def ensure_family(self,
store: Store,
family_info: dict,
app_tag: str = None):
"""Load a family with samples and link relations"""
customer_obj = self.ensure_customer(store)
family_obj = store.Family(
name=family_info["name"],
panels=family_info["panels"],
internal_id=family_info["internal_id"],
priority="standard",
)
family_obj = self.add_family(store,
family_obj=family_obj,
customer_id=customer_obj.internal_id)
app_tag = app_tag or "WGTPCFC030"
app_type = family_info.get("application_type", "wgs")
self.ensure_application_version(store, application_tag=app_tag)
data_analysis = family_info.get("data_analysis", "mip")
sample_objs = {}
for sample_data in family_info["samples"]:
sample_id = sample_data["internal_id"]
sample_obj = self.add_sample(
store,
customer_name=sample_data["name"],
gender=sample_data["sex"],
internal_id=sample_id,
data_analysis=data_analysis,
application_type=app_type,
ticket=sample_data["ticket_number"],
reads=sample_data["reads"],
)
sample_objs[sample_id] = sample_obj
for sample_data in family_info["samples"]:
sample_obj = sample_objs[sample_data["internal_id"]]
father = None
if sample_data.get("father"):
father = sample_objs[sample_data["father"]]
mother = None
if sample_data.get("mother"):
mother = sample_objs[sample_data["mother"]]
self.add_relationship(
store,
family=family_obj,
sample=sample_obj,
status=sample_data.get("status", "unknown"),
father=father,
mother=mother,
)
self.add_analysis(store, pipeline="pipeline", family=family_obj)
return family_obj
def fixture_analysis_store(base_store: Store, analysis_family: dict) -> Store:
"""Setup a store instance for testing analysis API."""
customer = base_store.customer("cust000")
family = base_store.Family(
data_analysis=analysis_family["data_analysis"],
name=analysis_family["name"],
panels=analysis_family["panels"],
internal_id=analysis_family["internal_id"],
priority=Priority.standard.name,
)
family.customer = customer
base_store.add(family)
application_version = base_store.application("WGSPCFC030").versions[0]
for sample_data in analysis_family["samples"]:
sample = base_store.add_sample(
name=sample_data["name"],
sex=sample_data["sex"],
internal_id=sample_data["internal_id"],
ticket=sample_data["ticket_number"],
reads=sample_data["reads"],
capture_kit=sample_data["capture_kit"],
)
sample.family = family
sample.application_version = application_version
sample.customer = customer
base_store.add(sample)
base_store.commit()
for sample_data in analysis_family["samples"]:
sample_obj = base_store.sample(sample_data["internal_id"])
link = base_store.relate_sample(
family=family,
sample=sample_obj,
status=sample_data["status"],
father=base_store.sample(sample_data["father"])
if sample_data.get("father") else None,
mother=base_store.sample(sample_data["mother"])
if sample_data.get("mother") else None,
)
base_store.add(link)
base_store.commit()
yield base_store
def ensure_case_from_dict(
store: Store,
case_info: dict,
app_tag: str = None,
ordered_at: datetime = None,
completed_at: datetime = None,
created_at: datetime = datetime.now(),
):
"""Load a case with samples and link relations"""
customer_obj = StoreHelpers.ensure_customer(store)
case_obj = store.Family(
name=case_info["name"],
panels=case_info["panels"],
internal_id=case_info["internal_id"],
ordered_at=ordered_at,
data_analysis=case_info.get("data_analysis", str(Pipeline.MIP_DNA)),
data_delivery=case_info.get("data_delivery", str(DataDelivery.SCOUT)),
created_at=created_at,
action=case_info.get("action"),
)
case_obj = StoreHelpers.add_case(
store, case_obj=case_obj, customer_id=customer_obj.internal_id
)
app_tag = app_tag or "WGSPCFC030"
app_type = case_info.get("application_type", "wgs")
StoreHelpers.ensure_application_version(store, application_tag=app_tag)
sample_objs = {}
for sample_data in case_info["samples"]:
sample_id = sample_data["internal_id"]
sample_obj = StoreHelpers.add_sample(
store,
gender=sample_data["sex"],
name=sample_data.get("name"),
internal_id=sample_id,
application_type=app_type,
ticket=sample_data["ticket_number"],
reads=sample_data["reads"],
capture_kit=sample_data["capture_kit"],
)
sample_objs[sample_id] = sample_obj
for sample_data in case_info["samples"]:
sample_obj = sample_objs[sample_data["internal_id"]]
father = None
if sample_data.get("father"):
father = sample_objs[sample_data["father"]]
mother = None
if sample_data.get("mother"):
mother = sample_objs[sample_data["mother"]]
StoreHelpers.add_relationship(
store,
case=case_obj,
sample=sample_obj,
status=sample_data.get("status", "unknown"),
father=father,
mother=mother,
)
StoreHelpers.add_analysis(
store,
pipeline=Pipeline.MIP_DNA,
case=case_obj,
completed_at=completed_at or datetime.now(),
)
return case_obj
