def test_non_supported_organism(self):
fake_reference_folder = FakeReferenceFolder()
test_tools.mock_file_existence(
existing_files=fake_reference_folder.resources
)
with self.assertRaises(NeofoxConfigurationException):
ReferenceFolder(organism="rat")
def test_one_resource_do_not_exist(self):
fake_reference_folder = FakeReferenceFolder()
test_tools.mock_file_existence(
existing_files=fake_reference_folder.resources[
1 : len(fake_reference_folder.resources)
],
non_existing_files=[fake_reference_folder.resources[0]],
)
with self.assertRaises(NeofoxConfigurationException):
ReferenceFolder()
def setUp(self):
self.variables = {
neofox.NEOFOX_BLASTP_ENV: "/path/to/blastp",
neofox.NEOFOX_NETMHC2PAN_ENV: "/path/to/netmhc2pan",
neofox.NEOFOX_NETMHCPAN_ENV: "/path/to/netmhcpan",
neofox.NEOFOX_RSCRIPT_ENV: "/path/to/rscript",
neofox.NEOFOX_MIXMHCPRED_ENV: "/path/to/mixmhcpred",
neofox.NEOFOX_MIXMHC2PRED_ENV: "/path/to/mixmhc2pred",
neofox.NEOFOX_PRIME_ENV: "/path/to/prime",
}
self.non_existing = "/path/to/nothing"
self.non_executable = "/path/to/something/not/executable"
test_tools.mock_file_existence(
existing_files=list(self.variables.values()) + [self.non_executable],
non_existing_files=[self.non_existing],
)
test_tools.mock_file_is_executable(
executable_files=list(self.variables.values()),
non_executable_files=[self.non_executable],
)
def test_organism_human(self):
fake_reference_folder = FakeReferenceFolder()
test_tools.mock_file_existence(
existing_files=fake_reference_folder.resources
)
ReferenceFolder(organism=ORGANISM_HOMO_SAPIENS)
def test_organism_mouse(self):
fake_reference_folder = FakeReferenceFolder(organism=ORGANISM_MUS_MUSCULUS)
test_tools.mock_file_existence(
existing_files=fake_reference_folder.resources
)
ReferenceFolder(organism=ORGANISM_MUS_MUSCULUS)
def test_all_resources_exist(self):
fake_reference_folder = FakeReferenceFolder()
test_tools.mock_file_existence(
existing_files=fake_reference_folder.resources
)
ReferenceFolder()