firelyteam/ronfhir

R on FHIR

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 'Firely .NET SDK', 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)

ronfhir's Issues

client$continue is throwing 401 due to indiscriminate prepending of endpoint to subsequent page

Show example use

This is super cool project.

it would be nice to see this mimic the call like this one below
from http://docs.smarthealthit.org/

$ curl https://sb-fhir-dstu2.smarthealthit.org/api/smartdstu2/open/Patient/SMART-1551992
-H 'Accept: application/json'
{
"resourceType": "Patient",
"active": true,
"name": [{
"use": "official",
"family": ["Coleman"],
"given": ["Lisa","P."]
}],
"gender": "female",
"birthDate": "1948-04-14",
...
}

better quoting in example

in AMIA tutorial, you used \ to escape "

better approach would be to do ' my text with "quotes" '

it would make the tutorial much more readable!

here:

Support for FHIR R4

Do you plan to add support for FHIR R4? Currently, there is an error

"R on FHIR is not compatible with 4 only with STU 3"

when I try to authenticate to an R4 FHIR server.

Thank you,

Jakob