build.yaml

steps:
  - kind: buildImage2
    name: git_make_bash_image
    dockerFile:
      inline: |
        FROM {{ global.docker_root_image }}
        RUN apt-get update && apt-get install -y git make bash
  - kind: runImage
    name: merge_code
    image:
      valueFrom: git_make_bash_image.image
    script: |
      set -ex
      cd /io
      mkdir repo
      cd repo
      {{ code.checkout_script }}
      make -C hail python-version-info
      git rev-parse HEAD > git_version
    outputs:
      - from: /io/repo/
        to: /repo
      - from: /io/repo/hail/python/hail/hail_version
        to: /hail_version
      - from: /io/repo/hail/python/hail/hail_pip_version
        to: /hail_pip_version
      - from: /io/repo/git_version
        to: /git_version
    dependsOn:
      - git_make_bash_image
  - kind: buildImage2
    name: hail_ubuntu_image
    dockerFile: /io/hail-ubuntu/Dockerfile
    contextPath: /io/hail-ubuntu
    publishAs: hail-ubuntu
    inputs:
      - from: /repo/docker/hail-ubuntu
        to: /io/hail-ubuntu
    dependsOn:
      - merge_code
  - kind: createNamespace
    name: default_ns
    namespaceName: default
    public: true
    secrets:
      - gcr-pull-key
      - gcr-push-service-account-key
      - hail-ci-0-1-github-oauth-token
      - test-gsa-key
      - test-aws-key
      - test-azure-key
      - auth-oauth2-client-secret
      - zulip-config
      - benchmark-gsa-key
      - billing-monitor-gsa-key
      - hail-ci-0-1-service-account-key
      - test-dataproc-service-account-key
  - kind: buildImage2
    name: echo_image
    dockerFile: /io/echo/Dockerfile
    contextPath: /io/echo
    publishAs: echo
    resources:
      storage: 10Gi
      cpu: "2"
      memory: 7.5Gi
    inputs:
      - from: /repo/echo
        to: /io/echo
    dependsOn:
      - hail_ubuntu_image
      - merge_code
  - kind: deploy
    name: deploy_echo
    namespace:
      valueFrom: default_ns.name
    config: echo/deployment.yaml
    dependsOn:
      - default_ns
      - echo_image
  - kind: deploy
    name: deploy_batch_sa
    namespace:
      valueFrom: default_ns.name
    config: batch/service-account.yaml
    dependsOn:
      - default_ns
  - kind: deploy
    name: deploy_ci_agent
    namespace:
      valueFrom: default_ns.name
    config: ci/ci-agent.yaml
    dependsOn:
      - default_ns
  - kind: deploy
    name: deploy_test_batch_sa
    namespace:
      valueFrom: default_ns.name
    config: batch/test-sa.yaml
    dependsOn:
      - default_ns
  - kind: buildImage2
    name: base_image
    dockerFile: /io/repo/docker/Dockerfile.base
    contextPath: /io/repo
    publishAs: base
    resources:
      storage: 10Gi
      cpu: "2"
      memory: 7.5Gi
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - hail_ubuntu_image
      - merge_code
  - kind: runImage
    name: check_hail
    image:
      valueFrom: base_image.image
    script: |
      set -ex
      cd /io/repo
      make check-hail
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - base_image
      - merge_code
  - kind: buildImage2
    name: service_base_image
    dockerFile: /io/repo/docker/Dockerfile.service-base
    contextPath: /io/repo
    publishAs: service-base
    resources:
      storage: 10Gi
      cpu: "2"
      memory: 7.5Gi
    dependsOn:
      - base_image
      - merge_code
    inputs:
      - from: /hail_version
        to: /io/repo/hail_version
      - from: /repo
        to: /io/repo
  - kind: runImage
    name: check_services
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex
      cd /io/repo
      {% if 'target_sha' in code %}
      export HAIL_TARGET_SHA={{ code.target_sha }}
      {% endif %}
      make -k check-services
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - service_base_image
      - merge_code
  - kind: buildImage2
    name: create_certs_image
    dockerFile: /io/tls/Dockerfile
    contextPath: /io/tls
    publishAs: create_certs_image
    inputs:
      - from: /repo/tls
        to: /io/tls
    dependsOn:
      - hail_ubuntu_image
      - merge_code
  - kind: runImage
    name: create_ssl_config_hail_root
    image:
      valueFrom: create_certs_image.image
    script: |
      openssl req -new -x509 -subj /CN=hail-root -nodes -newkey rsa:4096 -keyout hail-root-key.pem -out hail-root-cert.pem
      until kubectl get secret -n {{ default_ns.name }} ssl-config-hail-root
      do
          kubectl create secret generic -n {{ default_ns.name }} ssl-config-hail-root \
                  --from-file=hail-root-key.pem \
                  --from-file=hail-root-cert.pem
      done
    serviceAccount:
      name: admin
      namespace:
        valueFrom: default_ns.name
    scopes:
      - test
      - dev
    dependsOn:
      - default_ns
      - create_certs_image
  - kind: runImage
    name: create_certs
    image:
      valueFrom: create_certs_image.image
    script: |
      set -ex
      python3 create_certs.py \
              {{ default_ns.name }} \
              config.yaml \
              /ssl-config-hail-root/hail-root-key.pem \
              /ssl-config-hail-root/hail-root-cert.pem
    serviceAccount:
      name: admin
      namespace:
        valueFrom: default_ns.name
    secrets:
      - name: ssl-config-hail-root
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config-hail-root
    dependsOn:
      - default_ns
      - create_certs_image
      - create_ssl_config_hail_root
  - kind: createDatabase
    name: test_database_instance
    databaseName: test-instance
    migrations: []
    namespace:
      valueFrom: default_ns.name
    scopes:
      - test
    dependsOn:
      - default_ns
  - kind: runImage
    name: create_database_server_config
    image:
      valueFrom: base_image.image
    script: |
     kubectl -n {{ default_ns.name }} get -o json secret {{ test_database_instance.admin_secret_name }} | jq '{apiVersion, kind, type, data, metadata: {name: "database-server-config"}}' | kubectl -n {{ default_ns.name }} apply -f -
    serviceAccount:
      name: admin
      namespace:
        valueFrom: default_ns.name
    scopes:
      - test
    dependsOn:
      - default_ns
      - base_image
      - test_database_instance
  - kind: runImage
    name: delete_auth_tables
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex
      mysql --defaults-extra-file=/sql-config/sql-config.cnf < /io/sql/delete-auth-tables.sql
    inputs:
      - from: /repo/auth/sql
        to: /io/sql
    secrets:
      - name: database-server-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /sql-config
    runIfRequested: true
    scopes:
      - dev
    dependsOn:
      - default_ns
      - service_base_image
      - merge_code
  - kind: createDatabase
    name: auth_database
    databaseName: auth
    migrations:
      - name: initial
        script: /io/sql/initial.sql
      - name: copy-paste-tokens
        script: /io/sql/copy-paste-tokens.sql
      - name: drop-bucket
        script: /io/sql/drop-bucket.sql
      - name: add-trial-billing-project
        script: /io/sql/add-trial-billing-project.sql
      - name: add-roles
        script: /io/sql/add-roles.sql
    inputs:
      - from: /repo/auth/sql
        to: /io/sql
    namespace:
      valueFrom: default_ns.name
    shutdowns:
      - kind: Deployment
        namespace:
          valueFrom: default_ns.name
        name: auth
    dependsOn:
      - default_ns
      - merge_code
      - delete_auth_tables
  - kind: runImage
    name: create_deploy_config
    image:
      valueFrom: base_image.image
    script: |
      set -ex
      # k8s deploy config
      cat > deploy-config.json <<EOF
      {"location":"k8s","default_namespace":"{{ default_ns.name }}","domain":"{{ global.domain }}"}
      EOF
      kubectl -n {{ default_ns.name }} create secret generic deploy-config \
              --from-file=./deploy-config.json \
              --save-config --dry-run=client -o yaml \
          | kubectl -n {{ default_ns.name }} apply -f -
      # gce deploy config
      cat > deploy-config.json <<EOF
      {"location":"gce","default_namespace":"{{ default_ns.name }}","domain":"{{ global.domain }}"}
      EOF
      kubectl -n {{ default_ns.name }} create secret generic gce-deploy-config \
              --from-file=./deploy-config.json \
              --save-config --dry-run=client -o yaml \
          | kubectl -n {{ default_ns.name }} apply -f -
    serviceAccount:
      name: admin
      namespace:
        valueFrom: default_ns.name
    dependsOn:
      - default_ns
      - base_image
  - kind: deploy
    name: deploy_admin_pod
    namespace:
      valueFrom: default_ns.name
    config: admin-pod/admin-pod.yaml
    scopes:
      - deploy
      - dev
    dependsOn:
      - default_ns
      - service_base_image
      - create_deploy_config
      - create_certs
  - kind: runImage
    name: create_session_key
    image:
      valueFrom: base_image.image
    script: |
      set -ex
      # create session keys
      N=$(kubectl -n {{ default_ns.name }} get secret --ignore-not-found=true --no-headers session-secret-key | wc -l | tr -d '[:space:]')
      if [[ $N != 0 ]]; then
        exit
      fi
      mkdir /session-secret-key
      cat > generate-session-key.py <<EOF
      import base64
      from cryptography import fernet
      with open('/session-secret-key/session-secret-key', 'wb') as f:
          f.write(base64.urlsafe_b64decode(fernet.Fernet.generate_key()))
      EOF
      python3 generate-session-key.py
      kubectl -n {{ default_ns.name }} create secret generic session-secret-key --from-file=/session-secret-key/session-secret-key
    serviceAccount:
      name: admin
      namespace:
        valueFrom: default_ns.name
    dependsOn:
      - default_ns
      - base_image
  - kind: runImage
    name: create_test_gsa_keys
    image:
      valueFrom: service_base_image.image
    script: |
      kubectl -n {{ default_ns.name }} get -o json secret test-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "atgu-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
      kubectl -n {{ default_ns.name }} get -o json secret test-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "auth-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
      kubectl -n {{ default_ns.name }} get -o json secret test-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "batch-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
      kubectl -n {{ default_ns.name }} get -o json secret test-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "benchmark-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
      kubectl -n {{ default_ns.name }} get -o json secret test-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "ci-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
      kubectl -n {{ default_ns.name }} get -o json secret test-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "query-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
      kubectl -n {{ default_ns.name }} get -o json secret test-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "test-dev-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
      kubectl -n {{ default_ns.name }} get -o json secret test-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "grafana-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
    scopes:
      - test
      - dev
    serviceAccount:
      name: admin
      namespace:
        valueFrom: default_ns.name
    dependsOn:
      - default_ns
      - service_base_image
  - kind: buildImage2
    name: auth_image
    dockerFile: /io/repo/auth/Dockerfile
    contextPath: /io/repo
    publishAs: auth
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - service_base_image
      - merge_code
  - kind: deploy
    name: deploy_auth_driver_service_account
    namespace:
      valueFrom: default_ns.name
    config: auth/auth-driver-service-account.yaml
    dependsOn:
      - default_ns
  - kind: runImage
    name: create_accounts
    image:
      valueFrom: auth_image.image
    script: |
      set -ex
      export PROJECT={{ global.project }}
      export ZONE={{ global.zone }}
      export HAIL_PROJECT={{ global.project }}
      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
      export HAIL_SCOPE={{ scope }}
      python3 /io/bootstrap_create_accounts.py
    serviceAccount:
      name: admin
      namespace:
        valueFrom: default_ns.name
    secrets:
      - name:
          valueFrom: auth_database.user_secret_name
        namespace:
          valueFrom: default_ns.name
        mountPath: /sql-config
      - name: database-server-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /database-server-config
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: auth-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /auth-gsa-key
    inputs:
      - from: /repo/ci/bootstrap_create_accounts.py
        to: /io/bootstrap_create_accounts.py
    dependsOn:
      - default_ns
      - deploy_test_batch_sa
      - auth_database
      - auth_image
      - create_deploy_config
      - deploy_auth_driver_service_account
      - create_test_gsa_keys
  - kind: runImage
    name: create_initial_user
    runIfRequested: true
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex
      python3 /io/create_initial_account.py {{ code.username }} {{ code.email }}
    secrets:
      - name:
          valueFrom: auth_database.user_secret_name
        namespace:
          valueFrom: default_ns.name
        mountPath: /sql-config
    inputs:
      - from: /repo/ci/create_initial_account.py
        to: /io/create_initial_account.py
    dependsOn:
      - default_ns
      - service_base_image
      - merge_code
      - auth_database
  - kind: buildImage2
    name: hail_build_image
    dockerFile: /io/hail/Dockerfile.hail-build
    contextPath: /io/hail
    publishAs: hail-build
    inputs:
      - from: /repo/hail
        to: /io/hail
    dependsOn:
      - base_image
      - merge_code
  - kind: buildImage2
    name: hail_run_image
    dockerFile: /io/hail/Dockerfile.hail-run
    contextPath: /io/hail
    publishAs: hail-run
    resources:
      storage: 10Gi
      cpu: "2"
      memory: 7.5Gi
    inputs:
      - from: /repo/hail
        to: /io/hail
    dependsOn:
      - service_base_image
      - merge_code
  - kind: buildImage2
    name: hail_run_tests_image
    dockerFile: /io/hail/Dockerfile.hail-run-tests
    contextPath: /io/hail
    publishAs: hail-run-tests
    inputs:
      - from: /repo/hail
        to: /io/hail
    dependsOn:
      - hail_run_image
      - merge_code
  - kind: buildImage2
    name: benchmark_image
    dockerFile: /io/repo/benchmark-service/Dockerfile
    contextPath: /io/repo
    publishAs: benchmark
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - service_base_image
      - merge_code
  - kind: runImage
    name: check_benchmark_service
    image:
      valueFrom: benchmark_image.image
    script: |
      set -ex
      SITE_PACKAGES=$(pip3 show benchmark | grep Location | sed 's/Location: //')
      python3 -m flake8 $SITE_PACKAGES/benchmark
      python3 -m pylint --rcfile pylintrc benchmark --score=n
    dependsOn:
      - benchmark_image
  - kind: buildImage2
    name: monitoring_image
    dockerFile: /io/repo/monitoring/Dockerfile
    contextPath: /io/repo
    publishAs: monitoring
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - service_base_image
      - merge_code
  - kind: buildImage2
    name: batch_image
    dockerFile: /io/batch/Dockerfile
    contextPath: /io/batch/
    publishAs: batch
    inputs:
      - from: /repo/batch
        to: /io/batch
    dependsOn:
      - service_base_image
      - merge_code
  - kind: runImage
    name: render_grafana_nginx_conf
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex
      cd /io/repo/grafana
      {% if deploy %}
      DEPLOY=true
      {% else %}
      DEPLOY=false
      {% endif %}
      python3 ../ci/jinja2_render.py '{"deploy": '${DEPLOY}', "default_ns": {"name": "{{ default_ns.name }}"}}' nginx.conf nginx.conf.out
    inputs:
      - from: /repo
        to: /io/repo
    outputs:
      - from: /io/repo/grafana/nginx.conf.out
        to: /grafana/nginx.conf.out
    dependsOn:
      - default_ns
      - service_base_image
      - merge_code
  - kind: buildImage2
    name: grafana_nginx_image
    dockerFile: /io/grafana/Dockerfile.nginx
    contextPath: /io/grafana
    publishAs: grafana
    inputs:
      - from: /repo/grafana
        to: /io/grafana
      - from: /grafana/nginx.conf.out
        to: /io/grafana/nginx.conf.out
    dependsOn:
      - hail_ubuntu_image
      - render_grafana_nginx_conf
      - merge_code
  - kind: buildImage2
    name: test_ci_image
    dockerFile: /io/repo/ci/Dockerfile.test
    contextPath: /io/repo
    publishAs: test-ci
    scopes:
      - test
      - dev
    inputs:
      - from: /repo
        to: /io/repo
      - from: /hail_version
        to: /io/repo/hail_version
    dependsOn:
      - base_image
      - merge_code
  - kind: buildImage2
    name: test_monitoring_image
    dockerFile: /io/repo/monitoring/Dockerfile.test
    contextPath: /io/repo
    publishAs: test-monitoring
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - service_base_image
      - merge_code
  - kind: buildImage2
    name: test_benchmark_image
    dockerFile: /io/repo/benchmark-service/Dockerfile.test
    contextPath: /io/repo
    publishAs: test-benchmark
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - service_base_image
      - merge_code
  - kind: buildImage2
    name: ci_image
    dockerFile: /io/repo/ci/Dockerfile
    contextPath: /io/repo
    publishAs: ci
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - service_base_image
      - merge_code
  - kind: buildImage2
    name: hail_buildkit_image
    dockerFile: /io/repo/ci/buildkit/Dockerfile
    contextPath: /io/repo/ci
    publishAs: hail-buildkit
    inputs:
      - from: /repo/ci
        to: /io/repo/ci
    dependsOn:
      - service_base_image
      - merge_code
  - kind: buildImage2
    name: ci_utils_image
    dockerFile: /io/ci/Dockerfile.ci-utils
    contextPath: /io/ci
    publishAs: ci-utils
    inputs:
      - from: /repo/ci
        to: /io/ci
    dependsOn:
      - service_base_image
      - merge_code
  - kind: runImage
    name: build_hail_jar_only
    image:
      valueFrom: hail_build_image.image
    resources:
      memory: 7.5G
      cpu: '4'
    script: |
      set -ex
      cd /io/repo/hail
      chmod 755 ./gradlew
      time retry ./gradlew --version
      time retry make shadowJar
    inputs:
      - from: /repo
        to: /io/repo
    outputs:
      - from: /io/repo/hail/build/libs/hail-all-spark.jar
        to: /just-jar/hail.jar
    dependsOn:
      - hail_build_image
      - merge_code
  - kind: runImage
    name: build_hail
    image:
      valueFrom: hail_build_image.image
    resources:
      memory: 7.5G
      cpu: '4'
    script: |
      set -ex
      cd /io/repo/hail
      chmod 755 ./gradlew
      time retry ./gradlew --version
      time retry make jars wheel HAIL_DEBUG_MODE=1
      (cd build/deploy/dist/ && tar -cvf debug-wheel-container.tar hail-*-py3-none-any.whl)
      cd /io/repo/hail
      mkdir build/debug_libs
      mv build/libs/hail-all-spark.jar build/debug_libs/
      mv build/libs/hail-all-spark-test.jar build/debug_libs/
      mv build/deploy/dist/debug-wheel-container.tar build/debug_libs
      time retry make jars python-version-info wheel
      time (cd python && zip -r hail.zip hail hailtop)
      time tar czf test.tar.gz -C python test
      time tar czf resources.tar.gz -C src/test resources
      time tar czf data.tar.gz -C python/hail/docs data
      (cd .. && time tar czf hail/website-src.tar.gz website)
      time tar czf cluster-tests.tar.gz python/cluster-tests
      (cd build/deploy/dist/ && tar -cvf wheel-container.tar hail-*-py3-none-any.whl)
      time TESTNG_SPLITS=5 python3 generate_splits.py
      time tar czf splits.tar.gz testng-splits-*.xml
    inputs:
      - from: /repo
        to: /io/repo
    outputs:
      - from: /io/repo/hail/build/libs/hail-all-spark.jar
        to: /hail.jar
      - from: /io/repo/hail/build/libs/hail-all-spark-test.jar
        to: /hail-test.jar
      - from: /io/repo/hail/build/debug_libs/hail-all-spark-test.jar
        to: /hail-debug-test.jar
      - from: /io/repo/hail/testng-build.xml
        to: /testng-build.xml
      - from: /io/repo/hail/testng-services.xml
        to: /testng-services.xml
      - from: /io/repo/hail/python/hail.zip
        to: /hail.zip
      - from: /io/repo/hail/build/deploy/dist/wheel-container.tar
        to: /wheel-container.tar
      - from: /io/repo/hail/build/debug_libs/debug-wheel-container.tar
        to: /debug-wheel-container.tar
      - from: /io/repo/hail/test.tar.gz
        to: /test.tar.gz
      - from: /io/repo/hail/resources.tar.gz
        to: /resources.tar.gz
      - from: /io/repo/hail/splits.tar.gz
        to: /splits.tar.gz
      - from: /io/repo/hail/data.tar.gz
        to: /data.tar.gz
      - from: /io/repo/hail/website-src.tar.gz
        to: /website-src.tar.gz
      - from: /io/repo/hail/cluster-tests.tar.gz
        to: /cluster-tests.tar.gz
    dependsOn:
      - hail_build_image
      - merge_code
  - kind: runImage
    name: build_hail_spark2.4.5
    image:
      valueFrom: hail_build_image.image
    resources:
      memory: 7.5G
      cpu: '4'
    script: |
      set -ex
      cd /io/repo/hail
      chmod 755 ./gradlew
      time retry ./gradlew --version
      export SPARK_VERSION="2.4.5" SCALA_VERSION="2.11.12"
      time retry make jars python-version-info wheel
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - hail_build_image
      - merge_code
  - kind: runImage
    name: build_hail_spark3.0.1
    image:
      valueFrom: hail_build_image.image
    resources:
      memory: 7.5G
      cpu: '4'
    script: |
      set -ex
      cd /io/repo/hail
      chmod 755 ./gradlew
      time retry ./gradlew --version
      export SPARK_VERSION="3.0.1" SCALA_VERSION="2.12.12"
      time retry make jars python-version-info wheel
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - hail_build_image
      - merge_code
  - kind: buildImage2
    name: batch_worker_image
    dockerFile: /io/repo/batch/Dockerfile.worker
    contextPath: /io/repo
    publishAs: batch-worker
    inputs:
      - from: /repo
        to: /io/repo
      - from: /hail_version
        to: /io/repo/hail_version
    dependsOn:
      - merge_code
      - hail_ubuntu_image
  - kind: buildImage2
    name: service_java_run_base_image
    dockerFile: /io/repo/docker/Dockerfile.service-java-run-base
    contextPath: /io/repo
    publishAs: service-java-run-base
    inputs:
      - from: /repo
        to: /io/repo
      - from: /hail_version
        to: /io/repo/hail_version
    dependsOn:
      - hail_ubuntu_image
      - merge_code
  - kind: buildImage2
    name: query_image
    dockerFile: /io/query/Dockerfile
    contextPath: /io/query/
    publishAs: query
    inputs:
      - from: /repo/query
        to: /io/query
      - from: /just-jar/hail.jar
        to: /io/query/hail.jar
    dependsOn:
      - service_java_run_base_image
      - build_hail_jar_only
      - merge_code
  - kind: deploy
    name: deploy_query_sa
    namespace:
      valueFrom: default_ns.name
    config: query/service-account.yaml
    dependsOn:
      - default_ns
  - kind: buildImage2
    name: memory_image
    dockerFile: /io/repo/memory/Dockerfile
    contextPath: /io/repo
    publishAs: memory
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - service_base_image
      - merge_code
  - kind: deploy
    name: deploy_memory_sa
    namespace:
      valueFrom: default_ns.name
    config: memory/service-account.yaml
    dependsOn:
      - default_ns
  - kind: buildImage2
    name: hail_repl_image
    dockerFile: /io/hail/Dockerfile.hail-repl
    contextPath: /io/hail
    publishAs: hail-run
    inputs:
      - from: /repo/hail
        to: /io/hail
      - from: /wheel-container.tar
        to: /io/hail/wheel-container.tar
    dependsOn:
      - base_image
      - build_hail
      - merge_code
  - kind: deploy
    name: deploy_hail_repl
    runIfRequested: true
    scopes:
      - dev
    namespace:
      valueFrom: default_ns.name
    config: hail/hail_repl.yaml
    dependsOn:
      - default_ns
      - hail_repl_image
  - kind: runImage
    name: upload_test_resources_to_gcs
    image:
      valueFrom: base_image.image
    script: |
      set -ex
      cd /io/repo/hail/
      gcloud -q auth activate-service-account --key-file=/test-gsa-key/key.json
      gsutil -m cp -r src/test/resources/* gs://{{ global.hail_test_gcs_bucket }}/{{ token }}/test/resources/
      gsutil -m cp -r python/hail/docs/data/* gs://{{ global.hail_test_gcs_bucket }}/{{ token }}/doctest/data/
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    inputs:
      - from: /repo/hail/src/test/resources
        to: /io/repo/hail/src/test/resources
      - from: /repo/hail/python/hail/docs/data
        to: /io/repo/hail/python/hail/docs/data
    dependsOn:
      - default_ns
      - base_image
      - merge_code
  - kind: runImage
    name: test_hail_java_0
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      mkdir -p src/test
      tar xzf resources.tar.gz -C src/test
      tar xzf splits.tar.gz
      export HAIL_TEST_SKIP_R=1
      export HAIL_GS_FS_TEST_RESOURCES=gs://{{ global.hail_test_gcs_bucket }}/{{ upload_test_resources_to_gcs.token }}/test/resources/fs
      export HAIL_TEST_GCS_BUCKET={{ global.hail_test_gcs_bucket }}
      java -cp hail-test.jar:$SPARK_HOME/jars/* org.testng.TestNG -listener is.hail.LogTestListener testng-splits-0.xml
    inputs:
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /hail-debug-test.jar
        to: /io/hail-test.jar
      - from: /splits.tar.gz
        to: /io/splits.tar.gz
    outputs:
      - from: /io/test-output
        to: /test-output
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - default_ns
      - upload_test_resources_to_gcs
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_hail_java_1
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      mkdir -p src/test
      tar xzf resources.tar.gz -C src/test
      tar xzf splits.tar.gz
      export HAIL_TEST_SKIP_R=1
      export HAIL_GS_FS_TEST_RESOURCES=gs://{{ global.hail_test_gcs_bucket }}/{{ upload_test_resources_to_gcs.token }}/test/resources/fs
      export HAIL_TEST_GCS_BUCKET={{ global.hail_test_gcs_bucket }}
      java -cp hail-test.jar:$SPARK_HOME/jars/* org.testng.TestNG -listener is.hail.LogTestListener testng-splits-1.xml
    inputs:
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /hail-debug-test.jar
        to: /io/hail-test.jar
      - from: /splits.tar.gz
        to: /io/splits.tar.gz
    outputs:
      - from: /io/test-output
        to: /test-output
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - default_ns
      - upload_test_resources_to_gcs
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_hail_java_2
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      mkdir -p src/test
      tar xzf resources.tar.gz -C src/test
      tar xzf splits.tar.gz
      export HAIL_TEST_SKIP_R=1
      export HAIL_GS_FS_TEST_RESOURCES=gs://{{ global.hail_test_gcs_bucket }}/{{ upload_test_resources_to_gcs.token }}/test/resources/fs
      export HAIL_TEST_GCS_BUCKET={{ global.hail_test_gcs_bucket }}
      java -cp hail-test.jar:$SPARK_HOME/jars/* org.testng.TestNG -listener is.hail.LogTestListener testng-splits-2.xml
    inputs:
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /hail-debug-test.jar
        to: /io/hail-test.jar
      - from: /splits.tar.gz
        to: /io/splits.tar.gz
    outputs:
      - from: /io/test-output
        to: /test-output
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - default_ns
      - upload_test_resources_to_gcs
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_hail_java_3
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      mkdir -p src/test
      tar xzf resources.tar.gz -C src/test
      tar xzf splits.tar.gz
      export HAIL_TEST_SKIP_R=1
      export HAIL_GS_FS_TEST_RESOURCES=gs://{{ global.hail_test_gcs_bucket }}/{{ upload_test_resources_to_gcs.token }}/test/resources/fs
      export HAIL_TEST_GCS_BUCKET={{ global.hail_test_gcs_bucket }}
      java -cp hail-test.jar:$SPARK_HOME/jars/* org.testng.TestNG -listener is.hail.LogTestListener testng-splits-3.xml
    inputs:
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /hail-debug-test.jar
        to: /io/hail-test.jar
      - from: /splits.tar.gz
        to: /io/splits.tar.gz
    outputs:
      - from: /io/test-output
        to: /test-output
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - default_ns
      - upload_test_resources_to_gcs
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_hail_java_4
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      mkdir -p src/test
      tar xzf resources.tar.gz -C src/test
      tar xzf splits.tar.gz
      export HAIL_TEST_SKIP_R=1
      export HAIL_GS_FS_TEST_RESOURCES=gs://{{ global.hail_test_gcs_bucket }}/{{ upload_test_resources_to_gcs.token }}/test/resources/fs
      export HAIL_TEST_GCS_BUCKET={{ global.hail_test_gcs_bucket }}
      java -cp hail-test.jar:$SPARK_HOME/jars/* org.testng.TestNG -listener is.hail.LogTestListener testng-splits-4.xml
    inputs:
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /hail-debug-test.jar
        to: /io/hail-test.jar
      - from: /splits.tar.gz
        to: /io/splits.tar.gz
    outputs:
      - from: /io/test-output
        to: /test-output
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - default_ns
      - upload_test_resources_to_gcs
      - hail_run_tests_image
      - build_hail
  - kind: buildImage2
    name: hail_base_image
    dockerFile: /io/repo/hail/Dockerfile.hail-base
    contextPath: /io/repo
    publishAs: hail-base
    resources:
      storage: 10Gi
      cpu: "2"
      memory: 7.5Gi
    inputs:
      - from: /repo
        to: /io/repo
      - from: /hail.jar
        to: /io/repo/hail.jar
      - from: /hail.zip
        to: /io/repo/hail.zip
    dependsOn:
      - hail_run_image
      - build_hail
      - merge_code
  - kind: buildImage2
    name: hail_pip_installed_python37_image
    dockerFile: /io/repo/hail/Dockerfile.hail-pip-installed-python37
    contextPath: /io/repo
    publishAs: hail-pip-installed-python37
    inputs:
      - from: /repo
        to: /io/repo
      - from: /wheel-container.tar
        to: /io/repo/wheel-container.tar
    dependsOn:
      - build_hail
      - hail_ubuntu_image
      - merge_code
  - kind: buildImage2
    name: hail_pip_installed_python36_image
    dockerFile: /io/repo/hail/Dockerfile.hail-pip-installed-python36
    contextPath: /io/repo
    publishAs: hail-pip-installed-python36
    inputs:
      - from: /repo
        to: /io/repo
      - from: /wheel-container.tar
        to: /io/repo/wheel-container.tar
    dependsOn:
      - build_hail
      - hail_ubuntu_image
      - merge_code
  - kind: runImage
    name: check_hail_python37
    image:
      valueFrom: hail_pip_installed_python37_image.image
    script: |
      set -x
      SITE_PACKAGES=$(pip3 show hail | grep Location | sed 's/Location: //')

      exit_status=0

      python3 -m flake8 --config setup.cfg $SITE_PACKAGES/hail $SITE_PACKAGES/hailtop || exit_status=$?
      python3 -m pylint --rcfile pylintrc hailtop || exit_status=$?
      # working around this: https://github.com/python/mypy/issues/7087
      ln -s $SITE_PACKAGES/hailtop hailtop
      mypy --config-file /setup.cfg -p hailtop || exit_status=$?

      exit $exit_status
    dependsOn:
      - hail_pip_installed_python37_image
  - kind: runImage
    name: check_hail_python36
    image:
      valueFrom: hail_pip_installed_python36_image.image
    script: |
      set -x
      SITE_PACKAGES=$(pip3 show hail | grep Location | sed 's/Location: //')

      exit_status=0

      python3 -m flake8 --config setup.cfg $SITE_PACKAGES/hail $SITE_PACKAGES/hailtop || exit_status=$?
      python3 -m pylint --rcfile pylintrc hailtop || exit_status=$?
      # working around this: https://github.com/python/mypy/issues/7087
      ln -s $SITE_PACKAGES/hailtop hailtop
      mypy --config-file /setup.cfg -p hailtop || exit_status=$?

      exit $exit_status
    dependsOn:
      - hail_pip_installed_python36_image
  - kind: buildImage2
    name: notebook_image
    dockerFile: /io/repo/notebook/Dockerfile
    contextPath: /io/repo/
    publishAs: notebook
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - service_base_image
      - merge_code
  - kind: runImage
    name: render_notebook_nginx_conf
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex
      cd /io/repo/notebook
      {% if deploy %}
      DEPLOY=true
      {% else %}
      DEPLOY=false
      {% endif %}
      python3 ../ci/jinja2_render.py '{"deploy": '${DEPLOY}', "default_ns": {"name": "{{ default_ns.name }}"}}' nginx.conf nginx.conf.out
    inputs:
      - from: /repo
        to: /io/repo
    outputs:
      - from: /io/repo/notebook/nginx.conf.out
        to: /notebook/nginx.conf.out
    dependsOn:
      - default_ns
      - service_base_image
      - merge_code
  - kind: buildImage2
    name: notebook_nginx_image
    dockerFile: /io/notebook/Dockerfile.nginx
    contextPath: /io/notebook
    publishAs: notebook_nginx
    inputs:
      - from: /repo/notebook
        to: /io/notebook
      - from: /notebook/nginx.conf.out
        to: /io/notebook/nginx.conf.out
    dependsOn:
      - hail_ubuntu_image
      - render_notebook_nginx_conf
      - merge_code
  - kind: runImage
    name: check_notebook
    image:
      valueFrom: notebook_image.image
    script: |
      set -ex
      SITE_PACKAGES=$(pip3 show notebook | grep Location | sed 's/Location: //')
      python3 -m flake8 $SITE_PACKAGES/notebook
      python3 -m pylint --rcfile pylintrc notebook
    dependsOn:
      - notebook_image
  - kind: runImage
    name: test_hail_python_0
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      tar xzf test.tar.gz
      tar xzf resources.tar.gz
      tar xzf data.tar.gz
      tar xvf debug-wheel-container.tar
      python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
      export HAIL_TEST_RESOURCES_DIR=./resources
      export HAIL_DOCTEST_DATA_DIR=./data
      export HAIL_TEST_GCS_BUCKET={{ global.hail_test_gcs_bucket }}
      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
      export HAIL_TEST_S3_BUCKET=hail-test-dy5rg
      export AWS_SHARED_CREDENTIALS_FILE=/test-aws-key/credentials
      export HAIL_TEST_AZURE_ACCOUNT=hailtest
      export HAIL_TEST_AZURE_CONTAINER=hail-test-4nxei
      export AZURE_APPLICATION_CREDENTIALS=/test-azure-key/credentials.json
      export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=0
      python3 -m pytest --ignore=test/hailtop/batch/ --ignore=test/hailtop/aiotools/test_copy.py --log-cli-level=INFO -s -vv --instafail --durations=50 test
    inputs:
      - from: /debug-wheel-container.tar
        to: /io/debug-wheel-container.tar
      - from: /test.tar.gz
        to: /io/test.tar.gz
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /data.tar.gz
        to: /io/data.tar.gz
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
      - name: test-aws-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-aws-key
      - name: test-azure-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-azure-key
    dependsOn:
      - default_ns
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_hail_python_1
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      tar xzf test.tar.gz
      tar xzf resources.tar.gz
      tar xzf data.tar.gz
      tar xvf debug-wheel-container.tar
      python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
      export HAIL_TEST_RESOURCES_DIR=./resources
      export HAIL_DOCTEST_DATA_DIR=./data
      export HAIL_TEST_GCS_BUCKET={{ global.hail_test_gcs_bucket }}
      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
      export HAIL_TEST_S3_BUCKET=hail-test-dy5rg
      export AWS_SHARED_CREDENTIALS_FILE=/test-aws-key/credentials
      export HAIL_TEST_AZURE_ACCOUNT=hailtest
      export HAIL_TEST_AZURE_CONTAINER=hail-test-4nxei
      export AZURE_APPLICATION_CREDENTIALS=/test-azure-key/credentials.json
      export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=1
      python3 -m pytest --ignore=test/hailtop/batch/ --ignore=test/hailtop/aiotools/test_copy.py --log-cli-level=INFO -s -vv --instafail --durations=50 test
    inputs:
      - from: /debug-wheel-container.tar
        to: /io/debug-wheel-container.tar
      - from: /test.tar.gz
        to: /io/test.tar.gz
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /data.tar.gz
        to: /io/data.tar.gz
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
      - name: test-aws-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-aws-key
      - name: test-azure-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-azure-key
    dependsOn:
      - default_ns
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_hail_python_2
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      tar xzf test.tar.gz
      tar xzf resources.tar.gz
      tar xzf data.tar.gz
      tar xvf debug-wheel-container.tar
      python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
      export HAIL_TEST_RESOURCES_DIR=./resources
      export HAIL_DOCTEST_DATA_DIR=./data
      export HAIL_TEST_GCS_BUCKET={{ global.hail_test_gcs_bucket }}
      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
      export HAIL_TEST_S3_BUCKET=hail-test-dy5rg
      export AWS_SHARED_CREDENTIALS_FILE=/test-aws-key/credentials
      export HAIL_TEST_AZURE_ACCOUNT=hailtest
      export HAIL_TEST_AZURE_CONTAINER=hail-test-4nxei
      export AZURE_APPLICATION_CREDENTIALS=/test-azure-key/credentials.json
      export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=2
      python3 -m pytest --ignore=test/hailtop/batch/ --ignore=test/hailtop/aiotools/test_copy.py --log-cli-level=INFO -s -vv --instafail --durations=50 test
    inputs:
      - from: /debug-wheel-container.tar
        to: /io/debug-wheel-container.tar
      - from: /test.tar.gz
        to: /io/test.tar.gz
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /data.tar.gz
        to: /io/data.tar.gz
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
      - name: test-aws-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-aws-key
      - name: test-azure-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-azure-key
    dependsOn:
      - default_ns
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_hail_python_3
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      tar xzf test.tar.gz
      tar xzf resources.tar.gz
      tar xzf data.tar.gz
      tar xvf debug-wheel-container.tar
      python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
      export HAIL_TEST_RESOURCES_DIR=./resources
      export HAIL_DOCTEST_DATA_DIR=./data
      export HAIL_TEST_GCS_BUCKET={{ global.hail_test_gcs_bucket }}
      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
      export HAIL_TEST_S3_BUCKET=hail-test-dy5rg
      export AWS_SHARED_CREDENTIALS_FILE=/test-aws-key/credentials
      export HAIL_TEST_AZURE_ACCOUNT=hailtest
      export HAIL_TEST_AZURE_CONTAINER=hail-test-4nxei
      export AZURE_APPLICATION_CREDENTIALS=/test-azure-key/credentials.json
      export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=3
      python3 -m pytest --ignore=test/hailtop/batch/ --ignore=test/hailtop/aiotools/test_copy.py --log-cli-level=INFO -s -vv --instafail --durations=50 test
    inputs:
      - from: /debug-wheel-container.tar
        to: /io/debug-wheel-container.tar
      - from: /test.tar.gz
        to: /io/test.tar.gz
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /data.tar.gz
        to: /io/data.tar.gz
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
      - name: test-aws-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-aws-key
      - name: test-azure-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-azure-key
    dependsOn:
      - default_ns
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_hail_python_4
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      tar xzf test.tar.gz
      tar xzf resources.tar.gz
      tar xzf data.tar.gz
      tar xvf debug-wheel-container.tar
      python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
      export HAIL_TEST_RESOURCES_DIR=./resources
      export HAIL_DOCTEST_DATA_DIR=./data
      export HAIL_TEST_GCS_BUCKET={{ global.hail_test_gcs_bucket }}
      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
      export HAIL_TEST_S3_BUCKET=hail-test-dy5rg
      export AWS_SHARED_CREDENTIALS_FILE=/test-aws-key/credentials
      export HAIL_TEST_AZURE_ACCOUNT=hailtest
      export HAIL_TEST_AZURE_CONTAINER=hail-test-4nxei
      export AZURE_APPLICATION_CREDENTIALS=/test-azure-key/credentials.json
      export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=4
      python3 -m pytest --ignore=test/hailtop/batch/ --ignore=test/hailtop/aiotools/test_copy.py --log-cli-level=INFO -s -vv --instafail --durations=50 test
    inputs:
      - from: /debug-wheel-container.tar
        to: /io/debug-wheel-container.tar
      - from: /test.tar.gz
        to: /io/test.tar.gz
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /data.tar.gz
        to: /io/data.tar.gz
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
      - name: test-aws-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-aws-key
      - name: test-azure-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-azure-key
    dependsOn:
      - default_ns
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_hail_python_copy
    image:
      valueFrom: hail_run_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      tar xzf test.tar.gz
      tar xvf debug-wheel-container.tar
      python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
      export HAIL_TEST_GCS_BUCKET={{ global.hail_test_gcs_bucket }}
      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
      export HAIL_TEST_S3_BUCKET=hail-test-dy5rg
      export AWS_SHARED_CREDENTIALS_FILE=/test-aws-key/credentials
      export HAIL_TEST_AZURE_ACCOUNT=hailtest
      export HAIL_TEST_AZURE_CONTAINER=hail-test-4nxei
      export AZURE_APPLICATION_CREDENTIALS=/test-azure-key/credentials.json
      python3 -m pytest --log-cli-level=INFO -s -vv --instafail --durations=50 -n 10 test/hailtop/aiotools/test_copy.py
    inputs:
      - from: /debug-wheel-container.tar
        to: /io/debug-wheel-container.tar
      - from: /test.tar.gz
        to: /io/test.tar.gz
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
      - name: test-aws-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-aws-key
      - name: test-azure-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-azure-key
    dependsOn:
      - default_ns
      - hail_run_image
      - build_hail
  - kind: runImage
    name: test_hail_python_unchecked_allocator
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      tar xzf test.tar.gz
      tar xzf resources.tar.gz
      tar xzf data.tar.gz
      tar xvf wheel-container.tar
      python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
      export HAIL_TEST_RESOURCES_DIR=./resources
      export HAIL_DOCTEST_DATA_DIR=./data
      export HAIL_TEST_GCS_BUCKET={{ global.hail_test_gcs_bucket }}
      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
      export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
      python3 -m pytest -m unchecked_allocator --ignore=test/hailtop/batch/ --log-cli-level=INFO -s -vv --instafail --durations=50 test
    inputs:
      - from: /wheel-container.tar
        to: /io/wheel-container.tar
      - from: /test.tar.gz
        to: /io/test.tar.gz
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /data.tar.gz
        to: /io/data.tar.gz
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - default_ns
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_hail_python_local_backend_0
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      tar xzf test.tar.gz
      tar xzf resources.tar.gz
      tar xzf data.tar.gz
      tar xvf debug-wheel-container.tar
      python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
      export HAIL_TEST_RESOURCES_DIR=./resources
      export HAIL_DOCTEST_DATA_DIR=./data
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=0
      export HAIL_QUERY_BACKEND=local
      python3 -m pytest --ignore=test/hailtop/ --log-cli-level=INFO -s -vv --instafail --durations=50 test
    inputs:
      - from: /debug-wheel-container.tar
        to: /io/debug-wheel-container.tar
      - from: /test.tar.gz
        to: /io/test.tar.gz
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /data.tar.gz
        to: /io/data.tar.gz
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - default_ns
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_hail_python_local_backend_1
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      tar xzf test.tar.gz
      tar xzf resources.tar.gz
      tar xzf data.tar.gz
      tar xvf debug-wheel-container.tar
      python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
      export HAIL_TEST_RESOURCES_DIR=./resources
      export HAIL_DOCTEST_DATA_DIR=./data
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=1
      export HAIL_QUERY_BACKEND=local
      python3 -m pytest --ignore=test/hailtop/ --log-cli-level=INFO -s -vv --instafail --durations=50 test
    inputs:
      - from: /debug-wheel-container.tar
        to: /io/debug-wheel-container.tar
      - from: /test.tar.gz
        to: /io/test.tar.gz
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /data.tar.gz
        to: /io/data.tar.gz
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - default_ns
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_hail_python_local_backend_2
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      tar xzf test.tar.gz
      tar xzf resources.tar.gz
      tar xzf data.tar.gz
      tar xvf debug-wheel-container.tar
      python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
      export HAIL_TEST_RESOURCES_DIR=./resources
      export HAIL_DOCTEST_DATA_DIR=./data
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=2
      export HAIL_QUERY_BACKEND=local
      python3 -m pytest --ignore=test/hailtop/ --log-cli-level=INFO -s -vv --instafail --durations=50 test
    inputs:
      - from: /debug-wheel-container.tar
        to: /io/debug-wheel-container.tar
      - from: /test.tar.gz
        to: /io/test.tar.gz
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /data.tar.gz
        to: /io/data.tar.gz
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - default_ns
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_hail_python_local_backend_3
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      tar xzf test.tar.gz
      tar xzf resources.tar.gz
      tar xzf data.tar.gz
      tar xvf debug-wheel-container.tar
      python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
      export HAIL_TEST_RESOURCES_DIR=./resources
      export HAIL_DOCTEST_DATA_DIR=./data
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=3
      export HAIL_QUERY_BACKEND=local
      python3 -m pytest --ignore=test/hailtop/ --log-cli-level=INFO -s -vv --instafail --durations=50 test
    inputs:
      - from: /debug-wheel-container.tar
        to: /io/debug-wheel-container.tar
      - from: /test.tar.gz
        to: /io/test.tar.gz
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /data.tar.gz
        to: /io/data.tar.gz
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - default_ns
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_hail_python_local_backend_4
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      tar xzf test.tar.gz
      tar xzf resources.tar.gz
      tar xzf data.tar.gz
      tar xvf debug-wheel-container.tar
      python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
      export HAIL_TEST_RESOURCES_DIR=./resources
      export HAIL_DOCTEST_DATA_DIR=./data
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=4
      export HAIL_QUERY_BACKEND=local
      python3 -m pytest --ignore=test/hailtop/ --log-cli-level=INFO -s -vv --instafail --durations=50 test
    inputs:
      - from: /debug-wheel-container.tar
        to: /io/debug-wheel-container.tar
      - from: /test.tar.gz
        to: /io/test.tar.gz
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /data.tar.gz
        to: /io/data.tar.gz
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - default_ns
      - hail_run_tests_image
      - build_hail
  - kind: runImage
    name: test_python_docs
    image:
      valueFrom: hail_base_image.image
    script: |
      set -ex
      cd /hail/python/hail
      python3 -m pytest --instafail \
        --doctest-modules \
        --doctest-glob='*.rst' \
        --ignore=docs/conf.py \
        --ignore=docs/doctest_write_data.py
    dependsOn:
      - hail_base_image
  - kind: runImage
    name: make_docs
    image:
      valueFrom: hail_base_image.image
    script: |
      set -ex
      export HAIL_SHORT_VERSION='0.2'
      export SPHINXOPTS='-tgenerate_notebook_outputs'

      mkdir -p {{ token }}/python
      cd {{ token }}
      unzip -q -d python /io/hail.zip

      tar xzf /io/website-src.tar.gz
      export HAIL_WEBSITE_DIR=$(pwd)/website/website/

      sed -E "s/\(hail\#([0-9]+)\)/(\[#\1](https:\/\/github.com\/hail-is\/hail\/pull\/\1))/g" \
        < python/hail/docs/change_log.md \
        | pandoc -o python/hail/docs/change_log.rst

      make -C python/hail/docs BUILDDIR=_build clean html
      make -C python/hailtop/batch/docs BUILDDIR=_build clean html

      mkdir -p www/docs
      mv python/hail/docs/_build/html www/docs/0.2
      mv python/hailtop/batch/docs/_build/html www/docs/batch

      HAIL_CACHE_VERSION=$(cat python/hail/hail_version)
      find www -iname *.html -type f -exec sed -i -e "s/\.css/\.css\?v\=$HAIL_CACHE_VERSION/" {} +;

      tar czf /io/www.tar.gz www
    resources:
      memory: 7.5G
      cpu: '2'
    inputs:
      - from: /hail.zip
        to: /io/hail.zip
      - from: /website-src.tar.gz
        to: /io/website-src.tar.gz
    outputs:
      - from: /io/www.tar.gz
        to: /www.tar.gz
    dependsOn:
      - hail_base_image
      - build_hail
  - kind: runImage
    name: make_pip_versioned_docs
    image:
      valueFrom: hail_run_image.image
    script: |
      set -ex

      cd /io/repo

      make -C hail python/hail/hail_pip_version

      # dev deploy elides the hail-is remote, add it and retrieve the tags
      git remote add hail-is https://github.com/hail-is/hail.git
      git fetch hail-is

      # 0.2.63 was the last old-style docs
      if [[ "$(cat hail/python/hail/hail_pip_version)" != "0.2.63" ]]
      then
          # downloading files from GCS changes permissions, so we reset all of that first
          git reset --hard HEAD
          # if the tag doesn't exist, this commit is the release
          git checkout $(cat hail/python/hail/hail_pip_version) || true
      fi

      PYTHONPATH=$PYTHONPATH:$(pwd)/hail/python make -C hail hail-docs-no-test batch-docs

      gsutil cp gs://hail-common/builds/0.1/docs/hail-0.1-docs-5a6778710097.tar.gz .
      mkdir hail/build/www/docs/0.1
      tar -xvf hail-0.1-docs-5a6778710097.tar.gz -C hail/build/www/docs/0.1 --strip-components 2

      tar czf /io/docs.tar.gz -C hail/build/www .
    resources:
      memory: 7.5G
      cpu: '2'
    inputs:
      - from: /repo
        to: /io/repo
    outputs:
      - from: /io/docs.tar.gz
        to: /docs.tar.gz
    dependsOn:
      - hail_run_image
      - merge_code
  - kind: deploy
    name: deploy_grafana
    namespace:
      valueFrom: default_ns.name
    config: grafana/deployment.yaml
    scopes:
      - deploy
      - dev
    dependsOn:
      - default_ns
      - base_image
      - grafana_nginx_image
      - create_certs
  - kind: runImage
    name: render_prom_nginx_conf
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex
      cd /io/repo/prometheus
      {% if deploy %}
      DEPLOY=true
      {% else %}
      DEPLOY=false
      {% endif %}
      python3 ../ci/jinja2_render.py '{"deploy": '${DEPLOY}', "default_ns": {"name": "{{ default_ns.name }}"}}' nginx.conf nginx.conf.out
    inputs:
      - from: /repo
        to: /io/repo
    outputs:
      - from: /io/repo/prometheus/nginx.conf.out
        to: /prometheus/nginx.conf.out
    dependsOn:
      - default_ns
      - service_base_image
      - merge_code
  - kind: buildImage2
    name: prom_nginx_image
    dockerFile: /io/prometheus/Dockerfile.nginx
    contextPath: /io/prometheus
    publishAs: prometheus
    inputs:
      - from: /repo/prometheus
        to: /io/prometheus
      - from: /prometheus/nginx.conf.out
        to: /io/prometheus/nginx.conf.out
    dependsOn:
      - hail_ubuntu_image
      - render_prom_nginx_conf
      - merge_code
  - kind: deploy
    name: deploy_prometheus
    namespace:
      valueFrom: default_ns.name
    config: prometheus/prometheus.yaml
    scopes:
      - deploy
      - dev
    dependsOn:
      - default_ns
      - prom_nginx_image
      - create_certs
  - kind: runImage
    name: create_dummy_oauth2_client_secret
    image:
      valueFrom: base_image.image
    script: |
      set -ex
      kubectl -n {{ default_ns.name }} create secret generic auth-oauth2-client-secret || true
    scopes:
      - test
      - dev
    dependsOn:
      - default_ns
      - base_image
  - kind: deploy
    name: deploy_auth
    namespace:
      valueFrom: default_ns.name
    config: auth/deployment.yaml
    wait:
      - kind: Service
        name: auth
        for: alive
      - kind: Service
        name: auth-driver
        for: alive
    dependsOn:
      - default_ns
      - create_deploy_config
      - create_session_key
      - auth_database
      - auth_image
      - create_dummy_oauth2_client_secret
      - create_certs
      - create_accounts
  - kind: runImage
    name: check_monitoring
    image:
      valueFrom: monitoring_image.image
    script: |
      set -ex
      SITE_PACKAGES=$(pip3 show monitoring | grep Location | sed 's/Location: //')
      python3 -m flake8 $SITE_PACKAGES/monitoring
      python3 -m pylint --rcfile pylintrc monitoring
    dependsOn:
      - monitoring_image
  - kind: runImage
    name: delete_monitoring_tables
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex
      mysql --defaults-extra-file=/sql-config/sql-config.cnf < /io/sql/delete-monitoring-tables.sql
    inputs:
      - from: /repo/monitoring/sql
        to: /io/sql
    secrets:
      - name: database-server-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /sql-config
    runIfRequested: true
    scopes:
      - dev
    dependsOn:
      - default_ns
      - service_base_image
      - merge_code
  - kind: createDatabase
    name: monitoring_database
    databaseName: monitoring
    migrations:
      - name: initial
        script: /io/sql/initial.sql
    inputs:
      - from: /repo/monitoring/sql
        to: /io/sql
    namespace:
      valueFrom: default_ns.name
    shutdowns:
      - kind: Deployment
        namespace:
          valueFrom: default_ns.name
        name: monitoring
    dependsOn:
      - default_ns
      - merge_code
      - delete_monitoring_tables
  - kind: deploy
    name: deploy_monitoring
    namespace:
      valueFrom: default_ns.name
    config: monitoring/deployment.yaml
    wait:
      - kind: Service
        name: monitoring
        for: alive
    dependsOn:
      - default_ns
      - monitoring_image
      - monitoring_database
      - deploy_auth
      - create_certs
      - create_accounts
  - kind: runImage
    name: test_monitoring
    image:
      valueFrom: test_monitoring_image.image
    script: |
      set -ex
      python3 -m pytest --log-cli-level=INFO -s -vv --instafail --durations=50 /test/
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-dev-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: ssl-config-monitoring-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
    timeout: 300
    dependsOn:
      - test_monitoring_image
      - create_deploy_config
      - create_accounts
      - default_ns
      - create_certs
      - deploy_monitoring
  - kind: runImage
    name: test_auth_copy_paste_login
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex

      export HAIL_DEPLOY_CONFIG_FILE=/deploy-config/deploy-config.json

      COPY_PASTE_TOKEN=$(hailctl curl {{ default_ns.name }} \
                         auth /api/v1alpha/copy-paste-token \
                         -fsSL \
                         --retry 3 \
                         --retry-delay 5 \
                         -XPOST)
      hailctl auth copy-paste-login "$COPY_PASTE_TOKEN" --namespace {{ default_ns.name }}

      if hailctl auth copy-paste-login "$COPY_PASTE_TOKEN" --namespace {{ default_ns.name }}
      then
          echo "reusing a token should not work, but did"
          exit 1
      fi

      COPY_PASTE_TOKEN=$(hailctl curl {{ default_ns.name }} \
                         auth /api/v1alpha/copy-paste-token \
                         -fsSL \
                         --retry 3 \
                         --retry-delay 5 \
                         -XPOST)
      python3 -c '
      from hailtop.auth import copy_paste_login;
      copy_paste_login("'$COPY_PASTE_TOKEN'", "{{ default_ns.name }}")
      '

      python3 -c '
      from hailtop.auth import copy_paste_login;
      import aiohttp
      try:
          copy_paste_login("'$COPY_PASTE_TOKEN'", "{{ default_ns.name }}")
          print("reusing a token should not work, but did")
          sys.exit(1)
      except aiohttp.client_exceptions.ClientResponseError as exc:
          assert(exc.status == 401)
      '
    secrets:
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
    dependsOn:
      - default_ns
      - create_accounts
      - deploy_auth
      - create_deploy_config
      - service_base_image
  - kind: runImage
    name: test_auth_copy_paste_login_timeout
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex

      export HAIL_DEPLOY_CONFIG_FILE=/deploy-config/deploy-config.json

      COPY_PASTE_TOKEN=$(hailctl curl {{ default_ns.name }} \
                         auth /api/v1alpha/copy-paste-token \
                         -fsSL \
                         --retry 3 \
                         --retry-delay 5 \
                         -XPOST)
      sleep $(( 5 * 60 + 1))
      if hailctl auth copy-paste-login "$COPY_PASTE_TOKEN" --namespace {{ default_ns.name }}
      then
          echo "using an expired token should not work, but did"
          exit 1
      fi

      python3 -c '
      import aiohttp
      from hailtop.auth import copy_paste_login;
      try:
          copy_paste_login("'$COPY_PASTE_TOKEN'", "{{ default_ns.name }}")
          print("using an expired token should not work, but did")
          sys.exit(1)
      except aiohttp.client_exceptions.ClientResponseError as exc:
          assert(exc.status == 401)
      '
    secrets:
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
    dependsOn:
      - default_ns
      - create_accounts
      - deploy_auth
      - create_deploy_config
      - service_base_image
  - kind: runImage
    name: delete_batch_tables
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex
      mysql --defaults-extra-file=/sql-config/sql-config.cnf < /io/sql/delete-batch-tables.sql
    inputs:
      - from: /repo/batch/sql
        to: /io/sql
    secrets:
      - name: database-server-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /sql-config
    runIfRequested: true
    scopes:
      - dev
    dependsOn:
      - default_ns
      - service_base_image
      - merge_code
  - kind: runImage
    name: delete_ci_tables
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex
      mysql --defaults-extra-file=/sql-config/sql-config.cnf < /io/sql/delete-ci-tables.sql
    inputs:
      - from: /repo/ci/sql
        to: /io/sql
    secrets:
      - name: database-server-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /sql-config
    runIfRequested: true
    scopes:
      - dev
    dependsOn:
      - default_ns
      - service_base_image
      - merge_code
  - kind: createDatabase
    name: ci_database
    databaseName: ci
    migrations:
      - name: initial
        script: /io/sql/initial.sql
      - name: invalidated-batches
        script: /io/sql/invalidated-batches.sql
    inputs:
      - from: /repo/ci/sql
        to: /io/sql
    namespace:
      valueFrom: default_ns.name
    shutdowns:
      - kind: Deployment
        namespace:
          valueFrom: default_ns.name
        name: ci
    dependsOn:
      - default_ns
      - merge_code
      - delete_ci_tables
  - kind: createDatabase
    name: batch_database
    databaseName: batch
    migrations:
      - name: initial
        script: /io/sql/initial.sql
      - name: insert-globals
        script: /io/sql/insert_globals.py
      - name: create-billing-projects
        script: /io/sql/create-billing-projects.sql
      - name: increase-spec-size
        script: /io/sql/increase-spec-size.sql
      - name: remove-fk-batches-user-resources
        script: /io/sql/remove-fk-batches-user-resources.sql
      - name: change-ready-cores-bigint
        script: /io/sql/change-ready-cores-bigint.sql
      - name: add-user-resources-ready-cores-token
        script: /io/sql/add-user-resources-ready-cores-token.sql
      - name: add-lock-in-share-mode
        script: /io/sql/add-lock-in-share-mode.sql
      - name: add-batch-create-token
        script: /io/sql/add-batch-create-token.sql
      - name: improve-cancel
        script: /io/sql/improve-cancel.sql
      - name: store-specs-in-gcs
        script: /io/sql/store-specs-in-gcs.sql
      - name: add-batches-time-closed
        script: /io/sql/add-batches-time-closed.sql
      - name: add-instance-zone
        script: /io/sql/add-instance-zone.sql
      - name: add-batches-time-created-index
        script: /io/sql/add-batches-time-created-index.sql
      - name: change-test-worker-disk-size
        script: /io/sql/change_test_worker_disk_size.py
      - name: add-resources
        script: /io/sql/add-resources.sql
      - name: insert-resources
        script: /io/sql/insert_resources.py
      - name: insert-standing-worker-globals
        script: /io/sql/insert_standing_worker_globals.py
      - name: insert-local-ssd-resource
        script: /io/sql/insert_local_ssd_resource.py
      - name: fix-mark-job-complete-on-error
        script: /io/sql/fix-mark-job-complete-on-error.sql
      - name: add-worker-pd-ssd-data-disk
        script: /io/sql/add-worker-pd-ssd-data-disk.sql
      - name: add-aggregated-batch-resources-tokens
        script: /io/sql/add-aggregated-batch-resources-tokens.sql
      - name: change-test-worker-pool-size
        script: /io/sql/change_test_worker_pool_size.py
      - name: add-test-dev-to-billing-project-users
        script: /io/sql/add-test-dev-to-billing-project-users.sql
      - name: add-status-flag-billing-projects
        script: /io/sql/add-status-flag-billing-projects.sql
      - name: add-aggregated-billing-project-resources
        script: /io/sql/add-aggregated-billing-project-resources.sql
      - name: add-enable-standing-worker
        script: /io/sql/add-enable-standing-worker.py
      - name: add-inst-colls
        script: /io/sql/add-inst-colls.sql
      - name: add-creating-job-state
        script: /io/sql/add-creating-job-state.sql
      - name: add-job-private-inst-coll
        script: /io/sql/add-job-private-inst-coll.sql
      - name: insert-nonpreemptible-resources
        script: /io/sql/insert_nonpreemptible_resources.py
      - name: fix-schedule-job
        script: /io/sql/fix-schedule-job.sql
      - name: increase-test-and-dev-pool-sizes
        script: /io/sql/increase-test-and-dev-pool-sizes.py
      - name: fix-provisioning-bug
        script: /io/sql/fix-provisioning-bug.sql
      - name: do-not-lock-entire-batch
        script: /io/sql/do-not-lock-entire-batch.sql
      - name: add-fail-fast
        script: /io/sql/add-fail-fast.sql
      - name: add-frozen-mode
        script: /io/sql/add-frozen-mode.sql
      - name: add-instance-config
        script: /io/sql/add-instance-config.sql
    inputs:
      - from: /repo/batch/sql
        to: /io/sql
    namespace:
      valueFrom: default_ns.name
    shutdowns:
      - kind: Deployment
        namespace:
          valueFrom: default_ns.name
        name: batch
      - kind: Deployment
        namespace:
          valueFrom: default_ns.name
        name: batch-driver
    dependsOn:
      - default_ns
      - merge_code
      - delete_batch_tables
  - kind: deploy
    name: deploy_batch
    namespace:
      valueFrom: default_ns.name
    config: batch/deployment.yaml
    wait:
      - kind: Service
        name: batch
        for: alive
      - kind: Service
        name: batch-driver
        for: alive
    dependsOn:
      - default_ns
      - deploy_batch_sa
      - create_accounts
      - batch_image
      - batch_worker_image
      - batch_database
      - deploy_auth
      - create_certs
  - kind: runImage
    name: create_billing_projects
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex
      # create billing projects and add users to them
      cat > create-billing-projects.py <<EOF
      import sys
      import json
      import asyncio
      import aiohttp
      from hailtop.utils import async_to_blocking
      from hailtop.batch_client.aioclient import BatchClient
      async def create(billing_project, user, limit=None):
          bc = BatchClient(None)
          try:
              try:
                  await bc.create_billing_project(billing_project)
              except aiohttp.ClientResponseError as e:
                  if e.status != 403 or 'already exists' not in e.message:
                       raise

              try:
                  await bc.add_user(user, billing_project)
              except aiohttp.ClientResponseError as e:
                  if e.status != 403 or 'already member of billing project' not in e.message:
                       raise

              await bc.edit_billing_limit(billing_project, limit)
          finally:
              await bc.close()
      async def main():
          {% if deploy %}
          benchmark_limit = 25
          {% else %}
          benchmark_limit = 5
          {% endif %}

          await asyncio.gather(*[
              create(billing_project="benchmark", user="benchmark", limit=benchmark_limit)
          ])
      async_to_blocking(main())
      EOF
      python3 create-billing-projects.py
    secrets:
      - name: test-dev-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
    dependsOn:
      - default_ns
      - service_base_image
      - create_deploy_config
      - create_accounts
      - deploy_batch
  - kind: deploy
    name: deploy_benchmark
    namespace:
      valueFrom: default_ns.name
    config: benchmark-service/deployment.yaml
    wait:
      - kind: Service
        name: benchmark
        for: alive
    dependsOn:
      - default_ns
      - benchmark_image
      - create_certs
      - deploy_auth
      - create_accounts
      - create_billing_projects
      - deploy_batch
  - kind: runImage
    name: test_benchmark
    image:
      valueFrom: test_benchmark_image.image
    script: |
      set -ex
      python3 -m pytest --log-cli-level=INFO -s -vv --instafail --durations=50 /test/
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-dev-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: ssl-config-benchmark-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
    timeout: 1200
    dependsOn:
      - test_benchmark_image
      - create_deploy_config
      - create_accounts
      - default_ns
      - create_certs
      - deploy_benchmark
  - kind: runImage
    name: upload_query_jar
    image:
      valueFrom: base_image.image
    script: |
      set -ex
      gcloud -q auth activate-service-account --key-file=/query-gsa-key/key.json

      {% if deploy %}
      destination=$(cat /global-config/hail_query_gcs_path)/jars/
      {% else %}
      destination=gs://{{ global.hail_test_gcs_bucket }}/{{ token }}/jars/
      {% endif %}

      gsutil -m cp /io/hail.jar ${destination}$(cat /io/git_version).jar
    secrets:
      - name: query-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /query-gsa-key
      - name: global-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /global-config
    inputs:
      - from: /just-jar/hail.jar
        to: /io/hail.jar
      - from: /git_version
        to: /io/git_version
    dependsOn:
      - default_ns
      - base_image
      - build_hail_jar_only
      - merge_code
      - create_test_gsa_keys
  - kind: deploy
    name: deploy_query
    namespace:
      valueFrom: default_ns.name
    config: query/deployment.yaml
    wait:
      - kind: Service
        name: query
        for: alive
    dependsOn:
      - default_ns
      - deploy_batch
      - query_image
      - deploy_query_sa
      - upload_query_jar
      - create_certs
  - kind: deploy
    name: deploy_memory
    namespace:
      valueFrom: default_ns.name
    config: memory/deployment.yaml
    wait:
      - kind: Service
        name: memory
        for: alive
    dependsOn:
      - default_ns
      - memory_image
      - deploy_memory_sa
      - create_certs
  - kind: runImage
    name: test_lsm
    image:
      valueFrom: base_image.image
    script: |
      cd /io/lsm
      make
      make test
    inputs:
      - from: /repo/lsm
        to: /io/lsm
    dependsOn:
      - base_image
      - merge_code
  - kind: buildImage2
    name: netcat_ubuntu_image
    dockerFile:
      inline: |
        FROM {{ hail_ubuntu_image.image }}
        RUN hail-apt-get-install netcat
    dependsOn:
      - hail_ubuntu_image
  - kind: buildImage2
    name: volume_image
    dockerFile:
      inline: |
        FROM {{ hail_ubuntu_image.image }}
        VOLUME ["/data"]
    dependsOn:
      - hail_ubuntu_image
  - kind: buildImage2
    name: workdir_image
    dockerFile:
      inline: |
        FROM {{ hail_ubuntu_image.image }}
        WORKDIR ["/work"]
    dependsOn:
      - hail_ubuntu_image
  - kind: buildImage2
    name: curl_image
    dockerFile:
      inline: |
        FROM {{ hail_ubuntu_image.image }}
        RUN hail-apt-get-install curl
    dependsOn:
      - hail_ubuntu_image
  - kind: runImage
    name: test_memory
    image:
      valueFrom: memory_image.image
    resources:
      memory: 3.75Gi
      cpu: '1'
    script: |
      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
      export PROJECT={{ global.project }}
      hailctl config set batch/bucket {{ global.hail_test_gcs_bucket }}
      python3 -m pytest --log-cli-level=INFO -s -vv --instafail --durations=50 /io/test/
    timeout: 600
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: ssl-config-memory-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    inputs:
      - from: /repo/memory/test
        to: /io/test
    dependsOn:
      - create_deploy_config
      - create_accounts
      - default_ns
      - merge_code
      - memory_image
      - deploy_memory
  - kind: runImage
    name: test_batch_0
    image:
      valueFrom: batch_image.image
    script: |
      set -ex
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=0
      export HAIL_GSA_KEY_FILE=/test-gsa-key/key.json
      export HAIL_BASE_IMAGE={{ base_image.image }}
      export CI_UTILS_IMAGE={{ ci_utils_image.image }}
      export HAIL_CURL_IMAGE={{ curl_image.image }}
      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
      export HAIL_NETCAT_UBUNTU_IMAGE={{ netcat_ubuntu_image.image }}
      export HAIL_VOLUME_IMAGE={{ volume_image.image }}
      export HAIL_WORKDIR_IMAGE={{ workdir_image.image }}
      export HAIL_HAIL_BASE_IMAGE={{ hail_base_image.image }}
      export DOCKER_PREFIX="{{ global.docker_prefix }}"
      export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
      export HAIL_TEST_TOKEN_FILE=/user-tokens/tokens.json
      export HAIL_TEST_DEV_TOKEN_FILE=/dev-tokens/tokens.json
      export HAIL_TOKEN="{{ token }}"
      export HAIL_SCOPE="{{ scope }}"
      hailctl config set batch/bucket {{ global.hail_test_gcs_bucket }}
      python3 -m pytest \
              --log-date-format="%Y-%m-%dT%H:%M:%S" \
              --log-format="%(asctime)s %(levelname)s %(name)s %(filename)s:%(lineno)d:%(funcName)s %(message)s" \
              --log-cli-level=INFO \
              -s \
              -vv \
              --instafail \
              -k "not test_scale and not test_invariants" \
              --durations=0 \
              /io/test/
    inputs:
      - from: /repo/batch/test
        to: /io/test
    port: 5000
    timeout: 1200
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: test-dev-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /dev-tokens
      - name: ssl-config-batch-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - create_deploy_config
      - create_accounts
      - default_ns
      - merge_code
      - base_image
      - hail_base_image
      - batch_image
      - ci_utils_image
      - deploy_batch
      - netcat_ubuntu_image
      - volume_image
      - workdir_image
      - curl_image
  - kind: runImage
    name: test_batch_1
    image:
      valueFrom: batch_image.image
    script: |
      set -ex
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=1
      export HAIL_GSA_KEY_FILE=/test-gsa-key/key.json
      export HAIL_BASE_IMAGE={{ base_image.image }}
      export CI_UTILS_IMAGE={{ ci_utils_image.image }}
      export HAIL_CURL_IMAGE={{ curl_image.image }}
      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
      export HAIL_NETCAT_UBUNTU_IMAGE={{ netcat_ubuntu_image.image }}
      export HAIL_VOLUME_IMAGE={{ volume_image.image }}
      export HAIL_WORKDIR_IMAGE={{ workdir_image.image }}
      export HAIL_HAIL_BASE_IMAGE={{ hail_base_image.image }}
      export DOCKER_PREFIX="{{ global.docker_prefix }}"
      export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
      export HAIL_TEST_TOKEN_FILE=/user-tokens/tokens.json
      export HAIL_TEST_DEV_TOKEN_FILE=/dev-tokens/tokens.json
      export HAIL_TOKEN="{{ token }}"
      export HAIL_SCOPE="{{ scope }}"
      hailctl config set batch/bucket {{ global.hail_test_gcs_bucket }}
      python3 -m pytest \
              --log-date-format="%Y-%m-%dT%H:%M:%S" \
              --log-format="%(asctime)s %(levelname)s %(name)s %(filename)s:%(lineno)d:%(funcName)s %(message)s" \
              --log-cli-level=INFO \
              -s \
              -vv \
              --instafail \
              -k "not test_scale and not test_invariants" \
              --durations=0 \
              /io/test/
    inputs:
      - from: /repo/batch/test
        to: /io/test
    port: 5000
    timeout: 1200
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: test-dev-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /dev-tokens
      - name: ssl-config-batch-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - default_ns
      - create_deploy_config
      - create_accounts
      - merge_code
      - base_image
      - hail_base_image
      - batch_image
      - ci_utils_image
      - deploy_batch
      - netcat_ubuntu_image
      - volume_image
      - workdir_image
      - curl_image
  - kind: runImage
    name: test_batch_2
    image:
      valueFrom: batch_image.image
    script: |
      set -ex
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=2
      export HAIL_GSA_KEY_FILE=/test-gsa-key/key.json
      export HAIL_BASE_IMAGE={{ base_image.image }}
      export CI_UTILS_IMAGE={{ ci_utils_image.image }}
      export HAIL_CURL_IMAGE={{ curl_image.image }}
      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
      export HAIL_NETCAT_UBUNTU_IMAGE={{ netcat_ubuntu_image.image }}
      export HAIL_VOLUME_IMAGE={{ volume_image.image }}
      export HAIL_WORKDIR_IMAGE={{ workdir_image.image }}
      export HAIL_HAIL_BASE_IMAGE={{ hail_base_image.image }}
      export DOCKER_PREFIX="{{ global.docker_prefix }}"
      export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
      export HAIL_TEST_TOKEN_FILE=/user-tokens/tokens.json
      export HAIL_TEST_DEV_TOKEN_FILE=/dev-tokens/tokens.json
      export HAIL_TOKEN="{{ token }}"
      export HAIL_SCOPE="{{ scope }}"
      hailctl config set batch/bucket {{ global.hail_test_gcs_bucket }}
      python3 -m pytest \
              --log-date-format="%Y-%m-%dT%H:%M:%S" \
              --log-format="%(asctime)s %(levelname)s %(name)s %(filename)s:%(lineno)d:%(funcName)s %(message)s" \
              --log-cli-level=INFO \
              -s \
              -vv \
              --instafail \
              -k "not test_scale and not test_invariants" \
              --durations=0 \
              /io/test/
    inputs:
      - from: /repo/batch/test
        to: /io/test
    port: 5000
    timeout: 1200
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: test-dev-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /dev-tokens
      - name: ssl-config-batch-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - create_deploy_config
      - create_accounts
      - default_ns
      - merge_code
      - base_image
      - hail_base_image
      - batch_image
      - ci_utils_image
      - deploy_batch
      - netcat_ubuntu_image
      - volume_image
      - workdir_image
      - curl_image
  - kind: runImage
    name: test_batch_3
    image:
      valueFrom: batch_image.image
    script: |
      set -ex
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=3
      export HAIL_GSA_KEY_FILE=/test-gsa-key/key.json
      export HAIL_BASE_IMAGE={{ base_image.image }}
      export CI_UTILS_IMAGE={{ ci_utils_image.image }}
      export HAIL_CURL_IMAGE={{ curl_image.image }}
      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
      export HAIL_NETCAT_UBUNTU_IMAGE={{ netcat_ubuntu_image.image }}
      export HAIL_VOLUME_IMAGE={{ volume_image.image }}
      export HAIL_WORKDIR_IMAGE={{ workdir_image.image }}
      export HAIL_HAIL_BASE_IMAGE={{ hail_base_image.image }}
      export DOCKER_PREFIX="{{ global.docker_prefix }}"
      export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
      export HAIL_TEST_TOKEN_FILE=/user-tokens/tokens.json
      export HAIL_TEST_DEV_TOKEN_FILE=/dev-tokens/tokens.json
      export HAIL_TOKEN="{{ token }}"
      export HAIL_SCOPE="{{ scope }}"
      hailctl config set batch/bucket {{ global.hail_test_gcs_bucket }}
      python3 -m pytest \
              --log-date-format="%Y-%m-%dT%H:%M:%S" \
              --log-format="%(asctime)s %(levelname)s %(name)s %(filename)s:%(lineno)d:%(funcName)s %(message)s" \
              --log-cli-level=INFO \
              -s \
              -vv \
              --instafail \
              -k "not test_scale and not test_invariants" \
              --durations=0 \
              /io/test/
    inputs:
      - from: /repo/batch/test
        to: /io/test
    port: 5000
    timeout: 1200
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: test-dev-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /dev-tokens
      - name: ssl-config-batch-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - create_deploy_config
      - create_accounts
      - default_ns
      - merge_code
      - base_image
      - hail_base_image
      - batch_image
      - ci_utils_image
      - deploy_batch
      - netcat_ubuntu_image
      - volume_image
      - workdir_image
      - curl_image
  - kind: runImage
    name: test_batch_4
    image:
      valueFrom: batch_image.image
    script: |
      set -ex
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=4
      export HAIL_GSA_KEY_FILE=/test-gsa-key/key.json
      export HAIL_BASE_IMAGE={{ base_image.image }}
      export CI_UTILS_IMAGE={{ ci_utils_image.image }}
      export HAIL_CURL_IMAGE={{ curl_image.image }}
      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
      export HAIL_NETCAT_UBUNTU_IMAGE={{ netcat_ubuntu_image.image }}
      export HAIL_VOLUME_IMAGE={{ volume_image.image }}
      export HAIL_WORKDIR_IMAGE={{ workdir_image.image }}
      export HAIL_HAIL_BASE_IMAGE={{ hail_base_image.image }}
      export DOCKER_PREFIX="{{ global.docker_prefix }}"
      export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
      export HAIL_TEST_TOKEN_FILE=/user-tokens/tokens.json
      export HAIL_TEST_DEV_TOKEN_FILE=/dev-tokens/tokens.json
      export HAIL_TOKEN="{{ token }}"
      export HAIL_SCOPE="{{ scope }}"
      hailctl config set batch/bucket {{ global.hail_test_gcs_bucket }}
      python3 -m pytest \
              --log-date-format="%Y-%m-%dT%H:%M:%S" \
              --log-format="%(asctime)s %(levelname)s %(name)s %(filename)s:%(lineno)d:%(funcName)s %(message)s" \
              --log-cli-level=INFO \
              -s \
              -vv \
              --instafail \
              -k "not test_scale and not test_invariants" \
              --durations=0 \
              /io/test/
    inputs:
      - from: /repo/batch/test
        to: /io/test
    port: 5000
    timeout: 1200
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: test-dev-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /dev-tokens
      - name: ssl-config-batch-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - create_deploy_config
      - create_accounts
      - default_ns
      - merge_code
      - base_image
      - hail_base_image
      - batch_image
      - ci_utils_image
      - deploy_batch
      - netcat_ubuntu_image
      - volume_image
      - workdir_image
      - curl_image
  - kind: runImage
    name: delete_test_billing_projects
    image:
      valueFrom: batch_image.image
    script: |
      export HAIL_TEST_DEV_TOKEN_FILE=/dev-tokens/tokens.json
      export HAIL_TOKEN="{{ token }}"
      cd /io/test
      python3 -c '
      import test_accounts
      import asyncio
      asyncio.get_event_loop().run_until_complete(test_accounts.delete_all_test_billing_projects())'
    inputs:
      - from: /repo/batch/test
        to: /io/test
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-dev-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /dev-tokens
      - name: ssl-config-batch-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
    alwaysRun: true
    dependsOn:
      - create_deploy_config
      - create_accounts
      - default_ns
      - merge_code
      - batch_image
      - deploy_batch
      - test_batch_0
      - test_batch_1
      - test_batch_2
      - test_batch_3
      - test_batch_4
  - kind: runImage
    name: create_ci_test_repo
    image:
      valueFrom: base_image.image
    script: |
      set -e
      TOKEN=$(cat /secret/ci-secrets/user1)
      REPO_NAME="ci-test-{{token}}"

      echo creating $REPO_NAME...
      curl -XPOST \
        -i \
        -fsSL \
        https://api.github.com/orgs/hail-ci-test/repos \
        -H "Authorization: token ${TOKEN}" \
        -d "{ \"name\" : \"$REPO_NAME\" }"

      # checkout new ci repo
      cd /io
      git clone https://$TOKEN@github.com/hail-ci-test/$REPO_NAME.git
      cd $REPO_NAME

      mkdir -p ./ci/test ./hail/
      cp /io/repo/ci/test/resources/build.yaml ./
      cp -R /io/repo/ci/* ./ci/
      cp /io/repo/tls/Dockerfile ./ci/test/resources/Dockerfile.certs
      cp /io/repo/tls/create_certs.py ./ci/test/resources/
      cp /io/repo/pylintrc ./
      cp /io/repo/setup.cfg ./
      cp -R /io/repo/docker ./
      cp -R /io/repo/gear ./
      cp -R /io/repo/hail/python ./hail/
      cp /io/repo/hail/Makefile ./hail/
      cp /io/repo/hail/env_var.mk ./hail/
      cp -R /io/repo/web_common ./
      cp /io/repo/hail/python/setup-hailtop.py ./hail/python/

      git config user.name ci
      git config user.email ci@hail.is
      git add * && git commit -m "setup repo"
      git push
    secrets:
      - name: hail-ci-0-1-service-account-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /secret/ci-secrets
    scopes:
      - test
      - dev
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - default_ns
      - base_image
      - merge_code
  - kind: deploy
    name: deploy_ci
    namespace:
      valueFrom: default_ns.name
    config: ci/deployment.yaml
    wait:
      - kind: Service
        name: ci
        for: alive
    dependsOn:
      - default_ns
      - create_database_server_config
      - ci_image
      - ci_utils_image
      - create_accounts
      - ci_database
      - deploy_auth
      - deploy_batch
      - create_ci_test_repo
      - deploy_ci_agent
      - create_certs
      - hail_buildkit_image
  - kind: runImage
    name: test_ci
    image:
      valueFrom: test_ci_image.image
    script: |
      set -ex
      export ORGANIZATION=hail-ci-test
      export REPO_NAME=ci-test-"{{ create_ci_test_repo.token }}"
      export NAMESPACE="{{ default_ns.name }}"
      python3 -m pytest --log-cli-level=INFO -s -vv --instafail --durations=50 /test/
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-dev-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: hail-ci-0-1-service-account-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /secret/ci-secrets
      - name: ssl-config-ci-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
    timeout: 5400
    scopes:
      - test
      - dev
    dependsOn:
      - create_deploy_config
      - create_accounts
      - default_ns
      - create_certs
      - deploy_ci
      - test_ci_image
      - create_ci_test_repo
  - kind: runImage
    name: test_hailtop_batch_0
    image:
      valueFrom: service_base_image.image
    script: |
      cd /io/hailtop
      set -ex
      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=0
      export DOCKER_PREFIX="{{ global.docker_prefix }}"
      export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
      export PYTHON_DILL_IMAGE="{{ global.docker_prefix }}/python-dill:3.7-slim"
      export HAIL_TEST_GCS_BUCKET="{{ global.hail_test_gcs_bucket }}"
      hailctl config set batch/billing_project test
      hailctl config set batch/bucket {{ global.hail_test_gcs_bucket }}
      python3 -m pytest \
              --durations=0 \
              --log-cli-level=INFO \
              -s \
              -vv \
              --instafail \
              /io/test/hailtop/batch/
    inputs:
      - from: /repo/hail/python/test
        to: /io/test
      - from: /repo/hail/python/hailtop
        to: /io/hailtop
    timeout: 1200
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
      - name: ssl-config-batch-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
    dependsOn:
      - create_deploy_config
      - create_accounts
      - default_ns
      - merge_code
      - service_base_image
      - deploy_batch
  - kind: runImage
    name: test_hailtop_batch_1
    image:
      valueFrom: service_base_image.image
    script: |
      cd /io/hailtop
      set -ex
      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=1
      export DOCKER_PREFIX="{{ global.docker_prefix }}"
      export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
      export PYTHON_DILL_IMAGE="{{ global.docker_prefix }}/python-dill:3.7-slim"
      export HAIL_TEST_GCS_BUCKET="{{ global.hail_test_gcs_bucket }}"
      hailctl config set batch/billing_project test
      hailctl config set batch/bucket {{ global.hail_test_gcs_bucket }}
      python3 -m pytest \
              --durations=0 \
              --log-cli-level=INFO \
              -s \
              -vv \
              --instafail \
              /io/test/hailtop/batch/
    inputs:
      - from: /repo/hail/python/test
        to: /io/test
      - from: /repo/hail/python/hailtop
        to: /io/hailtop
    timeout: 1200
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
      - name: ssl-config-batch-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
    dependsOn:
      - create_deploy_config
      - create_accounts
      - default_ns
      - merge_code
      - service_base_image
      - deploy_batch
  - kind: runImage
    name: test_hailtop_batch_2
    image:
      valueFrom: service_base_image.image
    script: |
      cd /io/hailtop
      set -ex
      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=2
      export DOCKER_PREFIX="{{ global.docker_prefix }}"
      export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
      export PYTHON_DILL_IMAGE="{{ global.docker_prefix }}/python-dill:3.7-slim"
      export HAIL_TEST_GCS_BUCKET="{{ global.hail_test_gcs_bucket }}"
      hailctl config set batch/billing_project test
      hailctl config set batch/bucket {{ global.hail_test_gcs_bucket }}
      python3 -m pytest \
              --durations=0 \
              --log-cli-level=INFO \
              -s \
              -vv \
              --instafail \
              /io/test/hailtop/batch/
    inputs:
      - from: /repo/hail/python/test
        to: /io/test
      - from: /repo/hail/python/hailtop
        to: /io/hailtop
    timeout: 1200
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
      - name: ssl-config-batch-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
    dependsOn:
      - create_deploy_config
      - create_accounts
      - default_ns
      - merge_code
      - service_base_image
      - deploy_batch
  - kind: runImage
    name: test_hailtop_batch_3
    image:
      valueFrom: service_base_image.image
    script: |
      cd /io/hailtop
      set -ex
      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=3
      export DOCKER_PREFIX="{{ global.docker_prefix }}"
      export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
      export PYTHON_DILL_IMAGE="{{ global.docker_prefix }}/python-dill:3.7-slim"
      export HAIL_TEST_GCS_BUCKET="{{ global.hail_test_gcs_bucket }}"
      hailctl config set batch/billing_project test
      hailctl config set batch/bucket {{ global.hail_test_gcs_bucket }}
      python3 -m pytest \
              --durations=0 \
              --log-cli-level=INFO \
              -s \
              -vv \
              --instafail \
              /io/test/hailtop/batch/
    inputs:
      - from: /repo/hail/python/test
        to: /io/test
      - from: /repo/hail/python/hailtop
        to: /io/hailtop
    timeout: 1200
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
      - name: ssl-config-batch-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
    dependsOn:
      - create_deploy_config
      - create_accounts
      - default_ns
      - merge_code
      - service_base_image
      - deploy_batch
  - kind: runImage
    name: test_hailtop_batch_4
    image:
      valueFrom: service_base_image.image
    script: |
      cd /io/hailtop
      set -ex
      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
      export PYTEST_SPLITS=5
      export PYTEST_SPLIT_INDEX=4
      export DOCKER_PREFIX="{{ global.docker_prefix }}"
      export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
      export PYTHON_DILL_IMAGE="{{ global.docker_prefix }}/python-dill:3.7-slim"
      export HAIL_TEST_GCS_BUCKET="{{ global.hail_test_gcs_bucket }}"
      hailctl config set batch/billing_project test
      hailctl config set batch/bucket {{ global.hail_test_gcs_bucket }}
      python3 -m pytest \
              --durations=0 \
              --log-cli-level=INFO \
              -s \
              -vv \
              --instafail \
              /io/test/hailtop/batch/
    inputs:
      - from: /repo/hail/python/test
        to: /io/test
      - from: /repo/hail/python/hailtop
        to: /io/hailtop
    timeout: 1200
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
      - name: ssl-config-batch-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
    dependsOn:
      - create_deploy_config
      - create_accounts
      - default_ns
      - merge_code
      - service_base_image
      - deploy_batch
  - kind: runImage
    name: test_batch_docs
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex
      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
      cd /io/hailtop/batch
      hailctl config set batch/billing_project test
      hailctl config set batch/bucket {{ global.hail_test_gcs_bucket }}
      python3 -m pytest --instafail \
        --doctest-modules \
        --doctest-glob='*.rst' \
        --ignore=docs/cookbook/files/ \
        --ignore=docs/conf.py
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    dependsOn:
      - create_deploy_config
      - create_accounts
      - default_ns
      - service_base_image
      - merge_code
      - deploy_batch
    timeout: 1200
    inputs:
      - from: /repo/hail/python/hailtop
        to: /io/hailtop
  - kind: createDatabase
    name: notebook_database
    databaseName: notebook
    migrations:
      - name: initial
        script: /io/sql/initial.sql
    inputs:
      - from: /repo/notebook/sql
        to: /io/sql
    namespace:
      valueFrom: default_ns.name
    shutdowns:
      - kind: Deployment
        namespace:
          valueFrom: default_ns.name
        name: notebook
    dependsOn:
      - default_ns
      - merge_code
  - kind: deploy
    name: deploy_notebook
    namespace:
      valueFrom: default_ns.name
    config: notebook/deployment.yaml
    dependsOn:
      - default_ns
      - create_session_key
      - notebook_image
      - notebook_nginx_image
      - deploy_auth
      - notebook_database
      - create_certs
    wait:
      - kind: Service
        name: notebook
        for: alive
  - kind: runImage
    name: cleanup_ci_test_repo
    image:
      valueFrom: base_image.image
    script: |
      set -e
      TOKEN=$(cat /secret/ci-secrets/user1)
      echo deleting ci-test-{{ create_ci_test_repo.token }}...
      curl -XDELETE \
        -ifsSL \
        https://api.github.com/repos/hail-ci-test/ci-test-{{ create_ci_test_repo.token }} \
        -H "Authorization: token ${TOKEN}"
    secrets:
      - name: hail-ci-0-1-service-account-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /secret/ci-secrets
    alwaysRun: true
    scopes:
      - test
      - dev
    dependsOn:
      - default_ns
      - base_image
      - create_ci_test_repo
      - deploy_ci
      - test_ci
  - kind: runImage
    name: deploy_hail
    script: |
      set -ex
      gcloud auth activate-service-account --key-file=/secrets/ci-deploy-0-1--hail-is-hail.json
      SPARK_VERSION=3.1.1
      BRANCH=0.2
      SHA="{{ code.sha }}"
      GS_JAR=gs://hail-common/builds/${BRANCH}/jars/hail-${BRANCH}-${SHA}-Spark-${SPARK_VERSION}.jar
      gsutil cp /io/hail.jar ${GS_JAR}
      gsutil acl set public-read ${GS_JAR}
      GS_HAIL_ZIP=gs://hail-common/builds/${BRANCH}/python/hail-${BRANCH}-${SHA}.zip
      gsutil cp /io/hail.zip ${GS_HAIL_ZIP}
      gsutil acl set public-read ${GS_HAIL_ZIP}
    image:
      valueFrom: base_image.image
    secrets:
      - name: ci-deploy-0-1--hail-is-hail
        namespace:
          valueFrom: default_ns.name
        mountPath: /secrets
    inputs:
      - from: /hail.jar
        to: /io/hail.jar
      - from: /hail.zip
        to: /io/hail.zip
    scopes:
      - deploy
    dependsOn:
      - default_ns
      - base_image
      - build_hail
  - kind: buildImage2
    name: blog_nginx_image
    dockerFile: /io/blog/Dockerfile.nginx
    contextPath: /io/blog
    publishAs: blog_nginx
    inputs:
      - from: /repo/blog
        to: /io/blog
    dependsOn:
      - hail_ubuntu_image
      - merge_code
  - kind: deploy
    name: deploy_blog
    namespace:
      valueFrom: default_ns.name
    config: blog/deployment.yaml
    wait:
      - kind: Service
        name: blog
        for: alive
        resource_type: statefulset
    dependsOn:
      - default_ns
      - blog_nginx_image
      - create_certs
  - kind: runImage
    name: test_dataproc
    image:
      valueFrom: ci_utils_image.image
    script: |
      set -ex

      cd /io/repo

      gcloud auth activate-service-account --key-file=/test-dataproc-service-account-key/test-dataproc-service-account-key.json
      gcloud config set project hail-vdc
      gcloud config set dataproc/region us-central1

      if git ls-remote --exit-code --tags origin $(cat /io/hail_pip_version)
      then
          echo "tag $HAIL_PIP_VERSION already exists"
          exit 0
      fi

      cd hail
      chmod 755 ./gradlew
      time retry ./gradlew --version
      make test-dataproc DEV_CLARIFIER=ci_test_dataproc/
    dependsOn:
      - ci_utils_image
      - default_ns
      - merge_code
    inputs:
      - from: /hail_pip_version
        to: /io/hail_pip_version
      - from: /repo
        to: /io/repo
    secrets:
      - name: test-dataproc-service-account-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-dataproc-service-account-key
    scopes:
      - deploy
      - dev
  - kind: runImage
    name: deploy
    image:
      valueFrom: ci_utils_image.image
    script: |
      set -ex
      cd /io

      gcloud auth activate-service-account --key-file=/ci-deploy-0-1--hail-is-hail/ci-deploy-0-1--hail-is-hail.json
      cp /pypi-credentials/pypirc $HOME/.pypirc
      printf 'Authorization: token ' > github-oauth
      cat /hail-ci-0-1-github-oauth-token/oauth-token >>github-oauth
      printf '#!/bin/bash\necho ' > git-askpass
      cat /hail-ci-0-1-github-oauth-token/oauth-token >>git-askpass
      chmod 755 git-askpass
      export GIT_ASKPASS=/io/git-askpass

      cd /io/repo/hail

      if git ls-remote --exit-code --tags origin $(cat /io/hail_pip_version)
      then
          echo "tag $HAIL_PIP_VERSION already exists"
          exit 0
      fi

      chmod 755 ./gradlew
      time retry ./gradlew --version
      make wheel upload-artifacts DEPLOY_REMOTE=origin

      bash scripts/deploy.sh $(cat /io/hail_pip_version) \
                             $(cat /io/hail_version) \
                             $(cat /io/git_version) \
                             origin \
                             /io/repo/hail/build/deploy/dist/hail-*-py3-none-any.whl \
                             /io/github-oauth
    inputs:
      - from: /hail_version
        to: /io/hail_version
      - from: /hail_pip_version
        to: /io/hail_pip_version
      - from: /git_version
        to: /io/git_version
      - from: /repo
        to: /io/repo
    secrets:
      - name: pypi-credentials
        namespace:
          valueFrom: default_ns.name
        mountPath: /pypi-credentials
      - name: ci-deploy-0-1--hail-is-hail
        namespace:
          valueFrom: default_ns.name
        mountPath: /ci-deploy-0-1--hail-is-hail
      - name: hail-ci-0-1-github-oauth-token
        namespace:
          valueFrom: default_ns.name
        mountPath: /hail-ci-0-1-github-oauth-token
    scopes:
      - deploy
      - dev
    dependsOn:
      - test_dataproc
      - default_ns
      - ci_utils_image
      - build_hail
      - merge_code
  - kind: buildImage2
    name: website_image
    dockerFile: /io/website/Dockerfile
    contextPath: /io/website
    publishAs: website
    inputs:
      - from: /repo/website
        to: /io/website
      - from: /docs.tar.gz
        to: /io/website/docs.tar.gz
    dependsOn:
      - service_base_image
      - make_pip_versioned_docs
  - kind: deploy
    name: deploy_website
    namespace:
      valueFrom: default_ns.name
    config: website/deployment.yaml
    wait:
      - kind: Service
        name: website
        for: alive
    dependsOn:
      - default_ns
      - website_image
      - create_certs
  - kind: runImage
    name: test_website
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex
      hailctl curl {{ default_ns.name }} www / \
              -vvv \
              -fsSL \
              --retry 3 \
              --retry-delay 5
    secrets:
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
    dependsOn:
      - default_ns
      - create_accounts
      - service_base_image
      - deploy_website
  - kind: buildImage2
    name: hail_public_image
    dockerFile: /io/hail/Dockerfile
    contextPath: /io/hail/
    publishAs: hail-public
    inputs:
      - from: /docker/hail
        to: /io/hail
      - from: /hail/hail_pip_version
        to: /io/hail/hail_pip_version
    dependsOn:
      - merge_code
      - hail_ubuntu_image
    scopes:
      - dev
  - kind: runImage
    name: test_hail_public_image
    image:
      valueFrom: hail_public_image.image
    script: |
      set -ex
      python3 -c 'import hail as hl; hl.balding_nichols_model(3, 100, 100)._force_count_rows()'
      python3 -c 'import numpy; import pandas; import sklearn; import matplotlib; import scipy'
      gsutil --version
    dependsOn:
      - hail_public_image
    scopes:
      - dev
  - kind: buildImage2
    name: genetics_public_image
    dockerFile: /io/genetics/Dockerfile
    contextPath: /io/genetics/
    publishAs: genetics-public
    inputs:
      - from: /repo/genetics
        to: /io/genetics
    dependsOn:
      - hail_public_image
      - merge_code
    scopes:
      - dev
  - kind: runImage
    name: test_genetics_public_image
    image:
      valueFrom: genetics_public_image.image
    script: |
      set -ex
      samtools --version
      plink --version
      plink2 --version
    dependsOn:
      - genetics_public_image
    scopes:
      - dev
  - kind: runImage
    name: test_hail_services_java
    image:
      valueFrom: hail_run_tests_image.image
    resources:
      memory: 7.5G
      cpu: '2'
    script: |
      set -ex
      cd /io
      mkdir -p src/test
      tar xzf resources.tar.gz -C src/test
      java -Xms7500M -Xmx7500M \
           -cp hail-test.jar:$SPARK_HOME/jars/* \
           org.testng.TestNG \
           -listener is.hail.LogTestListener \
           testng-services.xml
    inputs:
      - from: /resources.tar.gz
        to: /io/resources.tar.gz
      - from: /hail-test.jar
        to: /io/hail-test.jar
      - from: /testng-services.xml
        to: /io/testng-services.xml
    secrets:
      - name: test-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: ssl-config-services-java-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
    timeout: 1200
    dependsOn:
      - default_ns
      - create_certs
      - hail_run_tests_image
      - build_hail
      - deploy_batch
  - kind: runImage
    name: test_batch_invariants
    image:
      valueFrom: batch_image.image
    script: |
      python3 -m pytest --log-date-format="%Y-%m-%dT%H:%M:%S" --log-format="%(asctime)s %(levelname)s %(name)s %(filename)s:%(lineno)d:%(funcName)s %(message)s" --log-cli-level=INFO -s -vv --instafail -k "test_invariants" /io/test/
    inputs:
      - from: /repo/batch/test
        to: /io/test
    timeout: 300
    secrets:
      - name: gce-deploy-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /deploy-config
      - name: test-dev-tokens
        namespace:
          valueFrom: default_ns.name
        mountPath: /user-tokens
      - name: ssl-config-batch-tests
        namespace:
          valueFrom: default_ns.name
        mountPath: /ssl-config
    scopes:
      - test
      - dev
    dependsOn:
      - create_deploy_config
      - create_accounts
      - default_ns
      - merge_code
      - batch_image
      - deploy_batch
      - test_batch_0
      - test_batch_1
      - test_batch_2
      - test_batch_3
      - test_batch_4
      - test_ci
      - test_hailtop_batch_0
      - test_hailtop_batch_1
      - test_hailtop_batch_2
      - test_hailtop_batch_3
      - test_hailtop_batch_4
  - kind: runImage
    name: delete_batch_instances
    image:
      valueFrom: base_image.image
    alwaysRun: true
    script: |
      set -ex
      gcloud -q auth activate-service-account --key-file=/test-gsa-key/key.json
      set +e
      gcloud -q compute instances list \
          --filter 'tags.items=batch2-agent AND labels.namespace={{ default_ns.name }}' \
          --format="table[no-heading](zone.basename(), name)" \
          --project {{ global.project }} \
        | xargs -n2 -r sh -c 'gcloud -q compute instances delete --zone "$1" --project {{ global.project }} "$2" || true' argv0
      gcloud -q compute disks list \
          --filter 'labels.batch=1 AND labels.namespace={{ default_ns.name }}' \
          --format="table[no-heading](zone.basename(), name)" \
          --project {{ global.project }} \
        | xargs -n2 -r sh -c 'gcloud -q compute disks delete --zone "$1" --project {{ global.project }} "$2" || true' argv0
    secrets:
      - name: test-gsa-key
        namespace:
          valueFrom: default_ns.name
        mountPath: /test-gsa-key
    scopes:
      - dev
      - test
    dependsOn:
      - default_ns
      - base_image
      - test_batch_invariants
      - test_batch_0
      - test_batch_1
      - test_batch_2
      - test_batch_3
      - test_batch_4
      - test_ci
      - test_hailtop_batch_0
      - test_hailtop_batch_1
      - test_hailtop_batch_2
      - test_hailtop_batch_3
      - test_hailtop_batch_4
  - kind: runImage
    name: delete_atgu_tables
    image:
      valueFrom: service_base_image.image
    script: |
      set -ex
      mysql --defaults-extra-file=/sql-config/sql-config.cnf < /io/sql/delete-atgu-tables.sql
    inputs:
      - from: /repo/atgu/sql
        to: /io/sql
    secrets:
      - name: database-server-config
        namespace:
          valueFrom: default_ns.name
        mountPath: /sql-config
    runIfRequested: true
    scopes:
      - dev
    dependsOn:
      - default_ns
      - service_base_image
      - merge_code
  - kind: buildImage2
    name: atgu_image
    dockerFile: /io/repo/atgu/Dockerfile
    contextPath: /io/repo
    publishAs: atgu
    inputs:
      - from: /repo
        to: /io/repo
    dependsOn:
      - service_base_image
      - merge_code
  - kind: createDatabase
    name: atgu_database
    databaseName: atgu
    migrations:
      - name: initial
        script: /io/sql/initial.sql
    inputs:
      - from: /repo/atgu/sql
        to: /io/sql
    namespace:
      valueFrom: default_ns.name
    shutdowns:
      - kind: Deployment
        namespace:
          valueFrom: default_ns.name
        name: atgu
      - kind: Deployment
        namespace:
          valueFrom: default_ns.name
        name: atgu-driver
    dependsOn:
      - default_ns
      - merge_code
      - delete_atgu_tables
  - kind: deploy
    name: deploy_atgu
    namespace:
      valueFrom: default_ns.name
    config: atgu/deployment.yaml
    wait:
      - kind: Service
        name: atgu
        for: alive
    dependsOn:
      - default_ns
      - create_certs
      - create_accounts
      - deploy_auth
      - atgu_image
      - atgu_database