https://github.com/neelsoumya/dsmiscellaneous
Miscellaneous tools for use in DataSHIELD
https://github.com/neelsoumya/dsmiscellaneous
datashield teaching-materials
Last synced: over 1 year ago
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Miscellaneous tools for use in DataSHIELD
- Host: GitHub
- URL: https://github.com/neelsoumya/dsmiscellaneous
- Owner: neelsoumya
- License: gpl-3.0
- Created: 2021-12-07T17:01:57.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2023-04-17T09:08:20.000Z (about 3 years ago)
- Last Synced: 2025-01-08T08:47:17.072Z (over 1 year ago)
- Topics: datashield, teaching-materials
- Language: R
- Homepage:
- Size: 65.4 KB
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
# dsMiscellaneous
[](https://www.gnu.org/licenses/gpl-3.0.html)
## 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 < datashield_installer_basic.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
[](https://doi.org/10.5281/zenodo.5772831)