"""Phase 8: Metadata Audit — completeness, consistency, correctness.""" import json, time from pathlib import Path from collections import Counter import numpy as np OUT = Path("scripts/audit_reports") DATASET = "dataset/entries_final_v3.json" AUDIT_DIR = Path.cwd() if Path.cwd().name == "Scandium-Dataset" else Path("/home/shamique/Scandium Labs SSB/Scandium-Dataset") severity_counts = {"CRITICAL": 0, "HIGH": 0, "MEDIUM": 0, "LOW": 0, "PASS": 0} findings = [] def finding(severity, phase, check, status, detail): severity_counts[severity] += 1 findings.append({"severity": severity, "phase": phase, "check": check, "status": status, "detail": str(detail)[:200]}) s = "🔴" if severity == "CRITICAL" else "🟠" if severity == "HIGH" else "🟡" if severity == "MEDIUM" else "🔵" if severity == "LOW" else "✅" print(f" {s} [{severity:8s}] {check}: {str(detail)[:120]}") REQUIRED_FIELDS = ["source_id", "formula", "elements", "source", "space_group", "volume", "density", "structure_json", "quality_score", "quality_sub_scores", "quality_flags", "tier", "provenance", "nsites", "band_gap", "formation_energy_per_atom", "families"] def main(): print("=" * 60) print(" PHASE 8: METADATA AUDIT") print("=" * 60) with open(AUDIT_DIR / DATASET) as f: entries = json.load(f) N = len(entries) # Field completeness print(f"\n--- Field Completeness ---") field_missing = Counter() for field in REQUIRED_FIELDS: for e in entries: if field not in e or e[field] is None: field_missing[field] += 1 for field, count in sorted(field_missing.items()): bad = count > 0 sev = "PASS" if bad and count > N * 0.01: sev = "HIGH" if count > N * 0.1 else "MEDIUM" elif bad and count > 10: sev = "LOW" elif bad: sev = "PASS" finding(sev, "completeness", f"missing_{field}", f"{count:,} ({100*count/N:.1f}%)", "") # Check tier distribution print(f"\n--- Tier Distribution ---") tier_counts = Counter(e.get("tier") for e in entries) for tier, cnt in sorted(tier_counts.items()): print(f" {tier:12s}: {cnt:>7,}") if tier_counts.get("raw") is None: finding("LOW", "tiers", "no_raw_tier", "raw tier missing from frozen set", "") # Source distribution print(f"\n--- Source Distribution ---") src_counts = Counter(e.get("source") for e in entries) for src, cnt in sorted(src_counts.items()): print(f" {src:8s}: {cnt:>7,} ({100*cnt/N:.1f}%)") # Family distribution print(f"\n--- Family Distribution ---") family_counts = Counter() for e in entries: for fam in e.get("families", []): family_counts[fam] += 1 for fam, cnt in sorted(family_counts.most_common(20)): print(f" {fam:20s}: {cnt:>7,}") # Provenance completeness print(f"\n--- Provenance ---") prov_fields = 0 for e in entries: if e.get("provenance"): prov_fields += 1 print(f" Entries with provenance: {prov_fields:,} ({100*prov_fields/N:.1f}%)") if prov_fields < N: finding("HIGH", "provenance", "missing_provenance", f"{N - prov_fields:,} entries ({100*(N-prov_fields)/N:.1f}%) missing", "") else: finding("PASS", "provenance", "all_have_provenance", "", "") # Check duplicate_group metadata dg_cnt = sum(1 for e in entries if e.get("duplicate_group") is not None) print(f"\n Entries with duplicate_group: {dg_cnt:,} ({100*dg_cnt/N:.1f}%)") # Check that all entries have structure_json no_struct = sum(1 for e in entries if not e.get("structure_json")) if no_struct > 0: finding("CRITICAL", "structure", "missing_structure", f"{no_struct:,} ({100*no_struct/N:.1f}%)", "") else: finding("PASS", "structure", "all_have_structure", "", "") # Check structured_formula parity sf_missing = sum(1 for e in entries if not e.get("structured_formula")) if sf_missing > 0: finding("MEDIUM", "metadata", "missing_structured_formula", f"{sf_missing:,} entries", "") # ID format consistency print(f"\n--- ID Consistency ---") id_formats = Counter() for e in entries: mid = e.get("source_id", "") if mid.startswith("mp-"): id_formats["mp-"] += 1 elif mid.startswith("oqmd-"): id_formats["oqmd-"] += 1 elif mid.startswith("jv-") or mid.startswith("jarvis-"): id_formats["jarvis"] += 1 else: id_formats["other"] += 1 for fmt, cnt in sorted(id_formats.items()): print(f" {fmt:12s}: {cnt:>7,}") if id_formats.get("other", 0) > 0: finding("MEDIUM", "metadata", "nonstandard_ids", f"{id_formats['other']:,} nonstandard IDs", "") # Quality flags staleness (OQMD space_group flag vs actual space_group) stale_flags = 0 for e in entries: if e.get("source") == "oqmd" and e.get("space_group") is not None: flags = e.get("quality_flags", []) if "missing_spacegroup" in flags: stale_flags += 1 if stale_flags > 100: finding("MEDIUM", "metadata", "stale_quality_flags", f"{stale_flags:,} OQMD entries flagged missing_spacegroup but SG now populated", "flags need recalculation") elif stale_flags > 0: finding("LOW", "metadata", "stale_quality_flags", f"{stale_flags} entries", "") else: finding("PASS", "metadata", "flags_current", "", "") # Summary print(f"\n{'=' * 60}") print(f" PHASE 8 SUMMARY") print(f" CRITICAL: {severity_counts['CRITICAL']}") print(f" HIGH: {severity_counts['HIGH']}") print(f" MEDIUM: {severity_counts['MEDIUM']}") print(f" LOW: {severity_counts['LOW']}") print(f" PASS: {severity_counts['PASS']}") print(f"{'=' * 60}") report = { "phase": "Phase 8: Metadata Audit", "timestamp": time.strftime("%Y-%m-%d %H:%M:%S"), "field_completeness": dict(field_missing), "tier_distribution": dict(tier_counts), "source_distribution": dict(src_counts), "family_distribution": dict(family_counts), "id_formats": dict(id_formats), "stale_quality_flags": stale_flags, "findings": findings, "summary": dict(severity_counts), } with open(OUT / "phase8_metadata_audit.json", "w") as f: json.dump(report, f, indent=2) print(f"\n Report: {OUT / 'phase8_metadata_audit.json'}") if __name__ == "__main__": main()