def test_no_shape_throws(self):
noargs = emptyArgs()
with self.assertRaises(SystemExit):
check_argument_sanity(noargs)
self.assertEqual(
"No shape was selected. Pick a shape to build using the -s flag\n",
str(self.stderr))
def test_g_unknown_args(self):
self.invalidArgs.g = ["r_sphere:100", "l_cylinder:100"]
with self.assertRaises(SystemExit):
check_argument_sanity(self.invalidArgs)
self.assertEqual(
'You submitted the following geometric argument(s) using the -g flag, but shape "{:s}" does not use those parameters\n{:s}\n'
.format("sphere", "l_cylinder"), str(self.stderr))
def test_g_value_error(self):
self.invalidArgs.g = ["r_sphere:five"]
with self.assertRaises(SystemExit):
check_argument_sanity(self.invalidArgs)
self.assertEqual(
"Could not convert one or more -g arguments to float - check you inputs\n",
str(self.stderr))
def test_zo_inconvertible_to_float(self):
self.invalidArgs.z = "a"
with self.assertRaises(SystemExit):
check_argument_sanity(self.invalidArgs)
self.assertEqual(
'your input of "a" for zo could not be converted to a floating point number\n',
str(self.stderr))
def test_bad_shape_throws(self):
invalidArgs = self.validArgs
invalidArgs.s = "spere"
with self.assertRaises(SystemExit):
check_argument_sanity(invalidArgs)
self.assertEqual(
'Invalid shape selected with argument -s. "spere" is not a valid shape\n',
str(self.stderr))
def test_g_missing_arguments(self):
self.invalidArgs.s = "cylinder"
self.invalidArgs.g = ["r_cylinder:100"]
with self.assertRaises(SystemExit):
check_argument_sanity(self.invalidArgs)
self.assertEqual(
'The following required geometry argument(s) for the shape "{:s}" are missing :\n{:s}\n'
.format("cylinder", "l_cylinder"), str(self.stderr))
def test_input_suffix_check(self):
invalidArgs = self.validArgs
invalidArgs.f = "nonexistent"
with self.assertRaises(SystemExit):
check_argument_sanity(invalidArgs)
self.assertEqual(
'User input for option -f was "nonexistent", does not end in .gro or .pdb\nPlease use a valid suffix\n',
str(self.stderr))
def test_input_is_not_a_file(self):
invalidArgs = self.validArgs
invalidArgs.f = "nonexistent.pdb"
with self.assertRaises(SystemExit):
check_argument_sanity(invalidArgs)
self.assertEqual(
'Error: input file does not exist\nUser input for -f : {:s}\n'.
format(invalidArgs.f), str(self.stderr))
def test_fails_with_no_thickness(self):
invalidArgs = self.validArgs
invalidArgs.gen_dummy_particles = True
with self.assertRaises(SystemExit):
check_argument_sanity(invalidArgs)
self.assertEqual(
'Error: you requested dummy particles with the --gen_dummy_particles option, but did not specify the thickness with --dummy_grid_thickness\n',
str(self.stderr))
def test_fails_dummy_unit_conversion(self):
invalidArgs = self.validArgs
invalidArgs.gen_dummy_particles = True
invalidArgs.dummy_grid_thickness = "twenty"
with self.assertRaises(SystemExit):
check_argument_sanity(invalidArgs)
self.assertEqual(
'Error: your input of "{:s}" for dummy_grid_thickness could not be converted to a floating point number\n'
.format(invalidArgs.dummy_grid_thickness), str(self.stderr))
def test_output_error(self):
# write to a directory that doesn't exist
nonexistent_dir_path = 'nodir/output.pdb'
invalidArgs = self.validArgs
invalidArgs.o = nonexistent_dir_path
with self.assertRaises(SystemExit):
check_argument_sanity(invalidArgs)
self.assertEqual(
'I/O error while trying to write to {:s}\n'.format(invalidArgs.o),
str(self.stderr))
def test_zo_warning(self):
# first case with no zo
check_argument_sanity(self.invalidArgs)
self.assertEqual(
"WARNING : zo was not set with the -z flag. Will use a default value of 10 angstroms. This should lead to "
+
"sufficient accuracy of lipid areas for most purposes, but you should refer to the BUMPy publication to "
+
"ensure that the default value is sufficient for your simulation purposes\n",
str(self.stderr))
def test_input_permissions_error(self):
# set up a file with no read permissions
permissionless_file = "nopermissions.pdb"
open(permissionless_file, 'a').close()
os.chmod(permissionless_file, 000)
invalidArgs = self.validArgs
invalidArgs.f = permissionless_file
with self.assertRaises(SystemExit):
check_argument_sanity(invalidArgs)
os.remove(permissionless_file)
self.assertEqual(
'I/O error while trying to read from {:s}\n'.format(invalidArgs.f),
str(self.stderr))
def test_zo_too_many_values(self):
# now a zo too long
self.invalidArgs.z = "1:2:3"
with self.assertRaises(SystemExit):
check_argument_sanity(self.invalidArgs)
self.assertEqual("Too many zo values selected\n", str(self.stderr))
def test_no_g_option(self):
with self.assertRaises(SystemExit):
check_argument_sanity(self.invalidArgs)
self.assertEqual(
"Geometry field -g was not specified. Please specify geometry. For example, ./bumpy -s sphere -g r_sphere:100\n",
str(self.stderr))
def test_runs_successfully(self):
self.validArgs.gen_dummy_particles = True
self.validArgs.dummy_grid_thickness = 20
check_argument_sanity(self.validArgs)
def test_zo_multiple_negatives(self):
self.invalidArgs.z = "1:-1"
with self.assertRaises(SystemExit):
check_argument_sanity(self.invalidArgs)
self.assertEqual("zo cannot be negative\n", str(self.stderr))
def test_succeeds_with_good_parameters(self):
check_argument_sanity(self.validArgs)