Merge pull request #1008 from xcube-dev/forman-1007-mlds_issue_with_v…

…iewer_in_jl

Fix adding ml-datasets from S3 to viewer in JL

CHANGES.md

@@ -64,10 +64,22 @@
      To enforce the old behaviour, provide the `var_configs` keyword-argument
      and set `recover_nan` to `True` for desired variables.
 
+### Fixes
+
+* When using the `xcube.webapi.viewer.Viewer` class in Jupyter notebooks
+  multi-level datasets opened from S3 or from deeper subdirectories into
+  the local filesystem are now fully supported. (#1007)
+
 * The class `MaskSet()` of module `xcube.core.maskset` now correctly recognises
   the variable attributes `flag_values`, `flag_masks`, `flag_meanings` when
   their values are lists (ESA CCI LC data encodes them as JSON arrays). (#1002)
 
+* Fixed an issue with xcube server `/timeseries` endpoint that returned
+  status 500 if a given dataset used a CRS other geographic and the 
+  geometry was not a point. (#995) 
+
+* Fixed broken table of contents links in dataset convention document.
+
 
 ### Incompatible API changes
 
@@ -101,14 +113,6 @@
   - Removed endpoint `/datasets/{datasetId}/vars/{varName}/tiles2/{z}/{y}/{x}`
     from xcube server.
 
-### Fixes
-
-* Fixed an issue with xcube server `/timeseries` endpoint that returned
-  status 500 if a given dataset used a CRS other geographic and the 
-  geometry was not a point. (#995) 
-
-* Fixed broken table of contents links in dataset convention document.
-
 ### Other changes
 
 * Make tests compatible with PyTest 8.2.0. (#973)

test/webapi/viewer/test_viewer.py

@@ -9,6 +9,7 @@
 from typing import Optional, Any, Union
 
 import pytest
+from xcube.core.mldataset import BaseMultiLevelDataset
 
 from xcube.core.new import new_cube
 from xcube.server.api import ApiError
@@ -210,6 +211,21 @@ def test_add_and_remove_dataset(self):
         with pytest.raises(ApiError.NotFound):
             self.viewer.datasets_ctx.get_dataset_config(ds_id_2)
 
+    # Verifies https://github.com/xcube-dev/xcube/issues/1007
+    def test_add_dataset_with_slash_path(self):
+        viewer = self.get_viewer(STYLES_CONFIG)
+
+        ml_ds = BaseMultiLevelDataset(
+            new_cube(variables={"analysed_sst": 280.0}),
+            ds_id="mybucket/mysst.levels",
+        )
+        ds_id = viewer.add_dataset(ml_ds, title="My SST")
+
+        self.assertEqual("mybucket-mysst.levels", ds_id)
+
+        ds_config = self.viewer.datasets_ctx.get_dataset_config(ds_id)
+        self.assertEqual({"Identifier": ds_id, "Title": "My SST"}, ds_config)
+
     def test_add_dataset_with_style(self):
         viewer = self.get_viewer(STYLES_CONFIG)
 

xcube/core/mldataset/fs.py

@@ -50,6 +50,12 @@ def __init__(
             fs, path = fsspec.core.url_to_fs(path, **(fs_kwargs or {}))
         assert_instance(fs, fsspec.AbstractFileSystem, name="fs")
         assert_instance(path, str, name="data_id")
+        # TODO: Setting ds_id=path is likely the root cause for
+        #   https://github.com/xcube-dev/xcube/issues/1007.
+        #   Then, the actual fix is to replace slashes by dashes or underscores.
+        #   But this requires deeper investigation and more test cases.
+        #   A quick fix has been applied in `xcube.webapi.viewer.Viewer.add_dataset()`
+        #   implementation. forman, 2024-06-07
         super().__init__(ds_id=path)
         self._path = path
         self._fs = fs

xcube/webapi/compute/context.py

@@ -7,7 +7,7 @@
 import inspect
 import concurrent.futures
 import datetime
-from typing import Dict, Any, Optional, Callable
+from typing import Any, Optional, Callable
 import traceback
 
 import xarray as xr

xcube/webapi/datasets/context.py

@@ -183,6 +183,13 @@ def add_dataset(
             ml_dataset = BaseMultiLevelDataset(dataset, ds_id=ds_id)
         else:
             ml_dataset = dataset
+            if not ds_id:
+                _ds_id = ml_dataset.ds_id
+                # TODO: Fixes https://github.com/xcube-dev/xcube/issues/1007, but
+                #   this does not solve the likely root cause
+                #   in xcube.core.mldataset.fs.FsMultiLevelDataset, see ctor.
+                if "/" in _ds_id:
+                    ds_id = _ds_id.replace("/", "-")
             if ds_id:
                 ml_dataset = IdentityMultiLevelDataset(dataset, ds_id=ds_id)
             dataset = ml_dataset.base_dataset

xcube/webapi/viewer/viewer.py

@@ -7,7 +7,7 @@
 import socket
 import threading
 from pathlib import Path
-from typing import Optional, Union, Any, Tuple, Dict
+from typing import Any, Optional, Union
 from collections.abc import Iterable
 from collections.abc import Mapping
 
@@ -62,7 +62,7 @@ class Viewer:
     The `Viewer` class takes a xcube server configuration as first
     argument. More details regarding configuration parameters are given in the
     `server documentation <https://xcube.readthedocs.io/en/latest/cli/xcube_serve.html>`_.
-    The full configuration reference can be generated by excecuting CLI command
+    The full configuration reference can be generated by executing CLI command
     ``$ xcube serve --show configschema``.
 
     Args: