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
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
|
"""
Unit tests for interface
"""
# System imports
import os
import time
import unittest
import jsondiff
import sys
# airr imports
import airr
from airr.schema import ValidationError
# Paths
test_path = os.path.dirname(os.path.realpath(__file__))
data_path = os.path.join(test_path, 'data')
class TestInferface(unittest.TestCase):
def setUp(self):
print('-------> %s()' % self.id())
# Test data
self.rearrangement_good = os.path.join(data_path, 'good_rearrangement.tsv')
self.rearrangement_bad = os.path.join(data_path, 'bad_rearrangement.tsv')
self.rep_good = os.path.join(data_path, 'good_repertoire.yaml')
self.rep_bad = os.path.join(data_path, 'bad_repertoire.yaml')
self.germline_good = os.path.join(data_path, 'good_germline_set.json')
self.germline_bad = os.path.join(data_path, 'bad_germline_set.json')
self.genotype_good = os.path.join(data_path, 'good_genotype_set.json')
self.genotype_bad = os.path.join(data_path, 'bad_genotype_set.json')
self.combined_yaml = os.path.join(data_path, 'good_combined_airr.yaml')
self.combined_json = os.path.join(data_path, 'good_combined_airr.json')
# Output data
self.output_rep = os.path.join(data_path, 'output_rep.json')
self.output_good = os.path.join(data_path, 'output_data.json')
self.output_blank = os.path.join(data_path, 'output_blank.json')
# Expected output
self.shape_good = (9, 44)
self.shape_bad = (9, 44)
# Start timer
self.start = time.time()
def tearDown(self):
t = time.time() - self.start
print('<- %.3f %s()' % (t, self.id()))
# @unittest.skip('-> load(): skipped\n')
def test_load_rearrangement(self):
# Good data
result = airr.load_rearrangement(self.rearrangement_good)
self.assertTupleEqual(result.shape, self.shape_good, 'load(): good data failed')
# Bad data
result = airr.load_rearrangement(self.rearrangement_bad)
self.assertTupleEqual(result.shape, self.shape_bad, 'load(): bad data failed')
# @unittest.skip('-> repertoire_template(): skipped\n')
def test_repertoire_template(self):
try:
with self.assertWarns(DeprecationWarning, msg='repertoire_template(): failed to issue DeprecationWarning'):
rep = airr.repertoire_template()
airr.write_airr(self.output_blank, {'Repertoire': rep}, validate=False, debug=True)
except:
pass
# @unittest.skip('-> schema.template(): skipped\n')
def test_schema_template(self):
# Repertoire template
try:
data = airr.schema.RepertoireSchema.template()
valid = airr.schema.RepertoireSchema.validate_object(data)
self.assertTrue(valid, 'Schema.template("Repertoire"): repertoire template failed validation')
except:
self.assertTrue(False, 'Schema.template("Repertoire"): repertoire template failed validation')
# GermlineSet template
try:
data = airr.schema.GermlineSetSchema.template()
valid = airr.schema.GermlineSetSchema.validate_object(data)
self.assertTrue(valid, 'Schema.template("GermlineSet"): repertoire template failed validation')
except:
self.assertTrue(False, 'Schema.template("GermlineSet"): repertoire template failed validation')
# GenotypeSet template
try:
data = airr.schema.GenotypeSetSchema.template()
valid = airr.schema.GenotypeSetSchema.validate_object(data)
self.assertTrue(valid, 'Schema.template("GenotypeSet"): repertoire template failed validation')
except:
self.assertTrue(False, 'Schema.template("GenotypeSet"): repertoire template failed validation')
# @unittest.skip('-> validate(): skipped\n')
def test_validate_rearrangement(self):
# Good data
try:
result = airr.validate_rearrangement(self.rearrangement_good)
self.assertTrue(result, 'validate(): good data failed')
except:
self.assertTrue(False, 'validate(): good data failed')
# Bad data
try:
result = airr.validate_rearrangement(self.rearrangement_bad)
self.assertFalse(result, 'validate(): bad data failed')
except Exception as inst:
print(type(inst))
raise inst
# @unittest.skip('-> read_airr(): skipped\n')
def test_read_airr(self):
# Good data
print('--> Good data')
try:
data = airr.read_airr(self.rep_good, validate=True, debug=True)
except:
self.fail('read_airr(): good data failed')
# Bad data
print('--> Bad data')
with self.assertRaises(ValidationError, msg="read_airr(): bad data passed validation"):
data = airr.read_airr(self.rep_bad, validate=True, debug=True)
# Combined yaml
print('--> Combined YAML')
try:
data_yaml = airr.read_airr(self.combined_yaml, validate=True, debug=True)
except:
self.fail('read_airr(): combined yaml failed')
# Combined json
print('--> Combined JSON')
try:
data_json = airr.read_airr(self.combined_json, validate=True, debug=True)
except:
self.fail('read_airr(): combined json failed')
# Check equality of yaml and json
self.assertDictEqual(data_yaml, data_json, msg="read_airr(): yaml and json imports are not equal")
# @unittest.skip('-> validate_airr(): skipped\n')
def test_validate_airr(self):
# Good data
print('--> Good data')
# As array
try:
data = airr.read_airr(self.rep_good, validate=True, debug=True)
valid = airr.validate_airr(data, debug=True)
self.assertTrue(valid, 'validate_airr(): good data array failed')
except:
self.assertTrue(False, 'validate_airr(): good data array failed')
# As dict
try:
array = airr.read_airr(self.rep_good, validate=False, debug=False)
data = {'Repertoire': {x['repertoire_id']: x for x in array['Repertoire']}}
valid = airr.validate_airr(data, debug=True)
self.assertTrue(valid, 'validate_airr(): good data dict failed')
except:
self.assertTrue(False, 'validate_airr(): good data dict failed')
# Bad data
print('--> Bad data')
# As array
try:
data = airr.read_airr(self.rep_bad, validate=True, debug=True)
valid = airr.validate_airr(data, debug=True)
self.assertFalse(valid, 'validate_airr(): bad data array failed')
except ValidationError:
pass
except Exception as inst:
print(type(inst))
raise inst
# As dict
try:
array = airr.read_airr(self.rep_bad, validate=False, debug=False)
data = {'Repertoire': {x['repertoire_id']: x for x in array['Repertoire']}}
valid = airr.validate_airr(data, debug=True)
self.assertFalse(valid, 'validate_airr(): bad data dict failed')
except ValidationError:
pass
except Exception as inst:
print(type(inst))
raise inst
# @unittest.skip('-> load_repertoire(): skipped\n')
def test_load_repertoire(self):
# Good data
try:
with self.assertWarns(DeprecationWarning, msg='load_repertoire(): failed to issue DeprecationWarning'):
data = airr.load_repertoire(self.rep_good, validate=True, debug=True)
except:
self.assertTrue(False, 'load_repertoire(): good data failed')
# Bad data
try:
with self.assertWarns(DeprecationWarning, msg='load_repertoire(): failed to issue DeprecationWarning'):
data = airr.load_repertoire(self.rep_bad, validate=True, debug=True)
self.assertFalse(True, 'load_repertoire(): bad data passed')
except ValidationError:
pass
except Exception as inst:
print(type(inst))
raise inst
# @unittest.skip('-> write_repertoire(): skipped\n')
def test_write_repertoire(self):
# Good data
try:
with self.assertWarns(DeprecationWarning, msg='load_repertoire(): failed to issue DeprecationWarning'):
data = airr.load_repertoire(self.rep_good, validate=True, debug=True)
with self.assertWarns(DeprecationWarning, msg='write_repertoire(): failed to issue DeprecationWarning'):
result = airr.write_repertoire(self.output_rep, data['Repertoire'], debug=True)
with self.assertWarns(DeprecationWarning, msg='load_repertoire(): failed to issue DeprecationWarning'):
# verify we can read it
obj = airr.load_repertoire(self.output_rep, validate=True, debug=True)
# is the data identical?
if jsondiff.diff(obj['Repertoire'], data['Repertoire']) != {}:
print('Output data does not match', file=sys.stderr)
print(jsondiff.diff(obj, data), file=sys.stderr)
self.assertTrue(False, 'write_repertoire(): Output data does not match')
except:
self.assertTrue(False, 'write_repertoire(): good data failed')
# @unittest.skip('-> load_germline(): skipped\n')
def test_read_germline(self):
# Good data
try:
result = airr.read_airr(self.germline_good, validate=True, debug=True)
except ValidationError:
self.assertTrue(False, 'load_germline(): good data failed')
# Bad data
try:
result = airr.read_airr(self.germline_bad, validate=True, debug=True)
self.assertFalse(True, 'load_germline(): bad data succeeded')
except ValidationError:
pass
# @unittest.skip('-> validate_germline(): skipped\n')
def test_validate_germline(self):
# Good data
print('--> Good data')
try:
result = airr.read_airr(self.germline_good, validate=True, debug=True)
valid = airr.validate_airr(result, debug=True)
self.assertTrue(valid, 'validate_germline(): good data failed')
except ValidationError:
self.assertTrue(False, 'validate_germline(): good data failed')
# Bad data
print('--> Bad data')
try:
result = airr.read_airr(self.germline_bad, validate=True, debug=True)
valid = airr.validate_airr(result, debug=True)
self.assertFalse(valid, 'validate_germline(): bad data succeeded')
except ValidationError:
pass
# @unittest.skip('-> load_genotype(): skipped\n')
def test_read_genotype(self):
# Good data
print('--> Good data')
try:
result = airr.read_airr(self.genotype_good, validate=True, debug=True)
except ValidationError:
self.assertTrue(False, 'load_genotype(): good data failed')
# Bad data
print('--> Bad data')
try:
result = airr.read_airr(self.genotype_bad, validate=True, debug=True)
self.assertFalse(True, 'load_genotype(): bad data succeeded')
except ValidationError:
pass
# @unittest.skip('-> validate_genotype(): skipped\n')
def test_validate_genotype(self):
# Good data
print('--> Good data')
try:
result = airr.read_airr(self.genotype_good, validate=True, debug=True)
valid = airr.validate_airr(result, debug=True)
self.assertTrue(valid, 'validate_genotype(): good data failed')
except ValidationError:
self.assertTrue(False, 'validate_genotype(): good data failed')
# Bad data
print('--> Bad data')
try:
result = airr.read_airr(self.genotype_bad, validate=True, debug=True)
valid = airr.validate_airr(result, debug=True)
self.assertFalse(valid, 'validate_genotype(): bad data succeeded')
except ValidationError:
pass
# @unittest.skip('-> load_genotype(): skipped\n')
def test_write_airr(self):
# Good data as array
try:
repertoire_data = airr.read_airr(self.rep_good, validate=True, debug=True)
germline_data = airr.read_airr(self.germline_good, validate=True, debug=True)
genotype_data = airr.read_airr(self.genotype_good, validate=True, debug=True)
# combine together and write
obj = {}
obj['Repertoire'] = repertoire_data['Repertoire']
obj['GermlineSet'] = germline_data['GermlineSet']
obj['GenotypeSet'] = genotype_data['GenotypeSet']
airr.write_airr(self.output_good, obj, validate=True, debug=True)
# verify we can read it
data = airr.read_airr(self.output_good, validate=True, debug=True)
# is the data identical?
del data['Info']
if jsondiff.diff(obj, data) != {}:
print('Output data does not match', file=sys.stderr)
print(jsondiff.diff(obj, data), file=sys.stderr)
self.assertTrue(False, 'write_airr_data(): Output data does not match')
except Exception as inst:
self.assertTrue(False, 'write_airr_data(): good data failed')
print(type(inst))
raise inst
# Good data as dict
try:
# Load data
repertoire_array = airr.read_airr(self.rep_good, validate=True, debug=True)
germline_array = airr.read_airr(self.germline_good, validate=True, debug=True)
genotype_array = airr.read_airr(self.genotype_good, validate=True, debug=True)
# Build keyed representation
repertoire_data = {'Repertoire': {x['repertoire_id']: x for x in repertoire_array['Repertoire']}}
germline_data = {'GermlineSet': {x['germline_set_id']: x for x in germline_array['GermlineSet']}}
genotype_data = {'GenotypeSet': {x['receptor_genotype_set_id']: x for x in genotype_array['GenotypeSet']}}
# combine together and write
obj = {}
obj['Repertoire'] = repertoire_data['Repertoire']
obj['GermlineSet'] = germline_data['GermlineSet']
obj['GenotypeSet'] = genotype_data['GenotypeSet']
airr.write_airr(self.output_good, obj, validate=True, debug=True)
# verify we can read it
data = airr.read_airr(self.output_good, validate=True, debug=True)
# is the data identical?
del data['Info']
if jsondiff.diff(obj, data) != {}:
print('Output data does not match', file=sys.stderr)
print(jsondiff.diff(obj, data), file=sys.stderr)
self.assertTrue(False, 'write_airr_data(): Output data does not match')
except Exception as inst:
self.assertTrue(False, 'write_airr_data(): good data failed')
print(type(inst))
raise inst
if __name__ == '__main__':
unittest.main()
|
