diff --git a/.bumpversion.cfg b/.bumpversion.cfg index c52f3b3a46..7fd551a5cf 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 64.5.6 +current_version = 64.5.8 commit = True tag = True tag_name = v{new_version} diff --git a/cg/__init__.py b/cg/__init__.py index e977f9189d..e81465b9ab 100644 --- a/cg/__init__.py +++ b/cg/__init__.py @@ -1,2 +1,2 @@ __title__ = "cg" -__version__ = "64.5.6" +__version__ = "64.5.8" diff --git a/cg/store/crud/read.py b/cg/store/crud/read.py index 8b3a0e175e..29cbbf33f6 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, @@ -1031,11 +1011,11 @@ 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() - def get_families_with_samples(self) -> Query: + def get_cases_with_samples(self) -> Query: """Return all cases in the database with samples.""" return self._get_join_cases_with_samples_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, ) @@ -1238,7 +1218,7 @@ def observations_to_upload(self, workflow: Workflow = None) -> Query: CaseFilter.WITH_LOQUSDB_SUPPORTED_SEQUENCING_METHOD, ] records: Query = apply_case_filter( - cases=self.get_families_with_samples(), + cases=self.get_cases_with_samples(), filter_functions=case_filter_functions, workflow=workflow, ) @@ -1249,7 +1229,7 @@ def observations_to_upload(self, workflow: Workflow = None) -> Query: def observations_uploaded(self, workflow: Workflow = None) -> Query: """Return observations that have been uploaded.""" records: Query = apply_case_filter( - cases=self.get_families_with_samples(), + cases=self.get_cases_with_samples(), filter_functions=[CaseFilter.WITH_LOQUSDB_SUPPORTED_WORKFLOW], workflow=workflow, ) diff --git a/pyproject.toml b/pyproject.toml index ca07ee347e..7c0e9667fd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [tool.poetry] name = "cg" -version = "64.5.6" +version = "64.5.8" description = "Clinical Genomics command center" authors = ["Clinical Genomics "] readme = "README.md"