Fix broken JSON encoding

CHANGES.md

@@ -28,6 +28,13 @@
   is used to select dataset labels along a given dimension using
   user-defined predicate functions.
 
+* The xcube Python environment is now requiring 
+  `xarray >= 2022.6` and `zarr >= 2.11` to ensure sparse 
+  Zarr datasets can be written using `dataset.to_zarr(store)`. (#688)
+
+* Added new class `xcube.util.jsonencoder.NumpyJSONEncoder` that 
+  is used to serialize numpy-like scalar values to JSON.
+
 ### Fixes
 
 * The filesystem-based data stores for the "s3", "file", and "memory"

test/util/test_jsonencoder.py

@@ -0,0 +1,85 @@
+# The MIT License (MIT)
+# Copyright (c) 2022 by the xcube development team and contributors
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+
+import json
+import unittest
+
+import numpy as np
+import pytest
+
+from xcube.util.jsonencoder import NumpyJSONEncoder
+
+
+class NumpyJSONEncoderTest(unittest.TestCase):
+    TEST_DATA = {
+        "np_bool": np.bool(True),
+        "np_int8": np.int8(1),
+        "np_uint8": np.uint8(2),
+        "np_int16": np.int16(3),
+        "np_uint16": np.uint8(4),
+        "np_int32": np.int32(5),
+        "np_uint32": np.uint32(6),
+        "np_int64": np.int64(7),
+        "np_uint64": np.uint64(8),
+        "np_float32": np.float32(9.1),
+        "np_float64": np.float64(9.2),
+        "py_bool": True,
+        "py_int": 11,
+        "py_float": 12.3,
+        "py_str": "Hallo",
+        "py_null": None,
+    }
+
+    def test_fail_without_encoder(self):
+        with pytest.raises(TypeError):
+            json.dumps(
+                self.TEST_DATA,
+                indent=2,
+            )
+
+    def test_encoder_encodes_all(self):
+        text = json.dumps(
+            self.TEST_DATA,
+            indent=2,
+            cls=NumpyJSONEncoder
+        )
+        data = json.loads(text)
+        self.assertEqual(
+            {
+                "np_bool": bool(np.bool(True)),
+                "np_int8": int(np.int8(1)),
+                "np_uint8": int(np.uint8(2)),
+                "np_int16": int(np.int16(3)),
+                "np_uint16": int(np.uint8(4)),
+                "np_int32": int(np.int32(5)),
+                "np_uint32": int(np.uint32(6)),
+                "np_int64": int(np.int64(7)),
+                "np_uint64": int(np.uint64(8)),
+                "np_float32": float(np.float32(9.1)),
+                "np_float64": float(np.float64(9.2)),
+                "py_bool": True,
+                "py_int": 11,
+                "py_float": 12.3,
+                "py_str": "Hallo",
+                "py_null": None,
+            },
+            data
+        )

xcube/cli/io.py

@@ -370,7 +370,9 @@ def format_cell_value(value: Any) -> str:
 
         with open(output_file_path, 'w') as fp:
             if output_format == 'json':
-                json.dump(dict(stores=store_list), fp, indent=2)
+                from xcube.util.jsonencoder import NumpyJSONEncoder
+                json.dump(dict(stores=store_list), fp, indent=2,
+                          cls=NumpyJSONEncoder)
             else:
                 yaml.dump(dict(stores=store_list), fp, indent=2)
 

xcube/util/jsonencoder.py

@@ -0,0 +1,45 @@
+# The MIT License (MIT)
+# Copyright (c) 2022 by the xcube development team and contributors
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+
+import json
+
+import numpy as np
+
+
+class NumpyJSONEncoder(json.JSONEncoder):
+    """A JSON encoder that converts numpy-like
+    scalars into corresponding serializable Python objects.
+    """
+
+    def default(self, obj):
+        if hasattr(obj, 'dtype') and hasattr(obj, 'ndim'):
+            if obj.ndim == 0:
+                # For time being just handle scalars.
+                if np.issubdtype(obj.dtype, np.bool):
+                    return bool(obj)
+                if np.issubdtype(obj.dtype, np.integer):
+                    return int(obj)
+                elif np.issubdtype(obj.dtype, np.floating):
+                    return float(obj)
+                else:
+                    return str(obj)
+            # We may add serialization for N-D arrays here.
+        return json.JSONEncoder.default(self, obj)