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