Show example use

[vojtechhuser]

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",
...
}

[slaverman]

Hi, thank you for your input. See the code below how your search would look like with R on FHIR.

query <- c("active=true", "family=Coleman", "given=Lisa,P.", "gender=female", "birthDate=1948-04-14")
client$search("Patient", query)

We are still working on a proper README file with examples for the GitHub repo. The full documentation of R on FHIR is available on CRAN.

[vojtechhuser]

thanks for reply

[gadepallivs]

Hi, do you have updated README ? The current example on github opens a blank page for auth. Is the CRAN release a stable one or the project is under active development ? Thank you

[slaverman]

This version is stable, as well as the version on CRAN. Have you tried re-installing the httr package? Otherwise try with a different browser. For me it still works with httr v 1.4.0 and Firefox.

[gadepallivs]

may be I am missing something very basic here. This line of the code client <- fhirClient$new("https://vonk.fire.ly/") has only Endpoint, but no token or tokenUrl or authUrl. Do i need to download and setup the firly server on windows ? Below is what I did

library(RonFHIR)
#> Warning: package 'RonFHIR' was built under R version 3.5.3
library(httr)
#> Warning: package 'httr' was built under R version 3.5.3

# Setting up a fhirClient with OAuth 2.0
client <- fhirClient$new("https://vonk.fire.ly")
client
#> Endpoint: https://vonk.fire.ly/

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
  )
oauth_endpoint
#> <oauth_endpoint>
#>  authorize: ?aud=https://vonk.fire.ly/
# Below code opens a blank page --- 
# Waiting for authentication in browser...
# Press Esc/Ctrl + C to abort
# token <-
#   httr::oauth2.0_token(
#     endpoint = oauth_endpoint,
#     app = app,
#     scope = scopes
#   )

^{Created on 2019-03-19 by the reprex package (v0.2.1)}

Session info

sessionInfo()
#> R version 3.5.1 (2018-07-02)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 10 x64 (build 14393)
#> 
#> Matrix products: default
#> 
#> locale:
#> [1] LC_COLLATE=English_United States.1252 
#> [2] LC_CTYPE=English_United States.1252   
#> [3] LC_MONETARY=English_United States.1252
#> [4] LC_NUMERIC=C                          
#> [5] LC_TIME=English_United States.1252    
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] httr_1.4.0    RonFHIR_0.3.1
#> 
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_1.0.1      digest_0.6.18   R6_2.4.0        jsonlite_1.6   
#>  [5] magrittr_1.5    evaluate_0.13   highr_0.7       stringi_1.4.3  
#>  [9] curl_3.3        rmarkdown_1.12  tools_3.5.1     stringr_1.4.0  
#> [13] xfun_0.5        yaml_2.2.0      compiler_3.5.1  htmltools_0.3.6
#> [17] knitr_1.22

[slaverman]

The endpoint https://vonk.fire.ly/ is an open endpoint and does not require authentication. You can try the SMART sandbox --> http://docs.smarthealthit.org/sandbox/

[gadepallivs]

Hi @slaverman . I tried with the SMART sandbox. https://r3.smarthealthit.org/. It says requires authorization and does the same thing.
RonFHIR works with SMART/FHIR ? If so, can you share an example for bulk query ?
Thank you

Press Esc/Ctrl + C to abort

Not sure, what I am missing. can you share

client <- fhirClient$new("https://r3.smarthealthit.org")
Warning: The endpoint requires authorization.

[slaverman]

Bulk queries only work for Bulk data API's like https://bulk-data.smarthealthit.org/ or you can set up your own bulk server, see https://github.com/smart-on-fhir/bulk-data-server

If you have a Bulk data endpoint, you can use the snippet below.

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)