def test_dispatch_done(self):
with TempDirectory() as input_dir, TempDirectory() as output_dir:
mock_module.my_exception_string = ""
jacquard._dispatch([mock_module], ["mock_module",
input_dir.path,
output_dir.path])
actual_messages = self.output.getvalue().rstrip().split("\n")
self.assertRegexpMatches(actual_messages[-1], "Done")
def test_dispatch(self):
with TempDirectory() as input_dir, TempDirectory() as output_dir:
mock_module.my_exception_string = ""
jacquard._dispatch([mock_module], ["mock_module",
input_dir.path,
output_dir.path])
self.assertTrue(mock_module.execute_called)
self.assertTrue(mock_module.report_called)
self.assertTrue(MOCK_MOVE_TEMP_CONTENTS_CALLED)
def test_dispatch(self):
with TempDirectory() as input_dir, TempDirectory() as output_dir:
mock_module.my_exception_string = ""
jacquard._dispatch([mock_module], ["mock_module",
input_dir.path,
output_dir.path])
self.assertTrue(mock_module.execute_called)
self.assertTrue(mock_module.report_called)
self.assertTrue(MOCK_MOVE_TEMP_CONTENTS_CALLED)
def test_dispatch_doneWithWarnings(self):
with TempDirectory() as input_dir, TempDirectory() as output_dir:
mock_module.my_exception_string = ""
logger.WARNING_OCCURRED = True
jacquard._dispatch([mock_module], ["mock_module",
input_dir.path,
output_dir.path])
actual_messages = self.output.getvalue().rstrip().split("\n")
self.assertRegexpMatches(actual_messages[-1], r"Done. \(See warnings above\)")
logger.WARNING_OCCURRED = False
def test_dispatch_unknownCommand(self):
with TempDirectory() as input_dir, TempDirectory() as output_dir:
mock_module.my_exception_string = ""
with self.assertRaises(SystemExit) as exit_code:
jacquard._dispatch([mock_module], ["foo_command",
input_dir.path,
output_dir.path])
self.assertEquals(1, exit_code.exception.code)
self.assertRegexpMatches(self.output.getvalue(),
r"'foo_command' is not a Jacquard command; choose from 'mock_module'")
def test_dispatch_forceNonEmptyOutputDir(self):
with TempDirectory() as input_dir, TempDirectory() as output_dir:
output_dir.write("file1.vcf", b"foo")
mock_module.my_exception_string = ""
jacquard._dispatch([mock_module], ["mock_module",
input_dir.path,
output_dir.path,
"--force"])
self.assertTrue(1 == 1, "Force does not result in premature exit.")
def test_dispatch_nonEmptyOutputDir(self):
with TempDirectory() as input_dir, TempDirectory() as output_dir:
output_dir.write("file1.vcf", b"foo")
output_file = os.path.join(output_dir.path, "file1.vcf")
mock_module.my_exception_string = ""
mock_module.predicted_output = set(["file1.vcf"])
with self.assertRaises(SystemExit) as exit_code:
jacquard._dispatch([mock_module], ["mock_module",
input_dir.path,
output_file])
self.assertEqual(1, exit_code.exception.code)
def test_gracefulErrorMessageWhenUnanticipatedProblem(self):
with TempDirectory() as input_dir, TempDirectory() as output_dir:
mock_module.my_exception_string = "I'm feeling angry"
with self.assertRaises(SystemExit) as exit_code:
jacquard._dispatch([mock_module], ["mock_module",
input_dir.path,
output_dir.path])
self.assertEqual(1, exit_code.exception.code)
actual_messages = self.output.getvalue().rstrip().split("\n")
self.assertEquals(2, len(actual_messages))
self.assertRegexpMatches(actual_messages[0], "I'm feeling angry")
self.assertRegexpMatches(actual_messages[1], "Jacquard encountered an unanticipated problem.")
def assertCommand(self, command, expected_output_path):
jacquard._dispatch(jacquard._SUBCOMMANDS, command)
actual_output_path = command[2]
try:
if os.path.isfile(actual_output_path):
self._compare_files(actual_output_path, expected_output_path)
elif os.path.isdir(actual_output_path):
for output_filename in os.listdir(actual_output_path):
actual_output_file = os.path.join(actual_output_path,
output_filename)
expected_output_file = os.path.join(expected_output_path,
output_filename)
self._compare_files(actual_output_file,
expected_output_file)
except self.failureException as e:
msg = "discrepancy in command [{}]: {}".format(" ".join(command), e)
raise self.failureException(msg)