docs/operations.md

@@ -20,6 +20,20 @@ paper-atlas maintain arxiv-tags --db /data/paper-index/papers.sqlite \
 
 修复使用同一维护锁，分批提交并保存断点，保留 `custom:*` 和其他来源证据；失败后确认原因已解决，再增加 `--resume` 从上次提交位置继续。完成报告不能作为重新扫描的断点，重新核验应指定新报告。源审计和标签修复均保留 8 GiB 空闲空间，不能代替所有来源入库后的实体、投稿去重与完整性检查。
 
+修复结束后还须核对每条 arXiv 来源记录的类别集合，不能只看旧证据键是否清零。下面的只读审计比较来源 metadata 中的类别、所属论文实体和逐记录证据键，同时检查没有合法 arXiv 来源的类别行：
+
+```sh
+paper-atlas audit arxiv-tags --db /data/paper-index/papers.sqlite \
+  --repair-report /data/paper-index/collected/arxiv-tag-repair.json \
+  --out /data/paper-index/collected/arxiv-tag-coverage-audit.json
+```
+
+审计持有共享维护锁；修复或其他协调写入尚未结束时会拒绝运行。提供修复报告时，还会核对其已完成状态、数据库路径和固定来源范围。审计以一致的只读快照分批读取，记录完整扫描数量、缺失/多余证据、错误论文归属、残留旧键及少量异常样例，不修改主库。
+
+来源记录按整数主键区间读取，避免 SQLite 误选按 external_id 排列的来源索引、每批重新排序整个来源；其他来源交错在编号区间内时仍按 source_id 过滤。类别证据继续使用 source_record_id 索引批量读取。完整核验范围不因查询优化缩小。
+
+只有全量记录核对完毕且无差异时才标记 `passed`；存在差异为 `failed` 并返回非零退出码，解析或执行中断为 `error`。运行中的报告不能作为完成证明。重新核验须使用新输出路径，不能覆盖已有报告；该检查不替代最后的实体去重、外键、SQLite 与全文索引核验。
+
 ## 长期维护与更新
 
 1. 每次采集先核对来源、许可、可访问性、空闲空间和现有运行批次。保持低并发，遵守来源限流、重试与人机验证要求。

paper_atlas/audits/arxiv_tags.py

@@ -0,0 +1,143 @@
+"""Compare every arXiv record's category evidence with retained source metadata."""
+import argparse
+from collections import defaultdict
+from contextlib import closing
+import fcntl
+import json
+from pathlib import Path
+import sqlite3
+
+from paper_atlas.db.submissions import timestamp
+
+
+def save(path, state):
+    part = path.with_suffix('.part')
+    part.write_text(json.dumps(state, ensure_ascii=False, indent=2) + '\n')
+    part.replace(path)
+
+
+def audit(db, out, repair_report=None, batch_size=500):
+    db, out = Path(db).resolve(), Path(out).resolve()
+    if not db.is_file():
+        raise ValueError('Existing database required')
+    if not 1 <= batch_size <= 500:
+        raise ValueError('Batch size must be between 1 and 500')
+    if out == db or repair_report and out == Path(repair_report).resolve():
+        raise ValueError('Audit output must preserve its inputs')
+    out.parent.mkdir(parents=True, exist_ok=True)
+    with Path(str(db) + '.maintenance.lock').open('a') as maintenance, Path(str(out) + '.lock').open('a') as output_lock:
+        # A partial repair is not a useful full-category audit. This also keeps
+        # cooperating maintenance writers out for the entire read-only snapshot.
+        fcntl.flock(maintenance, fcntl.LOCK_SH | fcntl.LOCK_NB)
+        fcntl.flock(output_lock, fcntl.LOCK_EX | fcntl.LOCK_NB)
+        if out.exists():
+            raise ValueError('Audit report exists; select a new output path')
+        with closing(sqlite3.connect(db.as_uri() + '?mode=ro', uri=True)) as c:
+            c.execute('PRAGMA cache_size=-32768')
+            c.execute('BEGIN')
+            source = c.execute("SELECT id FROM sources WHERE name='arxiv'").fetchone()
+            if source is None:
+                raise ValueError('No imported arXiv source')
+            total, maximum = c.execute('SELECT count(*),COALESCE(max(id),0) FROM source_records WHERE source_id=?', source).fetchone()
+            if not total:
+                raise ValueError('No imported arXiv records')
+            scope = {'db': str(db), 'source_id': source[0], 'source_record_count': total,
+                     'maximum_source_record_id': maximum}
+            if repair_report:
+                repair = json.loads(Path(repair_report).read_text())
+                if repair.get('status') != 'complete' or repair.get('records_refreshed') != total:
+                    raise ValueError('Category repair has not completed this source inventory')
+                if any(repair.get(key) != value for key, value in scope.items()):
+                    raise ValueError('Repair report belongs to a different source inventory')
+            state = {**scope, 'started_at': timestamp(), 'status': 'running', 'records_checked': 0,
+                     'last_record_id': 0, 'expected_evidence': 0, 'actual_evidence': 0,
+                     'records_with_mismatches': 0, 'missing_evidence': 0, 'unexpected_evidence': 0,
+                     'legacy_evidence': 0, 'examples': [], 'repair_report': str(Path(repair_report).resolve()) if repair_report else None}
+            save(out, state)
+            try:
+                while True:
+                    # The (source_id,external_id) index orders by external ID,
+                    # so choosing it sorts the entire source again per batch.
+                    # This fixed ID interval must use the integer primary key.
+                    records = c.execute('''SELECT id,external_id,paper_id,metadata_json FROM source_records NOT INDEXED
+                        WHERE source_id=? AND id>? AND id<=? ORDER BY id LIMIT ?''',
+                        (source[0], state['last_record_id'], maximum, batch_size)).fetchall()
+                    if not records:
+                        break
+                    ids = [row[0] for row in records]
+                    actual = defaultdict(set)
+                    for record, paper, category, evidence in c.execute('''SELECT pt.source_record_id,pt.paper_id,t.value,pt.evidence_key
+                        FROM paper_tags pt JOIN tags t ON t.id=pt.tag_id WHERE t.namespace='arxiv:category'
+                        AND pt.source_record_id IN (''' + ','.join('?' for _ in ids) + ')', ids):
+                        actual[record].add((category, paper, evidence))
+                        state['legacy_evidence'] += evidence == 'arxiv:categories'
+                    for record, external, paper, payload in records:
+                        metadata = json.loads(payload)
+                        if not isinstance(metadata, dict):
+                            raise ValueError('arXiv source metadata must be an object')
+                        categories = metadata.get('categories')
+                        if categories is None:
+                            categories = ''
+                        if not isinstance(categories, str):
+                            raise ValueError('arXiv source categories must be text')
+                        evidence_key = f'arxiv:record:{record}:tags'
+                        expected = {(category, paper, evidence_key) for category in categories.split()}
+                        found = actual[record]
+                        missing, unexpected = expected - found, found - expected
+                        state['expected_evidence'] += len(expected)
+                        state['actual_evidence'] += len(found)
+                        state['missing_evidence'] += len(missing)
+                        state['unexpected_evidence'] += len(unexpected)
+                        if missing or unexpected:
+                            state['records_with_mismatches'] += 1
+                            if len(state['examples']) < 20:
+                                state['examples'].append({'record_id': record, 'external_id': external,
+                                    'paper_id': paper, 'missing': sorted(missing), 'unexpected': sorted(unexpected)})
+                        state['records_checked'] += 1
+                    state['last_record_id'] = ids[-1]
+                    if state['records_checked'] % 10000 < len(records):
+                        save(out, state)
+                        print(json.dumps({k: state[k] for k in ('status', 'records_checked', 'source_record_count', 'records_with_mismatches')}), flush=True)
+                if state['records_checked'] != total:
+                    raise ValueError('Audited record count differs from the fixed source inventory')
+                # Every category row must also have an arXiv source-record owner.
+                # The full namespace total catches orphan and wrong-source evidence
+                # that cannot appear in the per-record traversal above.
+                all_evidence = c.execute("SELECT count(*) FROM paper_tags pt JOIN tags t ON t.id=pt.tag_id WHERE t.namespace='arxiv:category'").fetchone()[0]
+                unscoped = all_evidence - state['actual_evidence']
+                if unscoped < 0:
+                    raise ValueError('Category evidence totals are inconsistent')
+                state.update(namespace_evidence=all_evidence, evidence_without_arxiv_record=unscoped)
+                if unscoped:
+                    state['unscoped_examples'] = [dict(zip(('paper_id', 'category', 'source_record_id', 'evidence_key'), row))
+                        for row in c.execute('''SELECT pt.paper_id,t.value,pt.source_record_id,pt.evidence_key
+                            FROM paper_tags pt JOIN tags t ON t.id=pt.tag_id
+                            LEFT JOIN source_records r ON r.id=pt.source_record_id
+                            WHERE t.namespace='arxiv:category' AND (r.source_id IS NULL OR r.source_id<>?) LIMIT 20''', source)]
+                passed = not state['records_with_mismatches'] and not unscoped
+                state.update(status='passed' if passed else 'failed', finished_at=timestamp(),
+                             note='Full per-record category, canonical paper and evidence-key equality. '
+                                  'Read-only; not a global paper deduplication or full database-integrity audit.')
+                save(out, state)
+            except BaseException as error:
+                state.update(status='error', error=str(error), finished_at=timestamp())
+                save(out, state)
+                raise
+    print(json.dumps(state), flush=True)
+    return state
+
+
+def main(argv=None, *, prog=None):
+    parser = argparse.ArgumentParser(prog=prog)
+    parser.add_argument('--db', required=True)
+    parser.add_argument('--out', required=True)
+    parser.add_argument('--repair-report')
+    parser.add_argument('--batch-size', type=int, default=500)
+    args = parser.parse_args(argv)
+    result = audit(args.db, args.out, args.repair_report, args.batch_size)
+    if result['status'] != 'passed':
+        raise SystemExit('arXiv category evidence audit failed; inspect the report')
+
+
+if __name__ == '__main__':
+    main()

paper_atlas/cli.py

@@ -30,6 +30,7 @@ COMMANDS = {
     ('audit','iclr'): ('paper_atlas.audits.iclr', {}, '核对 ICLR 快照与同届官方程序'),
     ('audit','iclr-legacy'): ('paper_atlas.audits.iclr_legacy', {}, '独立核验 ICLR 2020 旧目录投稿身份'),
     ('audit','arxiv'): ('paper_atlas.audits.arxiv', {}, '核验 arXiv 原始编号、重复行与 ZIP 完整性'),
+    ('audit','arxiv-tags'): ('paper_atlas.audits.arxiv_tags', {}, '逐记录核验 arXiv 类别及出处完整性'),
     ('audit','public-openreview'): ('paper_atlas.audits.public_openreview', {}, '核对公开负面决定与已有投稿历史'),
 }
 

tests/test_arxiv_tag_audit.py

@@ -0,0 +1,138 @@
+import fcntl
+import json
+from pathlib import Path
+import tempfile
+import unittest
+import sqlite3
+from unittest.mock import patch
+
+from paper_atlas.audits.arxiv_tags import audit, main
+from paper_atlas.db.store import Store
+from paper_atlas.ingestion.arxiv import refresh_categories
+
+
+class ArxivTagAuditTests(unittest.TestCase):
+    def setUp(self):
+        self.temp = tempfile.TemporaryDirectory()
+        self.addCleanup(self.temp.cleanup)
+        self.root = Path(self.temp.name)
+        self.db = self.root / 'papers.sqlite'
+        self.out = self.root / 'audit.json'
+        self.store = Store(self.db)
+        self.addCleanup(self.store.conn.close)
+        self.records = []
+        for external in ('one', 'two'):
+            paper, record = self.store.record('arxiv', external, 'https://arxiv.org/abs/' + external,
+                'Same research work', 'Abstract', [], {'doi': '10.1234/same'},
+                {'categories': 'cs.AI cs.LG cs.AI'})
+            refresh_categories(self.store, paper, record, 'cs.AI cs.LG cs.AI')
+            self.records.append(record)
+        self.paper = paper
+        tag = self.store.conn.execute("INSERT INTO tags(namespace,value) VALUES('custom:topic','cs.AI')").lastrowid
+        self.store.conn.execute("INSERT INTO paper_tags VALUES(?,?,NULL,'manual:1')", (paper, tag))
+        self.store.conn.commit()
+
+    def test_all_merged_records_keep_their_own_categories_and_custom_tags_are_untouched(self):
+        before = self.store.conn.execute('SELECT * FROM paper_tags ORDER BY evidence_key,tag_id').fetchall()
+        result = audit(self.db, self.out, batch_size=1)
+        self.assertEqual(result['status'], 'passed')
+        self.assertEqual(result['records_checked'], 2)
+        self.assertEqual(result['expected_evidence'], 4)
+        self.assertEqual(result['actual_evidence'], 4)
+        self.assertEqual(result['evidence_without_arxiv_record'], 0)
+        self.assertEqual(self.store.conn.execute('SELECT * FROM paper_tags ORDER BY evidence_key,tag_id').fetchall(), before)
+
+    def test_zero_legacy_keys_does_not_hide_missing_categories_and_cli_fails(self):
+        self.store.conn.execute("DELETE FROM paper_tags WHERE source_record_id IS NOT NULL")
+        self.store.conn.commit()
+        with self.assertRaises(SystemExit):
+            main(['--db', str(self.db), '--out', str(self.out)])
+        result = json.loads(self.out.read_text())
+        self.assertEqual(result['status'], 'failed')
+        self.assertEqual(result['legacy_evidence'], 0)
+        self.assertEqual(result['missing_evidence'], 4)
+        self.assertEqual(result['records_with_mismatches'], 2)
+
+    def test_wrong_canonical_paper_or_stale_key_is_detected(self):
+        other, _ = self.store.record('example', 'other', 'https://example.org', 'Different work', 'AB', [])
+        self.store.conn.execute("UPDATE paper_tags SET paper_id=?,evidence_key='arxiv:categories' WHERE source_record_id=?", (other, self.records[0]))
+        self.store.conn.commit()
+        result = audit(self.db, self.out)
+        self.assertEqual(result['status'], 'failed')
+        self.assertEqual(result['records_with_mismatches'], 1)
+        self.assertEqual(result['legacy_evidence'], 2)
+        self.assertEqual(result['missing_evidence'], 2)
+        self.assertEqual(result['unexpected_evidence'], 2)
+
+    def test_wrong_source_and_unowned_category_rows_cannot_escape_the_full_audit(self):
+        paper, record = self.store.record('example', 'other', 'https://example.org', 'Other work', 'AB', [])
+        tag = self.store.conn.execute("SELECT id FROM tags WHERE namespace='arxiv:category' AND value='cs.AI'").fetchone()[0]
+        self.store.conn.execute('INSERT INTO paper_tags VALUES(?,?,?,?)', (paper, tag, record, 'wrong-source'))
+        self.store.conn.execute('INSERT INTO paper_tags VALUES(?,?,NULL,?)', (paper, tag, 'unowned'))
+        self.store.conn.commit()
+        result = audit(self.db, self.out)
+        self.assertEqual(result['status'], 'failed')
+        self.assertEqual(result['records_with_mismatches'], 0)
+        self.assertEqual(result['evidence_without_arxiv_record'], 2)
+        self.assertEqual(len(result['unscoped_examples']), 2)
+
+    def test_active_writer_and_incomplete_repair_are_rejected_before_publishing(self):
+        with Path(str(self.db) + '.maintenance.lock').open('a') as lock:
+            fcntl.flock(lock, fcntl.LOCK_EX | fcntl.LOCK_NB)
+            with self.assertRaises(BlockingIOError):
+                audit(self.db, self.out)
+        self.assertFalse(self.out.exists())
+        repair = self.root / 'repair.json'
+        repair.write_text(json.dumps({'status': 'running'}))
+        with self.assertRaisesRegex(ValueError, 'not completed'):
+            audit(self.db, self.out, repair)
+        self.assertFalse(self.out.exists())
+
+    def test_repair_report_scope_and_completed_audit_are_not_silently_reused(self):
+        repair = self.root / 'repair.json'
+        repair.write_text(json.dumps({'status': 'complete', 'records_refreshed': 2, 'db': str(self.db),
+            'source_id': 1, 'source_record_count': 2, 'maximum_source_record_id': 999}))
+        with self.assertRaisesRegex(ValueError, 'different source inventory'):
+            audit(self.db, self.out, repair)
+        result = audit(self.db, self.out)
+        before = self.out.read_bytes()
+        with self.assertRaisesRegex(ValueError, 'report exists'):
+            audit(self.db, self.out)
+        self.assertEqual(self.out.read_bytes(), before)
+        self.assertEqual(result['status'], 'passed')
+
+    def test_invalid_source_metadata_is_an_error_not_a_partial_pass(self):
+        self.store.conn.execute('UPDATE source_records SET metadata_json=? WHERE id=?',
+                                (json.dumps({'categories': ['invalid']}), self.records[0]))
+        self.store.conn.commit()
+        with self.assertRaisesRegex(ValueError, 'categories must be text'):
+            audit(self.db, self.out)
+        self.assertEqual(json.loads(self.out.read_text())['status'], 'error')
+
+    def test_interleaved_sources_use_bounded_primary_key_batches_without_sorting(self):
+        self.store.record('example', 'interleaved', 'https://example.org', 'Other source', 'AB', [])
+        paper, record = self.store.record('arxiv', 'three', 'https://arxiv.org/abs/three',
+                                          'A third record', 'AB', [], metadata={'categories': 'cs.AI'})
+        refresh_categories(self.store, paper, record, 'cs.AI')
+        self.store.conn.commit()
+        queries = []
+        connect = sqlite3.connect
+        def traced(*args, **kwargs):
+            connection = connect(*args, **kwargs)
+            connection.set_trace_callback(queries.append)
+            return connection
+        with patch('paper_atlas.audits.arxiv_tags.sqlite3.connect', side_effect=traced):
+            result = audit(self.db, self.out, batch_size=1)
+        self.assertEqual(result['status'], 'passed')
+        self.assertEqual(result['records_checked'], 3)
+        self.assertEqual(result['last_record_id'], record)
+        batches = [sql for sql in queries if sql.startswith('SELECT id,external_id,paper_id,metadata_json')]
+        self.assertEqual(len(batches), 4)  # Includes the bounded final empty read.
+        for sql in batches:
+            plan = ' '.join(row[3] for row in self.store.conn.execute('EXPLAIN QUERY PLAN ' + sql))
+            self.assertIn('INTEGER PRIMARY KEY', plan)
+            self.assertNotIn('TEMP B-TREE', plan)
+
+
+if __name__ == '__main__':
+    unittest.main()