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Add column to determine if eligible for skip qc #2758

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@islean islean commented Dec 11, 2023

Description

As part of the ongoing developments to let some customers bypass our qc, we need to keep track of which applications are allowed. The ones currently allowed are described here https://github.com/Clinical-Genomics/project-planning/issues/485#issuecomment-1845032498. This PR adds a column to the Application table which shows whether the application is eligible for skipping qc.

Added

  • New is_eligible_for_skip_qc column to the Application table.

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-eligible-column -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 self-assigned this Dec 11, 2023
@clingen-sthlm clingen-sthlm temporarily deployed to stage December 11, 2023 14:20 Inactive
@clingen-sthlm clingen-sthlm temporarily deployed to stage December 11, 2023 14:27 Inactive
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islean commented Dec 11, 2023

image image image

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islean commented Dec 11, 2023

Downgrade successful:

INFO  [alembic.runtime.migration] Context impl MySQLImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.
fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
repository is clean
Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... /home/isak.ohlsson
done.
Log deploy... done.
cg, version 54.2.0
1d [isak.ohlsson@hasta:~] [S_base] 3m30s 

@islean islean marked this pull request as ready for review December 11, 2023 14:33
@islean islean requested a review from a team as a code owner December 11, 2023 14:33
def upgrade():
op.add_column(
"application",
sa.Column("is_eligible_for_skip_qc", sa.Boolean(), nullable=False),
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Might be necessary to provide a default value to the column here as well?

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Apparently not

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but maybe a good idea to set it to False as default, not sure.

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A bit unsure what it would add, given that the script has already been tested and added the column with False as default.

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👍

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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

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Looks good, but when are the values updated? Is it going to be a separate PR?

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islean commented Dec 12, 2023

Looks good, but when are the values updated? Is it going to be a separate PR?

It won't be an automatic thing, rather that lab or production need to be able to set this manually when adding new Applications. Or at least that is my understanding currently, need to check whether this solution is satisfactory.

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👍

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islean commented Dec 13, 2023

Upon discussion, this will start out as the customer's responsibility. So for now there is no reason to add this functionality.

@islean islean closed this Dec 13, 2023
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5 participants