def ensure_bed_version(store: Store, bed_name: str = "dummy_bed") -> models.ApplicationVersion:
"""Utility function to return existing or create bed version for tests"""
bed = store.bed(name=bed_name)
if not bed:
bed = store.add_bed(name=bed_name)
store.add_commit(bed)
version = store.latest_bed_version(bed_name)
if not version:
version = store.add_bed_version(bed, 1, "dummy_filename", shortname=bed_name)
store.add_commit(version)
return version
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
