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If the database is combined, running `./manage_db.sh upgrade` should upgrade BOTH models: gxy and tsi. However, if tsi uses a separate database, only the galaxy model should be updated. Also, see this for context: https://github.com/galaxyproject/galaxy/pull/13108#discussion_r789108576 See inline comments for more details. The new tests are examples of new behavior. All refactoring is directly related to the changes in this commit.