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Author SHA1 Message Date
John Chilton a28c9a3ff7 Merge pull request #11683 from mvdbeek/map_over_state_new_outputs 
Ensure new outputs have correct mapOver state
 2021-04-07 10:03:47 -04:00
John Chilton c1186c1d61 Merge pull request #11497 from bernt-matthias/topic/xsd-param-validator 
xsd: use validator as child of param
 2021-04-07 09:47:41 -04:00
John Chilton 071456f891 Merge pull request #11220 from gregvonkuster/mrcfile 
Add mrc datatype (and Python dependency)
 2021-04-07 09:45:32 -04:00
John Chilton bbf6eab81b Merge pull request #11234 from jmchilton/cleanup_webtransaction_0 
Remove some seemingly unused cruft in GalaxyWebTransaction
 2021-04-07 09:40:42 -04:00
mvdbeek 15e4fa650a Merge branch 'release_21.01' into dev 2021-04-07 14:33:19 +02:00
mvdbeek e22f218bcf Merge branch 'release_20.09' into release_21.01 2021-04-07 14:31:58 +02:00
mvdbeek 84e1d54140 Merge branch 'release_20.05' into release_20.09 2021-04-07 14:30:48 +02:00
mvdbeek b71a4c5bd9 Merge branch 'release_20.01' into release_20.05 2021-04-07 14:30:03 +02:00
Nicola Soranzo e1014acc9d Merge branch 'release_21.01' into dev 2021-04-07 13:13:29 +01:00
Dannon 7f519b4c8e Merge pull request #11794 from nsoranzo/release_21.01_fix_upstream_mod_zip_docs 
[21.01] Fix typo in `upstream_mod_zip` admin docs
 2021-04-06 22:12:45 -04:00
Nicola Soranzo 13d91da1f4 Fix typo in upstream_mod_zip admin docs 2021-04-06 20:04:19 +01:00
Estelle Ancelet d5cb3c3e2f Lower tool id case while populating resource params 2021-04-06 18:08:22 +02:00
John Chilton 7773814c06 Merge pull request #11769 from davelopez/support_permissions_in_files_sources 
Support role and group permissions in file sources plugins
 2021-04-06 11:14:20 -04:00
Marius van den Beek 4a46ea1509 Merge pull request #11779 from natefoo/installable 
Fixes for installed Galaxy
 2021-04-06 16:45:40 +02:00
Marius van den Beek 32cb259274 Merge pull request #11641 from natefoo/release-process-overhaul 
Overhaul make-based release process
 2021-04-06 16:45:12 +02:00
John Chilton 3c1f887f4f Merge pull request #11791 from hexylena/l10n 
Update localisation options to include Español
 2021-04-06 10:26:42 -04:00
Helena Rasche c96cda9eb5 Enable spanish 2021-04-06 12:47:53 +02:00
Helena Rasche fe79dd171f update defaults 2021-04-06 12:26:51 +02:00
davelopez e71b92a9f8 Add more tests for invalid expressions 2021-04-06 11:17:55 +02:00
davelopez f8ace37cb4 Add expression validation when the configuration is parsed. 
This will stop Galaxy from starting with an invalid expression defined in the configuration.
 2021-04-06 11:17:55 +02:00
davelopez 3a03ff470d Add common email related characters to DEFAULT_TOKEN_FORMAT 
This will fix the failing integration test.
 2021-04-06 11:17:55 +02:00
davelopez 847db78aa1 Add test for using expression rules in posix file source 2021-04-06 11:17:55 +02:00
davelopez f04e08584e Use BooleanExpressionEvaluator to check security rules for requires_roles and requires_groups 2021-04-06 11:17:55 +02:00
davelopez 03795b766e Add generic boolean expression evaluator + unit tests 2021-04-06 11:17:55 +02:00
davelopez 895c165414 Fix integration test failing by different response order 2021-04-06 11:17:55 +02:00
davelopez 6ef54d73c6 Add file sources access unit tests 2021-04-06 11:17:55 +02:00
davelopez 74ca28c3a8 Change requirement condition to both options. 
If the `requires_roles` and `requires_groups` options are defined, both must be satisfied.
 2021-04-06 11:17:55 +02:00
davelopez ed0af1aef1 Update integration tests 2021-04-06 11:17:55 +02:00
davelopez 0caf1395da Fix default query parameters value for RemoteFilesFormat to uri. 
The default value was set to `flat` and causing different behavior between the legacy and FastAPI endpoints for remote_files.
 2021-04-06 11:17:55 +02:00
davelopez 8e5259ae16 Add new options to pydantic models 2021-04-06 11:17:55 +02:00
davelopez d51f70efa5 Check user access in FileSource plugins 2021-04-06 11:17:55 +02:00
davelopez dc942ed48d Add new config options 2021-04-06 11:17:55 +02:00
davelopez 7f23534461 Add integration tests. 
Basic tests for the new `requires_roles` and `requires_groups` settings for FileSources using the posix plugin.
 2021-04-06 11:17:55 +02:00
Dannon fb4ad9e2ef Merge pull request #11777 from jmchilton/license 
Add an explicit statement of assent to licensing to the pull request template
 2021-04-05 22:01:09 -04:00
Sergey Golitsynskiy 5a127a7a70 Merge pull request #11790 from ic4f/dev_postgres_url 
Handle deprecated postgresql db urls; update postgres version in ci
 2021-04-05 19:06:11 -04:00
Sergey GolitsynskiyandNicola Soranzo 732ccc50da Fix character casing 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-04-05 19:05:33 -04:00
Sergey Golitsynskiy 179a6e4a17 Fix deprecated db urls in user config properties 2021-04-05 17:11:24 -04:00
Sergey Golitsynskiy 94cc475681 Update github workflows to use postgres 13 2021-04-05 15:08:34 -04:00
Sergey Golitsynskiy be4429e4fb Replace: s/postgres/posgresql in db URLs 
Was deprecated in SQLAlchemy 1.3, removed in SQLAlchemy 1.4
https://docs.sqlalchemy.org/en/14/changelog/changelog_14.html#change-3687655465c25a39b968b4f5f6e9170b
https://github.com/sqlalchemy/sqlalchemy/issues/4643
 2021-04-05 15:02:26 -04:00
Nate Coraor 698d95e52d Move all galaxy.util.* modules to the galaxy-util package. 2021-04-05 12:06:48 -04:00
Nate Coraor f6fdc66e23 Move all galaxy.datatypes.* modules to the galaxy-data package. 2021-04-05 12:02:08 -04:00
Nate Coraor a857929af5 Move all galaxy.model.* modules to the galaxy-data package. 2021-04-05 11:48:14 -04:00
John Chilton 95791b23fd Merge pull request #11783 from nsoranzo/use_assertRaisesRegex 
Use `assertRaisesRegex()` to fix new B017 linting errors
 2021-04-03 15:57:04 -04:00
Nicola Soranzo 20a4bcd519 Use assertRaisesRegex() to fix new B017 linting errors 
Fix the following errors reported by flake8-bugbear 21.4.3:

B017 assertRaises(Exception): should be considered evil. It can lead to
your test passing even if the code being tested is never executed due to a
typo. Either assert for a more specific exception (builtin or custom), use
assertRaisesRegex, or use the context manager form of assertRaises.
 2021-04-03 20:09:02 +01:00
John Chilton 5a2985db39 Merge pull request #11776 from dannon/scroll-library-list 
[21.01] Fix library scrolling
 2021-04-03 13:39:43 -04:00
John Chilton 394408a530 Merge pull request #11778 from jmchilton/pydantic_18 
Fix workflow refactor schema parsing for pydantic 1.8.
 2021-04-03 13:38:25 -04:00
Nicola Soranzo a150dd2b79 Merge pull request #11782 from galaxyproject/dev_auto_update_dependencies 
Update Python dependencies
 2021-04-03 18:27:28 +01:00
ic4f 2d7b8b40b0 Update Python dependencies 2021-04-03 04:34:36 +00:00
Björn Grüning 635c6f805a Merge pull request #11758 from bgruening/meryldb_new 
[21.0] add new datatype class for meryldb
 2021-04-02 22:43:09 +02:00
Nate Coraor d8aa5a3804 Add fastapi-utils to galaxy-webapps package requirements. 2021-04-02 16:01:34 -04:00