"""Derive atlas assembly-presence coverage directly from a full accession index."""
import argparse
from collections import Counter
from datetime import datetime,timezone
import json
from pathlib import Path
import sqlite3

if __name__=='__main__':
    p=argparse.ArgumentParser(description=__doc__)
    p.add_argument('--index',type=Path,required=True)
    p.add_argument('--output',type=Path,required=True)
    args=p.parse_args()
    with sqlite3.connect(args.index) as c:
        m=json.loads(c.execute("SELECT value FROM metadata WHERE key='manifest'").fetchone()[0])
        if not m.get('full_snapshot') or m.get('schema_version')!=3: raise ValueError('A complete compact index is required')
        accessions=[r[0] for r in c.execute('SELECT DISTINCT c.assembly_accession FROM contexts c WHERE EXISTS (SELECT 1 FROM segment_data s WHERE s.context_id=c.id) ORDER BY c.assembly_accession')]
        shards=Counter('/'.join(r[0].split('/')[1:3]) for r in c.execute('SELECT path FROM files'))
        fetched=c.execute('SELECT sum(bytes_read) FROM files').fetchone()[0]
    inventory={'created_at':datetime.now(timezone.utc).isoformat(),'listing_observed_at':m['inventory_at'],
        'annotation_bucket':m['bucket_id'],'scope':'Assemblies with published annotations; includes partial assemblies. Exact accession versions; no base completeness claim.',
        'method':'Distinct assembly IDs read directly from scalar metadata of every indexed published annotation Parquet object. No completion-marker or packed-input inference.',
        'annotation_object_count':m['source_count'],'shard_count':len(shards),'metadata_bytes_read':fetched,
        'inventory_fingerprint':m['inventory_sha256'],'accessions':accessions,
        'shards':[{'shard':s,'annotation_objects':n,'method':'annotation_metadata'} for s,n in sorted(shards.items())]}
    temp=args.output.with_suffix('.json.tmp'); temp.write_text(json.dumps(inventory)); temp.replace(args.output)
    print('Direct annotation assembly versions:',len(accessions),flush=True)