class TestImportLibraryPrepSamples(unittest.TestCase):
def setUp(self):
here = os.path.dirname(__file__)
file_name = r'BLA-32605-v.4.0_Samples_for_library_preparation_SampleForm_test till validering.xlsx'
file_path = os.path.join(here, file_name)
sample_column_index = 4
volume_column_index = 6
sample_column_name = 'SAMPLE ID'
here = os.path.dirname(__file__)
export_file_path = os.path.join(here, 'newfile.xlsx')
self.excel_reader = ImportSampleSubmission(file_path,
sample_column_index,
volume_column_index,
sample_column_name,
export_file_path)
def test_get_caption_row(self):
row_index = self.excel_reader._determine_caption_row_index()
self.assertEqual(3, row_index)
def test_list_all_samples_under_library_id_columns__entries_found(self):
samples = self.excel_reader._samples
self.assertEqual(11, len(samples))
self.assertEqual('SE-402', samples[0])
def test_validate(self):
error_messages = self.excel_reader.check_faulty_contents()
self.assertEqual(9, len(error_messages))
def setUp(self):
here = os.path.dirname(__file__)
file_name = r'BLA-32605-v.4.0_Samples_for_library_preparation_SampleForm_test till validering.xlsx'
file_path = os.path.join(here, file_name)
sample_column_index = 4
volume_column_index = 6
sample_column_name = 'SAMPLE ID'
here = os.path.dirname(__file__)
export_file_path = os.path.join(here, 'newfile.xlsx')
self.excel_reader = ImportSampleSubmission(file_path,
sample_column_index,
volume_column_index,
sample_column_name,
export_file_path)
def setUp(self):
here = os.path.dirname(__file__)
file_name = r'BLA-32606-v.5.0_Ready-made-libraries_SampleForm.xlsx'
file_path = os.path.join(here, file_name)
sample_column_index = 3
volume_column_index = 7
sample_column_name = 'LIBRARY ID'
here = os.path.dirname(__file__)
export_file_path = os.path.join(here, 'newfile.xlsx')
self.excel_reader = ImportSampleSubmission(file_path,
sample_column_index,
volume_column_index,
sample_column_name,
export_file_path)
class TestImportReadyMadeLibraries(unittest.TestCase):
def setUp(self):
here = os.path.dirname(__file__)
file_name = r'BLA-32606-v.5.0_Ready-made-libraries_SampleForm.xlsx'
file_path = os.path.join(here, file_name)
sample_column_index = 3
volume_column_index = 7
sample_column_name = 'LIBRARY ID'
here = os.path.dirname(__file__)
export_file_path = os.path.join(here, 'newfile.xlsx')
self.excel_reader = ImportSampleSubmission(file_path,
sample_column_index,
volume_column_index,
sample_column_name,
export_file_path)
def test_get_caption_row(self):
row_index = self.excel_reader._determine_caption_row_index()
self.assertEqual(5, row_index)
def test_list_all_samples_under_library_id_columns__three_entries_found(
self):
samples = self.excel_reader._samples
self.assertEqual(3, len(samples))
self.assertEqual('edvardsample', samples[0])
def test_read_empty_volume_value__parsed_value_is_magic_str(self):
contents = self.excel_reader.contents
empty_volume = contents[1][1]
self.assertEqual('None', empty_volume)
def test_read_numeric_volume__parsed_value_is_str(self):
contents = self.excel_reader.contents
numeric_volume = contents[0][1]
self.assertEqual('29', numeric_volume)
def validate(sample_column_index, volume_column_index, sample_column_name,
file_path):
logger = DefaultLogger()
import_excel = ImportSampleSubmission(
file_path, sample_column_index, volume_column_index,
sample_column_name, logger=logger)
error_messages = import_excel.check_faulty_contents()
if len(error_messages) > 0:
cache = PrintCache()
cache.print('These rows were faulty:')
for smp in error_messages:
cache.print(smp)
cache.copy_to_clipboard()
else:
print('No errors detected!')
if not import_excel.save_workbook():
print('Excel formatting cannot be updated because the file is already open. '
'Please close the file if you want excel formatting enabled!')
class TestImportReadyMadeLibraries(unittest.TestCase):
def setUp(self):
here = os.path.dirname(__file__)
file_name = r'BLA-32606-v.5.0_Ready-made-libraries_SampleForm.xlsx'
file_path = os.path.join(here, file_name)
export_path = os.path.join(here, 'newfile.xlsx')
self.export_path = export_path
sample_column_index = 3
volume_column_index = 7
sample_column_name = 'LIBRARY ID'
self.excel_reader = ImportSampleSubmission(
file_path,
sample_column_index,
volume_column_index,
sample_column_name,
export_to_file_path=export_path)
def test_export(self):
self.excel_reader.check_faulty_contents()
print('NewFile.xlsx is updated to: \n{}'.format(self.export_path))
self.assertEqual(1, 2)
@skip('')
def test_row_cols(self):
number_rows = self.excel_reader.number_rows()
number_cols = self.excel_reader.number_cols()
print('rows: {}, cols: {}'.format(number_rows, number_cols))
self.assertEqual(1, 2)
@skip('')
def test_print_sample_col(self):
self.excel_reader.print_sample_column()
self.assertEqual(1, 2)