def test_complete_job(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/example-job/complete/",
body='{"success": true, "error": ""}'
)
job_id = "example-job"
payload = {
'success': True, 'error': '',
'artifacts': [
{'artifact_type': "Demultiplexed",
'filepaths': [("fp1", "preprocessed_fasta"),
("fp2", "preprocessed_fastq")],
'can_be_submitted_to_ebi': True,
'can_be_submitted_to_vamps': True}]}
complete_job(self.qclient, job_id, payload)
def execute_job(server_url, job_id, output_dir):
"""Starts the plugin and executes the assigned task
Parameters
----------
server_url : str
The url of the server
job_id : str
The job id
Raises
------
RuntimeError
If there is a problem gathering the job information
"""
qclient = QiitaClient(server_url)
# Request job information
job_info = qclient.get("/qiita_db/jobs/%s" % job_id)
# Check if we have received the job information so we can start it
if job_info and job_info['success']:
# Starting the heartbeat
start_heartbeat(qclient, job_id)
# Execute the given task
task_name = job_info['command']
task = TASK_DICT[task_name]
if not exists(output_dir):
makedirs(output_dir)
try:
payload = task(qclient, job_id, job_info['parameters'],
output_dir)
except Exception:
exc_str = repr(traceback.format_exception(*sys.exc_info()))
error_msg = ("Error executing %s:\n%s" % (task_name, exc_str))
payload = format_payload(False, error_msg=error_msg)
# The job completed
complete_job(qclient, job_id, payload)
else:
raise RuntimeError("Can't get job (%s) information" % job_id)
def execute_job(server_url, job_id, output_dir):
"""Starts the plugin and executes the assigned task
Parameters
----------
server_url : str
The url of the server
job_id : str
The job id
Raises
------
RuntimeError
If there is a problem gathering the job information
"""
qclient = QiitaClient(server_url)
# Request job information
job_info = qclient.get("/qiita_db/jobs/%s" % job_id)
# Check if we have received the job information so we can start it
if job_info and job_info['success']:
# Starting the heartbeat
start_heartbeat(qclient, job_id)
# Execute the given task
task_name = job_info['command']
task = TASK_DICT[task_name]
if not exists(output_dir):
makedirs(output_dir)
try:
payload = task(qclient, job_id, job_info['parameters'], output_dir)
except Exception:
exc_str = repr(traceback.format_exception(*sys.exc_info()))
error_msg = ("Error executing %s:\n%s" % (task_name, exc_str))
payload = format_payload(False, error_msg=error_msg)
# The job completed
complete_job(qclient, job_id, payload)
else:
raise RuntimeError("Can't get job (%s) information" % job_id)
