def test_store_samples(orders_api, base_store, fastq_status_data):
# GIVEN a basic store with no samples and a fastq order
assert base_store.samples().count() == 0
assert base_store.families().count() == 0
submitter: FastqSubmitter = FastqSubmitter(lims=orders_api.lims,
status=orders_api.status)
# WHEN storing the order
new_samples = submitter.store_items_in_status(
customer=fastq_status_data["customer"],
order=fastq_status_data["order"],
ordered=dt.datetime.now(),
ticket=1234348,
items=fastq_status_data["samples"],
)
# THEN it should store the samples and create a case for each sample
assert len(new_samples) == 2
assert base_store.samples().count() == 2
assert base_store.families().count() == 2
first_sample = new_samples[0]
assert len(first_sample.links) == 1
family_link = first_sample.links[0]
assert family_link.family in base_store.families()
for sample in new_samples:
assert len(sample.deliveries) == 1
assert family_link.family.data_analysis
assert family_link.family.data_delivery == DataDelivery.FASTQ
def test_store_samples_sex_stored(orders_api, base_store, fastq_status_data):
# GIVEN a basic store with no samples and a fastq order
assert base_store.samples().count() == 0
assert base_store.families().count() == 0
submitter = FastqSubmitter(lims=orders_api.lims, status=orders_api.status)
# WHEN storing the order
new_samples = submitter.store_items_in_status(
customer=fastq_status_data["customer"],
order=fastq_status_data["order"],
ordered=dt.datetime.now(),
ticket=1234348,
items=fastq_status_data["samples"],
)
# THEN the sample sex should be stored
assert new_samples[0].sex == "male"
def test_store_samples_bad_apptag(orders_api, base_store, fastq_status_data):
# GIVEN a basic store with no samples and a fastq order
assert base_store.samples().count() == 0
assert base_store.families().count() == 0
for sample in fastq_status_data["samples"]:
sample["application"] = "nonexistingtag"
submitter = FastqSubmitter(lims=orders_api.lims, status=orders_api.status)
# THEN it should raise OrderError
with pytest.raises(OrderError):
# WHEN storing the order
submitter.store_items_in_status(
customer=fastq_status_data["customer"],
order=fastq_status_data["order"],
ordered=dt.datetime.now(),
ticket=1234348,
items=fastq_status_data["samples"],
)
def test_store_fastq_samples_tumour_wgs_to_fastq(orders_api, base_store,
fastq_status_data):
# GIVEN a basic store with no samples and a tumour fastq order as wgs
assert base_store.samples().count() == 0
assert base_store.families().count() == 0
base_store.application(
fastq_status_data["samples"][0]["application"]).prep_category = "wgs"
fastq_status_data["samples"][0]["tumour"] = True
submitter = FastqSubmitter(lims=orders_api.lims, status=orders_api.status)
# WHEN storing the order
new_samples = submitter.store_items_in_status(
customer=fastq_status_data["customer"],
order=fastq_status_data["order"],
ordered=dt.datetime.now(),
ticket=1234348,
items=fastq_status_data["samples"],
)
# THEN the analysis for the case should be FASTQ
assert new_samples[0].links[0].family.data_analysis == Pipeline.FASTQ
def test_store_fastq_samples_non_wgs_as_fastq(orders_api, base_store,
fastq_status_data):
# GIVEN a basic store with no samples and a fastq order as non wgs
assert base_store.samples().count() == 0
assert base_store.families().count() == 0
non_wgs_prep_category = "wes"
assert base_store.applications(category=non_wgs_prep_category)
for sample in fastq_status_data["samples"]:
sample["application"] = base_store.applications(
category=non_wgs_prep_category)[0].tag
submitter = FastqSubmitter(lims=orders_api.lims, status=orders_api.status)
# WHEN storing the order
new_samples = submitter.store_items_in_status(
customer=fastq_status_data["customer"],
order=fastq_status_data["order"],
ordered=dt.datetime.now(),
ticket=1234348,
items=fastq_status_data["samples"],
)
# THEN the analysis for the case should be fastq (none)
assert new_samples[0].links[0].family.data_analysis == Pipeline.FASTQ
def test_samples_to_status(fastq_order_to_submit):
# GIVEN fastq order with two samples
order = OrderIn.parse_obj(fastq_order_to_submit, OrderType.FASTQ)
# WHEN parsing for status
data = FastqSubmitter.order_to_status(order=order)
# THEN it should pick out samples and relevant information
assert len(data["samples"]) == 2
first_sample = data["samples"][0]
assert first_sample["name"] == "prov1"
assert first_sample["application"] == "WGSPCFC060"
assert first_sample["priority"] == "priority"
assert first_sample["tumour"] is False
assert first_sample["volume"] == "1"
# ... and the other sample is a tumour
assert data["samples"][1]["tumour"] is True
def fastq_status_data(fastq_order_to_submit):
"""Parse fastq order example."""
project: OrderType = OrderType.FASTQ
order: OrderIn = OrderIn.parse_obj(obj=fastq_order_to_submit,
project=project)
return FastqSubmitter.order_to_status(order=order)