add IlluminaFlowCellDevice model

[diitaz93]

Description

Closes https://github.com/Clinical-Genomics/add-new-tech/issues/2

Added

• IlluminaFlowCellDevice model
• Alembic migration

How to prepare for test

• Ssh to relevant server (depending on type of change)

How to test

• Do alembic -c $ALEMBIC_CG_STAGE upgrade fe23de4ed528
• Verify that the new alembic version is fe23de4ed528
• Verify that the new table ìllumina_flow_cell` exists
• Create a new entry in the run_device table of type ILLUMINA
• Create a new entry in the table illumina_flow_cell with the same id as the previous entry and mode 10B.
• Query the new table filtering by flow cells with mode == "10B"
• Do alembic -c $ALEMBIC_CG_STAGE downgrade 6e6c36d5157b

Expected test outcome

• Check that the filtering returns a flow cell and no errors are raised

Review

• Tests executed by SD
• "Merge and deploy" approved by CO
  Thanks for filling in who performed the code review and the test!

This version is a

• PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

• Deployed to stage:

Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... /home/js.diazboada
done.
Log deploy... done.
cg, version 60.7.25
[js.diazboada@hasta:~] [S_base] $ up

• Deployed to production:

Log deploy... done.
cg, version 60.7.25
remote: Enumerating objects: 615, done.
remote: Counting objects: 100% (615/615), done.
remote: Compressing objects: 100% (252/252), done.
remote: Total 615 (delta 452), reused 454 (delta 362), pack-reused 0
Receiving objects: 100% (615/615), 184.00 KiB | 0 bytes/s, done.
Resolving deltas: 100% (452/452), completed with 64 local objects.
From https://github.com/Clinical-Genomics/cg
   b511844..b624356  master     -> origin/master
   52e9972..27c2ff6  fix_dry_run_conflict -> origin/fix_dry_run_conflict
 * [new branch]      patch_taxprofiler_versions -> origin/patch_taxprofiler_versions
   fdb5e1a..4f27930  raredisease_store -> origin/raredisease_store
   4056ffa..92def7a  remove-FFPE-from-loqusdb -> origin/remove-FFPE-from-loqusdb
 * [new tag]         v60.7.25   -> v60.7.25
Already on 'master'
Your branch is behind 'origin/master' by 2 commits, and can be fast-forwarded.
  (use "git pull" to update your local branch)
Updating b511844..b624356
Fast-forward
 .bumpversion.cfg                                                   |  2 +-
 alembic/versions/2024_05_17_fe23de4ed528_add_illumina_flow_cell.py | 31 +++++++++++++++++++++++++++++++
 cg/__init__.py                                                     |  2 +-
 cg/constants/demultiplexing.py                                     |  2 +-
 cg/store/models.py                                                 | 13 +++++++++++++
 pyproject.toml                                                     |  2 +-
 6 files changed, 48 insertions(+), 4 deletions(-)
 create mode 100644 alembic/versions/2024_05_17_fe23de4ed528_add_illumina_flow_cell.py
/home/js.diazboada
INFO  [alembic.runtime.migration] Context impl MySQLImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.
INFO  [alembic.runtime.migration] Running upgrade 6e6c36d5157b -> fe23de4ed528, add_illumina_flow_cell
[js.diazboada@hasta:~] [P_base] $ 

[diitaz93]

Apparently what we called "flow cell model" (10B, 25B) is officially called "type", which is the field we use for polymorphism. I changed it to flow_cell_type, any other suggestions? @Vince-janv @ChrOertlin

[Vince-janv]

I think short and descriptive names for the fields are better. We already have a clear name for the Model, so we don't need to duplicate the information in the field name

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

[ChrOertlin]

Looks good