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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_chkensemble`.
"""
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_chkensemble'
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_valid_ensemble(self):
"""$ pdb_chkensemble data/ensemble_OK.pdb"""
fpath = os.path.join(data_dir, 'ensemble_OK.pdb')
sys.argv = ['', fpath]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
self.assertEqual(len(self.stdout), 1)
self.assertEqual(len(self.stderr), 0) # no errors
self.assertEqual(self.stdout[0],
"Ensemble of 2 models *seems* OK")
def test_ensemble_diffatom(self):
"""$ pdb_chkensemble data/ensemble_error_1.pdb"""
fpath = os.path.join(data_dir, 'ensemble_error_1.pdb')
sys.argv = ['', fpath]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(len(self.stderr), 3)
self.assertEqual(self.stderr,
["Models 1 and 2 differ:",
"Atoms in model 1 only:",
" 2 H ASN A 1 "])
def test_ensemble_nomodel(self):
"""$ pdb_chkensemble data/ensemble_error_2.pdb"""
fpath = os.path.join(data_dir, 'ensemble_error_2.pdb')
sys.argv = ['', fpath]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(len(self.stderr), 1)
self.assertEqual(self.stderr[0],
"ERROR!! MODEL record missing before ATOM at line '3'")
def test_ensemble_noendmdl(self):
"""$ pdb_chkensemble data/ensemble_error_3.pdb"""
fpath = os.path.join(data_dir, 'ensemble_error_3.pdb')
sys.argv = ['', fpath]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(len(self.stderr), 1)
self.assertEqual(self.stderr[0],
"ERROR!! ENDMDL record missing at line '10'")
def test_ensemble_noendmdl2(self):
"""$ pdb_chkensemble data/ensemble_error_4.pdb"""
fpath = os.path.join(data_dir, 'ensemble_error_4.pdb')
sys.argv = ['', fpath]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(len(self.stderr), 1)
self.assertEqual(self.stderr[0],
"ERROR!! MODEL record found before ENDMDL at line '6'")
def test_file_not_found(self):
"""$ pdb_chkensemble 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)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0][:22],
"ERROR!! File not found")
@unittest.skipIf(os.getenv('SKIP_TTY_TESTS'), 'skip on GHA - no TTY')
def test_helptext(self):
"""$ pdb_chkensemble"""
sys.argv = ['']
# Execute the script
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr, self.module.__doc__.split("\n")[:-1])
def test_invalid_option(self):
"""$ pdb_chkensemble -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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