GEN-3b: import notation normalization (Uw=G, Sls, deaf flag, tags)

genotype.py:
- Uw/uw aliased to G/g (same locus) so the D2 conflict group + pure-Uw
  cases stop being conflicts (Gg == Uwuw).
- Sls/WP recognized as a SECOND spotting locus (S(l)s(l)=WP het); carried
  into mapped8locus alongside Sp (Sp+Sls = Superschecke).
- dea/Dea/taub/hörend -> hearing/deaf phenotype FLAG (not a locus).
- WFNZ/RV/GV/DP -> provenance/breeding tags (not genotype, not conflicts).
- test_genotype.py: zero-dep unit tests for all four.

extract.py: surface deaf+tags on animals; dedup conflict detection now
compares the NORMALIZED genotype key (mapped8locus) instead of the raw
string, so Uw=G no longer triggers a conflict. Result: Konflikte 32 -> 27,
Zucht-Splits stays 0. Dedup identity = name + DOB + Zucht.

Backend: Gerbil.IsDeaf (bool?) + additive migration AddGerbilDeafFlag
(has-pending-model-changes clean) + GerbilDto/GerbilInput round-trip.
ImportService sets IsDeaf from animal.deaf and preserves Sls + tags + deaf
in RawImportData (kept out of the 8-locus compact Genotype contract until
GEN-3a adopts them).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This commit is contained in:
2026-06-06 10:26:01 +02:00
parent bd9cc83205
commit 2f089a902d
13 changed files with 1645 additions and 62 deletions

View File

@@ -102,6 +102,23 @@ namespace GerbilManager.Tests
Assert.Equal(2, await db.Litters.CountAsync());
}
[Fact]
public async Task Execute_persists_deaf_flag_and_preserves_sls_and_tags()
{
using var db = NewDb();
await new ImportService(db, _dir, _dir).RunAsync(execute: true);
var a1 = await db.Gerbils.SingleAsync(g => g.ExternalRef == "a1");
// GEN-3b: deafness is a persisted phenotype flag (NOT a genotype locus).
Assert.True(a1.IsDeaf);
// Sls (2nd spotting locus) + provenance tags are preserved in RawImportData
// (kept out of the 8-locus compact Genotype contract until GEN-3a adopts them).
Assert.Contains("Sls", a1.RawImportData!);
Assert.Contains("WFNZ", a1.RawImportData!);
// and Sls must NOT leak into the compact 8-locus genotype string
Assert.DoesNotContain("Sl", a1.Genotype!);
}
[Fact]
public void ComposeGenotype_strips_carets_and_fills_missing_loci()
{
@@ -139,7 +156,8 @@ namespace GerbilManager.Tests
[
{"id":"a1","name":"Kind Eins","dob":"01.02.2020","death":"","gender":null,
"farbschlag":"Agouti","farbschlagVariants":["Agouti"],
"genotype":{"mapped8locus":{"A":["a","a"],"C":["C","C"],"D":["D","?"],"E":["e","e^f"]},"rawGenotype":"aa CC D- ee[f]","unmappedTokens":[]},
"genotype":{"mapped8locus":{"A":["a","a"],"C":["C","C"],"D":["D","?"],"E":["e","e^f"],"Sls":["Sl","sl"]},"rawGenotype":"aa CC D- ee[f] WP dea WFNZ","unmappedTokens":[]},
"deaf":true,"tags":["WFNZ"],
"zucht":"","parentRefs":[],"photos":[],"sourceFiles":["f1"],"conflict":false,
"litterRef":{"litterId":"L1","method":"geburtsdatum+eltern","confidence":"hoch"}},
{"id":"a2","name":"Streit","dob":"01.01.2019","death":"","gender":null,