8734548414

Committed 18 Apr 2024 08:10AM UTC coverage: 83.899%. First build

Build # 8734548414

Build Type

Pull #3148

github

Committed by

web-flow

Commit Message

Merge ea1962572 into 23a7e4995

Pull Request Pull Request #3148: add(create validation case)

Run Details

1 of 179 new or added lines in 5 files covered. (0.56%)

19358 of 23073 relevant lines covered (83.9%)

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0.0

/cg/meta/create_validation_cases/validation_case_data.py

1	"""Model for down sampling meta data."""
2
NEW 3	import logging	×
NEW 4	from pathlib import Path	×
5
NEW 6	from cg.apps.housekeeper.hk import HousekeeperAPI	×
NEW 7	from cg.constants import DataDelivery, Priority	×
NEW 8	from cg.meta.create_validation_cases.validation_data_input import ValidationDataInput	×
NEW 9	from cg.store.models import ApplicationVersion, Case, Sample	×
NEW 10	from cg.store.store import Store	×
NEW 11	from cg.utils.calculations import multiply_by_million	×
12
NEW 13	LOG = logging.getLogger(__name__)	×
14
15
NEW 16	class ValidationCaseData:	×
NEW 17	def __init__(	×
18	self, status_db: Store, hk_api: HousekeeperAPI, validation_data_input: ValidationDataInput
19	):
20	"""Initialize the validation sample data and perform integrity checks."""
NEW 21	self.status_db: Store = status_db	×
NEW 22	self.housekeeper_api: HousekeeperAPI = hk_api	×
NEW 23	self.input_data: ValidationDataInput = validation_data_input	×
NEW 24	self.case_id: str = validation_data_input.case_id	×
NEW 25	self.case_name: str = validation_data_input.case_name	×
NEW 26	self.original_case: Case = self.get_case_to_copy()	×
NEW 27	self.original_samples: list[Sample] = self.get_samples_to_copy()	×
NEW 28	self.validation_samples: list[Sample] = self.get_validation_samples()	×
NEW 29	self.validation_case: Case = self._generate_validation_case()	×
NEW 30	LOG.info(f"Validation Data checks completed for {self.case_id}")	×
31
NEW 32	@staticmethod	×
NEW 33	def _validation_sample_name(sample: Sample) -> str:	×
34	"""Return a new validation sample identifier. The identifier removes "ACC" and prepends "VAL"."""
NEW 35	return sample.internal_id.replace("ACC", "VAL")	×
36
NEW 37	@property	×
NEW 38	def validation_case_name(	×
39	self,
40	) -> str:
41	"""Return a case name with _validation appended."""
NEW 42	return f"{self.case_name}_validation"	×
43
NEW 44	def get_samples_to_copy(self) -> list[Sample]:	×
45	"""
46	Return samples associated to a case.
47	"""
NEW 48	case: Case = self.status_db.get_case_by_internal_id(self.case_id)	×
NEW 49	return [sample.internal_id for sample in case._get_samples]	×
50
NEW 51	def get_case_to_copy(self) -> Case:	×
52	"""
53	Check if a case exists in StatusDB.
54	Raises: ValueError
55	"""
NEW 56	case: Case = self.status_db.get_case_by_internal_id(self.case_id)	×
NEW 57	if not case:	×
NEW 58	raise ValueError(f"Case {self.case_id} not found in StatusDB.")	×
NEW 59	return case	×
60
NEW 61	def _generate_validation_samples(	×
62	self,
63	original_sample: Sample,
64	) -> Sample:
65	"""
66	Generate a validation sample record for StatusDB.
67	The new sample contains the original sample internal id and meta data
68	"""
NEW 69	application_version: ApplicationVersion = self._get_application_version(original_sample)	×
NEW 70	sample_name: str = self._validation_sample_name(original_sample)	×
NEW 71	validation_sample: Sample = self.status_db.add_sample(	×
72	name=sample_name,
73	internal_id=sample_name,
74	sex=original_sample.sex,
75	order=original_sample.order,
76	from_sample=original_sample.internal_id,
77	tumour=original_sample.is_tumour,
78	priority=Priority.standard,
79	customer=original_sample.customer,
80	application_version=application_version,
81	received=original_sample.received_at,
82	prepared_at=original_sample.prepared_at,
83	last_sequenced_at=original_sample.last_sequenced_at,
84	)
NEW 85	return validation_sample	×
86
NEW 87	def get_validation_samples(self):	×
NEW 88	return [self._generate_validation_samples(sample) for sample in self.original_samples]	×
89
NEW 90	def _generate_validation_case(	×
91	self,
92	) -> Case:
93	"""
94	Generate a case for the validation samples.
95	The new case uses existing case data.
96	Customer will be set to cust000.
97	"""
NEW 98	if self.status_db.case_with_name_exists(case_name=self.validation_case_name):	×
NEW 99	raise ValueError(f"Case with name {self.case_name} already exists.")	×
NEW 100	validation_case: Case = self.status_db.add_case(	×
101	data_analysis=(
102	self.input_data.data_analysis
103	if self.input_data.data_analysis
104	else self.original_case.data_analysis
105	),
106	data_delivery=(
107	self.input_data.delivery
108	if self.input_data.delivery
109	else self.original_case.delivery
110	),
111	name=self.validation_case_name,
112	panels=self.original_case.panels,
113	priority=self.original_case.priority,
114	ticket=self.original_case.latest_ticket,
115	)
NEW 116	validation_case.orders.append(self.original_case.latest_order)	×
NEW 117	validation_case.customer = "cust000"	×
NEW 118	validation_case.is_compressible = False	×
NEW 119	return validation_case	×
120
NEW 121	@staticmethod	×
NEW 122	def _get_application_version(sample: Sample) -> ApplicationVersion:	×
123	"""Return the application version for a sample."""
NEW 124	return sample.application_version	×

Clinical-Genomics / cg / 8734548414

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