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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 •
edited

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.

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@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 jdavcs added this to In progress in Backend Working Group Oct 20, 2021
@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 moved this from In progress to Done in Backend Working Group 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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area/database Galaxy's database or data access layer area/testing kind/refactoring cleanup or refactoring of existing code, no functional changes
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