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.
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)
Download and install VirtualBox
Install Ubuntu (in Virtual Box if necessary)
Clone the repository
git clone https://github.com/neelsoumya/dsMiscellaneous
cd dsMiscellaneous
Run installer_unix.sh
chmod 7555 installer_unix.sh
./installer_unix.sh
Run the following from the terminal
R --no-save < datashield_installer_basic.R
or type R at the terminal and at the R command prompt type the following
install.packages('devtools')
library(devtools)
devtools::install_github('neelsoumya/dsMiscellaneous')
Start RStudio Server by typing the following command at the Terminal
rstudio-server startGo to Firefox, and type localhost:8787 to go to R Studio server
Download and install the development Virtual Machine in Virtual Box
Docker for DataSHIELD
From the Terminal run the following command
R --no-save < baby_steps.R
or in R Studio open and run the file baby_steps.R
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opal_instructions.txt
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instructions for uploading data dictionary, data and creating tables in Opal server
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Opal javascript code
https://opaldoc.obiba.org/en/latest/magma-user-guide/value/value.html
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Other resources about DataSHIELD and Opal
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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
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Testing and development
https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/735314034/Writing+some+tests
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Git tips and tricks
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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
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Creating your own VM (Virtual Machine)
https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/367656962/Vagrant -
DataSHIELD repository
https://opaldoc.obiba.org/en/latest/cookbook/index.html -
Demo servers
username: administrator password: password
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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.
Soumya Banerjee
If you find this helpful, please cite the following DOI
10.5281/zenodo.5772830
