From 860e0a8f1ed5424587564ab04f1318cf8ad27e05 Mon Sep 17 00:00:00 2001 From: Vincent Janvid <69356202+Vince-janv@users.noreply.github.com> Date: Tue, 15 Oct 2024 09:55:36 +0200 Subject: [PATCH] Fix(SPRING) Change decompression SLURM QOS to high (#3836)(patch) ## Description This PR changes the SLURM quality of service from low to high for SPRING decompression jobs. See #3804 ### Changed - Decompression SLURM QOS to high --- cg/apps/crunchy/crunchy.py | 2 +- tests/apps/crunchy/test_compress_fastq.py | 18 ++++++++++-------- 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/cg/apps/crunchy/crunchy.py b/cg/apps/crunchy/crunchy.py index adb2db33ed..8049d49245 100644 --- a/cg/apps/crunchy/crunchy.py +++ b/cg/apps/crunchy/crunchy.py @@ -294,7 +294,7 @@ def spring_to_fastq(self, compression_obj: CompressionData, sample_id: str = "") log_dir=log_dir.as_posix(), memory=self.slurm_memory, number_tasks=self.slurm_number_tasks, - quality_of_service=SlurmQos.LOW, + quality_of_service=SlurmQos.HIGH, ) sbatch_content: str = self.slurm_api.generate_sbatch_content(sbatch_parameters) sbatch_path = files.get_spring_to_fastq_sbatch_path( diff --git a/tests/apps/crunchy/test_compress_fastq.py b/tests/apps/crunchy/test_compress_fastq.py index eed56fb15a..7168ab0818 100644 --- a/tests/apps/crunchy/test_compress_fastq.py +++ b/tests/apps/crunchy/test_compress_fastq.py @@ -2,6 +2,7 @@ import logging from pathlib import Path +from unittest import mock import pytest from pydantic import ValidationError @@ -123,7 +124,6 @@ def test_spring_to_fastq( compression_object: CompressionData, spring_metadata_file: Path, crunchy_config: dict, - mocker, ): """Test SPRING to FASTQ method @@ -132,15 +132,17 @@ def test_spring_to_fastq( """ # GIVEN a crunchy-api given an existing SPRING metadata file assert spring_metadata_file.exists() - mocker_submit_sbatch = mocker.patch.object(SlurmAPI, "submit_sbatch") + crunchy_api = CrunchyAPI(crunchy_config) # GIVEN that the pending path does not exist - assert compression_object.pending_exists() is False + assert not compression_object.pending_exists() - # WHEN calling bam_to_cram method on bam-path - crunchy_api.spring_to_fastq(compression_obj=compression_object) + with mock.patch.object(SlurmAPI, "submit_sbatch", return_value=123456) as submit_sbatch: + # WHEN calling bam_to_cram method on bam-path + crunchy_api.spring_to_fastq(compression_obj=compression_object) + + # THEN _submit_sbatch method is and the qos is high + assert "--qos=high" in submit_sbatch.call_args[1]["sbatch_content"] - # THEN _submit_sbatch method is called - mocker_submit_sbatch.assert_called() # THEN assert that the pending path was created - assert compression_object.pending_exists() is True + assert compression_object.pending_exists()