| 85b0a2b | mvdbeek | 01 July 2024, 16:21:53 UTC | Merge branch 'release_23.0' into release_23.1 | 01 July 2024, 16:21:53 UTC |
| 502aeae | mvdbeek | 01 July 2024, 16:21:09 UTC | Merge branch 'release_22.05' into release_23.0 | 01 July 2024, 16:21:09 UTC |
| 569d653 | Marius van den Beek | 01 July 2024, 14:03:15 UTC | Merge pull request #18472 from bernt-matthias/22.05-bleach5.01 [22.05] pin bleach to 5.0.1 | 01 July 2024, 14:03:15 UTC |
| 95df247 | Matthias Bernt | 01 July 2024, 08:25:03 UTC | 22.05 pin bleach to 5.0.1 22.05 is currently failing planemo tests because bleach 5.0.0 has an error in its requirements that has been fixed here https://github.com/mozilla/bleach/pull/655 | 01 July 2024, 08:25:03 UTC |
| 9b60a8c | Martin Cech | 05 June 2024, 17:10:30 UTC | Merge pull request #18332 from mvdbeek/permission_fix [23.1] Make toolshed repo permissions world-readable | 05 June 2024, 17:10:30 UTC |
| 8ee3b90 | mvdbeek | 05 June 2024, 15:59:13 UTC | Make repo permissions world-readable | 05 June 2024, 15:59:13 UTC |
| 53b56a8 | Marius van den Beek | 04 June 2024, 16:22:08 UTC | Merge pull request #18279 from mvdbeek/server_external_hgweb [23.1] More fixes for running the TS with external hgweb | 04 June 2024, 16:22:08 UTC |
| 992777e | mvdbeek | 04 June 2024, 14:58:26 UTC | Fix typo | 04 June 2024, 15:00:43 UTC |
| 80e15b6 | mvdbeek | 03 June 2024, 17:42:37 UTC | Remove html parameter from handle_exception | 03 June 2024, 17:42:37 UTC |
| 2e8c0df | mvdbeek | 03 June 2024, 15:52:27 UTC | Test and lint fixes | 03 June 2024, 15:52:27 UTC |
| 4978d64 | mvdbeek | 03 June 2024, 13:45:41 UTC | Don't delete tempdir | 03 June 2024, 15:27:20 UTC |
| e267891 | mvdbeek | 31 May 2024, 15:56:15 UTC | Cast html=True to string I tried type overloads but they are incredibly verbose. | 03 June 2024, 15:27:20 UTC |
| ea6751a | mvdbeek | 31 May 2024, 15:42:30 UTC | Make repository creation slightly safer | 03 June 2024, 13:55:11 UTC |
| 1b985e7 | Marius van den Beek | 31 May 2024, 13:48:47 UTC | Fix exception handler type hints Thank you! Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 31 May 2024, 15:44:23 UTC |
| 36b69e1 | mvdbeek | 31 May 2024, 09:20:07 UTC | Fix TS admin panel | 31 May 2024, 09:46:49 UTC |
| 7a29691 | mvdbeek | 31 May 2024, 09:19:18 UTC | Return byte strings for error html | 31 May 2024, 09:37:28 UTC |
| 01e9f02 | mvdbeek | 31 May 2024, 09:18:27 UTC | Log exceptions regardless of error log middleware outcome | 31 May 2024, 09:37:28 UTC |
| 06b8db4 | mvdbeek | 29 May 2024, 16:56:30 UTC | Change hardcoded repo location in more place | 31 May 2024, 09:36:59 UTC |
| aeaafc0 | Marius van den Beek | 31 May 2024, 08:02:29 UTC | Merge pull request #18271 from jdavcs/231_ts_revision_tags [23.1] Add revision tags for TS migration in 23.1 | 31 May 2024, 08:02:29 UTC |
| 05eecfc | John Davis | 30 May 2024, 15:33:36 UTC | Add revision tags for TS migration in 23.1 | 30 May 2024, 15:36:57 UTC |
| 90c9d47 | Marius van den Beek | 30 May 2024, 13:46:20 UTC | Merge pull request #18267 from jdavcs/231_ts_migration [23.1] Add missing TS migration | 30 May 2024, 13:46:20 UTC |
| d0d16eb | John Davis | 30 May 2024, 13:34:38 UTC | Make column non-nullable | 30 May 2024, 13:34:38 UTC |
| 063d985 | mvdbeek | 30 May 2024, 09:50:43 UTC | Also set model to nullable=False | 30 May 2024, 09:50:43 UTC |
| 4099fcc | mvdbeek | 30 May 2024, 09:45:12 UTC | Set all old keys to deleted | 30 May 2024, 09:45:12 UTC |
| a774c92 | John Davis | 30 May 2024, 02:18:26 UTC | Add ts db migration: deleted column to api_keys tbl | 30 May 2024, 02:49:30 UTC |
| b121db5 | Nate Coraor | 29 May 2024, 15:58:14 UTC | Merge pull request #18256 from mvdbeek/server_external_hgweb [23.1] Minor fix to enable external hgweb process | 29 May 2024, 15:58:14 UTC |
| 410ccb9 | mvdbeek | 29 May 2024, 15:45:23 UTC | Fix up lock handling in hgweb_config_manager | 29 May 2024, 15:50:49 UTC |
| b00beec | mvdbeek | 29 May 2024, 15:44:55 UTC | Allow configuring hgweb repo prefix | 29 May 2024, 15:44:55 UTC |
| dc9e078 | Nicola Soranzo | 10 April 2024, 16:42:00 UTC | Merge branch 'release_23.0' into release_23.1 | 10 April 2024, 16:42:00 UTC |
| 659e87f | Nicola Soranzo | 10 April 2024, 12:20:48 UTC | Merge pull request #17955 from nsoranzo/release_23.0_fix_XForwardedHostMiddleware [23.0] Fix KeyError in ``XForwardedHostMiddleware`` | 10 April 2024, 12:20:48 UTC |
| 11bb4b4 | Nicola Soranzo | 10 April 2024, 11:08:11 UTC | Fix KeyError in ``XForwardedHostMiddleware`` when `REMOTE_ADDR` is not defined. Reported by @vazovn . Also fix typos in environment variable names. | 10 April 2024, 11:09:24 UTC |
| 796ed40 | mvdbeek | 09 April 2024, 13:57:03 UTC | Merge branch 'release_23.0' into release_23.1 | 09 April 2024, 13:57:03 UTC |
| 3abb181 | Marius van den Beek | 09 April 2024, 12:49:04 UTC | Merge pull request #17944 from nsoranzo/release_23.0_fix_17938 [23.] Fix output datatype when uncompressing a dataset with incorrect datatype | 09 April 2024, 12:49:04 UTC |
| 0611465 | Nicola Soranzo | 09 April 2024, 10:36:10 UTC | Fix output datatype when uncompressing a dataset with incorrect datatype with the ``CONVERTER_gz_to_uncompressed`` tool. Previously, if a user forced an incorrect datatype to a compressed input dataset (e.g. `fastqsanger` instead of `fastqsanger.gz`), then the output datatype assigned by this tool would be an invalid one (`fastqsan`). Fix #17938. | 09 April 2024, 10:39:39 UTC |
| 95a3797 | Marius van den Beek | 29 March 2024, 23:21:58 UTC | Merge pull request #17868 from mvdbeek/parse_extensions_as_lowercase_and_stripped [23.1] Normalize extensions when loading tool | 29 March 2024, 23:21:58 UTC |
| 45c4675 | mvdbeek | 29 March 2024, 21:11:47 UTC | Normalize extensions when loading tool Fixes https://github.com/galaxyproject/galaxy/issues/17864 | 29 March 2024, 21:15:34 UTC |
| 67ed6a7 | mvdbeek | 25 March 2024, 09:11:20 UTC | Merge branch 'release_23.0' into release_23.1 | 25 March 2024, 09:11:20 UTC |
| 77fc849 | Marius van den Beek | 25 March 2024, 09:10:50 UTC | Merge pull request #17828 from mvdbeek/fix_large_memory_usage_qza [23.0] Fix excessive memory usage for npz files | 25 March 2024, 09:10:50 UTC |
| 28c19eb | mvdbeek | 12 March 2024, 17:24:24 UTC | Assert that at least one file in npz zipfile ends with .npy from https://pydoc.dev/numpy/latest/numpy.lib.npyio.NpzFile.html: > NpzFile is used to load files in the NumPy .npz data archive format. It assumes that files in the archive have a .npy extension, other files are ignored. | 25 March 2024, 08:20:50 UTC |
| ed69e0f | Matthias Bernt | 12 March 2024, 13:07:47 UTC | Npz sniffing: do not read the whole file takes to much memory | 25 March 2024, 08:20:27 UTC |
| 4b3bc55 | Marius van den Beek | 18 March 2024, 07:26:55 UTC | Merge pull request #17736 from ahmedhamidawan/dataset_handle_missing_indexer [23.1] Handle missing indexer for a dataset | 18 March 2024, 07:26:55 UTC |
| d6914b7 | Ahmed Awan | 15 March 2024, 20:55:10 UTC | exception without the `try/catch` block Also, improve clarity a bit... | 17 March 2024, 18:22:58 UTC |
| b84f945 | Ahmed Awan | 14 March 2024, 20:19:24 UTC | [23.1] Handle missing indexer for a dataset In case a dataset does not have an indexer, raise an exception. Fixes the bug mentioned in https://github.com/galaxyproject/galaxy/pull/17639#issuecomment-1995990448 | 14 March 2024, 20:19:24 UTC |
| a3c14ea | Marius van den Beek | 08 March 2024, 14:01:15 UTC | Merge pull request #17639 from mvdbeek/fix_data_reault [23.1] Fix DataResult type | 08 March 2024, 14:01:15 UTC |
| 81086bf | mvdbeek | 08 March 2024, 11:03:48 UTC | Fix DataResult type None isn't valid for `List[Any]`. Fixes: ``` ValidationError 1 validation error for DataResult data Input should be a valid list [type=list_type, input_value=None, input_type=NoneType] For further information visit https://errors.pydantic.dev/2.5/v/list_type ``` | 08 March 2024, 11:04:14 UTC |
| fab4424 | John Davis | 04 March 2024, 17:58:03 UTC | Merge pull request #17577 from jdavcs/23.1_coalesce [23.1] Fix ancient bug: incorrect usage of func.coalesce in User model | 04 March 2024, 17:58:03 UTC |
| 021cb80 | John Davis | 01 March 2024, 22:22:34 UTC | Fix bug: this is not part of a sql stmt | 01 March 2024, 22:22:34 UTC |
| 3308279 | John Davis | 18 February 2024, 20:22:08 UTC | Merge branch 'release_23.0' into release_23.1 | 18 February 2024, 20:22:08 UTC |
| 91d9d49 | Marius van den Beek | 13 February 2024, 16:19:03 UTC | Merge pull request #17459 from mvdbeek/backport_public_hdca_check [23.1] Only check access permissions in `/api/{history_dataset_collection_id}/contents/{dataset_collection_id}` | 13 February 2024, 16:19:03 UTC |
| d18003e | Ahmed Awan | 12 February 2024, 16:30:13 UTC | add api test for hdcas in public histories being accessible | 13 February 2024, 14:01:58 UTC |
| 4eab971 | Ahmed Awan | 09 February 2024, 15:57:59 UTC | remove `check_ownership` from `dataset_collections.contents` ... since this api only needs to `check_accessible` as it is not modifying a collection | 13 February 2024, 14:01:56 UTC |
| 8c3d967 | Ahmed Awan | 08 February 2024, 19:14:31 UTC | fix published history collections are empty on expand Only check ownership in `__get_history_collection_instance` if: `collection_instance.history.published` = False | 13 February 2024, 14:00:39 UTC |
| c94ec0d | Marius van den Beek | 13 February 2024, 10:32:21 UTC | Merge pull request #17456 from davelopez/23.1_fix_bulk_operation_menu_bis [23.1] Fix history bulk operations menu (part 2) | 13 February 2024, 10:32:21 UTC |
| b7b5c05 | davelopez | 12 February 2024, 16:20:36 UTC | Increase readability | 12 February 2024, 16:20:36 UTC |
| 811f8cf | davelopez | 12 February 2024, 16:06:58 UTC | Fix bulk menu conditions | 12 February 2024, 16:06:58 UTC |
| 79fee2a | davelopez | 12 February 2024, 16:06:20 UTC | Add more test conditions for bulk menu | 12 February 2024, 16:06:20 UTC |
| f130a3e | davelopez | 12 February 2024, 10:17:31 UTC | Refactor test to reduce selector duplication | 12 February 2024, 10:17:31 UTC |
| d483675 | Marius van den Beek | 10 February 2024, 10:40:40 UTC | Merge pull request #17448 from ahmedhamidawan/23.0_datasetStore_saveDatasets_fix [23.0] Fix `datasetStore.saveDatasets` bug | 10 February 2024, 10:40:40 UTC |
| 9d0a200 | Marius van den Beek | 10 February 2024, 10:38:53 UTC | Merge pull request #17445 from nuwang/make_extra_props_more_defensive More defensive access of extra props in filesources | 10 February 2024, 10:38:53 UTC |
| 948c013 | Ahmed Awan | 09 February 2024, 20:59:56 UTC | [23.0] Fix `datasetStore.saveDatasets` bug When we update the datasets in the `datasetStore`, we can sometimes set multiple properties to undefined. This happens because a dataset in the store fetched from `/api/datasets/${id}` has a keys mismatch from a dataset coming from `/api/histories/${historyId}/contents` in `watchHistory`, where the latter has lesser keys. To address this, I replaced 'localItem' with 'item' in the loop that updates the keys, ensuring the correct properties are retained during the store update. | 09 February 2024, 20:59:56 UTC |
| 7bffadb | John Davis | 09 February 2024, 18:37:33 UTC | Merge branch 'release_23.0' into release_23.1 | 09 February 2024, 18:37:33 UTC |
| c7a5e4f | Nuwan Goonasekera | 09 February 2024, 11:11:45 UTC | Code review suggestion Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> | 09 February 2024, 14:07:52 UTC |
| bffb7a9 | nuwang | 09 February 2024, 10:27:29 UTC | Use dataclass to initialize default values | 09 February 2024, 11:29:33 UTC |
| ae982a2 | nuwang | 09 February 2024, 06:33:24 UTC | Add initializers to filesource options | 09 February 2024, 11:29:32 UTC |
| bed5c5e | Marius van den Beek | 09 February 2024, 08:29:50 UTC | Merge pull request #17446 from jdavcs/23.0_truebug [23.0] Fix bug: true >> True | 09 February 2024, 08:29:50 UTC |
| c1f0aad | John Davis | 09 February 2024, 06:09:00 UTC | Fix typo | 09 February 2024, 06:09:00 UTC |
| 0008b4d | mvdbeek | 08 February 2024, 11:21:53 UTC | Merge branch 'release_23.0' into release_23.1 | 08 February 2024, 11:21:53 UTC |
| 4c1c8e2 | Marius van den Beek | 08 February 2024, 11:20:32 UTC | Merge pull request #17384 from ahmedhamidawan/fix_genome_build_filter_postgres [23.0] Fix History contents `genome_build` filter postgresql bug | 08 February 2024, 11:20:32 UTC |
| 62ee88d | Marius van den Beek | 08 February 2024, 10:04:07 UTC | Merge pull request #17433 from davelopez/23.1_fix_bulk_operations_menu [23.1] Fix history bulk operations menu conditions | 08 February 2024, 10:04:07 UTC |
| cb97ef1 | Marius van den Beek | 08 February 2024, 09:55:36 UTC | Merge pull request #17426 from davelopez/23.1_encode_tool_link_consistently [23.1] Encode tool link consistently | 08 February 2024, 09:55:36 UTC |
| 52933ed | Nicola Soranzo | 07 February 2024, 22:48:53 UTC | Merge branch 'release_23.0' into release_23.1 | 07 February 2024, 22:48:53 UTC |
| c654c88 | Marius van den Beek | 07 February 2024, 14:42:28 UTC | Merge pull request #17429 from nsoranzo/release_23.0_python-multipart_0.0.7 [23.0] Update python-multipart to 0.0.7 | 07 February 2024, 14:42:28 UTC |
| f60f0ae | davelopez | 07 February 2024, 13:58:52 UTC | Fix new edge case where all items might be already deleted This case was previously prevented at the UI level but should be considered here. | 07 February 2024, 13:58:52 UTC |
| bc0b3eb | davelopez | 07 February 2024, 13:52:53 UTC | Fix menu display conditions to adapt to "any" filter | 07 February 2024, 13:52:53 UTC |
| 5f14cd2 | davelopez | 07 February 2024, 13:50:28 UTC | Add test coverage for "any" state in menu options | 07 February 2024, 13:50:28 UTC |
| de8d456 | Nicola Soranzo | 07 February 2024, 05:44:11 UTC | Add missing Werkzeug test requirement Used in `test/unit/util/test_get_url.py` since commit 69ebbb761aa610c1eab2f92a385c34b47259ac32 . Pin Werkzeug in `lib/galaxy/dependencies/dev-requirements.txt` to latest version compatible with pytest-httpserver 1.0.6 . Fix unit test collection error on Python 3.11: ``` File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.11/site-packages/pytest_httpserver/httpserver.py", line 26, in <module> from werkzeug.http import parse_authorization_header ImportError: cannot import name 'parse_authorization_header' from 'werkzeug.http' (/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.11/site-packages/werkzeug/http.py) ``` | 07 February 2024, 05:44:42 UTC |
| 10ace7b | Nicola Soranzo | 06 February 2024, 17:33:18 UTC | Update python-multipart to 0.0.7 xref: https://github.com/tiangolo/fastapi/security/advisories/GHSA-qf9m-vfgh-m389 | 06 February 2024, 17:33:21 UTC |
| d787727 | davelopez | 06 February 2024, 13:53:17 UTC | Add test case for tool IDs with `+` | 06 February 2024, 13:53:17 UTC |
| 22d5071 | davelopez | 06 February 2024, 13:30:49 UTC | Fix tool link encoding Makes it easier to share when pasting it in oder contexts outside the web browser. | 06 February 2024, 13:30:49 UTC |
| 71237cf | davelopez | 06 February 2024, 13:29:37 UTC | Add unit test for Tools copyLink utility | 06 February 2024, 13:29:37 UTC |
| f7e6d16 | David López | 02 February 2024, 09:26:18 UTC | Merge pull request #17388 from davelopez/update_webdav_conf_sample [23.1] Set webdav file source to use temp files by default | 02 February 2024, 09:26:18 UTC |
| 11fdad0 | Nicola Soranzo | 01 February 2024, 12:00:50 UTC | Merge branch 'release_23.0' into release_23.1 | 01 February 2024, 12:00:50 UTC |
| 504053c | Marius van den Beek | 31 January 2024, 17:58:39 UTC | Merge pull request #17404 from nsoranzo/release_23.0_fix_docs_upload [23.0] Fix uploading of docs for release_NN.N branches | 31 January 2024, 17:58:39 UTC |
| e82b950 | Nicola Soranzo | 31 January 2024, 17:18:10 UTC | Fix uploading of docs for release_NN.N branches | 31 January 2024, 17:18:10 UTC |
| 7d27634 | davelopez | 31 January 2024, 10:25:46 UTC | Give webdav plugin a clean temp directory Co-authored-by: mvdbeek <m.vandenbeek@gmail.com> | 31 January 2024, 10:25:46 UTC |
| 5ffa9e1 | Ahmed Hamid Awan | 30 January 2024, 19:57:09 UTC | move database_connection assignment after super()... Co-authored-by: John Davis <jdavcs@gmail.com> | 30 January 2024, 19:57:09 UTC |
| 3e94c4d | Ahmed Awan | 30 January 2024, 13:39:42 UTC | check dbkey: [".."] as well, fix mypy errors | 30 January 2024, 13:39:42 UTC |
| 5153394 | davelopez | 30 January 2024, 12:43:09 UTC | Set webdav plugin to use temp files by default it avoids the issue with loading the entire files into memory. | 30 January 2024, 12:43:09 UTC |
| ddf992c | davelopez | 30 January 2024, 12:41:21 UTC | Add comment on writable for webdav file source | 30 January 2024, 12:41:21 UTC |
| 1a81f75 | davelopez | 30 January 2024, 10:59:03 UTC | Update docs for webdav file source config Include docs and settings to avoid loading entire files into memory. | 30 January 2024, 11:23:17 UTC |
| 38b1107 | Ahmed Awan | 29 January 2024, 18:43:27 UTC | [23.0] Fix History contents `genome_build` filter postgresql bug Check the user's db connection and use appropriate query/function. | 29 January 2024, 18:43:27 UTC |
| 1fe37b0 | John Chilton | 22 January 2024, 18:54:08 UTC | Merge pull request #17337 from davelopez/23.1_fix_tag_edit_on_shared_pages [23.1] Disable tag editing on non-owned Pages | 22 January 2024, 18:54:08 UTC |
| d1eaff9 | davelopez | 22 January 2024, 15:39:38 UTC | Disable tag editing on non-owned Pages | 22 January 2024, 15:39:38 UTC |
| ac6fe73 | Marius van den Beek | 18 January 2024, 12:26:24 UTC | Merge pull request #17323 from galaxyproject/revert-15238-patch-13 | 18 January 2024, 12:26:24 UTC |
| 61f3db2 | Nuwan Goonasekera | 18 January 2024, 11:47:32 UTC | Revert "[23.1] Enable job resubmissions in k8s runner" | 18 January 2024, 11:47:32 UTC |
| b4b1def | Nuwan Goonasekera | 18 January 2024, 09:44:43 UTC | Merge pull request #15238 from pcm32/patch-13 [23.2] Enable job resubmissions in k8s runner | 18 January 2024, 09:44:43 UTC |
| 7f057c9 | Marius van den Beek | 16 January 2024, 13:58:12 UTC | Merge pull request #17268 from mvdbeek/fix_element_not_copied [23.1] Always copy datasets in collection builder modals | 16 January 2024, 13:58:12 UTC |
| 5ba634b | John Davis | 12 January 2024, 14:46:04 UTC | Merge pull request #17276 from mvdbeek/fix_nested_collection_serialization_in_to_cwl [23.1] Fix ``to_cwl`` for nested collections | 12 January 2024, 14:46:04 UTC |
| 0150291 | mvdbeek | 12 January 2024, 11:24:51 UTC | Fix ``to_cwl`` for nested collections Fixes ``` TypeError Object of type DatasetCollection is not JSON serializable ``` seen when running https://github.com/galaxyproject/iwc/pull/315 | 12 January 2024, 11:24:59 UTC |
| e4f8315 | mvdbeek | 11 January 2024, 11:33:12 UTC | Adjust selenium tests for new numbering | 11 January 2024, 12:34:29 UTC |
