Remove legacy Visualization Mako and Controllers #21133

guerler · 2025-10-22T09:11:44Z

Requires #21106. Removes legacy template-based visualization framework components, including visualization Mako templates and legacy visualization controller endpoints. With the addition of IGV, the removal of Trackster became possible, which in turn made visualizations fully API-driven and rendered entirely client-side, eliminating all server-side Mako dependencies. This resolves inconsistencies and enables the addition of new features to the visualization framework.

After this PR, the remaining makos in the Galaxy app that still need to be migrated are:

build_from_current_history.mako
copy_view.mako (WIP: Remove copy dataset mako #17507)
display.mako (WIP: Refactor display application handling #15076)
tool_runner.mako (WIP: Remove Tool Runner mako #21235)

Then we can finalize this project by moving the bootstrapping as outlined in #21153, making the Galaxy App mako-free.

How to test the changes?

(Select all options that apply)

I've included appropriate automated tests.
This is a refactoring of components with existing test coverage.
Instructions for manual testing are as follows:
1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

davelopez

Looks good from my limited knowledge of these components 👍
Some minor comments below.

lib/galaxy/visualization/plugins/plugin.py

lib/galaxy/visualization/plugins/registry.py

client/src/components/Markdown/Sections/VisualizationWrapper.vue

lib/galaxy/visualization/plugins/registry.py

lib/galaxy/visualization/plugins/plugin.py

lib/galaxy/visualization/plugins/registry.py

test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py

…ionWrapper

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>

…ry.py Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>

test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py

guerler · 2025-11-01T11:18:50Z

Remaining test failures are unrelated.

Updates the VisualizationWrapper component to define props using the `interface` and `defineProps` approach for improved type safety and readability.

Refactors the VisualizationDisplay component to improve code readability and maintainability.

Improves type safety and code clarity by defining interfaces for props and emits in the VisualizationFrame component. This change ensures that the component's properties and emitted events are strongly typed, reducing the risk of runtime errors and improving maintainability.

itisAliRH

Thank you @guerler! Works well for me.
I made some small changes.

guerler · 2025-11-03T16:00:27Z

Thank you so much for the review and help! 🙏

guerler added this to the 26.0 milestone Oct 22, 2025

guerler added area/UI-UX kind/refactoring cleanup or refactoring of existing code, no functional changes labels Oct 22, 2025

guerler force-pushed the remove_visualization_mako branch 2 times, most recently from c056cb8 to 8417c7c Compare October 22, 2025 15:41

guerler marked this pull request as ready for review October 23, 2025 06:57

guerler marked this pull request as draft October 23, 2025 08:57

guerler marked this pull request as ready for review October 23, 2025 14:20

guerler force-pushed the remove_visualization_mako branch from 358fb47 to 1e26e13 Compare October 23, 2025 19:16

guerler requested a review from itisAliRH October 23, 2025 19:19

guerler force-pushed the remove_visualization_mako branch from 0aad49e to 575f997 Compare October 27, 2025 11:24

guerler mentioned this pull request Oct 28, 2025

Move js-client bootstrapping to FastAPI #21153

Open

guerler requested a review from jmchilton October 28, 2025 08:02

guerler force-pushed the remove_visualization_mako branch 2 times, most recently from ae2a63f to 90105d4 Compare October 29, 2025 11:37

guerler requested a review from davelopez October 30, 2025 15:03

guerler force-pushed the remove_visualization_mako branch from b9d1bae to 2129a53 Compare October 30, 2025 17:46

davelopez reviewed Oct 31, 2025

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nsoranzo reviewed Oct 31, 2025

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nsoranzo reviewed Oct 31, 2025

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guerler added 9 commits October 31, 2025 18:19

Switch from VisualizationFrame with backend mako to client Visualizat…

dba1060

…ionWrapper

Switch to VisualizationWrapper

ce6f775

Dump legacy saved visualization controller endpoint

5f31037

Remove visualization rendering controller

a3d47dc

Remove rendered_saved from visualization framework

d672442

Remove server side rendering from visualization framework

e80f8d6

Remove mako based visualization layer from visualization framework

a716dfd

Remove visualization mako

f177a67

Keep href for now

072a845

guerler and others added 6 commits October 31, 2025 18:20

Update lib/galaxy/visualization/plugins/plugin.py

5dfd6d3

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>

Update test/unit/app/visualizations/plugins/test_VisualizationsRegist…

34ae6bc

…ry.py Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>

Update test/unit/app/visualizations/plugins/test_VisualizationsRegist…

3d61ead

…ry.py Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>

Update test/unit/app/visualizations/plugins/test_VisualizationsRegist…

a4d79cd

…ry.py Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>

Add typing import to registry.py

48da2bb

Add conditional StructuredApp import after last import

f534435

guerler force-pushed the remove_visualization_mako branch from 894ed2a to f534435 Compare October 31, 2025 15:20

nsoranzo reviewed Oct 31, 2025

View reviewed changes

test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py Show resolved Hide resolved

Remove template_cache_dir from test

8764d75

nsoranzo reviewed Oct 31, 2025

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guerler added 2 commits October 31, 2025 18:28

Apply additional StructuredApp mocking

e571dcd

Add explicit typing to plugins

c8a0827

nsoranzo reviewed Oct 31, 2025

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test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py Outdated Show resolved Hide resolved

Properly pass title prop to frame component

973b6d5

nsoranzo reviewed Oct 31, 2025

View reviewed changes

test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py Outdated Show resolved Hide resolved

Restore root and plugin path

fdf6013

guerler force-pushed the remove_visualization_mako branch from f442b4b to fdf6013 Compare October 31, 2025 15:55

guerler mentioned this pull request Nov 1, 2025

Consolidate Dataset State Display #21231

Draft

4 tasks

guerler mentioned this pull request Nov 1, 2025

Refactor display application handling #15076

Draft

4 tasks

guerler and others added 6 commits November 2, 2025 21:28

Use visualization frame for published visualizations

4e1b346

Add explicit types to refs in visualization display

a449af1

Add visualization config condition

14d9568

Refactors VisualizationWrapper props definition

51abfe9

Updates the VisualizationWrapper component to define props using the `interface` and `defineProps` approach for improved type safety and readability.

Improves VisualizationDisplay component

9966d69

Refactors the VisualizationDisplay component to improve code readability and maintainability.

itisAliRH approved these changes Nov 3, 2025

View reviewed changes

guerler merged commit 3730e0b into galaxyproject:dev Nov 3, 2025
61 of 65 checks passed

guerler deleted the remove_visualization_mako branch November 3, 2025 15:59

Remove legacy Visualization Mako and Controllers #21133

Remove legacy Visualization Mako and Controllers #21133

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guerler commented Oct 22, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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guerler commented Oct 22, 2025 •

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