def test_to_lims_mip(mip_order_to_submit):
# GIVEN a scout order for a trio
order_data = OrderIn.parse_obj(obj=mip_order_to_submit,
project=OrderType.MIP_DNA)
# WHEN parsing the order to format for LIMS import
samples: List[LimsSample] = build_lims_sample(customer="cust003",
samples=order_data.samples)
# THEN it should list all samples
assert len(samples) == 4
# THEN container should be 96 well plate for all samples
assert {sample.container for sample in samples} == {"96 well plate"}
# THEN container names should be the same for all samples
container_names = {
sample.container_name
for sample in samples if sample.container_name
}
assert container_names == {"CMMS"}
# ... and pick out relevant UDFs
first_sample: LimsSample = samples[0]
assert first_sample.well_position == "A:1"
assert first_sample.udfs.family_name == "family1"
assert first_sample.udfs.priority == "standard"
assert first_sample.udfs.application == "WGSPCFC030"
assert first_sample.udfs.source == "tissue (fresh frozen)"
assert first_sample.udfs.quantity == "220"
assert first_sample.udfs.customer == "cust003"
assert first_sample.udfs.volume == "1"
# THEN assert that the comment of a sample is a string
assert isinstance(samples[1].udfs.comment, str)
def test_to_lims_sarscov2(sarscov2_order_to_submit):
# GIVEN a sarscov2 order for samples
order_data = OrderIn.parse_obj(obj=sarscov2_order_to_submit,
project=OrderType.SARS_COV_2)
# WHEN parsing for LIMS
samples: List[LimsSample] = build_lims_sample(customer="cust000",
samples=order_data.samples)
# THEN it should have found the same number of samples
assert len(samples) == 5
# ... and pick out relevant UDFs
first_sample = samples[0].dict()
assert first_sample["udfs"]["collection_date"] == "2021-05-05"
assert first_sample["udfs"]["extraction_method"] == "MagNaPure 96"
assert first_sample["udfs"]["lab_code"] == "SE110 Växjö"
assert first_sample["udfs"]["organism"] == "SARS CoV-2"
assert first_sample["udfs"][
"original_lab"] == "Karolinska University Hospital Solna"
assert first_sample["udfs"]["original_lab_address"] == "171 76 Stockholm"
assert first_sample["udfs"]["pre_processing_method"] == "COVIDSeq"
assert first_sample["udfs"]["priority"] == "research"
assert first_sample["udfs"]["reference_genome"] == "NC_111"
assert first_sample["udfs"]["region"] == "Stockholm"
assert first_sample["udfs"]["region_code"] == "01"
assert first_sample["udfs"][
"selection_criteria"] == "1. Allmän övervakning"
assert first_sample["udfs"]["volume"] == "1"
def test_to_lims_fastq(fastq_order_to_submit):
# GIVEN a fastq order for two samples; normal vs. tumour
order_data = OrderIn.parse_obj(obj=fastq_order_to_submit,
project=OrderType.FASTQ)
# WHEN parsing the order to format for LIMS
samples: List[LimsSample] = build_lims_sample(customer="dummyCust",
samples=order_data.samples)
# THEN should "work"
assert len(samples) == 2
normal_sample = samples[0]
tumor_sample = samples[1]
# ... and pick out relevant UDF values
assert normal_sample.udfs.tumour is False
assert tumor_sample.udfs.tumour is True
assert normal_sample.udfs.volume == "1"
def test_to_lims_rml(rml_order_to_submit):
# GIVEN a rml order for four samples
order_data = OrderIn.parse_obj(obj=rml_order_to_submit,
project=OrderType.RML)
# WHEN parsing for LIMS
samples: List[LimsSample] = build_lims_sample(customer="dummyCust",
samples=order_data.samples)
# THEN it should have found the same number of samples
assert len(samples) == 4
# ... and pick out relevant UDFs
first_sample = samples[0]
assert first_sample.udfs.pool == "pool-1"
assert first_sample.udfs.volume == "30"
assert first_sample.udfs.concentration == "5.0"
assert first_sample.udfs.index == "IDT DupSeq 10 bp Set B"
assert first_sample.udfs.index_number == "1"
def test_to_lims_balsamic(balsamic_order_to_submit):
# GIVEN a cancer order for a sample
order_data = OrderIn.parse_obj(obj=balsamic_order_to_submit,
project=OrderType.BALSAMIC)
# WHEN parsing the order to format for LIMS import
samples: List[LimsSample] = build_lims_sample(customer="cust000",
samples=order_data.samples)
# THEN it should list all samples
assert len(samples) == 1
# ... and determine the container, container name, and well position
container_names = {
sample.container_name
for sample in samples if sample.container_name
}
# ... and pick out relevant UDFs
first_sample = samples[0].dict()
assert first_sample["name"] == "s1"
assert {sample.container for sample in samples} == set(["96 well plate"])
assert first_sample["udfs"]["data_analysis"] == str(Pipeline.BALSAMIC)
assert first_sample["udfs"]["application"] == "WGSPCFC030"
assert first_sample["udfs"]["sex"] == "M"
assert first_sample["udfs"]["family_name"] == "family1"
assert first_sample["udfs"]["customer"] == "cust000"
assert first_sample["udfs"]["source"] == "blood"
assert first_sample["udfs"]["volume"] == "1"
assert first_sample["udfs"]["priority"] == "standard"
assert container_names == set(["p1"])
assert first_sample["well_position"] == "A:1"
assert first_sample["udfs"]["tumour"] is True
assert first_sample["udfs"]["capture_kit"] == "other"
assert first_sample["udfs"]["tumour_purity"] == "75"
assert first_sample["udfs"]["formalin_fixation_time"] == "1"
assert first_sample["udfs"]["post_formalin_fixation_time"] == "2"
assert first_sample["udfs"]["tissue_block_size"] == "small"
assert first_sample["udfs"]["quantity"] == "2"
assert first_sample["udfs"]["comment"] == "other Elution buffer"
def test_to_lims_microbial(microbial_order_to_submit):
# GIVEN a microbial order for three samples
order_data = OrderIn.parse_obj(obj=microbial_order_to_submit,
project=OrderType.MICROSALT)
# WHEN parsing for LIMS
samples: List[LimsSample] = build_lims_sample(customer="cust000",
samples=order_data.samples)
# THEN it should "work"
assert len(samples) == 5
# ... and pick out relevant UDFs
first_sample = samples[0].dict()
assert first_sample["udfs"]["priority"] == "research"
assert first_sample["udfs"]["organism"] == "M.upium"
assert first_sample["udfs"]["reference_genome"] == "NC_111"
assert (first_sample["udfs"]["extraction_method"] ==
"MagNaPure 96 (contact Clinical Genomics "
"before submission)")
assert first_sample["udfs"]["volume"] == "1"