Stream: implementers

Topic: R on Fhir

rekha (Oct 22 2019 at 12:24):

Hi All,
Is there any documentation related to R on FHIR and what is mean by that. Can anyone suggest me??
Thanks in advance.

Andrew Wason (Oct 22 2019 at 14:07):

Redox has some info on it here https://www.redoxengine.com/fhir/

Grahame Grieve (Oct 22 2019 at 17:08):

first hit in google: https://github.com/FirelyTeam/RonFHIR

Ward Weistra (Oct 23 2019 at 08:39):

@Sander Laverman will also present on it in the upcoming DevDays in Amsterdam: https://www.devdays.com/amsterdam/schedule-2019/#event-765

rekha (Oct 23 2019 at 09:21):

Thank you all for the information provided.

Andrew Wason (Oct 23 2019 at 14:17):

It's not related, Redox calls their FHIR compatibility solution R^FHIR (Redox on FHIR). The "R" is for Redox, vs RonFHIR where the "R" is for the R language.

I am interested in using R with FHIR as well. However, did not succeed using the RonFHIR package. Used SMART on FHIR python library and pulled the data into R. However, this is again an open server. Could not really get SMART python library work with their test sandboxes or epic test. I currently have an app ( same app built it in R Shiny & Python flask) that works well with some test EHR data stored in files locally. This has to integrate with the EPIC EHR to pull the realt-time EHR data , and I understood that SMART is framework that would help me to get this task to communicate with EPIC via FHIR. I am not technically sound about EHR infra ( Neither FHIR or SMART) server concepts, tokens , oauth2 etc. Can someone please layout a step-wise tasks manner on what it takes to for an app to be able to launch on EPIC interface ( end user is doctor) ? So, I can get some expert help for specific task that I cannot do it myself.

Grahame Grieve (Oct 23 2019 at 17:36):

if you are using the RonFHIR library and it's not working, you probably need to report a very specific error message as an issue (or make a PR!) against the RonFHIR library @Sander Laverman unless you nominate a different place

rekha (Oct 24 2019 at 05:13):

Thanks @Andrew Wason, @gvs, @Grahame Grieve

Ward Weistra (Oct 24 2019 at 13:59):

@gvs What problem did you run into with R on FHIR? It currently only supports STU3. There's an example of using it with SMART on FHIR here: https://github.com/FirelyTeam/RonFHIR#fhirclient
For Python trouble you could try the #python channel. But as Grahame suggests you would need to share what you have tried and at what specific point you run into trouble.

gvs (Oct 24 2019 at 19:15):

@Ward Weistra , I tried the example on github page. for the Oauth2, rstudio Waiting for authentication in browser... Press Esc/Ctrl + C to abort. The browser does not open for me. I did contact @Sander Laverman , he was very prompt to reply suggested to update httr packages or other dependencies. I could not fix it, hence moved from R and tried python. Can you provide example with testable links for oauth2 using RonFHIR ( with tokens and other parameters it require) The example says to enter so and so information, but does not provide a working links. I tried some of the SMART open and OuAuth2 test ...could not get it work in R. For Python, could not get their Oauth2 work so far, but the basic or open api works. And, to share what I have tried...can I do it in this chat box or send email ? if so, which email

gvs (Oct 24 2019 at 19:18):

Setting up a fhirClient with OAuth 2.0

client <- fhirClient$new("Endpoint of FHIR server that supports SMART on FHIR OAuth2 access")
The github page does not provide the url to try. I tried different urls like https://r3.smarthealthit.org and so on, and it never worked. Can you provide which url works and what are the tokens associated ?

Last updated: Apr 12 2022 at 19:14 UTC

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