diff --git a/micall/tests/test_sample_sheet_parser.py b/micall/tests/test_sample_sheet_parser.py index 8364aeed1..05ec438af 100644 --- a/micall/tests/test_sample_sheet_parser.py +++ b/micall/tests/test_sample_sheet_parser.py @@ -731,6 +731,44 @@ def test_extra_commas(self): self.assertEqual(ss["Experiment Name"], "10-Jul-2014") + @unittest.expectedFailure + def test_underscores_in_sample_name(self): + """ + Extracts the correct project code having multiple options. + """ + + stub_sample_sheet = """ +[Header] +IEMFileVersion,3 +Investigator Name,RL +Project Name,10-Jul-2014_v1test +Experiment Name,10-Jul-2014_v1test +Date,07/10/2014 +Workflow,GenerateFASTQ +Assay,Nextera +Description,Nextera +Chemistry,Amplicon +[Reads] +251 +251 +[Settings] +[Data] +Sample_ID,Sample_Name,Sample_Plate,Sample_Well,index,index2,Sample_Project,Description,GenomeFolder +CFE_SomeId_10-Jul-2014_N501-N701_Sample1_Proj1,Sample1_Proj1,10-Jul-2014_testing,N/A,ACGTACGT,TGCATGCA,\ +10-Jul-2014_testing,Research:Sample1_Proj1:TRUE Comments:Sample1_Proj1:thisiscommentone \ +Disablecontamcheck:Sample1_Proj1:FALSE, +CFE_SomeId_10-Jul-2014_N501-N702_Sample2_Proj2,Sample2_Proj2,10-Jul-2014_testing,N/A,AAAAGGGG,CCCCTTTT,\ +10-Jul-2014_testing,Research:Sample2_Foo_Proj2:FALSE Comments:Sample2_Foo_Proj2:thisiscommenttwo \ +Chemistry:Sample2_Foo_Proj2:BreakingBad Disablecontamcheck:Sample2_Foo_Proj2:TRUE, +""" + + ss = sample_sheet_parser(StringIO(stub_sample_sheet)) + split_rows = ss['DataSplit'] + assert len(split_rows) == 2 + assert split_rows[0]['project'] == 'Proj1' + assert split_rows[1]['project'] == 'Proj2' + + def test_read_sample_sheet_overrides(tmpdir): sample_sheet_path = Path(str(tmpdir)) / 'SampleSheet.csv' overrides_path = sample_sheet_path.parent / 'SampleSheetOverrides.csv'