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1754 Commits
Author SHA1 Message Date
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
Sergey Golitsynskiy f32b220cf8 Modify behavior of legacy wrapper, add tests, refactor 
If the database is combined, running `./manage_db.sh upgrade` should upgrade
BOTH models: gxy and tsi. However, if tsi uses a separate database, only
the galaxy model should be updated.

Also, see this for context: https://github.com/galaxyproject/galaxy/pull/13108#discussion_r789108576

See inline comments for more details.

The new tests are examples of new behavior.

All refactoring is directly related to the changes in this commit.
 2022-03-09 18:41:03 -05:00
Sergey Golitsynskiy 537cf5d2aa Preserve manage_db.sh, but do not hide alembic 
- Preserves usage of legacy script while not hiding the Alembic script.
    (see manage_db.sh and run_alembic.sh)
- Adds documentation (see top of script files)
- Includes misc. relevant refactorings
- Includes unit tests for testing legacy script handling
 2022-03-09 18:41:03 -05:00
Sergey Golitsynskiy ee5a3450bb Update db index testing: test both models, gxy and tsi 
Also, remove unused env var
 2022-03-09 18:41:03 -05:00
Sergey Golitsynskiy 3c992a608f Add create/migrate scripts for Alembic dbs (squashed) 
Also add exec permissions to create/migrate python scripts.
(not sure this is required, adding for consistency with previous
version)

+ A few fixes for TS scripts, tests

Squashed:
- pick b62443245e Add create/migrate scripts for Alembic dbs
- squash 06f0a923ca Fix integration test (test only relevant for TS)
 2022-03-09 18:41:02 -05:00
Sergey Golitsynskiy ad2f2233a8 Add create/migrate scripts for tool shed 2022-03-09 18:41:02 -05:00
Nicola Soranzo a62e86fc2e Merge branch 'release_22.01' into dev 2022-03-04 17:02:22 +00:00
Nicola Soranzo e886d38171 Merge branch 'release_21.09' into release_22.01 2022-03-04 16:16:15 +00:00
mvdbeek 873d43eac2 Move tool shed and reports config schema to config package 
And restore unit tests to proper place.
 2022-03-03 16:57:39 +01:00
Nicola Soranzo 7f04b5d698 Merge branch 'release_22.01' into dev 2022-03-02 20:08:55 +00:00
Nate Coraor 6a20106694 Fix typo with metadata_file 2022-03-02 14:23:46 -05:00
Nate Coraor a9b4b632a9 Fix pgcleanup.py for datasets stored by UUID 2022-03-02 14:18:31 -05:00
mvdbeek 034f518e43 Move init_models_from_config to galaxy.model.mapping 2022-03-01 16:50:06 +01:00
mvdbeek c08a12f553 Drop get_database_url helper 
I don't see an advantage over accessing the config attribute instead.
 2022-03-01 16:50:06 +01:00
Nicola Soranzo 4a31207701 Merge branch 'release_22.01' into dev 2022-02-28 20:21:56 +00:00
mvdbeek f4183ac5a0 Drop scripts/nosetests.py 2022-02-28 15:24:07 +01:00
mvdbeek 400922a5a4 Drop pkg_resources 2022-02-28 14:07:08 +01:00
Nicola Soranzo 22f6674f8d Merge branch 'release_22.01' into dev 2022-02-24 11:56:51 +00:00
Marius van den BeekandNicola Soranzo bcbdb9184e Don't escape quotes 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-02-23 15:43:32 +01:00
Marius van den BeekandNicola Soranzo b439675a38 Tweak comment 
And no, we could read out the port from the uwsgi section, or decide to move it elsewhere.

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-02-23 12:59:23 +01:00
mvdbeek 3800ddf6ff Move up GUNICORN_CMD_ARGS 2022-02-23 10:33:44 +01:00