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5dccc48 mvdbeek 04 January 2024, 15:15:11 UTC Create version 23.1.4 04 January 2024, 15:15:11 UTC
d0a7562 Marius van den Beek 02 January 2024, 18:41:31 UTC Merge pull request #17236 from mvdbeek/fix_schema_integrity [23.1] Separate collection and non-collection data element 02 January 2024, 18:41:31 UTC
4027c99 mvdbeek 01 January 2024, 08:07:30 UTC Skip test when ftp.gnu.org not available 01 January 2024, 08:07:30 UTC
b1361c8 mvdbeek 31 December 2023, 16:20:43 UTC Separate collection and non-collection data element in tool schema. New lxml is more strict when validating the xml schema and fails with ``` lxml.etree.XMLSchemaParseError: complex type 'Output': The content model is not determinist., line 5329 ``` this is because `filter` and `discover_datasets` are present in OutputDataElement and OutputCollectionElement, making ``` <xs:sequence> <xs:group ref="OutputDataElement" minOccurs="0" maxOccurs="unbounded" /> <xs:group ref="OutputCollectionElement" minOccurs="0" maxOccurs="unbounded" /> </xs:sequence> ``` not deterministic. In any case this isn't an accurate model of what is allowed and parsed, as you can't use collection-specific discover_datasets options outside of a dataset collection. I **think** that the reason for adding OutputCollectionElement to the sequence is that you can have a `data` element nested in a `collection` element. To continue allowing this and making it more precise I've added an additional `OutputCollectionDataElement` type that is allowed within `collection`. This then should allow us to remove `OutputCollectionElement` from the `OutputData` type. A quick test against IUC and devteam revealed no problem with this approach per se, however it showed that https://github.com/galaxyproject/tools-iuc/blob/aa8360cb3ec9faf1488938a430855977632706ff/tools/krakentools/extract_kraken_reads.xml#L145 uses `change_format` which is not implemented for collections. 31 December 2023, 17:59:17 UTC
687bcf9 Björn Grüning 23 December 2023, 11:43:56 UTC Merge pull request #17231 from mvdbeek/convert_test_backport [23.1] Backport #17188: Fix for converter tests 23 December 2023, 11:43:56 UTC
4d07aa9 Björn Grüning 23 December 2023, 11:43:26 UTC Merge pull request #17232 from mvdbeek/session_order_fix [23.1] Fix User.current_galaxy_session 23 December 2023, 11:43:26 UTC
1113f4c mvdbeek 23 December 2023, 09:34:11 UTC Fix User.current_galaxy_session 23 December 2023, 09:34:11 UTC
07bf0d6 Matthias Bernt 14 December 2023, 13:50:11 UTC Also fix test of the vcf_to_vcf_bgzip_converter 23 December 2023, 09:27:01 UTC
dc8275c Matthias Bernt 14 December 2023, 11:20:55 UTC slighly more intrusive fix 23 December 2023, 09:27:01 UTC
e4993e6 Matthias Bernt 14 December 2023, 11:17:01 UTC unintrusive fix for converter tests 23 December 2023, 09:27:00 UTC
1ffcf8e Marius van den Beek 19 December 2023, 11:00:33 UTC Merge pull request #17210 from davelopez/23.1_partial_backport_of_#17058 [23.1] Fix `url_for` in tool error reports 19 December 2023, 11:00:33 UTC
af9ad60 davelopez 21 November 2023, 13:22:03 UTC Remove web dependency from tools/error_reports 19 December 2023, 09:59:06 UTC
10e3dcd davelopez 21 November 2023, 10:12:07 UTC Remove web dependency from tools/errors.py 19 December 2023, 09:58:49 UTC
f6c06f6 Marius van den Beek 14 December 2023, 08:26:49 UTC Merge pull request #17176 from davelopez/23.1_fix_workflow_index_total_matches [23.1] Fix workflow index total matches counting 14 December 2023, 08:26:49 UTC
fa585e1 davelopez 12 December 2023, 16:14:07 UTC Fix workflow index total matches wrong count 12 December 2023, 18:08:10 UTC
75c1122 davelopez 12 December 2023, 16:13:03 UTC Add test to check workflow index total matches 12 December 2023, 18:08:02 UTC
ac8cc32 mvdbeek 06 December 2023, 10:29:03 UTC Merge branch 'release_23.0' into release_23.1 06 December 2023, 10:29:03 UTC
f9be1a4 Marius van den Beek 06 December 2023, 10:28:40 UTC Merge pull request #17133 from mvdbeek/tusuploader_fix [23.0] Assert that tus uploader instance has URL 06 December 2023, 10:28:40 UTC
7f30bb9 mvdbeek 06 December 2023, 09:38:25 UTC Assert that tus uploader instance has URL Newer tusclient package allows passing in client in which case url can be None. 06 December 2023, 09:38:30 UTC
1d32c21 Dannon 01 December 2023, 17:11:33 UTC Merge pull request #17120 from guerler/fix_logout_23.1 [23.1] Properly clear session on OIDC logout 01 December 2023, 17:11:33 UTC
861a54b guerler 01 December 2023, 15:42:25 UTC Apply logout fix to properly clear session from @nuwang 01 December 2023, 15:42:25 UTC
316f8c1 mvdbeek 01 December 2023, 10:54:46 UTC Start work on 23.1.4.dev0 01 December 2023, 10:54:46 UTC
d7cc988 mvdbeek 01 December 2023, 10:54:43 UTC Create version 23.1.3 01 December 2023, 10:54:43 UTC
98dc9c9 Marius van den Beek 01 December 2023, 10:45:14 UTC Merge pull request #17116 from mvdbeek/fix_library_manifest_upload [23.1] Add missing optional description field, fixes ephemeris data library example 01 December 2023, 10:45:14 UTC
e502863 mvdbeek 01 December 2023, 09:50:47 UTC Add missing optional description field, fixes ephemeris data library example 01 December 2023, 10:00:52 UTC
0e3a0ca Martin Cech 30 November 2023, 20:57:34 UTC Merge pull request #17111 from dannon/backport-forcereload-display [23.1] Allow re-click of display with force reloading if already on the route. 30 November 2023, 20:57:34 UTC
43bcc91 Dannon Baker 06 November 2023, 16:19:56 UTC Allow re-click of display with force reloading if already on the route. This forces redisplay. Use our monkeypatched force nav when necessary instead of a reload 30 November 2023, 13:28:28 UTC
cb1bb4a mvdbeek 29 November 2023, 18:20:10 UTC Start work on 23.1.3.dev0 29 November 2023, 18:20:10 UTC
3642185 mvdbeek 29 November 2023, 18:20:07 UTC Create version 23.1.2 29 November 2023, 18:20:07 UTC
cd46ff3 Marius van den Beek 29 November 2023, 17:37:32 UTC Merge pull request #17102 from mvdbeek/fix_loading_default_tools_in_packaged_galaxy [23.1] Set correct tool_path for packaged galaxy 29 November 2023, 17:37:32 UTC
ac5ebae Marius van den Beek 29 November 2023, 17:09:20 UTC Merge pull request #17104 from dannon/fix-build-hash-backport [23.1] Ensure that plugin build hash actually has a git hash to compare with… 29 November 2023, 17:09:20 UTC
eea5851 Dannon Baker 29 November 2023, 16:55:16 UTC Ensure that plugin build hash actually has a git hash to compare with -- otherwise force rebuild. 29 November 2023, 16:59:23 UTC
63c7402 mvdbeek 29 November 2023, 14:45:50 UTC Set correct tool_path for packaged galaxy 29 November 2023, 14:50:16 UTC
6757936 Marius van den Beek 29 November 2023, 14:44:31 UTC Merge pull request #17099 from mvdbeek/fix_webapps [23.1] Fix web_apps dependencies 29 November 2023, 14:44:31 UTC
f3a6f4f Marius van den Beek 29 November 2023, 14:23:06 UTC Merge pull request #17100 from davelopez/23.1_implement_missing_s3fs_upload [23.1] Implement missing upload for S3 file sources 29 November 2023, 14:23:06 UTC
5a88391 davelopez 29 November 2023, 12:34:32 UTC Implement missing upload for S3 file sources 29 November 2023, 12:34:32 UTC
cb99976 mvdbeek 29 November 2023, 12:32:21 UTC Fix web_apps dependencies 29 November 2023, 12:32:21 UTC
e7b3a29 Martin Cech 28 November 2023, 19:51:38 UTC Merge pull request #17093 from davelopez/23.1_backport_#17042 [23.1] Allow relative URLs in broadcasts action links 28 November 2023, 19:51:38 UTC
6dbd233 David López 21 November 2023, 09:15:34 UTC Keep AbsoluteOrRelativeUrl as RelativeUrl for now This will always fall back to a string, but the intention of the code reads better and we may add some custom validation later to really check for the URL correctness. Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> 28 November 2023, 18:34:29 UTC
0ce70fb davelopez 16 November 2023, 18:01:50 UTC Add test for broadcasts action links 28 November 2023, 18:34:07 UTC
0171551 davelopez 16 November 2023, 17:14:02 UTC Allow relative action URLs in broadcasts 28 November 2023, 18:31:37 UTC
0487e63 Marius van den Beek 28 November 2023, 16:52:39 UTC Merge pull request #17080 from muon-spectroscopy-computational-project/larch_datatypes [23.1] Add support for larch datatypes 28 November 2023, 16:52:39 UTC
4a7dbe9 Martin Cech 27 November 2023, 22:07:26 UTC Merge pull request #17072 from mvdbeek/add_head_route_to_job_files [23.1] Add HEAD route to job_files endpoint 27 November 2023, 22:07:26 UTC
c3dbf7d Martin Cech 27 November 2023, 18:31:30 UTC Merge pull request #17088 from davelopez/23.1_fix_notifications_input_datetimes [23.1] Fix input dates in notifications: consider timezone offset 27 November 2023, 18:31:30 UTC
9b1fb5e davelopez 27 November 2023, 17:03:55 UTC Fix notification input timestamps: consider timezone 27 November 2023, 17:31:59 UTC
809d409 davelopez 27 November 2023, 17:02:32 UTC Add test to check notification input times 27 November 2023, 17:02:32 UTC
142ac4b John Chilton 27 November 2023, 15:49:49 UTC Merge pull request #17071 from mvdbeek/assert_dataset_collection_element_points_at_something [23.1] Assert that ``DatasetCollectioElement`` has an associated object 27 November 2023, 15:49:49 UTC
5a1f3f9 Marius van den Beek 27 November 2023, 10:46:57 UTC Merge pull request #17085 from mvdbeek/always_commit_no_rollback [23.1] Remove rollback from ``__check_jobs_at_startup`` 27 November 2023, 10:46:57 UTC
da387d4 mvdbeek 26 November 2023, 14:58:58 UTC Remove rollback from ``__check_jobs_at_startup`` I think the premise that we want to do a rollback on exceptions in this method is wrong (it **may** be correct apprach in other places in the codebase e.g. in `Tool.handle_single_execution()`). Here it prevents us from comitting anything inside the with statement (as the job_wrapper.fail method does). Here's the simplified issue: ```shell ❯ python -i scripts/db_shell.py -c config/galaxy.yml >>> with sa_session() as session, session.begin(): ... sa_session.execute(update(Job).where(Job.id == 1).values(state="error")) ... sa_session.commit() ... sa_session.execute(update(Job).where(Job.id == 1).values(state="ok")) ... sa_session.commit() ... <sqlalchemy.engine.cursor.LegacyCursorResult object at 0x11f1be350> Traceback (most recent call last): File "<stdin>", line 4, in <module> File "<string>", line 2, in execute File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1711, in execute conn = self._connection_for_bind(bind, close_with_result=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1552, in _connection_for_bind TransactionalContext._trans_ctx_check(self) File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/util.py", line 199, in _trans_ctx_check raise exc.InvalidRequestError( sqlalchemy.exc.InvalidRequestError: Can't operate on closed transaction inside context manager. Please complete the context manager before emitting further commands. ``` It is probably still worthwhile to have the job recovery be minimal and do things such as calling the job wrapper fail method that does actual work to the job handler as in https://github.com/galaxyproject/galaxy/pull/17083/, but that's refactoring that can be done on the dev branch and it still seems risky in the sense that we then need to be very careful in ensuring we don't commit anywhere else inside the scope of the begin() statement. Finally I don't think it makes sense that the startup check should ever cause the boot process to fail. This isn't a misconfiguration or even anything catastrophic for the remaining jobs and places unnecessary stress on admins and can basically break at any time and shouldn't cause a complete service failure. Fixes https://github.com/galaxyproject/galaxy/issues/17079 27 November 2023, 09:36:59 UTC
cfab9e8 Patrick Austin 24 November 2023, 13:23:15 UTC DatasetInstance -> DatasetProtocol in larch.py typehints 24 November 2023, 13:23:15 UTC
42a2219 Patrick Austin 24 November 2023, 12:03:36 UTC Merge branch 'release_23.1' into larch_datatypes 24 November 2023, 12:03:36 UTC
36616a8 Patrick Austin 24 November 2023, 12:02:01 UTC Use List from typing for typehint in larch.py 24 November 2023, 12:02:01 UTC
d8a80ef Patrick Austin 24 November 2023, 11:39:23 UTC Fix typo in AthenaProject sniffer 24 November 2023, 11:39:23 UTC
11f1b4f mvdbeek 23 November 2023, 11:29:15 UTC Add HEAD route to job_files endpoint 23 November 2023, 11:29:15 UTC
626237d mvdbeek 23 November 2023, 09:23:16 UTC Assert that prior to flush DatasetCollectioElement has an associated object 23 November 2023, 09:23:16 UTC
41b302d mvdbeek 22 November 2023, 17:56:20 UTC Merge branch 'release_23.0' into release_23.1 22 November 2023, 17:56:20 UTC
472ebfe Marius van den Beek 22 November 2023, 17:55:40 UTC Merge pull request #17067 from mvdbeek/fix_store_by_id_outputs_to_working_directory_extra_files [23.0] Fix extra files collection if using ``store_by="id"`` and `outputs_to_working_directory` 22 November 2023, 17:55:40 UTC
7fe19a7 mvdbeek 22 November 2023, 14:41:21 UTC Merge ``store_by="id"`` tests 22 November 2023, 17:55:03 UTC
5cf9f0e mvdbeek 22 November 2023, 14:37:46 UTC Fix extra files collection for outputs in ``store_by="id"`` object stores 22 November 2023, 14:38:27 UTC
4659546 Marius van den Beek 20 November 2023, 13:40:19 UTC Merge pull request #17048 from mvdbeek/prevent_workflow_submission_missing_input_value [23.1] Prevent workflow submission with missing input values 20 November 2023, 13:40:19 UTC
ddd2157 Dannon 20 November 2023, 12:40:02 UTC Merge pull request #17049 from davelopez/23.1_fix_broadcast_filtering_for_admins [23.1] Fix filtering of active broadcasts for admins 20 November 2023, 12:40:02 UTC
35c18ff mvdbeek 20 November 2023, 12:11:34 UTC Add test case 20 November 2023, 12:20:10 UTC
da127b5 mvdbeek 17 November 2023, 17:32:38 UTC Disallow empty inputs on required input parameters in simplified workflow form This is another attempt at https://github.com/galaxyproject/galaxy/issues/13220, but taking into account https://github.com/galaxyproject/galaxy/issues/13220#issuecomment-1068054414 by limiting this to the simplified workflow form, where we can assume input parameter optionality to have the correct meaning. This makes it harder to submit a mandatory text parameter that can be empty, but that is (at this point at least) a very fringe requirement. If really needed you can make the parameter optional (and use pick_value to fill in an empty string if null is not OK as a value). 17 November 2023, 17:32:44 UTC
8d514b1 davelopez 17 November 2023, 16:52:53 UTC Add tests for expired and unpublished broadcasts 17 November 2023, 16:52:53 UTC
c03eda8 davelopez 17 November 2023, 15:19:58 UTC Fix filtering of active broadcasts Admin users get all the broadcasts notifications regardless of their "activation" status so we need to apply the filtering also in the client. Regular users are not affected because they can only get active broadcasts. 17 November 2023, 16:47:00 UTC
e5d37d4 John Chilton 17 November 2023, 15:38:02 UTC Merge pull request #17036 from jmchilton/tool_panel_fixes [23.1] Fix duplicated tools in tool panel view section copying 17 November 2023, 15:38:02 UTC
26573dd mvdbeek 17 November 2023, 14:51:20 UTC Prevent workflow submission with validation errors And disable submit button when request is being handled. 17 November 2023, 14:52:10 UTC
3e13db9 mvdbeek 16 November 2023, 17:38:30 UTC Ensure we're not allowing None as non-optional workflow input 16 November 2023, 17:38:30 UTC
0e14241 mvdbeek 16 November 2023, 14:08:21 UTC Exclude multiple_versions from test_global_filters_on_integrated_panel 16 November 2023, 14:08:21 UTC
ca5fce7 mvdbeek 16 November 2023, 09:56:17 UTC Test tool shed version as well 16 November 2023, 10:52:30 UTC
c3dc92b mvdbeek 16 November 2023, 08:57:40 UTC Test that only latest version is loaded 16 November 2023, 10:52:19 UTC
f36b847 John Chilton 16 November 2023, 10:51:03 UTC Comment about new bug discovered. Lower priority though right? Come back and fix it in dev? 16 November 2023, 10:51:03 UTC
427677a Marius van den Beek 16 November 2023, 10:17:10 UTC Merge pull request #16988 from mvdbeek/warning_for_duplicate_log_files [23.1] Change log level for duplicate data table entries to warning 16 November 2023, 10:17:10 UTC
3e40895 John Chilton 15 November 2023, 19:12:07 UTC Fix duplicated tools in tool panel view section copying. 15 November 2023, 19:21:38 UTC
edcc043 John Chilton 15 November 2023, 16:02:52 UTC Make testing tool panel views a little easier. 15 November 2023, 16:04:28 UTC
d0c583e mvdbeek 13 November 2023, 14:06:55 UTC Merge branch 'release_23.0' into release_23.1 13 November 2023, 14:06:55 UTC
1b0c0bb Marius van den Beek 13 November 2023, 14:04:29 UTC Merge pull request #17013 from bernt-matthias/bump/conda [23.0] Upgrade minimum conda to be compatible with latest conda-build 13 November 2023, 14:04:29 UTC
0aafa22 Matthias Bernt 12 November 2023, 18:07:26 UTC bump required conda version potential solution for the build prblems in https://github.com/galaxyproject/planemo/pull/1388 13 November 2023, 12:19:10 UTC
70d4185 Martin Cech 10 November 2023, 23:53:23 UTC Merge pull request #17009 from mvdbeek/update_tar_to_directory_dependency [23.1] Update tar_to_directory dependency 10 November 2023, 23:53:23 UTC
643b0d4 Björn Grüning 10 November 2023, 19:56:26 UTC Merge pull request #17007 from mvdbeek/fix_copied_outputs_metadata [23.1] Fix copying metadata to copied job outputs 10 November 2023, 19:56:26 UTC
93d11dc mvdbeek 10 November 2023, 17:37:32 UTC Update tar_to_directory dependency Should fix: ``` Traceback (most recent call last): File "<string>", line 1, in <module> File "/usr/local/lib/python3.7/site-packages/galaxy/util/compression_utils.py", line 114, in extract common_prefix_dir = self.common_prefix_dir File "/usr/local/lib/python3.7/site-packages/galaxy/util/compression_utils.py", line 103, in common_prefix_dir if len(common_prefix) >= 1 and not common_prefix.endswith(os.sep) and self.isdir(self.getmember(common_prefix)) \ File "/usr/local/lib/python3.7/site-packages/galaxy/util/compression_utils.py", line 186, in isdir return getattr(self, 'isdir_%s' % self.type)(member) File "/usr/local/lib/python3.7/site-packages/galaxy/util/compression_utils.py", line 189, in isdir_tar return member.isdir() AttributeError: 'NoneType' object has no attribute 'isdir' ``` seen on usegalaxy.eu with https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE176031&format=file 10 November 2023, 17:37:34 UTC
2fc1b64 mvdbeek 10 November 2023, 14:12:37 UTC Fix copying metadata to copied job outputs Fixes https://github.com/galaxyproject/galaxy/issues/17003 10 November 2023, 17:03:45 UTC
f450dee Marius van den Beek 09 November 2023, 08:43:47 UTC Merge pull request #16965 from mvdbeek/dont_hold_on_to_job_object [23.1] Don't store job in JobIO instance attributes 09 November 2023, 08:43:47 UTC
0290219 Martin Cech 08 November 2023, 23:20:02 UTC Merge pull request #16999 from dannon/client-publish-23.1 [23.1] Client publication 08 November 2023, 23:20:02 UTC
2e92765 Dannon Baker 08 November 2023, 21:58:47 UTC Update cpy-cli utility. 08 November 2023, 21:58:47 UTC
f0c5024 Dannon Baker 08 November 2023, 21:53:28 UTC Update installer package to 23.1.1 08 November 2023, 21:53:28 UTC
4a2dc9e Dannon Baker 08 November 2023, 21:51:06 UTC Clean rebuild and publish 08 November 2023, 21:51:06 UTC
dc6af21 Dannon Baker 08 November 2023, 21:37:10 UTC Link installer package to galaxy release version 08 November 2023, 21:37:10 UTC
cb5d18d Dannon Baker 08 November 2023, 21:34:27 UTC Drop unused, unintentionally added package from galaxy client installer 08 November 2023, 21:34:27 UTC
97d09ce Dannon Baker 08 November 2023, 21:29:42 UTC Update Galaxy client installer package version for 23.1 08 November 2023, 21:29:45 UTC
2af38ac Dannon Baker 08 November 2023, 21:29:24 UTC Update 23.1 client package version. 08 November 2023, 21:29:24 UTC
5566be0 mvdbeek 02 November 2023, 13:08:56 UTC Don't store job in JobIO instance attributes and invalidate `_output_hdas_and_paths` when current session is not the same session that was used to populate `_output_hdas_and_paths`. The Job instance may originate from a session that is associated to another thread, and when that thread closes the session the instance (along with other instances retrieved through loading relationships) becomes detached. I am not sure at all if this will fix ``` DetachedInstanceError: Instance <HistoryDatasetAssociation at 0x7fe68bbf14f0> is not bound to a Session; attribute refresh operation cannot proceed (Background on this error at: https://sqlalche.me/e/14/bhk3) File "galaxy/jobs/runners/__init__.py", line 291, in prepare_job job_wrapper.prepare() File "galaxy/jobs/__init__.py", line 1248, in prepare tool_evaluator.set_compute_environment(compute_environment, get_special=get_special) File "galaxy/tools/evaluation.py", line 162, in set_compute_environment self.param_dict = self.build_param_dict( File "galaxy/tools/evaluation.py", line 204, in build_param_dict self.__populate_output_dataset_wrappers(param_dict, output_datasets, job_working_directory) File "galaxy/tools/evaluation.py", line 447, in __populate_output_dataset_wrappers param_dict[name] = DatasetFilenameWrapper( File "galaxy/tools/wrappers.py", line 403, in __init__ path_rewrite = compute_environment and compute_environment.output_path_rewrite(dataset_instance) File "galaxy/job_execution/compute_environment.py", line 132, in output_path_rewrite return str(self.job_io.get_output_path(dataset)) File "galaxy/job_execution/setup.py", line 226, in get_output_path if hda.id == dataset.id: File "sqlalchemy/orm/attributes.py", line 487, in __get__ return self.impl.get(state, dict_) File "sqlalchemy/orm/attributes.py", line 959, in get value = self._fire_loader_callables(state, key, passive) File "sqlalchemy/orm/attributes.py", line 990, in _fire_loader_callables return state._load_expired(state, passive) File "sqlalchemy/orm/state.py", line 712, in _load_expired self.manager.expired_attribute_loader(self, toload, passive) File "sqlalchemy/orm/loading.py", line 1369, in load_scalar_attributes raise orm_exc.DetachedInstanceError( ``` but it seems to make some sense. JobIO crosses thread boundaries as part of the job wrapper getting put into threading queues. Ideally we'd make sure that no ORM instance crosses the thread boundary (or we systematically re-associated with a session). I also tried flagging these patterns automatically using something like: ``` @event.listens_for(session, "persistent_to_detached") def on_detach(sess, instance): if not getattr(instance, "allow_detatch", False): raise Exception(f"{instance} detached. This ain't good for how we do things ?") ``` but it seems tricky to figure out when this is fine and when it is not. 08 November 2023, 18:25:15 UTC
977a9ac Marius van den Beek 08 November 2023, 15:54:15 UTC Merge pull request #16992 from dannon/empty-page-render-fix-backport [23.1] Empty page render fix - backport 08 November 2023, 15:54:15 UTC
496ecc2 Dannon Baker 07 November 2023, 15:46:45 UTC Fixes rendering of an empty page by ensuring default content, even if empty. 08 November 2023, 15:21:43 UTC
df9c9b5 Nicola Soranzo 08 November 2023, 14:26:53 UTC Merge pull request #16989 from mvdbeek/backport_maf_fix [23.1] Backport Fix maf_thread_for_species.py 08 November 2023, 14:26:53 UTC
4e15e69 Lucille Delisle 03 November 2023, 07:35:06 UTC Fix maf_thread_for_species.py 08 November 2023, 09:45:11 UTC
ec32669 mvdbeek 08 November 2023, 09:38:42 UTC Change log level for duplicate data table entries to warning Fixes https://github.com/galaxyproject/galaxy/issues/16987, though there's probably something to be done for loc files being loaded from tools. At the minimum this is a versioning issue, if a new version of featureCounts comes with a new built-in reference then an old version shouldn't use it, and vice-versa. Seems like a hard problem to solve. 08 November 2023, 09:38:47 UTC
d6cc9f0 Marius van den Beek 07 November 2023, 10:44:39 UTC Merge pull request #16981 from nsoranzo/release_23.1_routes_bug [23.1] Workaround issue in Routes 07 November 2023, 10:44:39 UTC
d8f490f Nicola Soranzo 06 November 2023, 14:52:31 UTC Workaround issue in routes Fix the following traceback: ``` Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: uvicorn.access INFO 2023-06-30 10:28:03,573 [pN:main.1,p:3528860,tN:MainThread] 193.156.42.8:0 - "HEAD /root/login HTTP/1.0" 500 Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: Exception in supplement: Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: Traceback (most recent call last): Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: File "/cluster/galaxy-test/srv/galaxy/server/lib/galaxy/web/framework/middleware/error.py", line 165, in __call__ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: app_iter = self.application(environ, sr_checker) Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: File "/cluster/galaxy-test/srv/galaxy/venv/lib64/python3.11/site-packages/paste/recursive.py", line 85, in __call__ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: return self.application(environ, start_response) Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: File "/cluster/galaxy-test/srv/galaxy/venv/lib64/python3.11/site-packages/paste/httpexceptions.py", line 640, in __call__ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: return self.application(environ, start_response) Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: File "/cluster/galaxy-test/srv/galaxy/server/lib/galaxy/web/framework/base.py", line 167, in __call__ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: return self.handle_request(environ, start_response) Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: File "/cluster/galaxy-test/srv/galaxy/server/lib/galaxy/web/framework/base.py", line 221, in handle_request Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: rc.environ = environ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: ^^^^^^^^^^ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: File "/cluster/galaxy-test/srv/galaxy/venv/lib64/python3.11/site-packages/routes/__init__.py", line 23, in __setattr__ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: self.load_wsgi_environ(value) Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: File "/cluster/galaxy-test/srv/galaxy/venv/lib64/python3.11/site-packages/routes/__init__.py", line 73, in load_wsgi_environ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: self.__shared_state.host += ':' + environ['SERVER_PORT'] Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: TypeError: can only concatenate str (not "int") to str ``` Reported by @vazovn : https://matrix.to/#/!rfLDbcWEWZapZrujix:gitter.im/$McOyd5Kmp-w-Z-bYbRUV42K30YhVvwRJtrCaxru-yf4?via=gitter.im&via=matrix.org 06 November 2023, 14:52:35 UTC
8768f3a Dannon 03 November 2023, 01:19:45 UTC Merge pull request #16961 from ahmedhamidawan/redirect_if_fixed_delegated_auth [23.1] Prevent Singular external auth users from disconnecting identity 03 November 2023, 01:19:45 UTC
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