def test_get_projects(self):
"""Test that getting the projects from a flowcell works
"""
# Assert that an empty file returns an empty list
fh, ssheet = tempfile.mkstemp(dir=self.rootdir, suffix=".csv")
os.close(fh)
self.assertListEqual([],sq.get_projects(ssheet),
"The list of projects for an empty file is not empty")
# Generate artificial samplesheet data
data = td.generate_samplesheet_data()
projects = {}
for d in data:
projects[d[-1]] = 1
# Write the data to a samplesheet
td._write_samplesheet(data,ssheet)
# Assert that the list of projects returned is the same that we generated
self.assertListEqual(sorted(projects.keys()),sorted(sq.get_projects(ssheet)),
"The list of projects does not match the original list")
# Assert that the list of projects returned is filtered as specified
self.assertListEqual([projects.keys()[-1]],sq.get_projects(ssheet,projects.keys()[-1]),
"The filtered list of projects does not match the expected")
def test_parse_samplesheet(self):
"""Write and parse a csv-file
"""
# Assert non-existing file raises exception
with self.assertRaises(IOError):
HiSeqRun.parse_samplesheet(os.path.join(self.rootdir,'non-existing-samplesheet'))
# Write a csv file with some bogus values
sdata = td.generate_samplesheet_data()
samplesheet = os.path.join(self.rootdir,'SampleSheet.csv')
HiSeqRun.write_samplesheet(sdata,samplesheet)
# Assert that the written data corresponds to the generated data
with open(samplesheet) as fh:
# Assert that header is correct
self.assertListEqual(HiSeqRun._samplesheet_header(),
fh.next().strip().split(","),
"Written header does not match expected header")
for entry in sdata:
# Assert that all rows have the correct values in the correct columns
self.assertListEqual([str(e) for e in entry],
fh.next().strip().split(","),
"Written data row does not match entry in generated samplesheet")
# Assert that all rows from samplesheet has been consumed
with self.assertRaises(StopIteration):
fh.next()
# Assert that the parsed data matches the generated data
data = HiSeqRun.parse_samplesheet(samplesheet)
self.assertEqual(len(sdata),
len(data),
"Number of parsed entries does not match number of generated entries")
for d in data:
self.assertListEqual([str(e) for e in sdata.pop(0)],
[d[col] for col in HiSeqRun._samplesheet_header()],
"Parsed data row does not match entry in generated samplesheet")
# Assert that filtering on lane returns expected output
lanes = list(set([d["Lane"] for d in data]))
obs_lane_data = HiSeqRun.parse_samplesheet(samplesheet,lane=lanes[-1])
exp_lane_data = [d for d in data if str(d["Lane"]) == str(lanes[-1])]
self.assertListEqual(sorted(obs_lane_data),
sorted(exp_lane_data),
"Parsed data row does not match entry in generated samplesheet")
def test_get_project_names(self):
"""Get the projects from a samplesheet
"""
# Assert that an empty file returns an empty list
fh, ssheet = tempfile.mkstemp(dir=self.rootdir, suffix=".csv")
os.close(fh)
self.assertListEqual([],HiSeqRun.get_project_names(ssheet),
"The list of projects for an empty file is not empty")
# Generate artificial samplesheet data
data = td.generate_samplesheet_data()
projects = {}
for d in data:
projects[d[-1]] = 1
# Write the data to a samplesheet
td._write_samplesheet(data,ssheet)
# Assert that the list of projects returned is the same that we generated
self.assertListEqual(sorted(projects.keys()),sorted(HiSeqRun.get_project_names(ssheet)),
"The list of projects does not match the original list")
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")
