| 250c9c2 | mvdbeek | 22 August 2022, 19:25:14 UTC | Update version to 22.01.1 | 22 August 2022, 19:25:14 UTC |
| 30dc1bf | Marius van den Beek | 18 August 2022, 17:21:23 UTC | Merge pull request #14440 from qiagu/dynamic_options [22.01] Revert startswith of tool parameter options | 18 August 2022, 17:21:23 UTC |
| 5f0fbb0 | Matthias Bernt | 18 August 2022, 12:30:14 UTC | fix docs | 18 August 2022, 12:30:14 UTC |
| 8ef9ef4 | Matthias Bernt | 18 August 2022, 12:28:55 UTC | fix test | 18 August 2022, 12:28:55 UTC |
| ea85cab | qiagu | 12 August 2022, 07:34:36 UTC | Revert startswith of tool parameter options | 18 August 2022, 09:04:12 UTC |
| 6db3224 | Dannon | 16 August 2022, 20:26:41 UTC | Merge pull request #14466 from nsoranzo/release_22.01_fix_docs [22.01] Fix doc versioning banner and other doc fixes | 16 August 2022, 20:26:41 UTC |
| 11c0c7b | Nicola Soranzo | 16 August 2022, 14:29:12 UTC | Fix doc versioning banner Currently doc builds for `release_22.01` and `master` branches incorrectly show the "This document is for an in-development version of Galaxy." warning banner. Partially backport commit 318a1d7056cc8a5b9f6b83ef1cd186d6ef8939d4 and drop the unused `TARGET_BRANCH` variable from `Makefile` which shadows the shell environment variable of the same name set in `.github/workflows/docs.yaml` and used in `doc/source/conf.versioning.py` . | 16 August 2022, 14:33:26 UTC |
| 69defb7 | Nicola Soranzo | 14 August 2022, 17:33:42 UTC | Doc fixes | 15 August 2022, 18:15:02 UTC |
| 6a3804b | Nicola Soranzo | 14 August 2022, 16:55:51 UTC | Update application documentation with: ``` make -C doc/ updaterst ``` | 14 August 2022, 17:39:19 UTC |
| 6c43d66 | Marius van den Beek | 26 July 2022, 12:26:15 UTC | Merge pull request #14373 from cat-bro/fix-IMPLICITLY_REQUIRED_TOOL_FILES-for-maxquant [22.01] Correct IMPLICITLY_REQUIRED_TOOL_FILES for some tools | 26 July 2022, 12:26:15 UTC |
| 25e847e | cat-bro | 22 July 2022, 15:54:36 UTC | Correct IMPLICITLY_REQUIRED_TOOL_FILES for some tools | 25 July 2022, 17:07:36 UTC |
| a20d796 | Marius van den Beek | 24 July 2022, 16:22:21 UTC | Merge pull request #14332 from bernt-matthias/topic/options-var [22.01] fix `startswith` attribute of `<options>` | 24 July 2022, 16:22:21 UTC |
| 21a7ad2 | Marius van den Beek | 24 July 2022, 16:17:39 UTC | Merge pull request #14363 from davelopez/fix_enable_account_interface [22.01] Fix enable_account_interface option hiding too much | 24 July 2022, 16:17:39 UTC |
| f2bdee4 | davelopez | 22 July 2022, 16:11:14 UTC | Display correct description in Manage Information | 22 July 2022, 16:11:14 UTC |
| b004c32 | davelopez | 22 July 2022, 16:10:19 UTC | Display Manage Cloud Auth user preferences always | 22 July 2022, 16:10:19 UTC |
| e775648 | davelopez | 22 July 2022, 16:09:23 UTC | Disable only specific inputs in user information | 22 July 2022, 16:09:23 UTC |
| a066a42 | David López | 21 July 2022, 08:37:44 UTC | Merge pull request #14355 from nsoranzo/release_22.01_fix_14348 [22.01] Workflow download API: check if a workflow is importable (not published) | 21 July 2022, 08:37:44 UTC |
| 2ff6aa5 | Nicola Soranzo | 21 July 2022, 02:27:43 UTC | Workflow download API: check if a workflow is importable (not published) Fix https://github.com/galaxyproject/galaxy/issues/14348 . | 21 July 2022, 02:28:36 UTC |
| 7054261 | Nicola Soranzo | 21 July 2022, 02:25:12 UTC | Add some type annotations | 21 July 2022, 02:25:12 UTC |
| ce0d3a7 | Marius van den Beek | 16 July 2022, 10:46:00 UTC | Merge pull request #14330 from nsoranzo/release_22.01_dataset_API_fix_extension_list_filter [22.01] Fix filtering by an extension list in dataset API | 16 July 2022, 10:46:00 UTC |
| fe06eea | Matthias Bernt | 15 July 2022, 08:49:12 UTC | fix test output | 15 July 2022, 08:49:12 UTC |
| d7272cc | M Bernt | 14 July 2022, 21:30:11 UTC | Update test/functional/tools/options_from_metadata_file.xml Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 14 July 2022, 21:30:11 UTC |
| d642ce3 | Matthias Bernt | 14 July 2022, 12:19:40 UTC | fix `startswith` attribute of `<options>` as documented in the xsd in addition fix https://github.com/galaxyproject/galaxy/issues/14324, i.e. document the `separator` attribute of options also doc that only 1MB is used and lines starting with `#` are always ignored | 14 July 2022, 12:19:40 UTC |
| 8321b86 | Nicola Soranzo | 13 July 2022, 19:22:52 UTC | Fix filtering by an extension list in dataset API Fix the following traceback: ``` 2022-07-13T20:32:11.5995637Z galaxy.web.framework.decorators ERROR 2022-07-13 20:20:39,564 [pN:main,p:2622,tN:worker 1] Uncaught exception in exposed API method: 2022-07-13T20:32:11.5995754Z Traceback (most recent call last): 2022-07-13T20:32:11.5996289Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/web/framework/decorators.py", line 320, in decorator 2022-07-13T20:32:11.5996434Z rval = func(self, trans, *args, **kwargs) 2022-07-13T20:32:11.5996812Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/webapps/galaxy/api/datasets.py", line 387, in index 2022-07-13T20:32:11.5996977Z trans, history_id, serialization_params, filter_parameters 2022-07-13T20:32:11.5997364Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/webapps/galaxy/services/datasets.py", line 214, in index 2022-07-13T20:32:11.5997749Z filters = self.history_contents_filters.parse_query_filters(filter_query_params) 2022-07-13T20:32:11.5998133Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/managers/base.py", line 1031, in parse_query_filters 2022-07-13T20:32:11.5998269Z return self.parse_filters(filter_params) 2022-07-13T20:32:11.5998634Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/managers/base.py", line 1040, in parse_filters 2022-07-13T20:32:11.5998770Z filter_ = self.parse_filter(attr, op, val) 2022-07-13T20:32:11.5999135Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/managers/base.py", line 1060, in parse_filter 2022-07-13T20:32:11.5999286Z orm_filter = self._parse_orm_filter(attr, op, val) 2022-07-13T20:32:11.5999683Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/managers/history_contents.py", line 528, in _parse_orm_filter 2022-07-13T20:32:11.5999828Z return super()._parse_orm_filter(attr, op, val) 2022-07-13T20:32:11.6000195Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/managers/base.py", line 1136, in _parse_orm_filter 2022-07-13T20:32:11.6000293Z orm_filter = op(val) 2022-07-13T20:32:11.6000703Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/operators.py", line 604, in in_ 2022-07-13T20:32:11.6000834Z return self.operate(in_op, other) 2022-07-13T20:32:11.6001252Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/elements.py", line 861, in operate 2022-07-13T20:32:11.6001467Z return op(self.comparator, *other, **kwargs) 2022-07-13T20:32:11.6001884Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/operators.py", line 1386, in in_op 2022-07-13T20:32:11.6001975Z return a.in_(b) 2022-07-13T20:32:11.6002370Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/operators.py", line 604, in in_ 2022-07-13T20:32:11.6002496Z return self.operate(in_op, other) 2022-07-13T20:32:11.6002903Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/type_api.py", line 1343, in operate 2022-07-13T20:32:11.6003001Z op, *other, **kwargs 2022-07-13T20:32:11.6003401Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/type_api.py", line 76, in operate 2022-07-13T20:32:11.6003546Z return o[0](self.expr, op, *(other + o[1:]), **kwargs) 2022-07-13T20:32:11.6003982Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/default_comparator.py", line 160, in _in_impl 2022-07-13T20:32:11.6004157Z roles.InElementRole, seq_or_selectable, expr=expr, operator=op 2022-07-13T20:32:11.6004557Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/coercions.py", line 189, in expect 2022-07-13T20:32:11.6004673Z element, argname=argname, **kw 2022-07-13T20:32:11.6005102Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/coercions.py", line 587, in _literal_coercion 2022-07-13T20:32:11.6005234Z self._raise_for_expected(element, **kw) 2022-07-13T20:32:11.6005662Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/coercions.py", line 283, in _raise_for_expected 2022-07-13T20:32:11.6005841Z util.raise_(exc.ArgumentError(msg, code=code), replace_context=err) 2022-07-13T20:32:11.6006258Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 207, in raise_ 2022-07-13T20:32:11.6006348Z raise exception 2022-07-13T20:32:11.6006989Z sqlalchemy.exc.ArgumentError: IN expression list, SELECT construct, or bound parameter object expected, got 'bam,txt'. 2022-07-13T20:32:11.6007456Z 127.0.0.1 - - [13/Jul/2022:20:20:39 +0000] "GET /api/datasets?limit=500&offset=0&order=create_time-dsc&history_id=4b187121143038ff&q=extension-in&qv=bam%2Ctxt HTTP/1.1" 500 - "-" "python-requests/2.28.1" ``` | 14 July 2022, 11:55:49 UTC |
| 80b726e | Dannon | 13 July 2022, 00:11:52 UTC | Merge pull request #14319 from mvdbeek/local_tool_version_switxh [22.01] Fix local version switching | 13 July 2022, 00:11:52 UTC |
| 3e08160 | mvdbeek | 12 July 2022, 17:26:18 UTC | Fix local version switching Fixes https://github.com/galaxyproject/galaxy/issues/14311. Problem is that we use `:key` in https://github.com/mvdbeek/galaxy/blob/9e4563d9eb5d8f38a48e1f01466d4fcd1fc66502/client/src/components/Form/FormDisplay.vue#L3, so that doesn't re-render when the tool id doesn't change (which is the case for local tools, but not toolshed tools). | 12 July 2022, 21:04:28 UTC |
| 9162d57 | Nicola Soranzo | 07 July 2022, 22:39:49 UTC | Merge pull request #14274 from mvdbeek/tighten_session_exception_handling | 07 July 2022, 22:39:49 UTC |
| 29bba73 | mvdbeek | 07 July 2022, 05:29:24 UTC | Drop exception catching when querying db for session Should fix users getting logged out if a OperationError occurs and they get a new session because of the too-wide exception handling. | 07 July 2022, 05:30:32 UTC |
| b6629d7 | Marius van den Beek | 02 July 2022, 14:27:33 UTC | Merge pull request #14246 from mvdbeek/tus_robustness_22_01 [22.01] Improve robustness of tus upload and calculation of progress | 02 July 2022, 14:27:33 UTC |
| 4793bbc | Dannon Baker | 02 July 2022, 11:45:53 UTC | Minor rename in uploadbox to use err var | 02 July 2022, 11:45:53 UTC |
| 2fc79b4 | mvdbeek | 01 July 2022, 15:56:35 UTC | Improve robustness of tus upload and calculation of progress We now don't let the upload fail at all and instead retry indefinitely. The progress report is also more accurate as we only report the progress of individual chunks that have been confirmed by the server. | 01 July 2022, 15:58:24 UTC |
| 7e70fa3 | Marius van den Beek | 29 June 2022, 15:33:05 UTC | Merge pull request #14221 from natefoo/resumable-upload-script-fix-22.01 [22.01] Fixes for the tus resumable upload command line script | 29 June 2022, 15:33:05 UTC |
| a4e2af9 | Nate Coraor | 28 June 2022, 19:59:44 UTC | Fixes for the tus resumable upload command line script | 29 June 2022, 12:42:24 UTC |
| 582a7b9 | Nicola Soranzo | 27 June 2022, 09:36:41 UTC | Merge pull request #14201 from hexylena/fix-video-link | 27 June 2022, 09:36:41 UTC |
| 6b9658e | Helena Rasche | 27 June 2022, 08:47:20 UTC | Replace mp4s with youtube links | 27 June 2022, 08:47:45 UTC |
| cf1a83b | Nicola Soranzo | 24 June 2022, 19:23:06 UTC | Merge pull request #14186 from davelopez/21.01_fix_histories_api_url_building | 24 June 2022, 19:23:06 UTC |
| cb83191 | davelopez | 24 June 2022, 12:39:09 UTC | Add API test to ensure URLs are generated | 24 June 2022, 16:49:26 UTC |
| 374fabb | davelopez | 24 June 2022, 12:01:48 UTC | Provide request context to `url_for` When using FastAPI, we need call `url_builder` to generate the correct API URL instead of the legacy `url_for`. Here we were missing the request context that provides this functionality. Also the name of the endpoint for `/api/histories/{id}` was missing. | 24 June 2022, 12:03:27 UTC |
| 216378a | Dannon | 23 June 2022, 17:53:46 UTC | Merge pull request #14168 from mvdbeek/fix_folder_import_22_01 Minimal fix for folder imports | 23 June 2022, 17:53:46 UTC |
| 5785342 | Nicola Soranzo | 23 June 2022, 13:44:11 UTC | Merge branch 'release_21.09' into release_22.01 | 23 June 2022, 13:44:11 UTC |
| 52de57b | Nicola Soranzo | 23 June 2022, 13:43:21 UTC | Merge branch 'release_21.05' into release_21.09 | 23 June 2022, 13:43:21 UTC |
| 00ba0a9 | Marius van den Beek | 23 June 2022, 13:35:52 UTC | Merge pull request #13907 from davelopez/21.05_fix_anonymous_import_histories [21.05] Fix condition importing histories anonymously | 23 June 2022, 13:35:52 UTC |
| d3b4ef8 | Nicola Soranzo | 23 June 2022, 13:30:57 UTC | Merge branch 'release_21.09' into release_22.01 | 23 June 2022, 13:30:57 UTC |
| fda88e4 | David López | 23 June 2022, 13:17:05 UTC | Merge pull request #14057 from mvdbeek/backport_session_fix [21.09][Backport] Add sessioncookie with ``SameSite=None; secure`` for tool_runner path | 23 June 2022, 13:17:05 UTC |
| 3b23791 | Nicola Soranzo | 23 June 2022, 13:10:47 UTC | Merge branch 'release_21.09' into release_22.01 | 23 June 2022, 13:10:47 UTC |
| 43e3cc8 | Marius van den Beek | 23 June 2022, 12:28:16 UTC | Merge pull request #14162 from mvdbeek/fix_bam_native_collection_download [22.01] Fix collection download for bam native files | 23 June 2022, 12:28:16 UTC |
| 8361240 | Marius van den Beek | 23 June 2022, 12:15:52 UTC | Merge pull request #14161 from mvdbeek/fix_dataset_controller_actions [21.09] Fix dataset controller actions (delete, purge, unhide) | 23 June 2022, 12:15:52 UTC |
| cab0049 | mvdbeek | 23 June 2022, 11:33:48 UTC | Minimal fix for folder imports | 23 June 2022, 11:36:00 UTC |
| a6ea0a6 | Marius van den Beek | 23 June 2022, 07:35:59 UTC | Merge pull request #14158 from mvdbeek/fix_set_user [22.01] Fix set_user function | 23 June 2022, 07:35:59 UTC |
| 6c872e7 | Marius van den Beek | 23 June 2022, 07:34:50 UTC | Merge pull request #14157 from mvdbeek/fix_streaming_response [22.01] Adapt byte content for StreamingResponse | 23 June 2022, 07:34:50 UTC |
| 6b55c93 | mvdbeek | 22 June 2022, 18:57:09 UTC | Fix collection download for bam native files Fixes https://sentry.galaxyproject.org/organizations/galaxy/issues/85033/?project=3&query=is%3Aunresolved&statsPeriod=14d: ``` AttributeError: 'NoneType' object has no attribute 'file_name' File "galaxy/webapps/galaxy/services/history_contents.py", line 482, in get_dataset_collection_archive_for_download return self.__stream_dataset_collection(trans, dataset_collection_instance) File "galaxy/webapps/galaxy/services/history_contents.py", line 503, in __stream_dataset_collection archive = hdcas.stream_dataset_collection( File "galaxy/managers/hdcas.py", line 37, in stream_dataset_collection write_dataset_collection(dataset_collection_instance, archive) File "galaxy/managers/hdcas.py", line 46, in write_dataset_collection for file_path, relpath in hda.datatype.to_archive(dataset=hda, name=name): File "galaxy/datatypes/binary.py", line 535, in to_archive file_paths.append(dataset.metadata.bam_index.file_name) ``` | 22 June 2022, 18:59:08 UTC |
| 3700be2 | mvdbeek | 22 June 2022, 18:28:15 UTC | Fix dataset controller actions We don't have a parent property anymore. That's been broken since 21.09. Fixes https://sentry.galaxyproject.org/organizations/galaxy/issues/4971/?project=3&query=is%3Aunresolved&statsPeriod=14d: ``` AttributeError: 'HistoryDatasetAssociation' object has no attribute 'parent' File "galaxy/webapps/galaxy/controllers/dataset.py", line 897, in _undelete while topmost_parent.parent: ``` | 22 June 2022, 18:34:18 UTC |
| bd73e06 | mvdbeek | 22 June 2022, 17:55:02 UTC | Fix set_user function Should fix https://sentry.galaxyproject.org/organizations/galaxy/issues/84836/?project=3&query=is%3Aunresolved&statsPeriod=14d: ``` AttributeError: 'NoneType' object has no attribute 'bootstrap_admin_user' File "uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi result = await app(self.scope, self.receive, self.send) File "uvicorn/middleware/proxy_headers.py", line 75, in __call__ return await self.app(scope, receive, send) File "fastapi/applications.py", line 269, in __call__ await super().__call__(scope, receive, send) File "starlette/applications.py", line 124, in __call__ await self.middleware_stack(scope, receive, send) File "starlette/middleware/errors.py", line 184, in __call__ raise exc File "starlette/middleware/errors.py", line 162, in __call__ await self.app(scope, receive, _send) File "starlette_context/middleware/raw_middleware.py", line 96, in __call__ await self.app(scope, receive, send_wrapper) File "starlette/middleware/base.py", line 69, in __call__ await response(scope, receive, send) File "starlette/responses.py", line 260, in __call__ await wrap(partial(self.listen_for_disconnect, receive)) File "anyio/_backends/_asyncio.py", line 662, in __aexit__ raise exceptions[0] File "starlette/responses.py", line 256, in wrap await func() File "starlette/responses.py", line 245, in stream_response async for chunk in self.body_iterator: File "starlette/middleware/base.py", line 58, in body_stream raise app_exc File "starlette/middleware/base.py", line 36, in coro await self.app(scope, request.receive, send_stream.send) File "starlette/middleware/base.py", line 69, in __call__ await response(scope, receive, send) File "starlette/responses.py", line 260, in __call__ await wrap(partial(self.listen_for_disconnect, receive)) File "anyio/_backends/_asyncio.py", line 662, in __aexit__ raise exceptions[0] File "starlette/responses.py", line 256, in wrap await func() File "starlette/responses.py", line 245, in stream_response async for chunk in self.body_iterator: File "starlette/middleware/base.py", line 58, in body_stream raise app_exc File "starlette/middleware/base.py", line 36, in coro await self.app(scope, request.receive, send_stream.send) File "starlette/exceptions.py", line 93, in __call__ raise exc File "starlette/exceptions.py", line 82, in __call__ await self.app(scope, receive, sender) File "fastapi/middleware/asyncexitstack.py", line 21, in __call__ raise e File "fastapi/middleware/asyncexitstack.py", line 18, in __call__ await self.app(scope, receive, send) File "starlette/routing.py", line 670, in __call__ await route.handle(scope, receive, send) File "starlette/routing.py", line 418, in handle await self.app(scope, receive, send) File "a2wsgi/wsgi.py", line 140, in __call__ return await responder(scope, receive, send) File "a2wsgi/wsgi.py", line 179, in __call__ raise self.exc_info[0].with_traceback( File "galaxy/web/framework/middleware/error.py", line 165, in __call__ app_iter = self.application(environ, sr_checker) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 29, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 159, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request trans = self.transaction_factory(environ) File "galaxy/webapps/base/webapp.py", line 105, in <lambda> self.set_transaction_factory(lambda e: self.transaction_chooser(e, galaxy_app, session_cookie)) File "galaxy/webapps/base/webapp.py", line 194, in transaction_chooser return GalaxyWebTransaction(environ, galaxy_app, self, session_cookie) File "galaxy/webapps/base/webapp.py", line 311, in __init__ self.error_message = self._authenticate_api(session_cookie) File "galaxy/webapps/base/webapp.py", line 541, in _authenticate_api self.user = None File "galaxy/webapps/base/webapp.py", line 451, in set_user if user.bootstrap_admin_user: ``` Not sure what I was thinking when I did this in https://github.com/galaxyproject/galaxy/pull/10823/files#diff-ca6cf7b8ec16cb97add6d9535857de123352878e979bcc16812cdfa23f22b204R360 If we have a boostrap_admin_user we certainly can't add it to a session, that would definitely fail. | 22 June 2022, 17:55:50 UTC |
| 40c5605 | mvdbeek | 22 June 2022, 17:17:10 UTC | Adapt byte content for StreamingResponse Fixes https://github.com/galaxyproject/galaxy/issues/14156 ``` TypeError: 'bytes' object is not an iterator File "starlette/middleware/base.py", line 69, in __call__ await response(scope, receive, send) File "starlette/responses.py", line 260, in __call__ await wrap(partial(self.listen_for_disconnect, receive)) File "anyio/_backends/_asyncio.py", line 662, in __aexit__ raise exceptions[0] File "starlette/responses.py", line 256, in wrap await func() File "starlette/responses.py", line 245, in stream_response async for chunk in self.body_iterator: File "starlette/middleware/base.py", line 58, in body_stream raise app_exc File "starlette/middleware/base.py", line 36, in coro await self.app(scope, request.receive, send_stream.send) File "starlette/exceptions.py", line 93, in __call__ raise exc File "starlette/exceptions.py", line 82, in __call__ await self.app(scope, receive, sender) File "fastapi/middleware/asyncexitstack.py", line 21, in __call__ raise e File "fastapi/middleware/asyncexitstack.py", line 18, in __call__ await self.app(scope, receive, send) File "starlette/routing.py", line 670, in __call__ await route.handle(scope, receive, send) File "starlette/routing.py", line 266, in handle await self.app(scope, receive, send) File "starlette/routing.py", line 68, in app await response(scope, receive, send) File "starlette/responses.py", line 260, in __call__ await wrap(partial(self.listen_for_disconnect, receive)) File "anyio/_backends/_asyncio.py", line 662, in __aexit__ raise exceptions[0] File "starlette/responses.py", line 256, in wrap await func() File "starlette/responses.py", line 245, in stream_response async for chunk in self.body_iterator: File "starlette/concurrency.py", line 63, in iterate_in_threadpool yield await anyio.to_thread.run_sync(_next, iterator) File "anyio/to_thread.py", line 31, in run_sync return await get_asynclib().run_sync_in_worker_thread( File "anyio/_backends/_asyncio.py", line 937, in run_sync_in_worker_thread return await future File "anyio/_backends/_asyncio.py", line 867, in run result = context.run(func, *args) File "starlette/concurrency.py", line 53, in _next return next(iterator) ``` | 22 June 2022, 17:18:59 UTC |
| da4438a | Nicola Soranzo | 20 June 2022, 18:43:47 UTC | Merge branch 'release_21.09' into release_22.01 | 20 June 2022, 18:43:47 UTC |
| 1d85f4f | Björn Grüning | 18 June 2022, 18:17:49 UTC | Merge pull request #14103 from mvdbeek/fix_contains_collection [22.01] Fix contains_collection check for empty root collections | 18 June 2022, 18:17:49 UTC |
| b08fe47 | John Chilton | 18 June 2022, 13:46:20 UTC | Merge pull request #14086 from mvdbeek/fix_rule_builder_integer_dataset [21.09] Fix rule builder input with integer values | 18 June 2022, 13:46:20 UTC |
| d36888a | mvdbeek | 17 June 2022, 18:52:56 UTC | Fix contains_collection check for empty root collections Comparing hdca_id with parent_id is just wrong, as hdca_id is the id for a `HistoryDatasetCollectionAssociation`, while `parent_id` is the id for a `DatasetCollection`. This happened to work regardless of the first if check if the root collection contains at least one DCE, but that won't work for collections without elements. | 18 June 2022, 11:23:25 UTC |
| a314bcb | mvdbeek | 17 June 2022, 10:08:29 UTC | Fix rule builder input with integer values Upload a dataset with the only content being `123`. Go to the upload module, select the `Rule-based` tab. Select `Load tabular data from: `History Dataset` and select the dataset you just uploaded. Without this fix you'd see ``` vue.runtime.esm.js?2b0e:1897 TypeError: selection.content.split is not a function at createCollectionViaRules (RuleBasedCollectionCreatorModal.js?46f9:63:1) at child.buildCollection (history-view-edit.js?0c85:387:1) at VueComponent._buildSelection (RulesInput.vue?5e16:199:1) at VueComponent._eventBuild (RulesInput.vue?5e16:164:1) at invokeWithErrorHandling (vue.runtime.esm.js?2b0e:1863:1) at HTMLButtonElement.invoker (vue.runtime.esm.js?2b0e:2184:1) at original._wrapper (vue.runtime.esm.js?2b0e:6961:1) ``` That because `selection.content` is an integer value. | 17 June 2022, 10:30:55 UTC |
| cba4677 | David López | 14 June 2022, 12:45:50 UTC | Merge pull request #14066 from mvdbeek/enable_legacy_url_for_in_fastapi_routes [22.01] Enable generating urls for WSGI routes within FastAPI routes | 14 June 2022, 12:45:50 UTC |
| 55cc411 | mvdbeek | 14 June 2022, 10:38:31 UTC | Enable generating urls for WSGI routes within FastAPI routes | 14 June 2022, 10:41:48 UTC |
| 055a642 | Nicola Soranzo | 13 June 2022, 20:44:05 UTC | Merge pull request #13642 from nsoranzo/release_22.01_fix_13637 [22.01] Only stream stdout/stderr on kubernetes | 13 June 2022, 20:44:05 UTC |
| 3db96f4 | Marius van den Beek | 13 June 2022, 17:03:51 UTC | Use single quote to refer to tool_stdout / tool_stderr path in command line Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 13 June 2022, 17:03:51 UTC |
| 6679571 | mvdbeek | 13 June 2022, 13:49:37 UTC | Improve tool_runner path construction That'll work without galaxy_url_prefix and seems a little more robust. | 13 June 2022, 16:56:21 UTC |
| 5448144 | mvdbeek | 13 June 2022, 16:00:47 UTC | Only ``stream`` stdout/stderr on kubernetes | 13 June 2022, 16:13:16 UTC |
| 0962144 | Nicola Soranzo | 30 March 2022, 17:35:18 UTC | Add test reproducing issue #13637 xref. https://github.com/galaxyproject/galaxy/issues/13637 | 13 June 2022, 15:16:06 UTC |
| dcd0473 | Marius van den Beek | 13 June 2022, 11:34:18 UTC | Merge pull request #14056 from mvdbeek/backport_datatype_fix [22.01][Backport] Fix composite data uploads that use substitute_name_with_metadata | 13 June 2022, 11:34:18 UTC |
| 55ecc38 | mvdbeek | 09 June 2022, 10:18:42 UTC | Add selenium test for ucsc table browser data source | 13 June 2022, 09:03:13 UTC |
| eec196b | mvdbeek | 09 June 2022, 09:12:00 UTC | Api test to verify tool runner session handling | 13 June 2022, 08:58:58 UTC |
| 7fd52cb | mvdbeek | 08 June 2022, 18:17:36 UTC | Add sessioncookie with SameSite=None; secure for tool_runner path That should fix https://github.com/galaxyproject/galaxy/issues/11066 / https://github.com/galaxyproject/galaxy/issues/11374. | 13 June 2022, 08:58:42 UTC |
| 88324fc | mvdbeek | 10 June 2022, 18:40:34 UTC | Fix composite data uploads that use substitute_name_with_metadata Fixes https://github.com/galaxyproject/galaxy/issues/14050 | 13 June 2022, 08:28:45 UTC |
| 6a00e75 | Nicola Soranzo | 06 June 2022, 10:25:14 UTC | Merge branch 'release_21.09' into release_22.01 | 06 June 2022, 10:25:14 UTC |
| c5527ed | Nicola Soranzo | 06 June 2022, 09:22:29 UTC | Merge pull request #14020 from nuwang/fix_missing_biotools | 06 June 2022, 09:22:29 UTC |
| 16d9981 | Nuwan Goonasekera | 06 June 2022, 06:15:55 UTC | Fix missing biotools package | 06 June 2022, 06:15:55 UTC |
| 6159fe2 | Nicola Soranzo | 06 June 2022, 01:04:09 UTC | Merge pull request #14018 from nuwang/fix_missing_webapp_packages | 06 June 2022, 01:04:09 UTC |
| 4a779c4 | Björn Grüning | 03 June 2022, 09:04:59 UTC | try fixing the integration tests | 05 June 2022, 22:35:22 UTC |
| 9fdb5f2 | David López | 12 April 2022, 11:42:57 UTC | Add type hint suggestion Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 05 June 2022, 18:28:50 UTC |
| 44bf638 | davelopez | 12 April 2022, 11:24:55 UTC | Fix mypy error | 05 June 2022, 18:28:38 UTC |
| 6e43464 | Nuwan Goonasekera | 05 June 2022, 18:08:05 UTC | Update packages/app/requirements.txt Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 05 June 2022, 18:08:05 UTC |
| c61e391 | Nuwan Goonasekera | 05 June 2022, 07:51:38 UTC | Add missing whoosh package to galaxy-app package requirements | 05 June 2022, 07:51:38 UTC |
| 635944a | Nuwan Goonasekera | 05 June 2022, 06:47:47 UTC | Also add missing error_reports.plugins | 05 June 2022, 06:47:47 UTC |
| dd0702e | Nuwan Goonasekera | 04 June 2022, 21:00:37 UTC | Add root webapp to webapp package | 04 June 2022, 21:11:58 UTC |
| 55a8ab1 | Marius van den Beek | 02 June 2022, 09:19:23 UTC | Merge pull request #13991 from mvdbeek/backport_compression_converter [22.01] Don't create a BGZF index when running the compressing converter | 02 June 2022, 09:19:23 UTC |
| 4588b8f | Nicola Soranzo | 26 May 2022, 18:21:07 UTC | Don't create a BGZF index when running the compressing converter The index file is not used because it is generated again in `set_meta()` for the `VcfGz` datatype, and ignored for all others. Additionally, the index file is currently generated alongside the input dataset, which fails when the input directory is not writeable (such as when running in a container). Fix https://github.com/galaxyproject/galaxy/issues/13916 . Also, replace outdated `tabix` requirement with the latest `htslib`. | 01 June 2022, 09:17:47 UTC |
| 468d5e0 | Marius van den Beek | 27 May 2022, 14:42:27 UTC | Merge pull request #13913 from bgruening/fix_job_stderr [22.01] Redirect stderr of trap cleanup | 27 May 2022, 14:42:27 UTC |
| 149af62 | John Chilton | 10 May 2022, 15:04:48 UTC | Fix typing for unpinned request dependency. | 27 May 2022, 12:03:57 UTC |
| 4ac1ff1 | mvdbeek | 27 May 2022, 11:48:42 UTC | Fix up unit tests | 27 May 2022, 11:48:42 UTC |
| e103175 | Dannon | 25 May 2022, 14:40:32 UTC | Merge pull request #13639 from davelopez/fix_quotas_form_field_population [22.01] Fix FormElement: doesn't populate options for parameters | 25 May 2022, 14:40:32 UTC |
| d42a149 | Marius van den Beek | 25 May 2022, 14:31:49 UTC | Merge pull request #13583 from bernt-matthias/lint-ftype-action [22.01] linter: allow setting output format with actions | 25 May 2022, 14:31:49 UTC |
| 1dadb3c | Marius van den Beek | 25 May 2022, 14:03:04 UTC | Merge pull request #13959 from mvdbeek/tighten_sniffers [22.01] Tighten sniffers | 25 May 2022, 14:03:04 UTC |
| ae69c52 | mvdbeek | 25 May 2022, 11:38:55 UTC | Tighten xyz sniffer | 25 May 2022, 11:38:55 UTC |
| dd156d0 | mvdbeek | 25 May 2022, 10:48:29 UTC | Tighten phylip sniffer | 25 May 2022, 10:51:08 UTC |
| 139963b | Björn Grüning | 25 May 2022, 06:46:42 UTC | Merge pull request #13957 from mvdbeek/use_info_log_level [22.01] Use INFO log level for irods | 25 May 2022, 06:46:42 UTC |
| 72e1654 | mvdbeek | 24 May 2022, 21:47:17 UTC | Use INFO log level for irods We've run out of disk space on usegalaxy.org due to these log messages. | 24 May 2022, 21:47:32 UTC |
| b85297c | John Chilton | 21 May 2022, 21:25:27 UTC | Merge pull request #13945 from mvdbeek/cleanup_tus_uploads [22.01] Remove tus uploads during fetch data job | 21 May 2022, 21:25:27 UTC |
| bd8f7e8 | mvdbeek | 20 May 2022, 15:36:28 UTC | Remove tus uploads after fetch data job | 20 May 2022, 15:41:03 UTC |
| 4e8819e | Björn Grüning | 13 May 2022, 14:18:58 UTC | use -f instead of /dev/null in the tests | 13 May 2022, 14:18:58 UTC |
| 2f52e36 | Björn Grüning | 13 May 2022, 14:16:13 UTC | missing ; | 13 May 2022, 14:16:13 UTC |
| 696c24f | Björn Grüning | 13 May 2022, 14:15:00 UTC | change second trap_command | 13 May 2022, 14:15:00 UTC |
| eac698e | Björn Grüning | 13 May 2022, 14:10:18 UTC | Update lib/galaxy/jobs/command_factory.py Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 13 May 2022, 14:10:18 UTC |
