Missed pending decompression check

[islean]

Description

If one runs cg decompress case <case_id> when the decompression has already been started, the logging is weird, stating that files undergoing decompression are missing on Hasta, and does not start decompression of the remaining files for the sample. This PR adds a check for pending compressions.

Fixed

• We check for pending decompressions in the decompress flow.

How to prepare for test

• Ssh to relevant server (depending on type of change)
• Use stage: us
• Paxa the environment: paxa
• Install on stage (example for Hasta):

  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b fix-decompression-logging -a

How to test

• Do ...

Expected test outcome

• Check that ...
• Take a screenshot and attach or copy/paste the output.

Review

• Tests executed by
• "Merge and deploy" approved by
  Thanks for filling in who performed the code review and the test!

This version is a

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

• Document in ...
• Deploy this branch on ...
• Inform to ...

[seallard]

Nice find 👍

[islean]

Tested on Hasta with a provided sample which had some pending decompressions and now the decompression finishes as expected:

Check if pending compression file exists
Compression/decompression is pending for H3F22DSX5_sample_id_S14_L003
SPRING to FASTQ decompression not possible for sample_id
Check if pending compression file exists
Compression/decompression is pending for H3F22DSX5_sample_id_S14_L003
Spring file /home/proj/stage/housekeeper-bundles/sample_id/2022-12-04/H3F22DSX5_sample_id_S14_L003.spring is already being decompressed.
Check if pending compression file exists
/home/proj/stage/housekeeper-bundles/sample_id/2022-12-04/H3F22DSX5_sample_id_S14_L001.crunchy.pending.txt does not exist
Check if SPRING archive file exists
Check if FASTQ pair exists
/home/proj/stage/housekeeper-bundles/sample_id/2022-12-04/H3F22DSX5_sample_id_S14_L001_R1_001.fastq.gz does not exist
Decompression is possible
Decompressing /home/proj/stage/housekeeper-bundles/sample_id/2022-12-04/H3F22DSX5_sample_id_S14_L001.spring to FASTQ format for sample sample_id
Creating pending flag /home/proj/stage/housekeeper-bundles/sample_id/2022-12-04/H3F22DSX5_sample_id_S14_L001.crunchy.pending.txt
Fetch SPRING metadata from /home/proj/stage/housekeeper-bundles/sample_id/2022-12-04/H3F22DSX5_sample_id_S14_L001.json
Created temporary dir /home/proj/stage/housekeeper-bundles/sample_id/2022-12-04/spring_hbv1pa70_decompress
Submit sbatch /home/proj/stage/housekeeper-bundles/sample_id/2022-12-04/H3F22DSX5_sample_id_S14_L001_decompress_spring.sh
Running command sbatch /home/proj/stage/housekeeper-bundles/sample_id/2022-12-04/H3F22DSX5_sample_id_S14_L001_decompress_spring.sh
Submitted batch job 5468609
Spring decompression running as job 5468609

[diitaz93]

Bra jobbat ⭐

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

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