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
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 1118 João Pedro Rodrigues
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
Unit Tests for `pdb_splitchain`.
"""
import os
import shutil
import sys
import tempfile
import unittest
from .config import data_dir
from .utils import OutputCapture
class TestTool(unittest.TestCase):
"""
Generic class for testing tools.
"""
def setUp(self):
# Dynamically import the module
name = 'pdbtools.pdb_splitchain'
self.module = __import__(name, fromlist=[''])
self.tempdir = tempfile.mkdtemp() # set temp dir
os.chdir(self.tempdir)
def tearDown(self):
os.chdir(os.path.dirname(os.path.abspath('.'))) # cd ../
shutil.rmtree(self.tempdir)
def exec_module(self):
"""
Execs module.
"""
with OutputCapture() as output:
try:
self.module.main()
except SystemExit as e:
self.retcode = e.code
self.stdout = output.stdout
self.stderr = output.stderr
return
def test_default(self):
"""$ pdb_splitchain data/dummy.pdb"""
# Copy input file to tempdir
# Simulate input
src = os.path.join(data_dir, 'dummy.pdb')
dst = os.path.join(self.tempdir, 'dummy.pdb')
shutil.copy(src, dst)
sys.argv = ['', dst]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
self.assertEqual(len(self.stdout), 0) # no output
self.assertEqual(len(self.stderr), 0) # no errors
# Read files created by script and then delete
ofiles = [f for f in os.listdir(self.tempdir) if f.startswith('dummy')]
self.assertEqual(len(ofiles), 4 + 1) # ori + 4 chains
# Make sure each file has the chain it should have
records = (('ATOM', 'HETATM', 'TER', 'ANISOU'))
for fpath in ofiles:
if fpath == 'dummy.pdb':
continue
with open(os.path.join(self.tempdir, fpath), 'r') as handle:
fname_chain = fpath.split('_')[1][:-4] # xxx_(X).pdb
pdb_chains = [l[21] for l in handle if l.startswith(records)]
self.assertEqual(fname_chain, list(set(pdb_chains))[0])
def test_run_fhandler(self):
"""pdb_splitchain.run(fhandler)"""
from pdbtools import pdb_splitchain
src = os.path.join(data_dir, 'dummy.pdb')
dst = os.path.join(self.tempdir, 'dummy.pdb')
shutil.copy(src, dst)
with open(dst, 'r') as fin:
pdb_splitchain.run(fin)
# Read files created by script and then delete
ofiles = [f for f in os.listdir(self.tempdir) if f.startswith('dummy')]
self.assertEqual(len(ofiles), 4 + 1) # ori + 4 chains
# Make sure each file has the chain it should have
records = (('ATOM', 'HETATM', 'TER', 'ANISOU'))
for fpath in ofiles:
if fpath == 'dummy.pdb':
continue
with open(os.path.join(self.tempdir, fpath), 'r') as handle:
fname_chain = fpath.split('_')[1][:-4] # xxx_(X).pdb
pdb_chains = [l[21] for l in handle if l.startswith(records)]
self.assertEqual(fname_chain, list(set(pdb_chains))[0])
def test_run_iterable(self):
"""pdb_splitchain.run(iterable)"""
from pdbtools import pdb_splitchain
src = os.path.join(data_dir, 'dummy.pdb')
dst = os.path.join(self.tempdir, 'dummy.pdb')
shutil.copy(src, dst)
with open(dst, 'r') as fin:
lines = fin.readlines()
pdb_splitchain.run(lines)
# Read files created by script and then delete
ofiles = [
f
for f in os.listdir(self.tempdir)
if f.startswith('splitchains')
]
self.assertEqual(len(ofiles), 4) # 4 chains
# Make sure each file has the chain it should have
records = (('ATOM', 'HETATM', 'TER', 'ANISOU'))
for fpath in ofiles:
with open(os.path.join(self.tempdir, fpath), 'r') as handle:
fname_chain = fpath.split('_')[1][:-4] # xxx_(X).pdb
pdb_chains = [l[21] for l in handle if l.startswith(records)]
self.assertEqual(fname_chain, list(set(pdb_chains))[0])
def test_run_iterable_with_name(self):
"""pdb_splitchain.run(iterable)"""
from pdbtools import pdb_splitchain
src = os.path.join(data_dir, 'dummy.pdb')
dst = os.path.join(self.tempdir, 'dummy.pdb')
shutil.copy(src, dst)
with open(dst, 'r') as fin:
lines = fin.readlines()
pdb_splitchain.run(lines, outname='newname')
# Read files created by script and then delete
ofiles = [f for f in os.listdir(self.tempdir) if f.startswith('newname')]
self.assertEqual(len(ofiles), 4) # 4 chains
# Make sure each file has the chain it should have
records = (('ATOM', 'HETATM', 'TER', 'ANISOU'))
for fpath in ofiles:
with open(os.path.join(self.tempdir, fpath), 'r') as handle:
fname_chain = fpath.split('_')[1][:-4] # xxx_(X).pdb
pdb_chains = [l[21] for l in handle if l.startswith(records)]
self.assertEqual(fname_chain, list(set(pdb_chains))[0])
def test_file_not_found(self):
"""$ pdb_splitchain not_existing.pdb"""
afile = os.path.join(data_dir, 'not_existing.pdb')
sys.argv = ['', afile]
self.exec_module()
self.assertEqual(self.retcode, 1) # exit code is 1 (error)
self.assertEqual(len(self.stdout), 0) # nothing written to stdout
self.assertEqual(self.stderr[0][:22],
"ERROR!! File not found") # proper error message
@unittest.skipIf(os.getenv('SKIP_TTY_TESTS'), 'skip on GHA - no TTY')
def test_file_missing(self):
"""$ pdb_splitchain -10"""
sys.argv = ['', '-10']
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0) # no output
self.assertEqual(self.stderr[0][:38],
"ERROR!! File not found or not readable")
@unittest.skipIf(os.getenv('SKIP_TTY_TESTS'), 'skip on GHA - no TTY')
def test_helptext(self):
"""$ pdb_splitchain"""
sys.argv = ['']
self.exec_module()
self.assertEqual(self.retcode, 1) # ensure the program exited gracefully.
self.assertEqual(len(self.stdout), 0) # no output
self.assertEqual(self.stderr, self.module.__doc__.split("\n")[:-1])
def test_invalid_option(self):
"""$ pdb_splitchain -A data/dummy.pdb"""
sys.argv = ['', '-A', os.path.join(data_dir, 'dummy.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0][:22],
"ERROR!! Script takes 1") # proper error message
if __name__ == '__main__':
from config import test_dir
mpath = os.path.abspath(os.path.join(test_dir, '..'))
sys.path.insert(0, mpath) # so we load dev files before any installation
unittest.main()
|
