inst/README.md

In explodecomputer/alspac: Data dictionary for ALSPAC

Update ALSPAC dictionary

Each time the R drive files are update, we need to collate all the meta data from each of the stata files. The create_dictionary_from_stata.R automates this process. But the script needs access to the R drive, and ideally runs in parallel and not through the VPN (which is very slow).

Solution is to run the script on the crashdown.epi.bris.ac.uk docker cluster. Steps are:

1. Create the Docker environment to run the script (just need to do this once)
2. Mount the R drive, run the script within Docker, unmount the R drive (do this for every update)
3. Update the GitHub repository to a new version and push
4. Update the Shiny app

1. Create docker environment

This can be done by running the following (from /path/to/alspac/inst). Build the docker image that installs the alspac R package

sudo docker build -t ralspac:latest .

2. Update the package

Mount the R drive using a samba share:

mkdir -p mnt
sudo mount -t cifs -o user=$USER,vers=3.0 //central-gpfs.isys.bris.ac.uk/ALSPAC-Data mnt

(Note that on the crashdown server crashdown.epi.bris.ac.uk needed to install the cifs-utils package in order to mount (e.g. sudo apt-get install cifs-utils).)

Update the dictionary within the container

cd ../
sudo docker run --rm -e PASSWORD=123qwe -p 8787:8787 \
-v "$(pwd):/home/rstudio/alspac" \
-v "$(pwd)/inst/mnt:/home/rstudio/mnt" \
-w /home/rstudio/alspac/inst \
--name ralspac ralspac:latest \
Rscript create_dictionary_from_stata.R /home/rstudio/mnt 4

Unmount the R drive

sudo umount inst/mnt

Note if that doesn't work then find which process is using it

sudo lsof inst/mnt

Then kill that process and unmount

sudo kill -9 <pid>; sudo umount inst/mnt

This should have edited the following file:

data/current.rdata

3. Commit and update package version

1. See the history of versions using git tag
2. Edit the ../DESCRIPTION file to bump to the next version
3. Commit the changes to the rdata files and the DESCRIPTION file
4. Tag the commit git tag <new tag>
5. Push git push origin <new tag>

4. Update Shiny app

See info here https://github.com/explodecomputer/alspac-shiny

Mac

or on mac

docker build --platform linux/amd64 -t ralspac:latest .

and run

cd ../

docker run --platform linux/amd64 --rm -e PASSWORD=123qwe -p 8787:8787 \
-v "$(pwd):/home/rstudio/alspac" \
-v "/Volumes/ALSPAC-DATA:/home/rstudio/mnt" \
-w /home/rstudio/alspac/inst \
--name ralspac ralspac:latest \
Rscript create_dictionary_from_stata.R /home/rstudio/mnt 1

explodecomputer/alspac documentation built on Feb. 16, 2024, 4:18 p.m.