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7651 Commits
Author SHA1 Message Date
Marius van den Beek fa64fc646d Merge pull request #15825 from bernt-matthias/validation_metadata 
Add ability to assert metadata properties on input dataset parameters
 2023-07-29 12:00:32 +02:00
mvdbeek 7cdb480595 Merge branch 'release_23.1' into dev 2023-07-29 11:50:34 +02:00
Nicola Soranzo e25e27b6bc Fix merge forward of commit 77c0e915b0 2023-07-29 00:54:17 +01:00
Nicola Soranzo d543702e4b pytest-postgresql requires psycopg 
See https://github.com/ClearcodeHQ/pytest-postgresql#how-to-use

Fix failing queue_worker unit tests when psycopg2 is installed
(otherwise they are skipped):

```
$ pytest test/unit/app/queue_worker/test_database_heartbeat.py::test_database_heartbeat[postgres_app]
...
_________________________________________________________________________ ERROR at setup of test_database_heartbeat[postgres_app] _________________________________________________________________________

request = <SubRequest 'database_app' for <Function test_database_heartbeat[postgres_app]>>

    @pytest.fixture(params=["postgres_app", "sqlite_app", "sqlite_rabbitmq_app"])
    def database_app(request):
        if request.param == "postgres_app":
            if not which("initdb"):
                pytest.skip("initdb must be on PATH for postgresql fixture")
            if not psycopg2:
                pytest.skip("psycopg2 must be installed for postgresql fixture")
        if request.param == "sqlite_rabbitmq_app":
            if not os.environ.get("GALAXY_TEST_AMQP_INTERNAL_CONNECTION"):
                pytest.skip("rabbitmq tests will be skipped if GALAXY_TEST_AMQP_INTERNAL_CONNECTION env var is unset")
>       return request.getfixturevalue(request.param)

test/unit/app/queue_worker/conftest.py:67:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
.venv/lib/python3.10/site-packages/pytest_postgresql/factories/process.py:147: in postgresql_proc_fixture
    with DatabaseJanitor(
.venv/lib/python3.10/site-packages/pytest_postgresql/janitor.py:54: in __init__
    check_for_psycopg()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

    def check_for_psycopg() -> None:
        """
        Function checks whether psycopg was imported.

        Raises ImportError if not.
        """
        if not psycopg:
>           raise ImportError("No module named psycopg. Please install psycopg.")
E           ImportError: No module named psycopg. Please install psycopg.

.venv/lib/python3.10/site-packages/pytest_postgresql/compat.py:35: ImportError
```

Also, remove check for `initdb` in PATH, because on Ubuntu it's installed
in `/usr/lib/postgresql/VERSION/bin/initdb` .
 2023-07-29 00:46:10 +01:00
mvdbeek b61fa18616 Fix `test_most_recently_used` 
I see this failing about 50% of the time, and if it fails history1 and
history2 have the same update time.
 2023-07-29 00:46:09 +01:00
mvdbeek 849219d45a Skip postgres unit tests from psycopg2 not installed 2023-07-29 00:46:09 +01:00
Dannon Baker e5d97e2a72 Merge remote-tracking branch 'upstream/release_23.0' into release_23.1 2023-07-28 15:22:46 -04:00
Matthias Bernt 77c0e915b0 fix regex for profile version 
- did not allow for new style profile versions (that may have only a
  single digit after the dot)
- fix: do not allow `,` in profile version
 2023-07-28 17:32:20 +02:00
mvdbeek fe08cc57c0 Merge branch 'release_23.1' into dev 2023-07-28 15:25:18 +02:00
Marius van den Beek 7bde06cc47 Merge pull request #16474 from nsoranzo/release_23.1_fix_16435 
[23.1] Restore resolution of Conda environments generated from non-lowercase package names
 2023-07-27 20:42:25 +02:00
Nicola Soranzo dd811cf0cc Restore resolution of Conda environments generated from non-lowercase package names 
Fix https://github.com/galaxyproject/galaxy/issues/16435 .
 2023-07-27 13:23:32 +01:00
davelopez e2576cb983 Add missing API endpoints to deal with archived cleanup 2023-07-27 13:23:35 +02:00
Dannon 26031d6a40 Merge pull request #16391 from davelopez/migrate_export_components_to_ts 
Migrate some Remote Files Export components to composition API + TS
 2023-07-27 05:20:06 +10:00
mvdbeek 493f17a323 Merge branch 'release_23.1' into dev 2023-07-26 14:22:48 +02:00
mvdbeek 9e97643df4 Merge branch 'release_23.0' into release_23.1 2023-07-26 14:19:38 +02:00
Matthias Bernt c684e0b305 also warn in case of a filter 2023-07-25 13:14:20 +02:00
Matthias Bernt 2775005b8e make duplicated label a warning 2023-07-25 13:14:20 +02:00
Matthias Bernt af797d92b4 fix linter: duplicated label check 
duplicated labels may be OK if there are filters
 2023-07-25 13:14:20 +02:00
Nicola Soranzo c7a38d06d5 Fix new errors from ruff 0.0.279 2023-07-23 16:25:27 +01:00
John Davis c6ec1dd12b Fix SA2.0 syntax in test_workflow_refactoring 
.unique() is required due to joint eager loading specified in the
StoredWorkflow model.
 2023-07-21 13:04:23 -04:00
John Davis 9db76ab147 Fix SA2.0 syntax (query->select) in integration tests 2023-07-21 13:04:23 -04:00
John Davis b0a765ded5 Fix SA20 syntax in test_vault_extra_prefs, refactor 2023-07-21 13:04:23 -04:00
John Davis e1f9d7d97a Fix SA20 syntax in test_local_job_cancel., refactor 2023-07-21 13:04:23 -04:00
John Davis bce033e3fd Fix SA20 syntax in test_vault_file_source, refactor 2023-07-21 13:04:23 -04:00
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 acda6d87a9 Drop redundant commented out test 
This does not test DatasetRBACPermissions; the create dataset function
is tested in TestDatasetManager.
 2023-07-21 13:02:59 -04:00
mvdbeek cbb011962d Merge branch 'release_23.1' into dev 2023-07-21 12:01:57 +02:00
John Davis 53c6fe8f44 Merge pull request #16384 from mvdbeek/job_cache_fixes_for_dces 
[23.1] Job cache fixes for DCEs
 2023-07-20 00:29:33 +10:00
mvdbeek 746f9bb088 Fix test discovery in vscode 
The vscode extension doesn't like the skip being raised during discovery
anymore.
 2023-07-18 12:32:04 +10:00
mvdbeek a5275e62e4 Fix test discovery in vscode 
The vscode extension doesn't like the skip being raised during discovery
anymore.
 2023-07-16 12:17:06 +10:00
John Davis c58f74228c Merge pull request #16232 from claudiofr/celery_url 
Limit number of celery task executions per second per user
 2023-07-15 16:17:42 +10:00
davelopez 00e4740ad8 Fix selenium selector for history import 2023-07-14 14:03:52 +02:00
davelopez 0367e0fbcf Add coverage for counting with archived histories 2023-07-13 11:31:51 +02:00
claudiofr ae56d7c006 Pass user id to celery tasks to enable new user rate limiting functionality. 
Remove unnecessary integration tests. Change calls to celery tasks to pass values
to new task_user_id parameter which is used for user rate limiting.
 2023-07-12 10:35:54 -04:00
claudiofr 05885febb3 Limit number of celery tasks that a user can run per second. 
Introduce a celery_user_rate_limit config parameter which
specifies how many tasks per second a user can execute. Create a
custom celery Task class called GalaxyTask with a before_start hook
that implements the rate limiting logic. Add a new table,
celery_user_rate_limit that tracks the last scheduled execution time
by user id. Add new integration test, test_celery_user_rate_limit.py.
 2023-07-12 10:35:54 -04:00
Nicola Soranzo 264747f172 Merge branch 'release_23.1' into dev 2023-07-12 14:29:56 +01:00
mvdbeek b2f044c295 Extend test to reproduce disk usage recalculation wrongly dropping to 0 when no quota source is defined 2023-07-07 22:09:49 +10:00
mvdbeek c6c46b2a23 Extend user disk usage recalculation test 
to include a distributed object store config with and without celery
enabled.
 2023-07-07 20:58:41 +10:00
Laila Los 7a44a166a4 fix selenium test 2023-07-07 04:39:35 +02:00
Rendani Gangazhe e428ca2b79 Fix copy paste error 2023-07-06 09:21:32 +02:00
Rendani Gangazhe 753d199542 Merge dev and resolve conflicts 2023-07-03 10:54:25 +02:00
Rendani Gangazhe aa4177c4ff Add unit tests for get_carbon_intensity_entry 2023-06-30 17:45:34 +02:00
mvdbeek f887311ab4 Merge branch 'release_23.1' into dev 2023-06-28 15:21:59 +02:00
davelopez 2298f42ed7 Update XSD schema docs 
- Remove checksum support for inputs for now
 2023-06-28 12:31:42 +02:00
davelopez 49719e20cc Partially revert #15510 
This solution was suboptimal as it moved around too much unnecessary data
 2023-06-28 12:28:06 +02:00
Nicola Soranzo 7a4505ef41 Ignore false positive `comparison-overlap` mypy error 
xref. https://github.com/python/mypy/issues/15509

Introduced in mypy 1.4.0 .
 2023-06-26 00:40:25 +01:00
claudiofr ae97462073 Move test_resolution_cache_db.py to test/unit/app/tools directory 
The test/unit/app directory tree has a test-requirements.txt file that
brings in dependencies required by database utility modules imported by
the unit test.
 2023-06-21 22:45:13 +02:00
claudiofr 17f22c28f3 Add new config parameters for citation database beaker cache in tool_shed yaml file 2023-06-21 22:45:12 +02:00
claudiofr fe63ba9dcf Clear the beaker caches after creating them on app startup 
Clear the caches in the event the cache type is database. This will
delete any rows in the cache table that could be left over from a
prior run of the app preventing an accumulation of stale data.
 2023-06-21 22:45:12 +02:00
claudiofr 2d3547a630 Change default beaker cache type to file for the 3 beaker caches. 2023-06-21 22:45:12 +02:00