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Added tests for new tools
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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. | ||
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""" | ||
Unit Tests for `pdb_delresname`. | ||
""" | ||
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import os | ||
import sys | ||
import unittest | ||
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from config import data_dir | ||
from utils import OutputCapture | ||
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class TestTool(unittest.TestCase): | ||
""" | ||
Generic class for testing tools. | ||
""" | ||
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def setUp(self): | ||
# Dynamically import the module | ||
name = 'pdbtools.pdb_delresname' | ||
self.module = __import__(name, fromlist=['']) | ||
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def exec_module(self): | ||
""" | ||
Execs module. | ||
""" | ||
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with OutputCapture() as output: | ||
try: | ||
self.module.main() | ||
except SystemExit as e: | ||
self.retcode = e.code | ||
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self.stdout = output.stdout | ||
self.stderr = output.stderr | ||
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return | ||
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def test_single_sele(self): | ||
"""$ pdb_delresname -ARG data/dummy.pdb""" | ||
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# Simulate input | ||
sys.argv = ['', '-ARG', os.path.join(data_dir, 'dummy.pdb')] | ||
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# Execute the script | ||
self.exec_module() | ||
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# Validate results | ||
self.assertEqual(self.retcode, 0) | ||
self.assertEqual(len(self.stdout), 128) | ||
self.assertEqual(len(self.stderr), 0) | ||
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def test_multiple_sele(self): | ||
"""$ pdb_delresname -ARG,CA data/dummy.pdb""" | ||
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# Simulate input | ||
sys.argv = ['', '-ARG,CA', os.path.join(data_dir, 'dummy.pdb')] | ||
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# Execute the script | ||
self.exec_module() | ||
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# Validate results | ||
self.assertEqual(self.retcode, 0) | ||
self.assertEqual(len(self.stdout), 127) | ||
self.assertEqual(len(self.stderr), 0) | ||
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def test_empty_sele(self): | ||
"""$ pdb_delresname - data/dummy.pdb""" | ||
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# Simulate input | ||
sys.argv = ['', '-', os.path.join(data_dir, 'dummy.pdb')] | ||
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# Execute the script | ||
self.exec_module() | ||
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# Validate results | ||
self.assertEqual(self.retcode, 1) | ||
self.assertEqual(len(self.stdout), 0) | ||
self.assertEqual(self.stderr[0][:22], | ||
"ERROR!! Residue name s") | ||
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def test_invalid_sele(self): | ||
"""$ pdb_delresname -ABCD data/dummy.pdb""" | ||
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# Simulate input | ||
sys.argv = ['', '-ABCD', os.path.join(data_dir, 'dummy.pdb')] | ||
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# Execute the script | ||
self.exec_module() | ||
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# Validate results | ||
self.assertEqual(self.retcode, 1) | ||
self.assertEqual(len(self.stdout), 0) | ||
self.assertEqual(self.stderr[0][:22], | ||
"ERROR!! Residue name i") | ||
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def test_file_not_found(self): | ||
"""$ pdb_delresname not_existing.pdb""" | ||
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afile = os.path.join(data_dir, 'not_existing.pdb') | ||
sys.argv = ['', afile] | ||
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self.exec_module() | ||
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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 | ||
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def test_file_missing(self): | ||
"""$ pdb_delresname -ARG""" | ||
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sys.argv = ['', '-ARG'] | ||
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self.exec_module() | ||
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self.assertEqual(self.retcode, 1) | ||
self.assertEqual(len(self.stdout), 0) # no output | ||
self.assertEqual(self.stderr[0], | ||
"ERROR!! No data to process!") | ||
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def test_helptext(self): | ||
"""$ pdb_delresname""" | ||
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sys.argv = [''] | ||
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self.exec_module() | ||
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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]) | ||
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def test_not_an_option(self): | ||
"""$ pdb_delresname 20 data/dummy.pdb""" | ||
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sys.argv = ['', '20', os.path.join(data_dir, 'dummy.pdb')] | ||
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self.exec_module() | ||
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self.assertEqual(self.retcode, 1) | ||
self.assertEqual(len(self.stdout), 0) | ||
self.assertEqual(self.stderr[0], | ||
"ERROR! First argument is not an option: '20'") | ||
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if __name__ == '__main__': | ||
from config import test_dir | ||
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mpath = os.path.abspath(os.path.join(test_dir, '..')) | ||
sys.path.insert(0, mpath) # so we load dev files before any installation | ||
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unittest.main() |
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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. | ||
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""" | ||
Unit Tests for `pdb_head`. | ||
""" | ||
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import os | ||
import sys | ||
import unittest | ||
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from config import data_dir | ||
from utils import OutputCapture | ||
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class TestTool(unittest.TestCase): | ||
""" | ||
Generic class for testing tools. | ||
""" | ||
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def setUp(self): | ||
# Dynamically import the module | ||
name = 'pdbtools.pdb_head' | ||
self.module = __import__(name, fromlist=['']) | ||
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def exec_module(self): | ||
""" | ||
Execs module. | ||
""" | ||
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with OutputCapture() as output: | ||
try: | ||
self.module.main() | ||
except SystemExit as e: | ||
self.retcode = e.code | ||
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self.stdout = output.stdout | ||
self.stderr = output.stderr | ||
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return | ||
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def test_valid_option(self): | ||
"""$ pdb_head -10 data/dummy.pdb""" | ||
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# Simulate input | ||
sys.argv = ['', '-10', os.path.join(data_dir, 'dummy.pdb')] | ||
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# Execute the script | ||
self.exec_module() | ||
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# Validate results | ||
self.assertEqual(self.retcode, 0) | ||
self.assertEqual(len(self.stdout), 10) | ||
self.assertEqual(len(self.stderr), 0) | ||
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def test_invalid_option(self): | ||
"""$ pdb_head --10 data/dummy.pdb""" | ||
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# Simulate input | ||
sys.argv = ['', '--10', os.path.join(data_dir, 'dummy.pdb')] | ||
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# Execute the script | ||
self.exec_module() | ||
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# Validate results | ||
self.assertEqual(self.retcode, 1) | ||
self.assertEqual(len(self.stdout), 0) | ||
self.assertEqual(self.stderr[0][:22], | ||
"ERROR!! Option must be") | ||
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def test_file_not_found(self): | ||
"""$ pdb_head not_existing.pdb""" | ||
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afile = os.path.join(data_dir, 'not_existing.pdb') | ||
sys.argv = ['', afile] | ||
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self.exec_module() | ||
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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 | ||
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def test_file_missing(self): | ||
"""$ pdb_head -10""" | ||
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sys.argv = ['', '-10'] | ||
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self.exec_module() | ||
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self.assertEqual(self.retcode, 1) | ||
self.assertEqual(len(self.stdout), 0) # no output | ||
self.assertEqual(self.stderr[0], | ||
"ERROR!! No data to process!") | ||
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def test_helptext(self): | ||
"""$ pdb_head""" | ||
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sys.argv = [''] | ||
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self.exec_module() | ||
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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]) | ||
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def test_not_an_option(self): | ||
"""$ pdb_head 20 data/dummy.pdb""" | ||
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sys.argv = ['', '20', os.path.join(data_dir, 'dummy.pdb')] | ||
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self.exec_module() | ||
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self.assertEqual(self.retcode, 1) | ||
self.assertEqual(len(self.stdout), 0) | ||
self.assertEqual(self.stderr[0], | ||
"ERROR! First argument is not an option: '20'") | ||
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if __name__ == '__main__': | ||
from config import test_dir | ||
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mpath = os.path.abspath(os.path.join(test_dir, '..')) | ||
sys.path.insert(0, mpath) # so we load dev files before any installation | ||
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unittest.main() |
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