Shiny app for ALSPAC searches

Updating

There are two parts to updating the website:

1. Updating the data dictionary in the R/alspac package

Connect to the R drive and clone the alspac R package. Full instructions are found here: https://github.com/explodecomputer/alspac#package-maintenance

2. Pushing those changes to the web application

If any changes are made to the shiny app then increment the version number by running

./update_version.sh <1/2/3>

The shiny app is deployed as a Docker container on crashdown.epi.bris.ac.uk. To update either because of changes to the app or the data dictionary, ssh into the server, clone the repository

git clone git@github.com:explodecomputer/alspac-shiny.git

Then build and deploy

cd alspac-shiny
./release.sh

Deployment

Every time a commit is pushed to the repo the docker image is rebuilt and pushed to https://hub.docker.com/repository/docker/explodecomputer/alspac-shiny/general.

You can trigger rebuilding (e.g. if the explodecomputer/alspac package is updated) by going to Actions, clicking the most recent job and clicking Re-run.

Then deploy using e.g.:

docker run -d \
  --name alspac-shiny \
  -p 8010:3838 \
  --restart=always \
  explodecomputer/alspac-shiny:latest

You can setup automatic updates with this:

docker run -d \
  --name alspac-shiny-watchtower \
  -v /var/run/docker.sock:/var/run/docker.sock \
  containrrr/watchtower \
  alspac-shiny

Notes on CI/CD (not currently working)

• https://gist.github.com/Daniel-ltw/552b90800b07c22e4a83dfa68ada6318
• https://github.com/orgs/community/discussions/26323

LEGACY: On Shiny server:

#!/bin/bash

maintenance=${1}

sudo R -e 'devtools::install_github("explodecomputer/alspac")'
sudo R -e 'devtools::install_github("rstudio/DT")'

cd ${HOME}/repo/alspac-shiny

git fetch
git pull
if [[ -n "$maintenance" ]]; then
        echo "deploying maintenance page"
        git checkout maintenance
        git pull
fi
sudo rm -r /srv/shiny-server/alspac/*
sudo cp -r * /srv/shiny-server/alspac/


if [[ -n "$maintenance" ]]; then
        git checkout master
fi

sudo systemctl restart shiny-server

To do

• Separate into Search and Browse
• Add search bar. Use typeahead: https://github.com/ThomasSiegmund/shinyTypeahead
• Search brings up a filtered table based on grep of the searched word
• Filter by tags or categories (lables 1-3)
• Filter by dataset - have an inventory of datasets including their details.
• Link to pdfs

Notes

Colours

• http://www.color-hex.com/color/c9002f
• ALSPAC background colour: #c9002f
• Selected colour: #7d001d
• Hover colour: #960023