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Author SHA1 Message Date
Ahmed Awan 11d4a9165a [25.0] Rerun workflows for the correct version/instance 
In `GET /api/workflows/{encoded_workflow_id}/download`, for the case when `instance = True`, we were correctly obtaining the stored workflow.

However, then in `WorkflowContentsManager.workflow_to_dict` we were not considering the case that when `instance = True`, we need to not return the `latest_workflow.workflow_to_dict`, and instead return the specific workflow instance which has been specified.

We did handle the case when `version` is explicitly provided here, but not instance.

Fixes https://github.com/galaxyproject/galaxy/issues/20223
 2025-05-20 13:46:51 -05:00
Dannon de116a52f3 Merge pull request #20302 from guerler/logo_height 
[25.0] Fix logo height
 2025-05-20 09:00:34 -04:00
Marius van den Beek 118b30d5fb Merge pull request #20300 from davelopez/25.0_fix_multi_url_proxy 
[25.0] Skip multiple pasted URLs when checking for remote Zip
 2025-05-20 14:45:50 +02:00
guerler ae853e0c8b Restore previous logo height 2025-05-20 05:55:35 -04:00
davelopez 305f6b8bb0 Add unit tests for URL validation in zipExplorer 2025-05-20 11:40:59 +02:00
davelopez f5b309d23f Skip multi-line text in URL validation function 
We only support single URLs for exploring Zip contents.
 2025-05-20 11:28:38 +02:00
Dannon 900ad2fbb7 Merge pull request #20289 from ahmedhamidawan/remove_redundant_job_id_from_job_success 
[25.0] Remove duplicated job id in job success view
 2025-05-19 18:20:31 -04:00
Ahmed Awan c15404785e [25.0] Remove duplicated job id in job success view 
Fixes https://github.com/galaxyproject/galaxy/issues/20238
 2025-05-19 11:58:28 -05:00
mvdbeek a92286ba8e Merge branch 'release_24.2' into release_25.0 2025-05-19 17:00:12 +02:00
mvdbeek 957f6f5475 Merge branch 'release_24.1' into release_24.2 2025-05-19 16:54:19 +02:00
Marius van den Beek c4605dad00 Merge pull request #20239 from natefoo/fix-ucsc-display-as 
[24.1] Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL
 2025-05-19 16:52:44 +02:00
Marius van den Beek e5af55199b Merge pull request #20281 from mvdbeek/httpx 
[25.0] Add non-dev httpx dependency
 2025-05-19 16:08:16 +02:00
mvdbeek 50ec064838 Add non-dev httpx dependency 2025-05-19 15:19:33 +02:00
Martin Cech 3df96589c9 Merge branch 'release_24.2' into release_25.0 2025-05-19 12:44:44 +02:00
Martin Cech 1f7f2e7845 Merge branch 'release_24.1' into release_24.2 2025-05-19 12:44:19 +02:00
Martin Cech 4e1acd06ce Merge branch 'release_24.0' into release_24.1 2025-05-19 12:43:58 +02:00
Martin Cech faa7442ee7 Merge branch 'release_23.2' into release_24.0 2025-05-19 12:43:20 +02:00
David López 1908fbf9c0 Merge pull request #20275 from guerler/fix_theme_selector 
[25.0] Fix theme selector
 2025-05-19 12:35:00 +02:00
Martin Cech 7d4b3de58f Merge branch 'release_23.1' into release_23.2 2025-05-19 12:32:42 +02:00
Marius van den Beek e2ad28d9c8 Merge pull request #20266 from mvdbeek/extend_custom_tool_schema 
[25.0] Add more descriptions to custom tool source schema
 2025-05-19 10:45:25 +02:00
Marius van den Beek afefbbbc8a Merge pull request #20271 from guerler/tabulator.000 
[25.0] Improve handling of very large files in Tabulator
 2025-05-18 10:41:24 +02:00
Ahmed Hamid Awan 7e9cf090dc Merge pull request #20277 from guerler/fix_headers 
[25.0] Fix inconsistent header sizes
 2025-05-18 02:56:44 +05:00
guerler 1ec265d1bd Adjust Workflow and other BreadCrumbHeaders for consistency 2025-05-17 16:47:45 -04:00
guerler 9184d515e4 Adjust notifications header button for consistency 2025-05-17 16:36:46 -04:00
guerler 2113c6e3cb Unify header size across user interface for consistency 2025-05-17 16:33:39 -04:00
guerler b164d346cd Fix theme selectors computed value getter 2025-05-17 14:21:39 -04:00
guerler 9ddaff343f Update tabulator version, improve handling of very large files 
Use Math.ceil when determining page count
 2025-05-17 13:04:23 -04:00
mvdbeek 0e13bacee5 Provide more field annotations 2025-05-17 18:58:15 +02:00
Ahmed Hamid Awan ceaf544668 Merge pull request #20267 from ahmedhamidawan/version-25.0.rc1 
[25.0] Update version to 25.0.rc1
 2025-05-16 23:05:57 +05:00
Ahmed Awan 669e4d54f5 Update version to 25.0.rc1 2025-05-16 12:07:36 -05:00
Ahmed Hamid Awan 4d1da5acac Merge pull request #20265 from ahmedhamidawan/dev_250_migrationtags 
Add 25.0 migration tags
 2025-05-16 21:51:35 +05:00
mvdbeek e2678e7088 Upgrade monaco-yaml 2025-05-16 18:46:13 +02:00
Ahmed Awan db80c5c03e Add 25.0 migration tags 2025-05-16 11:45:19 -05:00
Marius van den Beek dcfa9bb8cd Merge pull request #20260 from common-workflow-lab/metadata-CONVERTER_tar_to_directory 
Fix tool-provided metadata for CONVERTER_tar_to_directory
 2025-05-16 16:52:32 +02:00
mvdbeek a4bad06a06 Merge branch 'release_24.2' into dev 2025-05-16 16:24:49 +02:00
mvdbeek 2156e2d98e Merge branch 'release_24.1' into release_24.2 2025-05-16 16:23:56 +02:00
mvdbeek 9a0d482f1a Merge branch 'release_24.0' into release_24.1 2025-05-16 16:23:36 +02:00
Marius van den Beek 36ea7dadde Merge pull request #20259 from mvdbeek/fix_rerun_button_dynamic_tools 
Fix job rerun for dynamic tools
 2025-05-16 16:23:08 +02:00
Marius van den Beek 400a9f605b Merge pull request #20258 from mvdbeek/fix_job_summary 
[24.0] Fall back to name in job summary if no input label given
 2025-05-16 16:22:52 +02:00
Nicola Soranzo 663c08aec4 Fix tool-provided metadata for CONVERTER_tar_to_directory 
The metadata are in the "default" (not "legacy") format, so need to
use a newer tool profile.

Also:
- Use CDATA and `&&` in command
 2025-05-16 15:13:16 +02:00
Dannon 45fdb1de97 Merge pull request #20244 from dannon/group-it-versions 
[25.0] Group Tool Versions in IT Panel
 2025-05-16 07:40:02 -04:00
Marius van den Beek f87df96220 Merge pull request #20247 from mvdbeek/fix_activity_bar_in_setting 
Only show custom tool editor in activity bar settings when user has access
 2025-05-16 12:18:39 +02:00
mvdbeek 3eaa78b745 Fix job rerun for dynamic tools 
Fixes https://github.com/galaxyproject/galaxy/issues/20255
 2025-05-16 12:17:42 +02:00
mvdbeek 65df554439 Fall back to name in job summary if no input label given 2025-05-16 11:07:41 +02:00
mvdbeek 82e700dab1 Don't show user-defined-tools in activity bar settings if user doesn't have access 2025-05-16 11:06:37 +02:00
Marius van den Beek fdeb70dc8e Merge pull request #20245 from dannon/vue-tsc-again 2025-05-16 09:06:40 +02:00
Dannon Baker cf7091f9c7 Fix vue-tsc issue in ParameterStep; ensure items have valid IDs before rendering 2025-05-15 20:52:22 -04:00
Dannon Baker 4eb42ae8ce Additional tests including running IT display for InteractiveToolsPanel. 2025-05-15 18:02:11 -04:00
Dannon Baker 8935ae6d66 Refactoring tool-version handling into a separate util 2025-05-15 17:20:29 -04:00
Dannon Baker d906996de8 Fix version filtering logic in InteractiveToolsPanel to handle version suffixes and improve test coverage 2025-05-15 17:20:29 -04:00