def test_load_job_constants__no_file(self):
file_path = [
"src",
"biokbase",
"narrative",
"tests",
"data",
"job_constants",
"does_not_exist.json",
]
with self.assertRaises(FileNotFoundError):
load_job_constants(file_path)
def test_load_job_constants__missing_value(self):
file_path = [
"src",
"biokbase",
"narrative",
"tests",
"data",
"job_constants",
"job_config-missing-item.json",
]
with self.assertRaisesRegex(
ValueError,
"job_config.json is missing the following values for params: BATCH_ID, JOB_ID",
):
load_job_constants(file_path)
def test_load_job_constants__missing_section(self):
file_path = [
"src",
"biokbase",
"narrative",
"tests",
"data",
"job_constants",
"job_config-missing-datatype.json",
]
with self.assertRaisesRegex(
ValueError,
"job_config.json is missing the 'message_types' config section"
):
load_job_constants(file_path)
def test_load_job_constants__valid(self):
# the live file!
(params, message_types) = load_job_constants()
for item in ["BATCH_ID", "JOB_ID"]:
self.assertIn(item, params)
for item in ["STATUS", "RETRY", "INFO", "ERROR"]:
self.assertIn(item, message_types)
import copy
import threading
from typing import List, Union
from ipykernel.comm import Comm
from biokbase.narrative.jobs.util import load_job_constants
from biokbase.narrative.jobs.jobmanager import JobManager
from biokbase.narrative.exception_util import NarrativeException, JobRequestException
from biokbase.narrative.common import kblogging
(PARAM, MESSAGE_TYPE) = load_job_constants()
UNKNOWN_REASON = "Unknown reason"
JOB_NOT_PROVIDED_ERR = "job_id not provided"
JOBS_NOT_PROVIDED_ERR = "job_id_list not provided"
CELLS_NOT_PROVIDED_ERR = "cell_id_list not provided"
BATCH_NOT_PROVIDED_ERR = "batch_id not provided"
ONE_INPUT_TYPE_ONLY_ERR = "Please provide one of job_id, job_id_list, or batch_id"
INVALID_REQUEST_ERR = "Improperly formatted job channel message!"
MISSING_REQUEST_TYPE_ERR = "Missing request type in job channel message!"
LOOKUP_TIMER_INTERVAL = 5
class JobRequest(object):
"""
A small wrapper for job comm channel request data.
This generally comes in the form of a packet from the kernel Comm object.
It's expected to be a dict of the format: