Merge branch 'improving-h5-scalar-attribute-handling' into 'dev'

Improved the handling of numpy scalars in cfoods.h5.h5_attr_to_property

See merge request caosdb/caosdb-advanced-user-tools!84

src/caosadvancedtools/cfoods/h5.py

@@ -6,6 +6,8 @@
 # Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
 # Copyright (C) 2021 Henrik tom Wörden <h.tomwoerden@indiscale.com>
 # Copyright (C) 2021 Alexander Kreft
+# Copyright (C) 2021 Laboratory for Fluid Physics and Biocomplexity, 
+# Max-Planck-Insitute für Dynamik und Selbstorganisation <www.lfpn.ds.mpg.de>
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU Affero General Public License as
@@ -85,13 +87,13 @@ def h5_attr_to_property(val):
         if isinstance(val, np.ndarray):
             if val.ndim > 1:
                 return None, None
-
-            if val.ndim == 0:
-                raise NotImplementedError(
-                    "Code assumes that scalar values "
-                    "will not be given as np.ndarray objects")
-            val = list(val)
+        # The tolist method is on both numpy.ndarray and numpy.generic
+        # and properly converts scalars (including 0-dimensional
+        # numpy.ndarray) to Python scalars and 1D arrays to lists of
+        # Python scalars.
+        if val.ndim != 0:
             dtype = db.LIST(dtype)
+        val = val.tolist()
 
         # TODO this can eventually be removed
 

unittests/test_h5.py

@@ -181,4 +181,7 @@ class H5CFoodTest(unittest.TestCase):
         self.assertTupleEqual((None, None), h5_attr_to_property(test_integers_2d))
         self.assertTupleEqual((None, None), h5_attr_to_property(test_floats_2d))
 
-        self.assertRaises(NotImplementedError, h5_attr_to_property, np.array(1))
+        # Test scalar values given as np.array
+        self.assertTupleEqual((1, db.INTEGER), h5_attr_to_property(np.array(1)))
+        self.assertTupleEqual((1.123, db.DOUBLE), h5_attr_to_property(np.array(1.123)))
+        self.assertTupleEqual(('Hello World', db.TEXT), h5_attr_to_property(np.array("Hello World")))