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.
...
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
...
gravity can be used anywhere once the venv is activated.
2022-01-21 09:51:34 -05:00
mvdbeek
4484f0d2f3
Adjust release-diff.py
...
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
Nicola Soranzo
0bdc93a7cc
Drop support for Python 3.6, add Python 3.10
2021-12-08 08:14:10 +00:00
Nicola Soranzo
8b07805228
Merge branch 'release_21.09' into dev
2021-12-03 12:58:27 +00:00
Nicola Soranzo
b779aeb21a
Merge branch 'release_21.05' into release_21.09
2021-12-03 12:56:28 +00:00
Nicola Soranzo
262ab8386c
Increase pip minimum version in startup script
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Pip <19.0 cannot install abi3 wheels, so for example on Python >3.6 it
would (try to) build a cryptography wheel, which is not needed since
cp36-abi3 wheels are already available on PyPI:
https://cryptography.io/en/latest/faq/#why-are-there-no-wheels-for-my-python3-x-version
Fix https://github.com/galaxyproject/galaxy/issues/13023 .
xref: https://github.com/galaxyproject/planemo/issues/1208#issuecomment-984831111
2021-12-03 11:02:20 +00:00
Nicola Soranzo
bd0cefa020
Don't use triple-quoted strings as comments
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They are expressions that get uselessly evaluated.
These were reported as B018 errors by flake8-bugbear 21.11.28 , but B018 for
strings has then been disabled in 21.11.29 since these strings can also be
used as inline attribute doc strings or module variable docstrings (not our
case though).
2021-11-29 23:02:34 +00:00
Nicola Soranzo
1701d0ed67
Merge pull request #13002 from nsoranzo/unnecessary_lists
2021-11-29 18:35:38 +00:00
John Chilton
965f579c39
Merge pull request #13000 from mvdbeek/separate_celery_tasks
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Move ``galaxy_tasks`` decorator to ``galaxy.celery``
2021-11-29 11:41:55 -05:00
Nicola Soranzo
7b67cea7d0
Remove unnecessary list creations
2021-11-29 16:33:05 +00:00
mvdbeek
0091d37469
Add interactive shell for celery tasks
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That's pretty useful for developing new tasks or just running one-off
tasks.
2021-11-29 10:34:01 +01:00
mvdbeek
6036a234c1
Move galaxy_tasks decorator to galaxy.celery
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That means we can import additional tasks that use `galaxy_task` in
galaxy.celery.tasks without circular imports.
2021-11-29 10:34:01 +01:00
Nicola Soranzo
38c0a5aa50
Remove tests that are now passing from RED_TESTS
2021-11-26 18:21:58 +00:00
Nicola Soranzo
eeb8a4e6bd
Fix path handling in imported conformance tests
2021-11-25 13:37:44 +00:00
John Chilton
9a586a58b9
Add CWL conformance API tests
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1) Download conformance tests to `test/functional/tools/cwl_tools` where
they can be used also by framework and unit tests in the future.
2) Add populators to enable executing CWL conformance tests
3) Generate CWL conformance API tests only when needed for tests
2021-11-23 14:10:21 +00:00
mvdbeek
bc329c7b84
Merge branch 'release_21.09' into dev
2021-11-02 11:54:42 +01:00
mvdbeek
c657675d07
Adjust check_blocking_issues to PyGithub usage
2021-11-01 13:01:02 +01:00
mvdbeek
c378d08f19
Add release-diff.py to process
2021-11-01 12:37:53 +01:00
mvdbeek
a9058c54ba
Produce Literal Blocks for config value changes
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These scroll correctly and don't fail when config description changes
includes newlines or long text.
2021-11-01 12:37:53 +01:00
mvdbeek
3b0c86f563
Fix and update bootstrap_history
2021-10-31 16:24:38 +01:00
Nicola Soranzo
90a729e431
New pyupgrade fixes
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Found by running `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py36-plus`
2021-10-24 12:10:34 +01:00
mvdbeek
5cfa818207
Merge branch 'release_21.09' into dev
2021-10-22 22:21:17 +02:00
Dannon Baker
2dd0eed46b
Fix several 'to to' redundant word typos.
2021-10-21 12:28:45 -04:00
Sergey Golitsynskiy
5acbb140b1
Remove refs to ToolShedRepository.metadata in scripts/
2021-10-20 17:15:39 -04:00
mvdbeek
9f463b6f82
Adapt scripts/resumable_upload.py to fetch API
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Finding out that the `files` parameter is required took way more time
than I want to admit ... .
2021-10-13 18:05:42 +02:00
mvdbeek
600f59b0ee
Use client-logic to run upload tool
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It is pretty cool to use hooks and an alternative tool submission
endpoint, but this is less invasive. We'd have to do this anyway for
cases where the upload is already on the server and the pre-finish hook
doesn't fire.
2021-10-12 13:43:45 +02:00
mvdbeek
0e1ff5a30c
Adjust endpoint so it can receive tusd hooks
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Without any proxying and tusd running as a separate service:
``
tusd -upload-dir=./database/tmp -hooks-http=http://localhost:8000/api/upload/_resumable_upload -hooks-http-forward-headers=X-Api-Key --hooks-enabled-events=post-finish
```
Adjust ./database/tmp to new_file_path, and this should work. Now we
just need to proxy `api/upload/resumable_upload` to `<tusd_port>/files`
and we're good for a production setup.
2021-10-12 13:34:55 +02:00
mvdbeek
d08a08ac4c
Backend Prototype for resumable uploads via TUS
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The middleware can be replaced by running a [tusd
server](https://github.com/tus/tusd ) or
[nginx tus location](https://github.com/mmatuska/lua-tus-server ) in
front of Galaxy.
Includes a sample script that can upload datasets into a Galaxy history.
2021-10-12 13:34:53 +02:00
John Chilton
cd2e6527fc
Merge pull request #12255 from bernt-matthias/topic/deprecate_datamanager_version
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Deprecate data manager version
2021-09-08 14:36:01 -04:00
mvdbeek
ecc54ba00c
Merge branch 'release_21.05' into dev
2021-08-09 18:45:05 +02:00
Nate Coraor
038045a600
Add a GDPR-friendly user purge to pgcleanup.
2021-07-23 14:55:54 -04:00
Matthias Bernt
c2a113bc85
add script for fixing shed_data_manager_conf.xml
2021-07-14 17:13:26 +02:00
mvdbeek
fdb36c7ed7
Run client-y tests with --frozen-lockfile
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Seems to be best-practice and may be a little faster
2021-06-30 13:06:24 +02:00
mvdbeek
24d825856a
Merge branch 'release_21.05' into 'release_21.09'
2021-06-10 21:23:23 +02:00
Marius van den Beek
f115fee4a7
Merge pull request #11938 from mvdbeek/21.05_release_notes
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Release notes for 21.05
2021-06-10 20:34:50 +02:00
mvdbeek
91795d198d
Lint fix
2021-06-10 19:41:24 +02:00
Helena Rasche
364286df04
munge filenames
2021-06-10 18:59:56 +02:00
Helena Rasche
3093c2dcef
handle subsections of configurations a bit better
2021-06-10 18:56:17 +02:00
Helena Rasche
1c66b755a6
include config schemas in diffing
2021-06-10 18:52:59 +02:00
Sergey Golitsynskiy
680db562f7
Do not use legacy string interpolation on URL obj
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This fixes the pgcleanup script and an integration test.
The test fails because of an error in the script.
The error is caused by incorrect string formatting.
The new SQLAlchemy URL object extends collections.namedtuple, and a
tuple is incompatible with printf-style formating.
Ref:
https://github.com/sqlalchemy/sqlalchemy/blob/18dbd6aa12a7eca0acb1e2c4f752088e24d6adae/lib/sqlalchemy/engine/url.py#L36
https://docs.python.org/3/library/stdtypes.html#printf-style-string-formatting
2021-05-18 19:00:55 -04:00
Sergey Golitsynskiy
3cd1c7f1c7
Handle DedupedColumnCollection in db_indexes
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This should fix the `scripts/check_model.py` script and the database
indexes github workflow.
Accessing index columns has changed: index.columns gives access to a
DedupedColumnCollection instead of a ColumnCollection.
Columns can be accessed by key; keys are accessed via keys() attr.
Ref:
https://docs.sqlalchemy.org/en/14/changelog/migration_14.html#select-objects-and-derived-from-clauses-allow-for-duplicate-columns-and-column-labels
https://docs.sqlalchemy.org/en/14/core/sqlelement.html?highlight=dedupecolumncollection#sqlalchemy.sql.expression.ColumnCollection
2021-05-18 19:00:55 -04:00
mvdbeek
37a15c5319
Merge branch 'release_21.05' into dev
2021-05-18 09:52:08 +02:00
Dannon Baker
22e7601653
First pass fstring conversion
2021-05-11 13:47:00 -04:00
Nate Coraor