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Commit Graph
1724 Commits
Author SHA1 Message Date
mvdbeek 2468629452 Update release.sh script for new packaging layout 2022-08-23 16:04:24 +02:00
mvdbeek 18a9a39d97 Write admin announce, add deferred datasets to user announcement 2022-08-19 16:11:41 +02:00
mvdbeek 857c598065 Update a couple PR titles, strip trailing . from PR titles 2022-08-19 12:29:25 +02:00
Nicola Soranzo 961472cfff Merge branch 'release_22.01' into release_22.05 2022-08-16 23:25:42 +01:00
Nicola Soranzo 69defb7a20 Doc fixes 2022-08-15 19:15:02 +01:00
mvdbeek da334f1e42 Fix first startup when only python3 is on PATH 2022-08-08 16:28:26 +02:00
John Davis af81f2a01d Verify db initialization before running upgrade script 2022-07-13 16:38:11 -04:00
mvdbeek acb321bfd8 Merge branch 'release_22.01' into release_22.05 2022-07-02 18:07:38 +02:00
Nate Coraor a4e2af92b3 Fixes for the tus resumable upload command line script 2022-06-29 08:42:24 -04:00
Nicola Soranzo 2e2403e1e2 Prefer venv module over virtualenv 
if it's installed as part of the Python standard library.
 2022-06-17 00:33:14 +01:00
Dannon 4644922783 Merge pull request #13655 from mvdbeek/metadata_embed 
Create data_fetch and set_metadata celery tasks
 2022-06-07 10:27:06 -04:00
John Chilton 1c795891e3 Tour validation. 2022-06-02 14:53:55 -04:00
Sergey Golitsynskiy 7f09898636 Update inline documentation in scripts 2022-05-31 10:30:30 -04:00
mvdbeek ec939cc9f7 Fix a typo in celery_shell.py 2022-05-25 19:46:47 +02:00
Nicola Soranzo abb75416a3 Drop uncredit pull requestor list 
and give credit to everyone, as in GitHub auto-generated release
notes.
 2022-05-13 12:40:48 +01:00
Nicola Soranzo 1ec8652313 Fix type annotation and simplify script 
Use f-strings
 2022-05-12 16:38:12 +01:00
Nicola Soranzo 4bc75e4179 Replace committer name and GitHub username 
Follow up on commit 559b0d1245 .

Also:
- Remove former devteam members from uncredited pull requestor list.
 2022-05-12 16:38:12 +01:00
Nicola Soranzo 9dec207a52 Respect GRAVITY_STATE_DIR when activating venv 
So that:

export GRAVITY_STATE_DIR=/srv/galaxy/gravity
./run.sh

writes gravity state/log files to the right place.
 2022-05-10 15:57:42 +02:00
Nicola Soranzo 8afac1afd5 Use `load_app_properties()` to load Galaxy config file 
instead of directly loading it as YAML.
Will make it easier to uniformly deal with changes of format (e.g.
we are deprecating ini now).

Fix traceback:

```
Traceback (most recent call last):
  File "scripts/config_parse.py", line 31, in <module>
    main(args.config_file, args.setting)
  File "scripts/config_parse.py", line 16, in main
    gx_config = GalaxyAppConfiguration(**yaml.safe_load(open(config))["galaxy"])
  File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/__init__.py", line 125, in safe_load
    return load(stream, SafeLoader)
  File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/__init__.py", line 81, in load
    return loader.get_single_data()
  File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/constructor.py", line 49, in get_single_data
    node = self.get_single_node()
  File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/composer.py", line 39, in get_single_node
    if not self.check_event(StreamEndEvent):
  File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/parser.py", line 98, in check_event
    self.current_event = self.state()
  File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/parser.py", line 171, in parse_document_start
    raise ParserError(None, None,
yaml.parser.ParserError: expected '<document start>', but found '<scalar>'
  in "/tmp/tmpsffm7of5/galaxy.ini", line 3, column 1
```

when starting Galaxy with a `galaxy.ini` config file (though Galaxy startup
will still fail later).
 2022-04-26 09:48:18 +01:00
Björn Grüning 8885c3107d Merge pull request #13657 from dannon/configurable-plugin-dir 
Add support for gulp build process to use a configurable directory
 2022-04-12 15:16:30 +02:00
mvdbeek 6f3bdd39d9 Merge branch 'release_22.01' into dev 2022-04-08 10:13:24 +02:00
Nicola Soranzo 6d53620a52 Respect GRAVITY_STATE_DIR when activating venv 
So that:

export GRAVITY_STATE_DIR=/srv/galaxy/gravity
./run.sh

writes gravity state/log files to the right place.
 2022-04-06 23:48:18 +01:00
Nicola Soranzo 7ecd7f0cb8 Remove --wait startup option 
Follow-up on https://github.com/galaxyproject/galaxy/pull/13071 .
 2022-04-05 19:15:23 +01:00
Dannon Baker 274fcf3bb3 Isort 2022-04-05 13:42:32 -04:00
Dannon Baker 04ed93d81f Make sure config actually exists. Exits silently if nothing found or 
no matches.
 2022-04-05 09:34:11 -04:00
mvdbeek 89e06a06cc Update supervisor config when starting galaxy via run.sh 2022-04-05 11:14:11 +02:00
Dannon Baker fdcf8c086e Actually pass plugin path through to invoked build process 2022-04-04 15:15:10 -04:00
Dannon Baker 256a4495fe Pass config path to gulp 2022-04-04 10:15:55 -04:00
Dannon Baker 6240a5ab57 Slight reorg in common_startup 2022-04-04 08:55:46 -04:00
Dannon Baker cb94125acf Add simple script to load specific options from galaxy config and print either a single value resolved or the loaded config dict 2022-04-04 08:55:11 -04:00
mvdbeek 08d3078382 Drop docker swarn gie support 2022-03-23 18:38:53 +01:00
mvdbeek d6424b5e72 Drop more mappings that don't exist anymore 2022-03-21 13:14:43 +01:00
mvdbeek d844db440e Drop repair repository script, uses endpoint that doesn't exist anymore 2022-03-21 13:14:43 +01:00
mvdbeek 3badee379d Drop workflow import script that uses API endpoint that doesn't exist anymore 2022-03-21 13:14:43 +01:00
John Chilton 4e01cfe3eb Merge pull request #13562 from ic4f/dev_sa20_3 
Misc. SQLAlchemy 2.0 upgrades
 2022-03-20 18:37:17 -04:00
Nicola Soranzo 00f7522e7e Merge branch 'release_22.01' into dev 2022-03-19 01:57:33 +00:00
mvdbeek 4c7bfd1032 Fix tool shed bootstrapping script 2022-03-17 19:34:43 +01:00
mvdbeek e9d2d683d6 Add --capture-output when running gunicorn in daemon mode 2022-03-17 19:34:16 +01:00
Sergey Golitsynskiy 09be05082f Wrap sql stmt in text() (tool_shed, exluding migrate/versions) 2022-03-17 12:41:47 -04:00
Sergey Golitsynskiy 158b9f0a70 s/eagerload/joinedload (SQLAlchemy 2.0) 
Ref: https://docs.sqlalchemy.org/en/14/orm/loading_relationships.html?highlight=eagerload#sqlalchemy.orm.eagerload
 2022-03-16 16:48:33 -04:00
mvdbeek fd51314a88 Drop more uWSGI legacy things 2022-03-15 21:32:00 +01:00
mvdbeek b39e8ad9a2 First pass in dropping uwsgi specific things 2022-03-15 21:31:59 +01:00
mvdbeek 7c5068863f WIP remove paster/uwsgi 2022-03-15 21:31:59 +01:00
Marius van den Beek 550f47db9e Merge pull request #13540 from mvdbeek/dev 
Merge release_22.01 into dev
 2022-03-15 11:30:18 +01:00
mvdbeek faea1c8211 Merge branch 'release_22.01' into dev 2022-03-14 17:06:49 +01:00
Nicola Soranzo 0c80836c34 Upgrade syntax to Python 3.7 
using `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py37-plus`

Also more refactoring of Python files in `packages/` .
 2022-03-14 14:57:43 +00:00
mvdbeek 3fa572d612 First pass at supporting --preload and worker_id 
We do need to include some kind of worker id in the server_name. If we
don't do this and we start with multiple workers the internal
QueueWorker won't work and multiple processes can pick up the same job
if the web process is also a job handler.
 2022-03-10 17:15:37 +01:00
Sergey Golitsynskiy 6fd1a6ee16 Print result of script execution 2022-03-09 18:41:50 -05:00
Sergey Golitsynskiy 1a1ae8d3d2 Adapt manage_db.py for usegalaxy playbook; add tests 2022-03-09 18:41:50 -05:00
Sergey Golitsynskiy 92b2e67145 Apply black, isort (squashed) 
Squashed:
- pick 8a26c3c7af Fix import order in config
- squash ebe36de5fc Apply black, isort
 2022-03-09 18:41:49 -05:00