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6878 Commits
Author SHA1 Message Date
John Davis bd56131ebd Split script into admin and dev 
TODO: remove duplication between db.py and db_dev.py (split into
multiple commits is intentional)
 2022-09-28 15:45:00 -04:00
John Davis e43552fdc5 Rename db.sh > manage_db.sh, following code review feedback 2022-09-28 15:45:00 -04:00
John Davis 0c348a5759 Update test comments 2022-09-28 15:32:10 -04:00
John Davis dfd32a2ee8 Add type hints 2022-09-28 15:32:01 -04:00
John Davis 6fcc58a85c Drop LegacyScripts: no longer used 2022-09-28 15:31:25 -04:00
John Davis d8e8a8efb6 Add --raiseerr option; hide error traceback by default 2022-09-28 15:25:14 -04:00
John Davis b4b76c91a2 Add missing tests 2022-09-28 15:25:06 -04:00
John Davis bf83b4347a Fix mypy by asserting object before accessing its attributes 2022-09-28 15:24:40 -04:00
John Davis e0e30a5744 Fix packages tests: script is one level up 2022-09-28 15:24:26 -04:00
John Davis 3be7c53eb9 Fix linting 2022-09-28 15:24:16 -04:00
John Davis ab1854f3a7 Test against 1 or 2 databases 2022-09-28 15:23:50 -04:00
John Davis 887b882ff0 Add inline testing documentation 2022-09-28 15:23:42 -04:00
John Davis b64fda7478 Add initial draft 2022-09-28 15:23:21 -04:00
John Davis 4cd3291598 Refactor get_alembic_cfg: make available to other code 2022-09-28 15:23:09 -04:00
John Chilton ace1e13da3 Merge pull request #14641 from mvdbeek/fix_optional_data_input_submission_expanded_tool_form 
[22.05] Fix delayed optional data input handling
 2022-09-22 18:08:58 -04:00
mvdbeek 64cb245ddd Fix running subworkflows with disconnected optional/default inputs 2022-09-21 19:31:41 +02:00
Nicola Soranzo dc0ac34fc4 Merge pull request #14588 from mvdbeek/fix_noisy_exception_logging_when_unicode_null_in_session_key 
[22.05] Ensure guid is hexadecimal value
 2022-09-08 19:05:54 +01:00
mvdbeek aceaa698fc Ensure guid is hexadecimal value 2022-09-08 14:04:35 +02:00
Nicola Soranzo 70b2ea429c Merge branch 'release_22.01' into release_22.05 2022-09-06 12:12:21 +01:00
Nicola Soranzo 9f1d8d053b Merge branch 'release_21.09' into release_22.01 2022-09-06 11:36:36 +01:00
Nicola Soranzo 06baa27d05 Merge branch 'release_21.05' into release_21.09 2022-09-06 11:24:20 +01:00
Nicola Soranzo 8069584d0f Merge branch 'release_21.01' into release_21.05 2022-09-06 11:12:59 +01:00
mvdbeek d1b4f05345 Merge branch 'release_22.01' into release_22.05 2022-08-30 20:32:39 +02:00
Nicola Soranzo 6519604620 Add some type annotations 2022-08-30 14:34:54 +01:00
Nicola Soranzo 4faa486c49 Merge pull request #14526 from bernt-matthias/topic/fix-test-linters 
[22.05] Fix typos in test linter
 2022-08-30 12:16:10 +01:00
Nicola Soranzo 61b6eb1ee9 Fix more `discovered_datasets` typos 2022-08-30 09:57:26 +01:00
mvdbeek 3b583a12c7 Give a hint about newlines when datatype test fails 2022-08-29 17:53:00 +02:00
mvdbeek 60cda23970 Mock quay.io API calls, pass install=False to not pull docker images 2022-08-29 16:38:31 +02:00
mvdbeek c4f576ccf3 Fix cache lookup condition 2022-08-29 16:38:31 +02:00
mvdbeek c4a9050af9 Fix _namespace_has_repo if cache namespace cache key not present 2022-08-29 14:08:49 +02:00
Matthias Bernt a8a80cf431 fix typo in test linter 2022-08-29 11:36:59 +02:00
Matthias Bernt 59f77048ce test case showing failing set_meta 
broke in https://github.com/galaxyproject/galaxy/commit/7d0ec29fa06ae6f04c0ae6fc193a390bc11cddcd
 2022-08-25 16:45:26 +02:00
mvdbeek 94c75a083c Fix setting metadata elements in conditional tool action 
Fixes https://github.com/galaxyproject/galaxy/issues/14509
 2022-08-25 14:27:44 +02:00
mvdbeek 8a8acc625f Fix refactor action dropping outputs on subworkflow connection 
I thought it would be cleaner to make a distinction between the output
name and the output label when reasoning about a subworkflow step in
the context of a parent workflow
(https://github.com/galaxyproject/galaxy/pull/14473/commits/b0727be9e0b096a2dacacb767a1f4ac0fc3e6540#diff-a50bcc5c08ade11249449c4100ea8c286727df601b52a5b9588eb2a385d97da7R543),
in case we'd later want to do something with the label.

I don't think I thought about this correctly though,
and it breaks connections between steps that were made by referencing
the subworkflow's output name.

This wasn't necessary for the main goal of
https://github.com/galaxyproject/galaxy/pull/14473, so I'm partially
reverting that here.

Fixes https://github.com/galaxyproject/planemo/pull/1262#issuecomment-1223874571
 2022-08-23 14:12:29 +02:00
Nicola Soranzo b5a75cac27 Merge branch 'release_22.01' into release_22.05 2022-08-19 15:28:58 +01:00
Marius van den Beek cccdb496b8 Merge pull request #14482 from davelopez/22.05_fix_query_parameter_lists 
[22.05] Fix Jobs API index to accept query parameters as lists
 2022-08-19 13:23:32 +02:00
Dannon d1c66d61b5 Merge pull request #14473 from mvdbeek/change_datatype_problems 
[22.05] Fix effective datatype in workflow editor node terminals
 2022-08-19 06:32:49 -04:00
davelopez 1d59487365 Add unit tests for query_parameter_as_list 2022-08-19 08:59:02 +02:00
Matthias Bernt 8ef9ef4383 fix test 2022-08-18 14:28:55 +02:00
Nicola Soranzo 9915a6eeeb Merge pull request #14456 from mvdbeek/drop_tzinfo_when_parsing_datetime 
[22.05] Fix data_range_{min,max} parsing
 2022-08-17 20:06:43 +01:00
Marius van den BeekandNicola Soranzo 973d0779b6 Include timezone testing 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-08-17 18:43:57 +02:00
mvdbeek 6eb034706f Fix position of cleanenv flag in singularity command 
Fixes https://github.com/galaxyproject/galaxy/issues/14408#issuecomment-1216742827
 2022-08-17 09:53:08 +02:00
mvdbeek b0727be9e0 Fix change_datatype not reflected in tool and workflow output terminals 2022-08-16 15:46:11 +02:00
mvdbeek b0d9cff6c4 Add unit test 
That was meant to go into the first commit ...
 2022-08-16 13:12:28 +02:00
Marius van den Beek df3d5a1992 Merge pull request #14429 from mvdbeek/singularity_no_host_env_vars 
[22.05] Pass ``--cleanenv`` by default to singularity command
 2022-08-12 15:58:05 +02:00
mvdbeek 0560e43a48 Fix cache image singularity resolver if path contains uppercase chars 
Fixes https://github.com/galaxyproject/galaxy/issues/14425
 2022-08-11 13:32:21 +02:00
mvdbeek 0eff482466 Pass --cleanenv by default to singularity command 2022-08-10 16:52:59 +02:00
davelopez bcff4a1995 Update integration test 
Test boolean expression with group names containing spaces and surrounded by single quotes
 2022-08-05 15:56:21 +02:00
davelopez 4846d04dad Add unit test for quoted strings with spaces 2022-08-05 15:54:04 +02:00
davelopez af949c2fd3 Revert adding __hash__ to BaseDatabaseIdField 2022-08-04 11:23:31 +02:00