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Author SHA1 Message Date
mvdbeek 5e4e04d8b3 Add workflow that tests runtime data column parameters 
This test only needs the previous 2 commits to pass.
 2021-03-11 16:57:31 +01:00
mvdbeek 8146fcb50d Only strip c from column definition if it precedes integers 2021-03-11 16:57:31 +01:00
mvdbeek ca0af28d52 Fix workflow runs with data_column runtime parameter changes 
The issue is that the fallback when no data is available uses the
default tool state but ignores values that are set at runtime.

Fixes https://github.com/galaxyproject/galaxy/issues/11593
 2021-03-11 16:56:13 +01:00
Dannon f5ad06ff68 Merge pull request #11541 from OlegZharkov/release_21.01 
[21.01] fix Upload button tool-tip for screenshooter
 2021-03-10 11:22:31 -05:00
John Chilton b28b784406 Merge pull request #11585 from mvdbeek/backport_empty_column_fix 
[21.01] Backport Handle the case where column list is a comma-separated string
 2021-03-10 09:38:48 -05:00
Dannon 520d599376 Merge pull request #11583 from mvdbeek/dockefile_build_backport 
[21.01] Dockerfile build backport
 2021-03-10 08:26:05 -05:00
Dannon 3cafcfde49 Merge pull request #11584 from mvdbeek/backport_oidc_logout 
[21.01] Backport oidc logout fix
 2021-03-10 07:55:45 -05:00
Kaivan Kamali b023970196 Added a default value to fix a broken framework test. 2021-03-10 10:26:41 +01:00
Kaivan Kamali d423b29336 Added another test for when columns are a comma separated string 2021-03-10 10:26:41 +01:00
Marius van den Beek 61b7cdd504 Add regression test for allowing data column selection on empty files 
A test for https://github.com/galaxyproject/galaxy/pull/10981.
 2021-03-10 10:26:41 +01:00
Kaivan Kamali 6e74674775 Removed whitespace 2021-03-10 10:26:41 +01:00
Kaivan Kamali 3e6aee1b4e Using utility function per code review feedback. 2021-03-10 10:26:41 +01:00
Kaivan Kamali 42a103291e Handle the case where column list is a comma-separated string 2021-03-10 10:26:41 +01:00
Juleen Graham a8a581b30b fix jslint error 2021-03-10 10:23:18 +01:00
Juleen Graham 347388326e Implement logout without extra api call 
utilise localStorage
 2021-03-10 10:23:18 +01:00
Juleen Graham d6c019306d remove unnecessary import 2021-03-10 10:23:18 +01:00
Juleen Graham 857508d059 prettier 2021-03-10 10:23:18 +01:00
Juleen Graham 30eacaa8a4 log out of oidc on galaxy logout 2021-03-10 10:23:18 +01:00
Nuwan Goonasekera cbe56641ff Don't remove node in docker build 2021-03-10 10:18:06 +01:00
Nuwan Goonasekera 98a7cc12c5 Added docker build hook with buildkit 2021-03-10 10:18:06 +01:00
Nuwan Goonasekera cc81ecd716 Parallelize client and server builds in dockerfile 2021-03-10 10:18:06 +01:00
Marius van den Beek 90e4f0c434 Merge pull request #11581 from jmchilton/files_plugin_error 
[21.01] Improve feedback for remote file listing exceptions.
 2021-03-10 09:48:34 +01:00
Marius van den Beek 517e6f924b Merge pull request #11577 from abretaud/gxit_home 
[21.01] Fix $HOME for some gxit requiring a specific one
 2021-03-09 17:55:14 +01:00
John Chilton 6a8725a641 Bug fix - poor feedback for remote file listing exceptions. 2021-03-09 11:21:03 -05:00
Oleg Zharkov e048262963 remove d50 2021-03-09 17:17:51 +02:00
Dannon 910821f6bf Merge pull request #11542 from mvdbeek/workflow_terminal_update_fixes 
[21.01] Fix workflow terminals not updating appropriately
 2021-03-09 09:30:46 -05:00
mvdbeek 45460cfac8 Merge branch 'release_20.09' into release_21.01 2021-03-09 15:27:49 +01:00
Anthony Bretaudeau b0fc281d54 Fix $HOME for some gxit requiring a specific one 2021-03-09 15:10:41 +01:00
Dannon 1eb0628046 Merge pull request #11576 from mvdbeek/fix_hid_name_in_dropped_value 
[21.01] Fix name and hid when selecting uploaded datasets
 2021-03-09 07:47:18 -05:00
Dannon 6f73a3590f Merge pull request #11572 from mvdbeek/tooltip_auto_positioning 
[21.01] Fix upload button tooltip blocking tool search field
 2021-03-09 07:45:13 -05:00
Dannon 81ddf7e1b5 Merge pull request #11574 from mvdbeek/anndata_select2_fix 
[20.09] Don't display obs_names in select list
 2021-03-09 07:38:13 -05:00
mvdbeek 09e3ebac41 Fix name and hid when selecting uploaded datasets 
in tool form or workflow form. Otherwise this would just display
`Selected: <hda_id>`.
 2021-03-09 12:19:22 +01:00
Marius van den Beek 2801c87468 Merge pull request #11457 from Nerdinacan/upload-select-button-11432 
Upload select button 11432
 2021-03-09 12:11:40 +01:00
mvdbeek 358a1e52a6 Don't display obs_names in select list 
This would result in thousands of select items, which breaks Select2
atm. Fixes https://github.com/galaxyproject/galaxy/issues/11406 while we
replace select2 hopefully soon.
 2021-03-09 11:37:46 +01:00
mvdbeek 5273f36520 Use tooltip auto positioning for upload button 
Fixes https://github.com/galaxyproject/galaxy/issues/11493
I think this tooltip isn't providing much, but at least it's
not getting in the way now.
 2021-03-09 10:51:18 +01:00
Marius van den Beek 54830aa1f7 Merge pull request #11540 from dannon/remote_user_logout 
[21.01] Remote user logout redirect fix
 2021-03-09 10:13:53 +01:00
Björn Grüning 91bda6127b Merge pull request #11567 from astrovsky01/paf_gz 
Add compressed paf datatype
 2021-03-09 08:36:35 +01:00
Alexander OSTROVSKY 58e183ae15 add compressed paf datatype 2021-03-08 13:59:19 -08:00
mvdbeek e49d6a3c46 Make NodeInput/NodeOutput reactive 2021-03-08 22:06:10 +01:00
John Chilton 6465b78836 Starting work on tool-util 21.1.0.dev7 2021-03-06 11:29:44 -05:00
Nicola Soranzo 2c0315731a Merge pull request #11555 from davebx/pb_datatype_release 
[21.01] Add display_in_upload for protobuf datatypes.
 2021-03-05 20:13:45 +00:00
John Chilton dc73f1f685 Merge pull request #11553 from jmchilton/rule_column_fix_2 
[21.01] Various Rule Builder Fixes
 2021-03-05 14:31:45 -05:00
Dave Bouvier 3c2f919ff0 Add display_in_upload for protobuf datatypes. 
These datatypes are used as an input for a tool, UShER, which is
currently being wrapped.
 2021-03-05 13:10:41 -05:00
John Chilton c7f52743b8 Fix typing handling around regex match group count. 
I can't tell when this broke.
 2021-03-05 12:35:00 -05:00
John Chilton 392c211119 Fix rule displays not using updated columns. 
Presumably broken with https://github.com/galaxyproject/galaxy/commit/f132f3ecbc416aeb24d96ff61a674fab7bb98bfa.
 2021-03-05 11:54:11 -05:00
Oleg Zharkov 802cd279ec tooltip wrapper 2021-03-05 18:17:30 +02:00
John Chilton ee2e0d4b82 Fix 'Method "l" has already been defined as a data property.' 
... in rule builder column selector.

```
[Vue warn]: Method "l" has already been defined as a data property.

found in

---> <ColumnSelector> at src/components/RuleBuilder/ColumnSelector.vue
       <RuleComponent> at src/components/RuleBuilder/RuleComponent.vue
         <RuleModalMiddle> at src/components/RuleBuilder/RuleModalMiddle.vue
           <StateDiv> at src/components/RuleBuilder/StateDiv.vue
             <Root>
```
 2021-03-05 09:48:32 -05:00
Marius van den Beek 5e763d1171 Merge pull request #11547 from bgruening/it_openrefine 
[21.01] allow using Openrefine without data inputs
 2021-03-05 13:45:28 +01:00
Marius van den Beek 768d1263a5 Merge pull request #11546 from bgruening/it_cellxgne 
[21.01] update the cellxgene IT container
 2021-03-05 13:45:11 +01:00
Marius van den Beek 43ceaad663 Merge pull request #11545 from bgruening/pyiron_updates 
[21.01] some pyiron interactive tools fixes from EU
 2021-03-05 13:44:46 +01:00