def test_unreadable_directory(self):
"""
Given an invalid directory (chmod 000), ensure the correct error is thown
:return:
"""
directory = path.join(path_to_module, "inaccessible_dir")
with self.assertRaises(DirectoryError) as context:
Parser.get_sample_sheet(directory)
self.assertEqual(context.exception.directory, directory)
def test_no_sheet_in_directory(self):
"""
Given an invalid directory, ensure an error is thrown
:return:
"""
directory = path.join(path_to_module, "three_dirs", "third")
with self.assertRaises(DirectoryError) as context:
Parser.get_sample_sheet(directory)
self.assertEqual(context.exception.directory, directory)
def test_parse_samples_valid(self):
"""
Verify samples created from parser match expected samples
:return:
"""
sheet_file = path.join(path_to_module, "fake_dir_data",
"SampleList.csv")
sample1 = model.Sample(
"my-sample-1",
"",
)
sample2 = model.Sample(
"my-sample-2",
"",
)
sample3 = model.Sample(
"my-sample-3",
"",
)
res = Parser().get_sequencing_run(sheet_file)
self.assertEqual(res.metadata, {'layoutType': 'PAIRED_END'})
self.assertEqual(res.project_list[0].id, "75")
self.assertEqual(res.project_list[1].id, "76")
self.assertEqual(res.project_list[0].sample_list[0].sample_name,
sample1.sample_name)
self.assertEqual(res.project_list[0].sample_list[1].sample_name,
sample2.sample_name)
self.assertEqual(res.project_list[1].sample_list[0].sample_name,
sample3.sample_name)
def test_build_valid_extra_line_on_sample_list(self):
"""
Ensure a valid SequencingRun is made when extra lines are present in sample list
:return:
"""
sheet_file = path.join(path_to_module, "fake_dir_data",
"SampleList_with_space.csv")
sequencing_run = Parser().get_sequencing_run(sheet_file)
# Returns a SequencingRun
self.assertEqual(type(sequencing_run), model.SequencingRun)
# Includes 2 projects
self.assertEqual(len(sequencing_run.project_list), 2)
# is of type Project
self.assertEqual(type(sequencing_run.project_list[0]), model.Project)
# Project has 2 samples
self.assertEqual(len(sequencing_run.project_list[0].sample_list), 2)
# Other Project has 1 sample
self.assertEqual(len(sequencing_run.project_list[1].sample_list), 1)
# samples are of type Sample
self.assertEqual(type(sequencing_run.project_list[0].sample_list[0]),
model.Sample)
# samples have SequenceFile
self.assertEqual(
type(sequencing_run.project_list[0].sample_list[0].sequence_file),
model.SequenceFile)
def test_build_valid(self):
"""
When given a valid directory, ensure a valid SequencingRun is built with Projects, Samples, ect
:return:
"""
sheet_file = path.join(path_to_module, "fake_dir_data",
"SampleList.csv")
sequencing_run = Parser().get_sequencing_run(sheet_file)
# Returns a SequencingRun
self.assertEqual(type(sequencing_run), model.SequencingRun)
# Includes 2 projects
self.assertEqual(len(sequencing_run.project_list), 2)
# is of type Project
self.assertEqual(type(sequencing_run.project_list[0]), model.Project)
# Project has 2 samples
self.assertEqual(len(sequencing_run.project_list[0].sample_list), 2)
# Other Project has 1 sample
self.assertEqual(len(sequencing_run.project_list[1].sample_list), 1)
# samples are of type Sample
self.assertEqual(type(sequencing_run.project_list[0].sample_list[0]),
model.Sample)
# samples have SequenceFile
self.assertEqual(
type(sequencing_run.project_list[0].sample_list[0].sequence_file),
model.SequenceFile)
def test_invalid_sample_sheets(self):
"""
Given an invalid sample sheet, ensure the correct errors are included in the validation result
:return:
"""
sample_sheet = path.join(path_to_module, "invalid_sample_sheet",
"SampleList.csv")
with self.assertRaises(ValidationError) as context:
Parser.get_sequencing_run(sample_sheet)
validation_result = context.exception.validation_result
self.assertEqual(type(validation_result), model.ValidationResult)
for error in validation_result.error_list:
self.assertEqual(type(error), SampleSheetError)
def test_find_none(self):
"""
Given a directory with no run directories in it, return a empty list
:return:
"""
directory = path.join(path_to_module, "no_dirs")
res = Parser().find_runs(directory)
self.assertEqual(res, [])
def test_valid_run(self):
"""
Given a valid sample sheet, ensure a sequencing run is created
:return:
"""
sample_sheet = path.join(path_to_module, "fake_dir_data",
"SampleList.csv")
res = Parser().get_sequencing_run(sample_sheet)
self.assertEqual(type(res), model.SequencingRun)
def test_valid_directory(self):
"""
test the file path of a valid sequencing run is gotten correctly
:return:
"""
directory = path.join(path_to_module, "three_dirs", "first")
file_path = path.join(directory, "SampleList.csv")
res = Parser().get_sample_sheet(directory)
self.assertEqual(res, file_path)
def test_find_dir(self):
"""
Given a valid run directory, show as new
:return:
"""
directory = path.join(path_to_module, "three_dirs", "first")
res = Parser().find_single_run(directory)
self.assertEqual(type(res), model.DirectoryStatus)
self.assertEqual(res.status, "new")
self.assertEqual(res.directory, directory)
def test_find_none(self):
"""
Given a directory with nothing in it, show as invalid
:return:
"""
directory = path.join(path_to_module, "no_dirs")
res = Parser().find_single_run(directory)
self.assertEqual(type(res), model.DirectoryStatus)
self.assertEqual(res.status, "invalid")
self.assertEqual(res.directory, directory)
def test_find_in_dir_with_three_dirs(self):
"""
Given a directory with directories in it (but no actual run at highest level), show as invalid
:return:
"""
directory = path.join(path_to_module, "three_dirs")
res = Parser().find_single_run(directory)
self.assertEqual(type(res), model.DirectoryStatus)
self.assertEqual(res.status, "invalid")
self.assertEqual(res.directory, directory)
def test_find_one_of_three(self):
"""
Given a directory with 3 potential run directories in it, determine which are new and invalid
:return:
"""
directory = path.join(path_to_module, "three_dirs")
dir_1 = path.join(directory, "first")
dir_2 = path.join(directory, "second")
dir_3 = path.join(directory, "third")
correct_dirs = [dir_1, dir_2, dir_3]
res = Parser().find_runs(directory)
self.assertIn(res[0].directory, correct_dirs)
self.assertIn(res[1].directory, correct_dirs)
self.assertIn(res[2].directory, correct_dirs)
for c_dir in res:
if c_dir.directory == dir_1:
self.assertEqual(c_dir.status, "new")
elif c_dir.directory == dir_2:
self.assertEqual(c_dir.status, "invalid")
elif c_dir.directory == dir_3:
self.assertEqual(c_dir.status, "invalid")