README.Rmd

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

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

<!-- badges: start -->
[![Build Status](https://travis-ci.org/molgenis/molgenis-r-armadillo.svg?branch=master)](https://travis-ci.org/molgenis/molgenis-r-armadillo)
[![CRAN status](https://www.r-pkg.org/badges/version/MolgenisArmadillo)](https://CRAN.R-project.org/package=MolgenisArmadillo)
[![codecov](https://codecov.io/gh/molgenis/molgenis-r-armadillo/branch/master/graph/badge.svg)](https://codecov.io/gh/molgenis/molgenis-r-armadillo)
<!-- badges: end -->

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.
Researchers can then analyse these datasets and datasets shared on other servers
using DataSHIELD.
Researchers will only be able to access aggregate information and cannot see
individual rows.

## 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.dev.molgenis.org",
      "https://armadillo-minio.dev.molgenis.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 throw away 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).