Delete clinvar_export app

[xiamaz]

@stolpeo Export the database and give tsv to @xiamaz

[xiamaz]

other steps will need to follow

[stolpeo]

Export added to Sharepoint under VarFish DHA/Data Dump/clinvar_export.tgz

[stolpeo]

Deleting an app that is registered as a ProjectAppPlugin is more complicated than thought. The plugins.py file can't be deleted because it is somehow required by the management command. The only thing is to add status = 2 to the plugin. But starting the server still searches for the app and requires an url entrypoint for the plugin, which will in return require views etc. In short, currently SODAR core does not allow to remove project app plugins.

[xiamaz]

@stolpeo Please check if this has been communicated as a SODAR-core ticket.

[stolpeo]

@mikkonie refers to the djangoplugins module that is used. apparently it is not developed anymore. any attempt to disable the app did not work.

[xiamaz]

After discussion, Manuel will handle this

[holtgrewe]

As written above by @stolpeo, we cannot completely delete the clinvar_export app because

1. migrations have to stay so all database models are removed
   • https://docs.djangoproject.com/en/5.0/howto/delete-app/ (also mentioned by @stolpeo earlier)
2. there is the described issue with the django plugins that we cannot solve right now

IIRC, @stolpe referred to @mikkonie's suggestion to address (2) by a two-step deployment process but I don't know whether we expect that to still work. For removing the models, we need a two-step deployment anyway (see django docs howto above).

We can work around the "clinvar_export" icon on the left being displayed by providing an invalid required permission as also done for the svs app. Superusers will still see the icon but normal users won't, so it's not an issue.

https://github.com/varfish-org/varfish-server/blob/909c4caae54b8253fafc235440d95757a007ec2c/backend/svs/plugins.py#L29-L30

I suggest the following resolution:

• remove everything EXCEPT for the plugin and the migrations
  • as far as I can see, @stolpeo already did this on the 1664-delete-clinvar_export-app branch
  • @stolpeo any other thing that should remain?
• document and mark the clinvar_export app to need a two-step-deployment for final removal at the same time that we do it for all of the other apps that we want to eventually remove

Effectively, a few files will stick around (as for the other apps where we want to get rid of all models) until the time of the two-step deployment for removal.