mysql demo db build #77
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 hosp/*.csv.gz ./ | |
| mv icu/*.csv.gz ./ | |
| mv 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 |