diff --git a/cg/store/crud/read.py b/cg/store/crud/read.py index 8b3a0e175e..b2cf67c277 100644 --- a/cg/store/crud/read.py +++ b/cg/store/crud/read.py @@ -11,20 +11,12 @@ from cg.constants.constants import CaseActions, CustomerId, PrepCategory, SampleType from cg.exc import CaseNotFoundError, CgError, OrderNotFoundError, SampleNotFoundError from cg.models.orders.constants import OrderType -from cg.server.dto.samples.collaborator_samples_request import ( - CollaboratorSamplesRequest, -) +from cg.server.dto.samples.collaborator_samples_request import CollaboratorSamplesRequest from cg.services.orders.order_service.models import OrderQueryParams from cg.store.base import BaseHandler from cg.store.exc import EntryNotFoundError -from cg.store.filters.status_analysis_filters import ( - AnalysisFilter, - apply_analysis_filter, -) -from cg.store.filters.status_application_filters import ( - ApplicationFilter, - apply_application_filter, -) +from cg.store.filters.status_analysis_filters import AnalysisFilter, apply_analysis_filter +from cg.store.filters.status_application_filters import ApplicationFilter, apply_application_filter from cg.store.filters.status_application_limitations_filters import ( ApplicationLimitationsFilter, apply_application_limitations_filter, @@ -34,23 +26,14 @@ apply_application_versions_filter, ) from cg.store.filters.status_bed_filters import BedFilter, apply_bed_filter -from cg.store.filters.status_bed_version_filters import ( - BedVersionFilter, - apply_bed_version_filter, -) +from cg.store.filters.status_bed_version_filters import BedVersionFilter, apply_bed_version_filter from cg.store.filters.status_case_filters import CaseFilter, apply_case_filter -from cg.store.filters.status_case_sample_filters import ( - CaseSampleFilter, - apply_case_sample_filter, -) +from cg.store.filters.status_case_sample_filters import CaseSampleFilter, apply_case_sample_filter from cg.store.filters.status_collaboration_filters import ( CollaborationFilter, apply_collaboration_filter, ) -from cg.store.filters.status_customer_filters import ( - CustomerFilter, - apply_customer_filter, -) +from cg.store.filters.status_customer_filters import CustomerFilter, apply_customer_filter from cg.store.filters.status_illumina_flow_cell_filters import ( IlluminaFlowCellFilter, apply_illumina_flow_cell_filters, @@ -69,10 +52,7 @@ OrderTypeApplicationFilter, apply_order_type_application_filter, ) -from cg.store.filters.status_organism_filters import ( - OrganismFilter, - apply_organism_filter, -) +from cg.store.filters.status_organism_filters import OrganismFilter, apply_organism_filter from cg.store.filters.status_pacbio_smrt_cell_filters import ( PacBioSMRTCellFilter, apply_pac_bio_smrt_cell_filters, @@ -1031,7 +1011,7 @@ def get_samples_to_sequence(self) -> list[Sample]: ) return records.order_by(Sample.prepared_at).all() - def get_families_with_analyses(self) -> Query: + def get_cases_with_analyzes(self) -> Query: """Return all cases in the database with an analysis.""" return self._get_outer_join_cases_with_analyses_query() @@ -1062,7 +1042,7 @@ def get_cases_to_analyze(self, workflow: Workflow = None, limit: int = None) -> CaseFilter.FOR_ANALYSIS, ] cases = apply_case_filter( - cases=self.get_families_with_analyses(), + cases=self.get_cases_with_analyzes(), filter_functions=case_filter_functions, workflow=workflow, )