DB Dump #444
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| name: DB Dump | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| schedule: | |
| - cron: '0 0 * * *' | |
| jobs: | |
| sync: | |
| if: github.repository == 'PecanProject/bety' | |
| runs-on: ubuntu-latest | |
| services: | |
| postgres: | |
| image: mdillon/postgis:9.5 | |
| ports: | |
| - 5432:5432 | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Setup Database | |
| run: | | |
| psql -h localhost -U postgres -c "CREATE ROLE bety WITH LOGIN CREATEDB NOSUPERUSER NOCREATEROLE PASSWORD 'bety'" | |
| psql -h localhost -U postgres -c "CREATE DATABASE bety WITH OWNER bety" | |
| psql -h localhost -U postgres -d bety -c "CREATE EXTENSION postgis;" | |
| - name: Sync with EBI | |
| run: script/load.bety.sh -a "postgres" -p "-h localhost" -d "bety" -o bety -m 99 -r 0 -c -w http://www.betydb.org/dump/bety.tar.gz | |
| - name: Sync with BU | |
| run: script/load.bety.sh -a "postgres" -p "-h localhost" -d "bety" -o bety -m 99 -r 1 | |
| - name: Sync with BNL | |
| run: script/load.bety.sh -a "postgres" -p "-h localhost" -d "bety" -o bety -m 99 -r 2 -w ftp://anon:[email protected]/outgoing/betydb/bety.tar.gz | |
| - name: Sync with Wisconsin | |
| run: script/load.bety.sh -a "postgres" -p "-h localhost" -d "bety" -o bety -m 99 -r 5 -w http://tree.aos.wisc.edu:6480/sync/dump/bety.tar.gz | |
| - name: Dump Database | |
| run: | | |
| PG=$(docker ps | awk '/postgis/ { print $1 }') | |
| docker exec ${PG} pg_dump -h localhost -U postgres -F c bety > initdb/db.dump | |
| - name: Build Docker with Database dump | |
| run: | | |
| cd initdb | |
| docker build --tag image --file Dockerfile . | |
| - name: Build smaller dump for CI runs | |
| # update on scheduled runs, not every PR | |
| if: github.event.schedule != '' | |
| run: | | |
| # Nuke some large tables not used in testing | |
| # (to avoid foreign key constraints when deleting their child inputs) | |
| docker exec ${PG} psql -h localhost -U bety -c " | |
| TRUNCATE runs,likelihoods,benchmarks CASCADE" | |
| # Drop unneeded records from inputs table | |
| # (loop is because many are referenced only by descendent inputs | |
| # that are themselves deleted here.) | |
| while [ "$DEL_RES" != "DELETE 0" ]; do | |
| DEL_RES=$( | |
| docker exec ${PG} psql -h localhost -U bety -c " | |
| DELETE FROM inputs WHERE | |
| id NOT IN ( | |
| SELECT DISTINCT container_id FROM dbfiles | |
| WHERE container_type = 'Input' | |
| AND container_id IS NOT null) | |
| AND id NOT IN ( | |
| SELECT DISTINCT parent_id FROM inputs | |
| WHERE parent_id IS NOT null);" | |
| ) || break | |
| echo ${DEL_RES} | |
| done | |
| # CI tests don't need any records from the excluded tables, just schemas | |
| docker exec ${PG} pg_dump \ | |
| -h localhost -U bety \ | |
| --exclude-table-data='runs*' \ | |
| --exclude-table-data='inputs_runs*' \ | |
| --exclude-table-data='likelihoods*' \ | |
| --exclude-table-data='ensembles*' \ | |
| --exclude-table-data='posteriors_ensembles*' \ | |
| --exclude-table-data='benchmarks*' \ | |
| --exclude-table-data='reference_runs*' \ | |
| -F c \ | |
| bety > initdb/db.dump | |
| docker build --tag image_ci --file Dockerfile . | |
| - name: Login into registry | |
| run: | | |
| echo "${{ secrets.GITHUB_TOKEN }}" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin | |
| if [ -n "${{ secrets.DOCKERHUB_USERNAME }}" -a -n "${{ secrets.DOCKERHUB_PASSWORD }}" ]; then | |
| echo "${{ secrets.DOCKERHUB_PASSWORD }}" | docker login -u ${{ secrets.DOCKERHUB_USERNAME }} --password-stdin | |
| fi | |
| - name: Push docker image | |
| run: | | |
| IMAGE_ID=docker.pkg.github.com/${{ github.repository }}/db | |
| IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]') | |
| for T in $(date +'%Y-%V') 'latest'; do | |
| docker tag image $IMAGE_ID:$T | |
| docker push $IMAGE_ID:$T | |
| if [ -n "${{ secrets.DOCKERHUB_USERNAME }}" -a -n "${{ secrets.DOCKERHUB_PASSWORD }}" ]; then | |
| docker tag image pecan/db:$T | |
| docker push pecan/db:$T | |
| fi | |
| done | |
| if [ -n "$(docker image ls -q image_ci)" ]; then | |
| docker tag image_ci $IMAGE_ID:ci | |
| docker push $IMAGE_ID:ci | |
| docker tag image_ci pecan/db:ci | |
| docker push pecan/db:ci | |
| fi |