Keep stable paper identities separate from ambiguous title matches

Reviewed-on: #17

docs/usage.md

@@ -99,6 +99,8 @@ paper-atlas query --pg-service foundry-research \
 
 `--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。
 
+已有稳定标识或原来源记录匹配时，该身份优先；同标题、同作者的另一 arXiv 存档或扩展稿不会仅因相似标题被并入。没有身份锚点时，作者佐证的精确标题只有一个候选才可匹配；多个候选会报 `Ambiguous paper identity`，整个采集文件回滚并记录失败运行。应补有证据的标识或先核查版本关系，不删除重复候选或任取第一个。一个新来源明确同时携带两个既有稳定标识时，仍可按既有规则归并并保留投稿、标签和合并日志；未归并的同标题关系继续保留为待核查候选。这些规则不证明全库去重完成。
+
 ## 5. 投稿历史关系审计
 
 ```sh

paper_atlas/audits/public_openreview.py

@@ -39,7 +39,9 @@ def audit(db, inventory, out, *, pg_service=None, pg_schema=None):
             if json.loads(path.with_suffix('.manifest.json').read_text()) != manifest:
                 raise ValueError('Collected manifest differs from inventory')
             count = 0
-            for line in path.read_text().splitlines():
+            # Unicode paragraph/line separators are valid inside JSON strings;
+            # split physical byte lines, not Unicode text boundaries.
+            for line in path.read_bytes().splitlines():
                 row = json.loads(line)
                 if any(row[key] != manifest[key] for key in ('source', 'venue', 'year', 'track')):
                     raise ValueError('Record edition differs from inventory')

paper_atlas/db/store.py

@@ -95,13 +95,19 @@ class Store:
             matches.add(old[0])
         key = normalized(title)
         title_matches = c.execute('SELECT id,authors_json,abstract FROM papers WHERE title_key=?',(key,)).fetchall()
-        authors_set = author_keys(authors)
-        for paper,old_authors,old_abstract in title_matches:
-            overlap = authors_set & author_keys(json.loads(old_authors))
-            # Cross-platform title matching needs independent author corroboration.
-            same_source = c.execute('SELECT 1 FROM source_records WHERE paper_id=? AND source_id=? LIMIT 1',(paper,source_id)).fetchone()
-            if not same_source and len(key)>=25 and (len(overlap)>=2 or (overlap and abstract and abstract.strip()==(old_abstract or '').strip())):
-                matches.add(paper)
+        # An existing identifier/source record anchors the entity. Title
+        # similarity must not pull in another deposit or an extended version.
+        if not matches:
+            title_only_matches = set()
+            authors_set = author_keys(authors)
+            for paper,old_authors,old_abstract in title_matches:
+                overlap = authors_set & author_keys(json.loads(old_authors))
+                same_source = c.execute('SELECT 1 FROM source_records WHERE paper_id=? AND source_id=? LIMIT 1',(paper,source_id)).fetchone()
+                if not same_source and len(key)>=25 and (len(overlap)>=2 or (overlap and abstract and abstract.strip()==(old_abstract or '').strip())):
+                    title_only_matches.add(paper)
+            if len(title_only_matches)>1:
+                raise ValueError('Ambiguous paper identity: multiple author-corroborated title matches; provide verified identifiers')
+            matches = title_only_matches
         if matches:
             paper = min(matches)
             for other in sorted(matches-{paper}):

tests/test_index_core.py

@@ -53,6 +53,50 @@ class StoreTests(unittest.TestCase):
         self.assertNotEqual(other,paper)
         self.assertEqual(self.store.conn.execute('SELECT count(*) FROM match_candidates').fetchone()[0],1)
 
+    def test_identifier_anchor_does_not_absorb_a_same_title_arxiv_version(self):
+        conference,first=self.record('arxiv','1408.1485')
+        extended,second=self.record('arxiv','cs/0307069')
+        self.store.decision(extended,second,'ICLR',2025,'main','separate','https://example.org/reject','rejected','Reject')
+        resolved,_=self.record('dblp','conf/uai/example',{'arxiv':'1408.1485'})
+        self.assertEqual(resolved,conference);self.assertNotEqual(conference,extended)
+        c=self.store.conn
+        self.assertEqual(c.execute('SELECT count(*) FROM papers').fetchone()[0],2)
+        self.assertEqual(c.execute('SELECT paper_id FROM submissions').fetchone()[0],extended)
+        self.assertEqual(c.execute('SELECT count(*) FROM paper_merges').fetchone()[0],0)
+        self.assertEqual(c.execute('SELECT count(*) FROM match_candidates').fetchone()[0],1)
+        # A refresh of the anchored original source is equally unambiguous.
+        self.assertEqual(self.record('arxiv','1408.1485')[0],conference)
+        self.assertEqual(c.execute('SELECT count(*) FROM papers').fetchone()[0],2)
+
+    def test_ambiguous_title_aborts_whole_file_without_merging_existing_entities(self):
+        self.record('arxiv','1408.1485');self.record('arxiv','cs/0307069')
+        self.store.conn.commit()
+        rows=[{'source':'dblp','external_id':'conf/uai/new','url':'https://example.org/new',
+               'title':'An unrelated earlier record in this file','abstract':None,'authors':[],
+               'venue':'UAI','year':2001,'track':'main','status':'accepted'},
+              {'source':'dblp','external_id':'conf/uai/ambiguous','url':'https://example.org/ambiguous',
+               'title':'A sufficiently long example research paper title','abstract':None,
+               'authors':['Jane Doe','John Smith'],'identifiers':{'doi':'10.0000/not-yet-known'},
+               'venue':'UAI','year':2001,'track':'main','status':'accepted'}]
+        path=Path(self.tmp.name)/'ambiguous.jsonl'
+        path.write_text(''.join(json.dumps(row)+'\n' for row in rows))
+        path.with_suffix('.manifest.json').write_text(json.dumps({'source':'dblp','list_url':'https://example.org/list','count':2}))
+        with self.assertRaisesRegex(ValueError,'Ambiguous paper identity'):ingest_file(self.db,path)
+        c=self.store.conn
+        for table,count in [('papers',2),('source_records',2),('submissions',0),('decisions',0),('paper_merges',0)]:
+            self.assertEqual(c.execute('SELECT count(*) FROM '+table).fetchone()[0],count,table)
+        self.assertEqual(c.execute('SELECT status FROM ingest_runs').fetchone()[0],'failed')
+
+    def test_explicit_bridge_merges_only_its_identifier_matches(self):
+        first,_=self.record('arxiv','2601.00001',authors=['First Author'])
+        second,_=self.record('arxiv','2601.00002',{'doi':'10.0000/bridge'},authors=['Second Author'])
+        unrelated,_=self.record('arxiv','2601.00003')
+        resolved,_=self.record('official','bridge',{'arxiv':'2601.00001','doi':'10.0000/bridge'})
+        self.assertEqual(resolved,min(first,second))
+        self.assertEqual(self.store.conn.execute('SELECT count(*) FROM papers').fetchone()[0],2)
+        self.assertIsNotNone(self.store.conn.execute('SELECT 1 FROM papers WHERE id=?',(unrelated,)).fetchone())
+        self.assertEqual(self.store.conn.execute('SELECT count(*) FROM paper_merges').fetchone()[0],1)
+
     def test_manifest_count_mismatch_rolls_back_records(self):
         path=Path(self.tmp.name)/'source.jsonl'
         path.write_text(json.dumps({'source':'pmlr','external_id':'v1/paper','url':'https://example.org/paper','title':'Paper','abstract':'Abstract','authors':[],'venue':'ICML','year':2023,'track':'main','status':'accepted'})+'\n')

tests/test_postgres_ingestion.py

@@ -110,6 +110,34 @@ class PostgreSQLIngestionTests(unittest.TestCase):
         finally:
             reader.close()
 
+    def test_identity_anchor_keeps_other_arxiv_version_and_ambiguous_file_rolls_back(self):
+        title='An identical long research title shared by conference and extended versions'
+        authors=['Jane Doe','John Smith']
+        store=self.store()
+        try:
+            first,_=store.record('arxiv','1408.1485','https://arxiv.org/abs/1408.1485',title,'Conference abstract',authors)
+            second,_=store.record('arxiv','cs/0307069','https://arxiv.org/abs/cs/0307069',title,'Extended abstract',authors)
+            resolved,_=store.record('dblp','known','https://example.org/known',title,None,authors,{'arxiv':'1408.1485'})
+            self.assertEqual(resolved,first);self.assertNotEqual(first,second)
+            store.conn.commit()
+            self.assertEqual(store.conn.execute('SELECT count(*) FROM papers').fetchone()[0],3)
+            self.assertEqual(store.conn.execute('SELECT count(*) FROM paper_merges').fetchone()[0],1)  # migration fixture only
+            self.assertEqual(store.conn.execute('SELECT count(*) FROM match_candidates').fetchone()[0],1)
+        finally:store.conn.close()
+        rows=[self.row('official','earlier',status='accepted',venue='UAI',year=2001),
+              dict(self.row('official','ambiguous',status='accepted',venue='UAI',year=2001),
+                   title=title,abstract=None,authors=authors,identifiers={})]
+        with self.assertRaisesRegex(ValueError,'Ambiguous paper identity'):self.ingest(self.file('ambiguous-identity',rows))
+        store=self.store()
+        try:
+            self.assertEqual(store.conn.execute('SELECT count(*) FROM papers').fetchone()[0],3)
+            self.assertEqual(store.conn.execute('SELECT count(*) FROM source_records').fetchone()[0],4)
+            self.assertEqual(store.conn.execute('SELECT count(*) FROM submissions').fetchone()[0],1)
+            self.assertEqual(store.conn.execute('SELECT count(*) FROM paper_merges').fetchone()[0],1)
+            self.assertEqual(store.conn.execute('SELECT status FROM ingest_runs ORDER BY id DESC LIMIT 1').fetchone()[0],'failed')
+            self.assertEqual(store.conn.execute("SELECT count(*) FROM source_records WHERE external_id IN (?,?)",('earlier','ambiguous')).fetchone()[0],0)
+        finally:store.conn.close()
+
     def test_file_import_is_idempotent_and_refreshes_only_own_tags(self):
         row = self.row(); row['tags'] = [{'namespace': 'openreview_snapshot:area', 'value': 'theory'}]
         path = self.file('reject', [row]); self.ingest(path)

tests/test_public_openreview.py

@@ -152,6 +152,35 @@ class PublicOpenReviewTests(unittest.TestCase):
             finally:
                 store.conn.close()
 
+    def test_unicode_separators_in_abstract_survive_audit_and_import(self):
+        for separator in ('\u0085', '\u2028', '\u2029'):
+            with self.subTest(separator=repr(separator)), tempfile.TemporaryDirectory() as tmp:
+                root = Path(tmp)
+                abstract = 'First paragraph' + separator + 'Second paragraph'
+                result = self.collect(root / 'source', {
+                    'venues/icml/icml2025.jsonl': [self.row(abstract=abstract)]})
+                path = Path(result['files'][0]['file'])
+                data = path.read_bytes()
+                self.assertIn(separator.encode(), data)
+                self.assertEqual(data.count(b'\n'), 1)
+                db = root / 'db.sqlite'
+                store = Store(db)
+                store.conn.close()
+                inventory = root / 'source/public-openreview-inventory.json'
+                before = audit(db, inventory, root / 'before.json')
+                self.assertEqual(before['status'], 'ready_for_serial_import')
+                self.assertEqual(before['records_checked'], 1)
+                ingest_file(db, path)
+                after = audit(db, inventory, root / 'after.json')
+                self.assertEqual(after['status'], 'ready_for_serial_import')
+                self.assertEqual(after['existing_same_edition_attempts'], 1)
+                store = Store(db)
+                try:
+                    self.assertEqual(store.conn.execute(
+                        'SELECT abstract FROM source_records').fetchone()[0], abstract)
+                finally:
+                    store.conn.close()
+
 
 if __name__ == '__main__':
     unittest.main()