BugFix: Empty list as val in RMGObject.as_dict() and .make_object()

rmgpy/rmgobject.pyx

@@ -55,14 +55,13 @@ cdef class RMGObject(object):
             if val is not None and not callable(val) and val != '':
                 output_dict[attr] = val
         for key, val in output_dict.iteritems():
-            if isinstance(val, list) and isinstance(val[0], RMGObject):
+            if isinstance(val, list) and val and isinstance(val[0], RMGObject):
                 output_dict[key] = [v.as_dict() for v in val]
-            elif not isinstance(val, (int, float, str, dict)):
-                if isinstance(val, np.ndarray):
-                    output_dict[key] = val.tolist()
-                else:
-                    # this is an object, call as_dict() again
-                    output_dict[key] = val.as_dict()
+            elif isinstance(val, np.ndarray):
+                output_dict[key] = val.tolist()
+            elif not isinstance(val, (int, float, str, dict)) and val:
+                # this is an object, call as_dict() again
+                output_dict[key] = val.as_dict()
         return output_dict
 
     cpdef make_object(self, dict data, dict class_dict):
@@ -83,7 +82,7 @@ cdef class RMGObject(object):
                 obj.make_object(val, class_dict)
                 logging.debug("made object {0}".format(class_name))
                 data[key] = obj
-            elif isinstance(val, list) and isinstance(val[0], dict) and 'class' in val[0]:
+            elif isinstance(val, list) and val and isinstance(val[0], dict) and 'class' in val[0]:
                 # Call make_object to make a list of objects within the parent object (as in Conformer.Modes)
                 data[key] = list()
                 for entry in val:

rmgpy/rmgobjectTest.py

@@ -0,0 +1,258 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+###############################################################################
+#                                                                             #
+# RMG - Reaction Mechanism Generator                                          #
+#                                                                             #
+# Copyright (c) 2002-2019 Prof. William H. Green (whgreen@mit.edu),           #
+# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)   #
+#                                                                             #
+# 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.                                                   #
+#                                                                             #
+###############################################################################
+
+"""
+This script contains unit tests of the :mod:`rmgobject` module.
+"""
+
+import unittest
+
+import numpy as np
+
+from rmgpy.rmgobject import RMGObject
+
+################################################################################
+
+class PseudoRMGObject(RMGObject):
+    """
+    Child class of RMG Object with more attributes for testing.
+    """
+
+    def __init__(self, a=None, b=None, c=None, d=None):
+        self.a = a
+        self.b = b
+        self.c = c
+        self.d = d
+
+
+class TestRMGObject(unittest.TestCase):
+    """
+    Contains unit tests for the RMGObject class
+    """
+
+    def test_save_int(self):
+        """Test saving ints"""
+        obj = PseudoRMGObject(a=1, b=5)
+        result = obj.as_dict()
+
+        expected = {'class': 'PseudoRMGObject', 'a': 1, 'b': 5}
+
+        self.assertEqual(result, expected)
+
+    def test_read_int(self):
+        """Test reading ints"""
+        data = {'a': 1, 'b': 5}
+        obj = PseudoRMGObject()
+        obj.make_object(data, class_dict={'PseudoRMGObject': PseudoRMGObject})
+
+        self.assertIsInstance(obj.a, int)
+        self.assertEqual(obj.a, 1)
+        self.assertIsInstance(obj.b, int)
+        self.assertEqual(obj.b, 5)
+
+    def test_save_float(self):
+        """Test saving floats"""
+        obj = PseudoRMGObject(a=1.0, b=5.0)
+        result = obj.as_dict()
+
+        expected = {'class': 'PseudoRMGObject', 'a': 1.0, 'b': 5.0}
+
+        self.assertEqual(result, expected)
+
+    def test_read_float(self):
+        """Test reading floats"""
+        data = {'a': 1.0, 'b': 5.0}
+        obj = PseudoRMGObject()
+        obj.make_object(data, class_dict={'PseudoRMGObject': PseudoRMGObject})
+
+        self.assertIsInstance(obj.a, float)
+        self.assertEqual(obj.a, 1.0)
+        self.assertIsInstance(obj.a, float)
+        self.assertEqual(obj.b, 5.0)
+
+    def test_save_str(self):
+        """Test saving strings"""
+        obj = PseudoRMGObject(a='foo', b='bar')
+        result = obj.as_dict()
+
+        expected = {'class': 'PseudoRMGObject', 'a': 'foo', 'b': 'bar'}
+
+        self.assertEqual(result, expected)
+
+    def test_read_str(self):
+        """Test reading strings"""
+        data = {'a': 'foo', 'b': 'bar'}
+        obj = PseudoRMGObject()
+        obj.make_object(data, class_dict={'PseudoRMGObject': PseudoRMGObject})
+
+        self.assertEqual(obj.a, 'foo')
+        self.assertEqual(obj.b, 'bar')
+
+    def test_save_empty_str(self):
+        """Test saving empty strings"""
+        obj = PseudoRMGObject(a='', b='bar')
+        result = obj.as_dict()
+
+        expected = {'class': 'PseudoRMGObject', 'b': 'bar'}
+
+        self.assertEqual(result, expected)
+
+    def test_read_empty_str(self):
+        """Test reading empty strings"""
+        data = {'a': '', 'b': 'bar'}
+        obj = PseudoRMGObject()
+        obj.make_object(data, class_dict={'PseudoRMGObject': PseudoRMGObject})
+
+        self.assertEqual(obj.a, '')
+        self.assertEqual(obj.b, 'bar')
+
+    def test_save_dict(self):
+        """Test saving dictionaries"""
+        obj = PseudoRMGObject(a={'foo': 'bar'})
+        result = obj.as_dict()
+
+        expected = {'class': 'PseudoRMGObject', 'a': {'foo': 'bar'}}
+
+        self.assertEqual(result, expected)
+
+    def test_read_dict(self):
+        """Test reading dictionaries"""
+        data = {'a': {'foo': 'bar'}}
+        obj = PseudoRMGObject()
+        obj.make_object(data, class_dict={'PseudoRMGObject': PseudoRMGObject})
+
+        self.assertEqual(obj.a, {'foo': 'bar'})
+
+    def test_save_mix(self):
+        """Test saving mix of builtin types"""
+        obj = PseudoRMGObject(a=1, b=5.0, c='foobar', d={'foo': 'bar'})
+        result = obj.as_dict()
+
+        expected = {'class': 'PseudoRMGObject', 'a': 1, 'b': 5.0, 'c': 'foobar', 'd': {'foo': 'bar'}}
+
+        self.assertEqual(result, expected)
+
+    def test_read_mix(self):
+        """Test reading mix of builtin types"""
+        data = {'a': 1, 'b': 5.0, 'c': 'foobar', 'd': {'foo': 'bar'}}
+        obj = PseudoRMGObject()
+        obj.make_object(data, class_dict={'PseudoRMGObject': PseudoRMGObject})
+
+        self.assertIsInstance(obj.a, int)
+        self.assertEqual(obj.a, 1)
+        self.assertIsInstance(obj.b, float)
+        self.assertEqual(obj.b, 5.0)
+        self.assertEqual(obj.c, 'foobar')
+        self.assertEqual(obj.d, {'foo': 'bar'})
+
+    def test_save_numpy(self):
+        """Test saving numpy array"""
+        obj = PseudoRMGObject(a=np.array([1.0, 2.0, 3.0]))
+        result = obj.as_dict()
+
+        expected = {'class': 'PseudoRMGObject', 'a': [1.0, 2.0, 3.0]}
+
+        self.assertEqual(result, expected)
+
+    def test_save_object(self):
+        """Test saving another object"""
+        obj = PseudoRMGObject(a=PseudoRMGObject(b='foobar'))
+        result = obj.as_dict()
+
+        expected = {'class': 'PseudoRMGObject', 'a': {'class': 'PseudoRMGObject', 'b': 'foobar'}}
+
+        self.assertEqual(result, expected)
+
+    def test_read_object(self):
+        """Test reading an object"""
+        data = {'a': {'class': 'PseudoRMGObject', 'b': 'foobar'}}
+        obj = PseudoRMGObject()
+        obj.make_object(data, class_dict={'PseudoRMGObject': PseudoRMGObject})
+
+        self.assertIsInstance(obj.a, PseudoRMGObject)
+        self.assertEqual(obj.a.b, 'foobar')
+
+    def test_save_object_list(self):
+        """Test saving a list of objects"""
+        obj = PseudoRMGObject(a=[PseudoRMGObject(b='foobar'), PseudoRMGObject(c=5.0)])
+        result = obj.as_dict()
+
+        expected = {'class': 'PseudoRMGObject',
+                    'a': [{'class': 'PseudoRMGObject', 'b': 'foobar'},
+                          {'class': 'PseudoRMGObject', 'c': 5.0}]}
+
+        self.assertEqual(result, expected)
+
+    def test_read_object_list(self):
+        """Test reading a list of objects"""
+        data = {'a': [{'class': 'PseudoRMGObject', 'b': 'foobar'},
+                      {'class': 'PseudoRMGObject', 'c': 5.0}]}
+        obj = PseudoRMGObject()
+        obj.make_object(data, class_dict={'PseudoRMGObject': PseudoRMGObject})
+
+        self.assertIsInstance(obj.a, list)
+        self.assertEqual(len(obj.a), 2)
+        self.assertIsInstance(obj.a[0], PseudoRMGObject)
+        self.assertEqual(obj.a[0].b, 'foobar')
+        self.assertIsInstance(obj.a[1], PseudoRMGObject)
+        self.assertEqual(obj.a[1].c, 5.0)
+
+    def test_save_empty_list(self):
+        """Test saving an empty list"""
+        obj = PseudoRMGObject(a=[PseudoRMGObject(b='foobar'), PseudoRMGObject(c=5.0)], b=[])
+        result = obj.as_dict()
+
+        expected = {'class': 'PseudoRMGObject',
+                    'a': [{'class': 'PseudoRMGObject', 'b': 'foobar'},
+                          {'class': 'PseudoRMGObject', 'c': 5.0}],
+                    'b': []}
+
+        self.assertEqual(result, expected)
+
+    def test_read_empty_list(self):
+        """Test reading an smpty list"""
+        data = {'a': [{'class': 'PseudoRMGObject', 'b': 'foobar'},
+                      {'class': 'PseudoRMGObject', 'c': 5.0}],
+                'b': []}
+        obj = PseudoRMGObject()
+        obj.make_object(data, class_dict={'PseudoRMGObject': PseudoRMGObject})
+
+        self.assertIsInstance(obj.a, list)
+        self.assertEqual(len(obj.a), 2)
+        self.assertIsInstance(obj.a[0], PseudoRMGObject)
+        self.assertEqual(obj.a[0].b, 'foobar')
+        self.assertIsInstance(obj.a[1], PseudoRMGObject)
+        self.assertEqual(obj.a[1].c, 5.0)
+        self.assertEqual(obj.b, [])
+
+################################################################################
+
+if __name__ == '__main__':
+    unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))