Merge db back to dev

[eboileau]

Aims/objectives.

Finalise DB setup first phase, and merge back to dev.

A clear and concise description of todo items.

Address these issues before

• [x] Configuration Current setup: .env files are under scimodom/server/src/scimodom/, and flask run must be run there, and e.g. flask --app scimodom run will not work -> Error: Could not import 'scimodom.scimodom'. If runnign flask --app scimodom run from /scimodom/server, the env variables are not read -> sqlalchemy.exc.ArgumentError: Expected string or URL object, got None. For local vs. dev (and eventually e.g. production), we now rely on LOCAL_APP to be set/unset before calling the application. We could also do something like create_app(os.getenv('BOILERPLATE_ENV') or 'dev') see e.g. https://github.com/miguelgrinberg/flasky/blob/master/app/__init__.py#L20. In general, we need to cleanly sort how to handle this, and how to handle relative paths (location of .env files, and how to run the app w/ options). See also https://flask.palletsprojects.com/en/2.3.x/config/ and https://flask.palletsprojects.com/en/2.3.x/cli/

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• [x] The SMID returned when testing test_project_validate_existing_entry is not consistent. Where this stems from? Is this some test side-effect?
• [x] test_project_add_selection (ProjectService(Session(), project)._add_selection()) and test_project_create_project (ProjectService(Session(), project).create_project()) passed when adding a DetectionTechnology (w/ foreign key method.id), even without defining a DetectionMethod. With an in-memory sqlite, there is no error, but this doesn't work with mysql... why?
• [x] Test parametrization and side-effects, e.g. in test_dataset_create_eufid, define project = _get_project(project_template, case="two"), but use project_template in the function, it still picks the right project?? In general, we should simplify the parametrization/conditionals to make tests simpler, and also more isolated, where possible.

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• [x] Implement minimal API to query e.g. via curl base tables (modification, taxonomy, etc.), project, and dataset. This could be used to test, and also as a basis for the actual FE-API communication (and maintenance via API?).

[eboileau]

For testing, we have to deal with (not always very clearly defined) differences between in-memory sqlite and mysql. Closing this, but somehow we need to keep this in mind for writing tests. We can always revisit/refine existing tests to improve, TDD is an iterative process, no?

As for the API, the is yet to be set-up, formally speaking, but we have some template structure. I've done a quick prototyping for a typical search query, but until we go back to the Search View and FE-BE communication, it's not worth refining.