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Author SHA1 Message Date
Mason Houtz be81d2ec09 fixed styleguide 2021-02-22 09:25:04 -08:00
Björn Grüning a568eaee7d Merge pull request #11403 from bernt-matthias/topic/slurm-real-user 
Fix SLURM runner for real user setups and avoid uneccesary chowns
 2021-02-21 19:49:00 +01:00
John Chilton 8e5c8532c6 Merge pull request #11402 from OlegZharkov/selenium-test-dataset-permissions 
[Selenium] Test library dataset permissions
 2021-02-20 21:53:00 -05:00
Dannon c6e5989100 Merge pull request #11424 from ic4f/dev_api_test_fix 
Rename fixtures to fix test database object name conflict
 2021-02-20 01:29:09 -05:00
Sergey Golitsynskiy e6cdbb8497 Rename fixtures to fix test db object name conflict 2021-02-19 22:31:55 -05:00
John Chilton 63540d517f Merge pull request #11422 from ic4f/dev_mypy_pin 
Pin mypy to 0.790 to prevent linting errors when running v 0.8
 2021-02-19 21:00:54 -05:00
Sergey Golitsynskiy f3f6c26470 Pin mypy to 0.790 2021-02-19 15:29:46 -05:00
John Chilton f526611441 Merge pull request #11412 from davelopez/refactor_api_groups 
Refactor groups API logic into GroupsManager
 2021-02-19 14:11:25 -05:00
John Chilton 0973a5eef6 Merge pull request #11418 from davelopez/refactor_group_users_api 
Refactor group_users API logic into GroupUsersManager
 2021-02-19 14:10:54 -05:00
John Chilton 36612f9d57 Merge pull request #11417 from davelopez/refactor_group_role_api 
Refactor group_roles API logic into GroupRolesManager
 2021-02-19 14:10:43 -05:00
Nicola Soranzo 7dbdce3be2 Merge branch 'release_21.01' into dev 2021-02-19 18:03:30 +00:00
Nicola Soranzo 7ac4278feb Merge branch 'release_20.09' into release_21.01 2021-02-19 18:01:13 +00:00
Nicola Soranzo b93b81aaf2 Merge branch 'release_20.05' into release_20.09 2021-02-19 17:56:55 +00:00
Nicola Soranzo b6836cb06b Merge branch 'release_20.01' into release_20.05 2021-02-19 17:53:53 +00:00
Nicola Soranzo 320aae00fe Merge pull request #11410 from bernt-matthias/topic/fix-configfile-20.05 2021-02-19 16:45:59 +00:00
Marius van den Beek e43819f47e Merge pull request #11416 from nsoranzo/release_20.09_fix_sniffers_for_too_many_comments 
[20.09] Fix sniffers of interval datatypes for files starting with many comments
 2021-02-19 15:25:06 +01:00
davelopez 0b9e1bb4b4 Add type annotations to controller 2021-02-19 15:09:04 +01:00
davelopez f77ba2cdc2 Refactor manager logic 
- Adapt error handling
- Remove redundant exception logging
 2021-02-19 15:08:47 +01:00
davelopez b5988a8777 Move controller logic to GroupUsersManager 2021-02-19 14:33:32 +01:00
davelopez e3783deb17 Replace the old legacy_expose_api decorators 2021-02-19 14:25:28 +01:00
davelopez 470c658eba Add tests for group_users API 2021-02-19 14:22:02 +01:00
davelopez a1c2a77ef3 Add type annotations to controller 2021-02-19 13:00:14 +01:00
davelopez 6d5ab7a1ae Refactor manager logic 
- Adapt error handling
- Remove redundant exception logging
 2021-02-19 12:59:56 +01:00
Oleg Zharkov f880010b51 implement selenium test 2021-02-19 13:59:37 +02:00
Nicola Soranzo ebf996f8bc Set Vcf metadata also for VcfGz files 2021-02-19 11:50:57 +00:00
Nicola Soranzo 26f731f060 Fix sniffers of interval datatypes for files starting with many comments 
For files starting with >60 comment lines, the `sniff_prefix()` method of
Bed, Gff, Gff3 and Gtf classes was returning `True` when actually all
headers lines were skipped.

Also:
- Don't skip lines having more than one column just because the first
column is empty.
- Properly skip comment lines in `is_column_based()`
- Add test file which would have been incorrectly sniffed as `gtf` before.
  It still isn't sniffed as `gff3`, but that's fine because it has too many
  comment lines for the default header prefix.
 2021-02-19 11:50:52 +00:00
davelopez 3f49ea9213 Move controller logic to GroupRolesManager 2021-02-18 20:12:07 +01:00
davelopez 5b718f8c9b Replace the old legacy_expose_api decorators 2021-02-18 19:57:04 +01:00
davelopez 10ae171e52 Add tests for group_roles API 2021-02-18 19:50:05 +01:00
davelopez b0fcf86a0f Decode all ids and fetch them all in one query 
As @mvdbeek suggested
 2021-02-18 16:02:27 +01:00
Marius van den BeekandNicola Soranzo db1618fc6a Use multiline yaml 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-02-18 14:10:03 +00:00
mvdbeek a8adab100c Restore all integration subsets 2021-02-18 14:09:43 +00:00
mvdbeek fc1d74d1d3 Deploy postgresql and rabbitmq in kubernetes 
Setting up minikube stops the postgres and rabbitmq containers that are
set up by the workflow. These are setup with custom docker networks, so
it isn't trivial to restart them. Instead we just deploy them to
minikube.
 2021-02-18 14:09:34 +00:00
Marius van den Beek 998f092cf9 Merge pull request #11396 from mvdbeek/workflow_versions 
[20.01] Backport Fix TypeError in WorkflowsAPIController.get_versions()
 2021-02-18 14:55:42 +01:00
davelopez d38ba53b21 Fix groups update endpoint 
Prevent possible name duplication and add error handling.
Fix tests to assert 409 when the operation may result in a name conflict.
 2021-02-18 14:50:40 +01:00
davelopez 559ba46302 Refactor error handling logic 2021-02-18 14:50:40 +01:00
davelopez 71214ae567 Add basic type annotations 2021-02-18 14:50:40 +01:00
davelopez 4fdf4c50ef Refactor move controller logic into GroupsManager 2021-02-18 14:50:40 +01:00
davelopez 719d8139eb Replace legacy expose_api decorators xref #11252 2021-02-18 14:50:40 +01:00
davelopez 5e129c1f6a Add API tests for groups 2021-02-18 14:50:40 +01:00
Nicola Soranzo cf50e90f82 Sync social-auth-core requirement in data package 
v4.0.2 dropped support for Python 3.5
 2021-02-18 13:48:52 +00:00
Dannon f15cc2a892 Merge pull request #11347 from OlegZharkov/dataset-lib-permissions 
Dataset lib permissions Vue rewrite
 2021-02-18 08:20:42 -05:00
Matthias Bernt bd5e8f326c fix profile logic for configfile generation 
some follow up fixes to

https://github.com/galaxyproject/galaxy/pull/9279/files
https://github.com/galaxyproject/galaxy/pull/9776/files

- wrong profile for the profile test tool (it used 20.01, but should
have used 20.05)
- the non-profile test tool used wrong assumptions. now fixed
  and also tested against 19.09
- in the profile version `value_wrapper.value` needs to be casted
  for `multiple==False` otherwise we gat `"None"` (which I do not
  understand 100%)
 2021-02-18 12:33:07 +01:00
Matthias Bernt e2076fbb9d fix genration of config files 2021-02-18 12:33:07 +01:00
Nicola Soranzo 3040c38860 Merge pull request #11400 from mvdbeek/maintainence_bot_fix 2021-02-18 11:06:12 +00:00
Marius van den BeekandNicola Soranzo 8a4bfb829e Add unlabeled to workflow types 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-02-18 10:56:44 +01:00
Nicola Soranzo 03cd2f78cc Merge pull request #11405 from ic4f/dev_poetry_fix 
Decrease verbosity of messages in poetry
 2021-02-18 09:25:32 +00:00
Sergey Golitsynskiy 1ff303f30d Decrease verbosity of messages in poetry 
Fixes poetry bug
 2021-02-17 19:21:13 -05:00
John Chilton 04d875ba30 Merge pull request #11380 from bernt-matthias/topic/fix-configfile 
fix profile logic for configfile generation
 2021-02-17 16:57:42 -05:00
Matthias Bernt c18af6f5cf avoid unnecessary chowns 
in 6117d0cbe3 another reclaim_ownership was introduced. I observed
that this function is now called 3x. so lets just skip this
of the dir is already owned by the corresponding owner
 2021-02-17 22:18:03 +01:00