def add_application_object(
application: ApplicationSchema, sign: str, store: Store
) -> models.Application:
"""Adds an application from a raw application record"""
new_application: models.Application = store.add_application(
tag=application.tag,
category=application.prep_category,
description=application.description,
is_accredited=application.is_accredited == 1.0,
turnaround_time=application.turnaround_time,
minimum_order=application.minimum_order,
sequencing_depth=application.sequencing_depth,
target_reads=application.target_reads,
sample_amount=application.sample_amount,
sample_volume=application.sample_volume,
sample_concentration=application.sample_concentration,
priority_processing=application.priority_processing == 1.0,
details=application.details,
limitations=application.limitations,
percent_kth=application.percent_kth,
percent_reads_guaranteed=application.percent_reads_guaranteed,
comment=application.comment + " Added by %s" % sign,
is_archived=application.is_archived == 1.0,
is_external=application.is_external == 1.0,
created_at=datetime.now(),
)
return new_application
def add_application(
store: Store,
application_tag: str = "dummy_tag",
application_type: str = "wgs",
description: str = None,
is_archived: bool = False,
is_accredited: bool = False,
is_external: bool = False,
min_sequencing_depth: int = 30,
**kwargs,
) -> models.Application:
"""Utility function to add a application to a store"""
application = store.application(tag=application_tag)
if application:
return application
if not description:
description = "dummy_description"
application = store.add_application(
tag=application_tag,
category=application_type,
description=description,
is_archived=is_archived,
percent_kth=80,
percent_reads_guaranteed=75,
is_accredited=is_accredited,
limitations="A limitation",
is_external=is_external,
min_sequencing_depth=min_sequencing_depth,
**kwargs,
)
store.add_commit(application)
return application
def add_application(
store: Store,
application_tag: str = "dummy_tag",
application_type: str = "wgs",
description: str = None,
is_accredited: bool = False,
is_external: bool = False,
**kwargs,
) -> models.Application:
"""Utility function to add a application to a store"""
application = store.application(tag=application_tag)
if application:
return application
if not description:
description = "dummy_description"
application = store.add_application(
tag=application_tag,
category=application_type,
description=description,
percent_kth=80,
is_accredited=is_accredited,
limitations="A limitation",
is_external=is_external,
)
store.add_commit(application)
return application
def test_add_pool(store: Store):
# GIVEN a valid customer and a valid application_version
customer_group = store.add_customer_group("dummy_group", "dummy group")
new_customer = store.add_customer(
internal_id="cust000",
name="Test customer",
scout_access=True,
customer_group=customer_group,
invoice_address="skolgatan 15",
invoice_reference="abc",
)
store.add_commit(new_customer)
application = store.add_application(
tag="RMLS05R150",
category="rml",
description="Ready-made",
percent_kth=80,
sequencing_depth=0,
)
store.add_commit(application)
app_version = store.add_version(
application=application,
version=1,
valid_from=dt.today(),
prices={
"standard": 12,
"priority": 222,
"express": 123,
"research": 12
},
)
store.add_commit(app_version)
# WHEN adding a new pool into the database
new_pool = store.add_pool(
customer=new_customer,
name="Test",
order="Test",
ordered=dt.today(),
application_version=app_version,
data_analysis="fastq",
)
store.add_commit(new_pool)
# THEN the new pool should have no_invoice = False
pool = store.pools(customer=None).first()
assert pool.no_invoice is False
def ensure_applications(base_store: Store, active_applications: list,
inactive_applications: list):
"""Create some requested applications for the tests """
for active_application in active_applications:
if not base_store.application(active_application):
base_store.add_commit(
base_store.add_application(
active_application,
"mic",
"dummy_description",
is_archived=False,
percent_kth=80,
))
for inactive_application in inactive_applications:
if not base_store.application(inactive_application):
base_store.add_commit(
base_store.add_application(
inactive_application,
category="mic",
description="dummy_description",
is_archived=True,
percent_kth=80,
))
def add_application_from_raw(raw_application, sign, store: Store):
"""Adds an application from a raw application record"""
new_application = store.add_application(
tag=_get_tag_from_raw_application(raw_application),
category=raw_application["prep_category"],
description=raw_application["description"],
is_accredited=raw_application["is_accredited"] == 1.0,
turnaround_time=raw_application["turnaround_time"],
minimum_order=raw_application["minimum_order"],
sequencing_depth=raw_application["sequencing_depth"],
target_reads=raw_application["target_reads"],
sample_amount=raw_application["sample_amount"],
sample_volume=raw_application["sample_volume"],
sample_concentration=raw_application["sample_concentration"],
priority_processing=raw_application["priority_processing"] == 1.0,
details=raw_application["details"],
limitations=raw_application["limitations"],
percent_kth=raw_application["percent_kth"],
comment=raw_application["comment"] + " Added by %s" % sign,
is_archived=raw_application["is_archived"] == 1.0,
is_external=raw_application["is_external"] == 1.0,
created_at=datetime.now(),
)
return new_application
def fixture_base_store(store: Store, apptag_rna: str) -> Store:
"""Setup and example store."""
customer_group = store.add_customer_group("all_customers", "all customers")
store.add_commit(customer_group)
customers = [
store.add_customer(
"cust000",
"Production",
scout_access=True,
customer_group=customer_group,
invoice_address="Test street",
invoice_reference="ABCDEF",
),
store.add_customer(
"cust001",
"Customer",
scout_access=False,
customer_group=customer_group,
invoice_address="Test street",
invoice_reference="ABCDEF",
),
store.add_customer(
"cust002",
"Karolinska",
scout_access=True,
customer_group=customer_group,
invoice_address="Test street",
invoice_reference="ABCDEF",
),
store.add_customer(
"cust003",
"CMMS",
scout_access=True,
customer_group=customer_group,
invoice_address="Test street",
invoice_reference="ABCDEF",
),
]
store.add_commit(customers)
applications = [
store.add_application(
tag="WGXCUSC000",
category="wgs",
description="External WGS",
sequencing_depth=0,
is_external=True,
percent_kth=80,
percent_reads_guaranteed=75,
target_reads=10,
),
store.add_application(
tag="EXXCUSR000",
category="wes",
description="External WES",
sequencing_depth=0,
is_external=True,
percent_kth=80,
percent_reads_guaranteed=75,
target_reads=10,
),
store.add_application(
tag="WGSPCFC060",
category="wgs",
description="WGS, double",
sequencing_depth=30,
accredited=True,
percent_kth=80,
percent_reads_guaranteed=75,
target_reads=10,
),
store.add_application(
tag="RMLP05R800",
category="rml",
description="Ready-made",
sequencing_depth=0,
percent_kth=80,
percent_reads_guaranteed=75,
target_reads=10,
),
store.add_application(
tag="WGSPCFC030",
category="wgs",
description="WGS trio",
is_accredited=True,
sequencing_depth=30,
target_reads=30,
limitations="some",
percent_kth=80,
percent_reads_guaranteed=75,
),
store.add_application(
tag="METLIFR020",
category="wgs",
description="Whole genome metagenomics",
sequencing_depth=0,
target_reads=400000,
percent_kth=80,
percent_reads_guaranteed=75,
),
store.add_application(
tag="METNXTR020",
category="wgs",
description="Metagenomics",
sequencing_depth=0,
target_reads=200000,
percent_kth=80,
percent_reads_guaranteed=75,
),
store.add_application(
tag="MWRNXTR003",
category="mic",
description="Microbial whole genome ",
sequencing_depth=0,
percent_kth=80,
percent_reads_guaranteed=75,
target_reads=10,
),
store.add_application(
tag=apptag_rna,
category="tgs",
description="RNA seq, poly-A based priming",
percent_kth=80,
percent_reads_guaranteed=75,
sequencing_depth=25,
accredited=True,
target_reads=10,
),
store.add_application(
tag="VWGDPTR001",
category="cov",
description="Viral whole genome ",
sequencing_depth=0,
percent_kth=80,
percent_reads_guaranteed=75,
target_reads=10,
),
]
store.add_commit(applications)
prices = {"standard": 10, "priority": 20, "express": 30, "research": 5}
versions = [
store.add_version(application,
1,
valid_from=dt.datetime.now(),
prices=prices) for application in applications
]
store.add_commit(versions)
beds = [store.add_bed("Bed")]
store.add_commit(beds)
bed_versions = [store.add_bed_version(bed, 1, "Bed.bed") for bed in beds]
store.add_commit(bed_versions)
organism = store.add_organism("C. jejuni", "C. jejuni")
store.add_commit(organism)
yield store
