1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
|
# coding: utf-8
# /*##########################################################################
# Copyright (C) 2016-2017 European Synchrotron Radiation Facility
#
# 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.
#
# ############################################################################*/
"""Tests for dicttoh5 module"""
__authors__ = ["P. Knobel"]
__license__ = "MIT"
__date__ = "10/02/2017"
from collections import OrderedDict
import numpy
import os
import tempfile
import unittest
try:
import h5py
h5py_missing = False
except ImportError:
h5py_missing = True
from collections import defaultdict
from ..configdict import ConfigDict
from ..dictdump import dicttoh5, dicttojson, dicttoini, dump
from ..dictdump import h5todict, load
def tree():
"""Tree data structure as a recursive nested dictionary"""
return defaultdict(tree)
city_attrs = tree()
city_attrs["Europe"]["France"]["Grenoble"]["area"] = "18.44 km2"
city_attrs["Europe"]["France"]["Grenoble"]["inhabitants"] = 160215
city_attrs["Europe"]["France"]["Grenoble"]["coordinates"] = [45.1830, 5.7196]
city_attrs["Europe"]["France"]["Tourcoing"]["area"]
@unittest.skipIf(h5py_missing, "Could not import h5py")
class TestDictToH5(unittest.TestCase):
def setUp(self):
self.tempdir = tempfile.mkdtemp()
self.h5_fname = os.path.join(self.tempdir, "cityattrs.h5")
def tearDown(self):
os.unlink(self.h5_fname)
os.rmdir(self.tempdir)
def testH5CityAttrs(self):
filters = {'shuffle': True,
'fletcher32': True}
dicttoh5(city_attrs, self.h5_fname, h5path='/city attributes',
mode="w", create_dataset_args=filters)
h5f = h5py.File(self.h5_fname)
self.assertIn("Tourcoing/area", h5f["/city attributes/Europe/France"])
ds = h5f["/city attributes/Europe/France/Grenoble/inhabitants"]
self.assertEqual(ds[...], 160215)
# filters only apply to datasets that are not scalars (shape != () )
ds = h5f["/city attributes/Europe/France/Grenoble/coordinates"]
#self.assertEqual(ds.compression, "gzip")
self.assertTrue(ds.fletcher32)
self.assertTrue(ds.shuffle)
h5f.close()
ddict = load(self.h5_fname, fmat="hdf5")
self.assertAlmostEqual(
min(ddict["city attributes"]["Europe"]["France"]["Grenoble"]["coordinates"]),
5.7196)
@unittest.skipIf(h5py_missing, "Could not import h5py")
class TestH5ToDict(unittest.TestCase):
def setUp(self):
self.tempdir = tempfile.mkdtemp()
self.h5_fname = os.path.join(self.tempdir, "cityattrs.h5")
dicttoh5(city_attrs, self.h5_fname)
def tearDown(self):
os.unlink(self.h5_fname)
os.rmdir(self.tempdir)
def testExcludeNames(self):
ddict = h5todict(self.h5_fname, path="/Europe/France",
exclude_names=["ourcoing", "inhab", "toto"])
self.assertNotIn("Tourcoing", ddict)
self.assertIn("Grenoble", ddict)
self.assertNotIn("inhabitants", ddict["Grenoble"])
self.assertIn("coordinates", ddict["Grenoble"])
self.assertIn("area", ddict["Grenoble"])
class TestDictToJson(unittest.TestCase):
def setUp(self):
self.dir_path = tempfile.mkdtemp()
self.json_fname = os.path.join(self.dir_path, "cityattrs.json")
def tearDown(self):
os.unlink(self.json_fname)
os.rmdir(self.dir_path)
def testJsonCityAttrs(self):
self.json_fname = os.path.join(self.dir_path, "cityattrs.json")
dicttojson(city_attrs, self.json_fname, indent=3)
with open(self.json_fname, "r") as f:
json_content = f.read()
self.assertIn('"inhabitants": 160215', json_content)
class TestDictToIni(unittest.TestCase):
def setUp(self):
self.dir_path = tempfile.mkdtemp()
self.ini_fname = os.path.join(self.dir_path, "test.ini")
def tearDown(self):
os.unlink(self.ini_fname)
os.rmdir(self.dir_path)
def testConfigDictIO(self):
"""Ensure values and types of data is preserved when dictionary is
written to file and read back."""
testdict = {
'simple_types': {
'float': 1.0,
'int': 1,
'percent string': '5 % is too much',
'backslash string': 'i can use \\',
'empty_string': '',
'nonestring': 'None',
'nonetype': None,
'interpstring': 'interpolation: %(percent string)s',
},
'containers': {
'list': [-1, 'string', 3.0, False, None],
'array': numpy.array([1.0, 2.0, 3.0]),
'dict': {
'key1': 'Hello World',
'key2': 2.0,
}
}
}
dump(testdict, self.ini_fname)
#read the data back
readdict = load(self.ini_fname)
testdictkeys = list(testdict.keys())
readkeys = list(readdict.keys())
self.assertTrue(len(readkeys) == len(testdictkeys),
"Number of read keys not equal")
self.assertEqual(readdict['simple_types']["interpstring"],
"interpolation: 5 % is too much")
testdict['simple_types']["interpstring"] = "interpolation: 5 % is too much"
for key in testdict["simple_types"]:
original = testdict['simple_types'][key]
read = readdict['simple_types'][key]
self.assertEqual(read, original,
"Read <%s> instead of <%s>" % (read, original))
for key in testdict["containers"]:
original = testdict["containers"][key]
read = readdict["containers"][key]
if key == 'array':
self.assertEqual(read.all(), original.all(),
"Read <%s> instead of <%s>" % (read, original))
else:
self.assertEqual(read, original,
"Read <%s> instead of <%s>" % (read, original))
def testConfigDictOrder(self):
"""Ensure order is preserved when dictionary is
written to file and read back."""
test_dict = {'banana': 3, 'apple': 4, 'pear': 1, 'orange': 2}
# sort by key
test_ordered_dict1 = OrderedDict(sorted(test_dict.items(),
key=lambda t: t[0]))
# sort by value
test_ordered_dict2 = OrderedDict(sorted(test_dict.items(),
key=lambda t: t[1]))
# add the two ordered dict as sections of a third ordered dict
test_ordered_dict3 = OrderedDict()
test_ordered_dict3["section1"] = test_ordered_dict1
test_ordered_dict3["section2"] = test_ordered_dict2
# write to ini and read back as a ConfigDict (inherits OrderedDict)
dump(test_ordered_dict3,
self.ini_fname, fmat="ini")
read_instance = ConfigDict()
read_instance.read(self.ini_fname)
# loop through original and read-back dictionaries,
# test identical order for key/value pairs
for orig_key, section in zip(test_ordered_dict3.keys(),
read_instance.keys()):
self.assertEqual(orig_key, section)
for orig_key2, read_key in zip(test_ordered_dict3[section].keys(),
read_instance[section].keys()):
self.assertEqual(orig_key2, read_key)
self.assertEqual(test_ordered_dict3[section][orig_key2],
read_instance[section][read_key])
def suite():
test_suite = unittest.TestSuite()
test_suite.addTest(
unittest.defaultTestLoader.loadTestsFromTestCase(TestDictToIni))
test_suite.addTest(
unittest.defaultTestLoader.loadTestsFromTestCase(TestDictToH5))
test_suite.addTest(
unittest.defaultTestLoader.loadTestsFromTestCase(TestDictToJson))
test_suite.addTest(
unittest.defaultTestLoader.loadTestsFromTestCase(TestH5ToDict))
return test_suite
if __name__ == '__main__':
unittest.main(defaultTest="suite")
|
