Minor refinements in the links checking

[ypriverol]

Summary by CodeRabbit

• Navigation Updates

  • Repositioned Template Builder link to appear earlier in the navigation menu across all pages
  • Removed Dev Version navigation item

• Data Corrections & Standardization

  • Standardized SDRF dataset entries including organism names, disease classifications, instruments, and acquisition methods for consistency
  • Updated dataset metadata timestamp

[coderabbitai]

Caution

Review failed

The pull request is closed.

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: cbb7c314-76bd-4f65-a996-40a8401506d4

📥 Commits

Reviewing files that changed from the base of the PR and between 241e4a1 and 3b4bb1b.

⛔ Files ignored due to path filters (1)

• psi-document/sdrf-proteomics-specification-v1.1.0-dev.pdf is excluded by !**/*.pdf

📒 Files selected for processing (8)

• .lycheeignore
• scripts/inject-headers.py
• site/index.html
• site/quickstart.html
• site/sdrf-builder.html
• site/sdrf-data.json
• site/sdrf-explorer.html
• site/sdrf-terms.html

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📝 Walkthrough

Walkthrough

Reordered navigation links across multiple HTML pages and the header-injection script; updated .lycheeignore with additional entries and a relaxed ASCIIDoc-link regex; applied extensive SDRF JSON normalization including timestamp, capitalization, ordering, and instrument/disease list updates.

Changes

Cohort / File(s)	Summary
Lychee Configuration \.lycheeignore	Added CHANGELOG.md and LICENSE to ignore list; added .*\[.*$ regex to also match incomplete ASCIIDoc link syntax while keeping the existing complete-bracket rule.
Header Injection Script scripts/inject-headers.py	Reordered static navigation header templates/current-item markers across pages (moved Template Builder earlier); no runtime/injection logic changes.
Site Navigation HTML site/index.html, site/quickstart.html, site/sdrf-builder.html, site/sdrf-explorer.html, site/sdrf-terms.html	Moved "Template Builder" link to appear after "Templates" (before Tools); removed "Dev Version" from index; active nav classes updated to match new ordering.
SDRF Data site/sdrf-data.json	Large normalization: updated generated_at timestamp; standardized capitalization and canonicalization of organisms, diseases, instruments, acquisition methods; added missing instrument entries; reordered and adjusted many per-record lists and aggregated statistics.

Estimated code review effort

🎯 4 (Complex) | ⏱️ ~45 minutes

Possibly related PRs

• Minor changes in the html web page.  #806: Also modifies scripts/inject-headers.py and header/navigation HTML ordering/injection logic — closely related at the code/template level.

Suggested reviewers

• noatgnu

Poem

🐰 I nudged links to a tidier row,
Hopped through JSON, made values glow,
Ignored a few crumbs, smoothed the trail,
Template Builder now leads the grail.
A tiny hop, a tidy cheer — the site is crisp and clear! 🥕

✨ Finishing Touches

• 📝 Generate docstrings (stacked PR)
• 📝 Generate docstrings (commit on current branch)

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch dev

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