Prepare evidence-bound identifier additions without rewriting source records

Reviewed-on: #17

.gitea/workflows/check.yml

@@ -54,6 +54,7 @@ jobs:
               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','audit','histories','--help'],cwd=outside,check=True)
+              subprocess.run([python,'-I','-B','-m','paper_atlas','curate','identifiers','--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()"
               subprocess.run([python,'-I','-B','-c',smoke],cwd=outside,check=True)

docs/usage.md

@@ -2,6 +2,55 @@
 
 先在已确认的远程环境安装项目，使用 `paper-atlas`。从源码运行时，将命令前缀替换为 `python3 -B -m paper_atlas`，其余参数相同。数据目录位于仓库外。
 
+## 按证据补充稳定标识
+
+`paper-atlas curate identifiers --plan /data/review/plan.json --output /data/review/prepared`
+只生成新的 JSONL、manifest、证据副本及 `curation-report.json`，不会连接数据库。
+输出目录必须不存在，父目录必须已存在；任何输入或断言失败，都不发布本批输出。
+原始文件不变，未选中的记录逐字节保留。题名、作者、年份、页码、投稿决定、标签和既有 metadata
+均不重写，仅补充 `identifiers` 并追加 `metadata.identifier_curation` 证据链。
+
+计划格式如下（哈希占位符须替换为真实 SHA256，所有路径按命令当前目录解析）：
+
+```json
+{
+  "format_version": 1,
+  "inputs": [{
+    "file": "/data/review/uai2001.jsonl",
+    "sha256": "<JSONL 文件 SHA256>",
+    "manifest_sha256": "<同名 .manifest.json 文件 SHA256>"
+  }],
+  "assertions": [{
+    "source": "dblp",
+    "external_id": "conf/uai/example",
+    "record_sha256": "<原始物理行字节 SHA256，包含该行原有换行符>",
+    "identifiers": {"arxiv": "1408.1485"},
+    "evidence": [{
+      "file": "/data/review/primary-metadata.json",
+      "sha256": "<证据 JSON 文件 SHA256>",
+      "url": "https://example.org/primary-record",
+      "checked_at": "2026-11-08T08:00:00Z",
+      "note": "说明人工核对的题名、作者、出版版本和稳定标识证据"
+    }]
+  }]
+}
+```
+
+输入 manifest 必须包含 `source/venue/year/track/count/list_url/file_sha256`，且与逐条记录一致。
+断言必须唯一、准确命中一条记录。仅支持无版本后缀的 arXiv 编号与小写规范 DOI；
+已有同类标识不允许覆盖，相同值可以补记证据。证据只接受不超过 16 MiB 的 JSON 元数据文件，
+来源 URL 要求 HTTPS 且不含凭据，核查时间必须带时区；不下载论文 PDF。
+
+`verification_scope=input_and_evidence_integrity_only` 和 `semantic_identity_verified=false`
+明确表示哈希校验不能证明两条记录属于同一作品。请先独立核对版本关系；仅年份、页码或相同题名
+不能作为合并依据。存在来源冲突的行应继续暂缓。新 manifest 保留原来的 partial 状态及摘要缺失数，
+不会把补充编号伪装成来源覆盖或摘要补全。证据副本按 SHA256 保存在输出目录 `evidence/`，
+原计划也保存在 `plan.json`，供之后复查。
+
+文件生成后仍需另做当前 PostgreSQL 身份、投稿和决定冲突预检；导入运行时必须包含
+“稳定标识优先、多个标题候选则整文件回滚”的身份保护，再以 `import records` 独立导入并验收。
+该命令不会自动导入或合并实体，也不代表最终全库去重通过。
+
 ## PostgreSQL 查询
 
 在远程环境安装 `.[postgres]`，通过权限为 `0600` 的 libpq service 文件连接，不把密码放入 URL、命令行或仓库。
@@ -99,6 +148,8 @@ 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/cli.py

@@ -6,6 +6,7 @@ from paper_atlas import __version__
 
 
 COMMANDS = {
+    ('curate','identifiers'): ('paper_atlas.curation.identifiers', {}, '按证据补充稳定标识并生成独立待导入文件'),
     ('query',): ('paper_atlas.querying', {}, '查询论文、标签和投稿历史'),
     ('coverage',): ('paper_atlas.audits.coverage', {}, '查看全部候选会议的覆盖情况'),
     ('download',): ('paper_atlas.io.snapshots', {}, '下载并校验固定版本快照'),
@@ -48,7 +49,7 @@ def main(argv=None):
             leaf=commands.add_parser(route[0],help=help_text,add_help=False)
         else:
             if route[0] not in groups:
-                group=commands.add_parser(route[0],help={'collect':'采集来源元数据','catalogue':'盘点历史目录','import':'导入数据库','maintain':'维护数据库','audit':'核验数据'}[route[0]])
+                group=commands.add_parser(route[0],help={'collect':'采集来源元数据','catalogue':'盘点历史目录','import':'导入数据库','maintain':'维护数据库','audit':'核验数据','curate':'按证据整理元数据'}[route[0]])
                 groups[route[0]]=group.add_subparsers(dest='operation',required=True)
             leaf=groups[route[0]].add_parser(route[1],help=help_text,add_help=False)
         leaf.set_defaults(handler=(route,module,kwargs))

paper_atlas/curation/__init__.py

@@ -0,0 +1 @@
+"""Offline, evidence-bound preparation of metadata for separate ingestion."""

paper_atlas/curation/identifiers.py

@@ -0,0 +1,212 @@
+"""Add reviewed stable identifiers without rewriting bibliographic source fields.
+
+Hashes establish file integrity, not the truth of an identity assertion. Identity
+review and a fresh database preflight remain separate requirements.
+"""
+import argparse
+from datetime import datetime
+import hashlib
+import json
+from pathlib import Path
+import re
+import tempfile
+from urllib.parse import urlsplit
+
+
+SCOPE = 'input_and_evidence_integrity_only'
+MAX_METADATA_BYTES = 16 * 1024 * 1024
+
+
+def digest(data):
+    return hashlib.sha256(data).hexdigest()
+
+
+def object_keys(value, required, optional=()):
+    if not isinstance(value, dict) or not set(required) <= value.keys() or value.keys() - set(required) - set(optional):
+        raise ValueError('Missing or unsupported plan fields')
+
+
+def json_bytes(value):
+    return (json.dumps(value, ensure_ascii=False, separators=(',', ':'), allow_nan=False) + '\n').encode('utf-8')
+
+
+def decode(raw):
+    def unique(pairs):
+        result = {}
+        for key, value in pairs:
+            if key in result:
+                raise ValueError('Duplicate JSON key: ' + key)
+            result[key] = value
+        return result
+    return json.loads(raw, object_pairs_hook=unique,
+                      parse_constant=lambda value: (_ for _ in ()).throw(ValueError('Non-finite JSON value')))
+
+
+def metadata(path, expected=None):
+    with Path(path).open('rb') as stream:
+        raw = stream.read(MAX_METADATA_BYTES + 1)
+    if len(raw) > MAX_METADATA_BYTES:
+        raise ValueError('Metadata exceeds size limit')
+    if expected is not None:
+        check_hash(raw, expected)
+    return raw, decode(raw)
+
+
+def check_hash(raw, expected):
+    if not isinstance(expected, str) or not re.fullmatch('[0-9a-f]{64}', expected) or digest(raw) != expected:
+        raise ValueError('SHA256 mismatch')
+
+
+def identifier(scheme, value):
+    if not isinstance(value, str) or any(char.isspace() or ord(char) < 32 or ord(char) == 127 for char in value):
+        raise ValueError('Invalid identifier')
+    if scheme == 'arxiv':
+        pattern = r'(?:\d{2}(?:0[1-9]|1[0-2])\.\d{4,5}|[a-zA-Z][a-zA-Z.-]*/\d{2}(?:0[1-9]|1[0-2])\d{3})'
+        valid = re.fullmatch(pattern, value)
+    elif scheme == 'doi':
+        valid = re.fullmatch(r'10\.\d{4,9}/\S+', value) and value == value.lower()
+    else:
+        valid = False
+    if not valid:
+        raise ValueError('Unsupported or noncanonical identifier: ' + scheme)
+
+
+def prepare(plan_path, output):
+    plan_raw, plan = metadata(plan_path)
+    object_keys(plan, ('format_version', 'inputs', 'assertions'))
+    if type(plan['format_version']) is not int or plan['format_version'] != 1:
+        raise ValueError('Unsupported format version')
+    if not isinstance(plan['inputs'], list) or not plan['inputs'] or not isinstance(plan['assertions'], list) or not plan['assertions']:
+        raise ValueError('Inputs and assertions must be nonempty lists')
+    output = Path(output).absolute()
+    if output.exists():
+        raise ValueError('Output directory must not already exist')
+    if not output.parent.is_dir():
+        raise ValueError('Output parent directory must exist')
+    assertions = {}
+    evidence_files = {}
+    checked_evidence = {}
+    for assertion in plan['assertions']:
+        object_keys(assertion, ('source', 'external_id', 'record_sha256', 'identifiers', 'evidence'))
+        if any(not isinstance(assertion[key], str) or not assertion[key] for key in ('source', 'external_id')):
+            raise ValueError('Invalid source identity')
+        key = (assertion['source'], assertion['external_id'])
+        if key in assertions:
+            raise ValueError('Duplicate identity assertion')
+        ids = assertion['identifiers']
+        if not isinstance(ids, dict) or not ids:
+            raise ValueError('Identifiers must be a nonempty object')
+        for scheme, value in ids.items():
+            identifier(scheme, value)
+        if not isinstance(assertion['evidence'], list) or not assertion['evidence']:
+            raise ValueError('Evidence is required')
+        references = []
+        for evidence in assertion['evidence']:
+            object_keys(evidence, ('file', 'sha256', 'url', 'checked_at', 'note'))
+            if not all(isinstance(value, str) and value for value in evidence.values()):
+                raise ValueError('Invalid evidence fields')
+            url = urlsplit(evidence['url'])
+            if url.scheme != 'https' or not url.hostname or url.username or url.password:
+                raise ValueError('Evidence requires an HTTPS URL without credentials')
+            if datetime.fromisoformat(evidence['checked_at'].replace('Z', '+00:00')).utcoffset() is None:
+                raise ValueError('Evidence timestamp requires a timezone')
+            evidence_key = (str(Path(evidence['file']).absolute()), evidence['sha256'])
+            if evidence_key not in checked_evidence:
+                checked_evidence[evidence_key] = metadata(evidence['file'], evidence['sha256'])[0]
+            raw = checked_evidence[evidence_key]
+            evidence_files[evidence['sha256']] = raw
+            references.append({**evidence, 'file': 'evidence/' + evidence['sha256'] + '.json'})
+        assertions[key] = (assertion, references)
+    seen = set()
+    applied = set()
+    names = set()
+    report = {'format_version': 1, 'plan_sha256': digest(plan_raw),
+              'verification_scope': SCOPE, 'semantic_identity_verified': False,
+              'database_written': False, 'files': [], 'assertions_applied': 0, 'identifiers_added': 0}
+    with tempfile.TemporaryDirectory(prefix='.identifier-curation-', dir=output.parent) as temporary:
+        staging = Path(temporary) / 'prepared'
+        staging.mkdir()
+        (staging / 'evidence').mkdir()
+        (staging / 'plan.json').write_bytes(plan_raw)
+        for sha, raw in evidence_files.items():
+            (staging / 'evidence' / (sha + '.json')).write_bytes(raw)
+        for entry in plan['inputs']:
+            object_keys(entry, ('file', 'sha256', 'manifest_sha256'))
+            path = Path(entry['file'])
+            if path.suffix != '.jsonl' or path.name in names:
+                raise ValueError('Inputs require distinct JSONL basenames')
+            names.add(path.name)
+            _, manifest = metadata(path.with_suffix('.manifest.json'), entry['manifest_sha256'])
+            if not isinstance(manifest, dict) or not {'source','venue','year','track','count','list_url','file_sha256'} <= manifest.keys():
+                raise ValueError('Complete source manifest required')
+            if manifest['file_sha256'] != entry['sha256']:
+                raise ValueError('Manifest and plan hashes differ')
+            before = hashlib.sha256()
+            after = hashlib.sha256()
+            count = 0
+            with path.open('rb') as source, (staging / path.name).open('wb') as target:
+                for raw in source:
+                    before.update(raw)
+                    row = decode(raw)
+                    if any(row[field] != manifest[field] for field in ('source', 'venue', 'year', 'track')):
+                        raise ValueError('Record differs from source manifest')
+                    key = (row['source'], row['external_id'])
+                    if key in seen:
+                        raise ValueError('Duplicate source identity in input batch')
+                    seen.add(key)
+                    if key in assertions:
+                        assertion, references = assertions[key]
+                        check_hash(raw, assertion['record_sha256'])
+                        existing = row.get('identifiers', {})
+                        if existing is None:
+                            existing = {}
+                        if not isinstance(existing, dict):
+                            raise ValueError('Invalid existing identifiers')
+                        for scheme, value in assertion['identifiers'].items():
+                            if scheme in existing and existing[scheme] != value:
+                                raise ValueError('Existing identifier conflict')
+                        details = row.setdefault('metadata', {})
+                        if not isinstance(details, dict):
+                            raise ValueError('Invalid record metadata')
+                        history = details.setdefault('identifier_curation', [])
+                        if not isinstance(history, list):
+                            raise ValueError('Invalid curation history')
+                        history.append({'plan_sha256': digest(plan_raw), 'input_file_sha256': entry['sha256'],
+                                        'record_sha256': digest(raw), 'previous_identifiers': dict(existing),
+                                        'identifiers_asserted': assertion['identifiers'], 'evidence': references,
+                                        'verification_scope': SCOPE})
+                        report['identifiers_added'] += len(assertion['identifiers'].keys() - existing.keys())
+                        row['identifiers'] = {**existing, **assertion['identifiers']}
+                        raw = json_bytes(row)
+                        applied.add(key)
+                    target.write(raw)
+                    after.update(raw)
+                    count += 1
+            if before.hexdigest() != entry['sha256'] or not re.fullmatch('[0-9a-f]{64}', entry['sha256']):
+                raise ValueError('Input SHA256 mismatch')
+            if not count or type(manifest['count']) is not int or count != manifest['count']:
+                raise ValueError('Manifest count mismatch')
+            provenance = {'plan_sha256': digest(plan_raw), 'input_file_sha256': before.hexdigest(),
+                          'input_manifest_sha256': entry['manifest_sha256'], 'verification_scope': SCOPE}
+            prepared = {**manifest, 'file': str(output / path.name), 'file_sha256': after.hexdigest(),
+                        'identifier_curation': provenance}
+            (staging / path.with_suffix('.manifest.json').name).write_bytes(json_bytes(prepared))
+            report['files'].append({'file': str(output / path.name), 'count': count,
+                                    'input_sha256': before.hexdigest(), 'sha256': after.hexdigest()})
+        if applied != assertions.keys():
+            raise ValueError('Assertion target absent from input batch')
+        report['assertions_applied'] = len(applied)
+        (staging / 'curation-report.json').write_bytes(json_bytes(report))
+        # All files are on the same filesystem. No database or input mutation.
+        if output.exists():
+            raise ValueError('Output directory appeared during preparation')
+        staging.rename(output)
+    return report
+
+
+def main(argv=None, *, prog=None):
+    parser = argparse.ArgumentParser(prog=prog, description=__doc__)
+    parser.add_argument('--plan', required=True, type=Path)
+    parser.add_argument('--output', required=True, type=Path)
+    args = parser.parse_args(argv)
+    print(json.dumps(prepare(args.plan, args.output), ensure_ascii=False))

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_identifier_curation.py

@@ -0,0 +1,185 @@
+import copy
+import json
+from pathlib import Path
+import tempfile
+import unittest
+
+from paper_atlas.curation.identifiers import SCOPE, digest, json_bytes, prepare
+from paper_atlas.db.store import Store
+from paper_atlas.ingestion.records import ingest_file
+
+
+class IdentifierCurationTests(unittest.TestCase):
+    def setUp(self):
+        self.tmp = tempfile.TemporaryDirectory()
+        self.addCleanup(self.tmp.cleanup)
+        self.root = Path(self.tmp.name)
+        self.output = self.root / 'prepared'
+        self.row = {'source':'dblp','external_id':'conf/uai/example','url':'https://example.org/paper',
+                    'title':'A sufficiently long example research paper title','abstract':None,
+                    'authors':['Jane Doe','John Smith'],'venue':'UAI','year':2001,'track':'main',
+                    'status':'accepted','tags':[{'namespace':'dblp:topic','value':'version\u2029study\x00'}],
+                    'metadata':{'pages':'203-210','raw_title':'Original\u2029title'}}
+        self.evidence = self.root / 'evidence.json'
+        self.evidence.write_bytes(json_bytes({'url':'https://example.org/archive','comment':'Conference version'}))
+        self.path = self.root / 'records.jsonl'
+        self.raw = json_bytes(self.row)
+        self.path.write_bytes(self.raw)
+        self.manifest = {'source':'dblp','venue':'UAI','year':2001,'track':'main','count':1,
+                         'list_url':'https://example.org/list','file_sha256':digest(self.raw),
+                         'status':'partial','missing_abstract_count':1,'parser_version':2}
+        self.path.with_suffix('.manifest.json').write_bytes(json_bytes(self.manifest))
+        self.plan = {'format_version':1,'inputs':[self.input(self.path)],'assertions':[
+            {'source':'dblp','external_id':self.row['external_id'],'record_sha256':digest(self.raw),
+             'identifiers':{'arxiv':'1408.1485'},'evidence':[{
+                 'file':str(self.evidence),'sha256':digest(self.evidence.read_bytes()),
+                 'url':'https://example.org/archive','checked_at':'2026-11-08T08:00:00Z',
+                 'note':'Reviewed title, authors, publication and version evidence'}]}]}
+
+    def input(self, path):
+        return {'file':str(path),'sha256':digest(path.read_bytes()),
+                'manifest_sha256':digest(path.with_suffix('.manifest.json').read_bytes())}
+
+    def run_plan(self, plan=None):
+        path = self.root / 'plan.json'
+        path.write_bytes(json_bytes(self.plan if plan is None else plan))
+        return prepare(path, self.output)
+
+    def test_only_identifiers_and_provenance_change_and_raw_inputs_survive(self):
+        result = self.run_plan()
+        self.assertEqual(self.path.read_bytes(), self.raw)
+        prepared = json.loads((self.output / self.path.name).read_bytes())
+        provenance = prepared['metadata'].pop('identifier_curation')
+        self.assertEqual(prepared.pop('identifiers'), {'arxiv':'1408.1485'})
+        self.assertEqual(prepared, self.row)
+        self.assertEqual(provenance[0]['record_sha256'], digest(self.raw))
+        self.assertEqual((self.output / provenance[0]['evidence'][0]['file']).read_bytes(), self.evidence.read_bytes())
+        manifest = json.loads((self.output / 'records.manifest.json').read_bytes())
+        for key, value in self.manifest.items():
+            if key != 'file_sha256': self.assertEqual(manifest[key], value)
+        self.assertEqual(manifest['file_sha256'], digest((self.output / self.path.name).read_bytes()))
+        self.assertEqual(result['assertions_applied'], 1)
+        self.assertEqual(result['identifiers_added'], 1)
+        self.assertEqual(result['verification_scope'], SCOPE)
+        self.assertFalse(result['semantic_identity_verified'])
+        self.assertFalse(result['database_written'])
+        self.assertEqual(list(self.output.glob('*.jsonl')), [self.output / self.path.name])
+        with self.assertRaisesRegex(ValueError, 'already exist'): self.run_plan()
+
+    def test_late_invalid_file_publishes_nothing(self):
+        second = self.root / 'second.jsonl'
+        second.write_bytes(json_bytes({**self.row,'external_id':'second'}))
+        manifest = {**self.manifest,'file_sha256':digest(second.read_bytes()),'count':2}
+        second.with_suffix('.manifest.json').write_bytes(json_bytes(manifest))
+        self.plan['inputs'].append(self.input(second))
+        with self.assertRaisesRegex(ValueError, 'count mismatch'): self.run_plan()
+        self.assertFalse(self.output.exists())
+        self.assertFalse(list(self.root.glob('.identifier-curation-*')))
+        self.assertEqual(self.path.read_bytes(), self.raw)
+
+    def test_unasserted_rows_keep_exact_physical_bytes_and_doi_is_additive(self):
+        untouched = (json.dumps({**self.row,'external_id':'unselected'},ensure_ascii=False,indent=None) + '  ').encode()
+        self.path.write_bytes(self.raw + untouched)
+        self.path.with_suffix('.manifest.json').write_bytes(json_bytes({**self.manifest,
+            'file_sha256':digest(self.path.read_bytes()),'count':2,'missing_abstract_count':2}))
+        self.plan['inputs'] = [self.input(self.path)]
+        self.plan['assertions'][0]['identifiers']['doi'] = '10.1234/example'
+        result = self.run_plan()
+        with (self.output / self.path.name).open('rb') as stream:
+            first = json.loads(next(stream))
+            self.assertEqual(next(stream), untouched)
+        self.assertEqual(first['identifiers'], {'arxiv':'1408.1485','doi':'10.1234/example'})
+        self.assertEqual(result['identifiers_added'], 2)
+
+    def test_missing_duplicate_and_mismatched_assertions_fail_closed(self):
+        for mode in ('missing','duplicate','line_hash','duplicate_input'):
+            with self.subTest(mode=mode):
+                plan = copy.deepcopy(self.plan)
+                assertion = plan['assertions'][0]
+                if mode == 'missing': assertion['external_id'] = 'absent'
+                elif mode == 'duplicate': plan['assertions'].append(copy.deepcopy(assertion))
+                elif mode == 'line_hash': assertion['record_sha256'] = '0' * 64
+                else:
+                    other = self.root / 'duplicate.jsonl'
+                    other.write_bytes(self.raw)
+                    other.with_suffix('.manifest.json').write_bytes(json_bytes(self.manifest))
+                    plan['inputs'].append(self.input(other))
+                with self.assertRaises(ValueError): self.run_plan(plan)
+                self.assertFalse(self.output.exists())
+
+    def test_identifier_conflict_does_not_overwrite_and_same_value_is_auditable(self):
+        self.row['identifiers'] = {'arxiv':'cs/0307069'}
+        self.path.write_bytes(json_bytes(self.row))
+        self.manifest['file_sha256'] = digest(self.path.read_bytes())
+        self.path.with_suffix('.manifest.json').write_bytes(json_bytes(self.manifest))
+        self.plan['inputs'] = [self.input(self.path)]
+        self.plan['assertions'][0]['record_sha256'] = digest(self.path.read_bytes())
+        with self.assertRaisesRegex(ValueError, 'identifier conflict'): self.run_plan()
+        self.assertFalse(self.output.exists())
+        self.plan['assertions'][0]['identifiers']['arxiv'] = 'cs/0307069'
+        self.assertEqual(self.run_plan()['identifiers_added'], 0)
+
+    def test_unsupported_changes_identifiers_and_unbound_evidence_are_rejected(self):
+        for mode in ('title','bad_month','version','unknown_scheme','doi_case','evidence_hash','credentials','timestamp'):
+            with self.subTest(mode=mode):
+                plan = copy.deepcopy(self.plan)
+                assertion = plan['assertions'][0]
+                evidence = assertion['evidence'][0]
+                if mode == 'title': assertion['title'] = 'Rewrite forbidden'
+                elif mode == 'bad_month': assertion['identifiers'] = {'arxiv':'1413.12345'}
+                elif mode == 'version': assertion['identifiers'] = {'arxiv':'1408.1485v2'}
+                elif mode == 'unknown_scheme': assertion['identifiers'] = {'url':'https://example.org'}
+                elif mode == 'doi_case': assertion['identifiers'] = {'doi':'10.1234/UPPER'}
+                elif mode == 'evidence_hash': evidence['sha256'] = '0' * 64
+                elif mode == 'credentials': evidence['url'] = 'https://user:secret@example.org'
+                else: evidence['checked_at'] = '2026-11-08T08:00:00'
+                with self.assertRaises(ValueError): self.run_plan(plan)
+                self.assertFalse(self.output.exists())
+
+    def test_input_and_manifest_hashes_and_duplicate_json_keys_are_checked(self):
+        for mode in ('input','manifest','duplicate_json','invalid_evidence_json'):
+            with self.subTest(mode=mode):
+                plan = copy.deepcopy(self.plan)
+                if mode == 'input':
+                    plan['inputs'][0]['sha256'] = '0' * 64
+                elif mode == 'manifest':
+                    plan['inputs'][0]['manifest_sha256'] = '0' * 64
+                elif mode == 'duplicate_json':
+                    raw = self.raw[:-2] + b',"source":"dblp"}\n'
+                    self.path.write_bytes(raw)
+                    self.path.with_suffix('.manifest.json').write_bytes(json_bytes({**self.manifest,'file_sha256':digest(raw)}))
+                    plan['inputs'] = [self.input(self.path)]
+                else:
+                    self.evidence.write_bytes(b'not json')
+                    plan['assertions'][0]['evidence'][0]['sha256'] = digest(self.evidence.read_bytes())
+                with self.assertRaises(ValueError): self.run_plan(plan)
+                self.assertFalse(self.output.exists())
+                self.path.write_bytes(self.raw)
+                self.path.with_suffix('.manifest.json').write_bytes(json_bytes(self.manifest))
+
+    def test_curated_anchor_import_does_not_merge_extended_version_or_its_history(self):
+        db = self.root / 'papers.sqlite'
+        store = Store(db)
+        try:
+            original, _ = store.record('arxiv','1408.1485','https://example.org/one',self.row['title'],None,self.row['authors'],{'arxiv':'1408.1485'})
+            extended, record = store.record('arxiv','cs/0307069','https://example.org/two',self.row['title'],None,self.row['authors'],{'arxiv':'cs/0307069'})
+            store.decision(extended,record,'ICLR',2025,'main','another-attempt','https://example.org/reject','rejected','Reject')
+            store.conn.commit()
+        finally:
+            store.conn.close()
+        self.run_plan()
+        ingest_file(db,self.output / self.path.name)
+        store = Store(db)
+        try:
+            c = store.conn
+            self.assertEqual(c.execute('SELECT count(*) FROM papers').fetchone()[0], 2)
+            self.assertEqual(c.execute('SELECT paper_id FROM source_records WHERE external_id=?',(self.row['external_id'],)).fetchone()[0], original)
+            self.assertEqual(c.execute('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 v.acronym=?',('ICLR',)).fetchone()[0], extended)
+            self.assertEqual(c.execute('SELECT count(*) FROM paper_merges').fetchone()[0], 0)
+            self.assertEqual(c.execute('PRAGMA foreign_key_check').fetchall(), [])
+        finally:
+            store.conn.close()
+
+
+if __name__ == '__main__':
+    unittest.main()

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()