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Author SHA1 Message Date
mvdbeek 2d1b341fcd WIP: Drop uWSGI from scaling documentation 2022-02-15 17:22:58 +01:00
Marius van den Beek ed8fce2f89 Merge pull request #13333 from dannon/fix-toolbox-cache 
[22.01] Fix toolbox cache
 2022-02-15 12:23:39 +01:00
Dannon Baker f7e6061903 Fall back to localStorage when indexeddb is unavailable 2022-02-14 23:20:56 -05:00
Dannon Baker 9ca28b29bb deepmerge breaks vuex stores that shouldn't even be touched here -- back down to vuex-persist 2.3 until we replace all this with pinia and isolated stores 2022-02-14 22:34:54 -05:00
Dannon Baker 02df329f4c More explicit configuration of indexeddb for use in store 2022-02-14 21:05:13 -05:00
Dannon Baker a9f8ca99aa Swap in localForage for toolbox persistence; much larger capacity here 
and it's async.
 2022-02-14 21:05:13 -05:00
Dannon Baker 9da5ef6c93 Drop debugging 2022-02-14 21:05:13 -05:00
Dannon Baker 66081375db Drop vuex-persistedstate (deprecated now anyway), use vuex-persist instead 2022-02-14 21:05:13 -05:00
Marius van den Beek 267ff2103a Merge pull request #13363 from astrovsky01/workflow_input_tag_collections 
[22.01] Make workflow tag for input collections optional
 2022-02-12 11:11:44 +01:00
Alexander OSTROVSKY 972faaaea1 add optional for workflow tag input collections 2022-02-11 15:09:32 -08:00
Dannon 2f1c862a8f Merge pull request #13293 from mvdbeek/fix_text_parameter_connected_to_select 
[22.01] Fix construction of SelectToolParameter default value
 2022-02-11 13:12:12 -05:00
Marius van den Beek abb7a74395 Merge pull request #13347 from dannon/fix-toolid-urls 
[22.01] Fix toolbox handling of spaces in old tools
 2022-02-11 19:09:01 +01:00
Marius van den Beek e6a2d75472 Merge pull request #13356 from mvdbeek/release_22.01 
[22.01] Merge 21.09 into 22.01
 2022-02-11 15:20:28 +01:00
mvdbeek 973f6679d6 Merge branch 'release_21.09' into release_22.01 2022-02-11 13:29:04 +01:00
Dannon Baker 3e8b6a7092 Force encoding of toolbox's tool_id routing to use '%20' instead of '+', 
since we ignore + because it's a valid character.
 2022-02-10 08:29:55 -05:00
Marius van den Beek c1f959d909 Merge pull request #13330 from mvdbeek/exp_imp_anonymous 
[22.01] Fix history exports import by url
 2022-02-10 12:11:19 +01:00
Marius van den Beek 76a8e12d21 Merge pull request #13325 from mvdbeek/remap_fix_sentry 
[21.09] Fix resuming job when job has optional data parameters
 2022-02-10 11:19:20 +01:00
mvdbeek 96d89a4f5c Drop API key from more places 2022-02-09 17:38:10 +01:00
mvdbeek db6e2db4dc Endpoint needs to be sessionless as well 2022-02-09 17:30:34 +01:00
mvdbeek 925f44a16e Improve (history import) job error reporting 2022-02-09 17:30:12 +01:00
Nicola Soranzo bf3a5420ef Merge pull request #13317 from mvdbeek/fix_command_recording 2022-02-09 10:21:52 +00:00
mvdbeek 991f82b136 Fix history exports import by url 2022-02-08 22:56:57 +01:00
Marius van den BeekandNicola Soranzo 7c4905251c Get the needed ToolEvaluator.build return value by index 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-02-08 21:35:13 +01:00
Nicola Soranzo 76d2f6377a Merge pull request #13326 from dannon/backport-blame-ignore-revs 2022-02-08 16:04:13 +00:00
Dannon Baker 9cb0c45ca4 Add .git-blame-ignore-revs to 21.09. Without this, if you have set the 
file up in git config blame will blow up with something like `could not
open object name list: .git-blame-ignore-revs`.

I only included the relevant hashes here, will need to handle a merge as
it goes forward.
 2022-02-08 09:57:50 -05:00
mvdbeek 96e76c62d2 Don't record version command as part of command line 
Fixes https://github.com/galaxyproject/galaxy/issues/13306
 2022-02-08 15:52:06 +01:00
Marius van den Beek e9270c5299 Merge pull request #13324 from mvdbeek/minor_fixes_sentry 
Minor fixes from sentry data
 2022-02-08 15:46:02 +01:00
mvdbeek bec9d4b49f Fix resuming job when job has optional data parameters 
This fixes
```
ERROR    galaxy.tools.actions:__init__.py:683 Cannot remap rerun dependencies.
Traceback (most recent call last):
  File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 664, in _remap_job_on_rerun
    self.__remap_parameters(job_to_remap, jtid, jtod, out_data)
  File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 694, in __remap_parameters
    input_values = {p.name: json.loads(p.value) for p in job_to_remap.parameters}
  File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 694, in <dictcomp>
    input_values = {p.name: json.loads(p.value) for p in job_to_remap.parameters}
  File "/usr/local/Cellar/python@3.9/3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py", line 339, in loads
    raise TypeError(f'the JSON object must be str, bytes or bytearray, '
TypeError: the JSON object must be str, bytes or bytearray, not
NoneType
```

Optional data inputs or optional selects are stored as `None` (super
inconsistent, since most other parameters are stored as JOSN. We should
create "basic_2.py" using pydantic at one point not too far into the
future ...). This means we can't call `json.loads` on these. Fortunately
this is the only place we do it, and we don't need to consider optional
parameters here anyway.
 2022-02-08 15:45:01 +01:00
Nicola Soranzo 00b0846e8f Merge branch 'release_21.05' into release_21.09 2022-02-08 13:29:08 +00:00
Nicola Soranzo d27ded4d5a Merge pull request #13315 from mvdbeek/restore_metadata_size_limit 2022-02-08 11:14:26 +00:00
mvdbeek acd56abee8 Return DatasetChainModel 
Fixes failure to serialize the response.
 2022-02-08 11:33:05 +01:00
Marius van den Beek f15de14cbd Merge pull request #13313 from mvdbeek/tus_config_dir 
[22.01] Add config variable for setting tus upload directory
 2022-02-08 11:15:43 +01:00
Marius van den Beek bbf1a4bd7f Merge pull request #13322 from dannon/notification-compat 
[22.01] Ensure Notification API is available prior to trying to use it
 2022-02-08 11:14:59 +01:00
Dannon Baker e6e4ae4030 Add a check to see if the Notification API is available prior to trying 
to configure or send them.
 2022-02-07 20:38:28 -05:00
mvdbeek 25d58f678d Drop unncessary log statement 2022-02-07 22:34:56 +01:00
Marius van den Beek e5455a47f0 Merge pull request #13316 from mvdbeek/fix_failure_to_fail_job 
[21.09] Make __link_file_check more robust
 2022-02-07 15:29:56 +01:00
mvdbeek 83c0683e86 Restore Metadata size limit 
Broke in https://github.com/galaxyproject/galaxy/pull/11902
 2022-02-07 15:02:02 +01:00
Marius van den Beek 377a608c5c Merge pull request #13267 from bernt-matthias/doc/xsd-collection-types 
[22.01] Add missing collection types to xsd doc
 2022-02-07 13:34:00 +01:00
mvdbeek 37846b2d27 Make __link_file_check more robust 
There's no need to load the job and job parameters if the tool isn't
upload1. This should fix https://github.com/galaxyproject/galaxy/issues/13311
 2022-02-07 11:33:18 +01:00
mvdbeek ee4603d918 Provide fallback for old chunked API 2022-02-06 19:16:44 +01:00
mvdbeek 2895dd36e1 Add config variable for setting tus upload directory 2022-02-06 10:41:35 +01:00
Nicola Soranzo c1f7799f98 Merge branch 'release_21.09' into release_22.01 2022-02-04 15:36:47 +00:00
Marius van den BeekandDavid López 43474de368 Use Optional instead of Union with None 
Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>
 2022-02-04 15:33:32 +01:00
mvdbeek 8da2f9eb01 Produce boolean 2022-02-04 15:31:03 +01:00
mvdbeek 51d728b4c2 Move option restriction to separate method 2022-02-04 15:31:03 +01:00
Marius van den Beek 529d2e8e08 Merge pull request #13309 from bernt-matthias/topic/hdah-only-undeleted 
[22.01] Only create HDAH entries for undeleted HDAs
 2022-02-04 15:10:32 +01:00
Björn Grüning 44644a0175 Merge pull request #13304 from mvdbeek/fix_stopping_its_slurm 
[21.09] Fix stopping ITs on slurm
 2022-02-04 13:46:28 +01:00
Marius van den Beek bb299b9dff Merge pull request #13301 from Smithsonian/Fixfor13297 
[21.09] Fix univa job runner setup without nativeSpecification
 2022-02-04 13:13:46 +01:00
mvdbeek 6b65de8f38 Add selenium test for restrictOnConnections 2022-02-04 13:03:42 +01:00
mvdbeek 8d8f6cf84b Fix construction of SelectToolParameter default value 2022-02-04 13:03:01 +01:00