def testCreateSubmission(self):
"""Test create_submission correctly loads dummy information to submission_queue.json"""
service = 'service'
submissions = dict()
submissions[service] = dict()
presubmit_ids = ['foo', 'bar']
for pre_id in presubmit_ids:
submissions[service][pre_id] = pre_id
pre_len = len(submissions[service])
orch = orchestrator.Orchestrator()
util.save_json(self.queue_loc, submissions)
new_id = orch.create_submission(service, 'data', 'wf_type', 'wf_name',
'sample')
submissions = util.get_json(self.queue_loc)
for pre_id in presubmit_ids:
self.assertEqual(submissions[service][pre_id], pre_id)
# Check that new entry was added appropriately.
self.assertEqual(pre_len + 1, len(submissions[service]))
self.assertFalse(new_id in presubmit_ids)
self.assertTrue((new_id in submissions[service]))
# Check that entry has correct data.
self.assertEqual(submissions[service][new_id]['status'], 'RECEIVED')
self.assertEqual(submissions[service][new_id]['data'], 'data')
self.assertEqual(submissions[service][new_id]['wf_id'], 'wf_name')
self.assertEqual(submissions[service][new_id]['type'], 'wf_type')
self.assertEqual(submissions[service][new_id]['sample'], 'sample')
def update_submission_run(eval_id, submission_id, run_data):
"""
Update information for a workflow run.
"""
evals = get_json(EVALS_PATH)
evals[eval_id][submission_id]['run'] = run_data
save_json(EVALS_PATH, evals)
def update_submission_status(eval_id, submission_id, status):
"""
Update the status of a submission.
"""
evals = get_json(EVALS_PATH)
evals[eval_id][submission_id]['status'] = status
save_json(EVALS_PATH, evals)
def set_json(self, section, service, var2add):
try:
orchestrator_config = get_json(self.config_path)
orchestrator_config.setdefault(section, {})[service] = var2add
save_json(self.config_path, orchestrator_config)
except AttributeError:
raise AttributeError('The config file needs to be set: ' +
self.config_path)
def create_submission(wes_id, submission_data, wf_type, wf_name, sample):
submissions = get_json(queue_path())
submission_id = dt.datetime.now().strftime('%d%m%d%H%M%S%f')
submissions.setdefault(wes_id, {})[submission_id] = {
'status': 'RECEIVED',
'data': submission_data,
'wf_id': wf_name,
'type': wf_type,
'sample': sample
}
save_json(queue_path(), submissions)
logger.info(" Queueing Job for '{}' endpoint:"
"\n - submission ID: {}".format(wes_id, submission_id))
return submission_id
def testConfigs(self):
"""
Make sure that the various config fetching functions reads the right data from the config file.
This test checks that the following functions return as expected:
config.wf_config()
config.trs_config()
config.wes_config()
"""
c = config.Config(self.config_loc)
config_entries = {'workflows': c.wf_config,
'toolregistries': c.trs_config,
'workflowservices': c.wes_config}
for entry, get_func in config_entries.items():
config_file = util.get_json(c.config_path)
config_file[entry] = entry # X_config() returns whatever is stored here.
util.save_json(c.config_path, config_file)
self.assertEqual(get_func(), entry)
def create_submission(eval_id, submission_data, wes_id, type=None):
"""
Submit a new job request to an evaluation queue.
"""
evals = get_json(EVALS_PATH)
submission_id = dt.datetime.now().strftime('%d%m%d%H%M%S%f')
evals.setdefault(eval_id, {})[submission_id] = {
'status': 'RECEIVED',
'data': submission_data,
'wes_id': wes_id,
'type': type
}
save_json(EVALS_PATH, evals)
logger.info("Created new job submission:\n - submission ID: {}".format(
submission_id))
logger.debug("\n - evaluation queue: {} ({})"
"\n - data:\n{}".format(
eval_id, config.eval_config[eval_id]['workflow_id'],
json.dumps(submission_data, indent=2)))
return submission_id
def update_submission_run(wes_id, submission_id, param, status):
"""Update the status of a submission."""
submissions = get_json(queue_path())
submissions[wes_id][submission_id]['run'][param] = status
save_json(queue_path(), submissions)
def update_submission(self, wes_id, submission_id, param, status):
"""Update the status of a submission."""
submissions = get_json(self.queue_path)
submissions[wes_id][submission_id][param] = status
save_json(self.queue_path, submissions)