| """v2 step 5: metadata tables shipped with the release, built from what v2_verify.py OBSERVED in the written files. |
| |
| metadata/triplets.parquet one row per released triplet, sorted by saddle_ms_id: |
| saddle_ms_id, subset, split, file, reactant_row_id (ASE id of the reactant row in `file`; saddle = +1, |
| product = +2), chemical_system, reduced_formula, source_id |
| metadata/removed_duplicates.parquet one row per removed triplet, sorted by removed_saddle_ms_id: |
| removed_saddle_ms_id, removed_subset, kept_saddle_ms_id, kept_subset, reason ("duplicate", or "broken" for |
| the BROKEN triplets that v2_write.py leaves out, with null kept_saddle_ms_id and kept_subset) |
| usage: v2_metadata.py <observed.npz> <meta_dir> <duplicates.parquet> <out_root> |
| """ |
| import glob, os, sys |
| import numpy as np, pyarrow as pa, pyarrow.parquet as pq |
| obs, meta_dir, dup_file, out = sys.argv[1:5]; SUBS = ["lemat", "mp20bat", "oc20", "oc22"] |
| BROKEN = [35584423, 79800988] |
| O = np.load(obs); assert bool(O["passed"]), "verification did not pass - refusing to build metadata" |
| files, n, ms = O["shard"], O["n"], O["ms"] |
| fi = np.repeat(np.arange(len(files)), n); row = np.concatenate([np.arange(1, k + 1) for k in n]) |
| sad = ms % 3 == 1; s_ms, s_fi, s_row = ms[sad], fi[sad], row[sad] - 1 |
| assert (ms[np.flatnonzero(sad) - 1] == s_ms - 1).all() |
| M = [np.load(f) for f in sorted(glob.glob(f"{meta_dir}/*.npz"))] |
| mms = np.concatenate([m["ms"] for m in M]); o = np.argsort(mms); mms = mms[o] |
| msub, mcs, mfo, msrc = (np.concatenate([m[k] for m in M])[o] for k in ("sub", "chemsys", "formula", "source")) |
| p = np.searchsorted(mms, s_ms); assert (mms[p] == s_ms).all() |
| parts = np.array([f.split("/") for f in files]) |
| t = np.argsort(s_ms) |
| tab = pa.table({"saddle_ms_id": pa.array(s_ms[t], pa.int64()), |
| "subset": pa.array(parts[s_fi[t], 0]), "split": pa.array(parts[s_fi[t], 1]), |
| "file": pa.array(files[s_fi[t]]), "reactant_row_id": pa.array(s_row[t], pa.int32()), |
| "chemical_system": pa.array(mcs[p][t]), "reduced_formula": pa.array(mfo[p][t]), "source_id": pa.array(msrc[p][t])}) |
| assert (np.array([SUBS[x] for x in msub[p][t]]) == parts[s_fi[t], 0]).all(), "subset in meta != directory" |
| os.makedirs(f"{out}/metadata", exist_ok=True) |
| pq.write_table(tab, f"{out}/metadata/triplets.parquet", compression="zstd") |
| D = pq.read_table(dup_file); dms = np.asarray(D.column(0)); drep = np.asarray(D.column(1)); r = dms != drep |
| pd_ = np.searchsorted(mms, dms[r]); pk = np.searchsorted(mms, drep[r]); pb = np.searchsorted(mms, BROKEN) |
| dup = pa.table({"removed_saddle_ms_id": pa.array(dms[r], pa.int64()), "removed_subset": pa.array([SUBS[x] for x in msub[pd_]]), |
| "kept_saddle_ms_id": pa.array(drep[r], pa.int64()), "kept_subset": pa.array([SUBS[x] for x in msub[pk]]), |
| "reason": pa.array(["duplicate"] * int(r.sum()), pa.string())}) |
| brk = pa.table({"removed_saddle_ms_id": pa.array(BROKEN, pa.int64()), "removed_subset": pa.array([SUBS[x] for x in msub[pb]]), |
| "kept_saddle_ms_id": pa.array([None] * len(BROKEN), pa.int64()), "kept_subset": pa.array([None] * len(BROKEN), pa.string()), |
| "reason": pa.array(["broken"] * len(BROKEN), pa.string())}) |
| pq.write_table(pa.concat_tables([dup, brk]).sort_by("removed_saddle_ms_id"), f"{out}/metadata/removed_duplicates.parquet", compression="zstd") |
| assert not np.isin(dms[r], s_ms).any() and np.isin(drep[r], s_ms).all() and not np.isin(BROKEN, s_ms).any(), "removed/kept inconsistent with the files" |
| print(f"triplets.parquet: {tab.num_rows} rows; removed_duplicates.parquet: {int(r.sum())} duplicate + {len(BROKEN)} broken rows") |
|
|
