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Trailblazer priority control samples #3991

Merged
merged 22 commits into from
Dec 5, 2024
Merged

Trailblazer priority control samples #3991

merged 22 commits into from
Dec 5, 2024

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eliottBo
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@eliottBo eliottBo commented Dec 2, 2024 •
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Description

This PR closes #3889. The controls currently get express priority in TB. This PR will change this and the control cases will get the priority according to what is stated in statusDB however the slurm QOS will remain equivalent to express.

Fixed

  • Controls ran with slurm qos express have the priority in trailblazer corresponding to the priority in statusDB

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 [THIS-BRANCH-NAME] -a

How to test

  • Start a control case and check in TB stage the displayed priority

Expected test outcome

  • Check that the priority is not express in TB
  • Take a screenshot and attach or copy/paste the output.

Review

  • Tests executed by ELB
  • "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 ...

eliottBo and others added 17 commits December 2, 2024 10:17
@eliottBo
Add method to retrieve case priority for Trailblazer
e9164bc
@eliottBo
Define TrailblazerPriority
cd56d34
@eliottBo
Define map_to_trailblazer_priority
92731c3
@eliottBo
Replace slurm_quality_of_service by trailblazer priority
789fa9f
@eliottBo
Replace SlurmQos with TrailblazerPriority in DemultiplexingAPI
d7b111e
@eliottBo
Refactor DeliveryRsyncService to use TrailblazerPriority instead of S…
18bfe86 
…lurmQos
@eliottBo
Add test for retrieving TrailblazerPriority based on case priority
8a4388b
@eliottBo
Update DeliverFilesService to use map_to_trailblazer_priority for cas…
bb2e90c 
…e priority
@eliottBo
Update RawDataAnalysisService to use map_to_trailblazer_priority for …
686ca1f 
…case priority
@eliottBo
Update map_to_trailblazer_priority to reflect new priority mappings
21f5497
@eliottBo
Change trailblazer_priority property to return TrailblazerPriority type
3d4edd9
@eliottBo
Put back slurm_quality_of_service
51a97c0
@eliottBo
typo fix
954e3bb
@eliottBo
Add tests for map_to_trailblazer_priority and update docstring for te…
989e32b 
…st_get_trailblazer_priority
@eliottBo
Merge branch 'master' into trailblazer-priority
699e839
@eliottBo
Black formatting
5086180
@eliottBo
Merge branch 'trailblazer-priority' of https://github.com/Clinical-Ge…
38ce717 
…nomics/cg into trailblazer-priority
@eliottBo eliottBo marked this pull request as ready for review December 3, 2024 11:55
@eliottBo eliottBo requested a review from a team as a code owner December 3, 2024 11:55
@eliottBo eliottBo changed the title Trailblazer priority Trailblazer priority control samples Dec 4, 2024
@eliottBo eliottBo self-assigned this Dec 4, 2024
islean
islean approved these changes Dec 4, 2024
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@islean islean left a comment

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Looks good to me!

cg/meta/workflow/analysis.py Outdated Show resolved Hide resolved
cg/meta/workflow/utils/utils.py Outdated Show resolved Hide resolved
tests/meta/workflow/test_analysis.py Show resolved Hide resolved
@sonarqubecloud SonarQubeCloud
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sonarqubecloud bot commented Dec 4, 2024

Quality Gate Passed Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

@eliottBo eliottBo requested a review from islean December 4, 2024 12:25
@eliottBo
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eliottBo commented Dec 5, 2024 •
edited
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Tests in stage:

This works as intended

Slurm quality of service express when submitting

Screenshot 2024-12-05 at 10 07 45

Trailblazer priority High

Screenshot 2024-12-05 at 10 07 13

@eliottBo eliottBo merged commit c624ab0 into master Dec 5, 2024
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@eliottBo eliottBo deleted the trailblazer-priority branch December 5, 2024 09:28
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eliottBo commented Dec 5, 2024

Deployment:

Stage

Screenshot 2024-12-05 at 10 40 40

Screenshot 2024-12-05 at 10 37 24

Production:

Screenshot 2024-12-05 at 10 45 56

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@islean islean Awaiting requested review from islean

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Successfully merging this pull request may close these issues.

Bug: Control samples show up as 'Express' in Trailblazer
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@eliottBo @islean