uc-cdis / metadata-service / 22003496374

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[PD-78] GINO -> SQLAlchemy and upgrade to Python 3.13 (#159)

* initial GINO to SQLAlchemy structure

* core CRUD operations for metadata in DAL

* alias operations for metadata DAL

* use URL.create() sqlalchemy 2.0 compatibility, update lock

* add batch and index DAL methods, add full unit testing for DAL layer

* remove Gino

* Apply automatic documentation changes

* update DB_DRIVER default config

* undo change

* test

* test

* test ci db fix

* update migration

* update migration

* fix migration, seperate db op and migration

* update test_server.py

* change unit test --cov-fail-under to 91

* address comments

* Fix for coverage reporting when using sqlalchemy async sessions

* fix nginx

* fix docstring

* fix populate.py

* update Dockerfile

* remove a line

* remove some asserts in test

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Co-authored-by: mark xiao <xiao2@uchicago.edu>
Co-authored-by: markxiao <markxiao@users.noreply.github.com>

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