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Author SHA1 Message Date
John Chilton d99b7eddb0 Merge pull request #10360 from mvdbeek/skip_workflow_invocation_step_update_subquery 
[20.09] Don't use subquery to update workflow invocation step update time
 2020-10-05 13:04:07 -04:00
Marius van den BeekandDannon 1c76fbd18d Drop parens 
Thanks Dannon!

Co-authored-by: Dannon <dannon.baker@gmail.com>
 2020-10-05 17:18:12 +02:00
mvdbeek ecf34f3b37 Don't use subquery to update workflow invocation step update time 
Thanks Nate, I don't think the subqeury was needed.
 2020-10-05 15:55:49 +02:00
mvdbeek 048e3b7c4f Merge branch 'release_20.05' into release_20.09 2020-10-02 17:41:29 +02:00
Marius van den Beek dcb329be00 Merge pull request #10284 from OlegZharkov/quickfix_20.09 
[20.09] fix folder path
 2020-10-02 17:04:21 +02:00
John Chilton 076e640206 Merge pull request #10321 from nsoranzo/release_20.05_fix_use_shared_home_with_docker 
[20.05] Respect ``use_shared_home="false"`` when running tools in container
 2020-10-02 10:57:38 -04:00
Marius van den Beek 9a15b1a6b5 Merge pull request #10344 from mvdbeek/add_missing_index_migrations 
[20.09] Add missing index migrations
 2020-10-02 15:39:35 +02:00
mvdbeek 79a018f861 Merge branch 'release_20.05' into release_20.09 2020-10-02 15:37:45 +02:00
mvdbeek 71e01da20f Merge branch 'release_20.01' into release_20.05 2020-10-02 15:32:35 +02:00
Marius van den Beek 311cbe430a Merge pull request #10248 from dannon/refactor-logout 
[20.09] Logout fix and refactoring
 2020-10-02 15:31:07 +02:00
Dannon Baker 70060df180 Expect a transition here in selenium test when logout_all happens 2020-10-02 08:42:34 -04:00
Marius van den Beek 6f495fceb3 Merge pull request #10335 from simonbray/staging-with-id-20.09 
[20.09] Allow 'planemo run' to stage in existing datasets without reuploading
 2020-10-02 12:29:47 +02:00
Marius van den Beek 535e4c52a5 Merge pull request #10308 from nuwang/fix_k8s_job_cleanup_loop 
[20.01] Prevent endless cleanup loops when duplicate job or k8s job not found
 2020-10-02 12:28:31 +02:00
Marius van den Beek 1a8e271e01 Merge pull request #10342 from dannon/fix-toolbox-wrap-20.05 
[20.05] Use block elements for labels to handle wrapping indentation
 2020-10-02 12:25:35 +02:00
mvdbeek 3af877573a Cleanup add_index/drop_index 2020-10-02 11:41:37 +02:00
Dannon 1af5d5d45b Merge pull request #10341 from blankenberg/itsvalid20.09 
[20.09] enable validation of ITs
 2020-10-01 15:06:55 -04:00
Nuwan Goonasekera e0d221a97b Also check for expected output in k8s delete test 2020-10-02 00:11:50 +05:30
mvdbeek d97606186c Add missing indexes 2020-10-01 20:21:08 +02:00
mvdbeek 04186715e9 Drop unused models 2020-10-01 20:21:08 +02:00
Nuwan Goonasekera ada9ee648d Minor refactoring of k8s tests 2020-10-01 23:46:18 +05:30
Nuwan Goonasekera 5d1b54cf6c Added test to check that jobs fail when deleted directly via k8s api 2020-10-01 23:46:18 +05:30
Nuwan Goonasekera 9d311d4557 Prevent endless cleanup loops when duplicate k8s job or k8s job not found 2020-10-01 23:46:18 +05:30
Dannon Baker 5c00766d86 Use block elements for labels to handle wrapping indentation 2020-10-01 14:00:35 -04:00
John Chilton 341b80b63b Merge pull request #10337 from dannon/pytest_pin 
[20.01] Pin pytest < 6.1
 2020-10-01 09:44:29 -04:00
Daniel Blankenberg 1b4d0bf07b enable validation of ITs 2020-10-01 09:25:33 -04:00
Dannon bfce056b38 Merge pull request #10331 from mvdbeek/dont_raise_exception_when_no_session_found_for_resending_email 
[20.09] Handle resend_activation_email gracefully without session
 2020-10-01 09:13:35 -04:00
Simon BrayandNicola Soranzo 3780f54f75 remove path attribute from FileLiteralTarget class 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-10-01 09:13:05 +02:00
Dannon Baker ca529da26c Simplification, no need to grab Galaxy and userId given the component props 2020-09-30 23:29:59 -04:00
Dannon Baker 399939fdf8 Clientside-only user logout (currently only useful for after deletion; we generally want to invalidate the session as well) 2020-09-30 23:27:37 -04:00
Dannon Baker 9d2cc0da69 Fix python snake_case arg construction 2020-09-30 21:44:41 -04:00
Dannon Baker 657dbb1a13 Support logoutAll, fix bug in userPreferences where we said it was a full session logout, but it was only terminating the current one. 2020-09-30 21:44:41 -04:00
Dannon Baker 5ad5342953 Logout fix (logout when deleting account) and refactoring to use this 
single method everywhere we process logout in the client.  It should
probably live elsewhere.
 2020-09-30 21:44:41 -04:00
Dannon Baker 276d8dce22 Pin pytest < 6.1 for now (backport) 2020-09-30 16:26:49 -04:00
Dannon 97cd907cd3 Merge pull request #10332 from mvdbeek/strip_trailing_slash_from_tool_id 
[20.09] Strip trailing ``/`` from tool_id for data source redirects
 2020-09-30 11:55:34 -04:00
Dannon Baker 6c2d123ef1 Merge remote-tracking branch 'upstream/release_20.05' into release_20.09 2020-09-30 11:43:27 -04:00
Dannon Baker bcae7d41c9 Merge remote-tracking branch 'upstream/release_20.01' into release_20.05 2020-09-30 11:42:35 -04:00
Marius van den Beek 33cc0ef9a2 Merge pull request #10330 from mvdbeek/fix_download_of_composite_data_from_collections 
[20.09] Fix composite data download from collection
 2020-09-30 17:34:03 +02:00
Dannon acfe5624b6 Merge pull request #10333 from mvdbeek/viewport_fix 
[20.01] Fix wiggle estimated_display_viewport
 2020-09-30 11:15:57 -04:00
John Chilton 2b038d3d09 pytest breakage in package testing? 2020-09-30 10:57:49 -04:00
Simon Bray 7dceabe22c tidy 2020-09-30 16:52:15 +02:00
Simon Bray cb14ce8b60 remove copy_func, appears unnecessary 2020-09-30 16:52:07 +02:00
Simon Bray 177cb604d3 allow copying datasets rather than uploading in StagingInterface 2020-09-30 16:51:57 +02:00
mvdbeek 812015421d Drop msg from _archive_composite_dataset signature 2020-09-30 15:32:03 +02:00
Marius van den Beek acfa2663cf Merge pull request #15 from nsoranzo/simplify__archive_composite_dataset 
Simplify `Data._archive_composite_dataset()`
 2020-09-30 15:25:38 +02:00
Nicola Soranzo 5ce78cb5cd Simplify Data._archive_composite_dataset() 2020-09-30 12:21:20 +01:00
Marius van den Beek 456f58bbee Merge pull request #10287 from dannon/viz-fixes 
[20.09] Plugin watchBuilding, and fixes for several older visualization builds
 2020-09-30 13:18:53 +02:00
Marius van den Beek b7f6259b4c Merge pull request #10312 from nsoranzo/release_20.09_fix_Wav_parent 
[20.09] Fix ``Wav`` datatype to inherit from ``Audio``
 2020-09-30 13:14:59 +02:00
Marius van den Beek 9421fd9f79 Merge pull request #10329 from dannon/fix-double-masthead 
[20.09] Fix double masthead in some spaces
 2020-09-30 13:14:03 +02:00
Marius van den Beek f800e056e9 Merge pull request #10317 from dannon/fix-tool-search-result-delay 
[20.09] Fix tool search to not display 'no results' prior to result return
 2020-09-30 13:08:19 +02:00
mvdbeek 925f9cfb0e Fix wiggle estimated_display_viewport 
Broken in https://github.com/galaxyproject/galaxy/pull/9415, where I
used the wrong function name.
Fixes https://sentry.galaxyproject.org/sentry/main/issues/568813/:
```
AttributeError: module 'galaxy.util' has no attribute 'iter_readline_count'
  File "galaxy/datatypes/interval.py", line 1092, in get_estimated_display_viewport
    for line in util.iter_readline_count(fh, VIEWPORT_READLINE_BUFFER_SIZE):
```
 2020-09-30 12:43:53 +02:00