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fix: quoting parameters #355

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Merged
merged 10 commits into from
Sep 18, 2025
Merged

fix: quoting parameters #355

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7b9b425
fix: quoting every quotable paramter
cmeesters Sep 15, 2025
608cf05
fix: only format strings, where format strings are needed
cmeesters Sep 15, 2025
3b8e558
fix: testing for None is not necessary
cmeesters Sep 15, 2025
79fe868
fix: checking for str type for qos values was not necessary
cmeesters Sep 15, 2025
862d2df
fix: adapted code due to latest changes
cmeesters Sep 15, 2025
9a24e1c
refactor: comment about account/partition quoting is added
cmeesters Sep 15, 2025
3e45398
fix: allow for empty workdir
cmeesters Sep 15, 2025
c1f6ec4
fix: need to return empty string, too. for safe_quote
cmeesters Sep 16, 2025
a1ed3ff
fix: empty strings for constraint and qos allowed
cmeesters Sep 16, 2025
5ed6686
fix: formatting
cmeesters Sep 16, 2025
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27 changes: 19 additions & 8 deletions snakemake_executor_plugin_slurm/submit_string.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,16 @@
from snakemake_executor_plugin_slurm_jobstep import get_cpu_setting
from types import SimpleNamespace
import shlex


def safe_quote(value):
"""
Safely quote a parameter value using shlex.quote.
Handles None values and converts to string if needed.
"""
if value is None:
return ""
return shlex.quote(str(value))


def get_submit_command(job, params):
Expand All @@ -12,10 +23,10 @@ def get_submit_command(job, params):
call = (
f"sbatch "
f"--parsable "
f"--job-name {params.run_uuid} "
f'--output "{params.slurm_logfile}" '
f"--job-name {safe_quote(params.run_uuid)} "
f"--output {safe_quote(params.slurm_logfile)} "
f"--export=ALL "
f'--comment "{params.comment_str}"'
f"--comment {safe_quote(params.comment_str)}"
)

# No accout or partition checking is required, here.
Expand All @@ -29,18 +40,18 @@ def get_submit_command(job, params):
call += f" {params.partition}"

if job.resources.get("clusters"):
call += f" --clusters {job.resources.clusters}"
call += f" --clusters {safe_quote(job.resources.clusters)}"

if job.resources.get("runtime"):
call += f" -t {job.resources.runtime}"
call += f" -t {safe_quote(job.resources.runtime)}"

if job.resources.get("constraint") or isinstance(
job.resources.get("constraint"), str
):
call += f" -C '{job.resources.get('constraint')}'"
call += f" -C {safe_quote(job.resources.get('constraint'))}"

if job.resources.get("qos") or isinstance(job.resources.get("qos"), str):
call += f" --qos='{job.resources.qos}'"
call += f" --qos={safe_quote(job.resources.qos)}"

if job.resources.get("mem_mb_per_cpu"):
call += f" --mem-per-cpu {job.resources.mem_mb_per_cpu}"
Expand Down Expand Up @@ -77,6 +88,6 @@ def get_submit_command(job, params):
# ensure that workdir is set correctly
# use short argument as this is the same in all slurm versions
# (see https://github.com/snakemake/snakemake/issues/2014)
call += f" -D '{params.workdir}'"
call += f" -D {safe_quote(params.workdir)}"

return call
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