Nicola Soranzo
95ccefacb8
Improve type annotations for model store
...
and related files.
Follow-up on https://github.com/galaxyproject/galaxy/pull/14971 .
2022-11-30 01:45:56 +00:00
John Davis
29053fa9e4
Move test_dbscript into app
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JUSTIFICATION:
As per @jmchilton:
The package tests should pretend they don't have galaxy_directory()
available because they're meant to be installed into a Python env.
This test is fundamentally not testing anything about the Galaxy data
package - it is testing scripts placed in Galaxy root directory and that
would not be available in an installed Galaxy environment.
2022-11-21 18:12:04 -05:00
John Davis
4e5a94a2b2
Use resource_path for test_dbscript
2022-11-21 18:12:04 -05:00
John Davis
faf8efafd0
Use resource_path for test_migrations
2022-11-21 18:12:04 -05:00
John Davis
dd267e2d3e
Refactor test, use galaxy_directory()
2022-11-21 18:12:04 -05:00
John Davis
821b60f30a
Use galaxy_directory() instead of hacking the path
2022-11-21 18:12:04 -05:00
John Chilton
dac9f39266
Move model/mapping utils into packaged code for reuse by the tool shed.
2022-10-29 12:07:46 -04:00
davelopez
881c57eb64
Fix export history RO-Crate without workflows
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The workflows_directory may not exists if no workflow was invoked in the history.
Includes unit test + small tests refactor
2022-10-21 10:25:32 +02:00
Marius van den Beek
934369aa3a
Merge pull request #14792 from jdavcs/dev_sqlalchemy_engine_options
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Make connect_args for SQLAlchemy's engine configurable
2022-10-17 10:30:44 +02:00
John Davis
d957e143ea
Engine options are never null
2022-10-14 15:27:20 -04:00
John Davis
7578edbd00
Fix mypy error
2022-10-14 13:31:54 -04:00
John Davis
da87ca9209
Allow to set connect_args for SQLAlchemy's engine in config
2022-10-14 13:17:42 -04:00
davelopez
0356c2e01f
Add unit test for api_keys.deleted column
2022-09-30 16:39:12 +02:00
John Davis
1eb4d15f38
Split script into admin and dev
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TODO: remove duplication between db.py and db_dev.py (split into
multiple commits is intentional)
2022-09-16 00:39:44 -04:00
John Davis
b6a5286487
Rename db.sh > manage_db.sh, following code review feedback
2022-09-16 00:39:44 -04:00
John Davis
3c094790a1
Update test comments
2022-09-16 00:39:03 -04:00
John Davis
372d4af0b8
Add type hints
2022-09-16 00:39:03 -04:00
John Davis
1f5b0e6bba
Drop LegacyScripts: no longer used
2022-09-16 00:39:03 -04:00
John Davis
7e238bf591
Add --raiseerr option; hide error traceback by default
2022-09-16 00:39:03 -04:00
John Davis
959bc49e66
Add missing tests
2022-09-16 00:39:03 -04:00
John Davis
0745e2e05c
Fix mypy by asserting object before accessing its attributes
2022-09-16 00:39:03 -04:00
John Davis
89f753767b
Fix packages tests: script is one level up
2022-09-16 00:39:03 -04:00
John Davis
ac6b0ceee0
Fix linting
2022-09-16 00:39:03 -04:00
John Davis
0a798ea536
Test against 1 or 2 databases
2022-09-16 00:39:03 -04:00
John Davis
b30e4e14ae
Add inline testing documentation
2022-09-16 00:39:03 -04:00
John Davis
a69ab407a6
Add initial draft
2022-09-16 00:39:03 -04:00
John Davis
6abc9dc1c5
Refactor get_alembic_cfg: make available to other code
2022-09-16 00:39:03 -04:00
John Chilton
3dbe2891e7
Implement RO Crate export of Galaxy histories and invocations.
2022-09-13 19:20:48 -04:00
John Davis
def882932d
Add verify_db_is_initialized function; tests
2022-07-13 16:10:58 -04:00
John Davis
1e75d85fd4
Prevent accessing LegacyScripts.database before processing script args
2022-07-13 15:40:42 -04:00
Sergey Golitsynskiy
bf91dc5b75
Remove column update_time from model, tests
2022-06-01 18:30:30 -04:00
John Chilton
c5bf63bc91
Add DEFERRED datasets to Galaxy
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- Improves options and display around discarded datasets.
- Adds new APIs for importing model stores.
- Adds support to model store layer for importing/exporting workflow invocations and APIs and tests to support this.
- Add new DEFERRED dataset state - with APIs for materializing them or the option to defer them on the worker node if using tool_evaluation_strategy=remote on the job destination.
- UI and API options for uploading deferred datasets individually or into collections.
2022-05-23 19:48:47 -04:00
Sergey Golitsynskiy
34e8b182d4
Map Dataset declaratively
2022-04-29 13:37:32 -04:00
Sergey Golitsynskiy
cc1c2e4b94
Enable postgresql testing for new annotations module
2022-04-20 22:16:40 -04:00
Sergey Golitsynskiy
e9eb6c1500
Proof of concept: replace annotation mapping tests
2022-04-20 18:14:43 -04:00
Sergey Golitsynskiy
254830a33b
Add fixture for WorkflowStepAnnotationAssociation
2022-04-20 17:48:37 -04:00
Sergey Golitsynskiy
ed2798e044
Fix module path for remote unit tests
2022-04-20 17:03:03 -04:00
Sergey Golitsynskiy
52bb6c90e6
Fix linting
2022-04-20 16:23:05 -04:00
Sergey Golitsynskiy
95a4fd5667
Use plugins instead of importing fixtures directly
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Also handle setting the fully qualified module name depending on wht's
the cwd from which the test is executed.
2022-04-20 15:50:52 -04:00
Sergey Golitsynskiy
c9e3d340f6
Move tmp_dir fixture one level up
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Otherwise url_factory is not usable outside of migrations
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
1228bfa769
Refactor code for dropping postgres
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
495dd6daaf
Move last context managers out of migrations
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
c3059de4a5
Move disposing_engine out of migrations
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
eec0a87028
Move url_factory out of migrations
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Make available for use in other testing contexts.
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
476da34b7a
Move test revisions into testing_utils
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
f5c962d8d7
Move common.py to testing_utils
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
d2ecb7ee68
Fix linting (unused import)
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
0a7d2113bd
Factor out helper function (kill more dups)
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
9ae2d4e08f
Simplify (no need for scoped_session), consolidate redundant fixtures
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
1a95857271
Rename test modules for testing_utils
2022-04-20 10:28:03 -04:00
Nicola Soranzo