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 fixture_microbial_store_dummy_tag(microbial_store: Store,
helpers: StoreHelpers) -> Store:
"""Populate a microbial store with a extra dummy app tag"""
helpers.ensure_application(store=microbial_store,
tag="dummy_tag",
application_type="mic",
is_archived=False)
return microbial_store
def fixture_applications_store(store: Store, application_versions_file: str,
helpers: StoreHelpers) -> Store:
"""Return a store populated with applications from excel file"""
versions: Iterable[ApplicationVersionSchema] = parse_application_versions(
excel_path=application_versions_file)
for version in versions:
helpers.ensure_application(store=store, tag=version.app_tag)
return store
def fixture_rml_store(store: Store, helpers: StoreHelpers) -> Store:
"""Populate a store with microbial application tags"""
active_apptags = [
"RMLP10R300",
"RMLP10S130",
"RMLP15R100",
"RMLP15R200",
"RMLP15R400",
"RMLP15R500",
"RMLP15R750",
"RMLP15R825",
"RMLP15S100",
"RMLP15S125",
"RMLP15S150",
"RMLP15S175",
"RMLP15S200",
"RMLP15S225",
"RMLP15S425",
]
inactive_apptags = [
"RMLP05R800",
"RMLP15S250",
"RMLP15S275",
"RMLP15S300",
"RMLP15S325",
"RMLP15S350",
"RMLP15S375",
"RMLP15S400",
"RMLP15S450",
"RMLP15S475",
"RMLP15S500",
"RMLS05R200",
"RMLCUSR800",
"RMLCUSS160",
]
for app_tag in active_apptags:
helpers.ensure_application(store=store,
tag=app_tag,
application_type="rml",
is_archived=False)
for app_tag in inactive_apptags:
helpers.ensure_application(store=store,
tag=app_tag,
application_type="rml",
is_archived=True)
return store
def fixture_microbial_store(store: Store, helpers: StoreHelpers) -> Store:
"""Populate a store with microbial application tags"""
microbial_active_apptags = [
"MWRNXTR003", "MWGNXTR003", "MWMNXTR003", "MWLNXTR003"
]
microbial_inactive_apptags = ["MWXNXTR003", "VWGNXTR001", "VWLNXTR001"]
for app_tag in microbial_active_apptags:
helpers.ensure_application(store=store,
tag=app_tag,
application_type="mic",
is_archived=False)
for app_tag in microbial_inactive_apptags:
helpers.ensure_application(store=store,
tag=app_tag,
application_type="mic",
is_archived=True)
return store
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