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Refactor get latest analysis #264

Merged
merged 9 commits into from
Aug 29, 2023
Merged

Refactor get latest analysis #264

merged 9 commits into from
Aug 29, 2023

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henrikstranneheim
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@henrikstranneheim henrikstranneheim commented Aug 24, 2023 •
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Description

Refactor get_latest_analysis and migrate to CRUD.

Added

  • Tests

Changed

  • Refactor get_latest_analysis and migrate to CRUD.
  • Refactor tests
  • Rename case_id fixtures to case_name

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 refactor_get_latest_analysis -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 henrikstranneheim added the Project Task Part of a quarterly project label Aug 24, 2023
@henrikstranneheim henrikstranneheim requested a review from a team as a code owner August 24, 2023 08:43
@henrikstranneheim henrikstranneheim self-assigned this Aug 24, 2023
islean
islean approved these changes Aug 28, 2023
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Looks nice! 🔥

tests/cli/test_cli_core.py Outdated Show resolved Hide resolved
tests/cli/test_cli_core.py Show resolved Hide resolved
tests/cli/test_cli_core.py Show resolved Hide resolved
trailblazer/store/api.py Show resolved Hide resolved
@henrikstranneheim
Merge branch 'master' into refactor_get_latest_analysis
b8aff88 
# Conflicts:
#	tests/store/test_store_api.py
#	trailblazer/store/api.py
@henrikstranneheim
fix(review):
acd64c0
@sonarcloud
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sonarcloud bot commented Aug 28, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@clingen-sthlm clingen-sthlm temporarily deployed to stage August 29, 2023 12:25 Inactive
@henrikstranneheim
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CLI ✅

θ65° [henrik.stranneheim@hasta:~] [S_base] 2m51s $ trailblazer scan
slurm_load_jobs error: Invalid job id specified
Error updating analysis for: case - HYG7YDSXX : CalledProcessError
Error updating analysis for: case - gentleamoeba : FileNotFoundError
Error updating analysis for: case - masterimpala : FileNotFoundError
Error updating analysis for: case - starakita : FileNotFoundError
Error updating analysis for: case - goodrodent : FileNotFoundError
Error updating analysis for: case - strongbug : FileNotFoundError
Error updating analysis for: case - masterwombat : FileNotFoundError
Error updating analysis for: case - warmcalf : FileNotFoundError
Error updating analysis for: case - jointstag : FileNotFoundError
Error updating analysis for: case - finerobin : FileNotFoundError
Error updating analysis for: case - wantedhen : FileNotFoundError
Error updating analysis for: case - cleanleech : PermissionError
Error updating analysis for: case - socialearwig : FileNotFoundError
Error updating analysis for: case - topsdodo : FileNotFoundError
Error updating analysis for: case - usablefeline : PermissionError
Error updating analysis for: case - 233471 : FileNotFoundError
Error updating analysis for: case - crispshiner : FileNotFoundError
Error updating analysis for: case - supertiger : PermissionError
Error updating analysis for: case - fullfrog : FileNotFoundError
Error updating analysis for: case - toplouse : FileNotFoundError
Error updating analysis for: case - sunnycondor : FileNotFoundError
Error updating analysis for: case - keyeft : FileNotFoundError
Error updating analysis for: case - robustalien : PermissionError
Error updating analysis for: case - busyowl : PermissionError
Error updating analysis for: case - boldhound : PermissionError
Error updating analysis for: case - vastboar : FileNotFoundError
Error updating analysis for: case - topsworm : PermissionError
Error updating analysis for: case - setcolt : PermissionError
Error updating analysis for: case - proudfish : PermissionError
Error updating analysis for: case - funnyaphid : FileNotFoundError
Error updating analysis for: case - onestag : PermissionError
Error updating analysis for: case - newgopher : PermissionError
Error updating analysis for: case - helpedlab : MissingSqueueOutput
Error updating analysis for: case - goodbengal : MissingSqueueOutput
Error updating analysis for: case - grandaphid : PermissionError
All analyses updated!
[henrik.stranneheim@hasta:~] [S_base] 15s $ trailblazer ls
272007 | richurchin 2023-08-24 [WGS/QC]
272004 | truepigeon 2023-08-22 [WTS/FAILED]
272001 | cuddlyhen 2023-08-17 [WTS/FAILED]
271975 | ampleray 2023-07-25 [WTS/COMPLETED] - None
271971 | acetuna 2023-07-24 [TGS/COMPLETED] - None
271970 | uphippo 2023-07-24 [TGS/FAILED]
271969 | equalbug 2023-07-24 [TGS/FAILED]
271968 | unitedbeagle 2023-07-24 [TGS/COMPLETED] - None
271967 | setamoeba 2023-07-24 [TGS/COMPLETED] - None
271966 | fleetjay 2023-07-24 [WGS/FAILED]
271965 | civilsole 2023-07-24 [WGS/FAILED]
271957 | uphippo_rsync 2023-07-17 [OTHER/FAILED]
271955 | setamoeba_rsync 2023-07-17 [OTHER/FAILED]
271907 | equalbug_rsync 2023-07-07 [OTHER/FAILED]
271906 | equalbug_rsync 2023-07-07 [OTHER/FAILED]
271905 | equalbug_rsync 2023-07-07 [OTHER/FAILED]
271904 | H27CLDRX3 2023-06-30 [OTHER/COMPLETED] - None
271903 | intentcorgi 2023-06-27 [WGS/COMPLETED] - None
271902 | sharpwhale 2023-06-26 [WGS/COMPLETED] - None
271901 | safeguinea 2023-06-26 [WGS/COMPLETED] - None
271900 | onemite 2023-06-26 [WGS/COMPLETED] - None
271899 | brightcaiman 2023-06-26 [WGS/COMPLETED] - None
271897 | tenderoriole 2023-06-22 [TGS/COMPLETED] - None
271896 | strongbison 2023-06-22 [WES/COMPLETED] - None
271894 | sharppigeon 2023-06-22 [WGS/COMPLETED] - None
271892 | proudcougar 2023-06-22 [WGS/COMPLETED] - None
271890 | nextjackal 2023-06-22 [WGS/COMPLETED] - None
271889 | modernmule 2023-06-22 [WGS/COMPLETED] - None
271888 | intentmayfly 2023-06-22 [WGS/COMPLETED] - None
271887 | kindcaiman 2023-06-22 [WGS/COMPLETED] - None

Api ✅

Screenshot 2023-08-29 at 14 30 21

@henrikstranneheim henrikstranneheim merged commit 506e0d4 into master Aug 29, 2023
6 checks passed
@henrikstranneheim henrikstranneheim deleted the refactor_get_latest_analysis branch August 29, 2023 12:33
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@islean islean islean approved these changes

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