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440 Commits
Author SHA1 Message Date
John Chilton 7f7710d392 Implement recovering normalized workflow request from invocation. 2024-10-15 09:12:05 -04:00
John Davis 00bebee7c7 Add test exposing bug 
After user's email has been modified, we can't retrieve sharing roles
for that user
 2024-10-04 14:44:41 -04:00
Marius van den Beek 2ead0c41e9 Merge pull request #18807 from jmchilton/landing 2024-10-01 21:44:50 +02:00
Nicola Soranzo 136747e766 Type annotations and fixes 
- Use `galaxy.util.path.StrPath` everywhere
 2024-09-30 21:33:44 +01:00
John Chilton 93f2af6a44 Allow dataset and source checksum validation during materialization. 2024-09-30 13:25:02 -04:00
John Chilton 80aaff8d23 Plumbing for dereferencing URLs into datasets. 2024-09-30 13:25:02 -04:00
John Chilton 813ed02d53 Merge pull request #18886 from jdavcs/dev_db_test_update 
Refactor migration testing setup code
 2024-09-25 10:49:27 -04:00
Matthias Bernt 7dd606a6b2 Merge branch 'release_24.1' into dev 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_shed/HISTORY.rst
#	packages/tool_shed/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2024-09-25 14:29:37 +02:00
John Davis b57ec18991 Refactor migration testing setup code 
- Do not explicitly import fixtures (a little duplication is safer/cleaner)
- Move dangerous fixture into module to prevent accidental usage from other modules
- Ensure only one database is used for all tests in module
 2024-09-24 20:47:09 -04:00
John Davis 03641a98fa Fix migration data fixes tests 
When upgrading back to a valid revision, upgrade to head, not the
revision under test: we need the latest version of the model definition
in the database for the test to cleanup correctly.
 2024-09-24 16:16:05 -04:00
John Davis 5524ea77a7 Add tests for migration fixes 2024-09-23 23:52:05 -04:00
John Davis 2fc21f9962 Do not pass unnecessary arguments 2024-09-23 17:05:15 -04:00
John Davis 6c4ddeb91d Test that private roles are not assignable 2024-09-23 17:05:15 -04:00
John Davis 8c4a90010a Add tests for user and history default permissions 2024-09-23 17:05:15 -04:00
John Davis 19d76e9580 Fix mypy: statements are reachable 2024-09-23 17:05:15 -04:00
John Davis 4fb1c704d6 Rename verify_items helper to have_same_elements 
Improves readability of test code
 2024-09-23 15:49:01 -04:00
John Davis 004d46c7a4 Fix test database handling for db tests 2024-09-23 14:22:59 -04:00
John Davis 7739134485 Add unit tests for user/group/role associations 2024-09-23 14:22:59 -04:00
John Davis bef3888683 Refactor for testability: pass only session 
We don't need a ModelMapping instance here; without it we can
easily write unit tests.
 2024-09-23 14:22:59 -04:00
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 87573ee617 Add tests for migration data fixes 2024-09-21 00:18:02 -04:00
John Davis 4471c6a851 Refactor tests to reduce duplication 2024-09-21 00:17:20 -04:00
John Davis 600523b773 Fix test_galaxy_mapping to respect constraint 2024-09-20 17:24:20 -04:00
John Davis 11a25ae199 Fix test_quota to respect constraint 2024-09-20 17:24:20 -04:00
John Davis b261dea43a Randomize test user email to respect unique constraint 2024-09-20 17:24:20 -04:00
Nicola Soranzo e61f2e8999 Fix new E721 and F811 errors from ruff 0.5.0 2024-07-03 16:57:52 +01:00
John Davis 0712fbf538 Add test_history_update 2024-06-10 15:48:10 -04:00
John Davis fd29aab55d Drop test_tasks 
Tests SQLAlchemy (create foo + set foo.bar + load foo + check bar)
 2024-06-10 15:48:10 -04:00
John Davis 1d7d65568b Convert + improve test_job/task_metrics 2024-06-10 15:48:10 -04:00
John Davis 65530c9d59 Drop unused fixture arg 2024-06-10 15:48:10 -04:00
John Davis 5123c39298 Convert test_metadata_spec 2024-06-10 15:48:10 -04:00
John Davis e7d4270321 Drop test_basic 
Tests SQLAlchemy, user-history relationship mapping
 2024-06-10 15:48:10 -04:00
John Davis 83e124f4d1 Drop incomplete test 
No assert (only TODO); but would test SQLAlchemy
 2024-06-10 15:48:10 -04:00
John Davis 47a8bf7675 Drop test_tags 
Tests SQLAlchemy:

1. Create tag
2. Verify there's no FooTagAssociation with this tag
3. Add new FooTagAssociation to Foo and save to db
4. Verify there is one FooTagAssociation with this tag
 2024-06-10 15:48:10 -04:00
John Davis c8df2fdf30 Convert test_get_display_name 2024-06-10 15:48:10 -04:00
John Davis 23ae962bbf Convert hid tests 2024-06-10 15:48:10 -04:00
John Davis 2d4a65d915 Convert test_current_galaxy_sesssion 2024-06-10 15:48:10 -04:00
John Davis da3c885800 Convert test_history_contents 2024-06-10 15:48:10 -04:00
John Davis 1a4d6e651f Drop test_jobs 
Tested SQLAlchemy:
- create job
- set job.tool_id
- save, load job by id, verify job.tool_id
 2024-06-10 15:48:10 -04:00
John Davis 706079188d Drop test_dataset_job_relationship 
This tested SQLAlchemy:
1. create: dataset, job
2. set: dataset.job = job
3. save, then load dataset by dataset.id; verify that dataset.job = job
 2024-06-10 15:48:10 -04:00
John Davis 9572a93ac4 Convert test_ratings 2024-06-10 15:48:10 -04:00
John Davis 51ffbfd432 Convert test_default_disk_usage 2024-06-10 15:48:10 -04:00
John Davis 558d8364e9 More test-galaxy-mapping conversions 2024-06-10 15:48:10 -04:00
John Davis bc6fb8953d Improve test: enable db triggers; do not verify HistoryAudit table 
We do not verify the counts of rows in the HistoryAudit table because
with the db trigger enabled, those rows are created automatically.

Although it is possible to calculate the expected counts, those numbers
would be dependend on previous db statements executed in the same test,
and that calculation would be not straightforward, making the test
brittle and confusing.
 2024-06-10 15:48:10 -04:00
John Davis 7ad6d43418 Start replacing test_galaxy_mapping w/data access tests 2024-06-10 15:48:10 -04:00
John Davis 4aaed3e2c9 Move+test get_roles_by_ids 2024-06-10 15:48:10 -04:00
John Davis f91bd11052 Test User.username model definition (unique constraint) 2024-06-10 15:48:10 -04:00
John Davis 4329a5e603 webapps.galaxy.services.user.get_users_for_index: test + factor out 2024-06-10 15:48:10 -04:00
John Davis fabce5bdc4 security.get_private_user_role: test + factor out 2024-06-10 15:48:10 -04:00
John Davis b8e05af3be security.get_npns_roles: test + factor out 2024-06-10 15:48:10 -04:00