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7154 Commits
Author SHA1 Message Date
Marius van den Beek d689b79169 Merge pull request #15090 from davelopez/fix_task_history_export_ftp 
Fix export history to FTP using tasks
 2022-12-06 14:51:49 +01:00
Björn Grüning 6a5608bcd6 Merge pull request #15031 from jmchilton/structured_test_decorators 
Infrastructure for indicating Galaxy features being used by tests.
 2022-12-03 10:34:49 +01:00
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
davelopez efcf76e3b5 Return 404 when target expires or doesn't exists 2022-12-02 09:57:29 +01:00
John Davis 0aa0feb610 Merge pull request #15004 from jdavcs/dev_mypy_workflow 
Run mypy on a fully loaded galaxy venv for stricter type checking
 2022-11-30 22:30:37 -05:00
Martin Cech e4becc21a0 Merge pull request #14959 from bernt-matthias/topic/lint-expect_failure_num_outputs 
lint for coexisting expect_num_outputs and expect_failure
 2022-11-30 20:06:29 +01:00
John DavisandNicola Soranzo 02ea4f531e Drop unused attr 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-30 13:39:16 -05:00
John DavisandNicola Soranzo 67c7e7d1ac Use a simple cast instead of relying on dependency injection 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-30 13:33:42 -05:00
Nicola Soranzo 139d14e952 Fix `object_store type in MinimalToolApp` protocol 2022-11-30 17:55:04 +00:00
Nicola Soranzo 95ccefacb8 Improve type annotations for model store 
and related files.

Follow-up on https://github.com/galaxyproject/galaxy/pull/14971 .
 2022-11-30 01:45:56 +00:00
John Davis 71769182b6 Ignore 2 type errors in tests 2022-11-29 14:59:17 -05:00
John Davis cbabba8f49 Fix typing error in unit test 2022-11-29 14:59:17 -05:00
John Davis aba2b4c52a Fix mypy error (has-type) 
Fixes this error: (the value is of type sqlalchemy.orm.Session; I don't
know what it's not inferred)

test/unit/app/authnz/test_custos_authnz.py:225: error: Cannot determine type of "sa_session"  [has-type]
                    self.session = self.sa_session
 2022-11-29 14:59:17 -05:00
Martin Cech 85058e4331 Merge pull request #15018 from natefoo/job-conf-yaml 
Replace XML job conf sample with YAML
 2022-11-29 00:52:05 +01:00
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
Matthias Bernt 0b4d75419e lint for coexisting expect_num_outputs and expect_failure 
which makes no sense since output assumption are not checked
if an error occurs
 2022-11-28 14:07:53 +01:00
Nicola Soranzo de5e9c0e71 Add some type annotations to `WebApplication and GalaxyWebTransaction` 2022-11-28 04:50:03 +00:00
Nicola Soranzo c5868cc717 Add overloads to `listify()` type annotations 
Also:
- Add unit tests.
 2022-11-28 04:50:03 +00:00
Nicola Soranzo 807fdfa5af Type annotation fixes 2022-11-28 04:50:01 +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
John Chilton 5fb47ac23f WIP: selenium test decorators... 2022-11-26 11:31:13 -05:00
John Chilton 018d066e36 Useful test decorators and runtime support for annotating how tests will be used. 2022-11-26 11:28:36 -05:00
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
John Davis d11eab88aa Merge pull request #15010 from jdavcs/dev_galaxy_root_func 
Use galaxy_directory() util function to check if code is running from root or from packages
 2022-11-22 10:25:38 -05:00
John Davis f3b109a7a5 Merge pull request #14993 from jdavcs/dev_datatypes_contbl 
Refactor, add type hints to get_chunk() in datatypes
 2022-11-22 09:53:06 -05:00
John Davis e0145fad50 Rename template.py >> templates.py 2022-11-21 18:12:04 -05:00
John Davis 3b488017b1 Normalize path before checking basename 2022-11-21 18:12:04 -05:00
John Davis b2d6b8d40d Skip dbscript tests if running from packages; refactor util function 2022-11-21 18:12:04 -05:00
John Davis 116682a59f Do not call split on cmd: there may be spaces in path 2022-11-21 18:12:04 -05:00
John Davis b934b27ea0 Move custom tempates unit test into app; rm jinja2 package dep from config 2022-11-21 18:12:04 -05:00
John Davis 29053fa9e4 Move test_dbscript into app 
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 86cc0f2b69 Move custom templates into the config package 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
mvdbeek b3c0428ceb xfail kubernetes test_job_environment 2022-11-21 15:07:41 +01:00
mvdbeek 702bdc0ec9 Test that tempdir creation is possible 2022-11-21 11:44:24 +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
mvdbeek c01e6b8797 Install conda for framework tests 2022-11-20 08:58:33 +01:00
John Davis 44e7c97b6d Fix get_chunk(), add test 2022-11-18 18:24:54 -05:00
mvdbeek f24eaa581a Use APITestCase class to run framework tool tests 2022-11-18 18:35:15 +01:00
Nate Coraor 1cdb7b5bcd Replace XML job conf sample with YAML. 
Prefer loading job_conf.yml, fall back to job_conf.xml with a warning if
it exists.
 2022-11-17 19:58:24 -05:00