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
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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
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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
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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)
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Squashed:
- pick 8a26c3c7afebe36de5fc
2022-03-09 18:41:49 -05:00
Sergey Golitsynskiy
f32b220cf8
Modify behavior of legacy wrapper, add tests, refactor
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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
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- 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
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Also, remove unused env var
2022-03-09 18:41:03 -05:00
Sergey Golitsynskiy
3c992a608f
Add create/migrate scripts for Alembic dbs (squashed)
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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
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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
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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 Beek and Nicola Soranzo
bcbdb9184e
Don't escape quotes
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2022-02-23 15:43:32 +01:00
Marius van den Beek and Nicola Soranzo
b439675a38
Tweak comment
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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
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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
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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
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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
mvdbeek
d938357d8e
Update virtualenv
2022-02-11 17:25:50 +01:00
Dannon Baker
623a5e165a
Apply black formatting.
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Apply isort.
2022-02-03 07:42:20 -05:00
Nicola Soranzo
a8f5965ba6
Fix gravity requirement for Poetry
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For VCS references, need to specify the branch if it's not `master`.
Also:
- Update Poetry download link
- Require pip >= 19.3 to support direct references as requirement
specifiers
https://www.python.org/dev/peps/pep-0440/#direct-references
2022-01-31 15:09:35 +00:00
Nate Coraor
6c9d497e82
Only set $GALAXY_DAEMON_LOG when using gravity since other servers have
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their own means of setting a log file. Read the supervisor log if it
exists and the daemon log does not, since failure to start Galaxy will
prevent creation of the daemon log file.
When running first startup in CI, attempt to read log files from
multiple places to make debugging different types of failures possible.
2022-01-26 14:50:39 -05:00
Nate Coraor
1d21506f78
Set $GALAXY_DAEMON_LOG when running run.sh --daemon for compatibility.
2022-01-24 15:45:11 -05:00
Nate Coraor
096c75a1fb
No magic arg getter for gunicorn means we have to explicitly pass the
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sample config if necessary
2022-01-24 14:00:56 -05:00
Nate Coraor
98e1cd0c29
Set gunicorn worker for non-galaxy webapps
2022-01-24 10:20:59 -05:00
Nate Coraor
b3bd38be4a
Attempt to properly start reports
2022-01-21 15:45:10 -05:00
Nate Coraor
141e9008f4
Not all echos interpret backslash chars (and -e is not standard either)
2022-01-21 14:07:26 -05:00
Nate Coraor
080b92ad25
Add daemon mode options for Gravity
2022-01-21 13:51:53 -05:00
Nate Coraor
c9cf15576c
Move gunicorn to regular requirements (not just dev) and add uvloop.
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Swap circusd for gravity to start dev-mode/run.sh Galaxy.
2022-01-21 13:29:14 -05:00
Nate Coraor
a53ef1888d
If creating venv, modify activate to set $GRAVITY_STATE_DIR so that
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gravity can be used anywhere once the venv is activated.
2022-01-21 09:51:34 -05:00
mvdbeek
4484f0d2f3
Adjust release-diff.py
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For the 22.01 release I will just create symlinks to the old locations.
2022-01-19 18:20:19 +00:00
Nicola Soranzo
72874b74a5
Add tox environment and GitHub workflow for reports startup test
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Also:
- Fix tox envlist still using py36
- Partially fix running reports with `APP_WEBSERVER=dev`
2021-12-18 15:56:46 +00:00
mvdbeek
bab12662a9
Drop old sqlalchemy patterns
2021-12-16 12:30:49 +01:00
Nicola Soranzo
8c7477cab6
Test Galaxy release script
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xref. https://github.com/galaxyproject/galaxy/pull/11641#discussion_r764049621
2021-12-08 10:43:09 +00:00
mvdbeek