def test_validate_case_name(rml_order_to_submit: dict, base_store: Store,
helpers: StoreHelpers):
# GIVEN pool order with a case already all in the database
order: OrderIn = OrderIn.parse_obj(rml_order_to_submit, OrderType.RML)
sample: RmlSample
customer: models.Customer = helpers.ensure_customer(
store=base_store, customer_id=order.customer)
for sample in order.samples:
case = helpers.ensure_case(
store=base_store,
name=PoolSubmitter.create_case_name(ticket=order.ticket,
pool_name=sample.pool),
customer=customer,
data_analysis=Pipeline.FLUFFY,
data_delivery=DataDelivery.STATINA,
)
base_store.add_commit(case)
def test_clean_hk_bundle_files_dry_run(
caplog,
case_id: str,
cg_context: CGConfig,
cli_runner: CliRunner,
helpers: StoreHelpers,
mocker,
timestamp: datetime,
):
# GIVEN a housekeeper api with some alignment files
file_path = "path/to_file.cram"
tag = "cram"
hk_bundle_data = {
"name": case_id,
"created": timestamp,
"expires": timestamp,
"files": [
{
"path": file_path,
"archive": False,
"tags": [case_id, tag]
},
],
}
store = cg_context.status_db
case = helpers.ensure_case(store=store, case_id=case_id)
helpers.add_analysis(store=store,
case=case,
started_at=timestamp,
completed_at=timestamp)
helpers.ensure_hk_bundle(cg_context.housekeeper_api,
bundle_data=hk_bundle_data)
# WHEN running the clean command in dry run mode
caplog.set_level(logging.INFO)
result = cli_runner.invoke(hk_bundle_files,
["-c", case_id, "--dry-run", "--tags", tag],
obj=cg_context)
# THEN assert it exits with success
assert result.exit_code == 0
# THEN assert that the files where removed
assert f"{file_path} not on disk" in caplog.text
def fixture_rna_store(
base_store: Store,
helpers: StoreHelpers,
rna_case_id: str,
dna_case_id: str,
) -> Store:
"""Populate store with an rna case that is connected to a dna case via sample.subject_id"""
store: Store = base_store
# an existing RNA case with related sample
rna_case = helpers.ensure_case(
store=store,
name="rna_case",
customer=helpers.ensure_customer(store=store),
data_analysis=Pipeline.MIP_RNA,
data_delivery=DataDelivery.SCOUT,
)
rna_case.internal_id = rna_case_id
rna_sample_son = helpers.add_sample(store=store, name="rna_son", subject_id="son")
rna_sample_daughter = helpers.add_sample(
store=store, name="rna_daughter", subject_id="daughter"
)
rna_sample_mother = helpers.add_sample(store=store, name="rna_mother", subject_id="mother")
rna_sample_father = helpers.add_sample(store=store, name="rna_father", subject_id="father")
helpers.add_relationship(
store=store,
sample=rna_sample_son,
case=rna_case,
mother=rna_sample_mother,
father=rna_sample_father,
status="affected",
)
helpers.add_relationship(
store=store,
sample=rna_sample_daughter,
case=rna_case,
mother=rna_sample_mother,
father=rna_sample_father,
status="unaffected",
)
helpers.add_relationship(
store=store, sample=rna_sample_mother, case=rna_case, status="unaffected"
)
helpers.add_relationship(
store=store, sample=rna_sample_father, case=rna_case, status="affected"
)
for link in rna_case.links:
link.sample.internal_id = link.sample.name
# an existing DNA case with related sample
dna_case = helpers.ensure_case(
store=store,
name="dna_case",
customer=helpers.ensure_customer(store=store),
data_analysis=Pipeline.MIP_DNA,
data_delivery=DataDelivery.SCOUT,
)
dna_case.internal_id = dna_case_id
dna_sample_son = helpers.add_sample(store=store, name="dna_son", subject_id="son")
dna_sample_daughter = helpers.add_sample(
store=store, name="dna_daughter", subject_id="daughter"
)
dna_sample_mother = helpers.add_sample(store=store, name="dna_mother", subject_id="mother")
dna_sample_father = helpers.add_sample(store=store, name="dna_father", subject_id="father")
helpers.add_relationship(
store=store,
sample=dna_sample_son,
case=dna_case,
mother=dna_sample_mother,
father=dna_sample_father,
status="affected",
)
helpers.add_relationship(
store=store,
sample=dna_sample_daughter,
case=dna_case,
mother=dna_sample_mother,
father=dna_sample_father,
status="unaffected",
)
helpers.add_relationship(
store=store, sample=dna_sample_mother, case=dna_case, status="unaffected"
)
helpers.add_relationship(
store=store, sample=dna_sample_father, case=dna_case, status="affected"
)
for link in dna_case.links:
link.sample.internal_id = link.sample.name
store.commit()
return store
