README.md

In vjcitn/AnvBiocFHIR: Use pyAnVIL and SMART infrastructure to work with AnVIL FHIR in R

AnvBiocFHIR

This README is updated 29 May 2022.

A thorough introduction to FHIR in the NIH Cloud Interoperability project is provided in a jupyter notebook last edited in July 2020.

In the RStudio console, in May 2022, use

pip install pyAnVIL==0.1.1rc2
pip install git+https://github.com/smart-on-fhir/client-py#egg=fhirclient==4.0.0

to obtain necessary infrastructure.

The R package at github.com/vjcitn/AnvBiocFHIR uses basilisk to pin down all details of python infrastructure used to interface to the FHIR services in AnVIL.

Installation steps

Ensure that the .Renviron file in the home folder has a line PIP_USER=false.

Verify that the setting of PIP_USER is "false" using Sys.getenv("PIP_USER").

Install the package:

BiocManager::install("vjcitn/AnvBiocFHIR")

Instantiate the python infrastructure with

x = try(AnvBiocFHIR::abfhir_demo()) 

This will take some time to construct a conda environment.

Evaluate x to see a list of two Module objects produced by reticulate.

Demonstration

library(AnvBiocFHIR)
example(connect_smart)

On 29 May 2022 the result is

> unlist(lapply(res[1:5], function(x) x$id))
[1] "AnVIL-CMG-Broad-Muscle-Myoseq-WES"       
[2] "AnVIL-CMG-Broad-Orphan-Estonia-Ounap-WGS"
[3] "AnVIL-CMG-Broad-Brain-Gleeson-WES"       
[4] "AnVIL-CMG-Broad-Muscle-Topf-WES"         
[5] "AnVIL-CCDG-Broad-CVD-AFib-Duke-WGS"     

vjcitn/AnvBiocFHIR documentation built on May 31, 2022, 10:39 a.m.