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Author SHA1 Message Date
M BerntandNicola Soranzo 8a87d75b8d reformulation 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2023-11-24 16:24:33 +01:00
Matthias Bernt 16b2bf20b2 add docs for tool panel and panel view administration 2023-11-24 12:37:55 +01:00
Laila Los 788050d042 Merge pull request #17057 from guerler/grid_use_debounce 
Use debounce instead of timeout utility
 2023-11-21 14:56:34 +01:00
Marius van den Beek a758757551 Merge pull request #17056 from mvdbeek/dev 
Merge release_23.1 into dev
 2023-11-21 13:49:08 +01:00
Marius van den Beek 1181e7dde2 Merge pull request #17055 from bernt-matthias/topic/quote-singularity-env-params 
Quote singularity env parameters
 2023-11-21 09:48:45 +01:00
mvdbeek 686ec6fac4 Merge branch 'release_23.1' into dev 2023-11-21 09:36:51 +01:00
guerler d170374e9e Add grid list message hiding test case 2023-11-21 10:26:59 +03:00
guerler adefcb2989 Remove custom timeout utility 2023-11-21 09:47:10 +03:00
guerler 5948224c54 Hide grid message using debounce instead of custom timeout helper 2023-11-21 09:46:35 +03:00
Laila Los c88fa03833 Merge pull request #17053 from dannon/axios-16 
Upgrade axios to 1.6.2
 2023-11-21 00:12:37 +01:00
John Davis 36fc64ae3f Merge pull request #17025 from SergeyYakubov/optimize-object-store-pull 
optimize object store cache operations
 2023-11-20 10:47:37 -05:00
Matthias Bernt a0f0b83c1d quote singularity env parameters 
destination parameters that contain spaces, e.g.

```
<param id="singularity_env__JAVA_OPTIONS">-Xmx61g -Xms256m</param>
```

need quoting.
 2023-11-20 15:01:51 +01:00
Marius van den Beek 46595468fa Merge pull request #17048 from mvdbeek/prevent_workflow_submission_missing_input_value 
[23.1] Prevent workflow submission with missing input values
 2023-11-20 14:40:19 +01:00
Dannon Baker b67a32f270 Upgrade axios to 1.6.2 2023-11-20 07:44:35 -05:00
Dannon ddd2157c82 Merge pull request #17049 from davelopez/23.1_fix_broadcast_filtering_for_admins 
[23.1] Fix filtering of active broadcasts for admins
 2023-11-20 07:40:02 -05:00
Dannon 1666892918 Merge pull request #16892 from guerler/grids_vue 
Vueify Visualizations Grid
 2023-11-20 07:38:20 -05:00
mvdbeek 35c18ff7b0 Add test case 2023-11-20 13:20:10 +01:00
Nicola Soranzo 05fe2868f3 Merge pull request #17050 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2023-11-19 14:01:24 +00:00
galaxybot 0c081b1e91 Update Python dependencies 2023-11-18 03:11:31 +00:00
mvdbeek da127b5b83 Disallow empty inputs on required input parameters in simplified workflow form 
This is another attempt at
https://github.com/galaxyproject/galaxy/issues/13220, but taking into
account
https://github.com/galaxyproject/galaxy/issues/13220#issuecomment-1068054414
by limiting this to the simplified workflow form, where we can assume
input parameter optionality to have the correct meaning.

This makes it harder to submit a mandatory text parameter that can be
empty, but that is (at this point at least) a very fringe requirement.

If really needed you can make the parameter optional (and use pick_value
to fill in an empty string if null is not OK as a value).
 2023-11-17 18:32:44 +01:00
Yakubov, Sergey 892c9b1888 document object store cache configuration 2023-11-17 12:23:29 -05:00
Yakubov, Sergey 59be4046a9 comment changes to irods force write option 2023-11-17 12:13:49 -05:00
David López 257c2bb52c Merge pull request #17043 from ahmedhamidawan/open_history_storage_in_analysis 
Open `HistoryStorageOverview` in center panel from `HistoryPanel`
 2023-11-17 18:08:40 +01:00
Yakubov, Sergey b342f4ccb6 rename _sync_cache -> sync_cache 2023-11-17 12:08:28 -05:00
davelopez 8d514b1c3b Add tests for expired and unpublished broadcasts 2023-11-17 17:52:53 +01:00
davelopez c03eda8425 Fix filtering of active broadcasts 
Admin users get all the broadcasts notifications regardless of their "activation" status so we need to apply the filtering also in the client.

Regular users are not affected because they can only get active broadcasts.
 2023-11-17 17:47:00 +01:00
Martin Cech 8806d60b89 Merge pull request #17038 from ahmedhamidawan/workflow_editor_require_name 
Require name for workflows on save, set default to Unnamed Workflow
 2023-11-17 17:08:00 +01:00
John Chilton e5d37d48d3 Merge pull request #17036 from jmchilton/tool_panel_fixes 
[23.1] Fix duplicated tools in tool panel view section copying
 2023-11-17 10:38:02 -05:00
mvdbeek 26573dd7ed Prevent workflow submission with validation errors 
And disable submit button when request is being handled.
 2023-11-17 15:52:10 +01:00
David López fc01188332 Merge pull request #17032 from ElectronicBlueberry/notification-style 
Change Broadcast Notifications Style
 2023-11-17 13:14:39 +01:00
Laila Los aac6aa548e makeCompareFn anti-symmetric 2023-11-17 11:53:26 +01:00
Ahmed Awan e5ce95d6a2 Open HistoryStorageOverview in center panel from HistoryPanel 
Previously, if we clicked the History storage button for the current
history in the `HistoryPanel`, it took over the whole screen because
the `StorageDashboardRoutes` are not children of the `Analysis`
route.

Changed it so the `HistoryStorageOverview` route opens in the
center panel as an `Analysis` route (only from the `HistoryPanel`,
otherwise, it is still opened as one of the `StorageDashboardRoutes`)

Fixes https://github.com/galaxyproject/galaxy/issues/17026
 2023-11-16 20:06:56 -06:00
Ahmed Awan 3da9c41434 add api test for update workflow with empty name 2023-11-16 14:47:44 -06:00
guerler 8e23476a70 Fix typing warnings 2023-11-16 22:02:07 +03:00
Ahmed Awan ea8cffde35 backend: throw error if name is empty for PUT /api/workflows/{id} 
This is handled at the frontend in the editor to prevent this,
but still add additional checks in backend
 2023-11-16 12:39:04 -06:00
Yakubov, Sergey d0eef6ab3e use cache_updated_data=True for s3 tests 2023-11-16 13:22:09 -05:00
mvdbeek 3e13db9ee5 Ensure we're not allowing None as non-optional workflow input 2023-11-16 18:38:30 +01:00
guerler 3039faad7b Use IconDefinition instead of IconProp 2023-11-16 19:55:52 +03:00
guerler 3a54fdfc45 Remove unused shareindicator component section for now 2023-11-16 19:42:29 +03:00
Dannon 19b0ffde46 Merge pull request #17015 from ElectronicBlueberry/multiselect-style 
Restyle Vue Multiselect and Adapt Option Order
 2023-11-16 11:07:02 -05:00
Laila Los c90dfccc68 add tests for sorting and carousel 2023-11-16 17:04:48 +01:00
Laila Los a36b049d19 make urgent stand out more 
fix action links don't wrap on small screens
 2023-11-16 16:51:01 +01:00
Sergey YakubovandJohn Davis d930fc638d update comment about file check for cloud object store 
Co-authored-by: John Davis <jdavcs@gmail.com>
 2023-11-16 10:25:49 -05:00
Yakubov, Sergey 9858c5971b irods - download file even if already in cache 2023-11-16 10:11:50 -05:00
mvdbeek 0e142414cd Exclude multiple_versions from test_global_filters_on_integrated_panel 2023-11-16 15:08:21 +01:00
mvdbeek ca5fce7566 Test tool shed version as well 2023-11-16 05:52:30 -05:00
mvdbeek c3dc92b463 Test that only latest version is loaded 2023-11-16 05:52:19 -05:00
John Chilton f36b8474a3 Comment about new bug discovered. Lower priority though right? 
Come back and fix it in dev?
 2023-11-16 05:51:03 -05:00
Marius van den Beek e340737a3e Merge pull request #17037 from dannon/no-more-eventhub 
Remove eventHub custom module, swap to appropriate alternatives.
 2023-11-16 11:23:11 +01:00
Marius van den Beek 427677a540 Merge pull request #16988 from mvdbeek/warning_for_duplicate_log_files 
[23.1] Change log level for duplicate data table entries to warning
 2023-11-16 11:17:10 +01:00