Fix import FK fault: derived/back-linked litter referenced a not-yet-inserted parent
BUG (blocked the supervised live re-import): /import/execute threw Npgsql 23503 FK_Litters_Gerbils_FatherId and rolled back. Root cause was INSERT ORDERING — synthesized derived litters were SaveChanges()'d BEFORE the parent gerbils (created later in the animal loop), so the litter's Father/MotherId pointed at rows that didn't exist yet. The dry-run and the EF in-memory test provider don't enforce FKs, so it slipped through. Fix: - Stage synthesized litters in the context but DON'T save them early; the single SaveChanges after the animal loop lets EF order parents → litters → offspring (all FKs nullable). Saving litters first was the fault. - FK-integrity guard (god's spec): compute the persisted set (existing DB + this run's loadable) and null out any litter parent FK not in it; SKIP a derived litter whose BOTH parents are unresolvable (offspring loads with LitterId=null). Quarantined parents already resolve to null via ResolveParentGid; this is defense-in-depth + makes the invariant explicit. - Report litterParentFksDropped + derivedLittersSkipped (LitterSummary) + a German note — so a green dry-run (0/0) GUARANTEES execute won't FK-fault. Tests: two SQLite-backed regressions (SQLite enforces FKs, unlike the in-memory provider) — a derived litter with NEW chart parents executes without throwing, and a quarantined parent leaves that FK null. 120 C# tests + python green; no schema change (has-pending clean). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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@@ -1,5 +1,6 @@
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using GerbilManagerWebAPI.Import;
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using GerbilManagerWebAPI.Models;
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using Microsoft.Data.Sqlite;
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using Microsoft.EntityFrameworkCore;
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namespace GerbilManager.Tests
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@@ -191,6 +192,92 @@ namespace GerbilManager.Tests
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finally { try { Directory.Delete(dir, recursive: true); } catch { } }
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}
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[Fact]
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public async Task Execute_on_relational_db_with_new_chart_parents_does_not_FK_throw()
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{
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// Regression for FK_Litters_Gerbils_FatherId: a derived litter references parent gerbils
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// created in the SAME run, so they must be inserted before the litter. The EF in-memory
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// provider does NOT enforce FKs (which masked the bug), so this uses SQLite — which does.
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var dir = Path.Combine(Path.GetTempPath(), "fkfix-" + Guid.NewGuid().ToString("N"));
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Directory.CreateDirectory(dir);
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using var conn = new SqliteConnection("DataSource=:memory:");
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conn.Open();
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try
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{
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File.WriteAllText(Path.Combine(dir, "litters.json"), "[]");
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File.WriteAllText(Path.Combine(dir, "animals.json"), """
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[
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{"id":"papa","name":"Papa v.d. Test","dob":"01.01.2022","death":"","farbschlag":"",
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"genotype":{"mapped8locus":{},"rawGenotype":"","unmappedTokens":[]},"conflict":false},
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{"id":"mama","name":"Mama v.d. Test","dob":"02.02.2022","death":"","farbschlag":"",
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"genotype":{"mapped8locus":{},"rawGenotype":"","unmappedTokens":[]},"conflict":false},
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{"id":"c","name":"C","dob":"29.04.2024","death":"","farbschlag":"",
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"genotype":{"mapped8locus":{},"rawGenotype":"","unmappedTokens":[]},"conflict":false,
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"parentRefs":[
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{"name":"Papa v.d. Test","dob":"01.01.2022","roleGuess":"father","method":"chart-position","confidence":"medium"},
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{"name":"Mama v.d. Test","dob":"02.02.2022","roleGuess":"mother","method":"chart-position","confidence":"medium"}
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]}
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]
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""");
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var opts = new DbContextOptionsBuilder<ApplicationContext>().UseSqlite(conn).Options;
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using var db = new ApplicationContext(opts);
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await db.Database.EnsureCreatedAsync(); // schema WITH enforced FK constraints
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// must not throw FK_Litters_Gerbils_FatherId (parents inserted before the litter)
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var report = await new ImportService(db, dir, dir).RunAsync(execute: true);
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var c = await db.Gerbils.SingleAsync(g => g.ExternalRef == "c");
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Assert.NotNull(c.LitterId);
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var litter = await db.Litters.SingleAsync(l => l.Id == c.LitterId);
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Assert.Equal((await db.Gerbils.SingleAsync(g => g.ExternalRef == "papa")).Id, litter.FatherId);
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Assert.Equal(0, report.Litters.ParentFksDropped);
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Assert.Equal(0, report.Litters.DerivedSkipped);
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}
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finally { try { Directory.Delete(dir, recursive: true); } catch { } }
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}
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[Fact]
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public async Task Derived_litter_with_quarantined_parent_leaves_FK_null_no_throw()
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{
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// A chart parentRef pointing to a QUARANTINED (conflict) animal must not become an FK —
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// the derived litter keeps that side null; if both sides are unresolvable, no litter.
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var dir = Path.Combine(Path.GetTempPath(), "fkq-" + Guid.NewGuid().ToString("N"));
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Directory.CreateDirectory(dir);
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using var conn = new SqliteConnection("DataSource=:memory:");
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conn.Open();
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try
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{
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File.WriteAllText(Path.Combine(dir, "litters.json"), "[]");
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File.WriteAllText(Path.Combine(dir, "animals.json"), """
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[
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{"id":"badpa","name":"BadPapa v.d. Test","dob":"01.01.2022","death":"","farbschlag":"",
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"genotype":{"mapped8locus":{},"rawGenotype":"","unmappedTokens":[]},"conflict":true},
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{"id":"goodma","name":"GoodMama v.d. Test","dob":"02.02.2022","death":"","farbschlag":"",
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"genotype":{"mapped8locus":{},"rawGenotype":"","unmappedTokens":[]},"conflict":false},
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{"id":"c2","name":"C2","dob":"29.04.2024","death":"","farbschlag":"",
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"genotype":{"mapped8locus":{},"rawGenotype":"","unmappedTokens":[]},"conflict":false,
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"parentRefs":[
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{"name":"BadPapa v.d. Test","dob":"01.01.2022","roleGuess":"father","method":"chart-position","confidence":"medium"},
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{"name":"GoodMama v.d. Test","dob":"02.02.2022","roleGuess":"mother","method":"chart-position","confidence":"medium"}
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]}
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]
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""");
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var opts = new DbContextOptionsBuilder<ApplicationContext>().UseSqlite(conn).Options;
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using var db = new ApplicationContext(opts);
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await db.Database.EnsureCreatedAsync();
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await new ImportService(db, dir, dir).RunAsync(execute: true); // must not throw
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Assert.False(await db.Gerbils.AnyAsync(g => g.ExternalRef == "badpa")); // quarantined
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var c2 = await db.Gerbils.SingleAsync(g => g.ExternalRef == "c2");
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Assert.NotNull(c2.LitterId); // still linked (via mother)
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var litter = await db.Litters.SingleAsync(l => l.Id == c2.LitterId);
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Assert.Null(litter.FatherId); // quarantined father -> null FK
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Assert.Equal((await db.Gerbils.SingleAsync(g => g.ExternalRef == "goodma")).Id, litter.MotherId);
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}
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finally { try { Directory.Delete(dir, recursive: true); } catch { } }
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}
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[Fact]
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public void ComposeGenotype_strips_carets_and_fills_missing_loci()
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{
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