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1698 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
mvdbeek 89e06a06cc Update supervisor config when starting galaxy via run.sh 2022-04-05 11:14:11 +02:00
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
mvdbeek 31dd8e4b46 Fix tool_shed entrypoint and default port 2022-02-22 17:58:28 +01:00
Marius van den Beek fa3ae1d6c6 Merge pull request #13358 from mvdbeek/codecoverage 
Report code coverage (for pytest test suites)
 2022-02-18 17:02:50 +01:00
Dannon Baker 29a7489590 Merge remote-tracking branch 'upstream/release_22.01' into dev 2022-02-16 14:02:31 -05:00
Nate Coraor 0297eb1bc8 Ensure $GRAVITY_STATE_DIR is present in venv activate script any time 
run.sh/common_startup.sh is called normally (without --skip-venv or
--no-create-venv).
 2022-02-16 10:09:50 -05:00
Nate Coraor 85dcd60d4c Remove node_modules when upgrading Node 2022-02-14 10:31:46 -05:00
mvdbeek 4dca001b5d Do verify certs 
You'll be running into problems later on anyway, and it doesn't look
like there are builds with known shasums anymore for more recent
virtualenv zipapps.
 2022-02-11 17:25:50 +01:00