def submit_order(self, order: OrderIn) -> dict:
self._fill_in_sample_verified_organism(order.samples)
# submit samples to LIMS
project_data, lims_map = process_lims(lims_api=self.lims,
lims_order=order,
new_samples=order.samples)
# prepare order for status database
status_data = self.order_to_status(order)
self._fill_in_sample_ids(status_data["samples"],
lims_map,
id_key="internal_id")
# submit samples to Status
samples = self.store_items_in_status(
customer=status_data["customer"],
order=status_data["order"],
ordered=project_data["date"]
if project_data else dt.datetime.now(),
ticket=order.ticket,
items=status_data["samples"],
comment=status_data["comment"],
data_analysis=Pipeline(status_data["data_analysis"]),
data_delivery=DataDelivery(status_data["data_delivery"]),
)
return {"project": project_data, "records": samples}
def _process_case_samples(self, order: OrderIn) -> dict:
"""Process samples to be analyzed."""
project_data = lims_map = None
# submit new samples to lims
new_samples = [
sample for sample in order.samples if sample.internal_id is None
]
if new_samples:
project_data, lims_map = process_lims(lims_api=self.lims,
lims_order=order,
new_samples=new_samples)
status_data = self.order_to_status(order=order)
samples = [
sample for family in status_data["families"]
for sample in family["samples"]
]
if lims_map:
self._fill_in_sample_ids(samples, lims_map)
new_families = self.store_items_in_status(
customer=status_data["customer"],
order=status_data["order"],
ordered=project_data["date"]
if project_data else dt.datetime.now(),
ticket=order.ticket,
items=status_data["families"],
)
return {"project": project_data, "records": new_families}
def submit_order(self, order: OrderIn) -> dict:
"""Submit a batch of metagenome samples."""
project_data, lims_map = process_lims(lims_api=self.lims,
lims_order=order,
new_samples=order.samples)
status_data = self.order_to_status(order)
self._fill_in_sample_ids(status_data["samples"], lims_map)
new_samples = self.store_items_in_status(
customer=status_data["customer"],
order=status_data["order"],
ordered=project_data["date"],
ticket=order.ticket,
items=status_data["samples"],
)
self._add_missing_reads(new_samples)
return {"project": project_data, "records": new_samples}
def submit_order(self, order: OrderIn) -> dict:
status_data = self.order_to_status(order)
project_data, lims_map = process_lims(lims_api=self.lims,
lims_order=order,
new_samples=order.samples)
samples = [
sample for pool in status_data["pools"]
for sample in pool["samples"]
]
self._fill_in_sample_ids(samples, lims_map, id_key="internal_id")
new_records = self.store_items_in_status(
customer=status_data["customer"],
order=status_data["order"],
ordered=project_data["date"],
ticket=order.ticket,
items=status_data["pools"],
)
return {"project": project_data, "records": new_records}