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’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)

## End(Not run)

fhirClient

Description

Read and search only client in R for FHIR STU 3 and R4. Based on the official HL7 FHIR .NET API.

Usage

client <- fhirClient$new(endpoint, token = NULL)

client$read(location, summaryType = NULL, returnType = "parsed")
client$search(resourceType, criteria = NULL, includes = NULL, pageSize = NULL, summaryType = NULL, returnType = "parsed")
client$searchById(resourceType, id, includes = NULL, summaryType = NULL, returnType = "parsed")
client$wholeSystemSearch(criteria = NULL, includes = NULL, pageSize = NULL, summaryType = NULL, returnType = "parsed")
client$searchParams(params, resourceType = NULL, returnType = "parsed")
client$continue(bundle)


client$setToken(token)

client$endpoint
client$authUrl
client$tokenUrl
client$registerUrl
client$token

print(client)

Arguments

client

A fhirClient object.

endpoint

The URL of the server to connect to.

token

An ouath 2.0 Token (httr Token 2.0)

resourceType

The type of resource to search for.

id

The id of the Resource to search for.

summaryType

Whether to include only return a summary of the Resource(s).

location

The url of the Resource to fetch. This can be a Resource id url or a version-specific.

criteria

The search parameters to filter the Resources on. Each given string is a combined key/value pair (separated by '=').

includes

Paths to include in the search.

pageSize

Asks server to limit the number of entries per page returned.

query

A searchParams object containing the search parameters.

bundle

The bundle as received from the last response.

returnType

Specify the return type. This can be "parsed", "json" or "xml".

Details

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

$read() Fetches a typed Resource from a FHIR resource endpoint.

$search() Search for Resources of a certain type that match the given criteria.

$searchById() Search for Resources based on a Resource's id.

$wholeSystemSearch() Search for Resources across the whole server that match the given criteria.

$searchByQuery() Search for Resources based on a searchParams object.

$continue() Uses the FHIR paging mechanism to go navigate around a series of paged result Bundles.

$setToken() Saves an Oauth 2.0 token in a variable.

$endpoint Returns the endpoint.

$authUrl Returns the authorization server’s OAuth authorization endpoint.

$tokenUrl Returns the authorization server’s OAuth token endpoint.

$registerUrl Returns the endpoint where the client can register.

$token Returns the initialized token.

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

Examples

## Not run: 
# Setting up a fhirClient
client <- fhirClient$new("https://vonk.fire.ly")
# Read
client$read("Patient/example")

# Search
bundle <- client$search("Patient", c("name=Peter", "address-postalcode=3999"))

while(!is.null(bundle)){
   # Do something useful
   bundle <- client$continue(bundle)
}

## End(Not run)
## Not run: 
# Using Oauth 2.0
client <- fhirClient$new("https://vonk.fire.ly")

# Retrieving a token

client_id <- "id"
client_secret <- "secret"
app_name <- "TestApp"
scopes <- c("patient/*.read")

app <- httr::oauth_app(appname = app_name, client_id, client_secret)
oauth_endpoint <- httr::oauth_endpoint(
                  authorize = paste(client$authUrl, "?aud=", client$endpoint, sep=""),
                  access = client$tokenUrl)
  
token <- httr::oauth2.0_token(endpoint = oauth_endpoint, app = app, scope = scopes)

# Set a token and read a patient resource
client$setToken(token$credentials$access_token)

client$read("Patient/example")

# Token refresh
token <- token$refresh()

client$setToken(token$credentials$access_token)


## End(Not run)

searchParams

Description

An alternative way to specify a query is by creating a searchParams object and pass this to the fhirClient's searchByQuery. The searchParams class has a set of fluent calls to allow you to easily construct more complex queries. Based on the official HL7 FHIR .NET API.

Usage

query <- searchParams$new()

query$select(elements)
query$where(criteria)
query$include(path)
query$orderBy(paramName, sortOrder = "asc")
query$limitTo(count)
query$countOnly()
query$summaryOnly()
query$textOnly()
query$dataOnly()

Arguments

query

A searchParams object that contains all specified search criteria.

elements

Elements defined at the root level in the Resource.

criteria

The search parameters to filter the Resources on. Each given string is a combined key/value pair (separated by '=').

path

Paths to include in the search.

paramName

Name of the parameter to order by.

sortOrder

Direction of the order. Can be asc or desc (ascending and descending).

count

The number of returned Resources per page.

Details

$new() Creates a new searchParams object.

$select() Specify the elements to be returned as part of a Resource.

$where() Specify on which parameters to filter.

$include() Specify the paths to include.

$orderBy() Specify the order to return the results.

$limitTo() Specify how many Resources should be returned in a single page of a Bundle.

$countOnly() Specifiy to just return a count of the matching Resources, without returning the actual matches.

$summaryOnly() Specify to return only those elements marked as "summary" in the base definition of the Resource(s).

$textOnly() Specify to return only the "text" element, the 'id' element, the 'meta' element, and only top-level mandatory elements.

$dataOnly() Specify to remove the text element.

Examples

## Not run: 
# Setting up a fhirClient
client <- fhirClient$new("http://vonk.furore.com")

# Creating a new searchParams object
query <- searchParams$new()
query$select(c("name", "birthDate"))$where("given:exact=Peter")$orderBy("family")


peters <- client$searchByQuery(query, "Patient")
# equivalent:
# client$search("Patient", c("_elements=name,birthDate","given:exact=Peter", "_sort=family"))

while(!is.null(bundle)){
   # Do something useful
   peters <- client$continue(peters)
}

## End(Not run)