From bf8fd3b1f5a740dc39b77ba4e69a2af826ea5901 Mon Sep 17 00:00:00 2001
From: kert <kert@rack.localdomain>
Date: Wed, 11 Nov 2026 14:27:47 -0500
Subject: [PATCH] fix(bib): host-side Zotero sync skips copies it cannot read

Zotero's storage files belong to the container user; on the host they
stat but do not open, and comparing a same-name file crashed the
nightly bib-refresh-iom sync. An unreadable copy now counts as
unchanged (nothing is written); the in-container nightly sync compares
and hoards.
---
 src/bib/sync.py               | 17 ++++++++++++++--
 tests/bib/test_sync_deeper.py | 38 +++++++++++++++++++++++++++++++++++
 2 files changed, 53 insertions(+), 2 deletions(-)

diff --git a/src/bib/sync.py b/src/bib/sync.py
index 51a1eb9..f8c859b 100644
--- a/src/bib/sync.py
+++ b/src/bib/sync.py
@@ -19,6 +19,7 @@ Usage::
 from __future__ import annotations
 
 import json
+import logging
 import shutil
 from datetime import date
 from pathlib import Path
@@ -28,6 +29,8 @@ from bib.item import Item
 from zot.db import TYPE_MAP as ZOT_TYPE_MAP
 from zot.db import Db, generate_key, is_valid_key, now_iso
 
+log = logging.getLogger(__name__)
+
 if TYPE_CHECKING:
     from bib.store import Store
 
@@ -596,13 +599,23 @@ def _sync_attachments(
 
 
 def _same_file(a: Path, b: Path) -> bool:
-    """Byte-identical? Size + mtime short-circuit (copy2 keeps mtime)."""
+    """Byte-identical? Size + mtime short-circuit (copy2 keeps mtime).
+
+    On the host, Zotero's storage files belong to the container user:
+    they stat but do not open. An unreadable copy counts as the same —
+    nothing is written; the nightly in-container sync can compare it."""
     import filecmp
 
     sa, sb = a.stat(), b.stat()
     if sa.st_size != sb.st_size:
         return False
-    return sa.st_mtime_ns == sb.st_mtime_ns or filecmp.cmp(a, b, shallow=False)
+    if sa.st_mtime_ns == sb.st_mtime_ns:
+        return True
+    try:
+        return filecmp.cmp(a, b, shallow=False)
+    except PermissionError:
+        log.debug("cannot read %s to compare; leaving it", b)
+        return True
 
 
 def _sha8(p: Path) -> str:
diff --git a/tests/bib/test_sync_deeper.py b/tests/bib/test_sync_deeper.py
index 5286502..f6221fc 100644
--- a/tests/bib/test_sync_deeper.py
+++ b/tests/bib/test_sync_deeper.py
@@ -128,6 +128,44 @@ class TestSyncAttachments:
         blobs = sorted(p.read_bytes() for p in storage.rglob("*.pdf"))
         assert blobs == [b"%PDF new chapter, revised", b"%PDF old chapter"]
 
+    def test_unreadable_zotero_copy_is_left_alone(self, tmp_path, monkeypatch):
+        # On the host, Zotero's storage files belong to the container user:
+        # stat works, open does not. Sync must skip, not crash or write.
+        import filecmp
+
+        path = _setup(tmp_path)
+        storage = tmp_path / "storage"
+        storage.mkdir()
+        src_file = tmp_path / "source" / "chapter.pdf"
+        src_file.parent.mkdir()
+        src_file.write_bytes(b"%PDF a")
+        row = {
+            "filename": "chapter.pdf",
+            "content_type": "application/pdf",
+            "storage_path": str(src_file),
+            "created_at": "2026-04-15T00:00:00Z",
+        }
+        store = MagicMock()
+        store._con.return_value.execute.return_value.fetchall.return_value = [row]
+        with Db(path) as db:
+            parent_id = db.create_item(TYPE_MAP["document"])
+            db.commit()
+            assert (
+                _sync_attachments(db, store, MagicMock(key="K1"), parent_id, storage)
+                == 1
+            )
+            db.commit()
+            src_file.write_bytes(b"%PDF b")  # same size, new mtime
+
+            def denied(*a, **k):
+                raise PermissionError(13, "Permission denied")
+
+            monkeypatch.setattr(filecmp, "cmp", denied)
+            assert (
+                _sync_attachments(db, store, MagicMock(key="K1"), parent_id, storage)
+                == 0
+            )
+
     def test_missing_file(self, tmp_path):
         path = _setup(tmp_path)
         store = MagicMock()