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Author SHA1 Message Date
Marius van den BeekandNicola Soranzo e6b498ea80 Improve scaling documentation 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-02-21 20:52:16 +01:00
mvdbeek 79ed8de3fe Adjust pool example and dumb it down a little 
There's no "handler2" anymore that handles special and default jobs.
You can of course still set it up exactly as before, that's in the
test case.
 2022-02-19 19:36:57 +01:00
mvdbeek dfe372991d Drop TODO, it is implemented now 2022-02-19 19:36:57 +01:00
Marius van den BeekandNicola Soranzo 5d63a84b56 Mention systemd in starting and stopping section 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-02-18 14:22:40 +01:00
Marius van den Beek 29afb52d91 Move transparent starts into starting and stopping 2022-02-18 14:22:08 +01:00
mvdbeek df9338bec9 Describe startup and logging 2022-02-18 11:01:54 +01:00
mvdbeek 3cb8e8578a Add tentative instructions for setting number of processes in gravity section 2022-02-17 16:21:12 +01:00
mvdbeek 5e88eae47b Drop signals section 2022-02-16 20:01:29 +01:00
mvdbeek f0da15fbae Document job handler pool 2022-02-16 19:56:58 +01:00
mvdbeek 2a6491c9bc Fix typo 2022-02-16 19:56:58 +01:00
Marius van den BeekandNicola Soranzo 5b65486444 Use backticks around run.sh 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-02-16 19:53:29 +01:00
Marius van den BeekandNicola Soranzo 3af4671ffc Improve structure, add links 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-02-16 19:33:52 +01:00
mvdbeek 131af43957 Describe job handling 2022-02-16 19:31:27 +01:00
mvdbeek 7079008772 Recommend a proxy 
No, really, it's the better option.
 2022-02-16 19:00:27 +01:00
mvdbeek 5dc3a6f037 More progress, describe some basic gunicorn options 2022-02-16 18:41:43 +01:00
mvdbeek e7c37e60d5 Don't reference uwsgi only option in introductory statement 2022-02-15 17:26:58 +01:00
mvdbeek f4dd77b382 Downgrade pre-assignment to the fallback method it is 2022-02-15 17:25:35 +01:00
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