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6855 Commits
Author SHA1 Message Date
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
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
davelopez e5b11bb25b Add unit tests for DabaseIdFields hashing 2022-08-02 11:10:35 +02:00
Nicola Soranzo e383e593e0 Merge branch 'release_22.01' into release_22.05 2022-07-27 15:38:19 +01:00
Matthias Bernt fe06eea75d fix test output 2022-07-15 10:49:12 +02:00
M BerntandNicola Soranzo d7272cc987 Update test/functional/tools/options_from_metadata_file.xml 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-07-14 23:30:11 +02:00
Matthias Bernt d642ce34c8 fix startswith attribute of <options> 
as documented in the xsd

in addition fix https://github.com/galaxyproject/galaxy/issues/14324,
i.e. document the `separator` attribute of options

also doc that only 1MB is used and lines starting with `#` are always
ignored
 2022-07-14 14:19:40 +02:00
John Davis def882932d Add verify_db_is_initialized function; tests 2022-07-13 16:10:58 -04:00
John Davis 1e75d85fd4 Prevent accessing LegacyScripts.database before processing script args 2022-07-13 15:40:42 -04:00
Nicola Soranzo 9a08a76ac0 Merge pull request #14284 from mvdbeek/fix_json_encoding_things 2022-07-10 17:57:06 +01:00
mvdbeek 73c73e0822 Test Decimal/inf/nan value dumping 2022-07-08 19:39:38 +03:00
Nicola Soranzo d4d3485b72 Fix mypy reexport error for testfixtures 
Fix this mypy error for the galaxy-app package:

```
tests/app/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py:5: error:
Module "testfixtures" does not explicitly export attribute "log_capture";
implicit reexport disabled  [attr-defined]
    from testfixtures import log_capture
    ^
```
 2022-07-08 02:33:28 +01:00
Evan Bolyen 184f0d8eaf TST: fix qiime2.tabular auto-upload test 2022-07-05 09:43:30 -07:00
Evan Bolyen 9c06e232e1 lint: make format is neat 2022-07-05 09:43:30 -07:00
Evan Bolyen 88fed0ffff TST: added more tests 2022-07-05 09:43:30 -07:00
Oddant1 38b1bfc417 QIIME 2: Strip properties from semantic types (#2) 2022-07-05 09:43:30 -07:00
mvdbeek 22f761aa10 Fix validation of nested element fetch data payloads 
Fixes https://github.com/galaxyproject/galaxy/issues/14242
 2022-07-01 13:52:06 +02:00
mvdbeek 84ea10767a Unit test for No response returned error 2022-06-27 18:11:49 +02:00
mvdbeek df6551da78 Test that metadata validators work 2022-06-25 12:55:51 +02:00
mvdbeek 8178178736 Test deferred data with extended metadata and metadata files 
And also test that option filters work correctly.
 2022-06-25 12:55:51 +02:00
Nicola Soranzo d3b4ef81d0 Merge branch 'release_21.09' into release_22.01 2022-06-23 14:30:57 +01:00
mvdbeek f139d29f19 Drop custom fail_job method in pbs/chronos/pulsar 2022-06-23 10:38:54 +02:00
Marius van den Beek 759065dc82 Merge pull request #14100 from mvdbeek/upload_dir_fix 
[22.05] Write temporary files created within celery tasks to working directory
 2022-06-21 13:06:22 +02:00
Marius van den Beek 88163ff5da Merge pull request #14114 from mvdbeek/xfail_openpbs_test 
Mark openPBS integration test cases as xfail
 2022-06-21 13:05:17 +02:00
Dannon 155c1c6e48 Merge pull request #5378 from jmchilton/resource_requirements 
Allow specification of resource requirements in tools.
 2022-06-20 14:11:35 -04:00