def test_incomplete_delete(self):
"""Tests that when the --complete option is not specified, only the chemical name specified is removed from \
the library (and not its nicknames)."""
temp_file = NamedTemporaryFile("w+")
test_salt_and_pepper = chemical.Chemical(200, ["salt", "pepper"])
test_kcl = chemical.Chemical(123.4, ["KCl"])
test_pepper = chemical.Chemical(200, ["pepper"])
initial_library = {
"salt": test_salt_and_pepper,
"pepper": test_salt_and_pepper,
"KCl": test_kcl
}
after_delete = {"KCl": test_kcl, "pepper": test_pepper}
with mock.patch("buf.commands.chemical.chemical_library_file",
temp_file.name):
chemical.save_chemical_library(initial_library)
chemical.delete_chemical("salt",
complete_deletion=False,
prompt_for_confirmation=False)
self.assertEqual(after_delete, chemical.load_chemicals())
def test_correct_read(self):
"""Tests that the function correctly parses a file into a dictionary."""
one_chemical = chemical.Chemical(123.4, ["name1", "name2"])
other_chemical = chemical.Chemical(567.8, ["name3", "name4"])
chemical_dict = {
"name1": one_chemical,
"name2": one_chemical,
"name3": other_chemical,
"name4": other_chemical
}
with mock.patch("buf.commands.chemical.open") as mock_open:
mock_open.return_value.__enter__.return_value = StringIO(
str(one_chemical) + "\n" + str(other_chemical))
returned_dict = chemical.load_chemicals()
self.assertEqual(chemical_dict, returned_dict)
def test_spaces_in_name(self):
"""Tests that the function does not allow spaces to be in a chemical name."""
with mock.patch(
"buf.commands.chemical.error_messages.spaces_in_chemical_name",
side_effect=SystemExit) as mock_error:
nacl_chemical = chemical.Chemical(58.44, ["NaCl"])
with mock.patch("buf.commands.chemical.load_chemicals",
return_value={"NaCl": nacl_chemical}):
with self.assertRaises(SystemExit):
chemical.nickname_chemical("NaCl", ["new name"])
mock_error.assert_called_with("new name")
def test_step_making(self):
"""Test that the class properly converts a Recipe into a series of Steps."""
nacl = chemical.Chemical(58.44, ["NaCl"])
kcl = chemical.Chemical(74.55, ["KCl"])
test_recipe = recipe.Recipe("my_recipe", ["300mM", "4g"],
["NaCl", "KCl"])
with mock.patch("buf.commands.make.chemical.load_chemicals",
return_value={
"NaCl": nacl,
"KCl": kcl
}):
test_buffer_instructions = make.BufferInstructions(2, test_recipe)
correct_steps = [
make.Step(
"NaCl", "300mM",
unit.scale_and_round_physical_quantity(
58.44 * 0.3 * 2, "g")),
make.Step("KCl", "4g", "4.0g")
]
self.assertEqual(test_buffer_instructions.steps, correct_steps)
def test_molarity_units(self):
"""Tests that when a concentration in molar is passed into the function, it returns the chemicals molar mass \
* concentration in molar * buffer volume in litres, scaled and rounded properly."""
inputs = [i for i in range(1, 100)]
nacl = chemical.Chemical(58.44, ["NaCl"])
chemical_library = {"NaCl": nacl}
for buffer_volume in range(1, 10):
for input in inputs:
self.assertEqual(
unit.scale_and_round_physical_quantity(
58.44 * buffer_volume * input, "g"),
make.calculate_amount_to_add(buffer_volume,
str(input) + "M", "NaCl",
chemical_library))
def test_equals(self):
"""Tests that two chemicals with the same molar masses and names are said to be equal."""
one_chemical = chemical.Chemical(123.4, ["name1", "name2"])
other_chemical = chemical.Chemical(123.4, ["name1", "name2"])
self.assertEqual(one_chemical, other_chemical)
def test_string_cast(self):
"""Tests casting a Chemical object to a string."""
test_chemical = chemical.Chemical(300, ["salt", "pepper"])
self.assertTrue(str(test_chemical), "300 salt pepper")