LimsaR

A simple implementation of the SODAR API to access the SODAR features from R.

Installation

You can install the development version of LimsaR from GitHub with:

# install.packages("devtools")
devtools::install_github("bihealth/LimsaR")

Quick start

Authentication

First, you need to know what your SODAR server is. For example, it can be https://sodar-demo.cubi.bihealth.org/.

Second you need to get hold of the API token. Without the token, you will not be able to work with LimsaR.

Once you have the server and the token, say, 'asdfb891823basdfuwerbce', before you start working you need to configure your access.

library(LimsaR)
token <- "asdfb891823basdfuwerbce"
sodar_url <- c("https://sodar-demo.cubi.bihealth.org")
sodar_config(token, sodar_url)

If you are a user of cubi-tk, chances are you have already set up the SODAR configuration in your ~/.cubitkrc.toml file. In that case, you can use the configr package to load the configuration:

library(configr)

access <- read.config("~/.cubitkrc.toml")

sodar_config(sodar_api_token = access$global$sodar_api_token,
             sodar_url = access$global$sodar_server_url)

Working with SODAR

Now you can get a data frame containing the projects and categories that are visible to you:

projects <- sodar_project_list()

Or check exactly who you are:

sodar_whoami()

A large part of the SODAR API is implemented. You can create and modify the projects. You can upload and download sample sheets. You can create and manipulate tickets, landing zones and delete requests. For example, if you have a project UUID and the project has a study and iRODS associated, you can create a landing zone with

lz <- sodar_lz_create(project_uuid)
# gets the UUID of the LZ
lz_uuid <- lz$sodar_uuid

and then check its status, and validate and move it with

sodar_lz_status(lz_uuid)
sodar_lz_move(lz_uuid)

Why LimsaR

Limsa is "Soda" in Finnish.