Dynamic configuration

Description

Remove hard coded config, and provide a yaml instead.

Closes issues: LA-1520, LA-1513 Related issues:

• Read config from file at the environment variable ELLA_CONFIG
• Extracted most of the config into an example config.
• Removed default filter configuration. Filters now needs to be fully defined in the json-file.
• Frequency groups in filterconfig is now taken from filter config and not global config (LA-1513). This obviously require groups to be set explicitly in the filter config.
• Create shadow tables in temporary tables, before overwriting the existing shadow tables.
• Add checks on filter config import and usergroup import, that the configurations for frequency filter and ACMG are valid with the current AnnotationShadowFrequency table.
• Added json schema for config

Notes to reviewer

Some fields are left hardcoded in config.py (VEP consequences, clinvar descriptions). These are not really config-values, and should ideally not be in the config-object. Left it as is for now.

Type of change

Application (affects UI or general functionality):

• New feature
• Bug fix
• Improvement

Ops / admin / CI related only (not impacting users):

• New feature
• Bug fix
• Improvement

Tests

General

• Tests have been added that prove my fix is effective or that my feature works
• Related tests have been modified/removed

Hypothesis testing:

• Soak testing has been done
• Distribution between positive / negative cases has been checked

Database

• Includes changes to database schema
• Includes necessary database migrations

Configuration

• Includes changes to configuration
• Includes configuration migration instructions in documentation

Merge checklist

• Self-review of code performed
• Feature review against specification (if applicable)
• Need for documentation has been evaluated and, if necessary, updated
• Code and implementation is reviewed by other core developer (all changes, inc. changes based on initial review)