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Citation Validation

book/tools/scripts/content/README_CITATION_VALIDATION.md

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Citation Validation

Overview

The citation validation script ensures that all @key citation references in .qmd files have corresponding entries in their associated .bib files. This prevents Quarto build failures caused by missing bibliography entries.

Automatic Validation (Pre-commit Hook)

The validation runs automatically when you commit .qmd files:

bash
git add myfile.qmd
git commit -m "Update chapter"

If there are missing citations, the commit will fail with output like:

❌ CITATION VALIDATION FAILED

The following .qmd files reference citations that are missing from their .bib files:

📄 quarto/contents/core/conclusion/conclusion.qmd:
   ❌ @koomey2011web
   ❌ @han2015deep
   ❌ @openai2023gpt4
   ❌ @vaswani2017attention

Manual Validation

You can also run the validation manually:

Validate specific files

bash
python tools/scripts/content/validate_citations.py chapter.qmd

Validate all files in a directory

bash
python tools/scripts/content/validate_citations.py -d quarto/contents/core/

Quiet mode (only show errors)

bash
python tools/scripts/content/validate_citations.py -d quarto/contents/ --quiet

How It Works

  1. Extracts bibliography file: Reads the bibliography: field from the .qmd file's YAML frontmatter
  2. Finds citations: Scans the .qmd file for all @key patterns
  3. Filters false positives: Excludes cross-reference labels like @fig-, @tbl-, @sec-, etc.
  4. Validates: Checks that each citation key exists in the .bib file
  5. Reports: Lists any missing citations

Fixing Missing Citations

When validation fails, you have several options:

Option 1: Copy from another chapter's .bib file

  1. Search for the citation key in other .bib files:

    bash
    grep -r "@article{koomey2011web" quarto/contents/

  2. Copy the BibTeX entry to your chapter's .bib file

Option 2: Search online databases

Use tools like:

Option 3: Remove the citation

If the citation is no longer needed, remove the @key reference from the .qmd file.

Supported Citation Formats

The validator recognizes various citation formats:

  • [@key] - Standard citation
  • @key - Inline citation
  • [@key1; @key2] - Multiple citations
  • [-@key] - Suppress author citation
  • [@key, p. 123] - Citation with page numbers

Common Issues

False Positives

The validator filters out cross-references to figures, tables, sections, etc. These are not citations:

  • @fig-architecture ✓ (ignored)
  • @tbl-results ✓ (ignored)
  • @sec-introduction ✓ (ignored)
  • @eq-formula ✓ (ignored)

Bibliography File Not Found

If you see:

❌ Bibliography file not found: chapter.bib

Make sure:

  1. The .bib file exists in the same directory as the .qmd file
  2. The bibliography: field in the YAML frontmatter is correct

Integration with Build Process

This validation runs before the Quarto build, catching issues early:

Pre-commit → Citation Validation → Git Commit → Quarto Build

This saves time by preventing failed builds due to missing citations.

Examples

Successful validation

bash
$ python tools/scripts/content/validate_citations.py conclusion.qmd
✅ All citations validated successfully (1 files checked)

Failed validation

bash
$ python tools/scripts/content/validate_citations.py conclusion.qmd

❌ CITATION VALIDATION FAILED

📄 quarto/contents/core/conclusion/conclusion.qmd:
   ❌ @smith2020deep
   ❌ @jones2021ml

To fix these issues:
1. Find the citation entry in another chapter's .bib file
2. Copy the BibTeX entry to the appropriate .bib file
3. Or remove the citation reference if it's no longer needed

See Also

  • clean_bibliographies.py - Remove unused entries from .bib files
  • fix_bibliography.py - Update citation key formats
  • .pre-commit-config.yaml - Pre-commit hook configuration