New Production Deployment and Tool Tests #922
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| name: New Production Deployment and Tool Tests | |
| on: | |
| schedule: | |
| - cron: "0 0 * * *" | |
| - cron: "0 12 * * *" | |
| workflow_dispatch: | |
| inputs: | |
| chunk: | |
| description: 'Chunk to run. Valid range [0:13]. Out of range inputs will be ignored.' | |
| required: true | |
| default: '3' | |
| jobs: | |
| deploygke: | |
| env: | |
| GKE_ZONE: us-east1-b | |
| GKE_VERSION: "1.28" | |
| GXY_TMP: /tmp/gxy | |
| PREFIX: prod | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: 'read' | |
| id-token: 'write' | |
| outputs: | |
| prefix: ${{ steps.prefix.outputs.prefix }} | |
| steps: | |
| - name: Set prefix with date | |
| id: prefix | |
| run: echo "prefix=$(echo $PREFIX-$(date +'%y-%m-%d-%H-%M'))" >> $GITHUB_OUTPUT | |
| - uses: 'actions/checkout@v3' | |
| - id: 'Auth' | |
| uses: 'google-github-actions/auth@v0' | |
| with: | |
| workload_identity_provider: 'projects/526897014808/locations/global/workloadIdentityPools/galaxy-tests-identity-pool/providers/gxy-tests-provider' | |
| service_account: 'galaxy-tests-repo-actions-sa@anvil-and-terra-development.iam.gserviceaccount.com' | |
| - name: 'Set up Cloud SDK' | |
| uses: 'google-github-actions/setup-gcloud@v1' | |
| - name: gcloud version | |
| run: gcloud --version | |
| - name: Create GKE cluster | |
| run: gcloud container clusters create "${{steps.prefix.outputs.prefix}}" --cluster-version="$GKE_VERSION" --disk-size=100 --num-nodes=1 --machine-type=e2-custom-20-81920 --zone "$GKE_ZONE" | |
| testgalaxy1: | |
| needs: deploygke | |
| env: | |
| GKE_ZONE: us-east1-b | |
| GXY_TMP: /tmp/gxy | |
| GKM_VERSION: "2.8.1" | |
| USE_GKE_GCLOUD_AUTH_PLUGIN: True | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: 'read' | |
| id-token: 'write' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - id: 'Auth' | |
| uses: 'google-github-actions/auth@v0' | |
| with: | |
| workload_identity_provider: 'projects/526897014808/locations/global/workloadIdentityPools/galaxy-tests-identity-pool/providers/gxy-tests-provider' | |
| service_account: 'galaxy-tests-repo-actions-sa@anvil-and-terra-development.iam.gserviceaccount.com' | |
| - name: 'Set up Cloud SDK' | |
| uses: 'google-github-actions/setup-gcloud@v1' | |
| - name: Get cluster kubeconfig | |
| run: gcloud container clusters get-credentials "${{needs.deploygke.outputs.prefix}}" --zone "$GKE_ZONE" --project ${{ secrets.GCP_PROJECT_ID }} | |
| - name: Create two GCP Disks | |
| run: gcloud compute disks create "${{needs.deploygke.outputs.prefix}}-1-postgres-pd" --size 10Gi --zone "$GKE_ZONE" && gcloud compute disks create "${{needs.deploygke.outputs.prefix}}-1-nfs-pd" --size 250Gi --zone "$GKE_ZONE" | |
| - name: Setup gcloud auth plugin for kubectl and fetch creds | |
| run: | | |
| gcloud components install gke-gcloud-auth-plugin | |
| gcloud container clusters get-credentials "${{needs.deploygke.outputs.prefix}}" --zone "$GKE_ZONE" | |
| - name: Install Kubectl | |
| run: curl -LO "https://storage.googleapis.com/kubernetes-release/release/$(curl -s https://storage.googleapis.com/kubernetes-release/release/stable.txt)/bin/linux/amd64/kubectl" && chmod +x ./kubectl && sudo mv ./kubectl /usr/local/bin/kubectl && kubectl version | |
| - name: Install Helm | |
| run: curl https://raw.githubusercontent.com/helm/helm/master/scripts/get-helm-3 | bash | |
| - name: Add anvil repository | |
| run: helm repo add anvil https://github.com/cloudve/helm-charts/raw/anvil | |
| - name: Deploy GalaxyKubeMan | |
| continue-on-error: true | |
| run: > | |
| (time sh -c "helm install --create-namespace -n ${{needs.deploygke.outputs.prefix}}-1 ${{needs.deploygke.outputs.prefix}}-1 anvil/galaxykubeman\ | |
| --wait\ | |
| --wait-for-jobs\ | |
| --timeout 720s\ | |
| --version $GKM_VERSION\ | |
| --set galaxy.service.type=LoadBalancer\ | |
| --set galaxy.configs.\"galaxy\.yml\".galaxy.admin_users=\"tests@fake.org\"\ | |
| --set galaxy.configs.\"galaxy\.yml\".galaxy.master_api_key=galaxypassword\ | |
| --set galaxy.configs.\"galaxy\.yml\".galaxy.single_user=\"tests@fake.org\"\ | |
| --set galaxy.configs.\"job_conf\.yml\".runners.k8s.k8s_node_selector=\"cloud.google.com/gke-nodepool: default-pool\"\ | |
| --set 'galaxy.configs.job_conf\.yml.execution.environments.tpv_dispatcher.tpv_config_files={https://raw.githubusercontent.com/galaxyproject/tpv-shared-database/main/tools.yml,lib/galaxy/jobs/rules/tpv_rules_local.yml,https://gist.githubusercontent.com/afgane/68d1dbbe0af2468ba347dc74b6d3f7fa/raw/20edda50161bdcb74ff38935e7f76d79bfdaf303/tvp_rules_tests.yml}'\ | |
| --set galaxy.nodeSelector.\"cloud\.google\.com\/gke-nodepool\"=\"default-pool\"\ | |
| --set galaxy.persistence.storageClass=\"nfs-${{needs.deploygke.outputs.prefix}}-1\"\ | |
| --set galaxy.postgresql.galaxyDatabasePassword=${{secrets.COMMON_PASSWORD}}\ | |
| --set galaxy.postgresql.master.nodeSelector.\"cloud\.google\.com\/gke-nodepool\"=\"default-pool\"\ | |
| --set galaxy.postgresql.persistence.existingClaim=\"${{needs.deploygke.outputs.prefix}}-1-postgres-disk-pvc\"\ | |
| --set galaxy.rabbitmq.nodeSelector.\"cloud\.google\.com\/gke-nodepool\"=\"default-pool\"\ | |
| --set galaxy.rabbitmq.persistence.storageClassName=\"nfs-${{needs.deploygke.outputs.prefix}}-1\"\ | |
| --set galaxy.ingress.ingressClassName=\"\"\ | |
| --set galaxy.tusd.ingress.ingressClassName=\"\"\ | |
| --set cvmfs.cvmfscsi.cache.alien.pvc.storageClass=\"nfs-${{needs.deploygke.outputs.prefix}}-1\"\ | |
| --set nfs.nodeSelector.\"cloud\.google\.com\/gke-nodepool\"=\"default-pool\"\ | |
| --set nfs.persistence.existingClaim=\"${{needs.deploygke.outputs.prefix}}-1-nfs-disk-pvc\"\ | |
| --set nfs.storageClass.name=\"nfs-${{needs.deploygke.outputs.prefix}}-1\"\ | |
| --set persistence.nfs.name=\"${{needs.deploygke.outputs.prefix}}-1-nfs-disk\"\ | |
| --set persistence.nfs.persistentVolume.extraSpec.gcePersistentDisk.pdName=\"${{needs.deploygke.outputs.prefix}}-1-nfs-pd\"\ | |
| --set persistence.postgres.name=\"${{needs.deploygke.outputs.prefix}}-1-postgres-disk\"\ | |
| --set persistence.postgres.persistentVolume.extraSpec.gcePersistentDisk.pdName=\"${{needs.deploygke.outputs.prefix}}-1-postgres-pd\"") 1> "$GXY_TMP" 2>> "$GXY_TMP" | |
| - name: Print output | |
| run: cat "$GXY_TMP" | |
| - name: Helm get values | |
| run: helm get values -n ${{needs.deploygke.outputs.prefix}}-1 ${{needs.deploygke.outputs.prefix}}-1 | |
| - name: Get pods, pvc, and pv, sc | |
| run: kubectl get pods -n ${{needs.deploygke.outputs.prefix}}-1; kubectl get pvc -n ${{needs.deploygke.outputs.prefix}}-1; kubectl get pv -n ${{needs.deploygke.outputs.prefix}}-1; kubectl get sc -n ${{needs.deploygke.outputs.prefix}}-1 | |
| - name: Get events | |
| run: kubectl get events -n ${{needs.deploygke.outputs.prefix}}-1 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - name: Install required system packages | |
| run: sudo apt-get update && sudo apt-get install -y python3-h5py pkg-config libhdf5-dev | |
| - name: Install dependencies | |
| run: python -m pip install planemo ephemeris pysam "galaxy-tool-util>=21.1.0.dev6" bioblend Jinja2 matplotlib gxabm | |
| - uses: actions/checkout@v3 | |
| with: | |
| persist-credentials: false | |
| - name: Add report from this run | |
| run: bash ./.github/scripts/report_deployment.sh "$GXY_TMP" anvil-production ${{ secrets.GIT_TOKEN }} | |
| - name: Get Galaxy IP and port | |
| id: galaxy | |
| run: echo "url=$(echo \"http://$(kubectl get svc -n ${{needs.deploygke.outputs.prefix}}-1 ${{needs.deploygke.outputs.prefix}}-1-galaxy-nginx -o jsonpath='{.status.loadBalancer.ingress[0].ip}' | sed -e 's/\"//g'):$(kubectl get svc -n ${{needs.deploygke.outputs.prefix}}-1 ${{needs.deploygke.outputs.prefix}}-1-galaxy-nginx -o jsonpath='{.spec.ports[0].port}')$(kubectl get ingress -n ${{needs.deploygke.outputs.prefix}}-1 ${{needs.deploygke.outputs.prefix}}-1-galaxy -o jsonpath='{.spec.rules[0].http.paths[0].path}')/\")" >> $GITHUB_OUTPUT | |
| - name: Create remote single user | |
| run: curl ${{steps.galaxy.outputs.url}} | |
| - name: Create reports dir for this date | |
| id: reports | |
| run: | | |
| DIR=reports/anvil-production/tool-tests/${{needs.deploygke.outputs.prefix}}-1 | |
| mkdir -p $DIR | |
| echo "dir=$DIR" >> $GITHUB_OUTPUT | |
| # - name: Get tool list | |
| # run: cp production/anvil/tools.yaml reports/anvil-production/tools.yaml | |
| - name: Create and get API key | |
| run: echo "key=$(python .github/scripts/create_api_key.py ${{steps.galaxy.outputs.url}} galaxypassword)" >> $GITHUB_OUTPUT | |
| id: api | |
| - name: Configure ABM | |
| id: key | |
| run: | | |
| abm version | |
| cp -R .abm ~/.abm | |
| abm config url galaxy ${{ steps.galaxy.outputs.url }} | |
| echo "Key is ${{ steps.api.outputs.key }}" | |
| abm config key galaxy ${{ steps.api.outputs.key }} | |
| abm config show galaxy | |
| echo "key=$key" >> $GITHUB_OUTPUT | |
| - name: Split tool tests (workflow_dispatch) | |
| if: ${{ github.event_name == 'workflow_dispatch' }} | |
| run: python .github/scripts/get_chunk.py --chunk ${{ github.event.inputs.chunk }} -o ${{ steps.reports.outputs.dir }} reports/anvil-production/tools.yaml | |
| - name: Split tool tests (cron job) | |
| if: ${{ github.event_name != 'workflow_dispatch' }} | |
| run: python .github/scripts/get_chunk.py reports/anvil-production/tools.yaml -o ${{ steps.reports.outputs.dir }} | |
| - name: Generate a history name | |
| id: history | |
| run: echo "history_name=anvil-test-$(date '+%F-%H-%M')" >> $GITHUB_OUTPUT | |
| - name: Run tool tests | |
| continue-on-error: true | |
| run: sleep 30 && .github/scripts/run-galaxy-tests.sh ${{ steps.history.outputs.history_name }} ${{ steps.reports.outputs.dir }} | |
| # - name: Write job results | |
| # run: abm galaxy jobs list --history ${{ steps.history.outputs.history_name }} > ${{ steps.reports.outputs.dir }}/jobs.txt | |
| - name: Generate Jobs reports | |
| continue-on-error: true | |
| shell: bash | |
| run: | | |
| abm galaxy jobs list --history ${{ steps.history.outputs.history_name }} > ${{ steps.reports.outputs.dir }}/jobs.txt | |
| echo "Saving jobs that had errors." | |
| abm galaxy jobs list --state error | |
| for job in $(abm galaxy jobs list --state error | awk '{print $1}') ; do | |
| if [[ ! -e ${{ steps.reports.outputs.dir }}/errors ]] ; then | |
| mkdir -p ${{ steps.reports.outputs.dir }}/errors | |
| fi | |
| abm galaxy jobs show $job > ${{ steps.reports.outputs.dir }}/errors/$job.json | |
| done | |
| echo "Looking for paused jobs" | |
| abm galaxy jobs list --state paused | |
| for job in $(abm galaxy jobs list --state paused | awk '{print $1}') ; do | |
| echo "Job $job was paused" | |
| if [[ ! -e ${{ steps.reports.outputs.dir }}/paused ]] ; then | |
| mkdir -p ${{ steps.reports.outputs.dir }}/paused | |
| fi | |
| abm galaxy jobs show $job > ${{ steps.reports.outputs.dir }}/paused/$job.json | |
| done | |
| abm galaxy history summarize ${{ steps.history.outputs.history_name }} > ${{ steps.reports.outputs.dir }}/job-metrics.csv | |
| - name: Save job handler logs and node information | |
| continue-on-error: true | |
| shell: bash | |
| run: | | |
| pod=$(kubectl get pods -n ${{needs.deploygke.outputs.prefix}}-1 | grep galaxy-job | awk '{print $1}') | |
| kubectl logs -n ${{needs.deploygke.outputs.prefix}}-1 $pod > ${{ steps.reports.outputs.dir }}/job.log | |
| kubectl describe nodes > ${{ steps.reports.outputs.dir }}/node-info.txt | |
| - name: Create HTML report | |
| run: planemo test_reports ${{ steps.reports.outputs.dir }}/results.json --test_output_xunit ${{ steps.reports.outputs.dir }}/results.xunit --test_output ${{ steps.reports.outputs.dir }}/results.html | |
| - name: Update Readme | |
| run: python .github/scripts/update_readme.py ${{ steps.reports.outputs.dir }}/chunk.json reports/anvil-production/tool-tests/chunks.json reports/anvil-production/README.md | |
| - name: Add updated README from this run | |
| run: bash ./.github/scripts/report_tests.sh ${{ secrets.GIT_TOKEN }} "Updating anvil-production README for ${{needs.deploygke.outputs.prefix}}-1" reports/anvil-production | |
| cleanup: | |
| if: always() | |
| needs: [deploygke,testgalaxy1] | |
| env: | |
| GKE_ZONE: us-east1-b | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: 'read' | |
| id-token: 'write' | |
| steps: | |
| - uses: 'actions/checkout@v3' | |
| - id: 'Auth' | |
| uses: 'google-github-actions/auth@v0' | |
| with: | |
| workload_identity_provider: 'projects/526897014808/locations/global/workloadIdentityPools/galaxy-tests-identity-pool/providers/gxy-tests-provider' | |
| service_account: 'galaxy-tests-repo-actions-sa@anvil-and-terra-development.iam.gserviceaccount.com' | |
| - name: 'Set up Cloud SDK' | |
| uses: 'google-github-actions/setup-gcloud@v1' | |
| - name: Delete the GKE cluster | |
| continue-on-error: true | |
| run: gcloud container clusters delete "${{needs.deploygke.outputs.prefix}}" --zone "$GKE_ZONE" --quiet | |
| - name: Delete the two GCP Disks for first Galaxy | |
| run: gcloud compute disks delete "${{needs.deploygke.outputs.prefix}}-1-postgres-pd" --zone "$GKE_ZONE" --quiet && gcloud compute disks delete "${{needs.deploygke.outputs.prefix}}-1-nfs-pd" --zone "$GKE_ZONE" --quiet |