QuartzBio EDP for R

This package contains the QuartzBio EDP R language bindings for the EDP (Enterprise Data Platform) API.

Features:

Authentication
Parallelization of dataset queries
Progress report
S3 methods
Portability between most platforms: Linux, Windows, OS X.

Please see the legacy SolveBio documentation for more information about the platform.

Beta Release

on-going migration of legacy solvebio R API to the new quartzbio.edp package.
backwards compatibility is currently maintained by providing the legacy SolveBio R client with the new client.
See ChangeLog for updates

Installation

Installing this package requires an installed R environment.

installation from GitHub

remotes::install_github("quartzbio/quartzbio.edp", dependencies = TRUE)

RcppSimdJson and CXX17

quartzbio.edp uses the RcppSimdJson R package for speed.

But on some older systems, RcppSimdJson requires a CXX17 compatible C++ compiler, even when installed from a pre-compiled binary package..

In this case, you can manually install a CXX17 compiler. Here are some resources:

In any case, RcppSimdJson is optional. If not installed, quartzbio.edp will work seamlessly in degraded mode.

complete reproducible installation example using a tidyverse qbrocker image

# run a shell inside the tidyverse container
docker run -ti --rm rocker/tidyverse  bash

# use the pre-installed installGithub.r script
installGithub.r -d TRUE quartzbio/quartzbio.edp

### OR: run R and use the `install_github()` function
R
>remotes::install_github("quartzbio/quartzbio.edp", dependencies = TRUE)

documentation

Github public quartzbio.edp source repository
Github quartzbio.edp online package documentation

Usage

connection/authentication

See the Connection to an EDP host vignette for more details.

Get an Authentication Token. They can be obtained from Personal Access Tokens

Save it into the ~/.qb/edp.json file as the default EDP configuration profile.
Your ~/.qb/edp.json may look like:

{
  "default": {
    "secret": "PUT_HERE_TOUR_AUTHENTICATION_TOKEN",
    "host": "https://api.solvebio.com"
  }
}

The package functions will use this default profile by default if you do not use an explicit configuration. For example:

library(quartzbio.edp)
User()
Vaults()
Folders()

Articles

Vignettes

dragosmg/quartzbio.edp