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#!/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_splitseg`.
"""
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_splitseg'
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_run_fhandler(self):
"""pdb_splitseg.run(iterable)"""
from pdbtools import pdb_splitseg
# 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)
with open(dst, 'r') as fin:
pdb_splitseg.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), 2 + 1) # ori + 2 segments
# 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_seg = fpath.split('_')[1][:-4] # xxx_(X).pdb
pdb_segids = [l[72:76].strip() for l in handle
if l.startswith(records)]
self.assertEqual(fname_seg, list(set(pdb_segids))[0])
def test_run_iterable_with_name(self):
"""pdb_splitseg.run(iterable, outname='newname')"""
from pdbtools import pdb_splitseg
# 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)
with open(dst, 'r') as fin:
lines = fin.readlines()
pdb_splitseg.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), 2)
# 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_seg = fpath.split('_')[1][:-4] # xxx_(X).pdb
pdb_segids = [l[72:76].strip() for l in handle
if l.startswith(records)]
self.assertEqual(fname_seg, list(set(pdb_segids))[0])
def test_run_iterable(self):
"""pdb_splitseg.run(fhandler)"""
from pdbtools import pdb_splitseg
# 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)
with open(dst, 'r') as fin:
lines = fin.readlines()
pdb_splitseg.run(lines)
# Read files created by script and then delete
ofiles = [
f
for f in os.listdir(self.tempdir)
if f.startswith('splitsegs')]
self.assertEqual(len(ofiles), 2)
# 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_seg = fpath.split('_')[1][:-4] # xxx_(X).pdb
pdb_segids = [l[72:76].strip() for l in handle
if l.startswith(records)]
self.assertEqual(fname_seg, list(set(pdb_segids))[0])
def test_default(self):
"""$ pdb_splitseg 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), 2 + 1) # ori + 2 segments
# 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_seg = fpath.split('_')[1][:-4] # xxx_(X).pdb
pdb_segids = [l[72:76].strip() for l in handle
if l.startswith(records)]
self.assertEqual(fname_seg, list(set(pdb_segids))[0])
def test_file_not_found(self):
"""$ pdb_splitseg 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_splitseg -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_splitseg"""
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_splitseg -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()
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