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feat(refactor): get_families_with_samples #3927

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feat(refactor): get_families_with_samples #3927

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feat(refactor): get_families_with_samples
henrikstranneheim Nov 8, 2024
3644b52
Merge branch 'master' into refactor-get_families_with_samples
henrikstranneheim Nov 11, 2024
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40 changes: 30 additions & 10 deletions cg/store/crud/read.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,19 @@
from cg.exc import CaseNotFoundError, CgError, OrderNotFoundError, SampleNotFoundError
from cg.models.orders.constants import OrderType
from cg.server.dto.orders.orders_request import OrdersRequest
from cg.server.dto.samples.collaborator_samples_request import CollaboratorSamplesRequest
from cg.server.dto.samples.collaborator_samples_request import (
CollaboratorSamplesRequest,
)
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,
Expand All @@ -26,14 +34,23 @@
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,
Expand All @@ -52,7 +69,10 @@
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,
Expand Down Expand Up @@ -1015,7 +1035,7 @@ def get_families_with_analyses(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()

Expand Down Expand Up @@ -1211,7 +1231,7 @@ 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,
)
Expand All @@ -1222,7 +1242,7 @@ 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,
)
Expand Down
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