fix: Fix gene card link formatter for datavzrd report and update linkout styles

[fxwiegand]

This PR fixes an issue with jQuery not being accessible in the function by removing

$(function () {
        $('[data-toggle="tooltip"]').tooltip()
    });

which was unnecessary anyways.

Summary by CodeRabbit

• New Features

  • Enhanced visual presentation of gene card links with improved styling for tables and rows.
  • Updated header and row styles for better aesthetics and readability.

• Bug Fixes

  • Streamlined execution flow by removing unnecessary jQuery functions.

• Refactor

  • Improved structure and layout of the generated HTML for better user experience.

[coderabbitai]

Walkthrough

The changes involve a comprehensive update to the gene_card_link_formatter function in workflow/scripts/gene_card_link_formatter.js. Key modifications include the removal of the jQuery document ready function, enhancements to the visual presentation of the generated HTML table, and the introduction of new inline styles for table rows, cells, and headers. The overall structure of the HTML has been refined to improve layout aesthetics while maintaining the function's signature and return value.

Changes

File	Change Summary
workflow/scripts/gene_card_link_formatter.js	Significant modifications to the gene_card_link_formatter function, including removal of jQuery ready function, enhanced styling for table rows, cells, and headers, and overall structural improvements to the generated HTML.

Poem

In the garden where tables bloom,
Styles and colors chase away gloom.
Rows now dance with padding and cheer,
A button returns, bright and clear.
With each click, a link takes flight,
Formatting joy, a visual delight! 🐇✨

---

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

🪧 Tips

Chat

There are 3 ways to chat with CodeRabbit:

• Review comments: Directly reply to a review comment made by CodeRabbit. Example:
  • I pushed a fix in commit <commit_id>, please review it.
  • Generate unit testing code for this file.
  • Open a follow-up GitHub issue for this discussion.
• Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
  • @coderabbitai generate unit testing code for this file.
  • @coderabbitai modularize this function.
• PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
  • @coderabbitai gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.
  • @coderabbitai read src/utils.ts and generate unit testing code.
  • @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.
  • @coderabbitai help me debug CodeRabbit configuration file.

Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments.

CodeRabbit Commands (Invoked using PR comments)

• @coderabbitai pause to pause the reviews on a PR.
• @coderabbitai resume to resume the paused reviews.
• @coderabbitai review to trigger an incremental review. This is useful when automatic reviews are disabled for the repository.
• @coderabbitai full review to do a full review from scratch and review all the files again.
• @coderabbitai summary to regenerate the summary of the PR.
• @coderabbitai resolve resolve all the CodeRabbit review comments.
• @coderabbitai configuration to show the current CodeRabbit configuration for the repository.
• @coderabbitai help to get help.

Other keywords and placeholders

• Add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.
• Add @coderabbitai summary to generate the high-level summary at a specific location in the PR description.
• Add @coderabbitai anywhere in the PR title to generate the title automatically.

CodeRabbit Configuration File (.coderabbit.yaml)

• You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
• Please see the configuration documentation for more information.
• If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

• Visit our Documentation for detailed information on how to use CodeRabbit.
• Join our Discord Community to get help, request features, and share feedback.
• Follow us on X/Twitter for updates and announcements.

[coderabbitai]

Actionable comments posted: 3

🧹 Outside diff range and nitpick comments (2)

workflow/scripts/gene_card_link_formatter.js (2)

1-3: Consider adding input validation

The function assumes value will be a valid string containing comma-separated genes. Consider adding validation to handle edge cases like null, undefined, or malformed input.

 function gene_card_link_formatter(value, row) {
+    if (!value) return '';
     let genes = value.split(",");
+    genes = genes.filter(g => g.trim());  // Remove empty entries
     let rows = "";

---

12-23: Enhance accessibility and usability

1. The fixed max-height (30vh) might truncate content on smaller screens
2. Missing ARIA attributes for better screen reader support
3. Consider adding a caption or aria-label for the table

-    let table = `<div style="overflow-y: auto; max-height: 30vh; min-width: 140px;">
-                    <table style="border-collapse: collapse; width: 100%; box-shadow: 0 2px 10px rgba(0, 0, 0, 0.1);">
+    let table = `<div style="overflow-y: auto; max-height: max(30vh, 200px); min-width: 140px;">
+                    <table style="border-collapse: collapse; width: 100%; box-shadow: 0 2px 10px rgba(0, 0, 0, 0.1);"
+                           aria-label="Gene Cards References">

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 61b6005 and 33ba70b.

📒 Files selected for processing (1)

• workflow/scripts/gene_card_link_formatter.js (1 hunks)

🔇 Additional comments (1)

workflow/scripts/gene_card_link_formatter.js (1)

30-30: LGTM!

The return statement is clean and consistent.

[dlaehnemann]

LGTM. Many thanks for this cleanup!

[coderabbitai]

Actionable comments posted: 4

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 33ba70b and 7221fd3.

📒 Files selected for processing (1)

• workflow/scripts/gene_card_link_formatter.js (1 hunks)

🔇 Additional comments (1)

workflow/scripts/gene_card_link_formatter.js (1)

1-4: LGTM: Clean function structure and initialization

The function signature and initial setup are well-structured for handling multiple genes.