def deploy_postgres(settings):
print_separator("postgres")
docker_build("postgres", settings)
restore_seqr_db_from_backup = settings.get("RESTORE_SEQR_DB_FROM_BACKUP")
reset_db = settings.get("RESET_DB")
if reset_db or restore_seqr_db_from_backup:
# Since pgdata is stored on a persistent volume, redeploying does not get rid of it. If any existing pgdata is
# present, even if the databases are empty, postgres will not fully re-initialize the database. This is
# good if you want to keep the data across a deployment, but problematic if you actually need to rest and
# reinitialize the db. Therefore, when the database needs to be fully reinitialized, delete pgdata
run_in_pod(get_pod_name("postgres",
deployment_target=settings["DEPLOY_TO"]),
"rm -rf /var/lib/postgresql/data/pgdata",
verbose=True)
deploy_pod("postgres", settings, wait_until_pod_is_ready=True)
if restore_seqr_db_from_backup:
postgres_pod_name = get_pod_name(
"postgres", deployment_target=settings["DEPLOY_TO"])
_restore_seqr_db_from_backup(
postgres_pod_name, restore_seqr_db_from_backup,
settings.get("RESTORE_REFERENCE_DB_FROM_BACKUP"))
def open_shell_in_component(component,
deployment_target,
shell_path='/bin/bash'):
"""Open a command line shell in the given component"""
run_in_pod(component,
shell_path,
deployment_target=deployment_target,
is_interactive=True)
def _drop_seqr_db(postgres_pod_name):
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 'drop database reference_data_db'",
errors_to_ignore=["does not exist"],
verbose=True,
)
def reset_database(database=[], deployment_target=None):
"""Runs kubectl commands to delete and reset the given database(s).
Args:
component (list): one more database labels - "seqrdb"
deployment_target (string): value from DEPLOYMENT_TARGETS - eg. "gcloud-dev"
"""
if "seqrdb" in database:
postgres_pod_name = get_pod_name("postgres", deployment_target=deployment_target)
if not postgres_pod_name:
logger.error("postgres pod must be running")
else:
run_in_pod(postgres_pod_name, "psql -U postgres postgres -c 'drop database seqrdb'" % locals(), errors_to_ignore=["does not exist"])
run_in_pod(postgres_pod_name, "psql -U postgres postgres -c 'create database seqrdb'" % locals())
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:
_drop_seqr_db(postgres_pod_name)
if restore_seqr_db_from_backup:
_drop_seqr_db(postgres_pod_name)
_restore_seqr_db_from_backup(postgres_pod_name,
restore_seqr_db_from_backup)
else:
run_in_pod(
postgres_pod_name,
"psql -U postgres postgres -c 'create database seqrdb'",
errors_to_ignore=["already exists"],
verbose=True,
)
run_in_pod(
postgres_pod_name,
"psql -U postgres postgres -c 'create database reference_data_db'",
errors_to_ignore=["already exists"],
verbose=True,
)
deploy_pod("seqr", settings, wait_until_pod_is_ready=True)
def redeploy_seqr(deployment_target):
print_separator('re-deploying seqr')
seqr_pod_name = get_pod_name('seqr', deployment_target=deployment_target)
if not seqr_pod_name:
raise ValueError('No seqr pod found, unable to re-deploy')
sleep_until_pod_is_running('seqr', deployment_target=deployment_target)
run_in_pod(seqr_pod_name, 'git pull', verbose=True)
run_in_pod(seqr_pod_name, './manage.py migrate', verbose=True)
run_in_pod(seqr_pod_name, '/usr/local/bin/restart_server.sh')
def _restore_seqr_db_from_backup(postgres_pod_name, seqrdb_backup, reference_data_backup=None):
run_in_pod(postgres_pod_name, "psql -U postgres postgres -c 'create database seqrdb'", verbose=True)
run_in_pod(postgres_pod_name, "psql -U postgres postgres -c 'create database reference_data_db'", verbose=True)
run("kubectl cp '{backup}' {postgres_pod_name}:/root/$(basename {backup})".format(
postgres_pod_name=postgres_pod_name, backup=seqrdb_backup), verbose=True)
run_in_pod(
postgres_pod_name, "/root/restore_database_backup.sh postgres seqrdb /root/$(basename {backup})".format(
backup=seqrdb_backup), verbose=True)
run_in_pod(postgres_pod_name, "rm /root/$(basename {backup})".format(backup=seqrdb_backup, verbose=True))
if reference_data_backup:
run("kubectl cp '{backup}' {postgres_pod_name}:/root/$(basename {backup})".format(
postgres_pod_name=postgres_pod_name, backup=reference_data_backup), verbose=True)
run_in_pod(
postgres_pod_name, "/root/restore_database_backup.sh postgres reference_data_db /root/$(basename {backup})".format(
backup=reference_data_backup), verbose=True)
run_in_pod(postgres_pod_name, "rm /root/$(basename {backup})".format(backup=reference_data_backup, verbose=True))
