|
1
|
|
|
import unittest |
|
2
|
|
|
import os, shutil |
|
3
|
|
|
from os.path import abspath |
|
4
|
|
|
|
|
5
|
|
|
|
|
6
|
|
|
class ProvenanceContextApiTests(unittest.TestCase): |
|
7
|
|
|
|
|
8
|
|
|
def setUp(self): |
|
9
|
|
|
self.dbpath = os.path.expanduser(os.path.join('~','provenance_test.json')) |
|
10
|
|
|
if os.path.exists(self.dbpath): |
|
11
|
|
|
os.remove(self.dbpath) |
|
12
|
|
|
os.mkdir('temp') |
|
13
|
|
|
from niprov import ProvenanceContext |
|
14
|
|
|
self.provenance = ProvenanceContext() |
|
15
|
|
|
self.provenance.config.database_type = 'file' |
|
16
|
|
|
self.provenance.config.database_url = self.dbpath |
|
17
|
|
|
|
|
18
|
|
|
def tearDown(self): |
|
19
|
|
|
shutil.rmtree('temp') |
|
20
|
|
|
|
|
21
|
|
|
def touch(self, path): |
|
22
|
|
|
with open(path,'w') as tempfile: |
|
23
|
|
|
tempfile.write('0') |
|
24
|
|
|
|
|
25
|
|
|
def test_Relative_paths(self): |
|
26
|
|
|
self.provenance.discover('testdata') |
|
27
|
|
|
newfile = 'temp/smoothed.test' |
|
28
|
|
|
self.touch(newfile) |
|
29
|
|
|
self.provenance.log(newfile, 'test', 'testdata/eeg/stub.cnt') |
|
30
|
|
|
img = self.provenance.get().byLocation(newfile) |
|
31
|
|
|
|
|
32
|
|
View Code Duplication |
def test_Log(self): |
|
|
|
|
|
|
33
|
|
|
self.provenance.discover('testdata') |
|
34
|
|
|
newfile = 'temp/smoothed.test' |
|
35
|
|
|
self.touch(newfile) |
|
36
|
|
|
parent = os.path.abspath('testdata/eeg/stub.cnt') |
|
37
|
|
|
self.provenance.log(newfile, 'test', parent) |
|
38
|
|
|
testfpath = os.path.abspath(newfile) |
|
39
|
|
|
img = self.provenance.get().byLocation(testfpath) |
|
40
|
|
|
self.assertEqual(img.provenance['subject'], 'Jane Doe') |
|
41
|
|
|
self.assertEqual(img.provenance['size'], os.path.getsize(newfile)) |
|
42
|
|
|
|
|
43
|
|
View Code Duplication |
def test_Record_with_user(self): |
|
|
|
|
|
|
44
|
|
|
self.provenance.discover('testdata') |
|
45
|
|
|
newfile = 'temp/recorded.test' |
|
46
|
|
|
self.touch(newfile) |
|
47
|
|
|
parent = os.path.abspath('testdata/eeg/stub.cnt') |
|
48
|
|
|
self.provenance.record('echo hallo', newfile, parent, user='007') |
|
49
|
|
|
testfpath = os.path.abspath(newfile) |
|
50
|
|
|
img = self.provenance.get().byLocation(testfpath) |
|
51
|
|
|
self.assertEqual(img.provenance['user'], '007') |
|
52
|
|
|
|
|
53
|
|
|
def test_Export_Import(self): |
|
54
|
|
|
from niprov.exceptions import UnknownFileError |
|
55
|
|
|
self.provenance.discover('testdata') |
|
56
|
|
|
discoveredFile = os.path.abspath('testdata/eeg/stub.cnt') |
|
57
|
|
|
self.assertIsNotNone(self.provenance.get().byLocation(discoveredFile)) |
|
58
|
|
|
backupFilepath = self.provenance.backup() |
|
59
|
|
|
os.remove(self.dbpath) # get rid of existing data. |
|
60
|
|
|
self.assertIsNone(self.provenance.get().byLocation(discoveredFile)) |
|
61
|
|
|
self.provenance.importp(backupFilepath) |
|
62
|
|
|
self.assertIsNotNone(self.provenance.get().byLocation(discoveredFile)) |
|
63
|
|
|
|
|
64
|
|
|
@unittest.skip("Doesn't work on Travis right now.") |
|
65
|
|
|
def test_Attach_provenance_string_in_file_based_on_config(self): |
|
66
|
|
|
import nibabel |
|
67
|
|
|
self.provenance.config.attach = True |
|
68
|
|
|
newfile = os.path.abspath('temp/fileX.nii.gz') |
|
69
|
|
|
shutil.copy('testdata/nifti/fieldmap.nii.gz', newfile) |
|
70
|
|
|
self.provenance.add(newfile) |
|
71
|
|
|
img = nibabel.load(newfile) |
|
72
|
|
|
self.assertEqual(img.get_header().extensions.count('comment'), 1) |
|
73
|
|
|
self.assertEqual(img.get_header().extensions[0].get_code(), 6) |
|
74
|
|
|
content = img.get_header().extensions[0].get_content() |
|
75
|
|
|
self.assertIn('"path": "{0}"'.format(newfile), content) |
|
76
|
|
|
|
|
77
|
|
|
def test_Approval(self): |
|
78
|
|
|
self.provenance.discover('testdata') |
|
79
|
|
|
self.provenance.markForApproval(['testdata/parrec/T1.PAR', |
|
80
|
|
|
'testdata/parrec/T2.PAR']) |
|
81
|
|
|
imgs = self.provenance.markedForApproval() |
|
82
|
|
|
self.provenance.approve('testdata/parrec/T1.PAR') |
|
83
|
|
|
imgs = self.provenance.markedForApproval() |
|
84
|
|
|
|
|
85
|
|
|
def test_Comparison(self): |
|
86
|
|
|
# Given two PARREC images' provenance records |
|
87
|
|
|
par1 = self.provenance.add(abspath('testdata/parrec/T1.PAR')) |
|
88
|
|
|
par2 = self.provenance.add(abspath('testdata/parrec/T2.PAR')) |
|
89
|
|
|
# Comparing them returns a Diff object with methods testing equality |
|
90
|
|
|
self.assertFalse(self.provenance.compare(par1, par2).areEqual()) |
|
91
|
|
|
# Compare() can also be called as a method on the objects themselves, |
|
92
|
|
|
# and the Diff object has assert..() methods that raise AssertionErrors |
|
93
|
|
|
msgRegExp = ".*echo-time.*2\.08.*80\.0.*" |
|
94
|
|
|
with self.assertRaisesRegexp(AssertionError, msgRegExp): |
|
95
|
|
|
par1.compare(par2).assertEqualProtocol() |
|
96
|
|
|
|
|
97
|
|
|
def test_Search(self): |
|
98
|
|
|
x1 = self.provenance.add('x1', transient=True, |
|
99
|
|
|
provenance={'transformation':'needle and thread'}) |
|
100
|
|
|
x2 = self.provenance.add('x2/needle.y', transient=True, |
|
101
|
|
|
provenance={'transformation':'needle and thread'}) |
|
102
|
|
|
x3 = self.provenance.add('x3', transient=True, |
|
103
|
|
|
provenance={'transformation':'hammer and tongs'}) |
|
104
|
|
|
results = self.provenance.search('needle') |
|
105
|
|
|
self.assertEqual(len(results), 2) |
|
106
|
|
|
self.assertEqual(x2.provenance['id'], results[0].provenance['id']) |
|
107
|
|
|
self.assertEqual(x1.provenance['id'], results[1].provenance['id']) |
|
108
|
|
|
|
|
109
|
|
|
def test_GetModalities(self): |
|
110
|
|
|
self.provenance.discover('testdata') |
|
111
|
|
|
modalities = self.provenance.get().allModalities() |
|
112
|
|
|
self.assertIn('MRI', modalities) |
|
113
|
|
|
self.assertIn('DWI', modalities) |
|
114
|
|
|
self.assertIn('EEG', modalities) |
|
115
|
|
|
|
|
116
|
|
|
def test_Version_history(self): |
|
117
|
|
|
self.provenance.add('f', transient=True, provenance={'a':1}) |
|
118
|
|
|
img = self.provenance.get().byLocation('f') |
|
119
|
|
|
self.assertEqual(1, img.provenance['a']) |
|
120
|
|
|
self.provenance.add('f', transient=True, provenance={'a':2}) |
|
121
|
|
|
img = self.provenance.get().byLocation('f') |
|
122
|
|
|
self.assertEqual(2, img.provenance['a']) |
|
123
|
|
|
self.assertEqual(1, img.versions[-1]['a']) |
|
124
|
|
|
self.provenance.add('f', transient=True, provenance={'a':3}) |
|
125
|
|
|
img = self.provenance.get().byLocation('f') |
|
126
|
|
|
self.assertEqual(3, img.provenance['a']) |
|
127
|
|
|
self.assertEqual(2, img.versions[-1]['a']) |
|
128
|
|
|
self.assertEqual(1, img.versions[-2]['a']) |
|
129
|
|
|
|
|
130
|
|
View Code Duplication |
def test_If_no_parent_provided_found_copy_considered_parent(self): |
|
|
|
|
|
|
131
|
|
|
self.provenance.add('testdata/eeg/stub.cnt') |
|
132
|
|
|
self.touch('temp/orig.f') |
|
133
|
|
|
self.provenance.log('temp/orig.f', 'op1', 'testdata/eeg/stub.cnt') |
|
134
|
|
|
shutil.copy('temp/orig.f', 'temp/copy.f') |
|
135
|
|
|
self.touch('temp/child.f') |
|
136
|
|
|
child = self.provenance.log('temp/child.f', 'op2', 'temp/copy.f') |
|
137
|
|
|
self.assertEqual(child.provenance['subject'], 'Jane Doe') |
|
138
|
|
|
copy = self.provenance.get().byLocation('temp/copy.f') |
|
139
|
|
|
self.assertIn('temp/orig.f', copy.provenance['parents'][0]) |
|
140
|
|
|
|
|
141
|
|
|
def test_Differentiates_Fifs(self): |
|
142
|
|
|
""" |
|
143
|
|
|
The fields tested here are just a subset. |
|
144
|
|
|
""" |
|
145
|
|
|
fiftypes = {'ave': {'fif-type':'ave', 'dimensions':[2,401,701]}, |
|
146
|
|
|
'cov': {'fif-type':'cov', 'dimensions':[366, 366]}, |
|
147
|
|
|
'epo': {'fif-type':'epo', 'highpass':0.10000000149011612}, |
|
148
|
|
|
'fwd': {'fif-type':'fwd'}, |
|
149
|
|
|
'trans': {'fif-type':'trans'}} |
|
150
|
|
|
for ftype, fields in fiftypes.items(): |
|
151
|
|
|
pth = os.path.abspath('testdata/fif/test-{}.fif'.format(ftype)) |
|
152
|
|
|
img = self.provenance.add(pth) |
|
153
|
|
|
for field, expectedValue in fields.items(): |
|
154
|
|
|
self.assertIn(field, img.provenance) |
|
155
|
|
|
self.assertEqual(img.provenance[field], expectedValue) |
|
156
|
|
|
|
|
157
|
|
|
|
|
158
|
|
|
if __name__ == '__main__': |
|
159
|
|
|
unittest.main() |
|
160
|
|
|
|
|
161
|
|
|
|
ilogue /
niprov
Loading history...
