diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py index be487b4da675..6629e6911267 100644 --- a/lib/galaxy/managers/base.py +++ b/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: diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py index 7f57f698e5f2..31bf22ac6d20 100644 --- a/lib/galaxy/managers/workflows.py +++ b/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 diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index d2d9b0fcfba2..586543f0f9c4 100644 --- a/lib/galaxy/model/__init__.py +++ b/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): diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index c68d6c7dbe2f..3ebb25983862 100644 --- a/packages/app/HISTORY.rst +++ b/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 `_ in `#18094 `_ +* Allow purge query param, deprecate purge body param by `@mvdbeek `_ in `#18105 `_ +* Backport OIDC schema fix by `@mvdbeek `_ in `#18111 `_ +* Don't log exception if cancelled slurm job doesn't have stderr file by `@mvdbeek `_ in `#18121 `_ +* Downgrade missing output file in working directory to warning for failed jobs by `@mvdbeek `_ in `#18123 `_ +* Fix data default values not getting added to history by `@mvdbeek `_ in `#18132 `_ +* Drop redundant error message by `@mvdbeek `_ in `#18156 `_ +* Emit warning when user-cancelled job already complete by `@mvdbeek `_ in `#18178 `_ +* Avoid object store path lookup when constructing JobState object by `@mvdbeek `_ in `#18190 `_ +* Add string cast for dbkey / genome_build by `@mvdbeek `_ in `#18207 `_ +* Check dataset state when attempting to acces dataset contents by `@mvdbeek `_ in `#18214 `_ +* Don't set dataset peek for errored jobs by `@mvdbeek `_ in `#18231 `_ +* Raise exception when extracting dataset from collection without datasets by `@mvdbeek `_ in `#18249 `_ +* Skip tests if toolshed, dx.doi not responding by `@mvdbeek `_ in `#18250 `_ +* Don't attempt to download purged datasets by `@mvdbeek `_ in `#18278 `_ +* Check various preconditions in FeatureLocationIndexDataProvider by `@davelopez `_ in `#18283 `_ +* Don't serialize display application links for deleted datasets by `@mvdbeek `_ in `#18307 `_ +* Downgrade doi fetch error to debug by `@mvdbeek `_ in `#18330 `_ +* Fix authentication error for anonymous users querying jobs by `@davelopez `_ in `#18333 `_ +* Fix seek in slurm memory check by `@mvdbeek `_ in `#18338 `_ +* Do not copy purged outputs to object store by `@mvdbeek `_ in `#18342 `_ +* Kill pulsar job if job stopped on galaxy side by `@mvdbeek `_ in `#18348 `_ +* Allow DCE as outer input to to_cwl by `@mvdbeek `_ in `#18349 `_ +* Fix anonymous user job retrieval logic by `@davelopez `_ in `#18358 `_ +* Fix update group API payload model by `@davelopez `_ in `#18374 `_ +* Fix user's private role can be missing by `@davelopez `_ in `#18381 `_ +* Fix null inputs in database operation tools by `@mvdbeek `_ in `#18385 `_ +* Assign default ``data`` extension on discovered collection output by `@mvdbeek `_ in `#18389 `_ +* Fix ``get_accessible_job`` if called without session by `@mvdbeek `_ in `#18400 `_ +* Fix invocation step_job_summary for new collections by `@mvdbeek `_ in `#18402 `_ +* Really allow in-range validator for txt by `@bernt-matthias `_ in `#18411 `_ +* Fix collection map over status for dragged collections by `@mvdbeek `_ in `#18416 `_ +* Serialize purged flag for datasets in collections by `@davelopez `_ in `#18420 `_ + +============= +Other changes +============= + +* Minor linting cleanup by `@mvdbeek `_ in `#18421 `_ +* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek `_ in `#18428 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst index e87c36a52403..478c650147d7 100644 --- a/packages/auth/HISTORY.rst +++ b/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) ------------------- diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst index 746ecf383fc6..99cf5a295f22 100644 --- a/packages/config/HISTORY.rst +++ b/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 `_ in `#18111 `_ +* Minor fix to enable external hgweb process by `@mvdbeek `_ in `#18256 `_ + +============= +Other changes +============= + +* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek `_ in `#18428 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index 1d3a447f88ba..c5830a383e8b 100644 --- a/packages/data/HISTORY.rst +++ b/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 `_ in `#18175 `_ +* Don't set dataset peek for errored jobs by `@mvdbeek `_ in `#18231 `_ +* Transparently open compressed files in DatasetDataProvider by `@mvdbeek `_ in `#18248 `_ +* Raise exception when extracting dataset from collection without datasets by `@mvdbeek `_ in `#18249 `_ +* Set page importable to false when serializing by `@mvdbeek `_ in `#18263 `_ +* Fix first_dataset_element type hint by `@mvdbeek `_ in `#18284 `_ +* Do not copy purged outputs to object store by `@mvdbeek `_ in `#18342 `_ +* Fix user's private role can be missing by `@davelopez `_ in `#18381 `_ +* Assign default ``data`` extension on discovered collection output by `@mvdbeek `_ in `#18389 `_ + +============= +Other changes +============= + +* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek `_ in `#18428 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst index 2fc21b40fea9..5191875456bc 100644 --- a/packages/files/HISTORY.rst +++ b/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 `_ in `#18130 `_ +* Raise ``RequestParameterInvalidException`` when url is invalid by `@mvdbeek `_ in `#18155 `_ +* Fix error message when accessing restricted Zenodo records by `@davelopez `_ in `#18169 `_ +* Raise ``RequestParameterInvalidException`` if url can't be verified by `@mvdbeek `_ in `#18230 `_ +* Fix Invenio credentials handling by `@davelopez `_ in `#18255 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index 65d9d4244618..d89c9d3f956b 100644 --- a/packages/job_execution/HISTORY.rst +++ b/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 `_ in `#18122 `_ +* Don't commit in ``DeleteIntermediatesAction`` by `@mvdbeek `_ in `#18131 `_ +* Don't fail metadata if we only have an extra output files dir by `@mvdbeek `_ in `#18179 `_ +* Don't set dataset peek for errored jobs by `@mvdbeek `_ in `#18231 `_ +* Do not copy purged outputs to object store by `@mvdbeek `_ in `#18342 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index aa0c39f3599d..1ec5a397ab35 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/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) ------------------- diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst index 0db4ab93679c..34478a8509a9 100644 --- a/packages/navigation/HISTORY.rst +++ b/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) ------------------- diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index 2f6dc31f61a7..83d1be0a85bc 100644 --- a/packages/objectstore/HISTORY.rst +++ b/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 `_ in `#18208 `_ +* Only log error if deleting directory really failed by `@mvdbeek `_ in `#18236 `_ +* Do not copy purged outputs to object store by `@mvdbeek `_ in `#18342 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/schema/HISTORY.rst b/packages/schema/HISTORY.rst index 16def6b775a4..7643f7253ea0 100644 --- a/packages/schema/HISTORY.rst +++ b/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 `_ in `#17818 `_ +* Allow purge query param, deprecate purge body param by `@mvdbeek `_ in `#18105 `_ +* Fix deprecated `deprecated` argument by `@mvdbeek `_ in `#18119 `_ +* Fix users API serialization when listing users by `@davelopez `_ in `#18329 `_ +* Fix update group API payload model by `@davelopez `_ in `#18374 `_ +* Serialize purged flag for datasets in collections by `@davelopez `_ in `#18420 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index 5beab1aae25b..352222c56485 100644 --- a/packages/selenium/HISTORY.rst +++ b/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) ------------------- diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index 792c69a9334e..d54e5c7b5d05 100644 --- a/packages/test_api/HISTORY.rst +++ b/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 `_ in `#18105 `_ +* Prevent anonymous and inactive users from running workflows by `@ahmedhamidawan `_ in `#18192 `_ +* Check dataset state when attempting to acces dataset contents by `@mvdbeek `_ in `#18214 `_ +* Fix update group API payload model by `@davelopez `_ in `#18374 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index 29b159027296..27207a23e82a 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -4,11 +4,22 @@ History .. to_doc --------- -24.1.dev0 +24.2.dev0 --------- +------------------- +24.0.3 (2024-06-28) +------------------- + + +========= +Bug fixes +========= + +* Fix submitted value in workflow run form if data is constrained by tag filter by `@mvdbeek `_ in `#18193 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index 35bc848859c4..b013adb27de9 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -4,11 +4,23 @@ History .. to_doc --------- -24.1.dev0 +24.2.dev0 --------- +------------------- +24.0.3 (2024-06-28) +------------------- + + +========= +Bug fixes +========= + +* Skip tests if toolshed, dx.doi not responding by `@mvdbeek `_ in `#18250 `_ +* Move tool shed specific driver function to tool_shed.test by `@mvdbeek `_ in `#18296 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/tool_shed/HISTORY.rst b/packages/tool_shed/HISTORY.rst index 4d37ec4ce31c..5d11a8c9c5d1 100644 --- a/packages/tool_shed/HISTORY.rst +++ b/packages/tool_shed/HISTORY.rst @@ -4,11 +4,24 @@ History .. to_doc --------- -24.1.dev0 +24.2.dev0 --------- +------------------- +24.0.3 (2024-06-28) +------------------- + + +========= +Bug fixes +========= + +* Add ``hgweb_repo_prefix`` attribute to ``TestToolShedConfig`` by `@nsoranzo `_ in `#18268 `_ +* Fix tool_shed package unit tests by `@mvdbeek `_ in `#18327 `_ +* Fix one more tool shed unit test by `@mvdbeek `_ in `#18328 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index 1192cd5b732d..68ceea5daee3 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/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 `_ in `#18105 `_ +* Make sure that all Linter subclasses are imported for listing them by `@bernt-matthias `_ in `#18339 `_ +* Assign default ``data`` extension on discovered collection output by `@mvdbeek `_ in `#18389 `_ +* Allow in_range validator for selects by `@bernt-matthias `_ in `#18403 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/tours/HISTORY.rst b/packages/tours/HISTORY.rst index 98b94ca159cc..7be5cbb5acc2 100644 --- a/packages/tours/HISTORY.rst +++ b/packages/tours/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) ------------------- diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index f181c3c71bce..ab4df9270340 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -4,11 +4,22 @@ History .. to_doc --------- -24.1.dev0 +24.2.dev0 --------- +------------------- +24.0.3 (2024-06-28) +------------------- + + +========= +Bug fixes +========= + +* Use config_section to distinguish between galaxy and ts or other apps by `@jdavcs `_ in `#18215 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst index 364d1133a1d6..c9acce3bb7c7 100644 --- a/packages/web_apps/HISTORY.rst +++ b/packages/web_apps/HISTORY.rst @@ -4,11 +4,44 @@ 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 `_ in `#17818 `_ +* Raise exception if collection elements missing during download by `@jdavcs `_ in `#18094 `_ +* Allow purge query param, deprecate purge body param by `@mvdbeek `_ in `#18105 `_ +* Prevent anonymous and inactive users from running workflows by `@ahmedhamidawan `_ in `#18192 `_ +* Fix `make all histories private` with immutable histories by `@davelopez `_ in `#18200 `_ +* Fix pca 3d rendering of tabular files and visualization error handling in general by `@mvdbeek `_ in `#18211 `_ +* Check dataset state when attempting to acces dataset contents by `@mvdbeek `_ in `#18214 `_ +* Restrict job_files access to jobs that are not terminal by `@mvdbeek `_ in `#18217 `_ +* Raise appropriate exception if accessing deleted input file by `@mvdbeek `_ in `#18223 `_ +* Fix element serialization for collections that aren't populated yet by `@mvdbeek `_ in `#18235 `_ +* Skip new history creation if user is anonymous and login is required by `@mvdbeek `_ in `#18319 `_ +* Fix users API serialization when listing users by `@davelopez `_ in `#18329 `_ +* Fix authentication error for anonymous users querying jobs by `@davelopez `_ in `#18333 `_ +* Do not copy purged outputs to object store by `@mvdbeek `_ in `#18342 `_ +* Fix anonymous user job retrieval logic by `@davelopez `_ in `#18358 `_ +* Fix update group API payload model by `@davelopez `_ in `#18374 `_ +* Drop unnecessary escaping for workflow name and annotation by `@mvdbeek `_ in `#18376 `_ + +============= +Other changes +============= + +* Decrease log level for expected visualization errors by `@mvdbeek `_ in `#18229 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index f3bb5f762efd..fc1fe145db9c 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -4,11 +4,23 @@ History .. to_doc --------- -24.1.dev0 +24.2.dev0 --------- +------------------- +24.0.3 (2024-06-28) +------------------- + + +========= +Bug fixes +========= + +* Reset content-length for unhandled exceptions by `@mvdbeek `_ in `#18233 `_ +* More fixes for running the TS with external hgweb by `@mvdbeek `_ in `#18279 `_ + ------------------- 24.0.2 (2024-05-07) ------------------- diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst index bcb6837658c6..ae693b033ba2 100644 --- a/packages/web_stack/HISTORY.rst +++ b/packages/web_stack/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) -------------------