Merge branch 'master' into write_config_taxprofiler

.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}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "64.5.6"
+__version__ = "64.5.8"

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,
         )

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 <[email protected]>"]
 readme = "README.md"