def _run_workflow(time_elapsed_seconds=0.5, finish=True):
"""Mock a workflow run."""
id_ = uuid4()
workflow = Workflow(
id_=str(id_),
name="test_{}".format(id_),
owner_id=new_user.id_,
reana_specification=[],
type_="serial",
logs="",
status=RunStatus.created,
)
# start workflow
workflow.status = RunStatus.running
session.add(workflow)
session.commit()
termination_value = datetime.now() + timedelta(
seconds=time_elapsed_seconds)
class MockDatetime(datetime):
@classmethod
def now(cls):
return termination_value
if finish:
with mock.patch("reana_db.models.datetime", MockDatetime):
Workflow.update_workflow_status(session, workflow.id_,
RunStatus.finished)
return workflow
def _update_workflow_status(workflow, status, logs):
"""Update workflow status in DB."""
if workflow.status != status:
Workflow.update_workflow_status(Session, workflow.id_, status, logs,
None)
if workflow.git_ref:
_update_commit_status(workflow, status)
if status not in ALIVE_STATUSES:
workflow.run_finished_at = datetime.now()
workflow.logs = workflow.logs or ""
try:
workflow_engine_logs = _get_workflow_engine_pod_logs(workflow)
workflow.logs += workflow_engine_logs + "\n"
except REANAWorkflowControllerError as exception:
logging.error(
f"Could not fetch workflow engine pod logs for workflow {workflow.id_}."
f" Error: {exception}")
workflow.logs += "Workflow engine logs could not be retrieved.\n"
if RunStatus.should_cleanup_job(status):
try:
_delete_workflow_job(workflow)
except REANAWorkflowControllerError as exception:
logging.error(
f"Could not clean up workflow job for workflow {workflow.id_}."
f" Error: {exception}")
def initialize_krb5_token(workflow_uuid):
"""Create kerberos ticket from mounted keytab_file."""
cern_user = os.environ.get("CERN_USER")
keytab_file = os.environ.get("CERN_KEYTAB")
cmd = "kinit -kt /etc/reana/secrets/{} {}@CERN.CH".format(
keytab_file, cern_user)
if cern_user:
try:
subprocess.check_output(cmd, shell=True)
except subprocess.CalledProcessError as err:
msg = "Executing: {} \n Authentication failed: {}".format(cmd, err)
Workflow.update_workflow_status(
db_session=Session,
workflow_uuid=workflow_uuid,
status=None,
new_logs=msg,
)
logging.error(msg, exc_info=True)
sys.exit(1)
else:
msg = "CERN_USER is not set."
logging.error(msg, exc_info=True)
Workflow.update_workflow_status(db_session=Session,
workflow_uuid=workflow_uuid,
status=None,
new_logs=msg)
logging.error(msg, exc_info=True)
def _update_workflow_status(workflow_uuid, status, logs):
"""Update workflow status in DB."""
Workflow.update_workflow_status(Session, workflow_uuid, status, logs, None)
alive_statuses = \
[WorkflowStatus.created, WorkflowStatus.running, WorkflowStatus.queued]
if status not in alive_statuses:
_delete_workflow_engine_pod(workflow_uuid)
def publish_workflow_submission(workflow, user_id, parameters):
"""Publish workflow submission."""
from reana_server.status import NodesStatus
Workflow.update_workflow_status(Session, workflow.id_, RunStatus.queued)
scheduling_policy = REANA_WORKFLOW_SCHEDULING_POLICY
if scheduling_policy not in REANA_WORKFLOW_SCHEDULING_POLICIES:
raise ValueError(
'Workflow scheduling policy "{0}" is not valid.'.format(
scheduling_policy))
# No need to estimate the complexity for "fifo" strategy
if scheduling_policy == "fifo":
workflow_priority = 0
workflow_min_job_memory = 0
else:
total_cluster_memory = NodesStatus().get_total_memory()
complexity = _calculate_complexity(workflow)
workflow_priority = workflow.get_priority(total_cluster_memory)
workflow_min_job_memory = get_workflow_min_job_memory(complexity)
current_workflow_submission_publisher.publish_workflow_submission(
user_id=str(user_id),
workflow_id_or_name=workflow.get_full_workflow_name(),
parameters=parameters,
priority=workflow_priority,
min_job_memory=workflow_min_job_memory,
)
def _update_workflow_status(workflow_uuid, status, logs):
"""Update workflow status in DB."""
Workflow.update_workflow_status(Session, workflow_uuid, status, logs, None)
workflow = Session.query(Workflow).filter_by(id_=workflow_uuid)\
.one_or_none()
if workflow.git_ref:
_update_commit_status(workflow, status)
def _update_workflow_status(workflow_uuid, status, logs):
"""Update workflow status in DB."""
Workflow.update_workflow_status(Session, workflow_uuid, status, logs, None)
workflow = Session.query(Workflow).filter_by(id_=workflow_uuid)\
.one_or_none()
if workflow.git_ref:
_update_commit_status(workflow, status)
alive_statuses = \
[WorkflowStatus.created, WorkflowStatus.running, WorkflowStatus.queued]
if status not in alive_statuses:
_delete_workflow_engine_pod(workflow_uuid)
def _update_workflow_status(workflow, status, logs):
"""Update workflow status in DB."""
if workflow.status != status:
Workflow.update_workflow_status(Session, workflow.id_, status, logs, None)
if workflow.git_ref:
_update_commit_status(workflow, status)
alive_statuses = [
RunStatus.created,
RunStatus.running,
RunStatus.queued,
]
if status not in alive_statuses:
_delete_workflow_engine_pod(workflow)
def _update_workflow_status(workflow, status, logs):
"""Update workflow status in DB."""
if workflow.status != status:
Workflow.update_workflow_status(Session, workflow.id_, status, logs,
None)
if workflow.git_ref:
_update_commit_status(workflow, status)
alive_statuses = [
WorkflowStatus.created,
WorkflowStatus.running,
WorkflowStatus.queued,
]
if status not in alive_statuses:
workflow.run_finished_at = datetime.now()
_delete_workflow_engine_pod(workflow)
def on_message(self, workflow_submission, message):
"""On new workflow_submission event handler."""
if reana_ready():
message.ack()
workflow_submission = json.loads(workflow_submission)
logging.info(
'Starting queued workflow: {}'.format(workflow_submission))
workflow_submission['status'] = 'start'
response, http_response = current_rwc_api_client.api.\
set_workflow_status(**workflow_submission).result()
http_response_json = http_response.json()
if http_response.status_code == 200:
workflow_uuid = http_response_json['workflow_id']
status = http_response_json['status']
Workflow.update_workflow_status(Session, workflow_uuid, status)
else:
message.requeue()
def _update_workflow_status(workflow, status, logs):
"""Update workflow status in DB."""
if workflow.status != status:
Workflow.update_workflow_status(Session, workflow.id_, status, logs,
None)
if workflow.git_ref:
_update_commit_status(workflow, status)
if status not in ALIVE_STATUSES:
try:
workflow.run_finished_at = datetime.now()
if RunStatus.should_cleanup_job(status):
_delete_workflow_engine_pod(workflow)
except REANAWorkflowControllerError:
logging.error(
f"Could not clean up workflow engine for workflow {workflow.id_}"
)
workflow.logs += "Workflow engine logs could not be retrieved.\n"
def _update_workflow_status(workflow_uuid, status, logs):
"""Update workflow status in DB."""
Workflow.update_workflow_status(Session, workflow_uuid, status, logs, None)
