fix: read-only error for derive_label/add_table on a read-only container

CHANGELOG.md

@@ -6,6 +6,9 @@
 
 - Add `set_config()` (exported from `ngio` and `ngio.config`) to replace the global `NgioConfig` from code at any time. It replaces the previous configuration (a zarr setting forwarded earlier stays unless the new config sets it) and immediately applies the `s3fs` retry markers and the `zarr` section, so libraries can configure ngio without setting `NGIO_CONFIG_PATH` before `import ngio`.
 
+### Fixes
+
+- `derive_label` and `add_table` on a container opened with `mode="r"` that has no `labels`/`tables` group yet raise `NgioValueError("The group is read only. Cannot derive a label.")` (or `... add a table.`) instead of `NgioValidationError("No labels found in the image.")`: the missing group could not be created, and the error said it did not exist. Same for `OmeZarrPlate.add_table`. Reading on such a container (`list_labels`, `labels_container`) still reports "No labels found" ([#279](https://github.com/BioVisionCenter/ngio/issues/279)).
 - `axes_order` only virtualises canonical axes. A canonical axis (`t`, `c`, `z`, `y`, `x`) missing on disk still comes back as a singleton, by its canonical name or the name the `AxesSetup` maps to it, so one `"czyx"` keeps working on 2D and 3D data. Any other name that is not an axis of the image raises `NgioValueError` naming it, the full order, the image axes and the canonical set; it used to become a phantom dimension (`axes_order="czyq"` returned a 4D array with `x` dropped and a size-1 axis appended). The iterators run the check in the constructor instead of at the first read, and the duplicate-axis error names the repeated axis ([#277](https://github.com/BioVisionCenter/ngio/issues/277)).
 
 ### Tests

src/ngio/hcs/_plate.py

@@ -1002,6 +1002,8 @@ def add_table(
 
         If `backend` is `None` (default), the table's own backend is preserved.
         """
+        if self._group_handler.read_only:
+            raise NgioValueError("The group is read only. Cannot add a table.")
         self.tables_container.add(
             name=name, table=table, backend=backend, overwrite=overwrite
         )

src/ngio/images/_ome_zarr_container.py

@@ -178,6 +178,11 @@ def refresh(self) -> None:
         self._tables_container = None
         self._tables_absent = False
 
+    def _require_writable(self, action: str) -> None:
+        """Raise before a write that needs a group this container cannot create."""
+        if self._group_handler.read_only:
+            raise NgioValueError(f"The group is read only. Cannot {action}.")
+
     @property
     def images_container(self) -> ImagesContainer:
         """Return the images container.
@@ -820,6 +825,7 @@ def add_table(
 
         If `backend` is `None` (default), the table's own backend is preserved.
         """
+        self._require_writable("add a table")
         self.tables_container.add(
             name=name, table=table, backend=backend, overwrite=overwrite
         )
@@ -992,6 +998,7 @@ def derive_label(
             Label: The new derived label.
 
         """
+        self._require_writable("derive a label")
         if ref_image is None:
             ref_image = self.get_image()
         return self.labels_container.derive(

tests/unit/hcs/test_plate_edge_cases.py

@@ -154,6 +154,8 @@ def test_tables_container_missing_on_readonly_plate(tmp_path: Path):
     assert plate.list_tables() == []
     with pytest.raises(NgioValidationError, match="No tables found"):
         _ = plate.tables_container
+    with pytest.raises(NgioValueError, match="read only"):
+        plate.add_table("t", RoiTable(rois=[]))
 
 
 def test_typed_table_getters(tmp_path: Path):

tests/unit/images/test_container_errors.py

@@ -202,5 +202,11 @@ def test_labels_missing_on_read_only_container(tmp_path: Path):
 
     # a read-only container without a labels group degrades gracefully
     assert container.list_labels() == []
-    with pytest.raises(NgioValidationError):
+    with pytest.raises(NgioValidationError, match="No labels found"):
         _ = container.labels_container
+
+    # a write names the real problem: the group cannot be created (#279)
+    with pytest.raises(NgioValueError, match="read only"):
+        container.derive_label("x")
+    with pytest.raises(NgioValueError, match="read only"):
+        container.add_table("t", RoiTable(rois=[]))