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build.yaml
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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:
- name: auth-oauth2-client-secret
- name: registry-push-credentials
- name: hail-ci-0-1-github-oauth-token
- name: test-gsa-key
- name: test-aws-key
clouds:
- gcp
- name: test-azure-key
clouds:
- gcp
- name: zulip-config
- name: benchmark-gsa-key
- name: billing-monitor-gsa-key
clouds:
- gcp
- name: hail-ci-0-1-service-account-key
- name: test-dataproc-service-account-key
clouds:
- gcp
- name: batch-worker-ssh-public-key
clouds:
- azure
- kind: buildImage2
name: echo_image
dockerFile: /io/echo/Dockerfile
contextPath: /io/echo
publishAs: echo
resources:
storage: 10Gi
cpu: "2"
memory: standard
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: standard
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: standard
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
- name: rename-gsa-identity
script: /io/sql/rename-gsa-identity.sql
- name: support-azure-oauth
script: /io/sql/support-azure-oauth.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 -
# worker 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 worker-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: "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 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: worker-deploy-config
namespace:
valueFrom: default_ns.name
mountPath: /deploy-config
- name: auth-gsa-key
namespace:
valueFrom: default_ns.name
mountPath: /auth-gsa-key
- name: global-config
namespace:
valueFrom: default_ns.name
mountPath: /global-config
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
export NAMESPACE={{ default_ns.name }}
export CLOUD={{ global.cloud }}
python3 /io/create_initial_account.py {{ code.username }} {{ code.login_id }}
serviceAccount:
name: admin
namespace:
valueFrom: default_ns.name
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: standard
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
resources:
storage: 10Gi
cpu: "2"
memory: standard
- 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}', "global": {"domain": "{{ global.domain }}"}, "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: standard
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: standard
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/testng-fs.xml
to: /testng-fs.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: standard
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: standard
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: runImage
name: build_wheel_for_azure
image:
valueFrom: hail_build_image.image
resources:
memory: standard
cpu: '4'
script: |
set -ex
cd /io/repo/hail
chmod 755 ./gradlew
time retry ./gradlew --version
export SPARK_VERSION="3.0.2" SCALA_VERSION="2.12.10"
time retry make wheel
(cd build/deploy/dist/ && tar -cvf wheel-container.tar hail-*-py3-none-any.whl)
inputs:
- from: /repo
to: /io/repo
outputs:
- from: /io/repo/hail/build/deploy/dist/wheel-container.tar
to: /wheel-for-azure-container.tar
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_pip_installed_image
dockerFile: /io/hail/Dockerfile.hail-pip-installed
contextPath: /io/hail
publishAs: hail-run
inputs:
- from: /repo/hail
to: /io/hail
- from: /wheel-container.tar
to: /io/hail/wheel-container.tar
dependsOn:
- service_base_image
- build_hail
- merge_code
resources:
storage: 10Gi
cpu: "2"
memory: standard
- kind: runImage
name: upload_test_resources_to_blob_storage
image:
valueFrom: hail_pip_installed_image.image
script: |
set -ex
cd /io/repo/hail/
export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
python3 -m hailtop.aiotools.copy 'null' '[
{"from": "src/test/resources",
"to": "{{ global.test_storage_uri }}/{{ token }}/test/resources"},
{"from": "python/hail/docs/data",
"to": "{{ global.test_storage_uri }}/{{ 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
- hail_pip_installed_image
- merge_code
- kind: runImage
name: test_hail_java_0
image:
valueFrom: hail_run_tests_image.image
resources:
memory: standard
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
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-0
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_java_1
image:
valueFrom: hail_run_tests_image.image
resources:
memory: standard
cpu: '2'
script: |
set -ex
cd /io
mkdir -p src/test
tar xzf resources.tar.gz -C src/test
tar xzf splits.tar.gz