Update database collections #39

	name: Update database collections

	on:
	workflow_dispatch:
	schedule:
	- cron: "0 0 15 * *"

	concurrency:
	group: ${{ github.workflow }}-${{ github.head_ref \|\| github.ref }}
	cancel-in-progress: true

	jobs:
	download-and-build:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v2
	with:
	submodules: true
	fetch-depth: 0
	ref: main
	- name: Fetch GMT files
	id: gmts
	run: \|
	sudo apt-get update
	sudo apt-get install libcurl4-openssl-dev
	shiny_run/scripts/fetch_gmts.sh

	- name: Setup R
	uses: r-lib/actions/setup-r@v2

	- name: Install packages
	run: \|
	install.packages(c("dplyr","magrittr","httr","jsonlite","BiocManager"))
	BiocManager::install("rWikiPathways", ask = FALSE)
	shell: Rscript {0}

	- name: Build database
	run: \|
	Rscript -e "source('shiny_run/scripts/build_db_ghaction.R')"

	- name: Rotate and commit
	run: \|
	git config --global user.name 'GitHub Action'
	git config --global user.email '[email protected]'
	if [ "$(ls -A shiny_run/databases/temp)" ]; then
	git rm -f shiny_run/databases/archive/*.RData
	mkdir shiny_run/databases/archive
	git mv -f shiny_run/databases/*.RData shiny_run/databases/archive/
	mv shiny_run/databases/temp/*.RData shiny_run/databases/
	git add -f shiny_run/databases/*.RData
	git commit -m 'Update RData database collections'
	git push
	else
	echo "No new RData files"
	fi

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