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snakemake / snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster
MIT License
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fix: sbatch stderr parsing #2 #165

Closed cmeesters closed 2 weeks ago

cmeesters commented 2 weeks ago

next attempt to fix the behaviour described in #161

Summary by CodeRabbit

coderabbitai[bot] commented 2 weeks ago

[!CAUTION]

Review failed

The pull request is closed.

Walkthrough

The changes in this pull request focus on enhancing error handling in the snakemake_executor_plugin_slurm/__init__.py file during SLURM job submissions. The error-checking mechanism was refined to specifically look for the phrase "submission failed" in error outputs. Additionally, the run_job method now provides clearer feedback on job submission failures. Minor adjustments to comments and formatting were also made, but the overall control flow and method signatures remained unchanged.

Changes

File Path Change Summary
snakemake_executor_plugin_slurm/init.py Enhanced error handling in run_job method to check for specific error messages and improve feedback on job submission failures. Minor formatting and comment adjustments made.

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freekvh commented 2 weeks ago

I'm happy to report that it works as expected!

cmeesters commented 2 weeks ago

@fgvieira Hoi Filipe, time for another go? ;-)

fgvieira commented 2 weeks ago

Sure! :)

The two error messages are identical and that might make it a bit hard to figure out why it failed. Could we make one of the messages more specific?

cmeesters commented 2 weeks ago

Hm, I am open to suggestions, because, yes: to a human reader it looks redundant. I assume, that you are referring to lines 232-238? The thing is: one is catching an error from lauchning the process itself. If it occurs, the likely cause is a cluster failure of some kind, where sbatch does not work. The 2nd is checking, whether some weird admins overwrote sbatch and give additional output to stderr, which ordinarily only happens upon error. I have no idea how to merge this conceptionally. Do you?

fgvieira commented 2 weeks ago

I did not meant merge them, but maybe have slightly different error messages so it is easier to identify where the error comes from.

EDIT: made a suggestion

cmeesters commented 2 weeks ago

yeah, fine. Inserting a clarification and distinction is just good.

cmeesters commented 2 weeks ago

@fgvieira I truncated the error string again - otherwise the linter will fail. Breaking the string in a multiline string yielded ugly output. The current string is a compromise.