10264300180

Committed 06 Aug 2024 09:52AM UTC coverage: 84.348%. First build

Build # 10264300180

Build Type

Pull #3521

github

Committed by

web-flow

Commit Message

Merge 0567ad449 into ed66523ed

Pull Request Pull Request #3521: Add application to response

Run Details

49 of 55 new or added lines in 2 files covered. (89.09%)

20942 of 24828 relevant lines covered (84.35%)

0.84 hits per line

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34.48

/cg/services/sample_service/utils.py

from datetime import datetime

from cg.server.dto.samples.samples_response import (
    ApplicationDTO,
    ApplicationVersionDTO,
    CustomerDto,
    SampleDTO,
    SamplesResponse,
)
from cg.store.models import Application, ApplicationVersion, Sample


def get_cancel_comment(user_name: str) -> str:
    date: str = datetime.now().strftime("%Y-%m-%d")
    return f"Cancelled {date} by {user_name}"


def get_confirmation_message(sample_ids: list[str], case_ids: list[str]) -> str:
    message = f"Cancelled {len(sample_ids)} samples. "
    if case_ids:
        cases = ", ".join(case_ids)
        message += f"Found {len(case_ids)} cases with additional samples: {cases}."
    else:
        message += "No case contained additional samples."
    return message


def create_samples_response(samples: list[Sample]) -> SamplesResponse:
    sample_dtos = []
    for sample in samples:
        sample_dtos.append(create_sample_dto(sample))
    return SamplesResponse(samples=sample_dtos, total=len(samples))


def create_sample_dto(sample: Sample) -> SampleDTO:
    customer = create_customer_dto(sample)
    application = create_application_dto(sample.application_version.application)
    application_version = create_application_version_dto(sample.application_version)

    return SampleDTO(
        comment=sample.comment,
        customer=customer,
        internal_id=sample.internal_id,
        name=sample.name,
        phenotype_groups=sample.phenotype_groups,
        phenotype_terms=sample.phenotype_terms,
        priority=sample.priority,
        reference_genome=sample.reference_genome,
        status=sample.state,
        subject_id=sample.subject_id,
        tumour=sample.is_tumour,
        application=application,
        application_version=application_version,
    )


def create_customer_dto(sample: Sample) -> CustomerDto:
    return CustomerDto(
        internal_id=sample.customer.internal_id,
        name=sample.customer.name,
    )


def create_application_dto(application: Application) -> ApplicationDTO:
    return ApplicationDTO(
        id=application.id,
        tag=application.tag,
        prep_category=application.prep_category,
        is_external=application.is_external,
        description=application.description,
        is_accredited=application.is_accredited,
        turnaround_time=application.turnaround_time,
        minimum_order=application.minimum_order,
        sequencing_depth=application.sequencing_depth,
        min_sequencing_depth=application.min_sequencing_depth,
        target_reads=application.target_reads,
        percent_reads_guaranteed=application.percent_reads_guaranteed,
        sample_amount=application.sample_amount,
        sample_volume=application.sample_volume,
        sample_concentration=application.sample_concentration,
        sample_concentration_minimum=application.sample_concentration_minimum,
        sample_concentration_maximum=application.sample_concentration_maximum,
        sample_concentration_minimum_cfdna=application.sample_concentration_minimum_cfdna,
        sample_concentration_maximum_cfdna=application.sample_concentration_maximum_cfdna,
        priority_processing=application.priority_processing,
        details=application.details,
        limitations=application.details,
        percent_kth=application.percent_kth,
        comment=application.comment,
        is_archived=application.is_archived,
        created_at=application.created_at,
        updated_at=application.updated_at,
    )


def create_application_version_dto(version: ApplicationVersion) -> ApplicationVersionDTO:
    return ApplicationVersionDTO(
        id=version.id,
        version=version.version,
        valid_from=version.valid_from,
        price_standard=version.price_standard,
        price_priority=version.price_priority,
        price_express=version.price_express,
        price_research=version.price_research,
        price_clinical_trials=version.price_clinical_trials,
        comment=version.comment,
        created_at=version.created_at,
        updated_at=version.updated_at,
        application_id=version.application_id,
    )

1	from datetime import datetime	1✔
2
3	from cg.server.dto.samples.samples_response import (	1✔
4	ApplicationDTO,
5	ApplicationVersionDTO,
6	CustomerDto,
7	SampleDTO,
8	SamplesResponse,
9	)
10	from cg.store.models import Application, ApplicationVersion, Sample	1✔
11
12
13	def get_cancel_comment(user_name: str) -> str:	1✔
14	date: str = datetime.now().strftime("%Y-%m-%d")	×
15	return f"Cancelled {date} by {user_name}"	×
16
17
18	def get_confirmation_message(sample_ids: list[str], case_ids: list[str]) -> str:	1✔
19	message = f"Cancelled {len(sample_ids)} samples. "	×
20	if case_ids:	×
21	cases = ", ".join(case_ids)	×
22	message += f"Found {len(case_ids)} cases with additional samples: {cases}."	×
23	else:
24	message += "No case contained additional samples."	×
25	return message	×
26
27
28	def create_samples_response(samples: list[Sample]) -> SamplesResponse:	1✔
29	sample_dtos = []	×
30	for sample in samples:	×
31	sample_dtos.append(create_sample_dto(sample))	×
32	return SamplesResponse(samples=sample_dtos, total=len(samples))	×
33
34
35	def create_sample_dto(sample: Sample) -> SampleDTO:	1✔
NEW 36	customer = create_customer_dto(sample)	×
NEW 37	application = create_application_dto(sample.application_version.application)	×
NEW 38	application_version = create_application_version_dto(sample.application_version)	×
39
40	return SampleDTO(	×
41	comment=sample.comment,
42	customer=customer,
43	internal_id=sample.internal_id,
44	name=sample.name,
45	phenotype_groups=sample.phenotype_groups,
46	phenotype_terms=sample.phenotype_terms,
47	priority=sample.priority,
48	reference_genome=sample.reference_genome,
49	status=sample.state,
50	subject_id=sample.subject_id,
51	tumour=sample.is_tumour,
52	application=application,
53	application_version=application_version,
54	)
55
56
57	def create_customer_dto(sample: Sample) -> CustomerDto:	1✔
NEW 58	return CustomerDto(	×
59	internal_id=sample.customer.internal_id,
60	name=sample.customer.name,
61	)
62
63
64	def create_application_dto(application: Application) -> ApplicationDTO:	1✔
NEW 65	return ApplicationDTO(	×
66	id=application.id,
67	tag=application.tag,
68	prep_category=application.prep_category,
69	is_external=application.is_external,
70	description=application.description,
71	is_accredited=application.is_accredited,
72	turnaround_time=application.turnaround_time,
73	minimum_order=application.minimum_order,
74	sequencing_depth=application.sequencing_depth,
75	min_sequencing_depth=application.min_sequencing_depth,
76	target_reads=application.target_reads,
77	percent_reads_guaranteed=application.percent_reads_guaranteed,
78	sample_amount=application.sample_amount,
79	sample_volume=application.sample_volume,
80	sample_concentration=application.sample_concentration,
81	sample_concentration_minimum=application.sample_concentration_minimum,
82	sample_concentration_maximum=application.sample_concentration_maximum,
83	sample_concentration_minimum_cfdna=application.sample_concentration_minimum_cfdna,
84	sample_concentration_maximum_cfdna=application.sample_concentration_maximum_cfdna,
85	priority_processing=application.priority_processing,
86	details=application.details,
87	limitations=application.details,
88	percent_kth=application.percent_kth,
89	comment=application.comment,
90	is_archived=application.is_archived,
91	created_at=application.created_at,
92	updated_at=application.updated_at,
93	)
94
95
96	def create_application_version_dto(version: ApplicationVersion) -> ApplicationVersionDTO:	1✔
NEW 97	return ApplicationVersionDTO(	×
98	id=version.id,
99	version=version.version,
100	valid_from=version.valid_from,
101	price_standard=version.price_standard,
102	price_priority=version.price_priority,
103	price_express=version.price_express,
104	price_research=version.price_research,
105	price_clinical_trials=version.price_clinical_trials,
106	comment=version.comment,
107	created_at=version.created_at,
108	updated_at=version.updated_at,
109	application_id=version.application_id,
110	)

Clinical-Genomics / cg / 10264300180

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