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Convert install_model to declarative mapping #12756

Merged
merged 23 commits into from
Oct 21, 2021
Merged

Convert install_model to declarative mapping #12756

merged 23 commits into from
Oct 21, 2021

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jdavcs
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@jdavcs jdavcs commented Oct 20, 2021 •
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Progress toward #10369 and #12541 (and the no-longer-elusive declarative bliss)
(Same justification as in #12666)

To do:

  • Add mapping tests for all models
  • Map all models except ToolShedRepository declaratively
  • Map ToolShedRepository declaratively (requires solving the metadata attribute issue)

Technical dept:
I'll handle test setup duplication in the following PR (it's out of scope, better fit for a separate set of commits)

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.

License

  • 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 16 commits October 19, 2021 17:30
@jdavcs
Rename mapping test, add install_model_mapping test
e2c7403
@jdavcs
Add unit tests for install_model mapping
fb7f71a
@jdavcs
Setup install_model for remapping
6f45f26
@jdavcs
Add nonstandard test for ToolVersion relationships
29e1885
@jdavcs
Remove MigrateTools from model and mapping (note)
8f79a8f 
This class is not referenced in the codebase. The table has limited use,
but not through the model, so, I think, it shouldn't be part of the
model. The table is part of our SQLAlchemy Migrate setup, which is being
replaced with Alembic.
@jdavcs
Map RepositoryRepositoryDependencyAssociation declaratively
86a30bc 
Also, setup Base class for declarative
@jdavcs
Map RepositoryDependency declaratively
a3d7a37
@jdavcs
Map ToolDependency declaratively
92b32ba
@jdavcs
Map ToolVersion declaratively
1fe5e6d
@jdavcs
Map ToolVersionAssociation declaratively
191464f
@jdavcs
Remove backref from ToolShedRepository.tool_version
19dc5c9
@jdavcs
Remove backref from ToolShedRepository.tool_dependencies
f99a397
@jdavcs
Remove unnecessary primary_join attr
cf96467
@jdavcs
Fix SAWarning: add back_populates args
a8e3c84
@jdavcs
Drop redundant datatypes from fkeys
b0446b1
@jdavcs
Drop redundant model constructors
353ce42
@jdavcs jdavcs added status/WIP kind/refactoring cleanup or refactoring of existing code, no functional changes area/testing area/database Galaxy's database or data access layer labels Oct 20, 2021
@jdavcs jdavcs added this to the 22.01 milestone Oct 20, 2021
jdavcs added 5 commits October 20, 2021 17:15
@jdavcs
Map ToolShedRepository declaratively (see note)
d870278 
Rename metadata to metadata_. This will break things.
(we are only renaming the model attribute, not the table column)
Next step: rename all instances of [ToolShedRepository].metadata in code base.
@jdavcs
Remove refs to ToolShedRepository.metadata in test/
691a3f6
@jdavcs
Remove refs to ToolShedRepository.metadata in scripts/
5acbb14
@jdavcs
Replace all remaining instances of TSR.metadata
bd765b0
@jdavcs
Fix .metadata_ in tool_shed dir
404bac3
@jdavcs jdavcs force-pushed the dev_install_model_declarative branch from a44d779 to 404bac3 Compare October 21, 2021 00:59
@jdavcs jdavcs changed the title [WIP] Convert install_model to declarative mapping Convert install_model to declarative mapping Oct 21, 2021
@jdavcs jdavcs removed the status/WIP label Oct 21, 2021
@jdavcs jdavcs marked this pull request as ready for review October 21, 2021 01:28
@mvdbeek mvdbeek merged commit f302a2d into galaxyproject:dev Oct 21, 2021
@jdavcs jdavcs mentioned this pull request Oct 22, 2021
Merged
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@jdavcs jdavcs deleted the dev_install_model_declarative branch October 22, 2021 16:11
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