#!/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_gap`. """ 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_gap' 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_gap 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), 5) # no lines deleted self.assertEqual(len(self.stderr), 0) # no errors self.assertEqual(self.stdout, ["B:ARG4 < Seq. Gap > B:GLU6", "A:ASN1 < 9.42A > A:ASN1", "C:ARG5 < Seq. Gap > C:GLU2", "C:GLU2 < 95.75A > C:MET-1", "Found 4 gap(s) in the structure"]) def test_file_not_found(self): """$ pdb_gap 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 def test_helptext(self): """$ pdb_gap""" 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_gap -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()