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Resolve "Declarative base class should subclass DeclarativeBase"

Vetle Simensen requested to merge 2247-declarative-base-class-should-be-subclassing-declarativebase into epic-autumn-cleaning

Description

This MR replaces the use of declarative_base() with a Base class that inherits from DeclarativeBase. This change introduced a handful of type annotation errors and assorted issues (e.g. access of non-existing attributes, incorrect use of poorly named functions) that have been fixed.

Notes to review (code/docs/QA)

  • The changes to src/cli/commands/filterconfigs/filterconfigs.py could perhaps also be made simpler by explicitly defining relationships in the data models, rather than only relying on foreign key constraints of the various ids?
  • Is it correct that the SQL query in src/api/v1/resources/workflow/analysis.py is supposed to be a chain of joins?

Related issues

#2242 (closed)

Closes #2247 (closed)

Edited by Vetle Simensen

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