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v22.05.1.dev0
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31684 Commits
Author SHA1 Message Date
mvdbeek 88a986c578 Update version to 22.05.1.dev0 2022-08-22 23:14:27 +02:00
Nicola Soranzo 4fcbe80268 Doc fixes 2022-08-19 18:33:20 +01:00
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 1545b9da99 Simplify query_parameter_as_list 
And render the repeated parameter input in the docs.
The first parameter can be a comma-separated list of values
 2022-08-19 12:30:53 +02:00
Marius van den Beek 65c724ec66 Merge pull request #14475 from jancrichter/patch-1 
[22.05] Grep1 tool: fix keep_header option
 2022-08-19 11:43:38 +02:00
Matthias Bernt b1e7b895b5 fix deprection warning 
which pops up at every `planemo lint`:

```
galaxy/tool_util/deps/requirements.py:348: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
```
 2022-08-19 10:29:06 +02:00
davelopez 05ed92688c Fix Jobs API index endpoint 
Use the `query_parameter_as_list` dependency to support multiple ways of providing lists of values while rendering the API docs as a single string query parameter.
 2022-08-18 18:39:34 +02:00
davelopez 1a103279af Add query_parameter_as_list dependable 
Supports declaring query parameters as 'listified'
 2022-08-18 18:37:10 +02:00
mvdbeek 446b07b4c0 Adjust workflow safe tool version update range for Grep1 2022-08-18 17:50:21 +02:00
Marius van den Beek 01a4915e29 Merge pull request #14476 from bernt-matthias/topic/linter-fixes 
[22.05] Tool linter bug fixes
 2022-08-18 17:35:51 +02:00
M BerntandMarius van den Beek 2bd8044a4d Remove comment 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-08-18 17:18:36 +02:00
Matthias Bernt d7006d2429 add scool datatype 
used in IUC schicexplorer
 2022-08-18 16:50:47 +02:00
Matthias Bernt df81e5568c explicitly test for None 
found one tool where argument was "" due to macro usage
 2022-08-18 14:35:11 +02:00
Matthias Bernt d8036a8418 f-string fix 2022-08-18 14:35:11 +02:00
Matthias Bernt b41bc6d336 allow no_options validator for data and data_collection 2022-08-18 14:35:11 +02:00
Matthias Bernt 1ede9e839d xsd: allow 0 for bytes 2022-08-18 14:35:11 +02:00
Matthias Bernt 5f0fbb061b fix docs 2022-08-18 14:30:14 +02:00
qiagu ea85cab75a Revert startswith of tool parameter options 2022-08-18 11:04:12 +02:00
mvdbeek 685ac29018 Fix qunit tests 2022-08-18 10:18:46 +02:00
mvdbeek e35b82aef1 Selenium test for changing datatype 
In subworkflows and outside. All asserts terminal label.
 2022-08-18 10:18:10 +02:00
Nate Coraor 1ec5909b98 Merge pull request #14471 from natefoo/gravity-0.13.3 
[22.05] Bump Gravity version to 0.13.3
 2022-08-17 16:35:13 -04:00
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
Nate Coraor 69ca03e99a Bump Gravity version to 0.13.3 2022-08-17 13:48:39 -04:00
Marius van den Beek cd94ccb6c5 Merge pull request #14457 from natefoo/log-rotation 
[22.05] Add log rotation options and update logging documentation
 2022-08-17 19:24:07 +02:00
Dannon 7d2f8dcdc8 Merge pull request #14470 from mvdbeek/singularity_fix_cleanenv 
[22.05] Fix position of cleanenv flag in singularity command
 2022-08-17 06:34:51 -04:00
Marius van den Beek 1b1d015c3d Merge pull request #14467 from natefoo/disable-translogger 
[22.05] Disable translogger middleware by default
 2022-08-17 09:55:04 +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
Nicola Soranzo 961472cfff Merge branch 'release_22.01' into release_22.05 2022-08-16 23:25:42 +01:00
Nate Coraor d1b37347da Disable translogger middleware by default, use gunicorn.access (actually 
uvicorn.access) for transaction logging.
 2022-08-16 12:37:45 -04:00
mvdbeek b0727be9e0 Fix change_datatype not reflected in tool and workflow output terminals 2022-08-16 15:46:11 +02:00
Marius van den BeekandNicola Soranzo cd76fef415 Convert to UTC instead of stripping timezone 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-08-16 13:11:21 +02:00
Nate Coraor 3522fd3a49 Add log rotation options and update logging documentation 2022-08-15 20:54:02 -04:00
Enis Afgan e91a659f1f Merge pull request #14449 from nuwang/docker_k8s_ansible_fixes 
Docker k8s ansible fixes
 2022-08-15 19:20:03 +00:00
Nicola Soranzo 69defb7a20 Doc fixes 2022-08-15 19:15:02 +01:00
mvdbeek 414156af8a Fix data_range_{min,max} parsing 
All datetime values established via our sqlalchemy models don't include `tzinfo`.
Fixes
https://github.com/galaxyproject/galaxy/issues/14094#issuecomment-1215166187.

In general this is a bad thing, we should definitely be honoring
timezone info, but the rest of the app just assumes UTC, so this will
work.
 2022-08-15 17:59:25 +02:00
Marius van den Beek 71ec60337e Merge pull request #14452 from mvdbeek/22_05_routes_with_trailing_slashes 
[22.05] Register trailing slashes in API routes
 2022-08-15 15:33:07 +02:00
mvdbeek 5c993ac652 Use non-aliased group user url in tests 2022-08-15 12:35:39 +02:00
mvdbeek cd6ce8d5ef Register trailing slashes in API routes 2022-08-15 11:51:51 +02:00
Nuwan Goonasekera 6fff1e0877 Fix a minor typo 2022-08-14 18:09:36 +05:30
Nuwan Goonasekera c602933ac9 Revert "Fix minor typo" 
This reverts commit b41ccccda1.
 2022-08-14 18:04:02 +05:30
Nuwan Goonasekera b41ccccda1 Fix minor typo 2022-08-14 12:56:01 +05:30
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
Dannon 9c0fcad2cb Merge pull request #14417 from mvdbeek/crc32_for_specific_file_sizes 
[22.05] Calculate CRC32 for files in size between 1444 and 1459 bytes
 2022-08-12 09:52:34 -04:00
Marius van den Beek a9027459c3 Merge pull request #14426 from davelopez/22.05_make_contains_filter_case_insensitive 
[22.05] Make history contents filter with `contains` case insensitive
 2022-08-12 13:42:13 +02:00
Marius van den Beek bb19e41ebc Merge pull request #14277 from astrovsky01/agp_sniff 
[22.05] Make Agp set_meta more lenient
 2022-08-12 11:31:14 +02:00
Marius van den Beek 9dd74fc953 Merge pull request #14431 from mvdbeek/cached_image_path_identifier_fix 
[22.05] Fix cache image singularity resolver if path contains uppercase chars
 2022-08-12 11:21:49 +02:00
mvdbeek 034ea59200 Use func.lower and autoescape for contains filters 2022-08-11 19:38:27 +02:00
Marius van den BeekandNicola Soranzo b4a8c061c2 Use os.sep.join 
Much nicer!

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-08-11 17:21:34 +02:00