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🐛 Fix bug for legacy LSF system (v8.3) #35

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🐛 Fix bug for legacy LSF system (v8.3) #35

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15 changes: 14 additions & 1 deletion {{cookiecutter.profile_name}}/lsf_status.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,17 @@ class UnknownStatusLine(Exception):
ZOMBIE = "ZOMBI"


def extract_job_status(bjobs_output):
import re

response = bjobs_output.split('\n')
if len(response) != 2:
return "UNKNOWN"

response = response[1]
return re.split("[\\t\\r\\n ]+", response)[2]


class StatusChecker:
SUCCESS = "success"
RUNNING = "running"
Expand Down Expand Up @@ -70,7 +81,7 @@ def outlog(self) -> str:

@property
def bjobs_query_cmd(self) -> str:
return "bjobs -o 'stat' -noheader {jobid}".format(jobid=self.jobid)
return "bjobs {jobid}".format(jobid=self.jobid)

def _handle_unknown_job(self) -> str:
if self.kill_unknown:
Expand Down Expand Up @@ -105,6 +116,8 @@ def _query_status_using_bjobs(self) -> str:
)
)

output_stream = extract_job_status(output_stream)

if output_stream == UNKNOWN:
return self._handle_unknown_job()

Expand Down