Datasets:
File size: 10,621 Bytes
9ee1aa9 | 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 | """Build the combined IRexp release (v4 IR-attachment fix + 2026 SI expansion) with strict structure tiers.
Inputs are the final local artifacts; nothing is fetched. Output: ../data (chmod 600)."""
import gzip,json,os,re,collections,hashlib
from rdkit import Chem, RDLogger; RDLogger.DisableLog('rdApp.*')
import selfies as sf
OUT='/workspace/irexp_release_237k/data/'
V4R='/workspace/irexp_v4_build/release/data/'
V4T='/workspace/irexp_growth/RESOLVE_237k/work/v4_tiers_final.jsonl.gz'
SIH='/workspace/irexp_growth/harvest/out/'
SIT='/workspace/irexp_growth/audit_rudra/new_tiers_final.jsonl'
SIS='/workspace/irexp_growth/structures/'
BENCH=set(json.load(open('/workspace/irexp_v4_build/work/bench_ik14.json')))
LIC={'CC BY':'CC-BY','CC BY-NC':'CC-BY-NC','CC BY-NC-ND':'CC-BY-NC-ND','CC BY-NC-SA':'CC-BY-NC-SA','CC BY-SA':'CC-BY-SA','CC0':'CC0'}
def mol_fields(smi):
m=Chem.MolFromSmiles(smi) if smi else None
if m is None: return None
can=Chem.MolToSmiles(m)
try: s=sf.encoder(can)
except Exception: s=None
return dict(smiles=can,inchikey=Chem.MolToInchiKey(m),selfies=s,_mol=m)
import sys as _sys
_sys.path.insert(0,'/workspace/irexp_v4_build/spectro-agent'); _sys.path.insert(0,'/workspace/irexp_v4_build/spectro-agent/scripts')
from quarantine_structure_nmr import gate_record as _gate_record
def nmr_check(m,h,c):
"""spectro-agent scripts/quarantine_structure_nmr.py gate_record (same rules as the 2026-08-26 quarantine)."""
return [x for x in _gate_record({'smiles':Chem.MolToSmiles(m),'h_nmr':h,'c_nmr':c,'ir_bands_cm-1':[]}) if x!='no_smiles']
def bands_ok(b):
return all(350<=float(x)<=4000 for x in b)
pools=collections.defaultdict(list); quar=[]; stats=collections.Counter(); tiers=collections.Counter(); tiers_pool=collections.Counter()
# ---------- v4 rows ----------
T={}
for l in gzip.open(V4T,'rt'):
d=json.loads(l); T[d['id']]=d
for f,pool in [('irexp_commercial','commercial'),('irexp_non_commercial','non_commercial'),('irexp_sharealike','sharealike'),('irexp_other','other')]:
for l in gzip.open(V4R+f+'.jsonl.gz','rt'):
d=json.loads(l); t=T[d['id']]; tier=t['tier_final']
d['source_set']='pmc_v4' if pool!='sharealike' or d.get('pmcid') else 'chemotion'
if pool=='sharealike' and d.get('source'): d['source_set']='chemotion' if 'hemotion' in str(d.get('source')) else 'pmc_v4'
flags=[]
if t.get('formula_conflict'): flags.append('formula_conflict')
if t.get('pubchem_conflict'): flags.append('pubchem_conflict')
mf=None
if tier in 'ABCD' and t.get('smiles'):
mf=mol_fields(t['smiles'])
if mf is None: stats['v4_unparseable']+=1; tier='none'
if tier=='X':
if d.get('smiles'): stats['v4_x_structure_removed_'+pool]+=1
quar.append(dict(id=d['id'],license_pool=pool,source_set=d['source_set'],reasons=['tier_X:'+(t.get('x_reason') or t.get('base_why') or 'contradiction')]))
if mf:
if d.get('smiles') and Chem.MolToSmiles(Chem.MolFromSmiles(d['smiles']))==mf['smiles'] and d.get('selfies'):
mf['selfies']=d['selfies']
if not d.get('smiles'): stats['v4_structure_added_'+pool]+=1
d.update(smiles=mf['smiles'],inchikey=mf['inchikey'],selfies=mf['selfies'],has_structure=True)
else:
d.update(smiles=None,inchikey=None,selfies=None,has_structure=False)
d['structure_tier']=tier if tier in 'ABCD' else ('X' if tier=='X' else None)
d['structure_method']=(('ocsr:'+str(t['src_ocsr'].get('method'))) if t.get('src_ocsr') else t.get('method')) if mf else None
d['formula_match']=t.get('fm') if mf else None
d['structure_second_method']=('pubchem' if t.get('a_strict') else None) if tier=='A' else None
d['structure_flags']=flags
if mf:
q=nmr_check(mf['_mol'],d.get('h_nmr'),d.get('c_nmr'))
if q: quar.append(dict(id=d['id'],license_pool=pool,source_set=d['source_set'],inchikey=mf['inchikey'],reasons=q))
tiers[d['structure_tier'] or 'none']+=1; tiers_pool[(pool,d['structure_tier'] or 'none')]+=1
pools[pool].append(d)
stats['v4_rows']=sum(len(v) for v in pools.values())
# ---------- SI expansion ----------
NT={}
for l in open(SIT):
d=json.loads(l); NT[d['id']]=d
SFL={}
for f in ['structures_commercial.jsonl.gz','structures_non_commercial.jsonl.gz']:
for l in gzip.open(SIS+f,'rt'):
r=json.loads(l); SFL[r['id']]=r.get('ir_flags') or []
nsi=0
for p in ['commercial','non_commercial']:
for l in gzip.open(SIH+f'irexp_si_{p}.jsonl.gz','rt'):
s=json.loads(l); nsi+=1; t=NT[s['id']]; tier=t['tier']
b0=s['ir_bands_cm-1']; seenb=set(); nb=[]
for x in b0:
k=int(round(float(x)))
if k not in seenb: seenb.add(k); nb.append(x)
if len(nb)!=len(b0): stats['si_dup_int_band_rows_'+p]+=1
if len(nb)<3: stats['si_dropped_lt3_after_dedup_'+p]+=1; continue
lic=LIC.get(s['license'],s['license'])
d=dict(id=s['id'],**{'ir_bands_cm-1':nb,'ir_bands_old_cm-1':b0},ir_source=s['ir_source'],h_nmr=s.get('h_nmr'),c_nmr=s.get('c_nmr'),
smiles=None,selfies=None,inchikey=None,has_structure=False,source_doi='PMC:'+s['pmcid'][3:],license=lic,license_raw=s['license'],
license_pool=p,license_source='pmc_oa_s3',pmcid=s['pmcid'],doi=s.get('doi'),source_set='si_2026',si_label=s.get('label'),si_name=s.get('name'),
ir_raw=s.get('ir'),parser=s.get('parser'),ir_shared_in_paper=False,ir_table_flatten_suspect=None,ir_refetch_confirmed=False,ir_refetch_merged=False)
mf=None
if tier in ('A','B','C','D') and t.get('smiles'):
mf=mol_fields(t['smiles'])
if mf is None: stats['si_unparseable']+=1; tier='none'
if mf:
d.update(smiles=mf['smiles'],inchikey=mf['inchikey'],selfies=mf['selfies'],has_structure=True)
q=nmr_check(mf['_mol'],d.get('h_nmr'),d.get('c_nmr'))
if q: quar.append(dict(id=d['id'],license_pool=p,source_set='si_2026',inchikey=mf['inchikey'],reasons=q))
if tier=='X': quar.append(dict(id=d['id'],license_pool=p,source_set='si_2026',reasons=['tier_X:'+(t.get('x_reason') or 'contradiction')]))
d['structure_tier']=tier if tier in ('A','B','C','D','X') else None
meth=t.get('method')
if t.get('src')=='ocsr': meth='ocsr:'+str(meth)
d['structure_method']=meth if mf else None
d['formula_match']=t.get('formula_match') if mf else None
sm=[c for c in t.get('confirm',[]) if 'DISAGREES' not in c]
d['structure_second_method']=('; '.join(sm) or None) if d['structure_tier']=='A' else None
fl=list(SFL.get(s['id'],[]))
if any('DISAGREES' in c for c in t.get('confirm',[])): fl.append('pubchem_conflict')
d['structure_flags']=fl
tiers[d['structure_tier'] or 'none']+=1; tiers_pool[(p,d['structure_tier'] or 'none')]+=1
pools[p].append(d)
stats['si_rows_in']=nsi
grp=collections.Counter((r['pmcid'],tuple(int(round(float(x))) for x in r['ir_bands_cm-1'])) for p in ('commercial','non_commercial') for r in pools[p] if r['source_set']=='si_2026')
for p in ('commercial','non_commercial'):
for r in pools[p]:
if r['source_set']=='si_2026' and grp[(r['pmcid'],tuple(int(round(float(x))) for x in r['ir_bands_cm-1']))]>1: r['ir_shared_in_paper']=True; stats['si_ir_shared_in_paper']+=1
stats['si_rows_out']=sum(1 for p in ('commercial','non_commercial') for r in pools[p] if r['source_set']=='si_2026')
# ---------- write ----------
def w(name,rows):
path=OUT+name
with gzip.open(path,'wt',compresslevel=9) as g:
for r in rows: g.write(json.dumps(r,ensure_ascii=False)+'\n')
os.chmod(path,0o600); return len(rows)
counts={}
counts['commercial']=w('irexp_commercial.jsonl.gz',pools['commercial'])
res=[r for r in pools['commercial'] if r['has_structure']]
counts['resolved_commercial']=w('irexp_resolved_commercial.jsonl.gz',res)
tnb=[r for r in res if r['inchikey'][:14] not in BENCH]
counts['train_no_bench_commercial']=w('train_no_bench_commercial.jsonl.gz',tnb)
counts['non_commercial']=w('irexp_non_commercial.jsonl.gz',pools['non_commercial'])
counts['sharealike']=w('irexp_sharealike.jsonl.gz',pools['sharealike'])
counts['other']=w('irexp_other.jsonl.gz',pools['other'])
counts['structure_quarantine']=w('structure_quarantine.jsonl.gz',quar)
# seen papers: v4 list + SI list
seen=set(l.strip() for l in gzip.open('/workspace/irexp_v4_build/IRexp/data/seen_papers.txt.gz','rt') if l.strip())
n4=len(seen); seen|=set(l.strip() for l in open('/workspace/irexp_growth/harvest/seen_papers_si.txt') if l.strip())
with gzip.open(OUT+'seen_papers.txt.gz','wt') as g: g.write('\n'.join(sorted(seen))+'\n')
os.chmod(OUT+'seen_papers.txt.gz',0o600)
def agg(rows):
st=[r for r in rows if r['has_structure']]
return dict(records=len(rows),structure_linked=len(st),unique_inchikey=len({r['inchikey'] for r in st}),
bands=sum(len(r['ir_bands_cm-1']) for r in rows),papers=len({r.get('pmcid') or r.get('source_doi') for r in rows}),
tiers=dict(collections.Counter(r['structure_tier'] or 'none' for r in rows)),
by_set=dict(collections.Counter(r['source_set'] for r in rows)),
full_quadruple=sum(1 for r in st if r.get('h_nmr') and r.get('c_nmr')),
lt3=sum(1 for r in rows if len(r['ir_bands_cm-1'])<3),
band_out_of_range=sum(1 for r in rows if not bands_ok(r['ir_bands_cm-1'])))
# research corpus (incl. empty/unknown licence pool, not redistributed)
rc=collections.Counter();
for l in gzip.open(V4T,'rt'): rc[json.loads(l)['tier_final']]+=1
for d in NT.values(): rc[d['tier'] or 'none']+=1
N=sum(rc.values())
rep=dict(counts=counts,files={k:agg(v) for k,v in pools.items()},resolved_commercial=agg(res),train_no_bench_commercial=agg(tnb),
released_total=sum(len(v) for v in pools.values()),
research_corpus=dict(n=N,tiers=dict(rc),AB=rc['A']+rc['B'],AB_pct=round(100*(rc['A']+rc['B'])/N,2),AD=sum(rc[k] for k in 'ABCD'),AD_pct=round(100*sum(rc[k] for k in 'ABCD')/N,2)),
released_tiers=dict(tiers),tiers_by_pool={'%s/%s'%k:v for k,v in sorted(tiers_pool.items())},
stats=dict(stats),seen_papers=dict(v4=n4,total=len(seen)),quarantine_reasons=dict(collections.Counter(r['reasons'][0].split(':')[0] for r in quar)),
benchmark_ik14=len(BENCH))
json.dump(rep,open(OUT+'irexp_release_build_stats.json','w'),indent=1); os.chmod(OUT+'irexp_release_build_stats.json',0o600)
print(json.dumps(rep,indent=1))
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