Remove is deleted

[henrikstranneheim]

Description

Added

Changed

• Remove is deleted

Fixed

How to prepare for test

• ssh to hasta (depending on type of change)
• activate stage: us
• request trailblazer-stage on hasta: paxa
• install on stage:

  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_trailblazer -t trailblazer -b remove-is_deleted -a

• ssh to clinical-db (depending on type of change)
• install on stage:
  bash /home/proj/production/servers/resources/clinical-db.scilifelab.se/update-trailblazer-ui-stage.sh [THIS-BRANCH-NAME]

How to test

• login to ...
• 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

[henrikstranneheim]

Clinical-Genomics/cg#2790

[ChrOertlin]

Nice cleanup!

[seallard]

Looks good! We do call the endpoint from cg though, so we should create a separate PR which removes that call as well in cg. This PR can be merged once this has been merged Clinical-Genomics/cg#2817

[henrikstranneheim]

CLI and API 👍

trailblazer scan
Error updating analysis for: case - setcolt : [Errno 13] Permission denied: '/home/proj/production/microbial/results/reports/trailblazer/ACC9963_slurm_ids.yaml'
Error updating analysis for: case - handyshrimp : [Errno 2] No such file or directory: '/home/proj/production/mutant/cases/handyshrimp/results/trailblazer_config.yaml'
Error updating analysis for: case - divinetomcat : [Errno 13] Permission denied: '/home/proj/production/microbial/results/reports/trailblazer/ACC5119_slurm_ids.yaml'
Error updating analysis for: case - HW2V2DRX2 : [Errno 2] No such file or directory: '/home/proj/production/flowcells/novaseq/runs/230504_A00689_0805_AHW2V2DRX2/slurm_job_ids.yaml'
Error updating analysis for: case - savingstag : [Errno 2] No such file or directory: '/home/proj/production/mutant/cases/savingstag/results/trailblazer_config.yaml'
Error updating analysis for: case - topewe : [Errno 13] Permission denied: '/home/proj/production/microbial/results/reports/trailblazer/ACC12566_slurm_ids.yaml'
Error updating analysis for: case - fullgoat : [Errno 13] Permission denied: '/home/proj/production/microbial/results/reports/trailblazer/ACC12567_slurm_ids.yaml'
Error updating analysis for: case - bolddrum : [Errno 13] Permission denied: '/home/proj/production/microbial/results/reports/trailblazer/ACC12696_slurm_ids.yaml'
Error updating analysis for: case - abovehusky : [Errno 13] Permission denied: '/home/proj/production/microbial/results/reports/trailblazer/ACC12791_slurm_ids.yaml'
Error updating analysis for: case - chiefgannet : [Errno 13] Permission denied: '/home/proj/production/microbial/results/reports/trailblazer/ACC12956_slurm_ids.yaml'
Error updating analysis for: case - grandoyster : [Errno 13] Permission denied: '/home/proj/production/microbial/results/reports/trailblazer/ACC12967_slurm_ids.yaml'
Status in Tower: coolkodiak - 282044 - WPjrjs23yxQwq
Error logging case - coolkodiak :  JSONDecodeError
slurm_load_jobs error: Invalid job id specified
Error updating analysis for: case - HK33MDRX3 : Command '['squeue', '--jobs', '5793325', '--states=all', '--format', '%A,%j,%T,%l,%M,%S']' returned non-zero exit status 1.
slurm_load_jobs error: Invalid job id specified
Error updating analysis for: case - HGYFNBCX2 : Command '['squeue', '--jobs', '5793259', '--states=all', '--format', '%A,%j,%T,%l,%M,%S']' returned non-zero exit status 1.
slurm_load_jobs error: Invalid job id specified
Error updating analysis for: case - HM2LNBCX2 : Command '['squeue', '--jobs', '5793260', '--states=all', '--format', '%A,%j,%T,%l,%M,%S']' returned non-zero exit status 1.
slurm_load_jobs error: Invalid job id specified
Error updating analysis for: case - HK33MDRX3 : Command '['squeue', '--jobs', '5793325', '--states=all', '--format', '%A,%j,%T,%l,%M,%S']' returned non-zero exit status 1.
Status in Tower: bossyeti - 282911 - 2VkkGmKqN3ODMw
Error logging case - bossyeti :  ValidationError
Status in Tower: bossmink - 282987 - 2bBeabAPHeAl0P
Updated status unitedbeagle - 282989: completed
Updated status largeturtle_rsync - 282990: completed
Updated status lightkodiak_rsync - 282991: completed
Updated status wholecivet_rsync - 282992: completed
Updated status upwardstork_rsync - 282993: completed
Updated status suitedgrub_rsync - 282994: completed
Updated status suitedgrub_rsync - 282995: completed
Updated status suitedgrub_rsync - 282996: completed
Updated status upwardstork_rsync - 282997: completed
Updated status wholecivet_rsync - 282998: completed
Updated status equalbug_rsync - 282999: failed
Updated status uphippo_rsync - 283000: completed
Updated status stableraven_rsync - 283001: completed
Updated status uphippo_rsync - 283002: completed
Updated status equalbug_rsync - 283003: failed
Updated status uphippo_rsync - 283004: completed
Updated status equalbug_rsync - 283005: failed
Updated status equalbug_rsync - 283006: failed
Updated status discretelocust_partial - 283007: failed
All analyses updated!

[seallard]

👍

[sonarqubecloud]

Quality Gate passed

Kudos, no new issues were introduced!

0 New issues
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud