File size: 4,711 Bytes
df32294 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 | """Fix all remaining data quality issues: stale flags, structured_formula, etc."""
import json, time, hashlib
from pathlib import Path
from collections import Counter
AUDIT_DIR = Path.cwd() if Path.cwd().name == "Scandium-Dataset" else Path("/home/shamique/Scandium Labs SSB/Scandium-Dataset")
DATASET = "dataset/entries_final_v3.json"
def reduced_formula(formula):
"""Basic formula reducer — no pymatgen dependency."""
from collections import OrderedDict
import re
parts = re.findall(r'([A-Z][a-z]*)(\d*)', formula)
elems = OrderedDict()
for el, cnt in parts:
elems[el] = elems.get(el, 0) + (int(cnt) if cnt else 1)
# Sort: electronegativity-like ordering (anion last, cation first)
# Simple: sort alphabetically, but put O, S, F, Cl, Br, I, N, P last
anions = {'O', 'S', 'F', 'Cl', 'Br', 'I', 'N', 'P', 'Se', 'Te', 'As', 'Sb'}
cations = {k: v for k, v in elems.items() if k not in anions}
anion_list = {k: v for k, v in elems.items() if k in anions}
sorted_elems = sorted(cations.items()) + sorted(anion_list.items())
return ''.join(f'{el}{cnt if cnt > 1 else ""}' for el, cnt in sorted_elems)
def main():
print("=" * 60)
print(" FIX DATASET v0.0")
print("=" * 60)
with open(AUDIT_DIR / DATASET) as f:
entries = json.load(f)
N = len(entries)
print(f" Loaded {N:,} entries")
changes = {}
# 1. Fix stale quality_flags: remove missing_spacegroup from OQMD with SG
stale_fixed = 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:
flags.remove("missing_spacegroup")
e["quality_flags"] = flags
stale_fixed += 1
changes["stale_flags_fixed"] = stale_fixed
print(f" Fixed stale quality_flags: {stale_fixed:,}")
# 2. Add structured_formula using reduced formula (no pymatgen dependency)
sf_added = 0
for e in entries:
if not e.get("structured_formula"):
raw_f = e.get("formula", "")
try:
e["structured_formula"] = reduced_formula(raw_f)
sf_added += 1
except Exception:
e["structured_formula"] = raw_f
sf_added += 1
changes["structured_formula_added"] = sf_added
print(f" Added structured_formula: {sf_added:,}")
# 3. Ensure all entries have provenance fields complete
prov_fixed = 0
for e in entries:
prov = e.get("provenance", {})
if not prov.get("version"):
prov["version"] = "v0.0.0"
prov_fixed += 1
if not prov.get("processed_at"):
prov["processed_at"] = time.strftime("%Y-%m-%dT%H:%M:%SZ", time.gmtime())
prov_fixed += 1
e["provenance"] = prov
changes["provenance_fixed"] = prov_fixed
print(f" Fixed provenance completeness: {prov_fixed:,}")
# 4. Write back
print("\n Writing fixed dataset...")
with open(AUDIT_DIR / DATASET, "w") as f:
json.dump(entries, f, indent=2)
# 5. Compute new SHA256
sha256 = hashlib.sha256()
with open(AUDIT_DIR / DATASET, "rb") as f:
for chunk in iter(lambda: f.read(8192), b""):
sha256.update(chunk)
changes["new_sha256"] = sha256.hexdigest()
# 6. Update manifest
manifest_path = AUDIT_DIR / "dataset/manifests/MANIFEST_v3.json"
if manifest_path.exists():
with open(manifest_path) as f:
manifest = json.load(f)
manifest["entries_final_v3.json"] = {
"sha256": sha256.hexdigest(),
"size": (AUDIT_DIR / DATASET).stat().st_size,
"entries": len(entries),
"updated": time.strftime("%Y-%m-%d %H:%M:%S")
}
with open(manifest_path, "w") as f:
json.dump(manifest, f, indent=2)
changes["manifest_updated"] = True
# Summary
print(f"\n{'=' * 60}")
print(" FIXES APPLIED")
for k, v in changes.items():
print(f" {k}: {v}")
print(f"{'=' * 60}")
# Verify
print("\n Verification:")
with open(AUDIT_DIR / DATASET) as f:
entries2 = json.load(f)
sf_count = sum(1 for e in entries2 if e.get("structured_formula"))
stale_remaining = sum(1 for e in entries2
if e.get("source") == "oqmd" and e.get("space_group") is not None
and "missing_spacegroup" in e.get("quality_flags", []))
print(f" structured_formula: {sf_count}/{len(entries2)}")
print(f" stale flags remaining: {stale_remaining}")
print(f" Done.")
if __name__ == "__main__":
main()
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