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", "phenotipsdb", "mongodb"
deployment_target (string): value from DEPLOYMENT_TARGETS - eg. "minikube", "gcloud-dev", etc.
"""
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())
if "phenotipsdb" 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 xwiki postgres -c 'drop database xwiki'" % locals(), errors_to_ignore=["does not exist"])
run_in_pod(postgres_pod_name, "psql -U xwiki postgres -c 'create database xwiki'" % locals())
#run("kubectl exec %(postgres_pod_name)s -- psql -U postgres xwiki < data/init_phenotipsdb.sql" % locals())
if "mongodb" in database:
mongo_pod_name = get_pod_name("mongo", deployment_target=deployment_target)
if not mongo_pod_name:
logger.error("mongo pod must be running")
else:
run_in_pod(mongo_pod_name, "mongo datastore --eval 'db.dropDatabase()'" % locals())
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 load_example_project(deployment_target,
genome_version="37",
cpu_limit=None,
start_with_step=None):
"""Load example project
Args:
deployment_target (string): value from DEPLOYMENT_TARGETS - eg. "minikube", "gcloud-dev", etc.
genome_version (string): reference genome version - either "37" or "38"
"""
project_name = "1kg"
check_kubernetes_context(deployment_target)
pod_name = get_pod_name('seqr', deployment_target=deployment_target)
if not pod_name:
raise ValueError(
"No 'seqr' pod found. Is the kubectl environment configured in this terminal? and have either of these pods been deployed?"
% locals())
run_in_pod(
pod_name,
"wget -N https://storage.googleapis.com/seqr-reference-data/test-projects/1kg.ped"
% locals())
#run_in_pod(pod_name, "gsutil cp %(ped)s ." % locals())
# TODO call APIs instead?
run_in_pod(
pod_name,
"python2.7 -u -m manage create_project -p '1kg.ped' '%(project_name)s'"
% locals(),
verbose=True)
if genome_version == "37":
vcf_filename = "1kg.vcf.gz"
elif genome_version == "38":
vcf_filename = "1kg.liftover.GRCh38.vep.vcf.gz"
else:
raise ValueError("Unexpected genome_version: %s" % (genome_version, ))
load_dataset(
deployment_target,
project_name=project_name,
genome_version=genome_version,
sample_type="WES",
dataset_type="VARIANTS",
cpu_limit=cpu_limit,
start_with_step=start_with_step,
vcf=
"https://storage.googleapis.com/seqr-reference-data/test-projects/%(vcf_filename)s"
% locals())
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", "phenotipsdb",
deployment_target (string): value from DEPLOYMENT_TARGETS - eg. "minikube", "gcloud-dev", etc.
"""
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())
if "phenotipsdb" 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 xwiki postgres -c 'drop database xwiki'" %
locals(),
errors_to_ignore=["does not exist"])
run_in_pod(
postgres_pod_name,
"psql -U xwiki postgres -c 'create database xwiki'" % locals())
def create_user(deployment_target, email=None, password=None):
"""Creates a seqr superuser.
Args:
deployment_target (string): value from DEPLOYMENT_TARGETS - eg. "minikube", "gcloud-dev", etc.
email (string): if provided, user will be created non-interactively
password (string): if provided, user will be created non-interactively
"""
check_kubernetes_context(deployment_target)
if not email:
run_in_pod("seqr", "python -u manage.py createsuperuser" % locals(), is_interactive=True)
else:
logger.info("Creating user %(email)s" % locals())
run_in_pod("seqr",
"""echo "from django.contrib.auth.models import User; User.objects.create_superuser('%(email)s', '%(email)s', '%(password)s')" \| python manage.py shell""" % locals(),
print_command=False,
errors_to_ignore=["already exists"])
def create_user(deployment_target, email=None, password=None):
"""Creates a seqr superuser.
Args:
deployment_target (string): value from DEPLOYMENT_TARGETS - eg. "minikube", "gcloud-dev", etc.
email (string): if provided, user will be created non-interactively
password (string): if provided, user will be created non-interactively
"""
check_kubernetes_context(deployment_target)
if not email:
run_in_pod("seqr",
"python -u manage.py createsuperuser" % locals(),
is_interactive=True)
else:
logger.info("Creating user %(email)s" % locals())
run_in_pod(
"seqr",
"""echo "from django.contrib.auth.models import User; User.objects.create_superuser('%(email)s', '%(email)s', '%(password)s')" \| python manage.py shell"""
% locals(),
print_command=False,
errors_to_ignore=["already exists"])
def load_example_project(deployment_target, genome_version="37", cpu_limit=None, start_with_step=None):
"""Load example project
Args:
deployment_target (string): value from DEPLOYMENT_TARGETS - eg. "minikube", "gcloud-dev", etc.
genome_version (string): reference genome version - either "37" or "38"
"""
project_name = "1kg"
check_kubernetes_context(deployment_target)
pod_name = get_pod_name('seqr', deployment_target=deployment_target)
if not pod_name:
raise ValueError("No 'seqr' pod found. Is the kubectl environment configured in this terminal? and have either of these pods been deployed?" % locals())
run_in_pod(pod_name, "wget -N https://storage.googleapis.com/seqr-reference-data/test-projects/1kg.ped" % locals())
#run_in_pod(pod_name, "gsutil cp %(ped)s ." % locals())
# TODO call APIs instead?
run_in_pod(pod_name, "python2.7 -u -m manage create_project -p '1kg.ped' '%(project_name)s'" % locals(), verbose=True)
if genome_version == "37":
vcf_filename = "1kg.vcf.gz"
elif genome_version == "38":
vcf_filename = "1kg.liftover.GRCh38.vep.vcf.gz"
else:
raise ValueError("Unexpected genome_version: %s" % (genome_version,))
load_dataset(
deployment_target,
project_name=project_name,
genome_version=genome_version,
sample_type="WES",
dataset_type="VARIANTS",
cpu_limit=cpu_limit,
start_with_step=start_with_step,
vcf="https://storage.googleapis.com/seqr-reference-data/test-projects/%(vcf_filename)s" % locals())
def load_dataset(deployment_target, project_name, genome_version, sample_type, dataset_type, vcf, memory_to_use=None, cpu_limit=None, **kwargs):
"""Load dataset into elasticsearch.
"""
pod_name = get_pod_name('pipeline-runner', deployment_target=deployment_target)
# run load command
additional_load_command_args = " ".join("--%s '%s'" % (key.lower().replace("_", "-"), value) for key, value in kwargs.items() if value is not None)
if deployment_target == "minikube":
vcf_name = os.path.basename(vcf)
path_in_pod = "/data/{}".format(vcf_name)
if os.path.isfile(vcf):
run("kubectl cp '%(vcf)s' '%(pod_name)s:%(path_in_pod)s'" % locals()) # if local file path, copy file into pod
elif vcf.startswith("http"):
run_in_pod(pod_name, "wget -N %(vcf)s -O %(path_in_pod)s" % locals())
elif vcf.startswith("gs:"):
run_in_pod(pod_name, "gsutil cp -n %(vcf)s %(path_in_pod)s" % locals())
vcf = path_in_pod
total_memory = psutil.virtual_memory().total - 6*10**9 # leave 6Gb for other processes
memory_to_use = "%sG" % (total_memory / 2 / 10**9) if memory_to_use is None else memory_to_use # divide available memory evenly between spark driver & executor
cpu_limit = max(1, psutil.cpu_count() / 2) if cpu_limit is None else cpu_limit
load_command = """/hail-elasticsearch-pipelines/run_hail_locally.sh \
--driver-memory %(memory_to_use)s \
--executor-memory %(memory_to_use)s \
hail_scripts/v01/load_dataset_to_es.py \
--cpu-limit %(cpu_limit)s \
--genome-version %(genome_version)s \
--project-guid %(project_name)s \
--sample-type %(sample_type)s \
--dataset-type %(dataset_type)s \
--skip-validation \
--exclude-hgmd \
--vep-block-size 100 \
--es-block-size 10 \
--num-shards 1 \
--max-samples-per-index 99 \
%(additional_load_command_args)s \
%(vcf)s
""" % locals()
else:
load_command = """/hail-elasticsearch-pipelines/run_hail_on_dataproc.sh \
hail_scripts/v01/load_dataset_to_es.py \
--genome-version %(genome_version)s \
--project-guid %(project_name)s \
--sample-type %(sample_type)s \
--dataset-type %(dataset_type)s \
%(additional_load_command_args)s \
%(vcf)s
""" % locals()
run_in_pod(pod_name, load_command, verbose=True)
def load_dataset(deployment_target,
project_name,
genome_version,
sample_type,
dataset_type,
vcf,
memory_to_use=None,
cpu_limit=None,
**kwargs):
"""Load dataset into elasticsearch.
"""
pod_name = get_pod_name('pipeline-runner',
deployment_target=deployment_target)
# run load command
additional_load_command_args = " ".join(
"--%s '%s'" % (key.lower().replace("_", "-"), value)
for key, value in kwargs.items() if value is not None)
if deployment_target == "minikube":
vcf_name = os.path.basename(vcf)
path_in_pod = "/data/{}".format(vcf_name)
if os.path.isfile(vcf):
run("kubectl cp '%(vcf)s' '%(pod_name)s:%(path_in_pod)s'" %
locals()) # if local file path, copy file into pod
elif vcf.startswith("http"):
run_in_pod(pod_name,
"wget -N %(vcf)s -O %(path_in_pod)s" % locals())
elif vcf.startswith("gs:"):
run_in_pod(pod_name,
"gsutil cp -n %(vcf)s %(path_in_pod)s" % locals())
vcf = path_in_pod
total_memory = psutil.virtual_memory(
).total - 6 * 10**9 # leave 6Gb for other processes
memory_to_use = "%sG" % (
total_memory / 2 / 10**9
) if memory_to_use is None else memory_to_use # divide available memory evenly between spark driver & executor
cpu_limit = max(1,
psutil.cpu_count() /
2) if cpu_limit is None else cpu_limit
load_command = """/hail-elasticsearch-pipelines/run_hail_locally.sh \
--driver-memory %(memory_to_use)s \
--executor-memory %(memory_to_use)s \
hail_scripts/v01/load_dataset_to_es.py \
--cpu-limit %(cpu_limit)s \
--genome-version %(genome_version)s \
--project-guid %(project_name)s \
--sample-type %(sample_type)s \
--dataset-type %(dataset_type)s \
--skip-validation \
--exclude-hgmd \
--vep-block-size 100 \
--es-block-size 10 \
--num-shards 1 \
--max-samples-per-index 99 \
%(additional_load_command_args)s \
%(vcf)s
""" % locals()
else:
load_command = """/hail-elasticsearch-pipelines/run_hail_on_dataproc.sh \
hail_scripts/v01/load_dataset_to_es.py \
--genome-version %(genome_version)s \
--project-guid %(project_name)s \
--sample-type %(sample_type)s \
--dataset-type %(dataset_type)s \
%(additional_load_command_args)s \
%(vcf)s
""" % locals()
run_in_pod(pod_name, load_command, verbose=True)
def update_reference_data(deployment_target):
"""DEPRECATED. Load reference data into mongodb.
Args:
deployment_target (string): value from DEPLOYMENT_TARGETS - eg. "minikube", "gcloud-dev", etc.
"""
check_kubernetes_context(deployment_target)
pod_name = get_pod_name('seqr', deployment_target=deployment_target)
if not pod_name:
raise ValueError(
"No 'seqr' pods found. Is the kubectl environment configured in this terminal? and have either of these pods been deployed?"
% locals())
# commented out because this is not loaded from settings backup
#run_in_pod(pod_name, "python2.7 -u manage.py update_all_reference_data --omim-key '$OMIM_KEY'" % locals(), verbose=True, print_command=True)
run_in_pod(pod_name, "mkdir -p /seqr/data/reference_data")
run_in_pod(
pod_name,
"wget -N https://storage.googleapis.com/seqr-reference-data/seqr-resource-bundle.tar.gz -O /seqr/data/reference_data/seqr-resource-bundle.tar.gz"
)
run_in_pod(
pod_name,
"tar xzf /seqr/data/reference_data/seqr-resource-bundle.tar.gz -C /seqr/data/reference_data",
verbose=True)
run_in_pod(pod_name,
"rm /seqr/data/reference_data/seqr-resource-bundle.tar.gz")
# load legacy resources
run_in_pod(pod_name, "python -u manage.py load_resources", verbose=True)
run_in_pod(pod_name, "python -u manage.py load_omim", verbose=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_phenotips(settings):
print_separator("phenotips")
phenotips_service_port = settings["PHENOTIPS_SERVICE_PORT"]
restore_phenotips_db_from_backup = settings.get(
"RESTORE_PHENOTIPS_DB_FROM_BACKUP")
reset_db = settings.get("RESET_DB")
deployment_target = settings["DEPLOY_TO"]
if reset_db or restore_phenotips_db_from_backup:
delete_pod("phenotips", settings)
run_in_pod(
"postgres",
"psql -U postgres postgres -c 'drop database xwiki'" % locals(),
verbose=True,
errors_to_ignore=["does not exist"],
deployment_target=deployment_target,
)
elif settings["DELETE_BEFORE_DEPLOY"]:
delete_pod("phenotips", settings)
# init postgres
if not settings["ONLY_PUSH_TO_REGISTRY"]:
run_in_pod(
"postgres",
"psql -U postgres postgres -c \"create role xwiki with CREATEDB LOGIN PASSWORD 'xwiki'\""
% locals(),
verbose=True,
errors_to_ignore=["already exists"],
deployment_target=deployment_target,
)
run_in_pod(
"postgres",
"psql -U xwiki postgres -c 'create database xwiki'" % locals(),
verbose=True,
errors_to_ignore=["already exists"],
deployment_target=deployment_target,
)
run_in_pod(
"postgres",
"psql -U postgres postgres -c 'grant all privileges on database xwiki to xwiki'"
% locals(),
)
# build container
docker_build(
"phenotips", settings,
["--build-arg PHENOTIPS_SERVICE_PORT=%s" % phenotips_service_port])
if settings["ONLY_PUSH_TO_REGISTRY"]:
return
deploy_pod("phenotips", settings, wait_until_pod_is_ready=True)
for i in range(0, 3):
# opening the PhenoTips website for the 1st time triggers a final set of initialization
# steps which take ~ 1 minute, so run wget to trigger this
try:
run_in_pod(
"phenotips",
#command="wget http://localhost:%(phenotips_service_port)s -O test.html" % locals(),
command=
"curl --verbose -L -u Admin:admin http://localhost:%(phenotips_service_port)s -o test.html"
% locals(),
verbose=True)
except Exception as e:
logger.error(str(e))
if i < 2:
logger.info("Waiting for phenotips to start up...")
time.sleep(10)
if restore_phenotips_db_from_backup:
delete_pod("phenotips", settings)
postgres_pod_name = get_pod_name("postgres",
deployment_target=deployment_target)
run("kubectl cp '%(restore_phenotips_db_from_backup)s' %(postgres_pod_name)s:/root/$(basename %(restore_phenotips_db_from_backup)s)"
% locals(),
verbose=True)
run_in_pod(
"postgres",
"/root/restore_database_backup.sh xwiki xwiki /root/$(basename %(restore_phenotips_db_from_backup)s)"
% locals(),
deployment_target=deployment_target,
verbose=True)
run_in_pod(
"postgres",
"rm /root/$(basename %(restore_phenotips_db_from_backup)s)" %
locals(),
deployment_target=deployment_target,
verbose=True)
deploy_pod("phenotips", settings, wait_until_pod_is_ready=True)
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 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_phenotips(settings):
print_separator("phenotips")
phenotips_service_port = settings["PHENOTIPS_SERVICE_PORT"]
restore_phenotips_db_from_backup = settings.get("RESTORE_PHENOTIPS_DB_FROM_BACKUP")
reset_db = settings.get("RESET_DB")
deployment_target = settings["DEPLOY_TO"]
if reset_db or restore_phenotips_db_from_backup:
delete_pod("phenotips", settings)
run_in_pod("postgres", "psql -U postgres postgres -c 'drop database xwiki'" % locals(),
verbose=True,
errors_to_ignore=["does not exist"],
deployment_target=deployment_target,
)
elif settings["DELETE_BEFORE_DEPLOY"]:
delete_pod("phenotips", settings)
# init postgres
if not settings["ONLY_PUSH_TO_REGISTRY"]:
run_in_pod("postgres",
"psql -U postgres postgres -c \"create role xwiki with CREATEDB LOGIN PASSWORD 'xwiki'\"" % locals(),
verbose=True,
errors_to_ignore=["already exists"],
deployment_target=deployment_target,
)
run_in_pod("postgres",
"psql -U xwiki postgres -c 'create database xwiki'" % locals(),
verbose=True,
errors_to_ignore=["already exists"],
deployment_target=deployment_target,
)
run_in_pod("postgres",
"psql -U postgres postgres -c 'grant all privileges on database xwiki to xwiki'" % locals(),
)
# build container
docker_build("phenotips", settings, ["--build-arg PHENOTIPS_SERVICE_PORT=%s" % phenotips_service_port])
if settings["ONLY_PUSH_TO_REGISTRY"]:
return
deploy_pod("phenotips", settings, wait_until_pod_is_ready=True)
for i in range(0, 3):
# opening the PhenoTips website for the 1st time triggers a final set of initialization
# steps which take ~ 1 minute, so run wget to trigger this
try:
run_in_pod("phenotips",
#command="wget http://localhost:%(phenotips_service_port)s -O test.html" % locals(),
command="curl --verbose -L -u Admin:admin http://localhost:%(phenotips_service_port)s -o test.html" % locals(),
verbose=True
)
except Exception as e:
logger.error(str(e))
if i < 2:
logger.info("Waiting for phenotips to start up...")
time.sleep(10)
if restore_phenotips_db_from_backup:
delete_pod("phenotips", settings)
postgres_pod_name = get_pod_name("postgres", deployment_target=deployment_target)
run("kubectl cp '%(restore_phenotips_db_from_backup)s' %(postgres_pod_name)s:/root/$(basename %(restore_phenotips_db_from_backup)s)" % locals(), verbose=True)
run_in_pod("postgres", "/root/restore_database_backup.sh xwiki xwiki /root/$(basename %(restore_phenotips_db_from_backup)s)" % locals(), deployment_target=deployment_target, verbose=True)
run_in_pod("postgres", "rm /root/$(basename %(restore_phenotips_db_from_backup)s)" % locals(), deployment_target=deployment_target, verbose=True)
deploy_pod("phenotips", settings, wait_until_pod_is_ready=True)
def update_reference_data(deployment_target):
"""DEPRECATED. Load reference data into mongodb.
Args:
deployment_target (string): value from DEPLOYMENT_TARGETS - eg. "minikube", "gcloud-dev", etc.
"""
check_kubernetes_context(deployment_target)
pod_name = get_pod_name('seqr', deployment_target=deployment_target)
if not pod_name:
raise ValueError("No 'seqr' pods found. Is the kubectl environment configured in this terminal? and have either of these pods been deployed?" % locals())
# commented out because this is not loaded from settings backup
#run_in_pod(pod_name, "python2.7 -u manage.py update_all_reference_data --omim-key '$OMIM_KEY'" % locals(), verbose=True, print_command=True)
run_in_pod(pod_name, "mkdir -p /seqr/data/reference_data")
run_in_pod(pod_name, "wget -N https://storage.googleapis.com/seqr-reference-data/seqr-resource-bundle.tar.gz -O /seqr/data/reference_data/seqr-resource-bundle.tar.gz")
run_in_pod(pod_name, "tar xzf /seqr/data/reference_data/seqr-resource-bundle.tar.gz -C /seqr/data/reference_data", verbose=True)
run_in_pod(pod_name, "rm /seqr/data/reference_data/seqr-resource-bundle.tar.gz")
# load legacy resources
run_in_pod(pod_name, "python -u manage.py load_resources", verbose=True)
run_in_pod(pod_name, "python -u manage.py load_omim", verbose=True)
