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#!/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_element`.
"""
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_element'
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_element 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
element_cols = [l[76:78] for l in self.stdout]
# Test content
assigned = [l for l in element_cols if l.strip()]
self.assertEqual(len(assigned), 185) # ignore TER/END & headers
# Test order
element_list = [' ', ' ', ' ', ' ', ' ', ' ', '', '', '', '', '',
'', '', ' N', ' H', ' H', ' H', ' C', ' H', ' C', ' H',
' H', ' C', ' H', ' H', ' C', ' H', ' H', ' N', ' H',
' C', ' N', ' H', ' H', ' N', ' H', ' H', ' C', ' O',
' N', ' H', ' C', ' H', ' C', ' H', ' H', ' C', ' H',
' H', ' C', ' O', ' O', ' C', ' O', ' N', ' H', ' C',
' H', ' C', ' H', ' H', ' H', ' C', ' O', '', ' N',
' H', ' H', ' H', ' C', ' C', ' H', ' C', ' H', ' H',
' C', ' O', ' N', ' H', ' H', ' C', ' O', ' N', ' H',
' C', ' H', ' C', ' H', ' H', ' C', ' H', ' H', ' C',
' H', ' H', ' N', ' H', ' C', ' N', ' H', ' H', ' N',
' H', ' H', ' C', ' O', ' N', ' H', ' C', ' H', ' C',
' H', ' H', ' C', ' H', ' H', ' C', ' O', ' O', ' C',
' O', ' ', ' N', ' H', ' H', ' H', ' C', ' H', ' C',
' H', ' H', ' C', ' H', ' H', ' C', ' H', ' H', ' N',
' H', ' C', ' N', ' H', ' H', ' N', ' H', ' H', ' C',
' O', ' N', ' H', ' C', ' H', ' C', ' H', ' H', ' C',
' H', ' H', ' C', ' O', ' O', ' C', ' O', ' N', ' C',
' C', ' O', ' C', ' C', ' S', ' C', ' ', ' P', ' O',
' O', ' O', ' C', ' C', ' O', ' C', ' O', ' C', ' C',
' N', ' C', ' O', ' N', ' C', ' O', ' C', ' C', ' C',
'CA', ' O', ' O', ' O', ' O', ' O', ' O', ' O', ' O',
' ', '', '']
self.assertEqual(element_cols, element_list)
def test_file_not_found(self):
"""$ pdb_element 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_element"""
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_element -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()
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