Merge main and preserve coverage and history audit checks

.gitea/workflows/check.yml

@@ -53,6 +53,7 @@ jobs:
               subprocess.run([python,'-I','-B','-m','paper_atlas','import','arxiv','--help'],cwd=outside,check=True)
               subprocess.run([python,'-I','-B','-m','paper_atlas','maintain','backfill','--help'],cwd=outside,check=True)
               subprocess.run([python,'-I','-B','-m','paper_atlas','audit','public-openreview','--help'],cwd=outside,check=True)
+              subprocess.run([python,'-I','-B','-m','paper_atlas','coverage','--help'],cwd=outside,check=True)
               subprocess.run([python,'-I','-B','-m','paper_atlas','audit','histories','--help'],cwd=outside,check=True)
               subprocess.run([python,'-I','-B','-c','from paper_atlas.postgres.writer import PostgresStore, WriteConnection'],cwd=outside,check=True)
               smoke = "from paper_atlas.db.store import Store; from paper_atlas.config import DEFAULT_REGISTRY; import json; assert {'COLM','MM','MLSys'} <= {v['acronym'] for v in json.loads(DEFAULT_REGISTRY.read_text())['venues']}; s=Store('installed.sqlite'); s.conn.close()"

README.md

@@ -51,7 +51,8 @@ PGSERVICEFILE=/etc/paper-atlas/pg_service.conf paper-atlas query --pg-service fo
 PGSERVICEFILE=/etc/paper-atlas/pg_service.conf paper-atlas query --pg-service foundry-research --paper 123
 
 # 列出全部目标会议，包括尚未入库的项目
-paper-atlas coverage --db /data/paper-index/papers.sqlite \
+PGSERVICEFILE=/etc/paper-atlas/pg_service.conf paper-atlas coverage \
+  --pg-service foundry-research --pg-schema research \
   --out /data/paper-index/collected/venue-coverage-current.json
 
 # 采集与导入分开；这里只采集到独立文件

docs/operations.md

@@ -97,13 +97,16 @@ paper-atlas audit arxiv-tags --db /data/paper-index/papers.sqlite \
 采集文件、已入库的来源记录和去重论文实体是不同的计数。来源可能覆盖同一篇论文，同一篇论文也可能有多次投稿；不能把各批文件数量相加作为独立论文总数。实时统计与覆盖报告使用：
 
 ```sh
-paper-atlas query --db /data/paper-index/papers.sqlite --stats
+PGSERVICEFILE=/etc/paper-atlas/pg_service.conf paper-atlas query --pg-service foundry-research --pg-schema research --stats
-paper-atlas coverage --db /data/paper-index/papers.sqlite \
+PGSERVICEFILE=/etc/paper-atlas/pg_service.conf paper-atlas coverage \
+  --pg-service foundry-research --pg-schema research \
   --out /data/paper-index/collected/venue-coverage-current.json
 ```
 
 manifest 和采集器状态清单用于确认文件是否齐全及是否缺摘要；`ingest_runs` 和协调器日志用于确认主库导入是否成功。官方程序、书目目录和公开投稿快照分别保留，未出现在某份清单不等于被拒稿；第三方快照也不能代表平台当前全量状态。代码测试成功不能代替最终全库去重、完整性和逐届覆盖核验。
 
+`coverage` 的所有计数来自同一个只读快照。`latest_observed_status_counts` 按每次投稿的最新观察决定统计，`decision_observation_counts` 保留所有历史观察；重复来源不增加投稿数，缺少决定的投稿计入最新状态 unknown，但不凭空制造 unknown 决定。`source_record_counts` 统计来源在该届次的实际记录与缺摘要数，和 `sources` 中逐清单的预期/导入数量分开；身份补充清单与原始论文集清单可以描述同一条记录。来源缺摘要与论文实体从其他来源获得摘要也分别报告。报告仍将历史覆盖标为待独立审计，不能用某个清单 complete 或没有拒稿记录推断全会议覆盖。
+
 当前代码与合并状态以 [Pull Requests](https://gitea.entroia.com/Zayden-Jung/paper-atlas/pulls) 为准；CI 结果以对应提交的 Actions 检查为准。工作分支交付后等待用户手动合并。合并代码不自动部署、不自动启动采集，也不代表数据批次已完成。
 ## 修正已有 PMLR 投稿的轨道
 

docs/usage.md

@@ -83,11 +83,14 @@ paper-atlas query --pg-service foundry-research --query '"language model"' --lim
 paper-atlas query --pg-service foundry-research --tag arxiv:category=cs.AI
 paper-atlas query --pg-service foundry-research --venue ICLR --year 2025 --status rejected
 paper-atlas query --pg-service foundry-research --paper 123
-paper-atlas coverage --db /data/paper-index/papers.sqlite --out /data/paper-index/collected/coverage.json
+PGSERVICEFILE=/etc/paper-atlas/pg_service.conf paper-atlas coverage \
+  --pg-service foundry-research --pg-schema research --out /data/paper-index/collected/coverage.json
 ```
 
 `--status rejected` 筛选某次投稿的最新已知决定。它并不表示论文在所有会议均未录用；分析转投情况时查看该论文的完整投稿历史。年份表示会议届次，观察时间和决定日期分别保留。
 
+覆盖报告使用只读一致性快照，标明实际数据库和 schema，并列出零入库目标与注册表外的已入库会议。逐届、逐 track 分别列出最新观察状态的投稿数、全部决定观察数、各来源记录数，以及来源摘要和论文实体摘要的缺失数。摘要缺失指 NULL 或空字符串；有文字不代表内容已经完整核验。同一来源的多个清单 URL 可以重叠，不能把清单计数相加当作来源总量；零条拒稿也不证明该会议没有公开拒稿。SQLite 样本仍可显式使用 `--db`，生产报告应查询当前 PostgreSQL。
+
 例如，查找在 ICLR 有拒稿记录、但在其他已知投稿中已有录用的论文：
 
 ```sh

paper_atlas/audits/coverage.py

@@ -1,45 +1,136 @@
-"""Show every target venue, including those with no imported records."""
+"""Describe imported venue coverage without implying a complete census."""
 import argparse
-from paper_atlas.config import DEFAULT_REGISTRY
+from collections import defaultdict
 import json
 from pathlib import Path
 import sqlite3
 
+from paper_atlas.config import DEFAULT_REGISTRY
+from paper_atlas.db.backend import database_arguments, open_read_connection
 from paper_atlas.db.submissions import timestamp
+from paper_atlas.querying import LATEST_DECISION
 
 
-def report(db,registry):
+STATUSES = ('accepted', 'rejected', 'desk_rejected', 'withdrawn', 'under_review', 'unknown')
-    registry=json.loads(Path(registry).read_text());targets=registry['venues']
+
+
+def _status_counts(connection, *, latest):
+    if latest:
+        query = '''SELECT s.edition_id,COALESCE(d.status,'unknown') AS status,count(*) AS count
+            FROM submissions s LEFT JOIN decisions d ON d.submission_id=s.id AND ''' + LATEST_DECISION
+    else:
+        query = '''SELECT s.edition_id,COALESCE(d.status,'unknown') AS status,count(*) AS count
+            FROM submissions s JOIN decisions d ON d.submission_id=s.id'''
+    counts = defaultdict(dict)
+    for row in connection.execute(query + " GROUP BY s.edition_id,COALESCE(d.status,'unknown')"):
+        counts[row[0]][row[1]] = row[2]
+    return counts
+
+
+def report(db, registry, *, pg_service=None, pg_schema=None):
+    started_at = timestamp()
+    registry = json.loads(Path(registry).read_text())
+    targets = registry['venues']
     names = [row['acronym'].casefold() for row in targets]
-    if len(names)!=len(set(names)):raise ValueError('Duplicate target venue')
+    if len(names) != len(set(names)):
-    scope='(v.acronym=? COLLATE NOCASE OR EXISTS(SELECT 1 FROM venue_aliases a WHERE a.venue_id=v.id AND a.alias=? COLLATE NOCASE))'
+        raise ValueError('Duplicate target venue')
-    c=sqlite3.connect(Path(db).resolve().as_uri()+'?mode=ro',uri=True);c.row_factory=sqlite3.Row
+    scope = '''(lower(v.acronym)=lower(?) OR EXISTS(
+        SELECT 1 FROM venue_aliases a WHERE a.venue_id=v.id AND lower(a.alias)=lower(?)))'''
+    connection = open_read_connection(db, pg_service=pg_service, pg_schema=pg_schema)
+    if not pg_service:
+        connection.row_factory = sqlite3.Row
     try:
-        c.execute('BEGIN');venues=[]
+        if pg_service:
+            identity = connection.execute('SELECT current_database(),current_schema()').fetchone()
+            database, schema = identity[0], identity[1]
+        else:
+            database, schema = str(Path(db).resolve()), None
+        latest = _status_counts(connection, latest=True)
+        observations = _status_counts(connection, latest=False)
+        # Aggregate the paper join once for the whole snapshot. Repeating it
+        # for each registry target caused repeated scans on the production DB.
+        edition_counts = {}
+        for row in connection.execute('''SELECT s.edition_id,count(s.id) AS submissions,
+                count(DISTINCT s.paper_id) AS papers,
+                count(DISTINCT CASE WHEN p.abstract IS NULL OR p.abstract='' THEN s.paper_id END)
+                    AS papers_without_abstract_text
+                FROM submissions s LEFT JOIN papers p ON p.id=s.paper_id GROUP BY s.edition_id'''):
+            entry = dict(row)
+            edition_counts[entry.pop('edition_id')] = entry
+        source_counts = defaultdict(list)
+        for row in connection.execute('''SELECT s.edition_id,so.name AS source,
+                count(DISTINCT sr.id) AS source_records,
+                count(DISTINCT CASE WHEN sr.abstract IS NULL OR sr.abstract='' THEN sr.id END)
+                    AS source_records_without_abstract_text
+                FROM submission_sources ss JOIN submissions s ON s.id=ss.submission_id
+                JOIN source_records sr ON sr.id=ss.source_record_id JOIN sources so ON so.id=sr.source_id
+                GROUP BY s.edition_id,so.name ORDER BY s.edition_id,so.name'''):
+            entry = dict(row)
+            source_counts[entry.pop('edition_id')].append(entry)
+        venues, covered_venue_ids = [], set()
         for target in targets:
-            acronym=target['acronym'];params=(acronym,acronym)
+            acronym = target['acronym']
+            params = (acronym, acronym)
             editions = []
-            for row in c.execute('SELECT e.id,v.acronym AS canonical_venue,e.year,e.track,count(s.id) AS submissions,count(DISTINCT s.paper_id) AS papers FROM editions e JOIN venues v ON v.id=e.venue_id LEFT JOIN submissions s ON s.edition_id=e.id WHERE '+scope+' GROUP BY e.id ORDER BY e.year,e.track',params):
+            for row in connection.execute('''SELECT e.id,v.id AS venue_id,v.acronym AS canonical_venue,
+                    e.year,e.track FROM editions e JOIN venues v ON v.id=e.venue_id
+                    WHERE ''' + scope + '''
+                    ORDER BY e.year,e.track,v.acronym''', params):
                 edition = dict(row)
-                edition['sources']=[dict(source) for source in c.execute('SELECT so.name,es.status,es.expected_count,es.imported_count,es.list_url,es.last_success_at,es.last_error FROM edition_sources es JOIN sources so ON so.id=es.source_id WHERE es.edition_id=? ORDER BY so.name',(row['id'],))]
+                edition.update(edition_counts.get(row['id'], {
+                    'submissions': 0, 'papers': 0, 'papers_without_abstract_text': 0}))
+                covered_venue_ids.add(edition['venue_id'])
+                edition['latest_observed_status_counts'] = {status: latest[row['id']].get(status, 0) for status in STATUSES}
+                edition['decision_observation_counts'] = {status: observations[row['id']].get(status, 0) for status in STATUSES}
+                edition['source_record_counts'] = source_counts[row['id']]
+                edition['sources'] = [dict(source) for source in connection.execute('''SELECT so.name,
+                    es.status,es.expected_count,es.imported_count,es.list_url,es.last_success_at,es.last_error
+                    FROM edition_sources es JOIN sources so ON so.id=es.source_id
+                    WHERE es.edition_id=? ORDER BY so.name,es.list_url''', (row['id'],))]
                 editions.append(edition)
-            totals=c.execute('SELECT count(s.id),count(DISTINCT s.paper_id) FROM submissions s JOIN editions e ON e.id=s.edition_id JOIN venues v ON v.id=e.venue_id WHERE '+scope,params).fetchone()
+            totals = connection.execute('''SELECT count(s.id),count(DISTINCT s.paper_id)
-            venues.append({'acronym':acronym,'field':target['field'],'imported_submissions':totals[0],'distinct_papers':totals[1],
+                FROM submissions s JOIN editions e ON e.id=s.edition_id
+                JOIN venues v ON v.id=e.venue_id WHERE ''' + scope, params).fetchone()
+            venues.append({'acronym': acronym, 'field': target['field'],
+                'imported_submissions': totals[0], 'distinct_papers': totals[1],
                 'history_status': 'partial_history_pending_independent_audit' if totals[0] else 'no_imported_records',
                 'discovery_sources': target.get('discovery_sources', []), 'editions': editions})
-        return {'checked_at':timestamp(),'target_venue_count':len(targets),'venues_with_imported_records':sum(bool(v['imported_submissions']) for v in venues),
+        outside_registry = [dict(row) for row in connection.execute('''SELECT v.id AS venue_id,
-                'scope_note':registry['scope_note'],'interpretation':'All registry targets are listed. Edition source complete means that source file passed import checks; it does not prove full historical or abstract coverage. Papers can appear in multiple venues/years, so do not sum venue paper counts as a global total.',
+            v.acronym,count(s.id) AS submissions,count(DISTINCT s.paper_id) AS papers
-                'venues':venues}
+            FROM submissions s JOIN editions e ON e.id=s.edition_id JOIN venues v ON v.id=e.venue_id
-    finally:c.close()
+            GROUP BY v.id,v.acronym ORDER BY v.acronym''') if row[0] not in covered_venue_ids]
+        return {'report_started_at': started_at, 'checked_at': timestamp(),
+            'engine': 'postgresql' if pg_service else 'sqlite', 'database': database, 'schema': schema,
+            'pg_service': pg_service, 'target_venue_count': len(targets),
+            'venues_with_imported_records': sum(bool(v['imported_submissions']) for v in venues),
+            'scope_note': registry['scope_note'],
+            'interpretation': 'All registry targets are listed, including zero imports. '
+                'Latest status counts use the latest observed decision for each attempt; decision observations retain history. '
+                'Source record totals are per source and edition, not per list URL; multiple list entries may describe overlapping records. '
+                'Missing abstract text means NULL or empty string; nonempty text does not prove a complete abstract. '
+                'An edition source marked complete is not a proof of complete conference history or public rejection coverage. '
+                'Zero imported rejections does not establish that no rejections are public. '
+                'Papers can appear in several venues/years; do not sum venue paper counts as a global total.',
+            'venues': venues, 'imported_venues_outside_registry': outside_registry}
+    finally:
+        connection.close()
 
 
 def main(argv=None, *, prog=None):
-    parser=argparse.ArgumentParser(prog=prog);parser.add_argument('--db',required=True)
+    parser = argparse.ArgumentParser(prog=prog)
-    parser.add_argument('--registry',default=str(DEFAULT_REGISTRY));parser.add_argument('--out')
+    database_arguments(parser)
-    args=parser.parse_args(argv);result=report(args.db,args.registry);text=json.dumps(result,ensure_ascii=False,indent=2)
+    parser.add_argument('--registry', default=str(DEFAULT_REGISTRY))
+    parser.add_argument('--out')
+    args = parser.parse_args(argv)
+    result = report(args.db, args.registry, pg_service=args.pg_service, pg_schema=args.pg_schema)
+    text = json.dumps(result, ensure_ascii=False, indent=2)
     if args.out:
-        path=Path(args.out);stage=path.with_suffix('.part');stage.write_text(text+'\n');stage.replace(path)
+        path = Path(args.out)
-    else:print(text)
+        stage = path.with_suffix('.part')
+        stage.write_text(text + '\n')
+        stage.replace(path)
+    else:
+        print(text)
 
 
 if __name__ == '__main__':

tests/test_coverage_report.py

@@ -7,6 +7,34 @@ from paper_atlas.audits.coverage import report
 from paper_atlas.db.store import Store
 
 
+def add_coverage_evidence(store):
+    paper, record = store.record('official_metadata', 'known', 'https://example.org/known',
+        'Known paper with two source observations', 'Complete canonical abstract', ['Jane Doe', 'John Smith'],
+        {'openreview': 'coverageForum', 'arxiv': '2401.98765'})
+    edition = store.decision(paper, record, 'COLING+LREC', 2024, 'main', 'known',
+        'https://example.org/accept', 'accepted', 'Accept', aliases=['COLING', 'LREC'],
+        identities=[('openreview', 'coverageForum')], observed_at='2025-05-01T00:00:00Z')
+    same, mirror = store.record('bibliography', 'mirror', 'https://example.org/mirror',
+        'Known paper with two source observations', None, ['Jane Doe', 'John Smith'], {'openreview': 'coverageForum'})
+    store.decision(same, mirror, 'COLING+LREC', 2024, 'main', 'mirror', 'https://example.org/older',
+        'rejected', 'Reject', identities=[('openreview', 'coverageForum')],
+        observed_at='2025-05-01T00:00:00Z', decision_date='2025-04-30T00:00:00Z')
+    unknown, unknown_record = store.record('unknown_catalogue', 'unknown', 'https://example.org/unknown',
+        'Indexed work without a public decision', None, [])
+    store.decision(unknown, unknown_record, 'COLING+LREC', 2024, 'main', 'unknown',
+        'https://example.org/unknown', None, '', identities=[('openreview', 'unknownForum')])
+    same, later = store.record('official_metadata', 'later', 'https://example.org/later',
+        'Known paper with two source observations', 'Complete canonical abstract', ['Jane Doe', 'John Smith'],
+        {'openreview': 'coverageNext', 'arxiv': '2401.98765'})
+    store.decision(same, later, 'COLING+LREC', 2025, 'findings', 'later', 'https://example.org/later',
+        'accepted', 'Accept', identities=[('openreview', 'coverageNext')], observed_at='2025-06-01T00:00:00Z')
+    source = store.source('official_metadata', 'https://example.org')
+    for url, status in [('https://example.org/list', 'complete'), ('https://example.org/identity-refresh', 'partial')]:
+        store.conn.execute('''INSERT INTO edition_sources(edition_id,source_id,list_url,status,expected_count,imported_count)
+            VALUES(?,?,?,?,?,?)''', (edition, source, url, status, 1, 1))
+    store.conn.commit()
+
+
 class CoverageTests(unittest.TestCase):
     def setUp(self):
         self.tmp=tempfile.TemporaryDirectory();self.addCleanup(self.tmp.cleanup)
@@ -31,5 +59,46 @@ class CoverageTests(unittest.TestCase):
         self.store.conn.commit();coling=report(self.db,self.registry)['venues'][0]
         self.assertEqual(coling['imported_submissions'],2);self.assertEqual(coling['distinct_papers'],1)
 
+    def test_observations_attempts_and_missing_source_abstracts_stay_separate(self):
+        add_coverage_evidence(self.store)
+        result = report(self.db, self.registry)
+        self.assertEqual(result['engine'], 'sqlite')
+        self.assertEqual(result['database'], str(self.db))
+        coling = result['venues'][0]
+        self.assertEqual((coling['imported_submissions'], coling['distinct_papers']), (3, 2))
+        edition, findings = coling['editions']
+        self.assertEqual((edition['submissions'], edition['papers'], edition['papers_without_abstract_text']), (2, 2, 1))
+        self.assertEqual(edition['latest_observed_status_counts']['accepted'], 1)
+        self.assertEqual(edition['latest_observed_status_counts']['rejected'], 0)
+        self.assertEqual(edition['latest_observed_status_counts']['unknown'], 1)
+        self.assertEqual(edition['decision_observation_counts']['accepted'], 1)
+        self.assertEqual(edition['decision_observation_counts']['rejected'], 1)
+        self.assertEqual(edition['decision_observation_counts']['unknown'], 0)
+        counts = {row['source']: row for row in edition['source_record_counts']}
+        self.assertEqual(counts['bibliography']['source_records_without_abstract_text'], 1)
+        self.assertEqual(counts['official_metadata']['source_records'], 1)
+        self.assertEqual(len(edition['sources']), 2)
+        self.assertEqual(findings['track'], 'findings')
+        self.assertEqual(result['imported_venues_outside_registry'], [])
+
+    def test_missing_sqlite_audit_does_not_create_a_database(self):
+        path = self.root / 'absent.sqlite'
+        with self.assertRaisesRegex(ValueError, 'Existing database'):
+            report(path, self.registry)
+        self.assertFalse(path.exists())
+
+    def test_empty_editions_remain_visible_after_shared_aggregation(self):
+        self.store.conn.execute("INSERT INTO venues(acronym,name,field,venue_type) VALUES('AAAI','AAAI','general_ai','conference')")
+        venue = self.store.conn.execute("SELECT id FROM venues WHERE acronym='AAAI'").fetchone()[0]
+        self.store.conn.execute("INSERT INTO editions(venue_id,year,track) VALUES(?,2026,'main')", (venue,))
+        self.store.conn.commit()
+        aaai = report(self.db, self.registry)['venues'][1]
+        self.assertEqual(aaai['history_status'], 'no_imported_records')
+        self.assertEqual(len(aaai['editions']), 1)
+        edition = aaai['editions'][0]
+        self.assertEqual((edition['submissions'], edition['papers'], edition['papers_without_abstract_text']), (0, 0, 0))
+        self.assertEqual(sum(edition['latest_observed_status_counts'].values()), 0)
+        self.assertEqual(edition['source_record_counts'], [])
+
 
 if __name__=='__main__':unittest.main()

tests/test_postgres_ingestion.py

@@ -243,6 +243,50 @@ class PostgreSQLIngestionTests(unittest.TestCase):
         finally:
             reader.close()
 
+    def test_coverage_matches_sqlite_with_history_aliases_and_missing_source_abstracts(self):
+        from paper_atlas.audits.coverage import report
+        from tests.test_coverage_report import add_coverage_evidence
+        registry = self.root / 'venues.json'
+        registry.write_text(json.dumps({'scope_note': 'Candidate scope', 'venues': [
+            {'acronym': 'coling', 'field': 'language'}, {'acronym': 'AAAI', 'field': 'general_ai'}]}))
+        sample = Store(self.root / 'seed.sqlite')
+        try:
+            add_coverage_evidence(sample)
+        finally:
+            sample.conn.close()
+        store = self.store()
+        try:
+            add_coverage_evidence(store)
+        finally:
+            store.conn.close()
+        sqlite_report = report(self.root / 'seed.sqlite', registry)
+        observed = []
+        def reader(*args, **kwargs):
+            connection = open_read_connection(*args, **kwargs)
+            observed.append((connection.execute('SHOW transaction_read_only').fetchone()[0],
+                             connection.execute('SHOW transaction_isolation').fetchone()[0]))
+            return connection
+        with patch('paper_atlas.audits.coverage.open_read_connection', side_effect=reader):
+            actual = report(None, registry, pg_service=self.service, pg_schema=self.schema)
+        self.assertEqual(observed, [('on', 'repeatable read')])
+        self.assertEqual(actual['engine'], 'postgresql')
+        self.assertEqual(actual['schema'], self.schema)
+        self.assertEqual(actual['pg_service'], self.service)
+        def content(result):
+            values = json.loads(json.dumps(result['venues']))
+            for venue in values:
+                for edition in venue['editions']:
+                    for key in ('id', 'venue_id'):
+                        edition.pop(key)
+            return values
+        self.assertEqual(content(actual), content(sqlite_report))
+        self.assertEqual([r['acronym'] for r in actual['imported_venues_outside_registry']], ['ICLR'])
+        edition = actual['venues'][0]['editions'][0]
+        self.assertEqual(edition['latest_observed_status_counts']['accepted'], 1)
+        self.assertEqual(edition['latest_observed_status_counts']['unknown'], 1)
+        self.assertEqual(edition['decision_observation_counts']['rejected'], 1)
+        self.assertEqual(edition['papers_without_abstract_text'], 1)
+
     def test_backfill_merges_evidence_without_reimporting_or_losing_history(self):
         files = []
         for source, external, title in [('official', 'legacy', 'First bibliographic name'), ('openreview_snapshot', 'forum', 'Renamed submission')]: