Commit Graph

82281 Commits

Author SHA1 Message Date
John Chilton f91012244b New packages galaxy-tool-util-models, galaxy-tool-shed-schema.
The galaxy-tool-shed-schema package is basically pydantic models for the whole tool shed API. It is used by both the backend code for the new tool shed and the testing code that runs on both the old and new tool shed.

The creation of galaxy-tool-util-models package is something I've wanted to do for a while - it should solve some TODOs I've left in the base. I think beyond enabling galaxy-tool-shed-schema package - the other nice thing is that galaxy-schema code can now rely on various tool stuff without requiring dependency on any of the parser or runtime code.

This should also fix things for the new record types in #19377. I've introduced a type that can be used tools and is included schema for collection creation. The galaxy-tool-util-models packages can now be dependended on by galaxy-schema and galaxy-tool-util and these two packages do not need to depend on each other - either direction of that dependency would make me uncomfortable. xref
https://github.com/galaxyproject/galaxy/actions/runs/13704893929/job/38327692654?pr=19377
2025-04-16 12:47:37 +02:00
Marius van den Beek e8e167a8b9 Merge pull request #20020 from ahmedhamidawan/fix_keyed_cache_preventing_multiple_calls
Fix `keyedCache` never allowing multiple fetches
2025-04-16 12:43:53 +02:00
mvdbeek dc0244f66b Ensure isLoadingItem returns boolean 2025-04-16 09:24:56 +02:00
Marius van den Beek a031768f90 Merge pull request #20019 from ahmedhamidawan/merge_tabs_invocation_view
Merge Inputs/Parameters and Outputs/Collections Tabs
2025-04-16 08:54:21 +02:00
Ahmed Awan 6dd0a5d1d7 use a ref object to track requests instead of a Map 2025-04-15 20:48:18 -05:00
Ahmed Awan 30b9deb699 fix keyedCache never allowing multiple fetches
We just weren't deleting the existing promises.

Co-authored-by: Aysam Guerler <aysam.guerler@gmail.com>
2025-04-15 20:33:49 -05:00
Ahmed Awan 5b04e4da24 prevent many fetches for outputs if wf already terminal using lazy prop
Removes the `lazy` prop for inputs since ideally they don't change state and hence, don't need to be fetched everytime you switch to that tab.
2025-04-15 20:01:16 -05:00
Ahmed Awan f4ad106698 improve ParameterStep styling and convert to TS+Composition API 2025-04-15 19:09:14 -05:00
Ahmed Awan 9fc761f448 Merge Inputs/Parameters and Outputs/Collections Tabs
Fixes https://github.com/galaxyproject/galaxy/issues/20002
Fixes https://github.com/galaxyproject/galaxy/issues/20001
2025-04-15 19:06:10 -05:00
Aysam Guerler 56aa9e038b Merge pull request #20016 from mvdbeek/update_vitessce_package
Update vitessce version
2025-04-15 14:46:11 -04:00
mvdbeek 13bfe67125 Update vitessce version 2025-04-15 18:52:10 +02:00
mvdbeek 738bab5d4f Merge branch 'release_24.2' into dev 2025-04-15 18:27:11 +02:00
Marius van den Beek 0579f32671 Merge pull request #20010 from ahmedhamidawan/fix_job_states_summary_not_fetched_bug
[24.2] Ensure job states are fetched in invocation view
2025-04-15 18:21:59 +02:00
mvdbeek 29d3c23cf2 Merge branch 'release_24.2' into dev 2025-04-15 17:53:08 +02:00
Ahmed Awan 97a6ceed1a remove newHistoryTarget prop and instead check if history is different
This means that we show the little icon to switch to the history for the invocation if that history isn't current, regardless of if results were generated in a new history or not.
2025-04-15 10:13:35 -05:00
Marius van den Beek a8cf438ec5 Merge pull request #19763 from jmchilton/missing_functional_tool
Add missing test file.
2025-04-15 15:09:42 +02:00
Marius van den Beek e2647616c5 Fix typo
Co-authored-by: M Bernt <m.bernt@ufz.de>
2025-04-15 15:09:32 +02:00
Marius van den Beek 7a1ea09e9c Merge pull request #19949 from jmchilton/parameter_model_fixes_0
[24.2] Fix various parameter validation issues.
2025-04-15 15:08:28 +02:00
Marius van den Beek 3c09f7b618 Merge pull request #19688 from jmchilton/job_message_typing
Define simple models for job messages.
2025-04-15 15:07:51 +02:00
Ahmed Awan ba43210086 add jest to test new populated_state for job summary 2025-04-14 19:49:09 -05:00
Ahmed Awan 642ad39a5d use populated_state in the jobs summary to continue polling for states
As we can see this value being set in `summarize_invocation_jobs` here https://github.com/galaxyproject/galaxy/blob/4a0cca07d97d7bbd22eb39ddab38d4d4354aa4fa/lib/galaxy/managers/jobs.py#L957-L1000, `new` seems to be a non-terminal `populated_state`, meaning this summary will have updates which will eventually produce some state counts.

To fix the bug of never getting a state count for the invocation view before the scheduling state becomes terminal, we now wait for the state to be something else than `new`, and only then look for other reasons to stop polling.
2025-04-14 19:22:05 -05:00
Nicola Soranzo 1ab6a7bd0f Merge branch 'release_24.1' into release_24.2 2025-04-14 23:51:20 +01:00
Nicola Soranzo 3fe4e31108 Merge branch 'release_24.0' into release_24.1 2025-04-14 23:48:16 +01:00
Nicola Soranzo 3a7febab51 Merge branch 'release_23.2' into release_24.0 2025-04-14 23:47:33 +01:00
Nicola Soranzo a47c0df66c Merge branch 'release_23.1' into release_23.2 2025-04-14 23:46:37 +01:00
Nicola Soranzo 875866716c Merge pull request #20008 from nsoranzo/warn_redundant_casts
Enable ``warn_redundant_casts`` mypy option and drop redundant casts
2025-04-14 23:44:08 +01:00
Ahmed Awan a2dc1485c4 route to invocation on run
**For a singular invocation** (excluding cases of batch runs), we now push to the `workflows/invocations/{invocation_id}` route when the workflow is run.
Without this, we would stay on the `workflows/run` route and refreshing would take you back to the run form, instead of the invocation view.
2025-04-14 15:50:05 -05:00
Ahmed Awan 3dca5d9225 fix jobStatesSummary return type (should be allowed to return null) 2025-04-14 15:42:17 -05:00
Ahmed Awan 00aa61cbc0 [24.2] Ensure job states are fetched in invocation view
Fixes https://github.com/galaxyproject/galaxy/issues/20003

We weren't checking if the job states summary had been fetched before we had the
```
if (invocationSchedulingTerminal.value && jobCount.value === 0)
```
check. `jobCount` would always be 0 if the states summary hadn't been fetched yet.
2025-04-14 15:32:45 -05:00
John Chilton 4f65729284 Merge pull request #19898 from guerler/remove_legacy_viz_insert
Removes outdated Markdown visualization insertion wizard
2025-04-14 12:56:32 -04:00
John Chilton da81b5777d Merge pull request #19958 from guerler/markdown_editor.007
Allow resizing Visualizations in Markdown editor
2025-04-14 12:54:16 -04:00
Nicola Soranzo e9861aa672 Enable `warn_redundant_casts` mypy option and drop redundant casts 2025-04-14 16:33:35 +01:00
David López d44bac9efb Merge pull request #19992 from davelopez/24.2_fix_user_object_stores_updates
[24.2] Update selectable object stores after adding or editing them
2025-04-14 09:59:06 +02:00
Björn Grüning 9bea32e719 Merge pull request #19963 from ElectronicBlueberry/g-button-replacement-1
Button replacement batch 1
2025-04-12 12:16:36 +02:00
John Chilton bfc612e1ed Merge pull request #19962 from mvdbeek/job_cache_allow_different_names_when_possible
Job cache allow different names when possible
2025-04-11 15:58:15 -04:00
Dannon 395bcc04c3 Merge pull request #19983 from jmchilton/fix_dependencies_0
Unwind more client dependencies at top of stack.
2025-04-11 15:21:42 -04:00
Marius van den Beek fed8750d25 Merge pull request #19985 from mvdbeek/fix_collection_drag_and_drop
[24.2] Always set copy_elements to true
2025-04-11 20:57:28 +02:00
Nicola Soranzo 5c245f9431 Merge pull request #19991 from nsoranzo/type_annot_202504
Improve type annotation of tool parameter wrapping
2025-04-11 19:43:28 +01:00
Ahmed Hamid Awan b13f297167 Merge pull request #19785 from itisAliRH/g-card-initial
Introduce reusable GCard component for unified card layout
2025-04-11 21:56:53 +05:00
Dannon 0f8eb33d05 Merge pull request #19987 from dannon/wizard-rate-limit
[24.2] ChatGXY Error Handling
2025-04-11 11:59:20 -04:00
mvdbeek 4d0c507961 Test that nested collection map-over works fine with job cache 2025-04-11 16:11:49 +02:00
mvdbeek f55ae853ae Test cache with HDCA (renamed) input 2025-04-11 16:11:49 +02:00
mvdbeek 4256e1e648 Allow pulsar job runner to quit submission
if we found a cached job in job_wrapper.prepare call (i.e. we had to do
a second round of the job search where we ignore the name match
requirement).
All other runners work via tha BaseJobRunner class that already does
this.
2025-04-11 16:11:48 +02:00
mvdbeek 4a0cca07d9 Fix up hdca logic 2025-04-11 16:11:48 +02:00
mvdbeek 9589b0509a Tighten skipped job search 2025-04-11 16:11:47 +02:00
mvdbeek 9faa3657b9 Skip name match requirement for skipped jobs 2025-04-11 16:11:47 +02:00
mvdbeek 7cd1dff1cf Make job cache work for nested dces 2025-04-11 16:11:46 +02:00
mvdbeek b78f64bdb4 Don't submit job if we found cached job in second search 2025-04-11 16:11:46 +02:00
mvdbeek f1ad3488bd Fix output copying, otherwise new job elements would lose their dataset collection id 2025-04-11 16:11:45 +02:00
mvdbeek bfd3d1972a WIP: if not accessing input.name, allow input.name to differ 2025-04-11 16:11:43 +02:00