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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_rplchain`.
"""
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_rplchain'
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_option_1(self):
"""$ pdb_rplchain -D:Z data/dummy.pdb"""
sys.argv = ['', '-D:Z', os.path.join(data_dir, 'dummy.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 0)
self.assertEqual(len(self.stdout), 204)
self.assertEqual(len(self.stderr), 0)
records = (('ATOM', 'HETATM'))
chain_ids = set([l[21] for l in self.stdout if l.startswith(records)])
self.assertTrue('Z' in chain_ids)
self.assertTrue('D' not in chain_ids)
def test_option_2(self):
"""$ pdb_rplchain -A: data/dummy.pdb"""
# Simulate input
sys.argv = ['', '-A:', 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 = set([l[21] for l in self.stdout if l.startswith(records)])
self.assertTrue(' ' in chain_ids)
self.assertTrue('A' not in chain_ids)
def test_file_not_found(self):
"""$ pdb_rplchain -A not_existing.pdb"""
afile = os.path.join(data_dir, 'not_existing.pdb')
sys.argv = ['', '-A', 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_rplchain -A"""
sys.argv = ['', '-A']
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0) # no output
self.assertEqual(self.stderr[0],
"ERROR!! No data to process!")
@unittest.skipIf(os.getenv('SKIP_TTY_TESTS'), 'skip on GHA - no TTY')
def test_helptext(self):
"""$ pdb_rplchain"""
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_1(self):
"""$ pdb_rplchain -AH data/dummy.pdb"""
sys.argv = ['', '-AH', 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][:34],
"ERROR!! Invalid option value: 'AH'")
def test_invalid_option_2(self):
"""$ pdb_rplchain -AH: data/dummy.pdb"""
sys.argv = ['', '-AH:', 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][:47],
"ERROR!! Chain identifiers must be a single char")
def test_not_an_option(self):
"""$ pdb_rplchain 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],
"ERROR! First argument is not an option: 'A'")
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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