god added a `correctDob` (DD.MM.YYYY) decisions field: the matched (name+dob)
record is a DUPLICATE with a wrong birthdate → remap its DOB to correctDob so
dedup MERGES it into the canonical same-named animal. apply_dob_remaps runs
BEFORE dedup (it changes the dedup identity); tolerates a missing file; logged
as "DOB-Remaps: N". First use: Chelsea *15.10.2021 → *02.04.2021 (merges into
the canonical record). test_extract covers the remap + that both records then
share one name+dob identity.
Extractor-only. python + dotnet 121/121 green.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Breeder merge rule: when two source variants of the SAME animal differ ONLY
by a token PRESENT in one and ABSENT in the other — a whole locus (e.g. spsp
charted in one source, omitted in another) or a modifier on the same base
allele (e^f vs e, the [f] marker) — keep the present token; that is NOT a
conflict. Genuine VALUE contradictions still quarantine: different base
alleles (Ee↔ee), unknown-vs-filled (D-↔DD), different modifiers (c[h]↔c[chm]),
C-↔Cc[h], P-↔Pp.
Replaces the old `len(distinct normalized geno keys) > 1` test with
_genotype_conflict() (per-locus, per-allele compatibility; '?'-vs-filled is a
contradiction, modifier-present-vs-absent and whole-locus-absence are not).
Markers/flags (WP/DP/WFNZ/hörend) are already tags/flags, never genotype, so
they never reach conflict detection; empty Farbschlag/death already don't
conflict (only non-empty values are compared).
Clears Daja (keep spsp), Ichika (keep ee[f]) and the D4 marker cases:
Konflikte 19 -> 15. test_extract covers spsp/[f] present-vs-absent =
no conflict and the four genuine-contradiction shapes. python + dotnet
121/121 green; extractor-only.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
god maintains tools/import/conflict-decisions.json as Julian/his wife answer
the D-conflicts. extract.py now consumes it (apply_conflict_decisions): for an
animal matching normalize(name)+dob, it clears the conflict, marks
resolvedByDecision, and — when the decision carries a `genotype` (breeder
notation, parsed via genotype.py) and/or `farbschlag` — treats those as
AUTHORITATIVE. Tolerates a missing/empty/garbled file. Genuinely-unresolved
conflicts stay quarantined.
Loader (ImportService): SourceAnimal.ResolvedByDecision flows through; the
report surfaces Animals.ConflictsResolvedByDecision + a German note.
Result on real data: the 2 current decisions (Firefly D-/PP, WildFire PP)
un-quarantine → Konflikte 21 → 19. As god appends entries the count grows;
nothing else needed from me.
Tests: python test_extract (decision clears conflict + genotype authoritative
+ removes from conflicts list + tolerates missing file) and a C# loader test
(a resolved animal loads and is counted). Folded into the EXTRACT-BANDS branch
so the next re-extract applies band-aware Farbschlag + these decisions in one
pass. No schema change (JSON DTO fields). python + dotnet 121/121 green;
has-pending clean.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Structural fix (god, Julian-reported via 'C'): the loader ignored
SourceAnimal.ParentRefs, so animals whose ancestry exists only as
Stammbaum chart-position refs loaded with LitterId=null ("unbekannt").
ImportService now synthesizes/reuses a derived litter from parentRefs:
resolves father+mother via name+DOB, groups siblings (same parents+dob)
into one litter, sets Father/Mother + offspring LitterId, dates it to the
offspring DOB, and tags Notes "aus Stammbaum-Diagramm abgeleitet
(Konfidenz: …)" so it's transparent/reversible. Existing animals that
become linkable are re-linked on re-run (sweep-idempotent). Dry-run counts
included. Projected: ~124 loadable animals gain a parent link.
Box-colour = sex (Julian): blue box = male, white box = female. All 11
pedigrees encode this as a solid theme-8 (accent5/blue) fill vs no fill.
xlsx_util.cell_fill_sex reads it; extract.py sets animal.gender from the
box; ImportService.InferGender prefers it over sire/dam name inference.
Result: 306/306 loadable animals now sexed (154♂/152♀).
Extractor noise fix (god): reject Farbschlag values that are actually a
parent NAME bled across cells (contain v.d./von/of/gen.) — cleared phantom
conflicts (e.g. Chayton). Combined with GEN-3 Uw→G: Konflikte 32→21.
Also skip Excel "~$" lock files in the glob.
GEN-3a contract (Kevin): ComposeGenotype appends "Slsl" for WP/Sls
carriers (wild-type sl/sl omitted) so 8-locus strings stay unchanged.
Importer-only. The live re-import into Julian's DB stays a separate
supervised gated step. 95 C# tests + python genotype tests green;
has-pending-model-changes clean (no schema change on this branch).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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>
- survivedToGoHome: unlabeled Tabelle1 col E detected positionally; value-
adaptive row parsing recovers it from schema-shifted Tabelle2 rows too
(118 recovered, 79 confirmed by the E=F-TG-s identity)
- breakdown G -> males/females/stillborn/diedLater ('s' = died before Abgabe)
- validation: E = F - TG - s; 113 mismatches as German review-report warnings
- (name, Zucht) canonicalisation: [brackets] == of/von suffix ([ZdkC] ==
von den Kleinen Chaoten); Zucht = dedup discriminator (0 splits in data)
- animal->litter matching via DOB+(Vater,Mutter): 95 high-confidence,
40 date-only, 9 ambiguous; litterRef in animals.json
- regenerated report: 889 raw -> 574 unique (279 dated), 32 conflicts
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
