Subset AntibodyArray gene graphs; give the data table its samples

[jbrestel]

Follow-up to #214. Both fixes come from the same cause: the AntibodyArray EDA studies span two entities — the measurement sits on the gene entity, its identity and covariates on the parent sample entity — while every existing EDA gene graph is single-entity, so nothing had exercised that path.

displayMode: highlight → subset

EdaAntibodyArrayDatasets emitted the literal 'highlight'. A box plot has no per-point identity to highlight, so the plot was drawn from every gene's values rather than the gene whose record page it is. EdaCellularLocalizationDatasets already emits subset; this uses the same value.

Verified on PF3D7_1441400 (Loffler): the gene's 33 measurements span 8.60–12.63, while all 48,543 measurements in the study span 0.88–15.62. The plot now draws the former.

Data table: report the sample, and stop dropping rows

antibodyArrayDataTableGeneTableSql joined only the gene entity, so every row was a bare value with no indication of which sample it came from — 450 anonymous intensities for PF3D7_1441400. It now joins eda.ancestors_<study>_<entity> and reports sample, keeping only NORMALIZED_INTENSITY; the Sample and Normalized Intensity columns replace the old Variable/Value pair.

The template also used UNION, which deduplicates identical tuples. Two samples recording the same intensity for one gene collapsed into a single row, and all 33 rows of the constant Dataset variable collapsed into one. That is data loss rather than tidying, so this uses UNION ALL — which restores the 4 measurements it had been dropping for this gene. The empty seed row remains harmless, filtered out by the join on gene id.

After the change, for PF3D7_1441400:

dataset	rows	distinct samples	min	max
Crompton_Mali	421	421	4.1455	6.6524
Loffler_Natural_Infection	33	33	8.6037	12.6327

Rows equal distinct samples in both, and the Loffler range matches what the box plot draws — table and plot demonstrably read the same measurements.

Testing

Built on a dev instance (jbrestel.eupathdb.org, model UniDB) and verified with wdkQuery -showQuery plus the rendered SQL run against the appDb. Paired with VEuPathDB/web-monorepo#PENDING, which adds the box plot component the plot_type in EDAGeneGraphs.xls asks for.

🤖 Generated with Claude Code