John Davis
475f7227c4
Add future=True flag to SA engine
2023-12-12 09:54:08 -05:00
John Davis
95fa80105a
Fix "statement is being autocommitted" SA2.0 warning
2023-12-11 16:09:44 -05:00
Michael R. Crusoe
14fb5acc69
importlib_resources is only needed in Python 3.8
...
Add type hints + fixes
2023-11-27 00:01:54 +00:00
Yakubov, Sergey
c30a4c06c2
Replace file_name property with get_file_name function
2023-11-08 17:17:14 -05:00
mvdbeek
c62da4aa33
Merge branch 'release_23.1' into dev
2023-08-09 16:06:08 +02:00
mvdbeek
7329575bf4
Unit test fixes
2023-07-31 14:03:32 +02:00
John Davis
e54a2ec897
Fix SA2.0 syntax (query->select) in unit tests
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Includes multiple upgrades to syntax.
Ref: https://docs.sqlalchemy.org/en/20/changelog/migration_20.html#migration-orm-usage
2023-07-21 13:04:22 -04:00
John Davis
4f2ebe4846
Wrap session.flush in test.unit.data.model
2023-06-09 13:05:26 -04:00
mvdbeek
368dfb3119
Merge branch 'release_23.0' into dev
2023-06-06 15:55:12 +02:00
mvdbeek
7cb93b3d93
Support ro-crate >=0.8.0 and 0.7.0
...
I guess there's a chance downstream users may run into version conflicts
if we pin ro-cate to 0.7.0, and we also don't really want to bump stable
version dependencies.
2023-06-06 11:55:52 +02:00
John Davis
f532069517
Rename helper functions
2023-05-15 13:44:32 -04:00
John Davis
22218b5806
Allow for composite indexes and constraints; add tests
2023-05-15 11:23:01 -04:00
John Davis
98d884e5c5
Drop views
2023-04-13 18:53:44 -04:00
Nicola Soranzo
c655360e4e
Merge branch 'release_23.0' into dev
2023-04-05 12:39:43 +01:00
Paul De Geest and David López
2146f7d1ff
Update 2 test/unit/data/model/test_model_store.py
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Co-authored-by: David López <46503462+davelopez@users.noreply.github.com >
2023-03-30 13:33:55 +02:00
Paul De Geest and David López
98c71d1c70
Update 1 test/unit/data/model/test_model_store.py
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Co-authored-by: David López <46503462+davelopez@users.noreply.github.com >
2023-03-30 13:33:43 +02:00
pauldg
9105ba3ea5
formatting
2023-03-29 11:32:35 +02:00
pauldg
e2882dc54c
Changes to tests according to ro-crate
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metadata changes
2023-03-29 11:32:34 +02:00
John Davis
63224a626d
Drop mapping unit tests
2023-02-28 15:48:14 -05:00
John Davis
e6b9da9070
Factor out common code into migrations.base
2023-02-08 14:33:30 -05:00
John Davis
df0c6b6292
Move migration exception classes into their own module
2023-02-08 12:12:21 -05:00
John Davis
cc55636588
Improve migrations error handling
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1. Make message, class name more descriptive, specific
2. Generalize attributes, message, factor out upgrade script
to be applicable to multiple databases (galaxy, tool shed, etc.)
3. Use more specific errors; do not group together errors caused by an
outdated version in a database controlled by Alembic and a
database that doesn't have Alembic setup.
2023-02-08 00:33:48 -05:00
Nicola Soranzo
30f60493c3
Format Python code with black 23.1.0
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with manual fixes to 3 files to make them compatible with black 22.12.0 .
We need to keep black pinned at `<23` until we vendorise `packaging`, since
the new version of black depends on `packaging >=22.0` which is the version
where `LegacyVersion` (which we use for tool lineages) was removed.
2023-02-01 23:51:03 +00:00
pauldg
50ef6bcaeb
Added asserts for invocation with collections
2023-01-11 09:37:22 +01:00
pauldg
5253992928
added unit test for collections and fixed format
2023-01-11 09:37:22 +01:00
pauldg
7ebc1b3f4e
added job params to unit testing
2023-01-11 09:37:22 +01:00
pauldg
c49a38ca70
changes to unit tests
2023-01-11 09:37:22 +01:00
davelopez
e627c32769
Fix linting + mypy
2023-01-11 09:37:17 +01:00
pauldg
e42ca8c442
Fix missing export_files parameter in test
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export_files parameters missing in ROCrateArchiveModelExportStore
2023-01-11 09:28:14 +01:00
pauldg
3631d08f68
added additional unit tests for workflow invocation to rocrate export
2023-01-11 09:28:14 +01:00
davelopez and Paul De Geest
1dca3eedfd
Add a bit more metadata check to rocrate tests
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Co-authored-by: Paul De Geest <pauldegeest1@gmail.com >
2023-01-11 09:28:14 +01:00
John Chilton
2f46f05d48
Typing galaxy.security.
2022-12-12 14:18:28 -05:00
Nicola Soranzo
95ccefacb8
Improve type annotations for model store
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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