Nightly Round-Trip Tests (Public) #467
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| name: Nightly Round-Trip Tests (Public) | |
| on: | |
| schedule: | |
| - cron: "0 7 * * *" | |
| workflow_dispatch: | |
| env: | |
| python-version: "3.9" | |
| poetry-version: "1.2.1" | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout Our Code | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: '${{ github.ref }}' | |
| - name: Get GH Reference | |
| run: echo '${{ github.ref }}' >> ~/github.ref | |
| - name: Upload Ref | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: github_hash | |
| path: ~/github.ref | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.python-version }} | |
| - name: Install poetry | |
| run: python3 -m pip install poetry==${{ env.poetry-version }} | |
| - name: Install other python dependencies | |
| run: python3 -m pip install -r requirements.txt | |
| - name: build vcell-cli-utils package | |
| run: | | |
| cd vcell-cli-utils | |
| poetry install | |
| - name: build vcell-admin package | |
| run: | | |
| cd docker/swarm/vcell-admin | |
| poetry install | |
| - name: build vcell-opt package | |
| run: | | |
| cd pythonProject/vcell-opt | |
| poetry install | |
| - name: Setup Java for Build | |
| uses: actions/setup-java@v2 | |
| with: | |
| java-version: '8' | |
| distribution: 'adopt' | |
| cache: 'maven' | |
| # Get files from VCDB | |
| - name: Checkout Input Files | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: virtualcell/vcdb | |
| path: ./filesToTest | |
| - name: Put Files To Testing Directory | |
| run: mkdir -p $HOME/test_dir && cp $GITHUB_WORKSPACE/filesToTest/public/biomodel/vcml/* $HOME/test_dir | |
| - name: Build VCell Jars && Run Roundtrip Test | |
| run: mvn --batch-mode clean install dependency:copy-dependencies -Dgroups="org.vcell.test.Nightly" -Dvcell.vcmlLocation="$HOME/test_dir" | |
| # Report a Success | |
| - name: Report Results to Slack | |
| run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="$(cat $HOME/test_dir/results/rawRoundTripResults.txt)" https://slack.com/api/chat.postMessage | |
| # | |
| # - name: Set up Docker Buildx | |
| # uses: docker/setup-buildx-action@v2 | |
| # | |
| # - name: Build and Export | |
| # uses: docker/build-push-action@v3 | |
| # with: | |
| # context: . | |
| # file: ./Dockerfile | |
| # outputs: type=docker,dest=/tmp/image.tar | |
| # build-args: | # Max ram for Ubuntu GitHub workflow is 7GB (as of 12/9/22), using MB for precision (0.8 of 7gb) | |
| # MAX_JAVA_MEM=5734 | |
| # | |
| # - name: Upload Artifact | |
| # uses: actions/upload-artifact@v3 | |
| # with: | |
| # name: docker-image | |
| # path: /tmp/image.tar | |
| # Report a Problem to Slack | |
| - name: Report Problem to Slack | |
| if: ${{ failure() }} | |
| run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="Uh-Oh! The Nightly Testing Action on GitHub Failed ( ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} )! This may need attention..." https://slack.com/api/chat.postMessage | |
| # Tmate just in case | |
| - name: Setup tmate session 3 | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ failure() }} | |
| # export: | |
| # runs-on: ubuntu-20.04 | |
| # needs: build | |
| # steps: | |
| # - name: Create Docker Image Dir | |
| # run: mkdir /tmp/docker | |
| # | |
| # - name: Download Docker Image from `build` Job | |
| # uses: actions/download-artifact@v3 | |
| # with: | |
| # name: docker-image | |
| # path: /tmp/docker | |
| # | |
| # - name: Load Downloaded Docker Image | |
| # run: docker load --input /tmp/docker/$(ls /tmp/docker) | |
| # | |
| # # Get files from VCDB | |
| # - name: Checkout Input Files | |
| # uses: actions/checkout@v3 | |
| # with: | |
| # repository: virtualcell/vcdb | |
| # | |
| # - name: Prepare Output Directory | |
| # run: mkdir -p $GITHUB_WORKSPACE/export_conversion/output | |
| # | |
| # # Do the conversion | |
| # - name: Begin Conversion | |
| # #$(docker image ls | grep "<none>" | awk '{print $3;}') to get image id | |
| # run: docker run -v $GITHUB_WORKSPACE:/root $(docker image ls | grep "<none>" | awk '{print $3;}') export-omex-batch -i "/root/public/biomodel/vcml" -o "/root/export_conversion/output" -m SBML --writeLogFiles=true --validate # grabs image and runs | |
| # | |
| # # Parse the results | |
| # - name: Parse Results | |
| # run: | | |
| # cd $GITHUB_WORKSPACE/export_conversion/output | |
| # /bin/echo "biomodels processed $(cat jobLog.txt | grep START | wc -l)" >> ../export_results.txt | |
| # /bin/echo "biomodels succeeded $(cat jobLog.txt | grep MODEL,SUCC | wc -l)" >> ../export_results.txt | |
| # /bin/echo "simcontexts total $(cat jobLog.txt | grep TEXT | wc -l)" >> ../export_results.txt | |
| # /bin/echo "simcontexts failed $(cat jobLog.txt | grep TEXT,FAIL | wc -l)" >> ../import_results.txt | |
| # /bin/echo "simcontexts supported that failed $(cat jobLog.txt | grep TEXT,FAIL | grep -v supp | wc -l)" >> ../export_results.txt | |
| # /bin/echo "simcontexts math not equivalent $(cat jobLog.txt | grep TEXT,FAIL | grep -v supp | grep equiv | wc -l)" >> ../export_results.txt | |
| # /bin/echo "simcontexts divide by zero $(cat jobLog.txt | grep TEXT,FAIL | grep -v supp | grep divide | wc -l)" >> ../export_results.txt | |
| # /bin/echo "simcontexts duplicate IDs $(cat jobLog.txt | grep TEXT,FAIL | grep -v supp | grep duplicate | wc -l)" >> ../export_results.txt | |
| # /bin/echo "simcontexts null pointer $(cat jobLog.txt | grep TEXT,FAIL | grep -v supp | grep null | wc -l)" >> ../export_results.txt | |
| # /bin/echo "simcontexts structure mapping $(cat jobLog.txt | grep TEXT,FAIL | grep -v supp | grep struct | wc -l)" >> ../export_results.txt | |
| # /bin/echo "simcontexts other failure $(cat jobLog.txt | grep TEXT,FAIL | grep -v supp | grep -v struct | grep -v null | grep -v duplicate | grep -v divide | grep -v equiv | wc -l)" >> ../export_results.txt | |
| # /bin/echo "simulations total $(cat jobLog.txt | grep TION | wc -l)" >> ../export_results.txt | |
| # /bin/echo "simulations failed $(cat jobLog.txt | grep TION,FAIL | wc -l)" >> ../export_results.txt | |
| # /bin/echo "simulations supported that failed $(cat jobLog.txt | grep TION,FAIL | grep -v supp | wc -l)" >> ../export_results.txt | |
| # /bin/echo "simulations orphan overrides $(cat jobLog.txt | grep TION,FAIL | grep -v supp | grep Over | wc -l)" >> ../export_results.txt | |
| # /bin/echo "simulations unbound identifier $(cat jobLog.txt | grep TION,FAIL | grep -v supp | grep unbound | wc -l)" >> ../export_results.txt | |
| # /bin/echo "simulations other failure $(cat jobLog.txt | grep TION,FAIL | grep -v supp | grep -v Over | grep -v unbound | wc -l)" >> ../export_results.txt | |
| # | |
| # # Create tar of converted files | |
| # - name: Compress Converted Files | |
| # run: cd $GITHUB_WORKSPACE/export_conversion/output && sudo tar cf omexes.tar --wildcards *.omex | |
| # | |
| # # Upload Converted Files | |
| # - name: Upload Converted Files | |
| # uses: actions/upload-artifact@v3 | |
| # with: | |
| # name: omexes.tar | |
| # path: ~/work/vcell/vcell/export_conversion/output/omexes.tar # Action only has basic ~ based expansion, env variables dont appear to work | |
| # | |
| # # Upload Results | |
| # - name: Upload results of round-trip | |
| # uses: actions/upload-artifact@v3 | |
| # with: | |
| # name: export_results.txt | |
| # path: ~/work/vcell/vcell/export_conversion/export_results.txt | |
| # | |
| # - name: Upload original log of export | |
| # uses: actions/upload-artifact@v3 | |
| # with: | |
| # name: export_log_original | |
| # path: ~/work/vcell/vcell/export_conversion/output/jobLog.txt | |
| # | |
| # # Report a Problem to Slack | |
| # - name: Report Problem to Slack | |
| # if: ${{ failure() }} | |
| # run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="Uh-Oh! The *Export Step* of Nightly Testing Action on GitHub Failed ( ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} )! This may need attention..." https://slack.com/api/chat.postMessage | |
| # | |
| # # Tmate just in case | |
| # - name: Setup tmate session 3 | |
| # uses: mxschmitt/action-tmate@v3 | |
| # if: ${{ failure() }} | |
| # import: | |
| # runs-on: ubuntu-20.04 | |
| # needs: export | |
| # steps: | |
| # - name: Create working directory | |
| # run: mkdir ~/wrk | |
| # | |
| # - name: Download Docker Image from `build` Job | |
| # uses: actions/download-artifact@v3 | |
| # with: | |
| # name: docker-image | |
| # path: ~/wrk | |
| # | |
| # - name: Load Downloaded Docker Image | |
| # run: docker load --input ~/wrk/$(ls ~/wrk) | |
| # | |
| # # Make Input and Output Directory | |
| # - name: Make Input and Output Directory | |
| # run: mkdir -p ~/input_files/output && mkdir ~/input_files/input | |
| # | |
| # # Get the coverted omexes from before | |
| # - name: Download Converted COMBINE Archives | |
| # uses: actions/download-artifact@v3 | |
| # with: | |
| # name: omexes.tar | |
| # path: ~/input_files/input | |
| # | |
| # - name: Unpack Input Files | |
| # run: cd ~/input_files/input && sudo tar xvf $(ls *.tar) && rm $(ls *.tar) | |
| # | |
| # # Do the round trip | |
| # - name: Begin Round-Trip Import | |
| # #$(docker image ls | grep "<none>" | awk '{print $3;}') to get image id | |
| # run: docker run -v ~/input_files:/root $(docker image ls | grep "<none>" | awk '{print $3;}') import-omex-batch -d -i "/root/input" -o "/root/output" | |
| # | |
| # # Parse the results | |
| # - name: Parse Results | |
| # run: | | |
| # cd ~/input_files/output | |
| # /bin/echo "Biomodels processed $(cat jobLog.txt | grep '.omex,SUCC\|.omex,FAIL' | wc -l)" >> ~/import_results.txt | |
| # /bin/echo "Biomodels succeeded $(cat jobLog.txt | grep SUCC | wc -l)" >> ~/import_results.txt | |
| # /bin/echo "Biomodels that didn't converge $(cat jobLog.txt | grep SUCC | grep -v ',1' | wc -l)" >> ~/import_results.txt | |
| # | |
| # # Upload results | |
| # - name: Upload Results of Round-Trip | |
| # uses: actions/upload-artifact@v3 | |
| # with: | |
| # name: import_results.txt | |
| # path: ~/import_results.txt | |
| # | |
| # - name: Upload Results of Round-Trip | |
| # uses: actions/upload-artifact@v3 | |
| # with: | |
| # name: import_log_original | |
| # path: ~/input_files/output/jobLog.txt | |
| # | |
| # # Report a Problem to Slack | |
| # - name: Report Problem to Slack | |
| # if: ${{ failure() }} | |
| # run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="Uh-Oh! The *Import Step* of Nightly Testing Action on GitHub Failed ( ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} )! This may need attention..." https://slack.com/api/chat.postMessage | |
| # | |
| # # Tmate just in case | |
| # - name: Setup tmate session 3 | |
| # uses: mxschmitt/action-tmate@v3 | |
| # if: ${{ failure() }} | |
| # | |
| # summarize: | |
| # runs-on: ubuntu-20.04 | |
| # needs: import | |
| # steps: | |
| # - name: Make Results Directory | |
| # run: mkdir -p ~/results && cd ~/results | |
| # | |
| # - name: Download Export Results | |
| # uses: actions/download-artifact@v3 | |
| # with: | |
| # name: export_results.txt | |
| # path: ~/results | |
| # | |
| # - name: Download Import Results | |
| # uses: actions/download-artifact@v3 | |
| # with: | |
| # name: import_results.txt | |
| # path: ~/results | |
| # | |
| # - name: Compile Results | |
| # run: | | |
| # if [ $() -gt 50000] && [ $() -lt 120000 ]; then echo -n 'Good Morning! ' >> ~/results/summary.txt; fi | |
| # echo 'Here are the results of the Nightly Testing. Have a great day!' >> ~/results/summary.txt | |
| # echo '' >> ~/results/summary.txt | |
| # echo '-------- Export Results --------' >> ~/results/summary.txt | |
| # cat ~/results/export_results.txt >> ~/results/summary.txt | |
| # echo '-------- Import Results --------' >> ~/results/summary.txt | |
| # cat ~/results/import_results.txt >> ~/results/summary.txt | |
| # echo '' >> ~/results/summary.txt | |
| # | |
| # # Report a Success | |
| # - name: Report Results to Slack | |
| # run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="$(cat ~/results/summary.txt)" https://slack.com/api/chat.postMessage | |
| # | |
| # # Report a Problem to Slack | |
| # - name: Report Problem to Slack | |
| # if: ${{ failure() }} | |
| # run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="Oops! The *Summary Step* of Nightly Testing Action on GitHub Failed ( ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} ). Go see what happened!" https://slack.com/api/chat.postMessage | |
| # | |
| # - name: Setup tmate session 3 | |
| # uses: mxschmitt/action-tmate@v3 | |
| # if: ${{ failure() }} | |
| # |