class TestRunfolderRepository(unittest.TestCase):
expected_runfolders = FAKE_RUNFOLDERS
file_system_service = mock_file_system_service(fake_directories,
fake_projects)
repo = FileSystemBasedRunfolderRepository(
base_path="/foo", file_system_service=file_system_service)
def test_get_runfolders(self):
actual_runfolders = list(self.repo.get_runfolders())
self.assertListEqual(self.expected_runfolders, actual_runfolders)
for actual_runfolder in actual_runfolders:
for expected_runfolder in self.expected_runfolders:
if actual_runfolder == expected_runfolder:
self.assertListEqual(actual_runfolder.projects,
expected_runfolder.projects)
def test_get_runfolders_does_not_return_none_runfolder(self):
# Adding a directory which does not conform to the runfolder pattern
with_non_runfolder_dir = fake_directories + ["bar"]
file_system_service = mock_file_system_service(with_non_runfolder_dir,
fake_projects)
repo = FileSystemBasedRunfolderRepository(
base_path="/foo", file_system_service=file_system_service)
actual_runfolders = list(repo.get_runfolders())
self.assertListEqual(self.expected_runfolders, actual_runfolders)
def test_get_runfolder(self):
runfolder_name = "160930_ST-E00216_0111_BH37CWALXX"
actual_runfolder = self.repo.get_runfolder(runfolder_name)
self.assertIsInstance(actual_runfolder, Runfolder)
self.assertEqual(actual_runfolder.name, runfolder_name)
def test_get_runfolders_does_not_return_none_runfolder(self):
# Adding a directory which does not conform to the runfolder pattern
with_non_runfolder_dir = fake_directories + ["bar"]
file_system_service = mock_file_system_service(with_non_runfolder_dir,
fake_projects)
repo = FileSystemBasedRunfolderRepository(base_path="/foo",
file_system_service=file_system_service)
actual_runfolders = list(repo.get_runfolders())
self.assertListEqual(self.expected_runfolders, actual_runfolders)
def setUp(self):
self.runfolder = test_utils.UNORGANISED_RUNFOLDER
self.project = self.runfolder.projects[0]
self.fastq_files = [
sample_file.file_path for sample in self.project.samples
for sample_file in sample.sample_files
]
self.runfolder.checksums = {
os.path.relpath(sample_file.file_path,
os.path.dirname(self.runfolder.path)):
sample_file.checksum
for sample in self.project.samples
for sample_file in sample.sample_files
}
self.file_system_service = test_utils.mock_file_system_service(
[], [], fastq_files=self.fastq_files)
self.sample_repo = RunfolderProjectBasedSampleRepository(
file_system_service=self.file_system_service)