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Author SHA1 Message Date
mvdbeek 92a76e9fd4 Produce a clean list of dataset instances if not datasets in collection 2020-11-10 15:30:29 +01:00
John Chilton 39c7c3dfd4 Merge pull request #10668 from jmchilton/assert_ok_invocation 
wait_for_invocation should take in an assert_ok flag like other wait methods.
 2020-11-10 07:47:59 -05:00
Nicola Soranzo 719df27150 Merge pull request #10673 from galaxyproject/bernt-matthias-patch-1 
fix link to job config sample in docs
 2020-11-10 12:13:50 +00:00
Nicola Soranzo 41c649d667 Merge pull request #10669 from jmchilton/optional_inputs_api_test 
API workflow test showing structure of default/optionals parameters.
 2020-11-10 11:56:09 +00:00
M Bernt 963fb994dd fix link to job config sample in docs 2020-11-10 11:34:31 +01:00
John Chilton 08a4ddafd1 API workflow test showing structure of default/optionals parameters. 
- Shows how to find them, name of parameters, odd double encoding of tool_state, and shows parameters with default values are implicitly optional = True.
 2020-11-09 23:12:21 -05:00
John Chilton 220d441844 wait_for_invocation should take in an assert_ok flag like other wait methods. 2020-11-09 20:42:52 -05:00
Dannon 3337e249f5 Merge pull request #10489 from guerler/radio_buttons 
Revise style of radio button groups to improve visibility
 2020-11-09 15:20:17 -05:00
Marius van den Beek e2977fd24c Merge pull request #10659 from nsoranzo/merge_20.05 
Merge forward release_20.09
 2020-11-09 16:12:55 +01:00
Marius van den Beek 7eb7e6be54 Merge pull request #10658 from jmchilton/cwltool_rev 
Rev cwltool to 3.0.20201109103151
 2020-11-09 16:06:28 +01:00
Marius van den Beek fd627e3091 Merge pull request #10657 from jmchilton/workflow_step_type 
Refactor logic for workflow_step.input_type into model.
 2020-11-09 14:50:55 +01:00
Nicola Soranzo 9f4dcc924f Update cwltool 3.0.20201109103151 requirements 2020-11-09 13:40:17 +00:00
Dannon 38623472af Merge pull request #10583 from hexylena/extract-wf-primary 
Make extract wf action more visible
 2020-11-09 08:37:05 -05:00
Nicola Soranzo cb8a310e74 Merge branch 'release_20.09' into dev 2020-11-09 12:53:53 +00:00
mvdbeek cae46bd415 Rev cwltool with fix for opaque strings 2020-11-09 12:46:23 +01:00
John Chilton 15c81f8869 Rev cwltool. 2020-11-08 22:11:45 -05:00
John Chilton f1d601a138 Move logic for workflow_step.input_type into model. 2020-11-08 13:57:50 -05:00
John Chilton cef3b9ab5c Merge pull request #10619 from OlegZharkov/trs-auto-import 
auto-import workflow with trs
 2020-11-08 08:02:42 -05:00
Marius van den Beek 3519db8698 Merge pull request #10652 from OlegZharkov/fix-race-20.09 
[20.09] fix dataset_manipulation and logged_dataset_manipulation
 2020-11-07 19:44:06 +01:00
Marius van den Beek 44c99169ac Merge pull request #10650 from jmchilton/upload_object 
Fix ObjectUploadTarget handling in tool util staging code.
 2020-11-07 19:30:52 +01:00
John Chilton 177bd9f7fe Fix ObjectUploadTarget handling in tool util staging code. 
With test cases.
 2020-11-07 08:44:46 -05:00
Oleg Zharkov e95246cbcb move logged_dataset_manipulation and dataset_manipulation to computed 2020-11-07 13:07:07 +01:00
Marius van den Beek bcc7ea0afc Merge pull request #10637 from assuntad23/bugfix/SavedRulesSelectorIssues 
Fix saving rule builder rules when uploading in rule editing view
 2020-11-07 13:03:12 +01:00
Dannon 08e839538b Merge pull request #10499 from guerler/upload_button_revision 
Move upload button below Tool panel header, increase size, add label
 2020-11-07 06:58:44 -05:00
John Chilton 85d196e0e8 Merge pull request #10649 from nsoranzo/release_20.09_fix_lint.yaml 
[20.09] Fix cache key for lint CI workflow
 2020-11-06 20:33:52 -05:00
Nicola Soranzo c86989826a Fix cache key for lint CI workflow 
Also:
- test on Python 3.9 instead of 3.8
- update some action versions

xref. https://github.com/galaxyproject/galaxy/pull/10615#pullrequestreview-521926167
 2020-11-06 18:47:31 +00:00
Assunta DeSanto 7e18d65492 Merge branch 'bugfix/SavedRulesSelectorIssues' of https://github.com/assuntad23/galaxy into bugfix/SavedRulesSelectorIssues 2020-11-06 11:55:26 -05:00
Assunta DeSanto 2f0582e737 running Prettier 2020-11-06 11:52:09 -05:00
Assunta DeSanto 6fb0d8f824 fixing an error 2020-11-06 11:47:02 -05:00
mvdbeek 800e098dca Run prettier 2020-11-06 09:57:59 +01:00
Assunta DeSanto c4e47e6e10 Fixing unit tests 2020-11-06 09:57:59 +01:00
Assunta DeSanto 973a527c52 Fixing unit tests 2020-11-06 09:57:59 +01:00
Assunta DeSanto b011e2bb31 Fixing unit tests 2020-11-06 09:57:59 +01:00
Assunta DeSanto 12cbdd54c8 Moving data of saved rules to a separate component from the template view 2020-11-06 09:57:59 +01:00
Assunta DeSanto 3d2b6d40dd Fixing unit tests 2020-11-06 00:33:28 -05:00
Assunta DeSanto dedc2e79d7 Fixing unit tests 2020-11-06 00:30:08 -05:00
Assunta DeSanto 89007a80e5 Fixing unit tests 2020-11-06 00:17:25 -05:00
Assunta DeSanto 1d3a9ad8bd Moving data of saved rules to a separate component from the template view 2020-11-05 23:44:34 -05:00
Björn Grüning c060b64fd0 Merge pull request #10632 from mvdbeek/workflow_editor_fixes_2 
[20.09] Update input label on workflow node when input changes
 2020-11-06 00:03:23 +01:00
mvdbeek 7df17504bf Merge branch 'release_20.09' into dev 2020-11-05 19:03:01 +01:00
mvdbeek 1095e8ac2e Merge branch 'release_20.05' into release_20.09 2020-11-05 18:58:07 +01:00
mvdbeek ad7a6ca430 Update input label on workflow node when input changes 2020-11-05 18:49:22 +01:00
Aysam Guerler 844c4e50f4 Merge pull request #10626 from mvdbeek/workflow_editor_fixes 
[20.09] Fix Workflow node input terminal not updating
 2020-11-05 12:46:33 -05:00
Marius van den Beek 5a10667554 Merge pull request #10623 from mvdbeek/fix_static_welcome_html_link 
[20.09] Restore welcome html link for non-uwsgi setups
 2020-11-05 17:57:07 +01:00
John Chilton 97305501bd Merge pull request #10625 from bernt-matthias/topic/singularity-bind-spec 
Don't specify default bind type for singularity
 2020-11-05 09:24:03 -05:00
Sergey Golitsynskiy 017c7ee344 Merge pull request #10617 from ic4f/20.09_filepath_fix 
[20.09] Fix file_path bug; change default assignment of file_path and id/uuid
 2020-11-04 17:57:08 -05:00
mvdbeek 6e3e91b6a2 Fix updating workflow node input terminal 
This fixes a silent error when hitting
`this.outputTerminals[name].$el.remove();`

This seems to not be necessary, but it is super weird that there is no
error logged. I just found it by stepping through this line by line in
the debugger.

This fixes https://github.com/galaxyproject/galaxy/issues/10622
 2020-11-04 21:35:25 +01:00
Matthias Bernt f35d06eef0 omit default bind type for singularity 2020-11-04 21:31:05 +01:00
Nicola Soranzo 5ce152b279 Improve testing of _configure_dataset_storage() 2020-11-04 19:13:17 +00:00
mvdbeek a87781fe09 Restore welcome html link for non-uwsgi setups 
by restoring the symlink from lib/galaxy/webapps/base/static to static.

This is the default location for `/static/welcome.html` as set in https://github.com/galaxyproject/galaxy/blob/release_20.09/lib/galaxy/webapps/base/webapp.py#L1032).
This fixes the `Not Found` in the center panel for Selenium tests and
planemo.
I am not sure if this is the right fix w.r.t packaging.

Alternatively we could sett a default of `static/welcome.html` for `static_welcome_html`
(and putting this in the schema, I have the impression that some users think this is what
`welcome_url` does).
 2020-11-04 12:10:04 +01:00