def test_sample_prep__number_rows_and_columns_are_ok(self):
# Arrange
file = self._create_organization_file(prep_sample_submission_path())
handler = SampleSubmissionHandler(context=self.handler_context, app=self.app)
# Act
handler.handle(multi_format_file=file)
# Assert
rows = [line for line in handler.csv]
assert 3 == len(rows)
assert 28 == len(handler.csv.header)
def test_parse_prep_from_excel__internal_temp_file_is_deleted(self):
# Arrange
handler_context = HandlerContext(self.organization)
handler = SampleSubmissionHandler(handler_context, self.app)
org_file = self._create_organization_file(
prep_sample_submission_path())
# Act
handler.handle(org_file)
# Assert
assert os.path.exists(handler.temp_file_name) is False
def test_prep_submission__with_3_samples_on_plate__plate_navigation_to_sample_ok(self):
# Arrange
contents = read_binary_file(prep_sample_submission_path())
fileobj = BytesIO(contents)
# Act
plugins.load_handler_implementation(SubstancesSubmissionHandler, SampleSubmissionHandler)
self.app.substances.load_file(self.organization, "the_file.xlsx", fileobj)
# Assert
containers = ContainerRepository(self.organization)
plate1 = containers.get(name='YY-1111_PL1_org_190829')
assert plate1 is not None
assert plate1['A:1'].name == 'sample1'
def test_prep_submission__with_3_samples_on_plate__sample_navigation_to_plate_is_ok(self):
# Arrange
contents = read_binary_file(prep_sample_submission_path())
fileobj = BytesIO(contents)
# Act
plugins.load_handler_implementation(SubstancesSubmissionHandler, SampleSubmissionHandler)
self.app.substances.load_file(self.organization, "the_file.xlsx", fileobj)
# Assert
fetched_sample1 = ioc.app.substances.get_by_name('sample1')
from clims.models.location import Location
from clims.models.container import Container
assert isinstance(fetched_sample1.location, Location)
assert isinstance(fetched_sample1.location.container, Container)
assert isinstance(fetched_sample1.container, Plate96)
def test_sample_prep__all_sample_udf_good(self):
# Arrange
contents = read_binary_file(prep_sample_submission_path())
file_obj = BytesIO(contents)
# Act
plugins.load_handler_implementation(SubstancesSubmissionHandler,
SampleSubmissionHandler)
self.app.substances.load_file(self.organization, "the_file.xlsx",
file_obj)
# Assert
fetched_sample1 = ioc.app.substances.get_by_name('YY-1111-sample1')
assert fetched_sample1.concentration == 101
assert fetched_sample1.external_name == 'sample1'
assert fetched_sample1.volume == 30
assert fetched_sample1.sample_type == 'gDNA'
assert fetched_sample1.coverage == '60x'
assert fetched_sample1.volume_current == 30
assert fetched_sample1.sample_delivery_date == '190829'
assert fetched_sample1.container == 'YY-1111_PL1_org_190829'
assert fetched_sample1.application == 'WG re-seq'
assert fetched_sample1.species == 'Bos taurus'
assert fetched_sample1.library_preparation_kit == 'TruSeq DNA PCR-Free Sample Preparation kit LT'
assert fetched_sample1.libraries_per_sample == 1
assert fetched_sample1.insert_size == '350'
assert fetched_sample1.pooling == '10 libraries/pool'
assert fetched_sample1.special_info_library_prep is False
assert fetched_sample1.number_of_lanes == '2 flowcells/pool'
assert fetched_sample1.seq_instrument == 'NovaSeq S4'
assert fetched_sample1.read_length == '151x2'
assert fetched_sample1.conc_flowcell_pm == '300 pM'
assert fetched_sample1.phix_percent == 1
assert fetched_sample1.custom_seq_primer is False
assert fetched_sample1.special_info_sequencing is False
assert fetched_sample1.genotyping_id_panel is False
assert fetched_sample1.data_analysis == 'No'
def test_read_sample_submission_and_save_in_write_only_mode(self):
excel_rw = ExcelReadWriter()
excel_rw.load(prep_sample_submission_path())
excel_rw.write_to_new_file(new_excel_file_path())
def test_write_sample_submission_in_dual_mode__check_output_manually(self):
excel_rw = ExcelReadWriter()
excel_rw.load(prep_sample_submission_path(),
data_only=False,
read_only=False)
excel_rw.write_with_dual_mode(new_excel_file_path())