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Author SHA1 Message Date
mvdbeek b2097db85d Merge remote-tracking branch 'upstream/release_24.0' into release_24.1 2024-05-31 15:27:27 +02:00
Marius van den Beek d5e44b654a Merge pull request #18284 from mvdbeek/fix_up_first_dataset_element_type_hint 
[24.0] Fix first_dataset_element type hint
 2024-05-31 15:25:23 +02:00
mvdbeek 99aeadec06 Fix first_dataset_element type hint 2024-05-31 15:09:31 +02:00
Marius van den Beek 8dd7a9e570 Merge pull request #18263 from mvdbeek/page_summary_fix 
[24.0] Set page importable to false when serializing
 2024-05-31 12:37:30 +02:00
Marius van den Beek 93a07857c2 Merge pull request #18278 from mvdbeek/collection_download 
Don't attempt to download purged datasets
 2024-05-31 12:37:06 +02:00
Nicola Soranzo 761a8d9f04 Merge pull request #18236 from mvdbeek/none_delete_error 
[24.0] Only log error if deleting directory really failed
 2024-05-31 10:42:54 +01:00
Marius van den Beek 48231391a8 Drop key argument 
Did not want to do that actually
 2024-05-31 10:18:23 +02:00
Marius van den Beek fd1cb2726a Merge pull request #18252 from bernt-matthias/revert/17656 
[24.1] Remove linter for unstripped text content for tool xml leaves
 2024-05-31 10:03:52 +02:00
Marius van den Beek fb7d10b221 Merge pull request #18251 from davelopez/24.1_fix_history_export_error_handling 
[24.1] Fix history export error handling
 2024-05-31 10:01:55 +02:00
Marius van den Beek 942ddea389 Merge pull request #18255 from davelopez/24.0_fix_invenio_credentials_handling 
[24.0] Fix Invenio credentials handling
 2024-05-31 10:01:42 +02:00
John Chilton 4c8b4bf2a7 Merge pull request #18249 from mvdbeek/fix_no_elements_exception_extract_dataset 
[24.0] Raise exception when extracting dataset from collection without datasets
 2024-05-30 17:54:24 -04:00
John Chilton 1dd31f08f6 Merge pull request #18248 from mvdbeek/enable_transparent_use_of_compressed_datasets_in_DatasetDataProvider 
[24.0] Transparently open compressed files in DatasetDataProvider
 2024-05-30 17:53:20 -04:00
Martin Cech 8f4029cdda Merge pull request #18274 from jdavcs/241_result_mappings 
[24.1] Fix handler: access to result row items changed in SA2.0
 2024-05-30 23:07:35 +02:00
Martin Cech 0daf36d5d6 Merge pull request #18273 from nsoranzo/release_24.0_black 
[24.0] Format with black
 2024-05-30 23:03:56 +02:00
John Davis 534f933861 Fix SA20 bug 2024-05-30 15:19:38 -04:00
Nicola Soranzo 53bf8ce1de Format with black 2024-05-30 17:58:42 +01:00
Nicola Soranzo 3ea8de4ce5 Merge branch 'release_23.2' into release_24.0 2024-05-30 16:45:28 +01:00
Nicola Soranzo 94ebebf4ac Merge pull request #18268 from nsoranzo/release_23.2_fix_TestToolShedConfig 
[23.2] Add ``hgweb_repo_prefix`` attribute to ``TestToolShedConfig``
 2024-05-30 16:43:35 +01:00
John Davis 4dda05fbd3 Merge pull request #18270 from jdavcs/241_merge_24.0 
[24.1] Merge 24.0 into 24.1
 2024-05-30 11:40:45 -04:00
John Davis 4030c70e9f Merge 24.0 into 24.1 
Adjust TS api_keys model
- Boolean datatype dropped since it's inferred from the type hint
- nullable=False added
 2024-05-30 11:24:24 -04:00
John Davis 15a8e6cc9a Merge branch 'release_23.2' into release_24.0 2024-05-30 11:11:12 -04:00
John Davis dbd063e00d Merge release_23.1 into release_23.2 2024-05-30 10:57:20 -04:00
Nicola Soranzo 6d068ca5f9 Add `hgweb_repo_prefix attribute to TestToolShedConfig` 
Fix the following error in unit tests:

```
AttributeError: 'TestToolShedConfig' object has no attribute 'hgweb_repo_prefix'
```

caused by merging commit b00beec3d2
forward.
 2024-05-30 15:16:38 +01:00
Marius van den Beek 90c9d4756f Merge pull request #18267 from jdavcs/231_ts_migration 
[23.1] Add missing TS migration
 2024-05-30 15:46:20 +02:00
John Davis d0d16ebf49 Make column non-nullable 2024-05-30 09:34:38 -04:00
Nicola Soranzo 6ef6fc911f Merge branch 'release_24.0' into release_24.1 2024-05-30 13:03:12 +01:00
Nicola Soranzo 713556029d Merge branch 'release_23.2' into release_24.0 2024-05-30 12:51:06 +01:00
Nicola Soranzo bd9a16988e Merge branch 'release_23.1' into release_23.2 2024-05-30 12:41:23 +01:00
mvdbeek 063d985650 Also set model to nullable=False 2024-05-30 11:50:43 +02:00
mvdbeek 4099fcc15a Set all old keys to deleted 2024-05-30 11:45:12 +02:00
Marius van den Beek 0db89059ef Merge pull request #18250 from mvdbeek/test_robustness 
[24.0] Skip tests if toolshed, dx.doi not responding
 2024-05-30 09:48:26 +02:00
John Davis a774c9234c Add ts db migration: deleted column to api_keys tbl 2024-05-29 22:49:30 -04:00
mvdbeek 0b6d925b8a Set page importable to false when serializing 
Fixes https://github.com/galaxyproject/galaxy/issues/18258
 2024-05-29 18:46:44 +02:00
Nate Coraor b121db548c Merge pull request #18256 from mvdbeek/server_external_hgweb 
[23.1] Minor fix to enable external hgweb process
 2024-05-29 11:58:14 -04:00
mvdbeek 410ccb9ab2 Fix up lock handling in hgweb_config_manager 2024-05-29 17:50:49 +02:00
mvdbeek b00beec3d2 Allow configuring hgweb repo prefix 2024-05-29 17:44:55 +02:00
davelopez 7cfba26fe1 Fix Invenio credentials handling 
Only ask for token when is really required
 2024-05-29 16:51:00 +02:00
mvdbeek 2ea3d342cc Import tool shed url 2024-05-29 15:29:39 +02:00
Matthias Bernt c201daa7a8 remove linter for unstripped text content for tool xml leaves 
reverts #17656

we have to many xml nodes where this is allowed (e.g. command)
and limiting the linter to a statically defined list of node types
seemed difficult to maintain

replaced this with a change in the xsd that should lead to the
automatic removal of surplus white spaces (leading/trailing are removed,
multiple whitespaces are replaced by a single space) for some of the
node types that were the original motivation for the linter
(if this proves useful this could be used for more node types).
 2024-05-29 15:29:00 +02:00
davelopez ec451f26f7 Update watchHistory test to expect rethrowSimple error 
Instead of AxiosError
 2024-05-29 14:58:17 +02:00
davelopez 518b0257ac Add tests for fatal error loading history 2024-05-29 14:22:46 +02:00
davelopez 1884ec4765 Hide history export UI on fatal error and show alert 2024-05-29 14:19:50 +02:00
davelopez 16f3be6904 Refactor HistoryExport tests to use MockAxios 2024-05-29 14:18:46 +02:00
davelopez 7d5385107f Add optional parameter to historyStore.getHistoryById 
The `getHistoryById` function in `historyStore.ts` now accepts an optional parameter `shouldFetchIfMissing` which determines whether to load the history if it is not already in the store. If `shouldFetchIfMissing` is set to `false`, the function will return `null` instead of fetching the history.
 2024-05-29 14:17:16 +02:00
davelopez c9e6144451 Rethrow errors instead of just log them in historyStore 2024-05-29 14:15:59 +02:00
mvdbeek b0ea69e418 Fix import order 2024-05-29 13:58:09 +02:00
mvdbeek ce1582f46a Move assertions out request error handling 2024-05-29 13:50:29 +02:00
Marius van den BeekandNicola Soranzo 5d2ccdfbe7 Use variable 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-05-29 13:49:10 +02:00
mvdbeek d8379a79a1 Also skip unit test 2024-05-29 13:39:26 +02:00
Marius van den BeekandNicola Soranzo 74e8d3257b Make it an f-string 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-05-29 13:35:52 +02:00