Add visualization framework interface to cell-based markdown editor#19775
Add visualization framework interface to cell-based markdown editor#19775guerler merged 27 commits intogalaxyproject:devfrom
Conversation
faca1f8 to
a775454
Compare
8e5a464 to
3a20af6
Compare
9db1a84 to
f76c386
Compare
f76c386 to
60c88eb
Compare
d6786c3 to
c27bdee
Compare
|
Thanks for your detailed response on #19226 (comment) - I hadn't seen that until just now. Umm... I think you've addressed my concerns well enough - I still wish we had generic components for a set of charts even if ad hoc plugins are needed generally... but also you're right that these plugins are packaged and installed in a much more robust and forward/backward compatible way than they used to be and maybe this is enough and enough for now. I think this PR is really beautiful and exciting. |
|
|
||
| # Matches blocks of various types | ||
| GALAXY_FENCED_BLOCK = re.compile(r"^```\s*galaxy\s*(.*?)^```", re.MULTILINE | re.DOTALL) | ||
| VISUALIZATION_FENCED_BLOCK = re.compile(r"^```\s*visualization+\n\s*(.*?)^```", re.MULTILINE | re.DOTALL) |
There was a problem hiding this comment.
Given that galaxy encompasses all sorts of kinds of plugins - it seems disjoint that visualization is sort of standalone - wouldn't this syntax feel more internally consistent if it was galaxy_visualization as the syntax marker. It is a small point though - I think this could be fine despite the brain scratch it gives me.
There was a problem hiding this comment.
Good point — but I think visualization is better here since we don’t actually use any galaxy_-prefixed namespaces elsewhere. That said, I’m open to changing it in a follow-up if it keeps feeling off.
|
@jmchilton thank you so much for your review! |
Requires #19835. See discussion regarding visualizations in pages in #19226.
This PR integrates an interface for our new visualization framework into the cell-based Markdown editor. Only fully packaged, standalone visualizations—published as npm packages in accordance with our new framework—can be used in pages and reports. This ensures stability, preventing visualizations from breaking due to Galaxy updates or build system limitations. Additionally, this PR enables the cell-based Markdown editor for workflow reports and lays the groundwork for workflow-specific visualizations by integrating Vega and Vitessce cell/block types.
Usage in Pages (with preview):
Screen.Recording.2025-03-19.at.7.01.45.PM.mov
Usage in Workflow Reports (without preview):
Screen.Recording.2025-03-20.at.9.43.16.AM.mov
How to test the changes?
(Select all options that apply)
License