(Archiving) Add cascade property to Archive

islean commented 11 months ago

Description

When deleting a file entry in Housekeeper, any associated entry in the Archive table (i.e. with a matching file_id) should also be deleted. Currently one can not delete a file when there is an archive entry associated to it. This PR adds that cascade property and adds some tests.

Fixed

Deleting a file now cascades to the archive table.

Testing

How to prepare for test

[ ] ssh to Hasta
[ ] Test your branch with

housekeeper-test-deploy cascade-archive
housekeeper-test <command here>

Any migrations need to be applied manually with alembic against the stage database.

How to test

[ ] login to ...
[ ] do ...

Expected test outcome

[ ] check that ...
[ ] Take a screenshot and attach or copy/paste the output.

Review

[ ] code approved by
[ ] 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
[x] PATCH - when you make backwards compatible bug fixes or documentation/instructions

islean commented 11 months ago

Currently in stage when trying to delete a file with an associated Archive entry:

AssertionError: Dependency rule tried to blank-out primary key column 'archive.file_id' on instance '<Archive at 0x7f6a1cec2b90>'
1d [isak.ohlsson@hasta:~] [S_base] 8s 1 $

islean commented 11 months ago

In the feature branch:

θ60° 1d [isak.ohlsson@hasta:~] [S_base] $ housekeeper-test delete file 5057208
2023-12-11 15:59:06 hasta.scilifelab.se housekeeper.cli.core[167283] INFO Use root path /home/proj/stage/housekeeper-bundles
Remove file /home/proj/stage/housekeeper-bundles/isaks_test_bundle/2023-12-06/isaks_test_spring_file.spring from file system and database? [y/N]: y
2023-12-11 15:59:22 hasta.scilifelab.se housekeeper.cli.delete[167283] INFO file deleted
θ60° 1d [isak.ohlsson@hasta:~] [S_base] 21s $

sonarcloud[bot] commented 11 months ago

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

islean commented 11 months ago

Deployed to stage and production:

Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: /home/proj/stage/singularity_containers/housekeeper_temp.sif
Successfully pulled the latest Housekeeper image.
1d [isak.ohlsson@hasta:~] [base] 17s $

Clinical-Genomics / housekeeper