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fix parse_jobs_list_output parsing issues with SGE #52

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fix parse_jobs_list_output parsing issues with SGE #52

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622fc15
fix parse_jobs_list_output parsing issues
QuantumChemist Dec 13, 2024
9ab7041
removing some debugging prints
QuantumChemist Dec 13, 2024
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66 changes: 47 additions & 19 deletions src/qtoolkit/io/sge.py
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Original file line number Diff line number Diff line change
Expand Up @@ -260,11 +260,11 @@ def parse_job_output(self, exit_code, stdout, stderr) -> QJob | None: # aiida s
),
)

def _get_element_text(self, parent, tag_name):
def _get_element_text(self, parent, tag_name, default=None):
elements = parent.getElementsByTagName(tag_name)
if elements:
if elements and elements[0].childNodes:
return elements[0].childNodes[0].data.strip()
return None
return default

def _safe_int(self, value: str | None) -> int | None:
if value is None:
Expand Down Expand Up @@ -294,41 +294,69 @@ def parse_jobs_list_output(self, exit_code, stdout, stderr) -> list[QJob]:
except xml.parsers.expat.ExpatError:
raise OutputParsingError("XML parsing of stdout failed")

job_elements = xmldata.getElementsByTagName("job_list")
jobs_list = []
# Determine the structure of the XML
if xmldata.getElementsByTagName("job_list"):
# Handle job_list_u.xml structure
job_elements = xmldata.getElementsByTagName("job_list")
elif xmldata.getElementsByTagName("element"):
# Handle job_list.xml structure
job_elements = xmldata.getElementsByTagName("element")
else:
raise OutputParsingError("No recognizable job elements found in XML data")

for job_element in job_elements:
qjob = QJob()
qjob.job_id = self._get_element_text(job_element, "JB_job_number")
job_state_string = self._get_element_text(job_element, "state")
qjob.job_id = self._get_element_text(
job_element, "JB_job_number", default="Unknown"
)
qjob.name = self._get_element_text(
job_element, "JB_job_name", default="Unknown"
)
qjob.username = self._get_element_text(
job_element, "JB_owner", default="Unknown"
)

# Determine job state
job_state_string = self._get_element_text(
job_element, "state", default=None
)
if job_state_string is None:
job_state_string = self._get_element_text(
job_element, "JAT_status", default="Unknown"
)

try:
sge_job_state = SGEState(job_state_string)
qjob.sub_state = sge_job_state
qjob.state = sge_job_state.qstate
except ValueError:
raise OutputParsingError(
f"Unknown job state {job_state_string} for job id {qjob.job_id}"
print(
f"Unknown job state: {job_state_string} for job ID: {qjob.job_id}"
)
qjob.sub_state = None
qjob.state = None

qjob.sub_state = sge_job_state
qjob.state = sge_job_state.qstate
qjob.username = self._get_element_text(job_element, "JB_owner")
qjob.name = self._get_element_text(job_element, "JB_name")

# Collect additional job information
info = QJobInfo()
info.nodes = self._safe_int(
self._get_element_text(job_element, "num_nodes")
self._get_element_text(job_element, "num_nodes", default="0")
)
info.cpus = self._safe_int(
self._get_element_text(job_element, "num_proc", default="0")
)
info.cpus = self._safe_int(self._get_element_text(job_element, "num_proc"))
info.memory_per_cpu = self._convert_memory_str(
self._get_element_text(job_element, "hard resource_list.mem_free")
self._get_element_text(
job_element, "hard resource_list.mem_free", default="0"
)
)
info.partition = self._get_element_text(job_element, "queue")
info.time_limit = self._convert_str_to_time(
self._get_element_text(job_element, "hard resource_list.h_rt")
self._get_element_text(
job_element, "hard resource_list.h_rt", default="0"
)
)

qjob.info = info

jobs_list.append(qjob)

return jobs_list
Expand Down
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