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f4183ac5a03f543a16725d905972d70c0192b67f
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1653 Commits
Author SHA1 Message Date
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
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
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
Nicola Soranzo a8f5965ba6 Fix gravity requirement for Poetry 
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 
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 
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. 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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