12276038756

Committed 11 Dec 2024 12:08PM UTC coverage: 84.029%. First build

Build # 12276038756

Build Type

Pull #3936

github

Committed by

web-flow

Commit Message

Merge 4694dc240 into ab9ded5a4

Pull Request Pull Request #3936: (Improve order flow) Minimal implementation FASTQSubmission

Run Details

33 of 53 new or added lines in 11 files covered. (62.26%)

25391 of 30217 relevant lines covered (84.03%)

0.84 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

58.06

/cg/services/order_validation_service/workflows/fastq/validation_service.py

from cg.exc import OrderError
from cg.services.order_validation_service.errors.sample_errors import SampleError
from cg.services.order_validation_service.errors.validation_errors import ValidationErrors
from cg.services.order_validation_service.model_validator.model_validator import ModelValidator
from cg.services.order_validation_service.models.order import Order
from cg.services.order_validation_service.order_validation_service import OrderValidationService
from cg.services.order_validation_service.response_mapper import create_order_validation_response
from cg.services.order_validation_service.utils import (
    apply_order_validation,
    apply_sample_validation,
)
from cg.services.order_validation_service.workflows.fastq.models.order import FastqOrder
from cg.services.order_validation_service.workflows.fastq.validation_rules import SAMPLE_RULES
from cg.services.order_validation_service.workflows.order_validation_rules import ORDER_RULES
from cg.store.store import Store


class FastqValidationService(OrderValidationService):

    def __init__(self, store: Store):
        self.store = store

    def validate(self, raw_order: dict) -> dict:
        parsed_order, errors = ModelValidator.validate(order=raw_order, model=FastqOrder)
        if parsed_order:
            errors: ValidationErrors = self._perform_rule_validation(order=parsed_order)
        return create_order_validation_response(raw_order=raw_order, errors=errors)

    def _perform_rule_validation(self, order: FastqOrder) -> ValidationErrors:

        order_errors: list[OrderError] = apply_order_validation(
            rules=ORDER_RULES,
            order=order,
            store=self.store,
        )
        sample_errors: list[SampleError] = apply_sample_validation(
            rules=SAMPLE_RULES,
            order=order,
            store=self.store,
        )

        return ValidationErrors(
            sample_errors=sample_errors,
            order_errors=order_errors,
        )

    def parse_and_validate(self, raw_order: dict) -> FastqOrder | dict:
        parsed_order, errors = ModelValidator.validate(order=raw_order, model=FastqOrder)
        if parsed_order:
            errors: ValidationErrors = self._perform_rule_validation(order=parsed_order)
        if not errors.is_empty:
            return create_order_validation_response(raw_order=raw_order, errors=errors)
        return parsed_order

1	from cg.exc import OrderError	1✔
2	from cg.services.order_validation_service.errors.sample_errors import SampleError	1✔
3	from cg.services.order_validation_service.errors.validation_errors import ValidationErrors	1✔
4	from cg.services.order_validation_service.model_validator.model_validator import ModelValidator	1✔
5	from cg.services.order_validation_service.models.order import Order	1✔
6	from cg.services.order_validation_service.order_validation_service import OrderValidationService	1✔
7	from cg.services.order_validation_service.response_mapper import create_order_validation_response	1✔
8	from cg.services.order_validation_service.utils import (	1✔
9	apply_order_validation,
10	apply_sample_validation,
11	)
12	from cg.services.order_validation_service.workflows.fastq.models.order import FastqOrder	1✔
13	from cg.services.order_validation_service.workflows.fastq.validation_rules import SAMPLE_RULES	1✔
14	from cg.services.order_validation_service.workflows.order_validation_rules import ORDER_RULES	1✔
15	from cg.store.store import Store	1✔
16
17
18	class FastqValidationService(OrderValidationService):	1✔
19
20	def __init__(self, store: Store):	1✔
21	self.store = store	1✔
22
23	def validate(self, raw_order: dict) -> dict:	1✔
NEW 24	parsed_order, errors = ModelValidator.validate(order=raw_order, model=FastqOrder)	×
NEW 25	if parsed_order:	×
NEW 26	errors: ValidationErrors = self._perform_rule_validation(order=parsed_order)	×
27	return create_order_validation_response(raw_order=raw_order, errors=errors)	×
28
29	def _perform_rule_validation(self, order: FastqOrder) -> ValidationErrors:	1✔
30
31	order_errors: list[OrderError] = apply_order_validation(	×
32	rules=ORDER_RULES,
33	order=order,
34	store=self.store,
35	)
36	sample_errors: list[SampleError] = apply_sample_validation(	×
37	rules=SAMPLE_RULES,
38	order=order,
39	store=self.store,
40	)
41
42	return ValidationErrors(	×
43	sample_errors=sample_errors,
44	order_errors=order_errors,
45	)
46
47	def parse_and_validate(self, raw_order: dict) -> FastqOrder \| dict:	1✔
NEW 48	parsed_order, errors = ModelValidator.validate(order=raw_order, model=FastqOrder)	×
NEW 49	if parsed_order:	×
NEW 50	errors: ValidationErrors = self._perform_rule_validation(order=parsed_order)	×
NEW 51	if not errors.is_empty:	×
NEW 52	return create_order_validation_response(raw_order=raw_order, errors=errors)	×
NEW 53	return parsed_order	×

Clinical-Genomics / cg / 12276038756

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous