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Handle deprecated postgresql db urls; update postgres version in ci #11790

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merged 4 commits into from
Apr 5, 2021

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@jdavcs jdavcs commented Apr 5, 2021

What did you do?

  1. Updated db urls to use postgresql instead of postgres (deprecated in SQLAlchemy 1.3, removed in 1.4)
  2. Added automated fixing of deprecated values set by the user (a descriptive warning is logged)
  3. Updated pinned version in github workflows to postgres:13 (was 11 in all but one workflow)

Why did you make this change?

With the move to SQLAlchemy 1.4, database_connection values of the old postgres:// form will fail.
Ref: https://docs.sqlalchemy.org/en/14/changelog/changelog_14.html#change-3687655465c25a39b968b4f5f6e9170b
Updating the pin in github workflows from 11 to 13 is related cleanup.

How to test the changes?

(select the most appropriate option; if the latter, provide steps for testing below)

  • unit test added

@jdavcs jdavcs added kind/enhancement area/database Galaxy's database or data access layer area/configuration Galaxy's configuration system labels Apr 5, 2021
@jdavcs jdavcs added this to the 21.05 milestone Apr 5, 2021
@jdavcs jdavcs changed the title Update handling of postgresql Handle deprecated postgresql db urls; update postgres version in ci Apr 5, 2021
lib/galaxy/config/__init__.py Outdated Show resolved Hide resolved
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
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jdavcs commented Apr 5, 2021

Thank you, @nsoranzo!

@jdavcs jdavcs merged commit 5a127a7 into galaxyproject:dev Apr 5, 2021
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Thanks!

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