def deploy_seqr(settings):
print_separator("seqr")
if settings["BUILD_DOCKER_IMAGES"]:
seqr_git_hash = run("git log -1 --pretty=%h", errors_to_ignore=["Not a git repository"])
seqr_git_hash = (":" + seqr_git_hash.strip()) if seqr_git_hash is not None else ""
docker_build("seqr",
settings,
[
"--build-arg SEQR_SERVICE_PORT=%s" % settings["SEQR_SERVICE_PORT"],
"--build-arg SEQR_UI_DEV_PORT=%s" % settings["SEQR_UI_DEV_PORT"],
"-f deploy/docker/seqr/Dockerfile",
"-t %(DOCKER_IMAGE_NAME)s" + seqr_git_hash,
]
)
if settings["ONLY_PUSH_TO_REGISTRY"]:
return
restore_seqr_db_from_backup = settings.get("RESTORE_SEQR_DB_FROM_BACKUP")
reset_db = settings.get("RESET_DB")
deployment_target = settings["DEPLOY_TO"]
postgres_pod_name = get_pod_name("postgres", deployment_target=deployment_target)
if settings["DELETE_BEFORE_DEPLOY"]:
delete_pod("seqr", settings)
elif reset_db or restore_seqr_db_from_backup:
seqr_pod_name = get_pod_name('seqr', deployment_target=deployment_target)
if seqr_pod_name:
sleep_until_pod_is_running("seqr", deployment_target=deployment_target)
run_in_pod(seqr_pod_name, "/usr/local/bin/stop_server.sh", verbose=True)
if reset_db:
run_in_pod(postgres_pod_name, "psql -U postgres postgres -c 'drop database seqrdb'",
errors_to_ignore=["does not exist"],
verbose=True,
)
if restore_seqr_db_from_backup:
run_in_pod(postgres_pod_name, "psql -U postgres postgres -c 'drop database seqrdb'",
errors_to_ignore=["does not exist"],
verbose=True,
)
run_in_pod(postgres_pod_name, "psql -U postgres postgres -c 'create database seqrdb'", verbose=True)
run("kubectl cp '%(restore_seqr_db_from_backup)s' %(postgres_pod_name)s:/root/$(basename %(restore_seqr_db_from_backup)s)" % locals(), verbose=True)
run_in_pod(postgres_pod_name, "/root/restore_database_backup.sh postgres seqrdb /root/$(basename %(restore_seqr_db_from_backup)s)" % locals(), verbose=True)
run_in_pod(postgres_pod_name, "rm /root/$(basename %(restore_seqr_db_from_backup)s)" % locals(), verbose=True)
else:
run_in_pod(postgres_pod_name, "psql -U postgres postgres -c 'create database seqrdb'",
errors_to_ignore=["already exists"],
verbose=True,
)
deploy_pod("seqr", settings, wait_until_pod_is_ready=True)
def deploy_seqr(settings):
print_separator("seqr")
if settings["BUILD_DOCKER_IMAGES"]:
seqr_git_hash = run("git log -1 --pretty=%h", errors_to_ignore=["Not a git repository"])
seqr_git_hash = (":" + seqr_git_hash.strip()) if seqr_git_hash is not None else ""
docker_build("seqr",
settings,
[
"--build-arg SEQR_SERVICE_PORT=%s" % settings["SEQR_SERVICE_PORT"],
"--build-arg SEQR_UI_DEV_PORT=%s" % settings["SEQR_UI_DEV_PORT"],
"-f deploy/docker/seqr/Dockerfile",
"-t %(DOCKER_IMAGE_NAME)s" + seqr_git_hash,
]
)
if settings["ONLY_PUSH_TO_REGISTRY"]:
return
restore_seqr_db_from_backup = settings.get("RESTORE_SEQR_DB_FROM_BACKUP")
reset_db = settings.get("RESET_DB")
deployment_target = settings["DEPLOY_TO"]
postgres_pod_name = get_pod_name("postgres", deployment_target=deployment_target)
if settings["DELETE_BEFORE_DEPLOY"]:
delete_pod("seqr", settings)
elif reset_db or restore_seqr_db_from_backup:
seqr_pod_name = get_pod_name('seqr', deployment_target=deployment_target)
if seqr_pod_name:
sleep_until_pod_is_running("seqr", deployment_target=deployment_target)
run_in_pod(seqr_pod_name, "/usr/local/bin/stop_server.sh", verbose=True)
if reset_db:
run_in_pod(postgres_pod_name, "psql -U postgres postgres -c 'drop database seqrdb'",
errors_to_ignore=["does not exist"],
verbose=True,
)
if restore_seqr_db_from_backup:
run_in_pod(postgres_pod_name, "psql -U postgres postgres -c 'drop database seqrdb'",
errors_to_ignore=["does not exist"],
verbose=True,
)
run_in_pod(postgres_pod_name, "psql -U postgres postgres -c 'create database seqrdb'", verbose=True)
run("kubectl cp '%(restore_seqr_db_from_backup)s' %(postgres_pod_name)s:/root/$(basename %(restore_seqr_db_from_backup)s)" % locals(), verbose=True)
run_in_pod(postgres_pod_name, "/root/restore_database_backup.sh postgres seqrdb /root/$(basename %(restore_seqr_db_from_backup)s)" % locals(), verbose=True)
run_in_pod(postgres_pod_name, "rm /root/$(basename %(restore_seqr_db_from_backup)s)" % locals(), verbose=True)
else:
run_in_pod(postgres_pod_name, "psql -U postgres postgres -c 'create database seqrdb'",
errors_to_ignore=["already exists"],
verbose=True,
)
deploy_pod("seqr", settings, wait_until_pod_is_ready=True)
def deploy_elasticsearch_sharded(settings, component):
if settings["ONLY_PUSH_TO_REGISTRY"]:
return
print_separator(component)
if component == "es-master":
config_files = [
"%(DEPLOYMENT_TEMP_DIR)s/hail_elasticsearch_pipelines/kubernetes/elasticsearch-sharded/es-discovery-svc.yaml",
"%(DEPLOYMENT_TEMP_DIR)s/hail_elasticsearch_pipelines/kubernetes/elasticsearch-sharded/es-master.yaml",
]
elif component == "es-client":
config_files = [
"%(DEPLOYMENT_TEMP_DIR)s/hail_elasticsearch_pipelines/kubernetes/elasticsearch-sharded/es-svc.yaml",
"%(DEPLOYMENT_TEMP_DIR)s/hail_elasticsearch_pipelines/kubernetes/elasticsearch-sharded/es-client.yaml",
]
elif component == "es-data":
config_files = [
"%(DEPLOYMENT_TEMP_DIR)s/hail_elasticsearch_pipelines/kubernetes/elasticsearch-sharded/es-data-svc.yaml",
"%(DEPLOYMENT_TEMP_DIR)s/hail_elasticsearch_pipelines/kubernetes/elasticsearch-sharded/es-data-stateful.yaml",
]
elif component == "es-kibana":
config_files = [
"%(DEPLOYMENT_TEMP_DIR)s/hail_elasticsearch_pipelines/kubernetes/elasticsearch-sharded/es-kibana.yaml",
]
elif component == "kibana":
config_files = [
"%(DEPLOYMENT_TEMP_DIR)s/deploy/kubernetes/kibana/kibana.%(DEPLOY_TO_PREFIX)s.yaml",
]
else:
raise ValueError("Unexpected component: " + component)
if settings["DELETE_BEFORE_DEPLOY"]:
for config_file in config_files:
run("kubectl delete -f " + config_file % settings,
errors_to_ignore=["not found"])
for config_file in config_files:
run("kubectl apply -f " + config_file % settings)
if component in ["es-client", "es-master", "es-data", "es-kibana"]:
# wait until all replicas are running
num_pods = int(
settings.get(component.replace("-", "_").upper() + "_NUM_PODS", 1))
for pod_number_i in range(num_pods):
sleep_until_pod_is_running(component,
deployment_target=settings["DEPLOY_TO"],
pod_number=pod_number_i)
if component == "es-client":
run("kubectl describe svc elasticsearch")
def deploy_pod(component_label, settings, wait_until_pod_is_running=True, wait_until_pod_is_ready=False):
if settings["ONLY_PUSH_TO_REGISTRY"]:
return
run(" ".join([
"kubectl apply",
"-f %(DEPLOYMENT_TEMP_DIR)s/deploy/kubernetes/"+component_label+"/"+component_label+".%(DEPLOY_TO_PREFIX)s.yaml"
]) % settings)
if wait_until_pod_is_running:
sleep_until_pod_is_running(component_label, deployment_target=settings["DEPLOY_TO"])
if wait_until_pod_is_ready:
sleep_until_pod_is_ready(component_label, deployment_target=settings["DEPLOY_TO"])
def deploy_pod(component_label, settings, wait_until_pod_is_running=True, wait_until_pod_is_ready=False):
if settings["ONLY_PUSH_TO_REGISTRY"]:
return
run(" ".join([
"kubectl apply",
"-f %(DEPLOYMENT_TEMP_DIR)s/deploy/kubernetes/"+component_label+"/"+component_label+".%(DEPLOY_TO_PREFIX)s.yaml"
]) % settings)
if wait_until_pod_is_running:
sleep_until_pod_is_running(component_label, deployment_target=settings["DEPLOY_TO"])
if wait_until_pod_is_ready:
sleep_until_pod_is_ready(component_label, deployment_target=settings["DEPLOY_TO"])
def deploy_elasticsearch_sharded(settings, component):
if settings["ONLY_PUSH_TO_REGISTRY"]:
return
print_separator(component)
if component == "es-master":
config_files = [
"%(DEPLOYMENT_TEMP_DIR)s/hail_elasticsearch_pipelines/kubernetes/elasticsearch-sharded/es-discovery-svc.yaml",
"%(DEPLOYMENT_TEMP_DIR)s/hail_elasticsearch_pipelines/kubernetes/elasticsearch-sharded/es-master.yaml",
]
elif component == "es-client":
config_files = [
"%(DEPLOYMENT_TEMP_DIR)s/hail_elasticsearch_pipelines/kubernetes/elasticsearch-sharded/es-svc.yaml",
"%(DEPLOYMENT_TEMP_DIR)s/hail_elasticsearch_pipelines/kubernetes/elasticsearch-sharded/es-client.yaml",
]
elif component == "es-data":
config_files = [
"%(DEPLOYMENT_TEMP_DIR)s/hail_elasticsearch_pipelines/kubernetes/elasticsearch-sharded/es-data-svc.yaml",
"%(DEPLOYMENT_TEMP_DIR)s/hail_elasticsearch_pipelines/kubernetes/elasticsearch-sharded/es-data-stateful.yaml",
]
elif component == "es-kibana":
config_files = [
"%(DEPLOYMENT_TEMP_DIR)s/hail_elasticsearch_pipelines/kubernetes/elasticsearch-sharded/es-kibana.yaml",
]
elif component == "kibana":
config_files = [
"%(DEPLOYMENT_TEMP_DIR)s/deploy/kubernetes/kibana/kibana.%(DEPLOY_TO_PREFIX)s.yaml",
]
else:
raise ValueError("Unexpected component: " + component)
if settings["DELETE_BEFORE_DEPLOY"]:
for config_file in config_files:
run("kubectl delete -f " + config_file % settings, errors_to_ignore=["not found"])
for config_file in config_files:
run("kubectl apply -f " + config_file % settings)
if component in ["es-client", "es-master", "es-data", "es-kibana"]:
# wait until all replicas are running
num_pods = int(settings.get(component.replace("-", "_").upper()+"_NUM_PODS", 1))
for pod_number_i in range(num_pods):
sleep_until_pod_is_running(component, deployment_target=settings["DEPLOY_TO"], pod_number=pod_number_i)
if component == "es-client":
run("kubectl describe svc elasticsearch")
