Merge branch 'release_24.1' into dev

lib/galaxy/managers/base.py

@@ -178,7 +178,7 @@ def get_object(trans, id, class_name, check_ownership=False, check_accessible=Fa
         item = trans.sa_session.query(item_class).get(decoded_id)
         assert item is not None
     except Exception:
-        log.exception(f"Invalid {class_name} id ( {id} ) specified.")
+        log.warning(f"Invalid {class_name} id ( {id} ) specified.")
         raise exceptions.MessageException(f"Invalid {class_name} id ( {id} ) specified", type="error")
 
     if check_ownership or check_accessible:

lib/galaxy/managers/workflows.py

@@ -1856,10 +1856,14 @@ def __load_subworkflow_from_step_dict(
         embedded_subworkflow = step_dict.get("subworkflow", None)
         subworkflow_id = step_dict.get("content_id", None)
         if embedded_subworkflow and subworkflow_id:
-            raise Exception("Subworkflow step defines both subworkflow and content_id, only one may be specified.")
+            raise exceptions.RequestParameterInvalidException(
+                "Subworkflow step defines both subworkflow and content_id, only one may be specified."
+            )
 
         if not embedded_subworkflow and not subworkflow_id:
-            raise Exception("Subworkflow step must define either subworkflow or content_id.")
+            raise exceptions.RequestParameterInvalidException(
+                "Subworkflow step must define either subworkflow or content_id."
+            )
 
         if embedded_subworkflow:
             assert not dry_run

lib/galaxy/model/__init__.py

@@ -7665,7 +7665,7 @@ def get_internal_version(self, version):
         if version is None:
             return self.latest_workflow
         if len(self.workflows) <= version:
-            raise Exception("Version does not exist")
+            raise galaxy.exceptions.RequestParameterInvalidException("Version does not exist")
         return list(reversed(self.workflows))[version]
 
     def version_of(self, workflow):

packages/app/HISTORY.rst

@@ -4,11 +4,61 @@ History
 .. to_doc
 
 ---------
-24.1.dev0
+24.2.dev0
 ---------
 
 
 
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Raise exception if collection elements missing during download by `@jdavcs <https://github.com/jdavcs>`_ in `#18094 <https://github.com/galaxyproject/galaxy/pull/18094>`_
+* Allow purge query param, deprecate purge body param by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18105 <https://github.com/galaxyproject/galaxy/pull/18105>`_
+* Backport OIDC schema fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18111 <https://github.com/galaxyproject/galaxy/pull/18111>`_
+* Don't log exception if cancelled slurm job doesn't have stderr file by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18121 <https://github.com/galaxyproject/galaxy/pull/18121>`_
+* Downgrade missing output file in working directory to warning for failed jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18123 <https://github.com/galaxyproject/galaxy/pull/18123>`_
+* Fix data default values not getting added to history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18132 <https://github.com/galaxyproject/galaxy/pull/18132>`_
+* Drop redundant error message by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18156 <https://github.com/galaxyproject/galaxy/pull/18156>`_
+* Emit warning when user-cancelled job already complete by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18178 <https://github.com/galaxyproject/galaxy/pull/18178>`_
+* Avoid object store path lookup when constructing JobState object by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18190 <https://github.com/galaxyproject/galaxy/pull/18190>`_
+* Add string cast for dbkey / genome_build by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18207 <https://github.com/galaxyproject/galaxy/pull/18207>`_
+* Check dataset state when attempting to acces dataset contents by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18214 <https://github.com/galaxyproject/galaxy/pull/18214>`_
+* Don't set dataset peek for errored jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18231 <https://github.com/galaxyproject/galaxy/pull/18231>`_
+* Raise exception when extracting dataset from collection without datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18249 <https://github.com/galaxyproject/galaxy/pull/18249>`_
+* Skip tests if toolshed, dx.doi not responding by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18250 <https://github.com/galaxyproject/galaxy/pull/18250>`_
+* Don't attempt to download purged datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18278 <https://github.com/galaxyproject/galaxy/pull/18278>`_
+* Check various preconditions in FeatureLocationIndexDataProvider by `@davelopez <https://github.com/davelopez>`_ in `#18283 <https://github.com/galaxyproject/galaxy/pull/18283>`_
+* Don't serialize display application links for deleted datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18307 <https://github.com/galaxyproject/galaxy/pull/18307>`_
+* Downgrade doi fetch error to debug by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18330 <https://github.com/galaxyproject/galaxy/pull/18330>`_
+* Fix authentication error for anonymous users querying jobs by `@davelopez <https://github.com/davelopez>`_ in `#18333 <https://github.com/galaxyproject/galaxy/pull/18333>`_
+* Fix seek in slurm memory check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18338 <https://github.com/galaxyproject/galaxy/pull/18338>`_
+* Do not copy purged outputs to object store by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18342 <https://github.com/galaxyproject/galaxy/pull/18342>`_
+* Kill pulsar job if job stopped on galaxy side by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18348 <https://github.com/galaxyproject/galaxy/pull/18348>`_
+* Allow DCE as outer input to to_cwl by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18349 <https://github.com/galaxyproject/galaxy/pull/18349>`_
+* Fix anonymous user job retrieval logic by `@davelopez <https://github.com/davelopez>`_ in `#18358 <https://github.com/galaxyproject/galaxy/pull/18358>`_
+* Fix update group API payload model by `@davelopez <https://github.com/davelopez>`_ in `#18374 <https://github.com/galaxyproject/galaxy/pull/18374>`_
+* Fix user's private role can be missing by `@davelopez <https://github.com/davelopez>`_ in `#18381 <https://github.com/galaxyproject/galaxy/pull/18381>`_
+* Fix null inputs in database operation tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18385 <https://github.com/galaxyproject/galaxy/pull/18385>`_
+* Assign default ``data`` extension on discovered collection output  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18389 <https://github.com/galaxyproject/galaxy/pull/18389>`_
+* Fix ``get_accessible_job`` if called without session by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18400 <https://github.com/galaxyproject/galaxy/pull/18400>`_
+* Fix invocation step_job_summary for new collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18402 <https://github.com/galaxyproject/galaxy/pull/18402>`_
+* Really allow in-range validator for txt by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18411 <https://github.com/galaxyproject/galaxy/pull/18411>`_
+* Fix collection map over status for dragged collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18416 <https://github.com/galaxyproject/galaxy/pull/18416>`_
+* Serialize purged flag for datasets in collections by `@davelopez <https://github.com/davelopez>`_ in `#18420 <https://github.com/galaxyproject/galaxy/pull/18420>`_
+
+=============
+Other changes
+=============
+
+* Minor linting cleanup by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18421 <https://github.com/galaxyproject/galaxy/pull/18421>`_
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
+
 -------------------
 24.0.2 (2024-05-07)
 -------------------

packages/auth/HISTORY.rst

@@ -4,11 +4,17 @@ History
 .. to_doc
 
 ---------
-24.1.dev0
+24.2.dev0
 ---------
 
 
 
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 24.0.2 (2024-05-07)
 -------------------

packages/config/HISTORY.rst

@@ -4,11 +4,29 @@ History
 .. to_doc
 
 ---------
-24.1.dev0
+24.2.dev0
 ---------
 
 
 
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Backport OIDC schema fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18111 <https://github.com/galaxyproject/galaxy/pull/18111>`_
+* Minor fix to enable external hgweb process by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18256 <https://github.com/galaxyproject/galaxy/pull/18256>`_
+
+=============
+Other changes
+=============
+
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
+
 -------------------
 24.0.2 (2024-05-07)
 -------------------

packages/data/HISTORY.rst

@@ -4,11 +4,36 @@ History
 .. to_doc
 
 ---------
-24.1.dev0
+24.2.dev0
 ---------
 
 
 
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Downgrade count lines error to warning by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18175 <https://github.com/galaxyproject/galaxy/pull/18175>`_
+* Don't set dataset peek for errored jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18231 <https://github.com/galaxyproject/galaxy/pull/18231>`_
+* Transparently open compressed files in DatasetDataProvider by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18248 <https://github.com/galaxyproject/galaxy/pull/18248>`_
+* Raise exception when extracting dataset from collection without datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18249 <https://github.com/galaxyproject/galaxy/pull/18249>`_
+* Set page importable to false when serializing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18263 <https://github.com/galaxyproject/galaxy/pull/18263>`_
+* Fix first_dataset_element type hint by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18284 <https://github.com/galaxyproject/galaxy/pull/18284>`_
+* Do not copy purged outputs to object store by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18342 <https://github.com/galaxyproject/galaxy/pull/18342>`_
+* Fix user's private role can be missing by `@davelopez <https://github.com/davelopez>`_ in `#18381 <https://github.com/galaxyproject/galaxy/pull/18381>`_
+* Assign default ``data`` extension on discovered collection output  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18389 <https://github.com/galaxyproject/galaxy/pull/18389>`_
+
+=============
+Other changes
+=============
+
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
+
 -------------------
 24.0.2 (2024-05-07)
 -------------------

packages/files/HISTORY.rst

@@ -4,11 +4,26 @@ History
 .. to_doc
 
 ---------
-24.1.dev0
+24.2.dev0
 ---------
 
 
 
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix listing possibly untitled records in Invenio Plugin by `@davelopez <https://github.com/davelopez>`_ in `#18130 <https://github.com/galaxyproject/galaxy/pull/18130>`_
+* Raise ``RequestParameterInvalidException`` when url is invalid by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18155 <https://github.com/galaxyproject/galaxy/pull/18155>`_
+* Fix error message when accessing restricted Zenodo records by `@davelopez <https://github.com/davelopez>`_ in `#18169 <https://github.com/galaxyproject/galaxy/pull/18169>`_
+* Raise ``RequestParameterInvalidException`` if url can't be verified by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18230 <https://github.com/galaxyproject/galaxy/pull/18230>`_
+* Fix Invenio credentials handling by `@davelopez <https://github.com/davelopez>`_ in `#18255 <https://github.com/galaxyproject/galaxy/pull/18255>`_
+
 -------------------
 24.0.2 (2024-05-07)
 -------------------

packages/job_execution/HISTORY.rst

@@ -4,11 +4,26 @@ History
 .. to_doc
 
 ---------
-24.1.dev0
+24.2.dev0
 ---------
 
 
 
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Include traceback when logging email PJA exception by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18122 <https://github.com/galaxyproject/galaxy/pull/18122>`_
+* Don't commit in ``DeleteIntermediatesAction`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18131 <https://github.com/galaxyproject/galaxy/pull/18131>`_
+* Don't fail metadata if we only have an extra output files dir by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18179 <https://github.com/galaxyproject/galaxy/pull/18179>`_
+* Don't set dataset peek for errored jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18231 <https://github.com/galaxyproject/galaxy/pull/18231>`_
+* Do not copy purged outputs to object store by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18342 <https://github.com/galaxyproject/galaxy/pull/18342>`_
+
 -------------------
 24.0.2 (2024-05-07)
 -------------------

packages/job_metrics/HISTORY.rst

@@ -4,11 +4,17 @@ History
 .. to_doc
 
 ---------
-24.1.dev0
+24.2.dev0
 ---------
 
 
 
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 24.0.2 (2024-05-07)
 -------------------

packages/navigation/HISTORY.rst

@@ -4,11 +4,17 @@ History
 .. to_doc
 
 ---------
-24.1.dev0
+24.2.dev0
 ---------
 
 
 
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 24.0.2 (2024-05-07)
 -------------------

packages/objectstore/HISTORY.rst

@@ -4,11 +4,24 @@ History
 .. to_doc
 
 ---------
-24.1.dev0
+24.2.dev0
 ---------
 
 
 
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Include stack when reporting delete error by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18208 <https://github.com/galaxyproject/galaxy/pull/18208>`_
+* Only log error if deleting directory really failed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18236 <https://github.com/galaxyproject/galaxy/pull/18236>`_
+* Do not copy purged outputs to object store by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18342 <https://github.com/galaxyproject/galaxy/pull/18342>`_
+
 -------------------
 24.0.2 (2024-05-07)
 -------------------

packages/schema/HISTORY.rst

@@ -4,11 +4,27 @@ History
 .. to_doc
 
 ---------
-24.1.dev0
+24.2.dev0
 ---------
 
 
 
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* do not expand datasets that are known to be inaccessible by `@martenson <https://github.com/martenson>`_ in `#17818 <https://github.com/galaxyproject/galaxy/pull/17818>`_
+* Allow purge query param, deprecate purge body param by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18105 <https://github.com/galaxyproject/galaxy/pull/18105>`_
+* Fix deprecated `deprecated` argument by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18119 <https://github.com/galaxyproject/galaxy/pull/18119>`_
+* Fix users API serialization when listing users by `@davelopez <https://github.com/davelopez>`_ in `#18329 <https://github.com/galaxyproject/galaxy/pull/18329>`_
+* Fix update group API payload model by `@davelopez <https://github.com/davelopez>`_ in `#18374 <https://github.com/galaxyproject/galaxy/pull/18374>`_
+* Serialize purged flag for datasets in collections by `@davelopez <https://github.com/davelopez>`_ in `#18420 <https://github.com/galaxyproject/galaxy/pull/18420>`_
+
 -------------------
 24.0.2 (2024-05-07)
 -------------------

packages/selenium/HISTORY.rst

@@ -4,11 +4,17 @@ History
 .. to_doc
 
 ---------
-24.1.dev0
+24.2.dev0
 ---------
 
 
 
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 24.0.2 (2024-05-07)
 -------------------

packages/test_api/HISTORY.rst

@@ -4,11 +4,25 @@ History
 .. to_doc
 
 ---------
-24.1.dev0
+24.2.dev0
 ---------
 
 
 
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Allow purge query param, deprecate purge body param by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18105 <https://github.com/galaxyproject/galaxy/pull/18105>`_
+* Prevent anonymous and inactive users from running workflows by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18192 <https://github.com/galaxyproject/galaxy/pull/18192>`_
+* Check dataset state when attempting to acces dataset contents by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18214 <https://github.com/galaxyproject/galaxy/pull/18214>`_
+* Fix update group API payload model by `@davelopez <https://github.com/davelopez>`_ in `#18374 <https://github.com/galaxyproject/galaxy/pull/18374>`_
+
 -------------------
 24.0.2 (2024-05-07)
 -------------------