mvdbeek
69a3cda018
Fix history import when parent_hda not serialized
...
and make sure we include the parent_hda when exporting histories.
Fixes
https://sentry.galaxyproject.org/share/issue/20ee27f675ef476588bbe8ff273eaee7/ :
```
KeyError: '31e7840b5aedca43523bfcc8e2e9e56f'
File "galaxy/jobs/__init__.py", line 2039, in finish
task_wrapper = self.tool.exec_after_process(
File "galaxy/tools/__init__.py", line 3100, in exec_after_process
JobImportHistoryArchiveWrapper(self.app, job.id).cleanup_after_job()
File "galaxy/tools/imp_exp/__init__.py", line 81, in cleanup_after_job
model_store.perform_import(new_history, job=job, new_history=True)
File "galaxy/model/store/__init__.py", line 416, in perform_import
self._import_implicit_dataset_conversions(object_import_tracker)
File "galaxy/model/store/__init__.py", line 1280, in _import_implicit_dataset_conversions
idc.parent_hda = object_import_tracker.hdas_by_key[idc_attrs["parent_hda"]]
```
2024-09-23 11:07:20 +02:00
John Davis
7f83b903cb
Add history pruner + test
...
Add __init__.py to test.unit.data.model.db
2024-05-02 14:12:35 -04:00
John Davis
1773dca37a
Add model fixtures
2024-05-02 14:12:35 -04:00
John Davis
2652ec6510
Add conftest.py for db tests
2024-05-02 14:12:35 -04:00
John Davis
76c8003d4f
Drop unused mapping testing utilities and fixtures
2024-05-02 14:12:35 -04:00
mvdbeek
0456ff1cfd
Merge branch 'release_24.0' into dev
2024-05-02 11:32:44 +02:00
davelopez
b7eda89485
Add test to verify export dataset without hid works
2024-04-25 12:06:28 +02:00
John Davis
09fee6aaad
Remove future, autocommit args from session and engine creation
2024-04-05 13:54:39 -04:00
John Davis
f52d35bf7f
Use NullPool for sqlite engines
...
This restores the behavior under SQLAlchemy 1.4
(Note that we set the pool for sqlite only if it's not an in-memory db
2024-04-02 10:08:53 -04:00
John Davis
78a77d934a
Mypy: typing errors, misc. fixes
2024-04-02 10:08:53 -04:00
mvdbeek
6f08b9fc9c
Add unit test for updating output hda copies
2024-03-19 10:41:16 +01:00
Marius van den Beek
5f25655096
Merge pull request #17346 from jmchilton/model_store_fixes
...
Fix model store exports that include implicit conversions.
2024-02-08 10:59:36 +01:00
Nicola Soranzo
e975ca3754
Update to black 2024 stable style
2024-01-30 18:09:51 +00:00
John Chilton
4157042ffa
Fix overlapping names in extra files for model stores.
2024-01-25 10:03:44 -05:00
John Chilton
69b01ac0e8
Utilities for higher level composite tests in test_model_store.
2024-01-25 10:03:44 -05:00
John Chilton
3a71150819
Minimal test case demonstrating model stores break on implicit conversions.
2024-01-25 09:32:40 -05:00
John Chilton
936a35d90d
More de-duplication in test_model_store.py.
2024-01-25 09:32:35 -05:00
John Chilton
24d215c9e7
Reduce duplication in test_model_store.
2024-01-24 11:11:16 -05:00
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
mvdbeek