def _wait_until_pod_is_ready(component_label, deployment_target):
logger.info("waiting for \"%s\" to complete initialization" %
component_label)
while get_pod_status(component_label,
deployment_target,
status_type=POD_READY_STATUS) != "true":
time.sleep(5)
def _wait_until_pod_is_running(component_label,
deployment_target,
pod_number=0):
logger.info(
"waiting for \"%(component_label)s\" pod #%(pod_number)s to enter Running state"
% locals())
while get_pod_status(component_label,
deployment_target,
status_type=POD_RUNNING_STATUS,
pod_number=pod_number) != "Running":
time.sleep(5)
def port_forward(component_port_pairs=[],
deployment_target=None,
wait=True,
open_browser=False,
use_kubectl_proxy=False):
"""Executes kubectl command to forward traffic between localhost and the given pod.
While this is running, connecting to localhost:<port> will be the same as connecting to that port
from the pod's internal network.
Args:
component_port_pairs (list): 2-tuple(s) containing keyword to use for looking up a kubernetes
pod, along with the port to forward to that pod (eg. ('mongo', 27017), or ('phenotips', 8080))
deployment_target (string): "local", "gcloud-dev", etc. See constants.DEPLOYMENT_TARGETS.
wait (bool): Whether to block indefinitely as long as the forwarding process is running.
open_browser (bool): If component_port_pairs includes components that have an http server
(eg. "seqr" or "phenotips"), then open a web browser window to the forwarded port.
use_kubectl_proxy (bool): Whether to use kubectl proxy instead of kubectl port-forward
(see https://kubernetes.io/docs/tasks/access-application-cluster/access-cluster/#manually-constructing-apiserver-proxy-urls)
Returns:
(list): Popen process objects for the kubectl port-forward processes.
"""
procs = []
for component_label, port in component_port_pairs:
while get_pod_status(component_label, deployment_target) != "Running":
time.sleep(5)
logger.info("Forwarding port %s for %s" % (port, component_label))
pod_name = get_pod_name(component_label,
deployment_target=deployment_target)
if use_kubectl_proxy:
command = "kubectl proxy --port 8001"
else:
command = "kubectl port-forward %(pod_name)s %(port)s" % locals()
p = run_in_background(command)
if open_browser and component_label in COMPONENTS_TO_OPEN_IN_BROWSER:
if use_kubectl_proxy:
url = "http://localhost:8001/api/v1/namespaces/default/services/%(component_label)s:%(port)s/proxy/" % locals(
)
else:
url = "http://localhost:%s" % port
os.system("open " + url)
procs.append(p)
if wait:
wait_for(procs)
return procs
def print_log(components, deployment_target, enable_stream_log, wait=True):
"""Executes kubernetes command to print logs for the given pod.
Args:
components (list): one or more kubernetes pod labels (eg. 'phenotips' or 'nginx').
If more than one is specified, logs will be printed from all components in parallel.
deployment_target (string): "local", "gcloud-dev", etc. See constants.DEPLOYMENT_TARGETS.
enable_stream_log (bool): whether to continuously stream the log instead of just printing
the log up to now.
wait (bool): If False, this method will return without waiting for the log streaming process
to finish printing all logs.
Returns:
(list): Popen process objects for the kubectl port-forward processes.
"""
stream_arg = "-f" if enable_stream_log else ""
procs = []
for component_label in components:
while get_pod_status(component_label, deployment_target) != "Running":
time.sleep(5)
pod_name = get_pod_name(component_label,
deployment_target=deployment_target)
p = run_in_background("kubectl logs %(stream_arg)s %(pod_name)s" %
locals())
def print_command_log():
for line in iter(p.stdout.readline, ''):
logger.info(line.strip('\n'))
t = Thread(target=print_command_log)
t.start()
procs.append(p)
if wait:
wait_for(procs)
return procs
if "nginx" in components:
deploy_nginx(settings)
if "pipeline-runner" in components:
deploy_pipeline_runner(settings)
def delete_pod(component_label,
settings,
async=False,
custom_yaml_filename=None):
yaml_filename = custom_yaml_filename or (component_label +
".%(DEPLOY_TO_PREFIX)s.yaml")
deployment_target = settings["DEPLOY_TO"]
if get_pod_status(component_label, deployment_target) == "Running":
run(" ".join([
"kubectl delete",
"-f %(DEPLOYMENT_TEMP_DIR)s/deploy/kubernetes/" + component_label +
"/" + yaml_filename,
]) % settings,
errors_to_ignore=["not found"])
logger.info("waiting for \"%s\" to exit Running status" % component_label)
while get_pod_status(component_label, deployment_target) in [
"Running", "Terminating"
] and not async:
time.sleep(5)
def _wait_until_pod_is_ready(component_label, deployment_target):
if "kibana" in components:
deploy_kibana(settings)
if "nginx" in components:
deploy_nginx(settings)
if "pipeline-runner" in components:
deploy_pipeline_runner(settings)
def delete_pod(component_label, settings, async=False, custom_yaml_filename=None):
yaml_filename = custom_yaml_filename or (component_label+".%(DEPLOY_TO_PREFIX)s.yaml")
deployment_target = settings["DEPLOY_TO"]
if get_pod_status(component_label, deployment_target) == "Running":
run(" ".join([
"kubectl delete",
"-f %(DEPLOYMENT_TEMP_DIR)s/deploy/kubernetes/"+component_label+"/"+yaml_filename,
]) % settings, errors_to_ignore=["not found"])
logger.info("waiting for \"%s\" to exit Running status" % component_label)
while get_pod_status(component_label, deployment_target) in ["Running", "Terminating"] and not async:
time.sleep(5)
def _wait_until_pod_is_ready(component_label, deployment_target):
logger.info("waiting for \"%s\" to complete initialization" % component_label)
while get_pod_status(component_label, deployment_target, status_type=POD_READY_STATUS) != "true":
time.sleep(5)
# deploy_elasticsearch(settings)
# else:
# deploy_elasticsearch_sharded(settings)
#if "kibana" in components:
# deploy_kibana(settings)
if "nginx" in components:
deploy_nginx(settings)
def delete_pod(component_label, settings, async=False, custom_yaml_filename=None):
yaml_filename = custom_yaml_filename or (component_label+".%(DEPLOY_TO_PREFIX)s.yaml")
deployment_target = settings["DEPLOY_TO"]
if get_pod_status(component_label, deployment_target) == "Running":
run(" ".join([
"kubectl delete",
"-f %(DEPLOYMENT_TEMP_DIR)s/deploy/kubernetes/"+component_label+"/"+yaml_filename,
]) % settings, errors_to_ignore=["not found"])
logger.info("waiting for \"%s\" to exit Running status" % component_label)
while get_pod_status(component_label, deployment_target) == "Running" and not async:
time.sleep(5)
def _wait_until_pod_is_ready(component_label, deployment_target):
logger.info("waiting for \"%s\" to complete initialization" % component_label)
while get_pod_status(component_label, deployment_target, status_type=POD_READY_STATUS) != "true":
time.sleep(5)