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 |