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1760 Commits
Author SHA1 Message Date
John Chilton 4bd80ce6ef Flush out documentation and service-info for DRS API a bit. 2022-12-08 10:08:01 -05:00
John Chilton 8ff9fe2610 Implement initial GA4GH DRS Support. 
- Implement APIs for serving Galaxy's public datasets as DRS objects.
- Implement support in galaxy.files.uris for DRS URIs so that upload, etc... can use DRS URIs from other data repositories.

The ways this can be improved are endless:

- New object ID patterns can be implemented to allow access to composite data, metadata files from a bundle view of datasets.
- New object ID patterns can be implemented to allow access to collections as bundles of datasets.
- More auth types and AccessMethods could be implemented for loading datasets from clients.
- Some sort of scheme for providing authenticated URLs to non-public data could be implemented to provide access to more of Galaxy's data if user's can implement.

Despite all these limitations - I think having the guts in like this provide useful points for interested parties to go and add functionality to enable their desired usecases.
 2022-12-08 10:07:11 -05:00
guerler 72fd52f087 Deprecate brand title text option, logo now contains text 2022-11-30 17:19:07 -05:00
Linelle 9c5f5bc3a2 changed references from sample XML to sample YML 
added a sentence about where to find the XMLs as well in case people are still using those (it's me, i'm people)
 2022-11-30 14:50:19 -05:00
Linelle ec504562e3 change resubmission example link from xml to yml 
Test case for resubmission location used to be https://github.com/galaxyproject/galaxy/blob/dev/test/integration/resubmission_job_conf.xml which leads to 404, have changed it to https://github.com/galaxyproject/galaxy/blob/dev/test/integration/resubmission_job_conf.yml and made it linked text instead of plain URL
 2022-11-30 14:29:52 -05:00
Nate Coraor 1cdb7b5bcd Replace XML job conf sample with YAML. 
Prefer loading job_conf.yml, fall back to job_conf.xml with a warning if
it exists.
 2022-11-17 19:58:24 -05:00
Nate Coraor bb41d1f6e3 Merge pull request #14867 from dannon/release-next-update-23.1 
Update release-next to 23.0
 2022-11-16 12:21:04 -05:00
John Chilton 1a2a534695 Merge pull request #14965 from jmchilton/remove_no_longer_useful_wsgi_middleware 
Remove old WSGI middleware that is no longer useful.
 2022-11-10 23:13:45 +01:00
John Davis b11c18eb21 Merge pull request #14825 from neoformit/dev-html-email 
Looks great! Thanks, @neoformit 

For future ref/todo: we do need a more systematic/unified approach to handling path construction that handles tests that are arun both as standalone unit tests and as part of package tests (as per observation by @neoformit)
 2022-11-10 11:30:42 -05:00
John Chilton 92a885e280 Remove old WSGI middleware that is no longer useful. 2022-11-10 05:28:24 -05:00
Simon Bray 91674ac9de small change to job runner docs 
to state more explicitly what `check_watched_item()` should return
 2022-11-08 11:47:09 +01:00
Nicola Soranzo 581d001828 Remove unused `require_new and GALAXY_TEST_HISTORY_ID` 2022-11-07 15:44:02 +00:00
Nicola Soranzo afa7b713bc Replace `GALAXY_TEST_INCLUDE_SLOW env variable with external_dependency_management` pytest marker 
Fix mulled tests missing tests in `test/unit/tool_util/test_conda_resolution.py` .

Also:
- Add `coverage` tox factor to generate coverage report.
 2022-11-03 21:43:37 +00:00
DannonandNicola Soranzo 9f5ac39923 Apply suggestion swapping to 23.0. 
This seems the group leaning at this point, and it sounds good to me.

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-01 19:58:21 -04:00
mvdbeek eec177839f Drop scripts/function_tests.py 2022-11-01 18:45:08 +00:00
Nicola Soranzo 5ca0aea54a Drop nose 
It's deprecated and unmaintained, and is broken under Python 3.10 .
 2022-11-01 18:45:07 +00:00
Dannon Baker 4b681f1258 Update release-next to 23.1 2022-10-27 08:34:35 -04:00
Cameron Hyde e2119e4750 Update config description 2022-10-20 14:25:49 +10:00
Cameron Hyde dc27533344 Account activation email rendered from text/html templates 2022-10-20 14:06:17 +10:00
Dannon c7216e4b85 Merge pull request #14776 from mahendrapaipuri/add_request_obj_authmanager 
Make HTTP request object available to `AuthManager`
 2022-10-18 09:23:10 -04:00
Marius van den Beek 672ed4984f Merge pull request #14694 from sveinugu/dev 
Allow path-based interactive tools using nginx proxy
 2022-10-17 11:24:38 +02:00
Marius van den Beek 241da69672 Merge pull request #12288 from dannon/sorted-tools-in-sections 
Automatically sort tools in sections by name
 2022-10-17 10:49:17 +02:00
Marius van den Beek ce26561b33 Merge pull request #14708 from jdavcs/dev_celery_config 
Enable fine-grained celery configuration
 2022-10-17 10:37:24 +02:00
Marius van den BeekandNicola Soranzo a5dc788bf3 Tweak wording and example for verifying remote_ip in custom LDAP authenticator 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-10-17 10:33:29 +02:00
Marius van den Beek 934369aa3a Merge pull request #14792 from jdavcs/dev_sqlalchemy_engine_options 
Make connect_args for SQLAlchemy's engine configurable
 2022-10-17 10:30:44 +02:00
Nicola Soranzo 0391cd4b62 Rename FooBarTestCase test classes as TestFooBar in API, framework, performance, Selenium and ToolShed tests 
These are collected by pytest only because they are `unittest.TestCase` derived,
but normally pytest collects only test classes whose name starts with `Test`, see
https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes

Also:
- Some type annotations
 2022-10-15 17:54:31 +01:00
John Davis d310635895 Celery config option result_backend is required 2022-10-14 19:28:17 -04:00
John Davis d26ad37e97 Remove celery_backend from config_schema, use celery_conf instead 2022-10-14 19:28:17 -04:00
John Davis b6b49897dc Remove celery_broker from config_schema, use celery_conf instead 2022-10-14 19:28:17 -04:00
John Davis 2de79dd7d1 Add default task routes to config schema 2022-10-14 19:28:17 -04:00
John Davis 71829ae6af Add more details to setting db engine options to config schema 2022-10-14 13:18:35 -04:00
mahendrapaipuri c0002c1ffb Update authentication documentation with an example on how to use request object in auth flows 2022-10-14 09:46:59 +02:00
Nicola Soranzo 6069023d86 Merge pull request #14740 from bernt-matthias/topic/doc-security-datatables 
Extend security docs
 2022-10-13 14:29:52 +01:00
M BerntandMarius van den Beek ffc26d5ddd Update doc/source/admin/security.md 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-10-13 13:53:06 +02:00
Nicola Soranzo a81d680cca Merge branch 'release_22.05' into dev 2022-10-11 21:34:31 +01:00
Dannon Baker c8659d1d4a Add toolbox_auto_sort config option, expose in config manager. 2022-10-06 22:20:06 -04:00
M BerntandNicola Soranzo e8adc13324 Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-09-30 22:38:49 +02:00
M Bernt 37594348f9 Update doc/source/admin/security.md 2022-09-30 19:00:54 +02:00
John Davis 06744d4d0f Document use of release tags in manage_db.sh 2022-09-30 10:42:01 -04:00
Matthias Bernt eddd8e89a6 extend security docs 
by adding data referred by data tables
 2022-09-30 14:33:40 +02:00
John Davis 8538ab7fcb Fix same error in sample code in the rst doc file 2022-09-29 12:23:28 -04:00
John Davis 84f22bac77 Add db migration documentation to docs 2022-09-27 15:03:12 -04:00
John Davis 5a748bb867 Display 'Config Options' as subheading of 'Galaxy Configuration' 
This corrects a (supposedly) typo that prevented this to be displayed as
a subheading on this page: https://docs.galaxyproject.org/en/master/admin/index.html
 2022-09-27 15:03:03 -04:00
Nicola Soranzo 7f03d51c17 Document how to profile memory use in tests 2022-09-27 03:34:55 +01:00
Sveinung Gundersen 4ec8c4654e Added info on galaxy.yml config 2022-09-23 17:54:01 +02:00
Sveinung Gundersen 89bf7b1e52 Adding documentation and example nginx config to allow path-based interactive tools 2022-09-23 17:19:31 +02:00
Nicola Soranzo 331d0d2465 Merge pull request #14580 from nsoranzo/recommend_draft_instead_of_WIP 
[PROCEDURES] Recommend to use PR draft state instead of WIP title/label
 2022-09-15 19:05:40 +01:00
Nicola Soranzo e08deef224 Merge pull request #14592 from nsoranzo/misc_fixes_202209 
Misc fixes 202209
 2022-09-09 21:34:38 +01:00
Nicola Soranzo 157d9647ea Update docs on adding Python dependencies 
to use Wheelforge instead of Starforge.
 2022-09-09 17:26:30 +01:00
Nicola Soranzo 404da60afa Fix Tool Shed link 2022-09-09 17:20:24 +01:00