Prevent VARCHAR round-trip auto cast, check for duplicate primary keys and add preprocessing tests

[Taepper]

Summary

We now prevent VARCHAR round-trip auto cast which lead to a VARCHAR column being first cast into a json and back by duckdb automatically. We also added a test for this.

Additionally, I added a check and test for duplicate primary keys

PR Checklist

- [ ] All necessary documentation has been adapted or there is an issue to do so.

• The implemented feature is covered by an appropriate test.

[github-actions]

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Changelog:

0.3.1 (2024-10-24)

Bug Fixes

• preprocessing: error on duplicate primary keys (d28cae7)
• validate the column types earlier to prevent duckdb auto-casting to cast types with differing round-trip conversions (092e601)

[fengelniederhammer]

LGTM

[anna-parker]

Since this change the dummyOrganism is failing to start because

[2024-10-25 10:29:27.109] [logger] [error] [api.cpp:289] Unknown metadata type: pango_lineage

This isn't very important as we only use it in the dummyOrganism - but would be good to figure out why

[Taepper]

Apparently, the linter problem in the github runners is more involved than I can reproduce. I will merge this anyways, as these bugfixes are quite good to have upstream. Work on the build fixes will meanwhile continue, but can take up to 4 hours to see the result, as the ARM images often need to be rebuild (.. and use the very slow github virtualization)