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Author SHA1 Message Date
Marius van den Beek 2ea1b94e39 Merge pull request #11945 from nsoranzo/release_21.01_fix_mypy 
[21.01] Backport #11900
 2021-05-06 13:33:04 +02:00
John Chilton 75e93a5d43 Fix package CI. 2021-05-06 12:20:53 +01:00
Nicola Soranzo fa58f37f28 Merge branch 'release_20.09' into release_21.01 2021-05-06 11:39:48 +01:00
Marius van den Beek 40e73295a6 Merge pull request #11923 from cat-bro/fix_legacy_grids_state_column 
[21.01] update legacy_framework.grids.StateColumn (bug fix)
 2021-05-04 15:42:53 +02:00
cat-broandMarius van den Beek 4f8503be29 Update lib/galaxy/web/legacy_framework/grids.py 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-05-04 22:13:01 +10:00
cat-bro f4ec1bac83 update legacy_framework.grids.StateColumn: model_class.states is Enum now instead of Bunch 2021-05-04 18:47:24 +10:00
Marius van den Beek 8c029f5b04 Merge pull request #11881 from scholtalbers/swid-backport 
[21.01] Backport #11871
 2021-05-03 16:13:20 +02:00
Marius van den Beek 26049fa684 Merge pull request #11913 from mvdbeek/keep_original_keep_data 
[21.01] Use keep_original in pysam.tabix_index to not remove original data
 2021-05-03 11:44:19 +02:00
Martin Cech 31c67a2420 Merge pull request #11906 from dannon/viz-scaling-fix 
[21.01] Shared visualization display fix
 2021-04-30 11:40:05 +02:00
mvdbeek 6a209388ee Use keep_original in pysam.tabix_index to not remove original data 2021-04-29 22:37:41 +02:00
Dannon Baker e15ec9173c Use full page context (not just the short embed chunk) when injecting a viz in an iframe 2021-04-27 13:29:43 -04:00
Dannon ede2f0f6a8 Merge pull request #11896 from mvdbeek/backport_the_third 
[21.01] Backport of #11687: Expose command line if expose_dataset_path is set
 2021-04-26 15:08:37 -04:00
John Chilton 5c52b35dc7 Merge pull request #11897 from mvdbeek/fix_config_provider 
[21.01] Fix ``Delete account`` visibility
 2021-04-26 09:18:33 -04:00
mvdbeek 3897019f44 Fix config slot for ConfigProvider 2021-04-26 13:07:55 +02:00
mvdbeek 8e67d140fe Adjust test, only check for external_id as admin-only property 2021-04-26 12:24:37 +02:00
mvdbeek a1ccd5bb8f Expose commandline if expose_dataset_path is set 
This restores what templates/show_params.mako used to do prior to https://github.com/galaxyproject/galaxy/pull/10980/
Fixes https://github.com/galaxyproject/galaxy/issues/11651
 2021-04-26 12:24:37 +02:00
scholtalbersandSimon Bray ba1f4a3f7a Update lib/galaxy/model/__init__.py 
Co-authored-by: Simon Bray <32272674+simonbray@users.noreply.github.com>
 2021-04-22 14:51:37 +02:00
Simon Bray c799e4a455 expose StoredWorkflowId in invocation API 2021-04-22 11:39:49 +02:00
John Chilton 25861047a9 Merge pull request #11876 from natefoo/total-walltime-fix 
[20.09] Fix user total walltime calculation when jobs are missing states in job state history
 2021-04-21 14:21:59 -04:00
Nate Coraor e015db0244 No f-strings in 3.5. 2021-04-21 11:07:48 -04:00
Nate Coraor 55f4d5fdc1 Fix user total walltime calculation when jobs are missing states in job 
state history.
 2021-04-21 10:50:17 -04:00
Nate Coraor 69b65ac99a Merge remote-tracking branch 'upstream/release_20.09' into release_20.09 2021-04-21 10:39:33 -04:00
mvdbeek b2d63cd71b Merge branch 'release_20.09' into release_21.01 2021-04-20 11:12:23 +02:00
mvdbeek 9169f6c8d2 Merge branch 'release_20.05' into release_20.09 2021-04-20 11:10:25 +02:00
Marius van den Beek 9e62d11483 Merge pull request #11867 from rhpvorderman/fixwatchdog20.05 
Backport to 20.05: watchdog dependency check bugfix.
 2021-04-20 11:09:09 +02:00
Ruben Vorderman 8f324eceef Also check for boolean True, not just string 'True' when evaluating conditional dependencies. 
When people know how actual yaml works they might have

    galaxy:
        watch_tools: true

as their config. Which signifies an actual Boolean value. This should be considered by the script as well.
 2021-04-20 08:45:28 +02:00
Björn Grüning a844e2b188 Merge pull request #11838 from hexylena/patch-gtn-in-galaxy 
[21.01] Patch to click the button which should be more stable
 2021-04-15 21:08:36 +02:00
Marius van den Beek 9b11f1749f Merge pull request #11835 from mvdbeek/stop_thread 
[21.01]Join QueueWorker thread
 2021-04-14 17:25:33 +02:00
Helena Rasche 19d3119428 Patch to click the button which should be more stable 2021-04-14 17:08:05 +02:00
mvdbeek 99e3c0b2dc Join QueueWorker thread 
As we're supposed to do based on
https://docs.celeryproject.org/projects/kombu/en/stable/reference/kombu.mixins.html,
under should_stop:
"When this is set to true the consumer should stop consuming and return, so that it can be joined if it is the implementation of a thread."
This means less noise on application shutdown.
 2021-04-14 13:52:46 +02:00
Björn Grüning 9348fdae7f Merge pull request #11816 from mvdbeek/performance_fix_setup_external_metadata 
[21.01] Backport #11815: Don't write job and job-related attributes when creating export model
 2021-04-12 15:17:11 +02:00
mvdbeek 897590b2f3 Add separate option for including jobs to model store 2021-04-11 20:33:57 +02:00
mvdbeek 0a4aa468bf Don't write job and job-related attributes when creating export model 
These aren't used in regular jobs (should only be needed for history
export currently).
 2021-04-11 10:56:39 +02:00
Björn Grüning 08694fd05f Merge pull request #11802 from astrovsky01/jellyfish_db 
jellyfish db datatype
 2021-04-10 10:16:28 +02:00
Alexander OSTROVSKY 93d1c7a4e8 change extension 2021-04-08 09:34:31 -07:00
Alexander OSTROVSKY cf5b8d8805 jellyfish db datatype 2021-04-08 09:34:31 -07:00
Marius van den Beek c767adbed1 Merge pull request #11654 from brinkmanlab/revert_11448 
Refactor default mounting of $tmp_directory in containers
 2021-04-08 15:43:39 +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
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 5a2985db39 Merge pull request #11776 from dannon/scroll-library-list 
[21.01] Fix library scrolling
 2021-04-03 13:39:43 -04:00
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
Dannon Baker 19acbd5b34 Fix library scrolling 
For good this time, I hope.  As implemented, we always want that
container to take 100% height, handle its own padding,  and scroll
internal contents.
 2021-04-02 11:01:48 -04:00
Björn Grüning 2ae087b88c fix spelling in test 2021-04-01 21:02:51 +02:00
John Chilton 950856002f Merge pull request #11762 from mvdbeek/assorted_tool_shed_fixes 
[21.01] Assorted tool shed fixes
 2021-04-01 10:46:38 -04:00
John Chilton a6f3b255cb Merge pull request #11764 from mvdbeek/fix_format_input_implicit_conversion 
[21.01] Fix format="input" with implicit conversions
 2021-04-01 10:45:55 -04:00
Marius van den Beek b6c24cfce0 Merge pull request #11765 from almahmoud/webapp 
[21.01] galaxy.webapps.tool_shed to webapp.tool_shed
 2021-04-01 16:32:53 +02:00