Fix bibliography formatting for DOI-only citations - #52
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formatBibliographyFromData()'s DOI branch dropped the old `title ?: toolName` fallback, so meta.yml entries with a DOI but no publication.title produced anonymous bibliography entries (e.g. `<li>doi: ...</li>`) with no way to tell which tool they referenced. Restore the tool-name fallback in the title position and add a Spock spec covering the DOI-without-title and DOI-only cases. Regenerate the affected citations-on-the-fly and topic-channel-citations validation snapshots to reflect the now-named entries. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015EvrftaVNPDUPvdubjHepF
…ranches Per maintainer feedback, the meta-schema treats `publication` as all-or-nothing, so the previous `title ?: toolName` fallback was the wrong shape. Key the formatter on publication presence instead: - publication present -> author-led academic reference (Author. (year). title. source. doi: link) - no publication -> identify by tool name (toolName. doi: link) This fixes the original regression (bare-DOI tools rendered anonymously now carry the tool name) without injecting the tool name into entries that already have an author. Lightweight field guards remain so the partial publications still present in some modules degrade cleanly. Update the spec to assert the two-branch contract and the citations-on-the-fly snapshot (only the bare-DOI multiqc entry changes). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015EvrftaVNPDUPvdubjHepF
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Summary
Fixes bibliography formatting to properly identify DOI-only citation entries by tool name, while preserving author-led formatting for entries with full publication metadata. This addresses the issue raised in PR #51 where DOI-only citations were rendered anonymously.
Changes
Bibliography formatter logic (
NfcoreCitationUtils.formatBibliographyFromData):publicationobject first, rather than DOI presence"Author. (year). title. source. doi: link""toolname. doi: link"or"toolname. url"Test coverage (
NfcoreCitationUtilsTest):"DOI-only entries are named by tool, publication entries are author-led"to verify the two formatting pathsSnapshot updates:
Implementation Details
This change aligns with ADR-0002 (structured citations and MultiQC rendering) by ensuring the interim HTML-string output is correct while the migration to structured CSL-JSON output is underway. The fix ensures that the current bibliography rendering is consistent and unambiguous: entries with full publication metadata follow academic citation style, while entries with only a DOI or homepage are identified by tool name to avoid anonymous references.
https://claude.ai/code/session_015EvrftaVNPDUPvdubjHepF