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Add nallo loqusdb upload #4344

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@peterpru peterpru commented Apr 16, 2025 •
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Description

This PR allows uploading of Nallo data to loqusdb using cg, it does not include being part of the cg upload command, and will be added later.

For the reviewer, this is a copy of the raredisease upload code, the only change being the added --snv-gq-only tag.

Added

  • Nallo upload to loqusDB using cg

Changed

Fixed

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 add-nallo-loqusdb-upload

How to test

  • Do cg -l DEBUG upload observations massivegopher
  • Do cg delete observations massivegopher

Expected test outcome

  • Check that the commands exit successfully uploading/deleteing observations to loqusdb
    image

Review

  • Tests executed by PP & SD
  • "Merge and deploy" approved by SD &
    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 ...

@peterpru peterpru added the nallo label Apr 16, 2025
@diitaz93 diitaz93 linked an issue Apr 29, 2025 that may be closed by this pull request
New loqusDB instance for Revio samples #4322
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diitaz93 approved these changes Apr 29, 2025
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LGTM 👍

@diitaz93 diitaz93 marked this pull request as ready for review April 29, 2025 10:50
@diitaz93 diitaz93 requested a review from a team as a code owner April 29, 2025 10:50
@diitaz93 diitaz93 marked this pull request as draft April 29, 2025 11:36
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Test on stage failed due to output error on vcf files from Nallo

2025-04-29 13:34:33 hasta.scilifelab.se loqusdb.commands.load[110472] WARNING GQ is not defined in vcf header

@sonarqubecloud SonarQubeCloud
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Quality Gate Passed Quality Gate passed

Issues
0 New issues
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

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@diitaz93 diitaz93 diitaz93 approved these changes

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New loqusDB instance for Revio samples
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