List and report disk-passthrough saves as zarr backend files

src/polystore/zarr.py

@@ -39,6 +39,7 @@
 
 DEFAULT_PLATE_NAME = os.getenv("POLYSTORE_PLATE_NAME", "Polystore_Plate")
 DISK_PASSTHROUGH_EXTENSIONS = (".json", ".csv", ".txt", ".roi.zip", ".zip")
+ZARR_METADATA_FILENAMES = frozenset({"zarr.json", ".zgroup", ".zarray", ".zattrs", ".zmetadata"})
 
 
 def _get_attr(attrs: Any, key: str):
@@ -129,6 +130,26 @@ def output_format(self):
     def _is_disk_passthrough_path(path: str | Path) -> bool:
         return str(path).endswith(DISK_PASSTHROUGH_EXTENSIONS)
 
+    @classmethod
+    def _disk_passthrough_files(cls, directory: str | Path, *, recursive: bool) -> list[Path]:
+        """Files this backend saved on disk inside ``directory``, never its own metadata."""
+        root = Path(directory)
+        if not root.is_dir():
+            return []
+        entries = root.rglob("*") if recursive else root.iterdir()
+        return sorted(
+            entry
+            for entry in entries
+            if entry.name not in ZARR_METADATA_FILENAMES
+            and cls._is_disk_passthrough_path(entry)
+            and entry.is_file()
+        )
+
+    @staticmethod
+    def _declares_array_store(directory: str | Path) -> bool:
+        root = Path(directory)
+        return (root / "zarr.json").is_file() or (root / ".zgroup").is_file()
+
     def supports_file_path(self, path: str | Path) -> bool:
         return self._is_disk_passthrough_path(path) or super().supports_file_path(path)
 
@@ -722,6 +743,12 @@ def _matches_filters(name: str) -> bool:
                 return any(name.lower().endswith(ext.lower()) for ext in extensions)
             return True
 
+        # Disk-passthrough saves are this backend's files too: list them beside the arrays.
+        saved_on_disk = self._disk_passthrough_files(directory, recursive=recursive)
+        result.extend(path for path in saved_on_disk if _matches_filters(path.name))
+        if saved_on_disk and not self._declares_array_store(directory):
+            return result
+
         try:
             # Open zarr group and traverse OME-ZARR structure
             location = OmeZarrLocation(store, mode="r")
@@ -764,9 +791,7 @@ def delete(self, path: str | Path) -> None:
             IsADirectoryError: If path is a non-empty group
             StorageResolutionError: For unexpected failures
         """
-        # Passthrough to disk backend for text files (JSON, CSV, TXT)
-        path_str = str(path)
-        if path_str.endswith((".json", ".csv", ".txt")):
+        if self._is_disk_passthrough_path(path):
             from .backend_registry import get_backend_instance
 
             disk_backend = get_backend_instance(Backend.DISK.value)
@@ -953,6 +978,10 @@ def is_dir(self, path: str | Path) -> bool:
             NotADirectoryError: If resolved target is not a group
             StorageResolutionError: For symlink cycles or other failures
         """
+        if not self._declares_array_store(path) and self._disk_passthrough_files(
+            path, recursive=False
+        ):
+            return True
         if not isinstance(self._resolved_node(path), zarr.Group):
             raise NotADirectoryError(f"Zarr path is an array (file): {path}")
         return True

tests/test_zarr_backend.py

@@ -65,6 +65,44 @@ def test_zarr_declared_passthrough_support_batch_save_and_native_readback(tmp_pa
         assert backend.physical_source_path(path, base_path=tmp_path) == path
 
 
+def test_zarr_lists_and_reports_directories_of_its_passthrough_saves(tmp_path):
+    """A result directory holding only passthrough saves is this backend's directory."""
+    backend = ZarrStorageBackend()
+    results = tmp_path / "results"
+    paths = [results / "A01_details.csv", results / "A01_rois.roi.zip"]
+    for path in paths:
+        backend.save("payload" if path.suffix == ".csv" else b"zip", path)
+    assert all(backend.exists(path) for path in paths)
+    assert backend.is_dir(results)
+    assert backend.list_files(results) == sorted(paths)
+    assert backend.list_files(results, extensions={".csv"}) == [paths[0]]
+    assert backend.list_files(results, extensions={".tif"}) == []
+
+
+@pytest.mark.parametrize("name", ["table.csv", "rois.roi.zip", "bundle.zip"])
+def test_zarr_deletes_every_passthrough_save_it_wrote(tmp_path, name):
+    backend = ZarrStorageBackend()
+    path = tmp_path / "results" / name
+    backend.save("payload" if name.endswith(".csv") else b"zip", path)
+    backend.delete(path)
+    assert not path.exists()
+    assert not backend.exists(path)
+
+
+def test_zarr_lists_passthrough_saves_beside_arrays_without_store_metadata(tmp_path):
+    backend = ZarrStorageBackend()
+    store = tmp_path / "images"
+    array_path = store / "A01_s1.tif"
+    text_path = store / "positions.json"
+    backend.save(np.zeros((2, 3), dtype=np.uint16), array_path)
+    backend.save("[]", text_path)
+    assert backend.is_dir(store)
+    listed = backend.list_files(store)
+    assert text_path in listed
+    assert not any(path.name in zarr_module.ZARR_METADATA_FILENAMES for path in listed)
+    assert backend.list_files(store, extensions={".json"}) == [text_path]
+
+
 @pytest.mark.parametrize("reverse", [False, True])
 def test_zarr_mixed_passthrough_array_batch_rejects_before_any_writes(tmp_path, reverse):
     backend = ZarrStorageBackend()