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Add sample name validation for microbial fastq #4019

Merged
merged 3 commits into from
Dec 17, 2024
Merged

Add sample name validation for microbial fastq #4019

merged 3 commits into from
Dec 17, 2024

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islean
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@islean islean commented Dec 11, 2024

Description

This PR suggests that we disallow any orders reusing sample names within microbial fastq.

Added

Changed

  • Microbial fastq orders containing samples which the customer has used in a previous order do not pass validation.

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 [THIS-BRANCH-NAME] -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 ...

@islean islean requested a review from a team as a code owner December 11, 2024 13:17
ChrOertlin
ChrOertlin approved these changes Dec 12, 2024
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Looks good. We should consider splitting these order types though and treat each as their own instead of solving this with if statements. I think we would gain a bit more clarity that way.

cg/services/orders/validate_order_services/validate_microbial_order.py Show resolved Hide resolved
diitaz93
diitaz93 approved these changes Dec 16, 2024
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looks good 👍

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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

@clingen-sthlm clingen-sthlm temporarily deployed to stage December 17, 2024 08:15 Inactive
@islean
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islean commented Dec 17, 2024

Tested in stage:

image

@islean islean merged commit d1004b4 into master Dec 17, 2024
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@islean islean deleted the add-microbial-fastq-validation branch December 17, 2024 08:19
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islean commented Dec 17, 2024

Deployed to the VMs

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@ChrOertlin ChrOertlin ChrOertlin approved these changes

@diitaz93 diitaz93 diitaz93 approved these changes

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4 participants
@islean @ChrOertlin @diitaz93 @clingen-sthlm