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Author SHA1 Message Date
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 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 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
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
mvdbeek 2ea3d342cc Import tool shed url 2024-05-29 15:29:39 +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
mvdbeek 5f1ec2b06f Skip tests that require toolshed to be up if toolshed down 2024-05-29 13:30:22 +02:00
mvdbeek 229b1c5bcb Skip doi unit test if request fails 2024-05-29 13:30:22 +02:00
Ahmed Hamid Awan c2438b2f06 Merge pull request #18243 from davelopez/24.0_fix_userOwnsHistory_conditions 
[24.0] Fix userOwnsHistory conditions
 2024-05-28 12:12:06 -05:00
davelopez 1637e202e5 Adapt History SelectorModal test 2024-05-28 14:55:37 +02:00
davelopez fa73f2e9f4 Fix conditions for userOwnsHistory and isRegisteredUser 2024-05-28 14:54:40 +02:00
David López ce53c7cc03 Merge pull request #18235 from mvdbeek/accessible_followup 
[24.0] Fix element serialization for collections that aren't populated yet
 2024-05-28 09:58:31 +02:00
mvdbeek 0359063816 Fix element serialization for collections that aren't populated yet 
Fixes
https://github.com/galaxyproject/galaxy/pull/17818#issuecomment-2134060961:
```
AttributeError
'NoneType' object has no attribute 'dataset'
```
 2024-05-28 08:15:19 +02:00
Marius van den Beek 316eb5bf81 Merge pull request #18233 from mvdbeek/reset_content_length_if_no_error_handling 
[24.0] Reset content-length for unhandled exceptions
 2024-05-27 20:00:39 +02:00
John Chilton 98d8ae99b4 Merge pull request #18223 from mvdbeek/discriminate_inputs_deleted_job_files 
[24.0] Raise appropriate exception if accessing deleted input file
 2024-05-27 09:49:09 -04:00
John Chilton 82a54a5f62 Merge pull request #18229 from mvdbeek/decrease_visualization_log_level 
[24.0] Decrease log level for expected visualization errors
 2024-05-27 09:44:54 -04:00
John Chilton 62b53c5e2a Merge pull request #18231 from mvdbeek/set_peek_on_success_only 
[24.0] Don't set dataset peek for errored jobs
 2024-05-27 09:42:56 -04:00
John Chilton fef8341023 Merge pull request #18230 from mvdbeek/exception_handling_fetch_invalid_url 
[24.0] Raise ``RequestParameterInvalidException`` if url can't be verified
 2024-05-27 09:41:24 -04:00
mvdbeek 3c6a9a8eaf Reset content-length for unhandled exceptions 
This prevents `ProtocolError` caused by the error middleware not being
able to reset the content length. Only affects routes that explicitly
set the content-length and don't have a default response handler.

This is effectively the case when using `web.expose`. To test this,
make sure you get Galaxy's error middleware output in the browser
and your console.
```
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index c95d9df788..92b04684d3 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -456,6 +456,8 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
     def imp(self, trans, dataset_id=None, **kwd):
         """Import another user's dataset via a shared URL; dataset is added to user's current history."""
         # Set referer message.
+        trans.response.headers["content-length"] = 0
+        trans = None
         referer = trans.request.referer
         if referer and not referer.startswith(f"{trans.request.application_url}{url_for('/login')}"):
             referer_message = f"<a href='{escape(referer)}'>return to the previous page</a>"

```
 2024-05-27 11:37:54 +02:00
mvdbeek 54db4e9a7a Don't fail set_peek if file does not look like GRO file 2024-05-27 10:23:59 +02:00
mvdbeek 3cd64e7861 Refactor set_peek and move exception handling 2024-05-27 10:15:54 +02:00
mvdbeek 11ae179c9a Don't set dataset peek for errored jobs 
This is consistent with the extended metadata logic, and prevents:
```
Message
Job wrapper finish method failed
Stack Trace

Newest

IndexError
list index out of range
```
which only makes it harder to diagnose the actual error, which in the
case of https://sentry.galaxyproject.org/share/issue/831261683ce642a4976efa20a9a0e55c/
is `\nslurmstepd: error: *** JOB 1910486 ON js2-gpu-small0 CANCELLED AT 2024-05-26T23:30:00 DUE TO TIME LIMIT ***\n`
 2024-05-27 10:06:46 +02:00
mvdbeek 30b1f4b2f9 Raise RequestParameterInvalidException if url can't be verified 
Kind of a followup to
https://github.com/galaxyproject/galaxy/pull/18155.

Fixes:
```
ValueError
invalid literal for int() with base 10: 'sequences'
```
For the attempted url `"http://emp-single-end-sequences:sequences"`.
 2024-05-27 09:54:09 +02:00
mvdbeek ed70432254 Decrease visualization log level 
Minor followup to https://github.com/galaxyproject/galaxy/pull/18211.
If we've got a MessageException I don't think we need to log this as an
error, since we're also showing a reasonable message to the user.
 2024-05-27 09:09:59 +02:00
Marius van den Beek d8b827f50e Merge pull request #17818 from martenson/noexpand-private 
[24.0] do not expand datasets that are known to be inaccessible
 2024-05-25 15:53:03 +02:00
mvdbeek cc2f83dac0 Raise appropriate exception if accessing deleted input file 2024-05-24 18:26:18 +02:00
Marius van den Beek ae9ea865e1 Merge pull request #18214 from mvdbeek/error_messages_when_accessing_datasets_we_cannot_access 
[24.0] Check dataset state when attempting to acces dataset contents
 2024-05-24 16:02:33 +02:00
davelopez 0104764bb8 Make accessible optional in HDAObject 
It is probably enough to serialize the `accessible` property only when requesting collection contents displayed in the UI.
 2024-05-24 13:43:33 +02:00
davelopez 810b246fbf Avoid requesting details for inaccessible datasets 2024-05-24 11:09:59 +02:00
davelopez a0adf7e76b Add missing event declaration 
Fixes typescript error:
Argument of type '"edit"' is not assignable to parameter of type '"toggleHighlights"'
 2024-05-24 10:53:00 +02:00
davelopez afac2afa24 Serialize accessible field for collection elements 2024-05-24 10:50:08 +02:00
davelopez 7961b475bb Fix bool const OpenAPI TS schema conversion 2024-05-24 10:47:32 +02:00
Marius van den Beek 21a427213d Merge pull request #18217 from mvdbeek/tighten_job_access 
[24.0] Restrict job_files access to jobs that are not terminal
 2024-05-24 09:00:56 +02:00