RonFHIR (version 0.4.0)

fhirBulkClient: fhirBulkClient

Description

Bulk data client in R for FHIR STU 3.

Usage

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)

Arguments

bulkclient

A fhirBulkClient object.

endpoint

The URL of the server to connect to.

tokenURL

Authorization server<U+2019>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).

Details

$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.

Examples

# 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)
# }
# NOT RUN {
# }