12294344407

Committed 12 Dec 2024 10:19AM UTC coverage: 80.834%. First build

Build # 12294344407

Build Type

Pull #3936

github

Committed by

web-flow

Commit Message

Merge 82f219ba6 into ab9ded5a4

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

Run Details

34 of 52 new or added lines in 11 files covered. (65.38%)

13648 of 16884 relevant lines covered (80.83%)

1.5 hits per line

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56.67

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

from cg.exc import OrderError, OrderFormError
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.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:
        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:
            raise OrderFormError(message="Order form contained errors")
        return parsed_order

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

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