mysql demo db build #59
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| name: mysql demo db build | |
| on: | |
| pull_request_review: | |
| types: [submitted] | |
| jobs: | |
| mimic-iv-mysql: | |
| # only run if PR is approved | |
| if: github.event.review.state == 'approved' | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v3 | |
| - name: Download demo data | |
| uses: ./.github/actions/download-demo | |
| with: | |
| gcp-project-id: ${{ secrets.GCP_PROJECT_ID }} | |
| gcp-sa-key: ${{ secrets.GCP_SA_KEY }} | |
| - name: Extract demo data to local folder | |
| run: | | |
| mv demo/hosp/*.csv.gz ./ | |
| mv demo/icu/*.csv.gz ./ | |
| mv demo/ed/*.csv.gz ./ | |
| gzip -d *.csv.gz | |
| - name: Start MySQL service | |
| run: | | |
| sudo /etc/init.d/mysql start | |
| mysql -u root -proot -e "SET GLOBAL local_infile=1;" | |
| mysql -u root -proot -e "SET GLOBAL sql_notes=0;" | |
| mysql -u root -proot -e "create database mimic" | |
| - name: Load icu/hosp demo data | |
| run: | | |
| echo "Loading data into mysql." | |
| mysql -u root -proot --local-infile=1 mimic < mimic-iv/buildmimic/mysql/load.sql | |
| mysql -u root -proot mimic < mimic-iv/buildmimic/mysql/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 | |
| - name: Load ed demo data | |
| run: | | |
| echo "Loading data into mysql." | |
| mysql -u root -proot --local-infile=1 mimic < mimic-iv-ed/buildmimic/mysql/load.sql | |
| mysql -u root -proot mimic < mimic-iv-ed/buildmimic/mysql/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 |