def test_ready_made_libraries__all_udf_good(self):
# Arrange
parser = CsvParser(
handler_type='rml', project_code='XX-1111', path=rml_sample_submission_path_csv())
ReplaceWith.contents_bag = ContentsBag(
handler_type=parser.handler_type, project_code=parser.project_code, sample_list=parser.csv)
# Act
plugins.load_handler_implementation(SubstancesSubmissionHandler, SampleSubmissionHandler)
self.app.substances.load_file(self.organization, "the_file.xlsx", fake_file_obj)
# Assert
fetched_rml2 = ioc.app.substances.get_by_name('XX-1111-rml2')
assert fetched_rml2.external_name == 'rml2'
assert fetched_rml2.concentration == 2
assert fetched_rml2.volume == 30
assert fetched_rml2.sample_type == 'Ready-made library'
assert fetched_rml2.application == 'Ready-made library'
assert fetched_rml2.index_category is None
assert fetched_rml2.index_number == '64-160'
assert fetched_rml2.custom_index == 'GTCCGGC-AACCGAT'
assert fetched_rml2.sample_index == 'Custom (GTCCGGC-AACCGAT)'
assert fetched_rml2.volume_current == 30
assert fetched_rml2.sample_delivery_date == '190529'
assert fetched_rml2.container == 'XX-1111_PL1_org_190529'
assert fetched_rml2.species == 'Vulpes lagopus'
assert fetched_rml2.seq_instrument == 'HiSeqX'
assert fetched_rml2.read_length == '151x2'
assert fetched_rml2.number_of_lanes == '2 lanes/pool'
assert fetched_rml2.conc_flowcell_pm == 'To be decided after QC'
assert fetched_rml2.phix_percent == 1
assert fetched_rml2.custom_seq_primer is False
assert fetched_rml2.special_info_sequencing is False
assert fetched_rml2.rml_kit_protocol == 'Meyer&Kircher 2010'
def setUp(self):
self.register_extensible(PrepSample)
self.register_extensible(RmlSample)
self.register_extensible(Pool)
self.register_extensible(Plate96)
plugins.load_handler_implementation(SubstancesSubmissionHandler,
SampleSubmissionHandler)
logger = logging.getLogger('clims.files')
logger.setLevel(logging.CRITICAL)
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_rml_submission__with_three_samples_on_same_plate__one_plate_created(self):
# Arrange
parser = CsvParser(
handler_type='rml', project_code='XX-1111', path=rml_sample_submission_path_csv())
ReplaceWith.contents_bag = ContentsBag(
handler_type=parser.handler_type, project_code=parser.project_code, sample_list=parser.csv)
# Act
plugins.load_handler_implementation(SubstancesSubmissionHandler, SampleSubmissionHandler)
self.app.substances.load_file(self.organization, "the_file.xlsx", fake_file_obj)
# Assert
containers = ContainerRepository(self.organization)
fetched_plate = containers.get(name='XX-1111_PL1_org_190529')
assert fetched_plate is not None
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_rml_submission__with_three_samples__one_pool_created(self):
# Arrange
parser = CsvParser(
handler_type='rml', project_code='XX-1111', path=rml_sample_submission_path_csv())
ReplaceWith.contents_bag = ContentsBag(
handler_type=parser.handler_type, project_code=parser.project_code, sample_list=parser.csv)
# Act
plugins.load_handler_implementation(SubstancesSubmissionHandler, SampleSubmissionHandler)
self.app.substances.load_file(self.organization, "the_file.xlsx", fake_file_obj)
# Assert
pool = ioc.app.substances.get_by_name('XX-1111-Pool1')
assert pool is not None
assert pool.volume == 30
assert pool.concentration == 0.63
assert len(pool.parents) == 4
def test_sample_prep__all_udf_good(self):
# Arrange
parser = CsvParser(
handler_type='prep', project_code='YY-1111', path=prep_sample_submission_path_csv())
ReplaceWith.contents_bag = ContentsBag(
handler_type=parser.handler_type, project_code=parser.project_code, sample_list=parser.csv)
# Act
plugins.load_handler_implementation(SubstancesSubmissionHandler, SampleSubmissionHandler)
self.app.substances.load_file(self.organization, "the_file.xlsx", fake_file_obj)
# Assert
samples = ioc.app.substances
fetched_sample1 = samples.get(name='YY-1111-sample1')
fetched_sample2 = samples.get(name='YY-1111-sample2')
fetched_sample3 = samples.get(name='YY-1111-sample3')
assert fetched_sample2.number_of_lanes == '1 lane/pool'
assert fetched_sample3.number_of_lanes == '1 lane/pool'
assert fetched_sample1.name == 'YY-1111-sample1'
assert fetched_sample1.external_name == 'sample1'
assert fetched_sample1.concentration == 101
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.number_of_lanes == '2 flowcells/pool'
assert fetched_sample1.special_info_library_prep is False
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_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_sample_prep__with_use_of_load_file__3_concentration_values_ok(self):
# Arrange
parser = CsvParser(
handler_type='prep', project_code='YY-1111', path=prep_sample_submission_path_csv())
ReplaceWith.contents_bag = ContentsBag(
handler_type=parser.handler_type, project_code=parser.project_code, sample_list=parser.csv)
# Act
plugins.load_handler_implementation(SubstancesSubmissionHandler, SampleSubmissionHandler)
self.app.substances.load_file(self.organization, "the_file.xlsx", fake_file_obj)
# Assert
expected = {
'YY-1111-sample1': 101,
'YY-1111-sample2': 10,
'YY-1111-sample3': 10,
}
all_samples = ioc.app.substances.filter()
conc_dict = dict()
for sample in all_samples:
conc_dict[sample.name] = sample.concentration
assert expected == conc_dict