Merge pull request #600 from HopkinsIDD/dev_manuscript_fig5_fix #2130
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| name: unit-tests | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| pull_request: | |
| branches: | |
| - master | |
| - dev | |
| jobs: | |
| unit-tests: | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: docker://hopkinsidd/choleramappingpipeline:latest-dev | |
| options: --user root | |
| steps: | |
| - name: Remove unnecessary files | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Checkout Layers | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: HopkinsIDD/cholera-covariates | |
| ref: for_testing | |
| path: Layers/ | |
| lfs: true | |
| token: ${{ secrets.PERSONAL_TOKEN }} | |
| - name: Set up Rprofile | |
| run: cp Docker.Rprofile $HOME/.Rprofile | |
| shell: bash | |
| - name: Run taxdat tests | |
| run: | | |
| setwd("packages/taxdat") | |
| devtools::test(stop_on_failure=TRUE) | |
| shell: Rscript {0} | |
| - name: Ingest Covariates | |
| run: | | |
| service postgresql start | |
| bash grant_cholera_database.sh root | |
| export USER=root | |
| Rscript -e "install.packages('packages/taxdat',type='source',repos=NULL)" | |
| pwd | |
| Rscript Analysis/R/prepare_grid_cmd.R -d ./ -u root -r 1 -i TRUE -a KEN | |
| Rscript Analysis/R/prepare_grid_cmd.R -d ./ -u root -r 20 -i TRUE -a KEN | |
| Rscript Analysis/R/prepare_covariates_cmd.R -d ./Layers -u root -r 1 -t '1 years' -i TRUE -p FALSE -n 1 -o FALSE -x TRUE -m TRUE -c p -g 'public.grid_1_1' -a KEN | |
| Rscript Analysis/R/prepare_covariates_cmd.R -d ./Layers -u root -r 20 -t '1 years' -i TRUE -p FALSE -n 1 -o FALSE -x FALSE -m TRUE -c p,dw -g 'public.grid_20_20' -a KEN | |
| shell: bash | |
| - name: Run integration tests | |
| env: | |
| CHOLERA_API_USERNAME: ${{ secrets.CHOLERA_API_USERNAME }} | |
| CHOLERA_API_KEY: ${{ secrets.CHOLERA_API_KEY }} | |
| run: | | |
| service postgresql start | |
| bash grant_cholera_database.sh root | |
| export USER=root | |
| Rscript -e "install.packages('packages/taxdat',type='source',repos=NULL)" | |
| pwd | |
| cd test | |
| export PRODUCTION_RUN=FALSE | |
| Rscript run_tests.R | |
| shell: bash |