def _create_organization_file(self, file_path):
name = os.path.basename(file_path)
file_model = File.objects.create(
name=name,
type='substance-batch-file',
headers=list(),
)
contents = read_binary_file(file_path)
file_like_obj = BytesIO(contents)
file_model.putfile(file_like_obj)
return OrganizationFile(name=name, organization=self.organization, file=file_model)
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'