Add balsamic sample sex validation (#3665)

cg/services/order_validation_service/errors/case_sample_errors.py

@@ -133,3 +133,8 @@ class InvalidVolumeError(CaseSampleError):
 class InvalidBufferError(CaseSampleError):
     field: str = "elution_buffer"
     message: str = "The chosen buffer is not allowed when skipping reception control"
+
+
+class SexSubjectIdError(CaseSampleError):
+    field: str = "sex"
+    message: str = "Another sample with the same subject id has a different sex"

cg/services/order_validation_service/workflows/balsamic/rules/case_sample/rules.py

@@ -0,0 +1,30 @@
+from cg.services.order_validation_service.errors.case_sample_errors import SexSubjectIdError
+from cg.services.order_validation_service.workflows.balsamic.models.order import BalsamicOrder
+from cg.services.order_validation_service.workflows.balsamic.rules.case_sample.utils import (
+    has_sex_and_subject,
+)
+from cg.store.store import Store
+
+
+def validate_subject_sex_consistency(
+    order: BalsamicOrder,
+    store: Store,
+) -> list[SexSubjectIdError]:
+    errors: list[SexSubjectIdError] = []
+
+    for case_index, case in order.enumerated_new_cases:
+        for sample_index, sample in case.enumerated_new_samples:
+            if not has_sex_and_subject(sample):
+                continue
+
+            if store.sample_exists_with_different_sex(
+                customer_internal_id=order.customer,
+                subject_id=sample.subject_id,
+                sex=sample.sex,
+            ):
+                error = SexSubjectIdError(
+                    case_index=case_index,
+                    sample_index=sample_index,
+                )
+                errors.append(error)
+    return errors

cg/services/order_validation_service/workflows/balsamic/rules/case_sample/utils.py

@@ -0,0 +1,8 @@
+from cg.models.orders.sample_base import SexEnum
+from cg.services.order_validation_service.workflows.balsamic.models.sample import (
+    BalsamicSample,
+)
+
+
+def has_sex_and_subject(sample: BalsamicSample) -> bool:
+    return bool(sample.subject_id and sample.sex != SexEnum.unknown)

cg/services/order_validation_service/workflows/balsamic/validation_rules.py

@@ -20,6 +20,10 @@
     validate_volume_interval,
     validate_wells_contain_at_most_one_sample,
 )
+from cg.services.order_validation_service.workflows.balsamic.rules.case_sample.rules import (
+    validate_subject_sex_consistency,
+)
+
 
 CASE_RULES: list[callable] = [
     validate_case_internal_ids_exist,
@@ -43,4 +47,5 @@
     validate_subject_ids_different_from_sample_names,
     validate_volume_interval,
     validate_wells_contain_at_most_one_sample,
+    validate_subject_sex_consistency,
 ]

cg/store/crud/read.py

@@ -10,9 +10,13 @@
 from cg.constants import SequencingRunDataAvailability, Workflow
 from cg.constants.constants import CaseActions, CustomerId, PrepCategory, SampleType
 from cg.exc import CaseNotFoundError, CgError, OrderNotFoundError, SampleNotFoundError
+from cg.models.orders.sample_base import SexEnum
 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,
@@ -21,9 +25,6 @@
     ApplicationFilter,
     apply_application_filter,
 )
-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_application_limitations_filters import (
     ApplicationLimitationsFilter,
     apply_application_limitations_filter,
@@ -64,11 +65,13 @@
 )
 from cg.store.filters.status_invoice_filters import InvoiceFilter, apply_invoice_filter
 from cg.store.filters.status_order_filters import OrderFilter, apply_order_filters
-
-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 (
-    apply_pac_bio_smrt_cell_filters,
     PacBioSMRTCellFilter,
+    apply_pac_bio_smrt_cell_filters,
 )
 from cg.store.filters.status_panel_filters import PanelFilter, apply_panel_filter
 from cg.store.filters.status_pool_filters import PoolFilter, apply_pool_filter
@@ -91,12 +94,12 @@
     Invoice,
     Order,
     Organism,
+    PacBioSMRTCell,
     Panel,
     Pool,
     Sample,
     SampleRunMetrics,
     User,
-    PacBioSMRTCell,
 )
 
 LOG = logging.getLogger(__name__)
@@ -1562,3 +1565,20 @@ def get_case_ids_for_samples(self, sample_ids: list[int]) -> list[str]:
         for sample_id in sample_ids:
             case_ids.extend(self.get_case_ids_with_sample(sample_id))
         return list(set(case_ids))
+
+    def sample_exists_with_different_sex(
+        self,
+        customer_internal_id: str,
+        subject_id: str,
+        sex: SexEnum,
+    ) -> bool:
+        samples: list[Sample] = self.get_samples_by_customer_and_subject_id(
+            customer_internal_id=customer_internal_id,
+            subject_id=subject_id,
+        )
+        for sample in samples:
+            if sample.sex == SexEnum.unknown:
+                continue
+            if sample.sex != sex:
+                return True
+        return False

tests/services/order_validation_service/workflows/balsamic/conftest.py

@@ -0,0 +1,55 @@
+import pytest
+
+from cg.constants.constants import GenomeVersion, Workflow
+from cg.models.orders.sample_base import ContainerEnum, ControlEnum, SexEnum, StatusEnum
+from cg.services.order_validation_service.constants import MINIMUM_VOLUME
+from cg.services.order_validation_service.workflows.balsamic.constants import BalsamicDeliveryType
+from cg.services.order_validation_service.workflows.balsamic.models.case import BalsamicCase
+from cg.services.order_validation_service.workflows.balsamic.models.order import BalsamicOrder
+from cg.services.order_validation_service.workflows.balsamic.models.sample import BalsamicSample
+
+
+def create_sample(id: int) -> BalsamicSample:
+    return BalsamicSample(
+        name=f"name{id}",
+        application="PANKTTR020",
+        container=ContainerEnum.plate,
+        container_name="ContainerName",
+        control=ControlEnum.not_control,
+        require_qc_ok=True,
+        reference_genome=GenomeVersion.HG19,
+        sex=SexEnum.female,
+        source="source",
+        status=StatusEnum.affected,
+        subject_id=f"subject{id}",
+        well_position=f"A:{id}",
+        volume=MINIMUM_VOLUME,
+        is_tumour=False,
+    )
+
+
+def create_case(samples: list[BalsamicSample]) -> BalsamicCase:
+    return BalsamicCase(
+        name="name",
+        samples=samples,
+    )
+
+
+def create_order(cases: list[BalsamicCase]) -> BalsamicOrder:
+    return BalsamicOrder(
+        connect_to_ticket=True,
+        delivery_type=BalsamicDeliveryType.FASTQ_ANALYSIS,
+        name="order_name",
+        ticket_number="#12345",
+        workflow=Workflow.BALSAMIC,
+        user_id=1,
+        customer="cust000",
+        cases=cases,
+    )
+
+
+@pytest.fixture
+def valid_order() -> BalsamicOrder:
+    sample = create_sample(1)
+    case = create_case([sample])
+    return create_order([case])

tests/services/order_validation_service/workflows/balsamic/test_case_sample_rules.py

@@ -0,0 +1,32 @@
+from cg.models.orders.sample_base import SexEnum
+from cg.services.order_validation_service.errors.case_sample_errors import SexSubjectIdError
+from cg.services.order_validation_service.workflows.balsamic.models.order import BalsamicOrder
+from cg.services.order_validation_service.workflows.balsamic.rules.case_sample.rules import (
+    validate_subject_sex_consistency,
+)
+from cg.store.models import Sample
+from cg.store.store import Store
+
+
+def test_validate_sex_subject_id_clash(valid_order: BalsamicOrder, sample_store: Store):
+    # GIVEN an existing sample
+    sample = sample_store.session.query(Sample).first()
+
+    # GIVEN an order and sample with the same customer and subject id
+    valid_order.customer = sample.customer.internal_id
+    valid_order.cases[0].samples[0].subject_id = "subject"
+    sample.subject_id = "subject"
+
+    # GIVEN a sample in the order that has a different sex
+    valid_order.cases[0].samples[0].sex = SexEnum.female
+    sample.sex = SexEnum.male
+
+    # WHEN validating the order
+    errors = validate_subject_sex_consistency(
+        order=valid_order,
+        store=sample_store,
+    )
+
+    # THEN an error should be given for the clash
+    assert errors
+    assert isinstance(errors[0], SexSubjectIdError)