Description
Read and Search Interface to the 'HL7 FHIR' REST API.
Description
R on FHIR is an easy to use wrapper around the 'HL7 FHIR' REST API (STU 3 and R4). It provides tools to easily read and search resources on a FHIR server and brings the results into the R environment. R on FHIR is based on the FhirClient of the official 'HL7 FHIR .NET API', also made by Firely.
README.md
RonFHIR
R on FHIR is an easy to use wrapper around the 'HL7 FHIR' REST API (STU 3 and R4). It provides tools to easily read and search resources on a FHIR server and bring the results into the R environment. R on FHIR is based on the FhirClient of the official 'HL7 FHIR .NET API', also made by Firely.
Installation
# To download the latest release from CRAN use:
install.packages("RonFHIR")
# Or download the development version from GitHub:
# install.packages("devtools")
devtools::install_github("FirelyTeam/RonFHIR")
Overview
- Read
- Search
- GraphQL
- Operations
- Paging mechanism
- Fluent search calls
- OAuth 2.0
- Bulk Data
Usage
fhirClient
library(RonFHIR)
# Setting up a fhirClient
client <- fhirClient$new("https://vonk.fire.ly/")
# Setting up a fhirClient with OAuth 2.0
client <- fhirClient$new("Endpoint of FHIR server that supports SMART on FHIR OAuth2 access")
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$tokenUrl)
token <- httr::oauth2.0_token(endpoint = oauth_endpoint, app = app, scope = scopes)
client$setToken(token)
# Search
bundle <- client$search("Patient", c("name=Peter", "address-postalcode=3999"))
while(!is.null(bundle)){
# Do something useful here
# Go to the next page of the bundle using FHIRs paging mechanism
bundle <- client$continue(bundle)
}
# Searching with a 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"))
#GraphQL read
client$qraphQL("{id name{given,family}}", "Patient/example")
#GraphQL read
client$qraphQL("{PatientList(name:\"pet\"){name @first @flatten{family,given @first}}}")
# Operations
client$operation("Observation", name = "lastn")
fhirBulkClient
privatekey <- openssl::read_key("PrivateKey.pem")
# Create your claim
claim <- jose::jwt_claim(iss = "ServiceURL",
sub = "ClientID",
aud = "TokenURL",
# expiration date as epoch (5 minutes)
exp = as.integer(as.POSIXct( Sys.time() + 300)),
# 'random' number
jti = charToRaw(as.character(runif(1, 0.5, 100000000000))))
# Sign your claim with your private key
jwt <- jose::jwt_encode_sig(claim, privatekey)
# Define your scope(s)
scopes <- c("system/*.read", "system/CommunicationRequest.write")
# Create a new fhirBulkClient
bulkclient <- fhirBulkClient$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)