 John Chilton
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fef8341023
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Merge pull request #18230 from mvdbeek/exception_handling_fetch_invalid_url
[24.0] Raise ``RequestParameterInvalidException`` if url can't be verified
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2024-05-27 09:41:24 -04:00 |
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mvdbeek
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30b1f4b2f9
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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"`.
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2024-05-27 09:54:09 +02:00 |
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Marius van den Beek
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d8b827f50e
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Merge pull request #17818 from martenson/noexpand-private
[24.0] do not expand datasets that are known to be inaccessible
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2024-05-25 15:53:03 +02:00 |
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Marius van den Beek
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ae9ea865e1
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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
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2024-05-24 16:02:33 +02:00 |
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davelopez
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0104764bb8
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Make accessible optional in HDAObject
It is probably enough to serialize the `accessible` property only when requesting collection contents displayed in the UI.
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2024-05-24 13:43:33 +02:00 |
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davelopez
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810b246fbf
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Avoid requesting details for inaccessible datasets
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2024-05-24 11:09:59 +02:00 |
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davelopez
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a0adf7e76b
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Add missing event declaration
Fixes typescript error:
Argument of type '"edit"' is not assignable to parameter of type '"toggleHighlights"'
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2024-05-24 10:53:00 +02:00 |
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davelopez
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afac2afa24
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Serialize accessible field for collection elements
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2024-05-24 10:50:08 +02:00 |
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davelopez
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7961b475bb
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Fix bool const OpenAPI TS schema conversion
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2024-05-24 10:47:32 +02:00 |
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Marius van den Beek
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21a427213d
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Merge pull request #18217 from mvdbeek/tighten_job_access
[24.0] Restrict job_files access to jobs that are not terminal
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2024-05-24 09:00:56 +02:00 |
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Nicola Soranzo
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7ab747506a
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Merge pull request #18192 from ahmedhamidawan/prevent_anon_users_run_workflow
[24.0] Prevent anonymous and inactive users from running workflows
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2024-05-23 23:28:33 +01:00 |
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mvdbeek
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4e47b8de13
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Restrict job_files access to jobs that are not terminal
That should fix https://sentry.galaxyproject.org/share/issue/c4eb157823c240d5a664ec6517354db2/
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2024-05-23 23:11:38 +02:00 |
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John Davis
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1c11fe13ea
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Merge pull request #18215 from jdavcs/240_ts_db_script
[24.0] Use config_section to distinguish between galaxy and ts or other apps
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2024-05-23 15:40:28 -04:00 |
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Martin Cech
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1e59ea48b7
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Merge pull request #18212 from nsoranzo/release_24.0_backport_18197
[24.0] Backport #18197
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2024-05-23 21:03:53 +02:00 |
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John Davis
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a047ea0861
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Use config_section to distinguish between galaxy and ts or other apps
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2024-05-23 14:34:10 -04:00 |
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Dannon
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2ddea78aef
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Merge pull request #18203 from ahmedhamidawan/fix_content_item_on_error
[24.0] Add `GenericItem` error handling
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2024-05-23 13:58:51 -04:00 |
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mvdbeek
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59803e968e
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Check dataset state when attempting to acces dataset contents
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2024-05-23 18:45:13 +02:00 |
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Ahmed Hamid AwanandNicola Soranzo
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538570b3e2
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Update lib/galaxy/webapps/galaxy/services/workflows.py
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
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2024-05-23 11:05:41 -05:00 |
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Ahmed Hamid AwanandMarius van den Beek
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cef091bcd1
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Update client/src/components/History/Content/GenericItem.vue
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
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2024-05-23 11:00:37 -05:00 |
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Ahmed Awan
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1e94915c98
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add titles to Toasts for GenericItem
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2024-05-23 10:34:59 -05:00 |
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Nicola Soranzo
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9b70b7582d
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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 .
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2024-05-23 16:09:31 +01:00 |
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Nicola Soranzo
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028630afcb
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Update syntax for labeler action v5
See https://github.com/marketplace/actions/labeler#breaking-changes-in-v5
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2024-05-23 16:09:22 +01:00 |
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Nicola Soranzo
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b19136073e
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Use official minikube GitHub action
Cannot used the new default driver (`docker`) as it crashes the
PostgreSQL Docker container started via job services.
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2024-05-23 16:07:25 +01:00 |
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Nicola Soranzo
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de2d36afe2
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Update versions of GitHub actions
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2024-05-23 16:06:43 +01:00 |
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Nicola Soranzo
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4c4ed106a4
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Use job permissions instead of token
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2024-05-23 16:06:21 +01:00 |
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John Chilton
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37aeadd146
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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
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2024-05-23 09:10:36 -04:00 |
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Dannon
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326e29158f
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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
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2024-05-23 09:09:50 -04:00 |
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mvdbeek
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15fa3a43f7
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Fix display of error messages in visualizations
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2024-05-23 13:18:20 +02:00 |
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mvdbeek
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8fcc151f6f
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Limit templated visualization data, fix PCA plot for tabular datasets
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2024-05-23 13:18:20 +02:00 |
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Marius van den Beek
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3a89e74019
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Merge pull request #18194 from ahmedhamidawan/replace_multiselect_label_with_icon
[24.0] Replace `Multiselect` `selectLabel` with icons in `FormSelect`
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2024-05-23 11:48:36 +02:00 |
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Marius van den Beek
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825a045b0a
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Merge pull request #18208 from mvdbeek/exc_info_in_object_store_delete
[24.0] Include stack when reporting delete error
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2024-05-23 11:48:08 +02:00 |
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Marius van den Beek
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921f181510
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Merge pull request #18207 from mvdbeek/fix_genome_build_int
[24.0] Add string cast for dbkey / genome_build
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2024-05-23 11:47:06 +02:00 |
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Marius van den Beek
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154aaa162d
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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
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2024-05-23 11:31:32 +02:00 |
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mvdbeek
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6d930fdebd
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Include stack when reporting delete error
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2024-05-23 10:47:15 +02:00 |
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mvdbeek
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ccec683fb5
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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.
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2024-05-23 10:19:57 +02:00 |
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John Davis
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89b07fa4e3
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Merge pull request #18202 from jdavcs/240_ts_db_script
[24.0] Remove legacy code, reference to sqlalchemy migrate
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2024-05-22 17:35:24 -04:00 |
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Ahmed Awan
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09a91e0749
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[24.0] Add GenericItem error handling
`GenericItem` was missing a `onError` function. Now, it catches backend errors and displays a `Toast` message for any failed operation.
Fixes https://github.com/galaxyproject/galaxy/issues/18176
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2024-05-22 15:06:15 -05:00 |
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John Davis
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04e77ef134
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Remove legacy ref to sqlalchemy migrate
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2024-05-22 14:57:53 -04:00 |
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Ahmed Awan
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f516679399
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add api test for running workflow as anon user
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2024-05-22 13:47:19 -05:00 |
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Ahmed Awan
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d0e460cb40
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[24.0] Prevent anonymous users from running workflows
Fixes https://github.com/galaxyproject/galaxy/issues/18147
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2024-05-22 12:36:45 -05:00 |
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Ahmed Awan
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659c2fa3e1
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fix jests since each option is in a div instead of a span
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2024-05-22 12:24:23 -05:00 |
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Marius van den Beek
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eef864ae9b
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Merge pull request #18200 from davelopez/24.0_fix_make_private_immutable
[24.0] Fix `make all histories private` with immutable histories
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2024-05-22 16:52:57 +02:00 |
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davelopez
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ec2bd51374
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Remove unnecessary catch all
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2024-05-22 15:22:46 +02:00 |
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mvdbeek
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ab2086d5dd
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Also filter out matchedValues using tags
This now matched the filter in formattedOptions, so that upon first
rendering there's no discrepancy with currentValue.
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2024-05-22 15:14:12 +02:00 |
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mvdbeek
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d33b0d783c
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Fix Select value prop type
Can be string or array
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2024-05-22 15:14:01 +02:00 |
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mvdbeek
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bec8f0cd34
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Add selenium test that fails because wrong dataset is submitted
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2024-05-22 15:14:01 +02:00 |
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davelopez
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c1a8fd4895
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Drop redundant check after setting dataset permissions
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2024-05-22 14:58:42 +02:00 |
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davelopez
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f3c63541c6
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Allow to make private purged and archived histories
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2024-05-22 12:20:49 +02:00 |
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davelopez
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994be2f49a
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Do not fail hard when one history fails to be made private
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2024-05-22 11:59:00 +02:00 |
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davelopez
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4e03914bcc
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Raise appropriate API exceptions in history controller
Instead of the legacy ones.
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2024-05-22 11:49:27 +02:00 |
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