Gulum
ea79703dbf
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>
438 lines
22 KiB
C#
438 lines
22 KiB
C#
using System.Text.Json;
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using System.Text.RegularExpressions;
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using GerbilManagerWebAPI.Models;
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using Microsoft.EntityFrameworkCore;
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namespace GerbilManagerWebAPI.Import
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{
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/// <summary>
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/// FEAT-8c import loader. Consumes tools/import/output (animals.json + litters.json
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/// produced by extract.py) and loads conflict-free data into the database:
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/// litters first (Wurfchronik = authoritative), then animals matched onto them.
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///
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/// Load policy:
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/// - Litters: all created (idempotent by ExternalRef = source litter id).
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/// - Animals: created when they have a DOB and are NOT in conflict. The birth-litter
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/// link is set only for HIGH-confidence matches (litterRef.confidence == "hoch");
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/// date-only/ambiguous links are quarantined (animal loads with LitterId = null).
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/// - QUARANTINED (never loaded): conflicts + stubs (no DOB) — await the wife's review.
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/// Idempotent: re-running matches on ExternalRef and skips existing rows.
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/// Execute is gated by the endpoint; this service only acts when asked.
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/// </summary>
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public sealed class ImportService
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{
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private static readonly string[] LocusOrder = { "A", "C", "D", "E", "G", "P", "Sp", "Re" };
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private static readonly JsonSerializerOptions Json = new()
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{
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PropertyNameCaseInsensitive = true,
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};
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private const string ImportSourceTag = "FEAT-8 Stammbaum/Wurfchronik";
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private readonly ApplicationContext _db;
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private readonly string _sourceDir;
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private readonly string _photoRoot;
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/// <summary>Test-friendly constructor with explicit paths.</summary>
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public ImportService(ApplicationContext db, string sourceDir, string photoRoot)
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{
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_db = db;
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_sourceDir = sourceDir;
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_photoRoot = photoRoot;
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}
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public ImportService(ApplicationContext db, IConfiguration config, IWebHostEnvironment env)
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: this(db,
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config["Import:SourcePath"]
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?? Path.GetFullPath(Path.Combine(env.ContentRootPath, "..", "tools", "import", "output")),
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config["Photos:RootPath"] ?? Path.Combine(env.ContentRootPath, "photo-storage"))
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{
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}
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public async Task<ImportReport> RunAsync(bool execute)
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{
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var notes = new List<string>();
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var samples = new List<string>();
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var animals = Load<List<SourceAnimal>>("animals.json") ?? new();
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var litters = Load<List<SourceLitter>>("litters.json") ?? new();
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if (animals.Count == 0 && litters.Count == 0)
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notes.Add($"Keine Quelldaten gefunden in {_sourceDir} (animals.json/litters.json). extract.py zuerst ausführen.");
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// ---- categorise animals ----
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var loadable = new List<SourceAnimal>();
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int conflicts = 0, stubs = 0, dateOnly = 0, ambiguous = 0;
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foreach (var a in animals)
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{
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if (a.Conflict) { conflicts++; continue; }
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if (string.IsNullOrEmpty(a.Dob)) { stubs++; continue; }
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loadable.Add(a);
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var conf = a.LitterRef?.Confidence;
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if (a.LitterRef?.Candidates is { Count: > 0 }) ambiguous++;
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else if (conf == "niedrig") dateOnly++;
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}
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// existing rows (idempotency). Gerbils carry ExternalRef; Litters have no such
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// column, so we key litter idempotency on the stable (Name + Date) pair instead.
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var existingGerbilExtRefs = await _db.Gerbils
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.Where(g => g.ExternalRef != null)
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.Select(g => g.ExternalRef!).ToListAsync();
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var existingGerbilSet = existingGerbilExtRefs.ToHashSet();
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var existingLitterKeys = await _db.Litters
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.Select(l => new { l.Name, l.Date }).ToListAsync();
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var existingLitterKeySet = existingLitterKeys
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.Select(x => $"{x.Name}|{x.Date:yyyy-MM-dd}").ToHashSet();
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// colour-variety name -> id (case-insensitive)
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var varieties = await _db.ColorVarieties.Select(v => new { v.Id, v.Name }).ToListAsync();
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var varietyByName = varieties
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.GroupBy(v => v.Name.Trim().ToLowerInvariant())
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.ToDictionary(g => g.Key, g => g.First().Id);
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// gender inference from litter roles (sire -> male, dam -> female; both -> unknown)
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var sireNames = litters.Select(l => Normalize(StripZucht(l.SireName))).Where(s => s.Length > 0).ToHashSet();
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var damNames = litters.Select(l => Normalize(StripZucht(l.DamName))).Where(s => s.Length > 0).ToHashSet();
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// ---- litters: create map source.id -> Litter (for high-confidence animal links) ----
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int littersCreated = 0, littersExisting = 0;
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var litterIdMap = new Dictionary<string, Guid>(); // source litter id -> Litter.Id
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foreach (var sl in litters)
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{
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var date = ParseDate(sl.Date);
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var name = $"Wurf {sl.LitterId}".Trim();
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var key = $"{name}|{date:yyyy-MM-dd}";
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if (existingLitterKeySet.Contains(key)) { littersExisting++; continue; }
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var id = Guid.NewGuid();
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litterIdMap[sl.Id] = id;
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littersCreated++;
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if (execute && date is DateOnly d)
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{
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_db.Litters.Add(new Litter
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{
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Id = id,
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Name = name,
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Date = d,
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TotalBorn = sl.TotalBorn,
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Notes = string.IsNullOrWhiteSpace(sl.Note) ? null : sl.Note,
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PairingCode = string.IsNullOrWhiteSpace(sl.Zuchtnummer) ? null : sl.Zuchtnummer,
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});
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}
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if (samples.Count < 8 && date is not null)
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samples.Add($"Wurf: {name} ({sl.Date}) — {sl.DamName} × {sl.SireName}");
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}
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if (execute) await _db.SaveChangesAsync();
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// ---- animals ----
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int animalsCreated = 0, linked = 0, fbMatched = 0, fbUnmatched = 0, animalsExisting = 0;
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int photosAttached = 0, photosMissing = 0;
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var createdAnimalByName = new Dictionary<string, Guid>(); // normalized name -> gerbil id (for litter back-link)
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// name+DOB -> gid index, across EXISTING rows AND this run's planned animals, so that
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// chart-position parentRefs (PEDIGREE-LINK) can resolve a parent to a real gerbil id.
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var existingRows = await _db.Gerbils
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.Select(g => new { g.Id, g.Name, g.DateOfBirth, g.ExternalRef, g.LitterId }).ToListAsync();
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var gidByNameDob = new Dictionary<string, Guid>();
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foreach (var g in existingRows)
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gidByNameDob[NameDobKey(g.Name, g.DateOfBirth)] = g.Id;
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var existingLitterByExtRef = existingRows.Where(g => g.ExternalRef != null)
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.ToDictionary(g => g.ExternalRef!, g => g.LitterId);
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// PASS 1: assign ids + resolve fb/gender/Wurfchronik link (no writes yet).
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var plan = new List<AnimalPlan>();
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foreach (var a in loadable)
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{
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bool exists = existingGerbilSet.Contains(a.Id);
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var gid = exists ? gidByNameDob[NameDobKey(a.Name, ParseDate(a.Dob))] : Guid.NewGuid();
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Guid? wurfLitterId = null;
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if (a.LitterRef?.Confidence == "hoch" && a.LitterRef.Candidates is not { Count: > 0 }
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&& litterIdMap.TryGetValue(a.LitterRef.LitterId, out var lid))
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wurfLitterId = lid;
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Guid? colorVarietyId = null;
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var fbCandidates = new[] { a.Farbschlag }.Concat(a.FarbschlagVariants)
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.Where(s => !string.IsNullOrWhiteSpace(s));
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foreach (var fb in fbCandidates)
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if (varietyByName.TryGetValue(fb.Trim().ToLowerInvariant(), out var vid))
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{ colorVarietyId = vid; break; }
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var gender = InferGender(a, sireNames, damNames);
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var norm = Normalize(StripZucht(a.Name));
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if (norm.Length > 0) createdAnimalByName.TryAdd(norm, gid);
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if (!exists) gidByNameDob.TryAdd(NameDobKey(a.Name, ParseDate(a.Dob)), gid);
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var currentLitter = exists && existingLitterByExtRef.TryGetValue(a.Id, out var el) ? el : null;
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plan.Add(new AnimalPlan(a, gid, exists, wurfLitterId, currentLitter, colorVarietyId, gender));
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}
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// PASS 1.5: PEDIGREE-LINK — synthesize/reuse a litter from chart-position parentRefs for
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// any animal that has no Wurfchronik litter and isn't already litter-linked. Siblings
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// (same father+mother+dob) share one derived litter. Computed for dry-run counts too.
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int parentLinksAdded = 0, derivedLitters = 0;
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var synthLitterForGid = new Dictionary<Guid, Guid>(); // offspring gid -> synth litter id
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var synthLitters = new Dictionary<string, SynthLitter>(); // parents+date key -> synth litter
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foreach (var p in plan)
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{
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if (p.WurfLitterId is not null || p.CurrentLitterId is not null) continue;
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if (p.A.ParentRefs is not { Count: > 0 }) continue;
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var father = ResolveParentGid(p.A, "father", gidByNameDob);
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var mother = ResolveParentGid(p.A, "mother", gidByNameDob);
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if (father is null && mother is null) continue; // nothing resolvable to link
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var dob = ParseDate(p.A.Dob);
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var conf = p.A.ParentRefs.FirstOrDefault()?.Confidence ?? "medium";
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var key = $"{father}|{mother}|{dob:yyyy-MM-dd}";
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if (!synthLitters.TryGetValue(key, out var sl))
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{
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sl = new SynthLitter(Guid.NewGuid(), father, mother, dob, conf);
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synthLitters[key] = sl;
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derivedLitters++;
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}
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synthLitterForGid[p.Gid] = sl.Id;
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parentLinksAdded++;
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}
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// PASS 2: write (litters synthesized first so offspring FK resolves), then animals + photos.
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if (execute)
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{
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// reuse an existing litter with the same parents+date instead of duplicating.
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var existingLitterRows = await _db.Litters
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.Select(l => new { l.Id, l.FatherId, l.MotherId, l.Date }).ToListAsync();
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var litterByParentsDate = new Dictionary<string, Guid>();
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foreach (var l in existingLitterRows)
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litterByParentsDate[$"{l.FatherId}|{l.MotherId}|{l.Date:yyyy-MM-dd}"] = l.Id;
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foreach (var sl in synthLitters.Values.ToList())
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{
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var reuseKey = $"{sl.Father}|{sl.Mother}|{sl.Date:yyyy-MM-dd}";
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if (litterByParentsDate.TryGetValue(reuseKey, out var existingId))
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{
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// remap offspring to the existing litter; don't create a duplicate.
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foreach (var g in synthLitterForGid.Where(kv => kv.Value == sl.Id).Select(kv => kv.Key).ToList())
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synthLitterForGid[g] = existingId;
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derivedLitters--;
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continue;
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}
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_db.Litters.Add(new Litter
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{
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Id = sl.Id,
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Name = $"Wurf (aus Diagramm) {sl.Date:yyyy-MM-dd}".Trim(),
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Date = sl.Date ?? default,
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FatherId = sl.Father,
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MotherId = sl.Mother,
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Notes = $"aus Stammbaum-Diagramm abgeleitet (Konfidenz: {sl.Confidence})",
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});
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}
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await _db.SaveChangesAsync();
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}
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foreach (var p in plan)
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{
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Guid? litterId = p.WurfLitterId
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?? (synthLitterForGid.TryGetValue(p.Gid, out var slid) ? slid : (Guid?)null);
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if (litterId is not null) linked++;
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if (p.ColorVarietyId is null) fbUnmatched++; else fbMatched++;
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if (samples.Count < 16)
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samples.Add($"Tier: {p.A.Name} (*{p.A.Dob}), Genotyp {ComposeGenotype(p.A.Genotype)}"
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+ (litterId is not null ? (p.WurfLitterId is not null ? ", Wurf-verknüpft" : ", Eltern aus Diagramm") : "")
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+ (p.ColorVarietyId is not null ? $", Farbschlag „{p.A.Farbschlag}\"" : ""));
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if (p.Exists)
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{
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animalsExisting++;
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// re-link an existing animal that just became linkable (sweep idempotency).
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if (execute && p.CurrentLitterId is null && litterId is not null)
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{
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var row = await _db.Gerbils.FirstOrDefaultAsync(g => g.Id == p.Gid);
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if (row is not null) row.LitterId = litterId;
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}
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continue;
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}
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animalsCreated++;
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if (execute)
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{
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_db.Gerbils.Add(new Gerbil
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{
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Id = p.Gid,
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Name = p.A.Name,
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Gender = p.Gender,
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Status = GerbilStatus.Active,
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DateOfBirth = ParseDate(p.A.Dob),
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DateOfDeath = ParseDate(p.A.Death),
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LitterId = litterId,
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ColorVarietyId = p.ColorVarietyId,
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Genotype = ComposeGenotype(p.A.Genotype),
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IsDeaf = p.A.Deaf,
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ImportSource = ImportSourceTag,
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ExternalRef = p.A.Id,
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OriginBreeder = string.IsNullOrWhiteSpace(p.A.Zucht) ? null : p.A.Zucht.Trim(),
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RawImportData = JsonSerializer.Serialize(new
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{
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p.A.Genotype.RawGenotype,
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p.A.Genotype.UnmappedTokens,
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// GEN-3b: Sls (2nd spotting locus) preserved here until Kevin's GEN-3a
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// parser adopts it into the compact Genotype contract; tags + deaf too.
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Sls = p.A.Genotype.Mapped8locus.TryGetValue("Sls", out var sls) ? sls : null,
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p.A.Tags,
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p.A.Deaf,
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p.A.Zucht,
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p.A.SourceFiles,
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FarbschlagRaw = p.A.Farbschlag,
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}),
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});
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}
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// photos
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foreach (var rel in p.A.Photos)
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{
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var src = Path.Combine(_sourceDir, rel.Replace('/', Path.DirectorySeparatorChar));
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if (!File.Exists(src)) { photosMissing++; continue; }
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photosAttached++;
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if (execute)
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{
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Directory.CreateDirectory(_photoRoot);
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var fileName = $"{Guid.NewGuid():N}{Path.GetExtension(src)}";
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File.Copy(src, Path.Combine(_photoRoot, fileName), overwrite: true);
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_db.GerbilPhotos.Add(new GerbilPhoto
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{
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Id = Guid.NewGuid(),
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GerbilId = p.Gid,
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FileName = fileName,
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SortOrder = 0,
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CreatedAt = DateTimeOffset.UtcNow,
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});
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}
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}
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}
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if (execute) await _db.SaveChangesAsync();
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// ---- back-link Wurfchronik litter parents by name (best effort) ----
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if (execute)
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{
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foreach (var sl in litters)
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{
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if (!litterIdMap.TryGetValue(sl.Id, out var lid)) continue;
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var litter = await _db.Litters.FirstOrDefaultAsync(l => l.Id == lid);
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if (litter is null) continue;
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if (createdAnimalByName.TryGetValue(Normalize(StripZucht(sl.SireName)), out var fId))
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litter.FatherId = fId;
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if (createdAnimalByName.TryGetValue(Normalize(StripZucht(sl.DamName)), out var mId))
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litter.MotherId = mId;
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}
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await _db.SaveChangesAsync();
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}
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notes.Add("Quarantäne (kein Import): Konflikte + Stubs ohne Geburtsdatum + unsichere Wurf-Zuordnungen — warten auf die Prüfung durch die Züchterin.");
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if (parentLinksAdded > 0)
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notes.Add($"Stammbaum-Diagramm: {parentLinksAdded} Tiere über Eltern-Verknüpfung einem (abgeleiteten) Wurf zugeordnet ({derivedLitters} abgeleitete Würfe).");
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if (!execute) notes.Add("DRY-RUN: nichts gespeichert. /import/execute lädt die konfliktfreien Daten.");
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return new ImportReport(
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Executed: execute,
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Litters: new LitterSummary(litters.Count, littersCreated, littersExisting, derivedLitters),
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Animals: new AnimalSummary(
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animals.Count, animalsCreated, linked, fbMatched, fbUnmatched, animalsExisting,
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new QuarantineSummary(conflicts, stubs, dateOnly, ambiguous, conflicts + stubs),
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parentLinksAdded),
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Photos: new PhotoSummary(photosAttached, photosMissing),
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Samples: samples,
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Notes: notes);
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}
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private T? Load<T>(string file)
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{
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var path = Path.Combine(_sourceDir, file);
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if (!File.Exists(path)) return default;
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using var fs = File.OpenRead(path);
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return JsonSerializer.Deserialize<T>(fs, Json);
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}
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public static string ComposeGenotype(SourceGenotype g)
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{
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var tokens = LocusOrder.Select(locus =>
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{
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if (g.Mapped8locus.TryGetValue(locus, out var pair) && pair.Count == 2)
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return StripCaret(pair[0]) + StripCaret(pair[1]);
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return "??";
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}).ToList();
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// GEN-3a contract (Kevin): Sls is appended LAST and ONLY for carriers — the
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// wild-type sl/sl is omitted so existing 8-locus strings stay unchanged. WP het
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// renders as the trailing token "Slsl"; S(l)S(l) is lethal so never appears.
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if (g.Mapped8locus.TryGetValue("Sls", out var sls) && sls.Count == 2
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&& !(sls[0] == "sl" && sls[1] == "sl"))
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{
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tokens.Add(StripCaret(sls[0]) + StripCaret(sls[1]));
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}
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return string.Join(' ', tokens);
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}
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private static string StripCaret(string allele) => allele.Replace("^", "");
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private static Gender InferGender(SourceAnimal a, HashSet<string> sires, HashSet<string> dams)
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{
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// Box colour (blue=male, white=female) is the authoritative breeder signal — prefer it
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// over sire/dam name inference (PEDIGREE-LINK, Julian 2026-06-06).
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if (string.Equals(a.Gender, "male", StringComparison.OrdinalIgnoreCase)) return Gender.male;
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if (string.Equals(a.Gender, "female", StringComparison.OrdinalIgnoreCase)) return Gender.female;
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var n = Normalize(StripZucht(a.Name));
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bool isSire = sires.Contains(n), isDam = dams.Contains(n);
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if (isSire && !isDam) return Gender.male;
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if (isDam && !isSire) return Gender.female;
|
||
return Gender.unknown;
|
||
}
|
||
|
||
public static DateOnly? ParseDate(string s)
|
||
{
|
||
if (string.IsNullOrWhiteSpace(s)) return null;
|
||
var m = Regex.Match(s, @"(\d{1,2})\.(\d{1,2})\.(\d{2,4})");
|
||
if (!m.Success) return null;
|
||
int d = int.Parse(m.Groups[1].Value), mo = int.Parse(m.Groups[2].Value);
|
||
int y = int.Parse(m.Groups[3].Value);
|
||
if (y < 100) y += 2000;
|
||
try { return new DateOnly(y, mo, d); }
|
||
catch { return null; }
|
||
}
|
||
|
||
private static string StripZucht(string name)
|
||
{
|
||
var n = Regex.Replace(name ?? "", @"\[.*?\]", " ");
|
||
n = Regex.Replace(n, @"\s+(?:of|von\s+den|von\s+der|v\.\s?d\.|von)\s+.*$", "", RegexOptions.IgnoreCase);
|
||
return n.Trim();
|
||
}
|
||
|
||
private static string Normalize(string name)
|
||
{
|
||
var n = (name ?? "").ToLowerInvariant();
|
||
n = Regex.Replace(n, @"\bgen\.\b", " ");
|
||
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);
|
||
}
|
||
}
|