Keep operations guidance independent of stale batch and PR status

docs/operations.md

@@ -16,6 +16,16 @@
 
 2026-11-06 从目标服务器测试：Kaggle 元数据 GET 可下载；OpenReview 会议 group 接口可读，但 notes 接口返回 `ChallengeRequiredError`。这限制了直接补全；已使用来源可追溯的公开历史快照补充近期投稿与明确决定。仍不能用录用名单替代全部投稿，也不能声称覆盖了全部拒稿。
 
-已核验的采集文件计数：ICLR 2020–2026 主会 15,534 条、COLM 2024–2026 共 1,573 条，摘要均已取得；候选范围内的 PMLR 文件为 31,428 条，已剔除两份重复出版元数据。ACL Anthology 已选文件为 63,297 条，其中 15,147 条源记录缺摘要。这些是采集文件的来源记录数，不能相加当作去重论文数，也不能代替主库实时统计；实际入库量使用 paper-atlas query --stats 查看。
+## 查询批次与入库状态
 
-代码在 `codex/metadata-index` 工作分支交付，[Draft PR #1](https://gitea.entroia.com/Zayden-Jung/paper-atlas/pulls/1) 尚未合并，等待全量就绪后用户手动合并。各提交分别由远程 CI 验证，结果以对应提交的 Gitea Actions 检查为准。全量导入、其他会议适配器、去重复核和覆盖率核验继续进行，应随实际结果更新此说明。
+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
+paper-atlas coverage --db /data/paper-index/papers.sqlite \
+  --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。
+
+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。

docs/usage.md

@@ -42,13 +42,4 @@ paper-atlas coverage --db /data/paper-index/papers.sqlite --out /data/paper-inde
 
 `--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。
 
-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 query --db /data/paper-index/papers.sqlite \\
-  --venue ICLR --status rejected --outcome accepted
-```
-
-`known_acceptances` 列出目前仍为录用状态的各次投稿及会议、年份、track 和决定证据，`publication_outcome` 汇总为 accepted 或 no_known_acceptance。汇总会检查所有会议和 track，不把某次拒稿覆盖到整篇论文；同一次投稿的后续撤稿也会更新该次状态并保留原决定。no_known_acceptance 只表示现有来源中没有查到录用，不能称为“从未录用”。
-
 `--stats` 中 papers 是当前规则下的论文实体数；source_records 是来源记录数；decisions 是决定观察数。一个投稿可能有多个来源和多条观察，不能相加当作论文数。

paper_atlas/querying.py

@@ -5,22 +5,6 @@ import sqlite3
 from pathlib import Path
 
 
-LATEST_DECISION = '''NOT EXISTS (
-    SELECT 1 FROM decisions newer WHERE newer.submission_id=d.submission_id
-    AND (newer.observed_at,COALESCE(newer.decision_date,newer.observed_at),newer.id)
-      > (d.observed_at,COALESCE(d.decision_date,d.observed_at),d.id)
-)'''
-ACCEPTED_PAPERS = "SELECT s.paper_id FROM submissions s JOIN decisions d ON d.submission_id=s.id WHERE d.status='accepted' AND "+LATEST_DECISION
-
-
-def known_acceptances(conn,paper):
-    return [dict(row) for row in conn.execute('''SELECT s.id AS submission_id,v.acronym AS venue,e.year,e.track,
-        d.id AS decision_id,d.decision_date,d.observed_at,d.evidence_url
-        FROM submissions s JOIN editions e ON e.id=s.edition_id JOIN venues v ON v.id=e.venue_id
-        JOIN decisions d ON d.submission_id=s.id WHERE s.paper_id=? AND d.status='accepted' AND '''+LATEST_DECISION+
-        ' ORDER BY e.year,v.acronym,e.track,s.id',(paper,))]
-
-
 def main(argv=None, *, prog=None):
     parser = argparse.ArgumentParser(prog=prog)
     parser.add_argument('--db', required=True)
@@ -31,7 +15,6 @@ def main(argv=None, *, prog=None):
     parser.add_argument('--year', type=int)
     parser.add_argument('--track',help='Exact track, e.g. main, findings, workshop')
     parser.add_argument('--status', choices=['accepted','rejected','desk_rejected','withdrawn','under_review','unknown'])
-    parser.add_argument('--outcome',choices=['accepted','no_known_acceptance'],help='跨会议的已知录用情况；未查到录用不等于从未录用')
     parser.add_argument('--limit', type=int, default=20)
     parser.add_argument('--stats', action='store_true')
     args = parser.parse_args(argv)
@@ -42,10 +25,6 @@ def main(argv=None, *, prog=None):
         result = {name:conn.execute('SELECT count(*) FROM '+name).fetchone()[0] for name in ('papers','source_records','submissions','decisions','tags','match_candidates')}
         result['records_by_source'] = [dict(r) for r in conn.execute('SELECT s.name,count(r.id) AS imported_records FROM sources s LEFT JOIN source_records r ON r.source_id=s.id GROUP BY s.id ORDER BY s.name')]
         result['decision_events_by_status'] = [dict(r) for r in conn.execute('SELECT status,count(*) AS events FROM decisions GROUP BY status')]
-        accepted=conn.execute('SELECT count(DISTINCT paper_id) FROM ('+ACCEPTED_PAPERS+')').fetchone()[0]
-        result['papers_with_known_acceptance']=accepted
-        result['papers_without_known_acceptance']=result['papers']-accepted
-        result['outcome_scope']='Only imported evidence is known. No known acceptance is not proof that a paper was never accepted.'
         result['coverage'] = [dict(r) for r in conn.execute('SELECT status,count(*) AS sources FROM edition_sources GROUP BY status')]
         result['runs'] = [dict(r) for r in conn.execute('SELECT * FROM ingest_runs ORDER BY id DESC LIMIT 10')]
     else:
@@ -57,8 +36,6 @@ def main(argv=None, *, prog=None):
         if args.tag:
             namespace,value = args.tag.split('=',1)
             where.append('EXISTS(SELECT 1 FROM paper_tags pt JOIN tags t ON t.id=pt.tag_id WHERE pt.paper_id=p.id AND t.namespace=? AND t.value=?)'); params.extend([namespace,value])
-        if args.outcome:
-            where.append('p.id '+('IN' if args.outcome=='accepted' else 'NOT IN')+' ('+ACCEPTED_PAPERS+')')
         if args.venue or args.year or args.status or args.track:
             clause = ['1=1']
             if args.venue:
@@ -71,7 +48,14 @@ def main(argv=None, *, prog=None):
             if args.year:
                 clause.append('e.year=?'); params.append(args.year)
             if args.status:
-                latest='EXISTS (SELECT 1 FROM decisions d WHERE d.submission_id=s.id AND d.status=? AND '+LATEST_DECISION+')'
+                latest='''EXISTS (
+                    SELECT 1 FROM decisions d WHERE d.submission_id=s.id AND d.status=?
+                    AND NOT EXISTS (
+                        SELECT 1 FROM decisions newer WHERE newer.submission_id=d.submission_id
+                        AND (newer.observed_at,COALESCE(newer.decision_date,newer.observed_at),newer.id)
+                          > (d.observed_at,COALESCE(d.decision_date,d.observed_at),d.id)
+                    )
+                )'''
                 clause.append('(NOT EXISTS(SELECT 1 FROM decisions d WHERE d.submission_id=s.id) OR '+latest+')' if args.status=='unknown' else latest); params.append(args.status)
             where.append('p.id IN (SELECT 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 '+' AND '.join(clause)+')')
         sql = 'SELECT p.* FROM papers p'+(' WHERE '+' AND '.join(where) if where else '')+' ORDER BY p.id LIMIT ?'
@@ -81,8 +65,6 @@ def main(argv=None, *, prog=None):
             paper = dict(row)
             paper['authors'] = json.loads(paper.pop('authors_json'))
             paper['identifiers'] = [dict(r) for r in conn.execute('SELECT scheme,value FROM identifiers WHERE paper_id=?',(row['id'],))]
-            paper['known_acceptances']=known_acceptances(conn,row['id'])
-            paper['publication_outcome']='accepted' if paper['known_acceptances'] else 'no_known_acceptance'
             if args.paper is not None:
                 paper['tags'] = [dict(r) for r in conn.execute('SELECT t.namespace,t.value,pt.evidence_key FROM paper_tags pt JOIN tags t ON t.id=pt.tag_id WHERE pt.paper_id=?',(row['id'],))]
                 paper['sources'] = [dict(r) for r in conn.execute('SELECT s.name,r.external_id,r.url,r.title,r.abstract,r.retrieved_at FROM source_records r JOIN sources s ON s.id=r.source_id WHERE r.paper_id=?',(row['id'],))]
@@ -95,7 +77,6 @@ def main(argv=None, *, prog=None):
                         if conn.execute("SELECT 1 FROM sqlite_master WHERE type='table' AND name='decision_sources'").fetchone():
                             decision['sources']=[dict(r) for r in conn.execute('SELECT s.name,r.external_id,ds.source_decision_id FROM decision_sources ds JOIN source_records r ON r.id=ds.source_record_id JOIN sources s ON s.id=r.source_id WHERE ds.decision_id=?',(d['id'],))]
                         submission['decisions'].append(decision)
-                    submission['latest_status']=submission['decisions'][-1]['status'] if submission['decisions'] else 'unknown'
                     if conn.execute("SELECT 1 FROM sqlite_master WHERE type='table' AND name='submission_sources'").fetchone():
                         submission['sources']=[dict(r) for r in conn.execute('SELECT so.name,r.external_id,ss.source_submission_id FROM submission_sources ss JOIN source_records r ON r.id=ss.source_record_id JOIN sources so ON so.id=r.source_id WHERE ss.submission_id=?',(sub['id'],))]
                     submissions.append(submission)

tests/test_query.py

@@ -9,41 +9,6 @@ from paper_atlas.db.store import Store
 
 
 class QueryTests(unittest.TestCase):
-    def run_query(self,db,*args):
-        return json.loads(subprocess.run([sys.executable,'-B','-m','paper_atlas','query','--db',str(db),*args],check=True,capture_output=True,text=True).stdout)
-
-    def test_rejection_then_acceptance_at_another_venue_preserves_both_attempts(self):
-        with tempfile.TemporaryDirectory() as tmp:
-            db=Path(tmp)/'papers.sqlite';store=Store(db);self.addCleanup(store.conn.close)
-            paper,first=store.record('openreview_snapshot','forum1','https://example.org/1','Original title','Abstract',['Jane Doe'],{'arxiv':'2401.00001','openreview':'forum1'})
-            store.decision(paper,first,'ICLR',2024,'main','forum1','https://example.org/reject','rejected','Reject',identities=[('openreview','forum1')],observed_at='2024-02-01T00:00:00Z')
-            same,second=store.record('colm','forum2','https://example.org/2','Revised title','Revised abstract',['Jane Doe'],{'arxiv':'2401.00001','openreview':'forum2'})
-            store.decision(same,second,'COLM',2025,'main','forum2','https://example.org/accept','accepted','Accept',identities=[('openreview','forum2')],observed_at='2025-08-01T00:00:00Z')
-            store.conn.commit();self.assertEqual(same,paper)
-            rows=self.run_query(db,'--venue','ICLR','--status','rejected','--outcome','accepted')
-            self.assertEqual([row['id'] for row in rows],[paper])
-            self.assertEqual(rows[0]['publication_outcome'],'accepted')
-            self.assertEqual([a['venue'] for a in rows[0]['known_acceptances']],['COLM'])
-            detail=self.run_query(db,'--paper',str(paper))[0]
-            self.assertEqual([(s['acronym'],s['latest_status']) for s in detail['submissions']],[('ICLR','rejected'),('COLM','accepted')])
-            self.assertEqual(self.run_query(db,'--venue','ICLR','--status','rejected','--outcome','no_known_acceptance'),[])
-            self.assertEqual(self.run_query(db,'--stats')['papers_with_known_acceptance'],1)
-
-    def test_later_rejection_elsewhere_does_not_erase_acceptance_and_unknown_is_not_never(self):
-        with tempfile.TemporaryDirectory() as tmp:
-            db=Path(tmp)/'papers.sqlite';store=Store(db);self.addCleanup(store.conn.close)
-            paper,one=store.record('source','one','https://example.org/1','One paper','Abstract',[])
-            store.decision(paper,one,'COLM',2024,'main','one','https://example.org/accept','accepted','Accept',observed_at='2024-01-01T00:00:00Z')
-            store.decision(paper,one,'ICLR',2025,'main','two','https://example.org/reject','rejected','Reject',observed_at='2025-01-01T00:00:00Z')
-            unknown,_=store.record('arxiv','other','https://example.org/other','No observed submissions','Abstract',[])
-            store.conn.commit()
-            self.assertEqual([r['id'] for r in self.run_query(db,'--outcome','accepted')],[paper])
-            self.assertEqual([r['id'] for r in self.run_query(db,'--outcome','no_known_acceptance')],[unknown])
-            store.decision(paper,one,'COLM',2024,'main','one','https://example.org/withdraw','withdrawn','Withdrawn',observed_at='2026-01-01T00:00:00Z')
-            store.conn.commit();self.assertEqual(self.run_query(db,'--outcome','accepted'),[])
-            history=self.run_query(db,'--paper',str(paper))[0]
-            self.assertEqual([d['status'] for d in history['submissions'][0]['decisions']],['accepted','withdrawn'])
-
     def test_joint_conference_alias_does_not_duplicate_submission(self):
         with tempfile.TemporaryDirectory() as tmp:
             db=Path(tmp)/'papers.sqlite';store=Store(db);self.addCleanup(store.conn.close)