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Return working directory as part of the queue status #143

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Merged
merged 3 commits into from
Oct 25, 2022
+16 −7
Merged

Return working directory as part of the queue status #143

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b40bc62
Return working directory as part of the queue status
jan-janssen Oct 20, 2022
2edcb0e
Format black
pyiron-runner Oct 20, 2022
412527f
fix tests
jan-janssen Oct 20, 2022
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1 change: 1 addition & 0 deletions pysqa/wrapper/sge.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,5 +55,6 @@ def leaf_to_dict(leaf):
"user": df_merge.JB_owner,
"jobname": df_merge.JB_name,
"status": df_merge.state,
"working_directory": [""] * len(df_merge),
}
)
17 changes: 12 additions & 5 deletions pysqa/wrapper/slurm.py
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Expand Up @@ -29,7 +29,7 @@ def delete_job_command(self):

@property
def get_queue_status_command(self):
return ["squeue", "--format", "%A|%u|%t|%.15j", "--noheader"]
return ["squeue", "--format", "%A|%u|%t|%.15j|%Z", "--noheader"]

@staticmethod
def get_job_id_from_output(queue_submit_output):
Expand All @@ -39,20 +39,27 @@ def get_job_id_from_output(queue_submit_output):
def convert_queue_status(queue_status_output):
line_split_lst = [line.split("|") for line in queue_status_output.splitlines()]
if len(line_split_lst) != 0:
job_id_lst, user_lst, status_lst, job_name_lst = zip(
job_id_lst, user_lst, status_lst, job_name_lst, working_directory_lst = zip(
*[
(int(jobid), user, status.lower(), jobname)
for jobid, user, status, jobname in line_split_lst
(int(jobid), user, status.lower(), jobname, working_directory)
for jobid, user, status, jobname, working_directory in line_split_lst
]
)
else:
job_id_lst, user_lst, status_lst, job_name_lst = [], [], [], []
job_id_lst, user_lst, status_lst, job_name_lst, working_directory_lst = (
[],
[],
[],
[],
[],
)
df = pandas.DataFrame(
{
"jobid": job_id_lst,
"user": user_lst,
"jobname": job_name_lst,
"status": status_lst,
"working_directory": working_directory_lst,
}
)
df.loc[df.status == "r", "status"] = "running"
Expand Down
5 changes: 3 additions & 2 deletions tests/test_queueadapter.py
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Expand Up @@ -137,7 +137,7 @@ def test_interfaces(self):
self.assertEqual(self.slurm._adapter._commands.delete_job_command, ["scancel"])
self.assertEqual(
self.slurm._adapter._commands.get_queue_status_command,
["squeue", "--format", "%A|%u|%t|%.15j", "--noheader"],
["squeue", "--format", "%A|%u|%t|%.15j|%Z", "--noheader"],
)
self.assertEqual(self.moab._adapter._commands.submit_job_command, ["msub"])
self.assertEqual(
Expand All @@ -148,7 +148,7 @@ def test_interfaces(self):
)
self.assertEqual(
self.gent._adapter._commands.get_queue_status_command,
["squeue", "--format", "%A|%u|%t|%.15j", "--noheader"],
["squeue", "--format", "%A|%u|%t|%.15j|%Z", "--noheader"],
)

def test__list_command_to_be_executed(self):
Expand Down Expand Up @@ -254,6 +254,7 @@ def test_convert_queue_status(self):
"user": df_merge.user,
"jobname": df_merge.jobname,
"status": df_merge.status,
"working_directory": [""] * len(df_merge),
}
)
self.assertTrue(
Expand Down