Merge branch 'release_24.0' into dev

# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_shed/HISTORY.rst
#	packages/tool_shed/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
This commit is contained in:
mvdbeek
2024-05-02 12:27:11 +02:00
21 changed files with 275 additions and 2 deletions
+45 -1
View File
@@ -9,6 +9,50 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
=========
Bug fixes
=========
* Fix tool version switch in editor by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17858 <https://github.com/galaxyproject/galaxy/pull/17858>`_
* Fix workflow run form failing on certain histories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17869 <https://github.com/galaxyproject/galaxy/pull/17869>`_
* Always serialize element_count and populated when listing contents by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17890 <https://github.com/galaxyproject/galaxy/pull/17890>`_
* Fix saving workflows with freehand_comments only by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17901 <https://github.com/galaxyproject/galaxy/pull/17901>`_
* Always discard session after __handle_waiting_jobs is done by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17913 <https://github.com/galaxyproject/galaxy/pull/17913>`_
* Fix workflow run form for workflows with null rename PJA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17929 <https://github.com/galaxyproject/galaxy/pull/17929>`_
* Revert unnecessary error change by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17948 <https://github.com/galaxyproject/galaxy/pull/17948>`_
* Fix missing implicit conversion for mapped over jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17952 <https://github.com/galaxyproject/galaxy/pull/17952>`_
* Fix get_content_as_text for compressed text datatypes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17976 <https://github.com/galaxyproject/galaxy/pull/17976>`_
* Backport: Fix bug: call unique() on result, not select stmt by `@jdavcs <https://github.com/jdavcs>`_ in `#17981 <https://github.com/galaxyproject/galaxy/pull/17981>`_
* Fix `LengthValidator` if no value passed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17983 <https://github.com/galaxyproject/galaxy/pull/17983>`_
* Raise ``RequestParameterInvalidException`` if collection element has unknown extension by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17985 <https://github.com/galaxyproject/galaxy/pull/17985>`_
* Don't attempt to commit in dry_run mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17987 <https://github.com/galaxyproject/galaxy/pull/17987>`_
* Don't fail if reporting invalid parameter values by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18002 <https://github.com/galaxyproject/galaxy/pull/18002>`_
* Include exception info when something goes wrong while refreshing tokens by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18008 <https://github.com/galaxyproject/galaxy/pull/18008>`_
* Avoid exception when opening apply rules tool and no collection in history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18011 <https://github.com/galaxyproject/galaxy/pull/18011>`_
* Don't commit without having set a hid by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18014 <https://github.com/galaxyproject/galaxy/pull/18014>`_
* Raise appropriate exception if user forces a collection that is not populated with elements as input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18023 <https://github.com/galaxyproject/galaxy/pull/18023>`_
* Fix tag regex pattern by `@jdavcs <https://github.com/jdavcs>`_ in `#18025 <https://github.com/galaxyproject/galaxy/pull/18025>`_
* Fix History Dataset Association creation so that hid is always set by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18036 <https://github.com/galaxyproject/galaxy/pull/18036>`_
* Change wrong quota_source value from KeyError to ValueError by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18040 <https://github.com/galaxyproject/galaxy/pull/18040>`_
* Check database connection to issue a rollback if no connection by `@jdavcs <https://github.com/jdavcs>`_ in `#18070 <https://github.com/galaxyproject/galaxy/pull/18070>`_
============
Enhancements
============
* Fix remote files sources error handling by `@davelopez <https://github.com/davelopez>`_ in `#18027 <https://github.com/galaxyproject/galaxy/pull/18027>`_
=============
Other changes
=============
* Drop left-over debug statement by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17939 <https://github.com/galaxyproject/galaxy/pull/17939>`_
-------------------
24.0.0 (2024-04-02)
-------------------
@@ -52,7 +96,7 @@ Enhancements
* Vueify Admin User Grid by `@guerler <https://github.com/guerler>`_ in `#17030 <https://github.com/galaxyproject/galaxy/pull/17030>`_
* Remove web framework dependency from tools by `@davelopez <https://github.com/davelopez>`_ in `#17058 <https://github.com/galaxyproject/galaxy/pull/17058>`_
* Add select parameter with options from remote resources by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17087 <https://github.com/galaxyproject/galaxy/pull/17087>`_
* Expose more tool information / navigability in UI. by `@jmchilton <https://github.com/jmchilton>`_ in `#17105 <https://github.com/galaxyproject/galaxy/pull/17105>`_
* Expose more tool information / navigability in UI. by `@jmchilton <https://github.com/jmchilton>`_ in `#17105 <https://github.com/galaxyproject/galaxy/pull/17105>`_
* Vueify Admin Roles Grid by `@guerler <https://github.com/guerler>`_ in `#17118 <https://github.com/galaxyproject/galaxy/pull/17118>`_
* SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by `@jdavcs <https://github.com/jdavcs>`_ in `#17122 <https://github.com/galaxyproject/galaxy/pull/17122>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17123 <https://github.com/galaxyproject/galaxy/pull/17123>`_
+6
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@@ -9,6 +9,12 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
No recorded changes since last release
-------------------
24.0.0 (2024-04-02)
-------------------
+27
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@@ -9,6 +9,33 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
=========
Bug fixes
=========
* Invenio plugin fixes by `@davelopez <https://github.com/davelopez>`_ in `#17997 <https://github.com/galaxyproject/galaxy/pull/17997>`_
* clarify the object store relocate functionality by `@martenson <https://github.com/martenson>`_ in `#18033 <https://github.com/galaxyproject/galaxy/pull/18033>`_
* Updated the datatypes name for FASTK tool by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#18053 <https://github.com/galaxyproject/galaxy/pull/18053>`_
============
Enhancements
============
* Added 4dn_pairs and 4dn_pairsam datatypes by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#17875 <https://github.com/galaxyproject/galaxy/pull/17875>`_
* Add middleware for logging start and end of request by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18046 <https://github.com/galaxyproject/galaxy/pull/18046>`_
=============
Other changes
=============
* Rebuild config samples by `@davelopez <https://github.com/davelopez>`_ in `#17911 <https://github.com/galaxyproject/galaxy/pull/17911>`_
* Backport colabfold tar file datatype by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18029 <https://github.com/galaxyproject/galaxy/pull/18029>`_
-------------------
24.0.0 (2024-04-02)
-------------------
+24 -1
View File
@@ -9,6 +9,29 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
=========
Bug fixes
=========
* Always serialize element_count and populated when listing contents by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17890 <https://github.com/galaxyproject/galaxy/pull/17890>`_
* Fix deadlock that can occur when changing job state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17896 <https://github.com/galaxyproject/galaxy/pull/17896>`_
* Fix tool form building if select filters from unavailable dataset metadata by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17930 <https://github.com/galaxyproject/galaxy/pull/17930>`_
* Fix ``InvalidRequestError: Can't operate on closed transaction inside context manager. Please complete the context manager before emitting further commands.`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17932 <https://github.com/galaxyproject/galaxy/pull/17932>`_
* Never fail dataset serialization if display_peek fails by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17937 <https://github.com/galaxyproject/galaxy/pull/17937>`_
* Fix output datatype when uncompressing a dataset with incorrect datatype by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17944 <https://github.com/galaxyproject/galaxy/pull/17944>`_
* Use or copy StoredWorkflow when copying step by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17988 <https://github.com/galaxyproject/galaxy/pull/17988>`_
* Raise ``MessageException`` when report references invalid workflow output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18009 <https://github.com/galaxyproject/galaxy/pull/18009>`_
* Fix tag regex pattern by `@jdavcs <https://github.com/jdavcs>`_ in `#18025 <https://github.com/galaxyproject/galaxy/pull/18025>`_
* Fix History Dataset Association creation so that hid is always set by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18036 <https://github.com/galaxyproject/galaxy/pull/18036>`_
* Fix history export with missing dataset hids by `@davelopez <https://github.com/davelopez>`_ in `#18052 <https://github.com/galaxyproject/galaxy/pull/18052>`_
* Fix comments lost on import by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#18060 <https://github.com/galaxyproject/galaxy/pull/18060>`_
* Fix history update time after bulk operation by `@davelopez <https://github.com/davelopez>`_ in `#18068 <https://github.com/galaxyproject/galaxy/pull/18068>`_
-------------------
24.0.0 (2024-04-02)
-------------------
@@ -51,7 +74,7 @@ Enhancements
* port invocation API to fastapi by `@martenson <https://github.com/martenson>`_ in `#16707 <https://github.com/galaxyproject/galaxy/pull/16707>`_
* SQLAlchemy 2.0 upgrades (part 5) by `@jdavcs <https://github.com/jdavcs>`_ in `#16932 <https://github.com/galaxyproject/galaxy/pull/16932>`_
* Python 3.8 as minimum by `@mr-c <https://github.com/mr-c>`_ in `#16954 <https://github.com/galaxyproject/galaxy/pull/16954>`_
* Expose more tool information / navigability in UI. by `@jmchilton <https://github.com/jmchilton>`_ in `#17105 <https://github.com/galaxyproject/galaxy/pull/17105>`_
* Expose more tool information / navigability in UI. by `@jmchilton <https://github.com/jmchilton>`_ in `#17105 <https://github.com/galaxyproject/galaxy/pull/17105>`_
* Add support for (fast5.tar).xz binary compressed files by `@tuncK <https://github.com/tuncK>`_ in `#17106 <https://github.com/galaxyproject/galaxy/pull/17106>`_
* SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by `@jdavcs <https://github.com/jdavcs>`_ in `#17122 <https://github.com/galaxyproject/galaxy/pull/17122>`_
* Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by `@jdavcs <https://github.com/jdavcs>`_ in `#17132 <https://github.com/galaxyproject/galaxy/pull/17132>`_
+17
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@@ -9,6 +9,23 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
=========
Bug fixes
=========
* Invenio plugin fixes by `@davelopez <https://github.com/davelopez>`_ in `#17997 <https://github.com/galaxyproject/galaxy/pull/17997>`_
============
Enhancements
============
* Fix remote files sources error handling by `@davelopez <https://github.com/davelopez>`_ in `#18027 <https://github.com/galaxyproject/galaxy/pull/18027>`_
-------------------
24.0.0 (2024-04-02)
-------------------
+6
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@@ -9,6 +9,12 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
No recorded changes since last release
-------------------
24.0.0 (2024-04-02)
-------------------
+6
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@@ -9,6 +9,12 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
No recorded changes since last release
-------------------
24.0.0 (2024-04-02)
-------------------
+6
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@@ -9,6 +9,12 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
No recorded changes since last release
-------------------
24.0.0 (2024-04-02)
-------------------
+6
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@@ -9,6 +9,12 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
No recorded changes since last release
-------------------
24.0.0 (2024-04-02)
-------------------
+12
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@@ -9,6 +9,18 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
=========
Bug fixes
=========
* Fix tag regex pattern by `@jdavcs <https://github.com/jdavcs>`_ in `#18025 <https://github.com/galaxyproject/galaxy/pull/18025>`_
* Fix History Dataset Association creation so that hid is always set by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18036 <https://github.com/galaxyproject/galaxy/pull/18036>`_
-------------------
24.0.0 (2024-04-02)
-------------------
+11
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@@ -9,6 +9,17 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
=========
Bug fixes
=========
* Set from_tool_form: true when saving new workflow by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17972 <https://github.com/galaxyproject/galaxy/pull/17972>`_
-------------------
24.0.0 (2024-04-02)
-------------------
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@@ -9,6 +9,26 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
=========
Bug fixes
=========
* Fix tool version switch in editor by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17858 <https://github.com/galaxyproject/galaxy/pull/17858>`_
* Fix workflow run form failing on certain histories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17869 <https://github.com/galaxyproject/galaxy/pull/17869>`_
* Always serialize element_count and populated when listing contents by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17890 <https://github.com/galaxyproject/galaxy/pull/17890>`_
* Make `wait_for_history_jobs` look at jobs, not datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17892 <https://github.com/galaxyproject/galaxy/pull/17892>`_
* Fix missing implicit conversion for mapped over jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17952 <https://github.com/galaxyproject/galaxy/pull/17952>`_
* Fix get_content_as_text for compressed text datatypes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17976 <https://github.com/galaxyproject/galaxy/pull/17976>`_
* Raise appropriate exception if user forces a collection that is not populated with elements as input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18023 <https://github.com/galaxyproject/galaxy/pull/18023>`_
* Fix ``test_get_tags_histories_content`` test by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18026 <https://github.com/galaxyproject/galaxy/pull/18026>`_
* Ensure that offset and limit are never negative by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18044 <https://github.com/galaxyproject/galaxy/pull/18044>`_
* Fix history update time after bulk operation by `@davelopez <https://github.com/davelopez>`_ in `#18068 <https://github.com/galaxyproject/galaxy/pull/18068>`_
-------------------
24.0.0 (2024-04-02)
-------------------
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-------------------
24.0.1 (2024-05-02)
-------------------
=========
Bug fixes
=========
* Make `wait_for_history_jobs` look at jobs, not datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17892 <https://github.com/galaxyproject/galaxy/pull/17892>`_
* Fix missing implicit conversion for mapped over jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17952 <https://github.com/galaxyproject/galaxy/pull/17952>`_
-------------------
24.0.0 (2024-04-02)
-------------------
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-------------------
24.0.1 (2024-05-02)
-------------------
No recorded changes since last release
-------------------
24.0.0 (2024-04-02)
-------------------
+6
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@@ -9,6 +9,12 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
No recorded changes since last release
-------------------
24.0.0 (2024-04-02)
-------------------
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@@ -9,6 +9,17 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
=========
Bug fixes
=========
* Fix conditional Image imports by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17899 <https://github.com/galaxyproject/galaxy/pull/17899>`_
-------------------
24.0.0 (2024-04-02)
-------------------
+6
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@@ -9,6 +9,12 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
No recorded changes since last release
-------------------
24.0.0 (2024-04-02)
-------------------
+11
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@@ -9,6 +9,17 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
=========
Bug fixes
=========
* Fix conditional Image imports by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17899 <https://github.com/galaxyproject/galaxy/pull/17899>`_
-------------------
24.0.0 (2024-04-02)
-------------------
+20
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@@ -9,6 +9,26 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
=========
Bug fixes
=========
* Fix tool version switch in editor by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17858 <https://github.com/galaxyproject/galaxy/pull/17858>`_
* Fix workflow run form failing on certain histories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17869 <https://github.com/galaxyproject/galaxy/pull/17869>`_
* Ensure that offset and limit are never negative by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18044 <https://github.com/galaxyproject/galaxy/pull/18044>`_
* Fix history update time after bulk operation by `@davelopez <https://github.com/davelopez>`_ in `#18068 <https://github.com/galaxyproject/galaxy/pull/18068>`_
============
Enhancements
============
* Add middleware for logging start and end of request by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18046 <https://github.com/galaxyproject/galaxy/pull/18046>`_
-------------------
24.0.0 (2024-04-02)
-------------------
+11
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@@ -9,6 +9,17 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
=========
Bug fixes
=========
* Fix KeyError in ``XForwardedHostMiddleware`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17955 <https://github.com/galaxyproject/galaxy/pull/17955>`_
-------------------
24.0.0 (2024-04-02)
-------------------
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@@ -9,6 +9,12 @@ History
-------------------
24.0.1 (2024-05-02)
-------------------
No recorded changes since last release
-------------------
24.0.0 (2024-04-02)
-------------------