def test_write_warnings_with_limit():
summary = StudySummary()
summary.unmapped_samples.extend(
((f'run{i // 10}', f'sample{i}') for i in range(50)))
expected_warnings = """\
WARNING, some samples did not map to participant ids:
run0:
sample0
sample1
sample2
sample3
sample4
sample5
sample6
sample7
sample8
sample9
run1:
sample10
sample11
[8 more samples...]
[30 more samples in 3 more runs...]
"""
report = StringIO()
summary.write_warnings(report, limit=12)
assert report.getvalue() == expected_warnings
def test_write_warnings():
summary = StudySummary()
summary.unmapped_samples.extend((('200101_M11111', 'E0003-NFLHIVDNA_S3'),
('200101_M11111', 'E0007-NFLHIVDNA_S5'),
('200108_M11111', 'E0009-NFLHIVDNA_S2')))
expected_warnings = """\
WARNING, some samples did not map to participant ids:
200101_M11111:
E0003-NFLHIVDNA_S3
E0007-NFLHIVDNA_S5
200108_M11111:
E0009-NFLHIVDNA_S2
"""
report = StringIO()
summary.write_warnings(report)
assert report.getvalue() == expected_warnings