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Misc. SQLAlchemy 2.0 upgrades #13562

Merged
merged 12 commits into from
Mar 20, 2022
Merged

Misc. SQLAlchemy 2.0 upgrades #13562

merged 12 commits into from
Mar 20, 2022

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jdavcs
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@jdavcs jdavcs commented Mar 16, 2022 •
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Ref #12541

These are all safe and mostly trivial.

How to test the changes?

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  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

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  • I agree to license these contributions under Galaxy's current license.
  • I agree to allow the Galaxy committers to license these and all my past contributions to the core galaxy codebase under the MIT license. If this condition is an issue, uncheck and just let us know why with an e-mail to [email protected].

jdavcs added 6 commits March 16, 2022 12:16
@jdavcs
Fix implicit exection and autocommit (both removed in 2.0)
63e6134 
Ref:
https://docs.sqlalchemy.org/en/14/changelog/migration_20.html#library-level-but-not-driver-level-autocommit-removed-from-both-core-and-ormo
https://docs.sqlalchemy.org/en/14/changelog/migration_20.html#implicit-and-connectionless-execution-bound-metadata-removed

Exposed by the following tests:

test/unit/data/model/test_model_discovery.py::test_model_create_context_persist_hdas
test/unit/data/model/test_model_discovery.py::test_model_create_context_persist_error_hda
test/unit/data/model/test_model_discovery.py::test_persist_target_library_dataset
test/unit/data/model/test_model_discovery.py::test_persist_target_library_folder
test/unit/data/model/test_model_discovery.py::test_persist_target_hdca
  /home/sergey/0dev/galaxy/_galaxy/dev/lib/galaxy/model/triggers/utils.py:8: RemovedIn20Warning: The DDLElement.execute() method is considered legacy as of the 1.x series of SQLAlchemy and will be removed in 2.0. All statement execution in SQLAlchemy 2.0 is performed by the Connection.execute() method of Connection, or in the ORM by the Session.execute() method of Session. (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    cmd.execute(bind=engine)

test/unit/data/model/test_model_discovery.py::test_model_create_context_persist_hdas
test/unit/data/model/test_model_discovery.py::test_model_create_context_persist_error_hda
test/unit/data/model/test_model_discovery.py::test_persist_target_library_dataset
test/unit/data/model/test_model_discovery.py::test_persist_target_library_folder
test/unit/data/model/test_model_discovery.py::test_persist_target_hdca
  /home/sergey/0dev/galaxy/_galaxy/dev/lib/galaxy/model/triggers/utils.py:8: RemovedIn20Warning: The Engine.execute() method is considered legacy as of the 1.x series of SQLAlchemy and will be removed in 2.0. All statement execution in SQLAlchemy 2.0 is performed by the Connection.execute() method of Connection, or in the ORM by the Session.execute() method of Session. (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    cmd.execute(bind=engine)
@jdavcs
Use class attributes instead of strings in load options
25985fc 
Fixes multiple instances of RemovedIn20Warning
Joining / loading on relationships uses attributes, not strings
Ref: https://docs.sqlalchemy.org/en/14/changelog/migration_20.html#orm-query-joining-loading-on-relationships-uses-attributes-not-strings
@jdavcs
Use text() to wrap sql string
c2bee38 
Fixes RemovedIn20Warning
Ref: https://docs.sqlalchemy.org/en/14/changelog/migration_20.html#execute-method-more-strict-execution-options-are-more-prominent
@jdavcs
Use class attr in load options (all_roles())
0963a02
@jdavcs
Row.keys() removed in 2.0: use _fields instead; adjust test
ad0c79e 
Ref: https://docs.sqlalchemy.org/en/14/core/connections.html?highlight=row#sqlalchemy.engine.Row.keys
@jdavcs
Use text() to wrap sql
20f6e8d
@jdavcs jdavcs added kind/refactoring cleanup or refactoring of existing code, no functional changes area/database Galaxy's database or data access layer labels Mar 16, 2022
@jdavcs jdavcs added this to the 22.05 milestone Mar 16, 2022
@jdavcs jdavcs changed the title [WIP] Misc. SQLAlchemy 2.0 upgrades Misc. SQLAlchemy 2.0 upgrades Mar 17, 2022
@jdavcs jdavcs marked this pull request as ready for review March 17, 2022 16:43
@jmchilton jmchilton merged commit 4e01cfe into galaxyproject:dev Mar 20, 2022
@bgruening
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Very cool @ic4f :-)

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