README.Rmd

---
title: "MolgenisArmadillo"
output: github_document
---

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```{r, include = FALSE}
knitr::opts_chunk$set(
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Client to share data in a [MOLGENIS Armadillo DataSHIELD Service](https://github.com/molgenis/molgenis-service-armadillo/).

## Purpose
This library can be used by data managers to share datasets on a
MOLGENIS Armadillo server.

## Overview
The datasets are stored in shared folders on a MinIO file store. The MOLGENIS
Armadillo server has access to the file store and can load the data sets into
a shielded RServe environment so that researchers can call DataSHIELD analysis
methods on the data.

## Usage
Login to the service.
``` R
library('MolgenisArmadillo')
armadillo.login("https://armadillo-url-example.org")
```

Now you can create a project and upload tables to the project to share them for
analysis.
``` R
library(datasets)
armadillo.create_project("project")
armadillo.upload_table("project", "folder", iris)
```

Listing the tables.
``` R
armadillo.list_tables("project")
```

Removing the data from the storage. First you need to remove the content of a project before you can delete the project.
``` R
armadillo.delete_table("project", "folder", "iris")
armadillo.delete_project("project")
```

## Documentation
For more in depth documentation please check the [howto](https://molgenis.github.io/molgenis-r-armadillo/articles/MolgenisArmadillo.html).

## Armadillo 2
The newest version (2.x) of MolgenisArmadillo will be only compatible with Armadillo version 3. If you still use Armadillo 2, you should use the 1.1.13 version of MolgenisArmadillo. You can install this specific version using
the following commands:

For windows:
``` R
packageurl <- "https://cran.rstudio.com/bin/windows/contrib/4.2/MolgenisArmadillo_1.1.3.zip"
install.packages(packageurl, repos=NULL, type="source")
```

For Mac:
``` R
packageurl <- "https://cran.rstudio.com/bin/macosx/contrib/4.2/MolgenisArmadillo_1.1.3.tgz"
install.packages(packageurl, repos=NULL, type="source")
```

For Linux:
``` R
packageurl <- "https://cran.rstudio.com/src/contrib/MolgenisArmadillo_1.1.3.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
```

## For developers

- To build documentation, do `devtools::document()`
- To run all unit tests, do `devtools::test()`
- While writing code (or tests), you can use `devtools::load_all()` to quickly "install" the package.
- To run a single test file, open it in Rstudio and do `devtools::test_active_file()`
- To run the linter, do `devtools::lint()`. Tip: run it often :)
- To create new README from Rmd: run `devtools::build_readme()`