NightlyBMDB_CLI.yml

name: Nightly CLI Execution Tests (BMDB)
on:
  schedule:
    - cron: "0 7 * * *"
  workflow_dispatch:

env:
  python-version: "3.10"
  poetry-version: "1.2.1"

jobs:
  build:
    runs-on: ubuntu-22.04
    steps:
      - name: Checkout Our Code
        uses: actions/checkout@v4
        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@v5
        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
          poetry run python -m pytest

      - name: build vcell-admin package
        run: |
          cd docker/swarm/vcell-admin
          poetry install
          poetry run python -m pytest

      - name: build pythonCopasiOpt package
        run: |
          cd pythonCopasiOpt/vcell-opt
          poetry install
          poetry run python -m pytest

      - name: build pythonVtk package
        run: |
          cd pythonVtk
          poetry install
          poetry run python -m pytest

      - name: build vcutils package
        run: |
          cd python-utils
          poetry install
          poetry run python -m pytest

      - name: build python-restclient package
        run: |
          cd python-restclient
          poetry install
          poetry run python -m pytest

      - name: build vcelldata package
        run: |
          cd pythonData
          poetry install
          poetry run python -m pytest

      - name: Setup Java for Build
        uses: actions/setup-java@v4
        with:
          java-version: '17'
          distribution: 'temurin'
          cache: 'maven'

      - name: Build VCell Jars
        run: mvn clean install dependency:copy-dependencies -DskipTests=True

      - 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 *Build Step* of Nightly Execution 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() }}

  bmdb:
    runs-on: ubuntu-20.04
    needs: build
    strategy:
      matrix:
        sets: [ "0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19" ]
    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 BMDB
      - name: Checkout Input Files
        uses: actions/checkout@v4
        with:
          repository: sys-bio/temp-biomodels

      - name: Prepare sub directory
        run: |
          SOURCE_DIR="$GITHUB_WORKSPACE/omex_files"
          TARGET_DIR="$GITHUB_WORKSPACE/set_${{ matrix.sets }}"
          MOD_VALUE=${{ matrix.sets }}
          
          # make target dir
          mkdir $TARGET_DIR
          # loop through files in directory, increment indexing and separating files
          
          echo "Extracting tests"
          
          for file in $SOURCE_DIR/*; do
              # Is the file of the correct form?
              file_name=$(basename $file)
              if ! [[ $file_name =~ ^BIOMD[0-9]+\.omex$ ]]; then
                echo "Input is invalid. Expecting 'BIOMD##########.omex format, got '${file_name}'."
                continue
              fi

              number=$(echo "$file_name" | sed -n 's/^BIOMD\([0-9]\+\)\.omex$/\1/p' | sed 's/^0*//')

              # TODO: remove later - if number is greater than MAX_TEST_NUMBER or less than MIN_TEST_NUMBER then continue
              MIN_TEST_NUMBER=800
              MAX_TEST_NUMBER=2000
              if [ $number -lt $MIN_TEST_NUMBER ]; then
                  echo "Skipping ${file_name}"
                  continue
              fi
              if [ $number -gt $MAX_TEST_NUMBER ]; then
                  echo "Skipping ${file_name}"
                  continue
              fi
              if [ $number -eq 235 ] || [ $number -eq 255 ] || [ $number -eq 595 ] || [ $number -eq 1008 ]; then
                  echo "Skipping ${file_name} - too slow or otherwise misbehaved"
                  continue
              fi

              if [ $((number % ${{ strategy.job-total }})) -eq $((MOD_VALUE + 0)) ]; then
                  echo "Accepting ${file_name}"
                  cp ${file} $TARGET_DIR/
              fi
          done

      - name: Install JQ
        run: sudo apt update && sudo apt install jq -y

        # Do the execution
      - name: Begin Execution
        #$(docker image ls | grep "<none>" | awk '{print $3;}')  to get image id
        run: |
          # Prepare files
          set +e
          echo "[]" > ${{ github.workspace }}/total_exec_summary.json
          touch ${{ github.workspace }}/total_exec_summary.ndjson
          echo "[]" > ${{ github.workspace }}/full_tracer.json
          # The /* goes on the outside, otherwise bash just interprets a string!
          for file in "$GITHUB_WORKSPACE/set_${{ matrix.sets }}"/*; do
            if [ -f "$file" ]; then
              extensionless_name="${file%.*}"
              base_name="$(basename ${file})"
              base_extless_name="$(basename ${extensionless_name})"
              mkdir "${extensionless_name}_output"
              
              sim_input="/root/${base_name}"
              sim_output="/root/${base_extless_name}_output"
              echo -n "Running \"${file}\" in output folder \"${base_extless_name}_output\"..."
              vcell_result=$(docker run -v $GITHUB_WORKSPACE/set_${{ matrix.sets }}:/root $(docker image ls | grep "<none>" | awk '{print $3;}') execute-omex -d -i ${sim_input} -o ${sim_output} --timeout_ms=300000)
              echo "Done!"
              # Grab Summary
              echo -n "Obtaining Summary..."
              if [ -f "${GITHUB_WORKSPACE}/set_${{ matrix.sets }}/${base_extless_name}_output/exec_summary.json" ]
              then
                # Append to master summary in github workspace
                jq '. + [inputs]' ${{ github.workspace }}/total_exec_summary.json $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output -name exec_summary.json) > temp.json
                mv temp.json ${{ github.workspace }}/total_exec_summary.json
                # note that the exec_summary.json file is already only a single line of json text, so simple concatenation is fine
                find $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output -name exec_summary.json -exec cat {} + | sort > temp.ndjson
                cat temp.ndjson >> ${{ github.workspace }}/total_exec_summary.ndjson
                echo "Done!"
              else
                echo "No summary found in set $GITHUB_WORKSPACE/set_${{ matrix.sets }}"
              fi
          
              # Check for individual Failure (a.k.a. if we failed early)
              echo -n "Obtaining Execution Result..."
              status=$(cat "${GITHUB_WORKSPACE}/set_${{ matrix.sets }}/${base_extless_name}_output/exec_summary.json" | jq -r '.status')
              echo "${status}"
              # Note: `cat`ing "$vcell_result" will be the runting logging! 
              if [[ "${status}" == "FAILED" ]]; then
                # Copy error log to github workspace
                echo -n "Copying Failure Report..."
                echo "${base_extless_name}" >> $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output/errorLog.txt
                touch ${{ github.workspace }}/errors.report
                cat $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output/errorLog.txt >> ${{ github.workspace }}/errors.report
                echo "Done!"
              fi
          
              # Grab Trace
              # Check for individual Success
              echo -n "Obtaining Execution Tracer Logs..."
              if [ $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output -name tracer.json | wc -l) -ne 0 ]
              then
                echo -n "Copying Tracer Logs..."
                # Append to master trace in github workspace
                jq '. + inputs' ${{ github.workspace }}/full_tracer.json $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output -name tracer.json) > temp_2.json
                mv temp_2.json ${{ github.workspace }}/full_tracer.json
                echo "Done!"
              else
                echo "No trace found in set $GITHUB_WORKSPACE/set_${{ matrix.sets }}"
              fi
            fi
          echo "Completed processing of \"${file}\"!"
          echo "\n\n-----------------------------------------------------------------------------------------------\n\n"
          done


      - name: Check For Success
        run: |
          # If the error file exists, then we have failures to report and upload; else, we can just end here; the next job will process results
          if [ $(find ${{ github.workspace }} -name errors.report | wc -l) -eq 0 ]
          then
            exit 0
          fi
          echo "Models that failed:"
          cat ${{ github.workspace }}/errors.report

      - name: Upload failures
        uses: actions/upload-artifact@v3
        with:
          name: set_${{ matrix.sets }}.report
          path: ${{ github.workspace }}/errors.report

      - name: Upload summary as json
        uses: actions/upload-artifact@v3
        with:
          name: set_${{ matrix.sets }}.summary
          path: ${{ github.workspace }}/total_exec_summary.json

      - name: Upload summary as ndjson
        uses: actions/upload-artifact@v3
        with:
          name: set_${{ matrix.sets }}.summary_ndjson
          path: ${{ github.workspace }}/total_exec_summary.ndjson

      - name: Upload tracer
        uses: actions/upload-artifact@v3
        with:
          name: set_${{ matrix.sets }}.tracer
          path: ${{ github.workspace }}/full_tracer.json

      # 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 *BMDB Step* of Nightly **Execution** (set ${{ matrix.sets }}) 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() }}

  bmdb_results:
    runs-on: ubuntu-20.04
    needs: bmdb

    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)

      - name: Gather Artifacts
        uses: actions/download-artifact@v3
        with:
          path: ${{ github.workspace }}/bmdb-results

      - name: Install JQ
        run: sudo apt update && sudo apt install jq -y

      - name: Combine .report artifacts into one file
        run: cat $(find $GITHUB_WORKSPACE/bmdb-results -name 'errors.report') > $GITHUB_WORKSPACE/combined.txt

      - name: Combine .summary artifacts into one file
        run: jq -s 'add | sort_by(.file_path)' $(find "$GITHUB_WORKSPACE/bmdb-results" -name 'total_exec_summary.json') > $GITHUB_WORKSPACE/summary.json
        
      - name: Combine all .summary_ndjson artifacts into one file
        # note that the total_exec_summary.ndjson files are already line delimited json text, so simple concatenation is fine
        run: find $GITHUB_WORKSPACE/bmdb-results -name total_exec_summary.ndjson -exec cat {} + | sort > $GITHUB_WORKSPACE/exec_summary.ndjson

      - name: Upload combined exec_summary.ndjson file
        uses: actions/upload-artifact@v3
        with:
          path: ${{ github.workspace }}/exec_summary.ndjson
          name: exec_summary.ndjson

      - name: Combine .summary artifacts into one file
        run: jq -s 'add' $(find $GITHUB_WORKSPACE/bmdb-results -name 'full_tracer.json') > $GITHUB_WORKSPACE/tracer.json

      # run exec-report CLI command via docker to generate report using the exec_summary.ndjson file and the embedded test_cases.ndjson file
      - name: Run Docker test-report command
        run: docker run -v ${{ github.workspace }}:/root $(docker image ls | grep "<none>" | awk '{print $3;}') test-report -c SYSBIO_BIOMD --exec-summaries /root/exec_summary.ndjson --report-md /root/report.md

      - name: Upload generated report.md
        uses: actions/upload-artifact@v3
        with:
          name: report.md
          path: ${{ github.workspace }}/report.md

      - name: Upload complete, compiled summary
        uses: actions/upload-artifact@v3
        with:
          name: complete_summary.json
          path: ${{ github.workspace }}/summary.json

      - name: Upload  complete, compiled tracer
        uses: actions/upload-artifact@v3
        with:
          name: complete_tracer.json
          path: ${{ github.workspace }}/tracer.json

      - name: Post results to slack part 1
        run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="Here're the $(cat ${GITHUB_WORKSPACE}/combined.txt | wc -l) BMDB models that didn't pass:" https://slack.com/api/chat.postMessage

      - name: Post results to slack part 2
        run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="$(sort ${GITHUB_WORKSPACE}/combined.txt)" https://slack.com/api/chat.postMessage

      - name: Post results to slack part 3 (report.md from exec-report CLI command)
        run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="$(cat ${GITHUB_WORKSPACE}/report.md)" https://slack.com/api/chat.postMessage

      - name: Post results to slack part 4
        run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="To see detailed logs of the BMDB results, see - ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}. Go see what happened!" https://slack.com/api/chat.postMessage