkclient$deleteBulkRequest(requestNumber)
bulkclient$retrieveToken(jwt, scopes, tokenURL = NULL)
bulkclient$setToken(token)

print(bulkclient)

bulkclient: A fhirBulkClient object.
endpoint: The URL of the server to connect to.
tokenURL: Authorization server’s endpoint.
token: Acces token.
criteria: The search parameters to filter the Resources on. Each given string is a combined key/value pair (separated by '=').
groupId: Id of the Group resource.
requestNumber: Number of the request in the queue.
returnType: Specify the return type. This can be "parsed" or "ndjson".
deleteFromQueue: If the request needs to be deleted from the queue after it's been downloaded.
jwt: JSON Web Token signed with the app's private key (RSA SHA-256).
scopes: Desired scope(s).

$new() Creates a new fhirBulkClient using a given endpoint. If the endpoint does not end with a slash (/), it will be added.

$patientExport() Request all data on all patients. Possible to filter the results with the _outputFormat, _since and _type parameters. The request will be added to the queue.

$groupExport() Request all data of a patientgroup. Possible to filter the results with the _outputFormat, _since and _type parameters. The request will be added to the queue.

$wholeSystemExport() Request all data. Possible to filter the results with the _outputFormat, _since and _type parameters. The request will be added to the queue.

$getBulkStatus() Update and return the queue to see the progress of your requests.

$downloadBulk() Download a request from the queue.

$deleteBulkRequest() Cancel a request from the queue.

$retrieveToken() Retrieve a token from the authentication server.

$setToken Set a token.

print(p) or p$print() Shows which endpoint is configured.

## Not run: 
# Read your private key
privatekey <- openssl::read_key("PrivateKey.pem")

# Create your claim
claim <- jose::jwt_claim(iss = "ServiceURL",
                         sub = "ClientID",
                         aud = "TokenURL",
                         
			                    # expiration date as epoch (5 minutes)
                         exp = as.integer(as.POSIXct( Sys.time() + 300)), 
                         
   			                # 'random' number
                         jti = charToRaw(as.character(runif(1, 0.5, 100000000000)))) 

# Sign your claim with your private key
jwt <- jose::jwt_encode_sig(claim, privatekey)

# Define your scope(s)
scopes <- c("system/*.read", "system/CommunicationRequest.write")

# Create a new fhirBulkClient
bulkclient <- fhirBulkClient$new("FHIRBulkServerURL", tokenURL = "TokenURL")

# Retrieve your token
token <- bulkclient$retrieveToken(jwt, scopes)

# Set your token
bulkclient$setToken(token$access_token)

# Request a download for Patient Cohort 3
bulkclient$groupExport(3)

# Request the progress of the requests
bulkclient$getBulkStatus()

# When the downloads a available, download the bulkdata
patient_cohort_3 <- bulkclient$downloadBulk(1)

View(patient_cohort_3)

## End(Not run)