GerbilManager/tools/import

GerbilManager import tooling (FEAT-8b)

One-off migration tooling (Python, no third-party deps) that turns Julian's wife's hand-built spreadsheets into normalised JSON for review and, later, import. This is not product code — it lives outside the app and is run manually.

See the format analysis in FEAT-8a-format-spec.md (Pam's hive workspace).

What it does

extract.py runs stages 1–2 of the pipeline:

1. Extract (stage 1)
   • 10 Stammbaum pedigree charts → animals (name, DOB, death, Farbschlag, genotype, breeder, positionally-reconstructed parent links, photos).
   • Wurfchronik litter chronicle → litters (date, dam, sire, Wurfstärke, sex breakdown, Zuchtnummer, notes). Columns are read by header row because the two sheets use different schemas.
   • Embedded photos (xl/media) → output/photos/<animal-slug>/, mapped to the animal by drawing anchor position.
2. Dedup + review (stage 2)
   • Merge animals on normalise(call-name) + DOB, with the Zucht as discriminator (Julian's ruling: Wurfchronik [brackets] ≡ Stammbaum of/von <line> suffix — both are the breeding line; same name+DOB but different Zucht stays two animals).
   • Match animals onto Wurfchronik litters (litterRef) via DOB + (Vater, Mutter) — the Pam-validated build order (chronicle litters are canonical).
   • Emit a German-language output/review-report.md for the breeder to verify (merges, conflicts, ambiguous/incomplete entries, unmapped genotype tokens, litter data-quality warnings).
   • Nothing is loaded into the database — stage 3 (API load) is separate and waits on DATA-2 + FEAT-1b phase 2.

Wurfchronik column semantics (Julian, authoritative)

A Wurfbezeichnung · B Geburtsdatum · C Mutter · D Vater ([…] = Zucht, & = multiple sires) · E survivedToGoHome (Tabelle1 only, unlabeled — detected positionally) · F Wurfstärke → totalBorn · G breakdown Männchen,Weibchen,TG,s → males/females/stillborn/diedLater (s = died after birth, before Abgabe) · last column → note. Validation: E should equal F − TG − s; mismatches become German warnings in the review report (data-quality signal, not an import blocker). A few Tabelle2 rows shift these columns — they are read value-adaptively and flagged with a warning.

Genotypes are mapped to the frozen 8-locus contract (A C D E G P Sp Re) while preserving everything: genotype.mapped8locus, genotype.rawGenotype (verbatim), genotype.unmappedTokens (e.g. the Uw locus, markers WFNZ/WP/DP). A - (unknown second allele) maps to ?.

Run

cd tools/import
python extract.py                       # uses the default source paths
python extract.py --stammbaeume "<dir>" --wurfchronik "<file.xlsx>"

Requires Python 3. Re-runnable / idempotent — re-run when more files arrive (Wurfchronik Teil2+, or new charts).

Output (tools/import/output/, git-ignored except the report)

File	Contents
animals.json	deduped animals with genotype, parentRefs, photos, sourceFiles
litters.json	litters from the Wurfchronik
photos/<slug>/…	extracted, anchor-mapped images
review-report.md	human review deliverable (committed)

Files

• xlsx_util.py — dependency-free .xlsx reader (zip + XML): shared strings, cells by reference, image/drawing anchors.
• genotype.py — genotype notation parser → 8-locus mapping + raw + unmapped.
• extract.py — the pipeline (stages 1–2).