clean_value work (#2129)

* common/test_hashing: add tests for truncation of subnormals, infs and nans

fixes: #2123

* o/i/g/node.clean_value: make inf/nan raise an exception

part of #2124

aiida/common/test_hashing.py

@@ -17,6 +17,7 @@
 import itertools
 import collections
 import uuid
+import math
 from datetime import datetime
 
 import numpy as np
@@ -27,7 +28,7 @@
 except ImportError:
     import unittest
 
-from aiida.common.hashing import make_hash, create_unusable_pass, is_password_usable
+from aiida.common.hashing import make_hash, create_unusable_pass, is_password_usable, truncate_float64
 from aiida.common.folders import SandboxFolder
 
 
@@ -46,6 +47,22 @@ def test_is_usable(self):
         self.assertFalse(is_password_usable('random string without hash identification'))
 
 
+class TruncationTest(unittest.TestCase):
+    """
+    Tests for the truncate_* methods
+    """
+
+    def test_nan(self):
+        self.assertTrue(math.isnan(truncate_float64(np.nan)))
+
+    def test_inf(self):
+        self.assertTrue(math.isinf(truncate_float64(np.inf)))
+        self.assertTrue(math.isinf(truncate_float64(-np.inf)))
+
+    def test_subnormal(self):
+        self.assertTrue(np.isclose(truncate_float64(1.0e-308), 1.0e-308, atol=1.0e-309))
+
+
 class MakeHashTest(unittest.TestCase):
     """
     Tests for the make_hash function.

aiida/orm/implementation/general/node.py

@@ -16,6 +16,8 @@
 import logging
 import importlib
 import collections
+import numbers
+import math
 
 import six
 
@@ -51,13 +53,20 @@ def clean_value(value):
     # Must be imported in here to avoid recursive imports
     from aiida.orm.data import BaseType
 
+    def clean_builtin(val):
+        if isinstance(val, numbers.Real) and (math.isnan(val) or math.isinf(val)):
+            # see https://www.postgresql.org/docs/current/static/datatype-json.html#JSON-TYPE-MAPPING-TABLE
+            raise ValidationError("nan and inf/-inf can not be serialized to the database")
+
+        return val
+
     if isinstance(value, BaseType):
-        return value.value
-    elif isinstance(value, dict):
+        return clean_builtin(value.value)
+
+    if isinstance(value, dict):
         # Check dictionary before iterables
         return {k: clean_value(v) for k, v in value.items()}
-    elif (isinstance(value, collections.Iterable) and
-          not isinstance(value, six.string_types)):
+    if (isinstance(value, collections.Iterable) and not isinstance(value, six.string_types)):
         # list, tuple, ... but not a string
         # This should also properly take care of dealing with the
         # basedatatypes.List object
@@ -67,7 +76,8 @@ def clean_value(value):
     # itself - it's not super robust, but relies on duck typing
     # (e.g. if there is something that behaves like an integer
     # but is not an integer, I still accept it)
-    return value
+
+    return clean_builtin(value)
 
 
 class _AbstractNodeMeta(ABCMeta):