dsMiscellaneous

Introduction

dsMiscellaneous is a set of miscellaneous development tools and beginner's resources for use in DataSHIELD.

DataSHIELD is a platform for privacy preserving federated analysis.

https://github.com/datashield

Files

installer_unix.sh Installer in UNIX (shell script)

installation_steps_workflow.md Installation steps for DataSHIELD

datashield_installer_basic.R R installation script to install R packages for DataSHIELD

baby_steps.R First coding project in DataSHIELD

ds.retStr.R First client side script to learn coding in DataSHIELD

     https://github.com/neelsoumya/dsBaseClient/blob/test_functions_branch/R/ds.retStr.R

retStrDS.R First server side script to learn coding in DataSHIELD

     https://github.com/neelsoumya/dsBase/blob/test_functions_branch/R/retStrDS.R

testthat.R Simple R script for using testthat for unit testing

teaching_resources.md Teaching resources using DataSHIELD

opal_instructions.txt Instructions for setting up and using Opal server (data warehouse)

Installation

Download and install VirtualBox

• https://www.virtualbox.org/wiki/Downloads

Install Ubuntu (in Virtual Box if necessary)

• https://ubuntu.com/download/desktop

Clone the repository

```r git clone https://github.com/neelsoumya/dsMiscellaneous

cd dsMiscellaneous

```

Run installer_unix.sh

```r chmod 7555 installer_unix.sh

./installer_unix.sh

```

Run the following from the terminal

```r

R --no-save < datashieldinstallerbasic.R

```

or type R at the terminal and at the R command prompt type the following

```r

install.packages('devtools') library(devtools)

devtools::install_github('neelsoumya/dsMiscellaneous')

```

Start RStudio Server by typing the following command at the Terminal

r rstudio-server start

Go to Firefox, and type localhost:8787 to go to R Studio server

Download and install the development Virtual Machine in Virtual Box

• https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/1658093595/RStudio+Server+based+Development+VM

Docker for DataSHIELD

• https://wilmarigl.de/?p=424

Usage

From the Terminal run the following command

```r

R --no-save < baby_steps.R

```

or in R Studio open and run the file baby_steps.R

Instructions for using DataSHIELD as a developer

• opal_instructions.txt

  • instructions for uploading data dictionary, data and creating tables in Opal server

  • Opal javascript code

    https://opaldoc.obiba.org/en/latest/magma-user-guide/value/value.html

• Other resources about DataSHIELD and Opal

  • Opal

         https://opaldoc.obiba.org/en/latest/cookbook/index.html
    

    • Installation of virtual machines and DataSHIELD

      https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/931069953/Installation+Training+Hub-+DataSHIELD+v6

    • Virtual Box VM download

      https://www.virtualbox.org/wiki/Downloads

    • Ubuntu ISO image

      https://ubuntu.com/download/desktop

    • Installation of development VM

      https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/1658093595/RStudio+Server+based+Development+VM

    • Installation for development environment

    https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/12943461/Getting+started * Testing and development

    https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/735314034/Writing+some+tests * Git tips and tricks

    https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/1006633032/GitHub+Bring+edits+from+another+repository+to+your+own * Developer tips and tricks

    https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/702218241/Developer+Tricks+and+Tips

     https://isglobal-brge.github.io/resource_bookdown/package-info.html#example-of-datashield-package-development
    

    • Setting up Opal server and loading data

    https://gitlab.inesctec.pt/wp4-recap/wp4_workshop/-/wikis/opal * Creating your own VM (Virtual Machine)

         https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/367656962/Vagrant 
    

    • DataSHIELD repository

    https://github.com/datashield

         https://opaldoc.obiba.org/en/latest/cookbook/index.html
    

    • Demo servers

    https://opal-demo.obiba.org/

    username: administrator password: password

    https://datashield-demo.obiba.org/

Acknowledgements

We acknowledge the help and support of the DataSHIELD technical team. We are especially grateful to Tom RP Bishop, Elaine Smith, Eleanor Hyde, Stuart Wheater, Yannick Marcon, Paul Burton, Demetris Avraam, Patricia Ryser-Welch, Kevin Rue-Albrecht and Wolfgang Viechtbauer for fruitful discussions and feedback.

Contact

Soumya Banerjee

sb2333@cam.ac.uk

Citation

If you find this helpful, please cite the following DOI

10.5281/zenodo.5772830