Commit 3cd860f1 authored by John Davis's avatar John Davis
Browse files

Add last PRs, fix markup typo

parent 1e430104
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+156 −0
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@@ -124,6 +124,12 @@ Tool enhancements

.. enhancement_tag_workflows

* Fix problem with multiple layers in workflow metrics
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19283`_
* Fix workflow metrics chart style
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19291`_
Workflow enhancements
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

@@ -232,6 +238,15 @@ Admin enhancements

.. enhancement

* List private file sources first in Remote Files Dialog
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19455`_
* Various list of pairs builder usability fixes
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19248`_
* Fix to not display upload when creating collections from existing datasets
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19373`_
Misc. enhancements
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

@@ -484,6 +499,9 @@ Misc. enhancements

.. small_enhancement

* Release testing - selenium tests for workflow invocation export
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19262`_
* Update versions of GitHub actions
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18197`_
@@ -581,6 +599,9 @@ Fixes

.. bug_tag_viz

* Prevent cycling through failing conversion jobs in trackster
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19494`_
Vizualization fixes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

@@ -617,6 +638,18 @@ Tool fixes

.. bug_tag_workflows

* Fix error message when subworkflow input connection missing
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19526`_
* Also check `trs_tool_id` for imported workflow indicator
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19460`_
* Set a hard limit of 100 invocations per request in api/invocations
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19497`_
* Fix import of previously-deleted TRS workflow
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19311`_
Workflow fixes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

@@ -659,6 +692,21 @@ UI fixes

.. bug_tag_jobs

* Use instance wide default ``real_system_username`` if not defined on destination
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19544`_
* Fix job parameter summary for inputs without label
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19427`_
* Serialize message exceptions on execution error
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19483`_
* Partial backport of `#19331 <https://github.com/galaxyproject/galaxy/issues/19331>`__
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19342`_
* Fixes for console logging
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19381`_
Job fixes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

@@ -668,8 +716,116 @@ Job fixes

.. bug_tag_admin

* Downgrade 'InteractiveTools are not enabled' to warning
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19518`_
.. bug

* Use visualizations api in trackster
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19495`_
* Fix extracting workflows from purged and deleted histories
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19525`_
* Fix WSGI response status handling in controller methods
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19520`_
* Fix remap for parameter called id
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19532`_
* Fix admin cancel job message not being displayed to the user
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19537`_
* Provide guidance in case of deadlock during db migration
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19551`_
* Update 24.2 db revision tags
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19550`_
* Fix to only show ChatGXY when available
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19389`_
* Display upload help highlight only once and include Rule-based upload info
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19393`_
* Show message for mixed extensions in collection creator
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19404`_
* Fix Activity Bar state lost on page reload
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19426`_
* Show Keycloak provider label in UI
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19447`_
* `mulled-build-tool` fix for packages wo version
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19450`_
* Fix parsing of validators with inf limits
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19459`_
* Fix help text overflow breaking tool inspector
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19465`_
* Fix object not found handling
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19468`_
* Remove print statement
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19469`_
* Bump typescript target to es2020
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19473`_
* Fail with error message when submitting invalid request
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19489`_
* Fix invocation query in JobInformation.vue component
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19496`_
* Fix minor typo in event name in collection creator
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19499`_
* Fix library dataset current user potentially null
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19505`_
* Fix workflowID assignment in Markdown.vue
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19507`_
* Skip token refresh without refresh token in psa
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19514`_
* Fix tool search constantly loading bug
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19528`_
* Add tool_id index on job table
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19543`_
* Outputs filter linter fixes
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19208`_
* Fix some collection builder help and language choices
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19244`_
* Only allow moving activity bar icons when editing the bar
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19258`_
* Fix CollectionCreatorModal being reopened on history
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19276`_
* Fix invocation metrics usability by providing job context
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19279`_
* Fix inconsistent tab handling in invocation view
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19298`_
* Don't show published workflows in workflow activity of workflow editor
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19312`_
* Fix timeout handling for planemo / galaxy-tool-util
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19384`_
* Fix for empty string in regex validator message
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19387`_
Misc. fixes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

+3 −0
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@@ -178,6 +178,9 @@ Visualizations
===========================================================

.. visualizations
* Prevent cycling through failing conversion jobs in trackster
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19494`_
* Update visualizations package versions
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19232`_
+56 −0
Original line number Diff line number Diff line

.. github_links
.. _Pull Request 19471: https://github.com/galaxyproject/galaxy/pull/19471
.. _Pull Request 19495: https://github.com/galaxyproject/galaxy/pull/19495
.. _Pull Request 19525: https://github.com/galaxyproject/galaxy/pull/19525
.. _Pull Request 19520: https://github.com/galaxyproject/galaxy/pull/19520
.. _Pull Request 19494: https://github.com/galaxyproject/galaxy/pull/19494
.. _Pull Request 19532: https://github.com/galaxyproject/galaxy/pull/19532
.. _Pull Request 19537: https://github.com/galaxyproject/galaxy/pull/19537
.. _Pull Request 19526: https://github.com/galaxyproject/galaxy/pull/19526
.. _Pull Request 19544: https://github.com/galaxyproject/galaxy/pull/19544
.. _Pull Request 19551: https://github.com/galaxyproject/galaxy/pull/19551
.. _Pull Request 19550: https://github.com/galaxyproject/galaxy/pull/19550
.. _Pull Request 19389: https://github.com/galaxyproject/galaxy/pull/19389
.. _Pull Request 19393: https://github.com/galaxyproject/galaxy/pull/19393
.. _Pull Request 19404: https://github.com/galaxyproject/galaxy/pull/19404
.. _Pull Request 19426: https://github.com/galaxyproject/galaxy/pull/19426
.. _Pull Request 19427: https://github.com/galaxyproject/galaxy/pull/19427
.. _Pull Request 19447: https://github.com/galaxyproject/galaxy/pull/19447
.. _Pull Request 19450: https://github.com/galaxyproject/galaxy/pull/19450
.. _Pull Request 19455: https://github.com/galaxyproject/galaxy/pull/19455
.. _Pull Request 19459: https://github.com/galaxyproject/galaxy/pull/19459
.. _Pull Request 19460: https://github.com/galaxyproject/galaxy/pull/19460
.. _Pull Request 19465: https://github.com/galaxyproject/galaxy/pull/19465
.. _Pull Request 19468: https://github.com/galaxyproject/galaxy/pull/19468
.. _Pull Request 19469: https://github.com/galaxyproject/galaxy/pull/19469
.. _Pull Request 19473: https://github.com/galaxyproject/galaxy/pull/19473
.. _Pull Request 19483: https://github.com/galaxyproject/galaxy/pull/19483
.. _Pull Request 19489: https://github.com/galaxyproject/galaxy/pull/19489
.. _Pull Request 19496: https://github.com/galaxyproject/galaxy/pull/19496
.. _Pull Request 19497: https://github.com/galaxyproject/galaxy/pull/19497
.. _Pull Request 19499: https://github.com/galaxyproject/galaxy/pull/19499
.. _Pull Request 19505: https://github.com/galaxyproject/galaxy/pull/19505
.. _Pull Request 19507: https://github.com/galaxyproject/galaxy/pull/19507
.. _Pull Request 19514: https://github.com/galaxyproject/galaxy/pull/19514
.. _Pull Request 19518: https://github.com/galaxyproject/galaxy/pull/19518
.. _Pull Request 19528: https://github.com/galaxyproject/galaxy/pull/19528
.. _Pull Request 19543: https://github.com/galaxyproject/galaxy/pull/19543
.. _Pull Request 19208: https://github.com/galaxyproject/galaxy/pull/19208
.. _Pull Request 19244: https://github.com/galaxyproject/galaxy/pull/19244
.. _Pull Request 19248: https://github.com/galaxyproject/galaxy/pull/19248
.. _Pull Request 19254: https://github.com/galaxyproject/galaxy/pull/19254
.. _Pull Request 19258: https://github.com/galaxyproject/galaxy/pull/19258
.. _Pull Request 19262: https://github.com/galaxyproject/galaxy/pull/19262
.. _Pull Request 19276: https://github.com/galaxyproject/galaxy/pull/19276
.. _Pull Request 19279: https://github.com/galaxyproject/galaxy/pull/19279
.. _Pull Request 19283: https://github.com/galaxyproject/galaxy/pull/19283
.. _Pull Request 19284: https://github.com/galaxyproject/galaxy/pull/19284
.. _Pull Request 19288: https://github.com/galaxyproject/galaxy/pull/19288
.. _Pull Request 19291: https://github.com/galaxyproject/galaxy/pull/19291
.. _Pull Request 19298: https://github.com/galaxyproject/galaxy/pull/19298
.. _Pull Request 19311: https://github.com/galaxyproject/galaxy/pull/19311
.. _Pull Request 19312: https://github.com/galaxyproject/galaxy/pull/19312
.. _Pull Request 19342: https://github.com/galaxyproject/galaxy/pull/19342
.. _Pull Request 19373: https://github.com/galaxyproject/galaxy/pull/19373
.. _Pull Request 19381: https://github.com/galaxyproject/galaxy/pull/19381
.. _Pull Request 19384: https://github.com/galaxyproject/galaxy/pull/19384
.. _Pull Request 19387: https://github.com/galaxyproject/galaxy/pull/19387
.. _Pull Request 19351: https://github.com/galaxyproject/galaxy/pull/19351
.. _Pull Request 19332: https://github.com/galaxyproject/galaxy/pull/19332
.. _Pull Request 19350: https://github.com/galaxyproject/galaxy/pull/19350
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