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782 Commits
Author SHA1 Message Date
davelopez 48c9d6f7c8 Relax file source access requirements in tests 
By default the user must have the required role and groups. To simplify the setup of other tests, by default `PosixFileSourceSetup` will not require groups unless explicitly specified in the test.
This way we are always testing the default `test user` access through the role.
 2022-12-02 13:12:28 +01:00
davelopez 3b89e982fb Add failing test for export to FTP using tasks 2022-12-02 09:59:09 +01:00
John Davis 71769182b6 Ignore 2 type errors in tests 2022-11-29 14:59:17 -05:00
John Chilton a558037321 Merge pull request #14971 from mr-c/mypy_0.990 
bonus Python typing
 2022-11-28 20:50:49 +01:00
Nicola Soranzo 962def5bb8 Merge branch 'release_22.05' into dev 2022-11-28 15:22:49 +00:00
Nicola Soranzo 9980ebebab Merge pull request #15039 from mvdbeek/fix_tmpdir_mounting 
[22.05] Mount ``$TMPDIR``, ``$TMP`` and ``$TEMP`` into container
 2022-11-28 13:09:06 +00:00
Michael R. Crusoe 75ba9cfd13 Even more typing 2022-11-28 04:50:00 +00:00
Michael R. Crusoe 2e69f64496 mypy 0.991 + bonus extra typing 2022-11-28 04:50:00 +00:00
Nicola Soranzo 4a7e25e665 Use `history_id` fixture instead of instance attribute. More type annotations 2022-11-23 04:04:51 +00:00
Nicola Soranzo 3f005412ec Fix Integeration typo 2022-11-23 01:20:00 +00:00
Nicola Soranzo 6609989136 Fix test_objectstore_datatype_upload.py . More type annotations 2022-11-23 01:19:59 +00:00
Michael R. Crusoe 95ea3a2d95 use history_id fixture instead of instance variable with the same name 2022-11-23 01:19:59 +00:00
mvdbeek b3c0428ceb xfail kubernetes test_job_environment 2022-11-21 15:07:41 +01:00
mvdbeek b6117ee3df Fix metadata setting for discovered datasets with extended metadata 
Fixes https://github.com/galaxyproject/galaxy/issues/15036
 2022-11-20 16:02:15 +01:00
davelopez 0c2f9d98de Add test for metadata generation 2022-11-17 11:10:36 +01:00
davelopez fb66f4c1f1 Do not force all datasets as discarded on import by default 2022-11-17 11:10:36 +01:00
davelopez 80feaafdda Add test to import history from file source using tasks 
Currently the test will fail because the imported datasets are in the "discarded" state.
 2022-11-17 11:10:36 +01:00
mvdbeek bac4736e05 Merge remote-tracking branch 'upstream/release_22.05' into dev 2022-11-16 12:07:04 +01:00
mvdbeek 693b25bfa6 Test x-accel/x-sendfile support 2022-11-15 19:44:42 +01:00
Dannon af90d66216 Merge pull request #14981 from davelopez/22.05_fix_invalid_quota_amount 
[22.05] Fix invalid quota amount
 2022-11-14 10:39:19 -05:00
davelopez f9efd46945 Add test for invalid quota amount 2022-11-14 12:04:43 +01:00
Marius van den Beek e3a91ab217 Merge pull request #14863 from jmchilton/puslar_extended_metadata_fixes 
Various Pulsar extended metadata fixes
 2022-11-08 11:51:59 +01:00
Marius van den Beek 261af2a5c6 Merge pull request #14739 from nsoranzo/replace_unittest.TestCase 
Replace ``unittest.TestCase`` in API, framework, performance, Selenium and ToolShed tests
 2022-11-07 21:13:05 +01:00
John Chilton 25eb7ea906 Merge pull request #14873 from mvdbeek/enable_restriceted_value_guessing_for_subworkflow_inputs 
Fix restricted values for parameter connected to subworkflow input
 2022-11-07 17:38:04 +01:00
Nicola Soranzo 81ddcde33e Rename class which is not derived from `TestCase` 
to make `.ci/check_test_class_names.sh` happy.
 2022-11-07 15:44:03 +00:00
Nicola Soranzo 3a8997ccf2 Replace `unittest.TestCase` in API, framework, performance, Selenium and ToolShed tests 
In API tests, replace no more working `uses_test_history` decorator (because
the `history_id` method parameter is interpreted as a fixture) with a real
class-level pytest fixture.
As a consequence, replace use of `self.history_id` in API tests because it
interferes with the class-level `history_id` fixture.

Also:
- Some type annotations
 2022-11-07 15:44:01 +00:00
John Chilton 89394bd8b9 Progress toward fixing extended metadata with Pulsar 2022-11-02 08:59:12 -04:00
Nicola Soranzo 5ca0aea54a Drop nose 
It's deprecated and unmaintained, and is broken under Python 3.10 .
 2022-11-01 18:45:07 +00:00
mvdbeek accdea9b14 Always inject all modules, then compute runtime state 2022-10-29 22:11:03 +02:00
Marius van den Beek a052f0baba Merge pull request #14714 from kxk302/idle_connection_pool_cleaner 
Idle connection pool cleaner
 2022-10-18 23:46:26 +02:00
Kaivan Kamali 587169394f REduced refresh time and monitor interval so test completes more quickly 2022-10-17 16:35:35 -04:00
John Chilton 5a3069d283 Pulsar infrastructure improvements for TES execution and MQ-less Kubernetes. 
Updating the Pulsar job runner/client for https://github.com/galaxyproject/pulsar/pull/302 and as described in the new docs at https://pulsar.readthedocs.io/en/latest/containers.html.
 2022-10-16 09:56:58 +02:00
davelopez c776c8169a Validate BioCompute Objects against schema in tests 2022-10-14 12:20:24 +02:00
davelopez 0950722c7c Exclude null values when serializing BCO 
+ fix typo
 2022-10-14 12:20:24 +02:00
davelopez 2140df7eed Add basic BCO export integration tests 2022-10-14 12:20:24 +02:00
Kaivan Kamali 75fcf3fcd3 Instantiating multiple instances of a specific upload test classes results in hng threads. Circumvented this by subclassing the Irods test class. 2022-10-12 12:21:13 -04:00
John Chilton 84005605c8 Extend tool shed install testing to include index API. 2022-10-10 11:19:18 -04:00
Kaivan Kamali 941f54f6b7 New IrodsUploadTestDatatypeDataTestCase for idle connection test 2022-10-07 15:02:35 -04:00
Kaivan Kamali 7d93b39bcc Merge branch 'dev' of https://github.com/galaxyproject/galaxy into idle_connection_pool_cleaner 2022-09-27 12:30:38 -04:00
Nicola Soranzo c35d8f2a06 Replace `unittest.TestCase` with pytest-based partial re-implementation 
Also:
- Rename `FooBarTestCase` test classes as `TestFooBar`. These were collected
  by pytest only because they were `unittest.TestCase` derived, but normally
  pytest collects only test classes whose name starts with `Test`, see
  https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes
 2022-09-27 03:34:58 +01:00
Nicola Soranzo 7646d9eb7b Workaround for abstract test classes 2022-09-27 03:34:56 +01:00
Nicola Soranzo 30d8d2ba66 Remove unused function 2022-09-27 03:34:56 +01:00
Nicola Soranzo 3091737ab9 Misc test fixes 2022-09-27 03:34:55 +01:00
Kaivan Kamali d42df2cb1a Created integration test for connection pool monitor. Revised connection pool monitor thread creation/destruction. 2022-09-26 17:12:30 -04:00
Kaivan Kamali 38b149b187 Added start() to BaseObjectStore, so if needed, object store post fork functions can be called by app 2022-09-23 15:31:28 -04:00
John Chilton 357a2ee954 Improved assertion in error in failing test. 2022-09-22 18:05:33 -04:00
Nicola Soranzo b5c7e2c86a Replace `self.assert* method calls with plain asserts in test/` 
using https://github.com/pytest-dev/unittest2pytest with the following command:

```
unittest2pytest -f self_assert -w -n test/
```

(excluding ``self.assertRaises*`` method calls).
 2022-09-21 23:50:05 +01:00
Kaivan Kamali 6105688bef Added connection pool monitor, to remove stale idle connections. 2022-09-20 15:27:31 -04:00
John Davis 4c7d6805e7 Drop integration test for config defaults 2022-09-16 15:31:55 -04:00
davelopez 0128e05a23 Fix export ro-crate to file source 
Write to the store the correct archive file
 2022-09-16 17:19:49 +02:00