Replace SQLAlchemy Migrate with Alembic#13108

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jdavcs wants to merge 61 commits intogalaxyproject:devfrom jdavcs:dev_alembic20

+3,626-12,864

Commits on Mar 1, 2022

Add alembic to dependencies
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Add testing infrastructure
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Add alembic infrastructure
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Add alembic dir to ignore list in run_tests
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Add alembic dir to ignore list in package tests
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Move engine_options default arg initialization to engine_factory
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Remove migrations test from first starup workflow
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Add workflow for migration tests
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Run tests under Python 3.7
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Move triggers out of migrate directory
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Integrate migrations design into config and model code
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Handle error when revision not found; add test case
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Avoid extra trip to db via lazy load of alembic version heads
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Use correct db options for both engines; resolve todos
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Fix mypy error
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Add informative log/error messages; add tests for new methods
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Drop config.database_create_tables (not used)
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Drop app.new_installation (not used)
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Don't use triple-quoted strings as comments in tests
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Setup infrastructure for running db scripts
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Add create/migrate scripts for tool shed
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Add create/migrate scripts for Alembic dbs
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Fix integration test (test only relevant for TS)
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Fix mypy error
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When overriding, override.
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Update data package (requirements, packages, includes)
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Move helper function out of migrate into triggers
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Remove galaxy.model.migrate files
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Remove galaxy.model.tool_shed_install.migrate files
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Move is-one-db check into model.database_utils
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Update data package entry point in orm.scripts.py
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Remove outdated parts from orm.scripts.py
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Update db index testing: test both models, gxy and tsi
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Add a comment on sqlalchemy-migrate to pyproject.toml
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Address existing mypy error (see note)
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Dispose of engines when invoked via script
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Add type hints to migrations modules
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Type-ignore alembic type hint bug
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Add type hints to common module in migration tests
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Remove circular dependency between migrations and config
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Add migrations README
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Add prev. version 180 as new revision.
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Preserve manage_db.sh, but do not hide alembic
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Update README: rename script, add legacy script, simplify upgrade steps.
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Modify behavior of legacy wrapper, add tests, refactor
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Check for table existence for vault (see note)
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Stub out config call in test_scripts; fixes package test
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Update manage_db.sh ($@ > "$@")

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Update manage_db.sh ($@ > "$@")

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Update manage_db.sh (use single = in [ ])

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Fix import order in config
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Apply black, isort
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Remove old migrate files (fix rebase)
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Change latest db version to 180
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Adapt manage_db.py for usegalaxy playbook; add tests
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Fix some of the package tests
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Fix path for package tests
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Print result of script execution
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One engine for 2 dbs logically equiv to 2 refs to same engine
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Change handling of unrecognized revisions; improve log messages
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Remove vault table revision (part of 22.01)
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