README.md

In hms-dbmi/pic-sure-biodatacatalyst-r-adapter-hpds: Simplified R library to communicate with HPDS-hosted services on the BioData Catalyst network

pic-sure-biodatacatalyst-r-adapter-hpds

Adapter Development

Generally, devtools::check() can be used in the R shell to check that documentation is up to date, unit tests are passing with a clean environment, and other possible problems.

Local Mac Installation

Install libgit2 locally, so devtools can be installed.

brew install R libgit2
R
Sys.setenv(TAR = "/usr/bin/tar")
options(unzip = "internal")
install.packages("devtools")
install.packages("urltools")
devtools::install_github("hms-dbmi/pic-sure-r-client", force=T)
devtools::install_github("hms-dbmi/pic-sure-r-adapter-hpds", force=T)
devtools::install("<full path to your local repo copy>/pic-sure-biodatacatalyst-r-adapter-hpds", force=T)

Running unit tests

Start R in this directory and run devtools::test() to execute all the unit tests available. For more information on unit testing in R, see R-Pkg's testing chapter and R-Lib's testthat package.

Run pseudo tests (manual integration)

Start R on the command line and install the latest copy of the library. Then source the pseudo tests, source("pseudo-tests/quick-check.R") and run them with a pic-sure url and your auth token, runtest(url, token).

Documentation

Documentation is generated from roxygen comments. To update, start R in this directory and run devtools::document() to regenerate the manual pages.

hms-dbmi/pic-sure-biodatacatalyst-r-adapter-hpds documentation built on Sept. 24, 2022, 9:24 a.m.