def test__get_project_analysis_dir(self):
"""Test that getting the project analysis folder behaves as expected
"""
# Assert that none is returned when no folder exists
proj = td.generate_project()
self.assertIsNone(sq.get_project_analysis_dir(self.rootdir,proj),
"Did not return empty result for non-existing folders")
# Assert that none is still returned when some mismatching folders exist
for n in range(5):
os.mkdir(os.path.join(self.rootdir,td.generate_project()))
self.assertIsNone(sq.get_project_analysis_dir(self.rootdir,proj),
"Did not return empty result for mismatching folders")
# Assert that a file with the same name as the project is not returned
projdir = os.path.join(self.rootdir,proj)
utils.touch_file(projdir)
self.assertIsNone(sq.get_project_analysis_dir(self.rootdir,proj),
"Returned a file with matching name. Should only return folders")
os.unlink(projdir)
# Assert that the corrct folder is returned when it exists
os.mkdir(projdir)
self.assertEqual(projdir,sq.get_project_analysis_dir(self.rootdir,proj),
"The expected project folder was not returned")
def test__get_project_analysis_dir(self):
"""Test that getting the project analysis folder behaves as expected
"""
# Assert that none is returned when no folder exists
proj = td.generate_project()
self.assertIsNone(sq.get_project_analysis_dir(self.rootdir,proj),
"Did not return empty result for non-existing folders")
# Assert that none is still returned when some mismatching folders exist
for n in range(5):
os.mkdir(os.path.join(self.rootdir,td.generate_project()))
self.assertIsNone(sq.get_project_analysis_dir(self.rootdir,proj),
"Did not return empty result for mismatching folders")
# Assert that a file with the same name as the project is not returned
projdir = os.path.join(self.rootdir,proj)
utils.touch_file(projdir)
self.assertIsNone(sq.get_project_analysis_dir(self.rootdir,proj),
"Returned a file with matching name. Should only return folders")
os.unlink(projdir)
# Assert that the corrct folder is returned when it exists
os.mkdir(projdir)
self.assertEqual(projdir,sq.get_project_analysis_dir(self.rootdir,proj),
"The expected project folder was not returned")
def test_get_project_samples(self):
"""Test that getting the project samples from a samplesheet behaves as expected
"""
# Generate artificial samplesheet data
data = td.generate_samplesheet_data()
fh, ssheet = tempfile.mkstemp(dir=self.rootdir, suffix=".csv")
os.close(fh)
td._write_samplesheet(data,ssheet)
# Assert that getting samples for a non-existing project returns an empty list
self.assertListEqual([],sq.get_project_samples(ssheet,td.generate_project()),
"Getting samples for a non-existing project returned unexpected output")
# Iterate over the projects and assert that the returned samples are correct
samples = {}
for row in data:
if row[9] not in samples:
samples[row[9]] = []
samples[row[9]].append(row[2])
for proj, sample in samples.items():
self.assertListEqual(sorted(sample),sorted(sq.get_project_samples(ssheet,proj)),
"The returned list of samples did not match the original")
