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Author SHA1 Message Date
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
Nicola Soranzo 7ab747506a Merge pull request #18192 from ahmedhamidawan/prevent_anon_users_run_workflow 
[24.0] Prevent anonymous and inactive users from running workflows
 2024-05-23 23:28:33 +01:00
mvdbeek 4e47b8de13 Restrict job_files access to jobs that are not terminal 
That should fix https://sentry.galaxyproject.org/share/issue/c4eb157823c240d5a664ec6517354db2/
 2024-05-23 23:11:38 +02:00
John Davis 1c11fe13ea Merge pull request #18215 from jdavcs/240_ts_db_script 
[24.0] Use config_section to distinguish between galaxy and ts or other apps
 2024-05-23 15:40:28 -04:00
Martin Cech 1e59ea48b7 Merge pull request #18212 from nsoranzo/release_24.0_backport_18197 
[24.0] Backport #18197
 2024-05-23 21:03:53 +02:00
John Davis a047ea0861 Use config_section to distinguish between galaxy and ts or other apps 2024-05-23 14:34:10 -04:00
Dannon 2ddea78aef Merge pull request #18203 from ahmedhamidawan/fix_content_item_on_error 
[24.0] Add `GenericItem` error handling
 2024-05-23 13:58:51 -04:00
mvdbeek 59803e968e Check dataset state when attempting to acces dataset contents 2024-05-23 18:45:13 +02:00
Ahmed Hamid AwanandNicola Soranzo 538570b3e2 Update lib/galaxy/webapps/galaxy/services/workflows.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-05-23 11:05:41 -05:00
Ahmed Hamid AwanandMarius van den Beek cef091bcd1 Update client/src/components/History/Content/GenericItem.vue 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2024-05-23 11:00:37 -05:00
Ahmed Awan 1e94915c98 add titles to Toasts for GenericItem 2024-05-23 10:34:59 -05:00
Nicola Soranzo 9b70b7582d Exclude bcsl.ts test files from CodeQL code scanning 
Fix errors like:

```
lib/galaxy/datatypes/test/test_file3.bcsl.ts#L2C12:12: A parse error
occurred: `';' expected.`. Check the syntax of the file. If the file
is invalid, correct the error or
[exclude](https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/customizing-code-scanning)
the file from analysis.
```

seen in https://github.com/galaxyproject/galaxy/actions/runs/9170180020/job/25211944475 .
 2024-05-23 16:09:31 +01:00
Nicola Soranzo 028630afcb Update syntax for labeler action v5 
See https://github.com/marketplace/actions/labeler#breaking-changes-in-v5
 2024-05-23 16:09:22 +01:00
Nicola Soranzo b19136073e Use official minikube GitHub action 
Cannot used the new default driver (`docker`) as it crashes the
PostgreSQL Docker container started via job services.
 2024-05-23 16:07:25 +01:00
Nicola Soranzo de2d36afe2 Update versions of GitHub actions 2024-05-23 16:06:43 +01:00
Nicola Soranzo 4c4ed106a4 Use job permissions instead of token 2024-05-23 16:06:21 +01:00
John Chilton 37aeadd146 Merge pull request #18179 from mvdbeek/fix_extra_files_dir_only_collection_pulsar 
[24.0] Don't fail metadata if we only have an extra output files dir
 2024-05-23 09:10:36 -04:00
Dannon 326e29158f Merge pull request #18211 from mvdbeek/fix_pca_3d_rendering_and_error_handling 
[24.0] Fix pca 3d rendering of tabular files and visualization error handling in general
 2024-05-23 09:09:50 -04:00
mvdbeek 15fa3a43f7 Fix display of error messages in visualizations 2024-05-23 13:18:20 +02:00
mvdbeek 8fcc151f6f Limit templated visualization data, fix PCA plot for tabular datasets 2024-05-23 13:18:20 +02:00
Marius van den Beek 3a89e74019 Merge pull request #18194 from ahmedhamidawan/replace_multiselect_label_with_icon 
[24.0] Replace `Multiselect` `selectLabel` with icons in `FormSelect`
 2024-05-23 11:48:36 +02:00
Marius van den Beek 825a045b0a Merge pull request #18208 from mvdbeek/exc_info_in_object_store_delete 
[24.0] Include stack when reporting delete error
 2024-05-23 11:48:08 +02:00
Marius van den Beek 921f181510 Merge pull request #18207 from mvdbeek/fix_genome_build_int 
[24.0] Add string cast for dbkey / genome_build
 2024-05-23 11:47:06 +02:00
Marius van den Beek 154aaa162d Merge pull request #18193 from mvdbeek/fix_tag_filter_workflow_run_form 
[24.0] Fix submitted value in workflow run form if data is constrained by tag filter
 2024-05-23 11:31:32 +02:00
mvdbeek 6d930fdebd Include stack when reporting delete error 2024-05-23 10:47:15 +02:00
mvdbeek ccec683fb5 Add string cast for dbkey / genome_build 
pydantic v1 would automatically apply the string casting.
I've verified that we raise RequestParameterInvlalid for new requests.
 2024-05-23 10:19:57 +02:00
John Davis 89b07fa4e3 Merge pull request #18202 from jdavcs/240_ts_db_script 
[24.0] Remove legacy code, reference to sqlalchemy migrate
 2024-05-22 17:35:24 -04:00