def test_add_family_bad_data_delivery(
cli_runner: CliRunner, base_context: CGConfig, helpers: StoreHelpers
):
"""Test to add a case using only the required arguments"""
# GIVEN a database with a customer and an panel
# WHEN adding a case without data delivery
disk_store: Store = base_context.status_db
customer: models.Customer = helpers.ensure_customer(store=disk_store)
customer_id = customer.internal_id
panel: models.Panel = helpers.ensure_panel(store=disk_store)
panel_id = panel.name
name = "case_name"
non_existing_data_delivery = "aws"
result = cli_runner.invoke(
add,
[
"case",
"--panel",
panel_id,
"--analysis",
CLI_OPTION_ANALYSIS,
"--data-delivery",
non_existing_data_delivery,
customer_id,
name,
],
obj=base_context,
)
# THEN it should not be added
assert result.exit_code != 0
assert disk_store.Family.query.count() == 0
def test_add_family_bad_panel(cli_runner: CliRunner, base_context: CGConfig, helpers: StoreHelpers):
"""Test to add a case using a non-existing panel"""
# GIVEN a database with a customer
disk_store: Store = base_context.status_db
# WHEN adding a case
customer: models.Customer = helpers.ensure_customer(store=disk_store)
customer_id = customer.internal_id
panel_id = "dummy_panel"
name = "dummy_name"
result = cli_runner.invoke(
add,
[
"family",
"--panel",
panel_id,
"--analysis",
CLI_OPTION_ANALYSIS,
"--data-delivery",
CLI_OPTION_DELIVERY,
customer_id,
name,
],
obj=base_context,
)
# THEN it should complain about missing panel instead of adding a case
assert result.exit_code == 1
assert disk_store.Family.query.count() == 0
def test_add_family_priority(cli_runner: CliRunner, base_context: CGConfig, helpers: StoreHelpers):
"""Test that the added case get the priority we send in"""
# GIVEN a database with a customer and an panel
disk_store: Store = base_context.status_db
# WHEN adding a case
customer: models.Customer = helpers.ensure_customer(store=disk_store)
customer_id = customer.internal_id
panel: models.Panel = helpers.ensure_panel(store=disk_store)
panel_id = panel.name
name = "case_name"
priority = "priority"
result = cli_runner.invoke(
add,
[
"family",
"--panel",
panel_id,
"--priority",
priority,
"--analysis",
CLI_OPTION_ANALYSIS,
"--data-delivery",
CLI_OPTION_DELIVERY,
customer_id,
name,
],
obj=base_context,
)
# THEN it should be added
assert result.exit_code == 0
assert disk_store.Family.query.count() == 1
assert disk_store.Family.query.first().priority_human == priority
def test_add_sample_required(cli_runner: CliRunner, base_context: CGConfig,
helpers: StoreHelpers):
# GIVEN a database with a customer and an application
disk_store: Store = base_context.status_db
sex = "male"
application_tag = "dummy_tag"
helpers.ensure_application(store=disk_store, tag=application_tag)
helpers.ensure_application_version(store=disk_store,
application_tag=application_tag)
customer: models.Customer = helpers.ensure_customer(store=disk_store)
customer_id = customer.internal_id
name = "sample_name"
# WHEN adding a sample
result = cli_runner.invoke(
add,
[
"sample",
"--sex",
sex,
"--application",
application_tag,
customer_id,
name,
],
obj=base_context,
)
# THEN it should be added
assert result.exit_code == 0
assert disk_store.Sample.query.count() == 1
assert disk_store.Sample.query.first().name == name
assert disk_store.Sample.query.first().sex == sex
def test_add_family_required(cli_runner: CliRunner, base_context: CGConfig, helpers: StoreHelpers):
"""Test to add a case using only the required arguments"""
# GIVEN a database with a customer and an panel
disk_store: Store = base_context.status_db
customer: models.Customer = helpers.ensure_customer(store=disk_store)
customer_id = customer.internal_id
panel: models.Panel = helpers.ensure_panel(store=disk_store)
panel_id = panel.name
name = "case_name"
# WHEN adding a panel
result = cli_runner.invoke(
add,
[
"family",
"--panel",
panel_id,
"--analysis",
CLI_OPTION_ANALYSIS,
"--data-delivery",
CLI_OPTION_DELIVERY,
customer_id,
name,
],
obj=base_context,
)
# THEN it should be added
assert result.exit_code == 0
assert disk_store.Family.query.count() == 1
assert disk_store.Family.query.first().name == name
assert disk_store.Family.query.first().panels == [panel_id]
def test_add_sample_bad_application(cli_runner: CliRunner,
base_context: CGConfig,
helpers: StoreHelpers):
# GIVEN a database with a customer
disk_store: Store = base_context.status_db
# WHEN adding a sample
sex = "male"
application = "dummy_application"
customer: models.Customer = helpers.ensure_customer(store=disk_store)
customer_id = customer.internal_id
name = "dummy_name"
result = cli_runner.invoke(
add,
[
"sample",
"--sex",
sex,
"--application",
application,
customer_id,
name,
],
obj=base_context,
)
# THEN it should complain about missing application instead of adding a sample
assert result.exit_code == 1
assert disk_store.Sample.query.count() == 0
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_get_family_by_name(cli_runner: CliRunner, base_context: CGConfig,
helpers: StoreHelpers):
# GIVEN A database with a customer in it
status_db: Store = base_context.status_db
customer: models.Customer = helpers.ensure_customer(store=status_db)
customer_id = customer.internal_id
# WHEN trying to get a non-existing case by name
result = cli_runner.invoke(
get,
[
"family",
"-c",
customer_id,
"-n",
"dummy-case-name",
],
obj=base_context,
)
# THEN it should not crash
assert result.exit_code == 0
def test_add_sample_downsampled(
cli_runner,
base_context: CGConfig,
disk_store: Store,
application_tag: str,
helpers: StoreHelpers,
):
# GIVEN a database with a customer and an application
helpers.ensure_application(store=disk_store, tag=application_tag)
helpers.ensure_application_version(store=disk_store,
application_tag=application_tag)
customer: models.Customer = helpers.ensure_customer(store=disk_store)
customer_id = customer.internal_id
sex = "male"
name = "sample_name"
downsampled_to = "123"
# WHEN adding a sample
result = cli_runner.invoke(
add,
[
"sample",
"--sex",
sex,
"--application",
application_tag,
"--downsampled",
downsampled_to,
customer_id,
name,
],
obj=base_context,
)
# THEN it should be added
assert result.exit_code == 0
assert disk_store.Sample.query.count() == 1
assert str(
disk_store.Sample.query.first().downsampled_to) == downsampled_to
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