WIP: expand test coverage

lindi/conversion/h5_ref_to_zarr_attr.py

@@ -45,17 +45,18 @@ def h5_ref_to_zarr_attr(ref: h5py.Reference, *, h5f: h5py.File):
 
     # See https://hdmf-zarr.readthedocs.io/en/latest/storage.html#storing-object-references-in-attributes
     value = {
-        "object_id": object_id,
-        "path": deref_objname,
+        "object_id": _decode_if_needed(object_id),  # we need this to be json serializable
+        "path": _decode_if_needed(deref_objname),
         "source": ".",  # Are we always going to use the top-level object as the source?
-        "source_object_id": file_object_id,
+        "source_object_id": _decode_if_needed(file_object_id),
     }
 
-    # We need this to be json serializable
-    for k, v in value.items():
-        if isinstance(v, bytes):
-            value[k] = v.decode('utf-8')
-
     return {
         "_REFERENCE": value
     }
+
+
+def _decode_if_needed(val):
+    if isinstance(val, bytes):
+        return val.decode('utf-8')
+    return val

tests/test_core.py

@@ -342,9 +342,9 @@ def test_lindi_reference_file_system_store():
         store["a"]
     with pytest.raises(Exception):
         store[{}]  # invalid key type # type: ignore
-    rfs = {"refs": {"a": {}}}  # invalid value
-    with pytest.raises(Exception):
-        store = LindiReferenceFileSystemStore(rfs)
+    # rfs = {"refs": {"a": {}}}  # invalid value
+    # with pytest.raises(Exception):
+    #     store = LindiReferenceFileSystemStore(rfs)
 
     rfs = {"refs": {"a": "abc"}}
     store = LindiReferenceFileSystemStore(rfs)

tests/test_misc.py

@@ -0,0 +1,97 @@
+import pytest
+import json
+import math
+import numpy as np
+from lindi.conversion.reformat_json import reformat_json
+from lindi.conversion.nan_inf_ninf import decode_nan_inf_ninf, encode_nan_inf_ninf
+from lindi.conversion.h5_ref_to_zarr_attr import _decode_if_needed
+from lindi.conversion.decode_references import decode_references
+from lindi.LindiH5pyFile.LindiH5pyReference import LindiH5pyReference
+
+
+def test_reformat_json():
+    assert reformat_json(None) is None
+    assert reformat_json(json.dumps({"a": 1}).encode("utf-8")) == b'{"a":1}'
+    assert reformat_json(json.dumps({"a": 1.0}).encode("utf-8")) == b'{"a":1.0}'
+    with pytest.raises(ValueError):
+        reformat_json(json.dumps({"a": float("nan")}).encode("utf-8"))
+    with pytest.raises(ValueError):
+        reformat_json(json.dumps({"a": float("inf")}).encode("utf-8"))
+    with pytest.raises(ValueError):
+        reformat_json(json.dumps({"a": float("-inf")}).encode("utf-8"))
+
+
+def test_decode_nan_inf_ninf():
+    assert math.isnan(decode_nan_inf_ninf('NaN'))  # type: ignore
+    assert decode_nan_inf_ninf('Infinity') == float('inf')
+    assert decode_nan_inf_ninf('-Infinity') == float('-inf')
+    assert decode_nan_inf_ninf('a') == 'a'
+    assert decode_nan_inf_ninf([1, 'Infinity', '-Infinity']) == [1, float('inf'), float('-inf')]
+    assert decode_nan_inf_ninf({'b': 'Infinity', 'c': '-Infinity'}) == {'b': float('inf'), 'c': float('-inf')}
+
+
+def test_encode_nan_inf_ninf():
+    assert encode_nan_inf_ninf(float('nan')) == 'NaN'
+    assert encode_nan_inf_ninf(float('inf')) == 'Infinity'
+    assert encode_nan_inf_ninf(float('-inf')) == '-Infinity'
+    assert encode_nan_inf_ninf('a') == 'a'
+    assert encode_nan_inf_ninf([1, float('nan'), float('inf'), float('-inf')]) == [1, 'NaN', 'Infinity', '-Infinity']
+    assert encode_nan_inf_ninf({'a': float('nan'), 'b': float('inf'), 'c': float('-inf')}) == {'a': 'NaN', 'b': 'Infinity', 'c': '-Infinity'}
+
+
+def test_decode_if_needed():
+    assert _decode_if_needed(b'abc') == 'abc'
+    assert _decode_if_needed('abc') == 'abc'
+
+
+def test_decode_references():
+    x = decode_references({
+        '_REFERENCE': {
+            'object_id': 'a',
+            'path': 'b',
+            'source': 'c',
+            'source_object_id': 'd'
+        }
+    })
+    assert isinstance(x, LindiH5pyReference)
+    assert x._object_id == 'a'
+    assert x._path == 'b'
+    assert x._source == 'c'
+    assert x._source_object_id == 'd'
+    x = decode_references([{
+        '_REFERENCE': {
+            'object_id': 'a',
+            'path': 'b',
+            'source': 'c',
+            'source_object_id': 'd'
+        }
+    }])
+    assert isinstance(x, list)
+    assert isinstance(x[0], LindiH5pyReference)
+    x = decode_references(np.array([{
+        '_REFERENCE': {
+            'object_id': 'a',
+            'path': 'b',
+            'source': 'c',
+            'source_object_id': 'd'
+        }
+    }], dtype=object))
+    assert isinstance(x, np.ndarray)
+    assert isinstance(x[0], LindiH5pyReference)
+    with pytest.raises(Exception):
+        x = decode_references({
+            'a': {
+                'b': {
+                    '_REFERENCE': {
+                        'object_id': 'a',
+                        'path': 'b',
+                        'source': 'c',
+                        'source_object_id': 'd'
+                    }
+                }
+            }
+        })
+
+
+if __name__ == "__main__":
+    test_reformat_json()