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
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2018 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_segxchain`.
"""
import os
import sys
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_segxchain'
self.module = __import__(name, fromlist=[''])
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_segxchain data/dummy.pdb"""
# Simulate input
sys.argv = ['', os.path.join(data_dir, 'dummy.pdb')]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
self.assertEqual(len(self.stdout), 204) # no lines deleted
self.assertEqual(len(self.stderr), 0) # no errors
records = (('ATOM', 'HETATM'))
chain_ids = [l[21] for l in self.stdout if l.startswith(records)]
# Test content
unique_chain_ids = sorted(set(chain_ids))
self.assertEqual(unique_chain_ids, [' ', 'A', 'Z'])
# Test order
chain_list = [' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', 'A', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z',
'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z',
' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ']
self.assertEqual(chain_ids, chain_list)
def test_file_not_found(self):
"""$ pdb_segxchain not_existing.pdb"""
# Error (file not found)
afile = os.path.join(data_dir, 'not_existing.pdb')
sys.argv = ['', afile]
# Execute the script
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_helptext(self):
"""$ pdb_segxchain"""
sys.argv = ['']
# Execute the script
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_segxchain -A data/dummy.pdb"""
sys.argv = ['', '-A', os.path.join(data_dir, 'dummy.pdb')]
# Execute the script
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0][:36],
"ERROR!! Script takes 1 argument, not")
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()
|
