Feat delete#96
Conversation
|
Warning Rate limit exceeded
Your organization is not enrolled in usage-based pricing. Contact your admin to enable usage-based pricing to continue reviews beyond the rate limit, or try again in 42 minutes and 27 seconds. ⌛ How to resolve this issue?After the wait time has elapsed, a review can be triggered using the We recommend that you space out your commits to avoid hitting the rate limit. 🚦 How do rate limits work?CodeRabbit enforces hourly rate limits for each developer per organization. Our paid plans have higher rate limits than the trial, open-source and free plans. In all cases, we re-allow further reviews after a brief timeout. Please see our FAQ for further information. ℹ️ Review info⚙️ Run configurationConfiguration used: Organization UI Review profile: CHILL Plan: Pro Run ID: 📒 Files selected for processing (1)
📝 WalkthroughWalkthroughUpdated the Cytoscape network widget's JavaScript to add edge deletion functionality via right-click or Ctrl+Click. Introduced a Changes
Sequence DiagramsequenceDiagram
participant User
participant Cytoscape as Cytoscape<br/>(Frontend)
participant Shiny as Shiny<br/>(Backend)
alt Right-Click or Ctrl+Click
User->>Cytoscape: cxttap event on edge
Cytoscape->>Cytoscape: deleteEdge(edge)
Cytoscape->>Shiny: Send input event<br/>(edge_deleted)
Shiny->>Shiny: Process deletion event
Cytoscape->>Cytoscape: Remove edge from graph
else Plain Click
User->>Cytoscape: tap event on edge
Cytoscape->>Shiny: Send input event<br/>(edge_clicked)
Cytoscape->>User: Open evidence link
end
Estimated code review effort🎯 2 (Simple) | ⏱️ ~10 minutes Possibly related PRs
Poem
🚥 Pre-merge checks | ✅ 2 | ❌ 1❌ Failed checks (1 inconclusive)
✅ Passed checks (2 passed)
✏️ Tip: You can configure your own custom pre-merge checks in the settings. ✨ Finishing Touches🧪 Generate unit tests (beta)
Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out. Comment |
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 2
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Inline comments:
In `@inst/htmlwidgets/cytoscapeNetwork.js`:
- Around line 459-462: The delete-edge interaction path currently calls
deleteEdge(edge) and returns without updating the legend; add a call to
buildLegend() immediately after deleteEdge(edge) (before the return) so the
legend is rebuilt from the updated cy.edges() when an edge is removed (same
branch handling evt.type === "cxttap" or evt.originalEvent.ctrlKey). Ensure you
reference the existing deleteEdge and buildLegend functions so the legend
refresh happens as part of the same interaction flow.
- Around line 454-461: The current combined event handler (cy.on("cxttap tap",
"edge", ...)) returns early for edges with edge.data("edge_type") ===
"ptm_attachment", preventing the delete branch from ever running; remove that
early return and instead only skip PTM edges in the evidence-link-specific code
path so ptm_attachment edges can still be deleted via the Ctrl+Click/right-click
branch (keep references to the existing cy.on handler and deleteEdge(edge) call
and move the ptm_attachment check into the evidence-link/evidence-link-handling
block).
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
⚙️ Run configuration
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
Run ID: 1452d959-8410-475d-871e-1ea19cd48597
📒 Files selected for processing (1)
inst/htmlwidgets/cytoscapeNetwork.js
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## devel #96 +/- ##
=======================================
Coverage 76.79% 76.79%
=======================================
Files 8 8
Lines 1030 1030
=======================================
Hits 791 791
Misses 239 239 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
2 participants
Motivation and Context
The PR adds interactive edge deletion functionality to the Cytoscape network visualization widget. Users can now remove edges (connections between proteins) directly from the network by right-clicking or using Ctrl+Click, enabling dynamic network refinement and exploration. The feature maintains backward compatibility by keeping plain left-click behavior for opening evidence links.
Solution Summary
The implementation introduces a
deleteEdge()helper function in the JavaScript widget that removes edges from the graph and notifies the R/Shiny server of deletions. The event handler logic was refactored to support both deletion (right-click/Ctrl+Click) and navigation (plain click) actions on edges, with the "prevent default" behavior removed as indicated in the commit message.Detailed Changes
deleteEdge(edge)helper function that:${el.id}_edge_deletedcontaining the deleted edge'ssource,target, andinteractionproperties when Shiny is availabletaphandler to combined"cxttap tap"handler:deleteEdge()${el.id}_edge_clickedeventTesting
No new unit tests have been added or modified to verify the edge deletion functionality. The existing test file
tests/testthat/test-utils_cytoscapeNetwork.Rdoes not include tests for the JavaScript widget's interactive features or the new deletion capability.Coding Guidelines
The implementation adheres to the existing code standards: