Rename the Variation record to Variant; add a precomputed SNV characteristics search

[jbrestel]

Model-side of the SNV work. Must merge together with ApiCommonWebService PR #20 — that PR's plugin advertises a span_snp_density column and validateColumns rejects it unless this PR's wsColumn declaration is present.

Renames the Variation record to Variant

The record class was Variation while every source_id it holds reads Variant_<sequence>_<location>, and its own attributes already said "Variant Type" and "Variant Call Set". "Variation" is the phenomenon; a record is one concrete allele at a locus.

Renames the WDK layer only — record class, question set and its five searches, query sets, param set, category ontology nodes, and six model files — and sets displayName to Short Variant / Short Variants, naming what the record actually holds (SNVs and small indels).

Deliberately unchanged: urlName stays variation so existing record URLs resolve (the feature is not public yet, so this can move separately); variation_sample_meta{,_a,_b} and chromosomeOptionalForVariations are contracts with the HSSS plugins and renaming them breaks the searches at run time, not build time.

The four HSSS searches now lead with SNV — HSSS computes over single-nucleotide variants only and cannot return an indel however the record class is named. VariantBySourceId is not prefixed, because an ID lookup goes to the tuning table and does return both.

Adds GenesByVariantCharacteristics

A precomputed sibling to GenesByNgsSnps. That one runs HSSS over a user-selected sample set and takes minutes; this reads apidbtuning.GeneVariationSummary, returns in milliseconds, and reports the same numbers as the gene record page. Neither replaces the other — dropping the HSSS search would delete the sample-set comparison, and without this one the record page and the search disagree about the same gene with no explanation.

Filtering is one filterParam over sixteen statistics, not sixteen range params. The range-param version was built first and abandoned: a numberRangeParam cannot express "untouched", so every range applies on every run and any gene NULL in that column is excluded — and GeneVariationSummary NULLs its frequency statistics below their allele floors by design, which for tbruTREU927 is 100% of rows for three columns. Working around that needed a full-span escape clause with bounds hardcoded in two files, which then broke when NumberRangeParamHandler rounded a value onto the declared ceiling. The filterParam has none of it, and distributions come from the data rather than from hand-declared bounds.

Result columns reuse the transcript record's own attributes rather than new dynamic ones — gene_pi_n_pi_s there is gvs.pi_n_pi_s_snpeff, the same column the filter reads, so the filtered value and the displayed value agree by construction.

Corrects GenesByNgsSnps labels

Its statistics changed in PR #20, so the strings describing them changed with them: density is now genuinely CDS with the old gene-span value beside it, the ratio says it is site-normalized, "Nonsynonymous SNPs" → Missense SNVs (it never included stop-gained), "Non-coding SNPs" → Unclassified SNVs (class 0 means no product byte was available). All eight result columns carry a (sample group) qualifier, since a results table can hold them next to the whole-cohort columns from the gene record.

Also adds span_snp_density to both postCacheUpdateSql blocks, not just the wsColumn list — those blocks enumerate result columns explicitly and backfill sibling transcripts, so omitting it would leave siblings NULL while matched transcripts carried a value.

Verification

Built and exercised on a dev instance throughout. Category tree keeps all 59 nodes after the rename with no stale VariationRecordClass references; all five renamed searches resolve with expandParams; the new search's filter distributions match SQL (impact classes sum to all 5,579 pfal genes; piN/piS reports exactly the 2,370 genes that have a value).

Note on scope

This branch carries ~90 prior commits of dnaseq work authored before this session — CNV search ports, the GeneVariationSummary tuning table, gene-record variation wiring. They are on the branch but are not part of this change.

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Related PRs

The variants work spans four repos. These four merge together — ApiCommonModel's record rename is a contract the other three depend on by name:

• ApiCommonModel Rename the Variation record to Variant; add a precomputed SNV characteristics search #212 — record rename + precomputed SNV characteristics search
• ApiCommonWebService Fix SNV density and dN/dS in the sample-set SNV search, and revive its test suite ApiCommonWebService#20 — density and dN/dS fixes, test-suite repair
• ApiCommonWebsite Prefix HSSS result IDs with Variant_ instead of NGS_SNP. ApiCommonWebsite#310 — HSSS result-ID prefix (NGS_SNP. → Variant_)
• web-monorepo Show the Variant record id without the record-type prefix web-monorepo#1841 — record-heading override, filename tracking the rename

Coupling worth knowing when sequencing the merges: #1841's customization is resolved by recordClass.fullName, so without #212 it matches nothing and the override silently stops applying — no error, just the default heading back. #310's prefix and #20's separator together produce the ids #212's record class resolves; any two without the third leaves HSSS emitting ids the record class rejects.

Related but independent, cherry-picked onto master — merge before the four above:

• EbrcModelCommon Optional dataset gate for presenter template injection (partial-appDb builds) EbrcModelCommon#131 — optional dataset gate for presenter template injection. Not part of the variants work; needed to build a site against a partial appDb.

The release note originally in VEuPathDB/ApiCommonWebsite#310 has been deferred (reverted in 965009fdd) because its date attribute was an unresolvable placeholder. Recover the drafted text with git show a039aeee9 in ApiCommonWebsite and re-PR it once the release date is known.