Gulum/GerbilManager
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

PEDIGREE-LINK: chart parentRefs→litters, box-colour=sex, name-bleed fix

Browse Source 
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>
This commit is contained in:
Gulum
2026-06-06 10:48:30 +02:00
parent a57b481a7e
commit ea79703dbf
6 changed files with 304 additions and 58 deletions
Download Patch File Download Diff File Expand all files Collapse all files

9
GerbilManagerWebAPI/Import/ImportModels.cs
View File

@@ -39,7 +39,9 @@ namespace GerbilManagerWebAPI.Import
{
public string Name { get; set; } = "";
public string Dob { get; set; } = "";
public string RoleGuess { get; set; } = "";
public string RoleGuess { get; set; } = ""; // "father" | "mother"
public string Method { get; set; } = ""; // e.g. "chart-position"
public string Confidence { get; set; } = ""; // "hoch" | "medium" | "niedrig"
}
public sealed class SourceLitterRef
@@ -73,7 +75,7 @@ namespace GerbilManagerWebAPI.Import
IReadOnlyList<string> Samples,
IReadOnlyList<string> Notes);
public sealed record LitterSummary(int InSource, int Created, int AlreadyImported);
public sealed record LitterSummary(int InSource, int Created, int AlreadyImported, int DerivedFromChart = 0);
public sealed record AnimalSummary(
int InSource,
@@ -82,7 +84,8 @@ namespace GerbilManagerWebAPI.Import
int FarbschlagMatched,
int FarbschlagUnmatched,
int AlreadyImported,
QuarantineSummary Quarantined);
QuarantineSummary Quarantined,
int ParentLinksFromChart = 0);
public sealed record QuarantineSummary(
int Conflicts,

205
GerbilManagerWebAPI/Import/ImportService.cs
View File

@@ -128,74 +128,165 @@ namespace GerbilManagerWebAPI.Import
int photosAttached = 0, photosMissing = 0;
var createdAnimalByName = new Dictionary<string, Guid>(); // normalized name -> gerbil id (for litter back-link)
// name+DOB -> gid index, across EXISTING rows AND this run's planned animals, so that
// chart-position parentRefs (PEDIGREE-LINK) can resolve a parent to a real gerbil id.
var existingRows = await _db.Gerbils
.Select(g => new { g.Id, g.Name, g.DateOfBirth, g.ExternalRef, g.LitterId }).ToListAsync();
var gidByNameDob = new Dictionary<string, Guid>();
foreach (var g in existingRows)
gidByNameDob[NameDobKey(g.Name, g.DateOfBirth)] = g.Id;
var existingLitterByExtRef = existingRows.Where(g => g.ExternalRef != null)
.ToDictionary(g => g.ExternalRef!, g => g.LitterId);
// PASS 1: assign ids + resolve fb/gender/Wurfchronik link (no writes yet).
var plan = new List<AnimalPlan>();
foreach (var a in loadable)
{
if (existingGerbilSet.Contains(a.Id)) { animalsExisting++; continue; }
animalsCreated++;
bool exists = existingGerbilSet.Contains(a.Id);
var gid = exists ? gidByNameDob[NameDobKey(a.Name, ParseDate(a.Dob))] : Guid.NewGuid();
Guid? litterId = null;
Guid? wurfLitterId = null;
if (a.LitterRef?.Confidence == "hoch" && a.LitterRef.Candidates is not { Count: > 0 }
&& litterIdMap.TryGetValue(a.LitterRef.LitterId, out var lid))
{
litterId = lid;
linked++;
}
wurfLitterId = lid;
Guid? colorVarietyId = null;
var fbCandidates = new[] { a.Farbschlag }.Concat(a.FarbschlagVariants)
.Where(s => !string.IsNullOrWhiteSpace(s));
foreach (var fb in fbCandidates)
{
if (varietyByName.TryGetValue(fb.Trim().ToLowerInvariant(), out var vid))
{ colorVarietyId = vid; break; }
}
if (colorVarietyId is null) fbUnmatched++; else fbMatched++;
var gender = InferGender(a, sireNames, damNames);
var gid = Guid.NewGuid();
var norm = Normalize(StripZucht(a.Name));
if (norm.Length > 0) createdAnimalByName.TryAdd(norm, gid);
if (!exists) gidByNameDob.TryAdd(NameDobKey(a.Name, ParseDate(a.Dob)), gid);
var currentLitter = exists && existingLitterByExtRef.TryGetValue(a.Id, out var el) ? el : null;
plan.Add(new AnimalPlan(a, gid, exists, wurfLitterId, currentLitter, colorVarietyId, gender));
}
// PASS 1.5: PEDIGREE-LINK — synthesize/reuse a litter from chart-position parentRefs for
// any animal that has no Wurfchronik litter and isn't already litter-linked. Siblings
// (same father+mother+dob) share one derived litter. Computed for dry-run counts too.
int parentLinksAdded = 0, derivedLitters = 0;
var synthLitterForGid = new Dictionary<Guid, Guid>(); // offspring gid -> synth litter id
var synthLitters = new Dictionary<string, SynthLitter>(); // parents+date key -> synth litter
foreach (var p in plan)
{
if (p.WurfLitterId is not null || p.CurrentLitterId is not null) continue;
if (p.A.ParentRefs is not { Count: > 0 }) continue;
var father = ResolveParentGid(p.A, "father", gidByNameDob);
var mother = ResolveParentGid(p.A, "mother", gidByNameDob);
if (father is null && mother is null) continue; // nothing resolvable to link
var dob = ParseDate(p.A.Dob);
var conf = p.A.ParentRefs.FirstOrDefault()?.Confidence ?? "medium";
var key = $"{father}|{mother}|{dob:yyyy-MM-dd}";
if (!synthLitters.TryGetValue(key, out var sl))
{
sl = new SynthLitter(Guid.NewGuid(), father, mother, dob, conf);
synthLitters[key] = sl;
derivedLitters++;
}
synthLitterForGid[p.Gid] = sl.Id;
parentLinksAdded++;
}
// PASS 2: write (litters synthesized first so offspring FK resolves), then animals + photos.
if (execute)
{
// reuse an existing litter with the same parents+date instead of duplicating.
var existingLitterRows = await _db.Litters
.Select(l => new { l.Id, l.FatherId, l.MotherId, l.Date }).ToListAsync();
var litterByParentsDate = new Dictionary<string, Guid>();
foreach (var l in existingLitterRows)
litterByParentsDate[$"{l.FatherId}|{l.MotherId}|{l.Date:yyyy-MM-dd}"] = l.Id;
foreach (var sl in synthLitters.Values.ToList())
{
var reuseKey = $"{sl.Father}|{sl.Mother}|{sl.Date:yyyy-MM-dd}";
if (litterByParentsDate.TryGetValue(reuseKey, out var existingId))
{
// remap offspring to the existing litter; don't create a duplicate.
foreach (var g in synthLitterForGid.Where(kv => kv.Value == sl.Id).Select(kv => kv.Key).ToList())
synthLitterForGid[g] = existingId;
derivedLitters--;
continue;
}
_db.Litters.Add(new Litter
{
Id = sl.Id,
Name = $"Wurf (aus Diagramm) {sl.Date:yyyy-MM-dd}".Trim(),
Date = sl.Date ?? default,
FatherId = sl.Father,
MotherId = sl.Mother,
Notes = $"aus Stammbaum-Diagramm abgeleitet (Konfidenz: {sl.Confidence})",
});
}
await _db.SaveChangesAsync();
}
foreach (var p in plan)
{
Guid? litterId = p.WurfLitterId
?? (synthLitterForGid.TryGetValue(p.Gid, out var slid) ? slid : (Guid?)null);
if (litterId is not null) linked++;
if (p.ColorVarietyId is null) fbUnmatched++; else fbMatched++;
if (samples.Count < 16)
samples.Add($"Tier: {a.Name} (*{a.Dob}), Genotyp {ComposeGenotype(a.Genotype)}"
+ (litterId is not null ? ", Wurf-verknüpft" : "")
+ (colorVarietyId is not null ? $", Farbschlag „{a.Farbschlag}\"" : ""));
samples.Add($"Tier: {p.A.Name} (*{p.A.Dob}), Genotyp {ComposeGenotype(p.A.Genotype)}"
+ (litterId is not null ? (p.WurfLitterId is not null ? ", Wurf-verknüpft" : ", Eltern aus Diagramm") : "")
+ (p.ColorVarietyId is not null ? $", Farbschlag „{p.A.Farbschlag}\"" : ""));
if (p.Exists)
{
animalsExisting++;
// re-link an existing animal that just became linkable (sweep idempotency).
if (execute && p.CurrentLitterId is null && litterId is not null)
{
var row = await _db.Gerbils.FirstOrDefaultAsync(g => g.Id == p.Gid);
if (row is not null) row.LitterId = litterId;
}
continue;
}
animalsCreated++;
if (execute)
{
_db.Gerbils.Add(new Gerbil
{
Id = gid,
Name = a.Name,
Gender = gender,
Id = p.Gid,
Name = p.A.Name,
Gender = p.Gender,
Status = GerbilStatus.Active,
DateOfBirth = ParseDate(a.Dob),
DateOfDeath = ParseDate(a.Death),
DateOfBirth = ParseDate(p.A.Dob),
DateOfDeath = ParseDate(p.A.Death),
LitterId = litterId,
ColorVarietyId = colorVarietyId,
Genotype = ComposeGenotype(a.Genotype),
IsDeaf = a.Deaf,
ColorVarietyId = p.ColorVarietyId,
Genotype = ComposeGenotype(p.A.Genotype),
IsDeaf = p.A.Deaf,
ImportSource = ImportSourceTag,
ExternalRef = a.Id,
OriginBreeder = string.IsNullOrWhiteSpace(a.Zucht) ? null : a.Zucht.Trim(),
ExternalRef = p.A.Id,
OriginBreeder = string.IsNullOrWhiteSpace(p.A.Zucht) ? null : p.A.Zucht.Trim(),
RawImportData = JsonSerializer.Serialize(new
{
a.Genotype.RawGenotype,
a.Genotype.UnmappedTokens,
p.A.Genotype.RawGenotype,
p.A.Genotype.UnmappedTokens,
// GEN-3b: Sls (2nd spotting locus) preserved here until Kevin's GEN-3a
// parser adopts it into the compact Genotype contract; tags + deaf too.
Sls = a.Genotype.Mapped8locus.TryGetValue("Sls", out var sls) ? sls : null,
a.Tags,
a.Deaf,
a.Zucht,
a.SourceFiles,
FarbschlagRaw = a.Farbschlag,
Sls = p.A.Genotype.Mapped8locus.TryGetValue("Sls", out var sls) ? sls : null,
p.A.Tags,
p.A.Deaf,
p.A.Zucht,
p.A.SourceFiles,
FarbschlagRaw = p.A.Farbschlag,
}),
});
}
// photos
foreach (var rel in a.Photos)
foreach (var rel in p.A.Photos)
{
var src = Path.Combine(_sourceDir, rel.Replace('/', Path.DirectorySeparatorChar));
if (!File.Exists(src)) { photosMissing++; continue; }
@@ -208,7 +299,7 @@ namespace GerbilManagerWebAPI.Import
_db.GerbilPhotos.Add(new GerbilPhoto
{
Id = Guid.NewGuid(),
GerbilId = gid,
GerbilId = p.Gid,
FileName = fileName,
SortOrder = 0,
CreatedAt = DateTimeOffset.UtcNow,
@@ -218,7 +309,7 @@ namespace GerbilManagerWebAPI.Import
}
if (execute) await _db.SaveChangesAsync();
// ---- back-link litter parents by name (best effort) ----
// ---- back-link Wurfchronik litter parents by name (best effort) ----
if (execute)
{
foreach (var sl in litters)
@@ -235,14 +326,17 @@ namespace GerbilManagerWebAPI.Import
}
notes.Add("Quarantäne (kein Import): Konflikte + Stubs ohne Geburtsdatum + unsichere Wurf-Zuordnungen — warten auf die Prüfung durch die Züchterin.");
if (parentLinksAdded > 0)
notes.Add($"Stammbaum-Diagramm: {parentLinksAdded} Tiere über Eltern-Verknüpfung einem (abgeleiteten) Wurf zugeordnet ({derivedLitters} abgeleitete Würfe).");
if (!execute) notes.Add("DRY-RUN: nichts gespeichert. /import/execute lädt die konfliktfreien Daten.");
return new ImportReport(
Executed: execute,
Litters: new LitterSummary(litters.Count, littersCreated, littersExisting),
Litters: new LitterSummary(litters.Count, littersCreated, littersExisting, derivedLitters),
Animals: new AnimalSummary(
animals.Count, animalsCreated, linked, fbMatched, fbUnmatched, animalsExisting,
new QuarantineSummary(conflicts, stubs, dateOnly, ambiguous, conflicts + stubs)),
new QuarantineSummary(conflicts, stubs, dateOnly, ambiguous, conflicts + stubs),
parentLinksAdded),
Photos: new PhotoSummary(photosAttached, photosMissing),
Samples: samples,
Notes: notes);
@@ -263,7 +357,16 @@ namespace GerbilManagerWebAPI.Import
if (g.Mapped8locus.TryGetValue(locus, out var pair) && pair.Count == 2)
return StripCaret(pair[0]) + StripCaret(pair[1]);
return "??";
});
}).ToList();
// GEN-3a contract (Kevin): Sls is appended LAST and ONLY for carriers — the
// wild-type sl/sl is omitted so existing 8-locus strings stay unchanged. WP het
// renders as the trailing token "Slsl"; S(l)S(l) is lethal so never appears.
if (g.Mapped8locus.TryGetValue("Sls", out var sls) && sls.Count == 2
&& !(sls[0] == "sl" && sls[1] == "sl"))
{
tokens.Add(StripCaret(sls[0]) + StripCaret(sls[1]));
}
return string.Join(' ', tokens);
}
@@ -271,6 +374,11 @@ namespace GerbilManagerWebAPI.Import
private static Gender InferGender(SourceAnimal a, HashSet<string> sires, HashSet<string> dams)
{
// Box colour (blue=male, white=female) is the authoritative breeder signal — prefer it
// over sire/dam name inference (PEDIGREE-LINK, Julian 2026-06-06).
if (string.Equals(a.Gender, "male", StringComparison.OrdinalIgnoreCase)) return Gender.male;
if (string.Equals(a.Gender, "female", StringComparison.OrdinalIgnoreCase)) return Gender.female;
var n = Normalize(StripZucht(a.Name));
bool isSire = sires.Contains(n), isDam = dams.Contains(n);
if (isSire && !isDam) return Gender.male;
@@ -304,5 +412,26 @@ namespace GerbilManagerWebAPI.Import
n = Regex.Replace(n, @"[^a-z0-9äöüß]", "");
return n;
}
/// <summary>Dedup identity for parent resolution: normalized call-name + DOB.</summary>
private static string NameDobKey(string name, DateOnly? dob) =>
$"{Normalize(StripZucht(name))}|{dob:yyyy-MM-dd}";
/// <summary>Resolve a chart-position parentRef (by role) to a known gerbil id, or null.</summary>
private static Guid? ResolveParentGid(SourceAnimal a, string role, Dictionary<string, Guid> gidByNameDob)
{
var pr = a.ParentRefs.FirstOrDefault(p =>
string.Equals(p.RoleGuess, role, StringComparison.OrdinalIgnoreCase));
if (pr is null || string.IsNullOrWhiteSpace(pr.Name)) return null;
return gidByNameDob.TryGetValue(NameDobKey(pr.Name, ParseDate(pr.Dob)), out var id) ? id : null;
}
/// <summary>Per-animal plan computed before any write so synthesis can run in dry-run too.</summary>
private sealed record AnimalPlan(
SourceAnimal A, Guid Gid, bool Exists, Guid? WurfLitterId,
Guid? CurrentLitterId, Guid? ColorVarietyId, Gender Gender);
/// <summary>A litter synthesized from chart-position parentRefs (PEDIGREE-LINK).</summary>
private sealed record SynthLitter(Guid Id, Guid? Father, Guid? Mother, DateOnly? Date, string Confidence);
}
}