| """Prove that a rebuilt spectral_library only changed what it was supposed to change. |
| |
| Compares a backup copy of ``assets/reactions/spectral_library`` (``--before``) with the rebuilt one (``--after``): |
| |
| * every compound entry that existed before is value-identical in every JSON file, except |
| - IR records listed in the FT/IR-4700 correction overlay (``--overlay``; the 24 mis-decoded spectra), which must |
| now equal the overlay's corrected values (grid, peaks, x range, header fields, y transform), and |
| - IR records the fixed decoder excludes (real-refractive-index-only optical-constant files), which must be listed |
| in ``excluded_spectra`` of the new ir_spectra.json, together with the matching ``index.json → ir_spectra`` count; |
| * unaffected IR records keep their order inside each compound; |
| * new compound ids are reported (they may only be added, never replace an existing id). |
| |
| Writes a JSON report (``--report``) and exits 1 on any unexpected difference. |
| |
| Usage: python -I verify_rebuild.py --before <backup dir> [--after assets/reactions/spectral_library] |
| [--overlay <jasco_ftir4700_ir_library/templates.json>] [--report out.json] |
| """ |
| from __future__ import annotations |
|
|
| import argparse |
| import json |
| from pathlib import Path |
|
|
| ROOT = Path(__file__).resolve().parents[2] |
| BACKUP = Path("../backups/spectral_library_2026-10-14") |
| OVERLAY_FIELDS = ("absorbance_normalized", "peaks_cm-1", "x_range_cm-1", "title", "state", "sampling", "resolution", "y_units_original", "y_transform") |
| FILES = ("compounds.json", "gc_retention.json", "ir_spectra.json", "ms_ei.json", "uv_vis.json", "nmr.json", "hplc_uv.json", "index.json") |
|
|
|
|
| def load(p: Path) -> dict: |
| return json.loads(p.read_text(encoding="utf-8")) |
|
|
|
|
| def main() -> int: |
| ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) |
| ap.add_argument("--before", type=Path, default=BACKUP / "spectral_library") |
| ap.add_argument("--after", type=Path, default=ROOT / "assets" / "reactions" / "spectral_library") |
| ap.add_argument("--overlay", type=Path, default=BACKUP / "aux" / "reactions" / "jasco_ftir4700_ir_library" / "templates.json") |
| ap.add_argument("--report", type=Path, default=None) |
| args = ap.parse_args() |
|
|
| overlay = {(t["compound_id"], t["nist_index"]): t for t in load(args.overlay)["templates"]} |
| ir_after_doc = load(args.after / "ir_spectra.json") |
| excluded = {(sid, e["nist_index"]) for sid, rows in ir_after_doc.get("excluded_spectra", {}).items() for e in rows} |
| report = {"before": str(args.before), "after": str(args.after), "overlay": str(args.overlay), "files": {}, "errors": []} |
| err = report["errors"].append |
|
|
| for name in FILES: |
| b = load(args.before / name) |
| a = load(args.after / name) |
| bc, ac = b["compounds"], a["compounds"] |
| missing = sorted(set(bc) - set(ac)) |
| added = sorted(set(ac) - set(bc)) |
| if missing: |
| err(f"{name}: compounds removed: {missing}") |
| changed_meta = sorted(k for k in set(a) | set(b) if k != "compounds" and a.get(k) != b.get(k)) |
| identical, differing, expected = 0, [], [] |
| for sid in sorted(set(bc) & set(ac)): |
| if name == "ir_spectra.json": |
| before_recs = {r["nist_index"]: r for r in bc[sid]} |
| after_recs = {r["nist_index"]: r for r in ac[sid]} |
| order_b = [r["nist_index"] for r in bc[sid] if (sid, r["nist_index"]) not in overlay and (sid, r["nist_index"]) not in excluded] |
| order_a = [r["nist_index"] for r in ac[sid] if (sid, r["nist_index"]) not in overlay] |
| if order_b != order_a: |
| err(f"{name}:{sid}: order/set of unaffected records changed {order_b} -> {order_a}") |
| for idx, rb in before_recs.items(): |
| key = (sid, idx) |
| if key in excluded: |
| if idx in after_recs: |
| err(f"{name}:{sid}#{idx}: listed as excluded but still stored") |
| expected.append({"record": f"{sid}__ir_{idx}", "change": "excluded (real-index-only optical-constant file)"}) |
| continue |
| ra = after_recs.get(idx) |
| if ra is None: |
| err(f"{name}:{sid}#{idx}: record disappeared"); continue |
| if key in overlay: |
| ov = overlay[key] |
| bad = [f for f in OVERLAY_FIELDS if ra.get(f) != ov.get(f)] |
| if bad: |
| err(f"{name}:{sid}#{idx}: does not match the overlay in {bad}") |
| n_changed = sum(1 for p, q in zip(ra["absorbance_normalized"], rb["absorbance_normalized"]) if p != q) |
| expected.append({"record": f"{sid}__ir_{idx}", "change": "corrected; equals overlay", "grid_points_changed_vs_before": n_changed, |
| "overlay_reason": ov["overrides"]["reason"]}) |
| continue |
| if ra == rb: |
| identical += 1 |
| else: |
| differing.append(f"{sid}#{idx}: " + ",".join(sorted(k for k in set(ra) | set(rb) if ra.get(k) != rb.get(k)))) |
| for idx in after_recs: |
| if idx not in before_recs: |
| err(f"{name}:{sid}#{idx}: new IR record for an existing compound") |
| continue |
| eb, ea = bc[sid], ac[sid] |
| if eb == ea: |
| identical += 1 |
| continue |
| keys = sorted(k for k in set(ea or {}) | set(eb or {}) if (ea or {}).get(k) != (eb or {}).get(k)) if isinstance(ea, dict) and isinstance(eb, dict) else ["<value>"] |
| n_excl = sum(1 for (s, _i) in excluded if s == sid) |
| if name == "index.json" and keys == ["ir_spectra"] and eb["ir_spectra"] - ea["ir_spectra"] == n_excl: |
| expected.append({"record": sid, "change": f"ir_spectra count {eb['ir_spectra']} -> {ea['ir_spectra']} (excluded real-index-only files)"}) |
| continue |
| differing.append(f"{sid}: {keys}") |
| for d in differing: |
| err(f"{name}: unexpected difference {d}") |
| report["files"][name] = {"compared_entries": len(set(bc) & set(ac)) if name != "ir_spectra.json" else sum(len(v) for k, v in bc.items() if k in ac), |
| "identical_entries": identical, "expected_changes": expected, "unexpected_differences": differing, |
| "added_compounds": len(added), "added_ids": added, "top_level_keys_changed": changed_meta} |
| overlay_keys_checked = sum(1 for e in report["files"]["ir_spectra.json"]["expected_changes"] if e["change"].startswith("corrected")) |
| if overlay_keys_checked != len(overlay): |
| err(f"overlay records checked {overlay_keys_checked} != {len(overlay)}") |
| report["summary"] = {"overlay_records_matched": overlay_keys_checked, "excluded_records": len(excluded), |
| "unaffected_ir_records_identical": report["files"]["ir_spectra.json"]["identical_entries"], |
| "pass": not report["errors"]} |
| text = json.dumps(report, ensure_ascii=False, indent=1) |
| if args.report: |
| args.report.parent.mkdir(parents=True, exist_ok=True) |
| args.report.write_text(text + "\n", encoding="utf-8") |
| print(json.dumps({"summary": report["summary"], "errors": report["errors"][:20], |
| "per_file": {k: {kk: v[kk] for kk in ("compared_entries", "identical_entries", "added_compounds", "top_level_keys_changed")} | {"expected_changes": len(v["expected_changes"])} |
| for k, v in report["files"].items()}}, ensure_ascii=False, indent=1)) |
| return 0 if not report["errors"] else 1 |
|
|
|
|
| if __name__ == "__main__": |
| raise SystemExit(main()) |
|
|
