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Merge pull request #1400 from MIT-LCP/gh_action_dependency
GitHub actions refactor
2 parents 5d0e11d + 57a7504 commit a3159d9

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‎.github/actions/download-demo/action.yml‎

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name: "Download MIMIC-IV Demo"
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description: "Downloads MIMIC-IV demo data from GCP"
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inputs:
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gcp-project-id:
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required: true
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description: "The Google Cloud Project ID used for billing usage"
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gcp-sa-key:
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required: true
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description: "The service account key used to authenticate with GCP"
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runs:
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using: "composite"
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steps:
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- name: Authenticate with GCP
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uses: 'google-github-actions/auth@v0'
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with:
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project_id: ${{ inputs.gcp-project-id }}
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credentials_json: ${{ inputs.gcp-sa-key }}
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- name: Set up Cloud SDK
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uses: 'google-github-actions/setup-gcloud@v0'
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- name: Download demo data from GCP
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run: |
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echo "Downloading MIMIC-IV demo from GCP."
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gsutil -q -u $PROJECT_ID -m cp -r gs://mimic-iv-archive/v2.0/demo ./
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env:
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PROJECT_ID: ${{ inputs.gcp-project-id }}
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shell: bash

‎.github/workflows/build-db.yml‎

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‎.github/workflows/mysql.yml‎

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name: mysql demo db build
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on:
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pull_request_review:
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types: [submitted]
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jobs:
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mimic-iv-mysql:
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# only run if PR is approved
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if: github.event.review.state == 'approved'
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runs-on: ubuntu-22.04
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steps:
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- name: Check out repository code
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uses: actions/checkout@v3
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- name: Download demo data
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uses: ./.github/actions/download-demo
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with:
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gcp-project-id: ${{ secrets.GCP_PROJECT_ID }}
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gcp-sa-key: ${{ secrets.GCP_SA_KEY }}
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- name: Extract demo data to local folder
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run: |
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mv demo/hosp/*.csv.gz ./
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mv demo/icu/*.csv.gz ./
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mv demo/ed/*.csv.gz ./
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gzip -d *.csv.gz
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- name: Start MySQL service
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run: |
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sudo /etc/init.d/mysql start
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mysql -u root -proot -e "SET GLOBAL local_infile=1;"
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mysql -u root -proot -e "SET GLOBAL sql_notes=0;"
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mysql -u root -proot -e "create database mimic"
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- name: Load icu/hosp demo data
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run: |
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echo "Loading data into mysql."
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mysql -u root -proot --local-infile=1 mimic < mimic-iv/buildmimic/mysql/load.sql
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mysql -u root -proot mimic < mimic-iv/buildmimic/mysql/validate_demo.sql > results
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# if we find "FAILED", then we did not pass the build
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if grep -F -q "FAILED" results; then
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echo "Failed the following row counts:"
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head -n 1 results
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grep "FAILED" results
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exit 1
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else
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echo "Built and loaded demo data successfully."
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cat results
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fi
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- name: Load ed demo data
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run: |
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echo "Loading data into mysql."
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mysql -u root -proot --local-infile=1 mimic < mimic-iv-ed/buildmimic/mysql/load.sql
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mysql -u root -proot mimic < mimic-iv-ed/buildmimic/mysql/validate_demo.sql > results
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# if we find "FAILED", then we did not pass the build
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if grep -F -q "FAILED" results; then
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echo "Failed the following row counts:"
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head -n 1 results
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grep "FAILED" results
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exit 1
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else
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echo "Built and loaded demo data successfully."
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cat results
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fi

‎.github/workflows/psql.yml‎

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

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