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psql demo db build

psql demo db build #74

Workflow file for this run

name: psql demo db build
on:
pull_request_review:
types: [submitted]
jobs:
mimic-iv-psql:
# only run if PR is approved
if: github.event.review.state == 'approved'
runs-on: ubuntu-latest
container: node:latest
services:
# Label used to access the service container
postgres:
# Docker Hub image
image: postgres
env:
POSTGRES_PASSWORD: postgres
# Set health checks to wait until postgres has started
options: >-
--health-cmd pg_isready
--health-interval 10s
--health-timeout 5s
--health-retries 5
steps:
- name: Check out repository code
uses: actions/checkout@v3
- name: Download demo data
uses: ./.github/actions/download-demo
- name: Install postgresql-client
run: |
apt-get update
apt-get install --yes --no-install-recommends postgresql-client
- name: Load icu/hosp data into PostgreSQL
run: |
echo "Loading data into psql."
psql -q -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/create.sql
psql -q -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/load_gz.sql
echo "Validating build."
psql -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/validate_demo.sql > results
# if we find "FAILED", then we did not pass the build
if grep -F -q "FAILED" results; then
echo "Failed the following row counts:"
head -n 1 results
grep "FAILED" results
exit 1
else
echo "Built and loaded demo data successfully."
cat results
fi
env:
POSTGRES_HOST: postgres
PGPASSWORD: postgres
BUILDCODE_PATH: mimic-iv/buildmimic/postgres
- name: Build mimic-iv concepts
run: |
psql -h $POSTGRES_HOST -U postgres -f postgres-functions.sql
psql -h $POSTGRES_HOST -U postgres -f postgres-make-concepts.sql
working-directory: ./mimic-iv/concepts_postgres
env:
POSTGRES_HOST: postgres
PGPASSWORD: postgres
- name: Load ed data into PostgreSQL
run: |
echo "Loading data into psql."
psql -q -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/create.sql
psql -q -h $POSTGRES_HOST -U postgres -v mimic_data_dir=ed/ -f ${BUILDCODE_PATH}/load_gz.sql
echo "Validating build."
psql -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/validate_demo.sql > results
# if we find "FAILED", then we did not pass the build
if grep -F -q "FAILED" results; then
echo "Failed the following row counts:"
head -n 1 results
grep "FAILED" results
exit 1
else
echo "Built and loaded demo data successfully."
cat results
fi
env:
# The hostname used to communicate with the PostgreSQL service container
POSTGRES_HOST: postgres
PGPASSWORD: postgres
# The default PostgreSQL port
POSTGRES_PORT: 5432
BUILDCODE_PATH: mimic-iv-ed/buildmimic/postgres