Remove unnecessary rules (#3664) (patch)

* Remove unnecessary rules

* Remove unnecessary rules

* Remove unnecessary rules

cg/services/order_validation_service/errors/case_sample_errors.py

@@ -79,11 +79,6 @@ class MotherNotInCaseError(CaseSampleError):
     message: str = "Mother must be in the same case"
 
 
-class StatusMissingError(CaseSampleError):
-    field: str = "status"
-    message: str = "Carrier status is required"
-
-
 class SampleDoesNotExistError(CaseSampleError):
     field: str = "internal_id"
     message: str = "The sample does not exist"
@@ -94,11 +89,6 @@ class SexMissingError(CaseSampleError):
     message: str = "Sex is required"
 
 
-class SourceMissingError(CaseSampleError):
-    field: str = "source"
-    message: str = "Source is required"
-
-
 class SubjectIdSameAsCaseNameError(CaseSampleError):
     field: str = "subject_id"
     message: str = "Subject id must be different from the case name"

cg/services/order_validation_service/errors/sample_errors.py

@@ -49,16 +49,6 @@ class OrganismDoesNotExistError(SampleError):
     message: str = "Organism does not exist"
 
 
-class ElutionBufferMissingError(SampleError):
-    field: str = "elution_buffer"
-    message: str = "Buffer is required"
-
-
-class ExtractionMethodMissingError(SampleError):
-    field: str = "extraction_method"
-    message: str = "Extraction method is required"
-
-
 class SampleNameNotAvailableError(SampleError):
     field: str = "name"
     message: str = "Sample name already used in previous order"

cg/services/order_validation_service/models/case.py

@@ -7,25 +7,28 @@
 from cg.services.order_validation_service.models.existing_sample import ExistingSample
 from cg.services.order_validation_service.models.sample import Sample
 
+NewSample = Annotated[Sample, Tag("new")]
+ExistingSampleType = Annotated[ExistingSample, Tag("existing")]
+
 
 class Case(BaseModel):
     name: str = Field(pattern=NAME_PATTERN, min_length=2, max_length=128)
     priority: PriorityTerms = PriorityTerms.STANDARD
     samples: list[
         Annotated[
-            Annotated[Sample, Tag("new")] | Annotated[ExistingSample, Tag("existing")],
+            NewSample | ExistingSampleType,
             Discriminator(has_internal_id),
         ]
     ]
 
-    @property
-    def enumerated_samples(self):
-        return enumerate(self.samples)
-
     @property
     def is_new(self) -> bool:
         return True
 
+    @property
+    def enumerated_samples(self):
+        return enumerate(self.samples)
+
     @property
     def enumerated_new_samples(self):
         samples: list[tuple[int, Sample]] = []

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

@@ -24,8 +24,6 @@
     SampleDoesNotExistError,
     SampleNameRepeatedError,
     SexMissingError,
-    SourceMissingError,
-    StatusMissingError,
     SubjectIdSameAsCaseNameError,
     SubjectIdSameAsSampleNameError,
     WellPositionMissingError,
@@ -232,16 +230,6 @@ def validate_sex_required_for_new_samples(order: OrderWithCases, **kwargs) -> li
     return errors
 
 
-def validate_source_required(order: OrderWithCases, **kwargs) -> list[SourceMissingError]:
-    errors: list[SourceMissingError] = []
-    for case_index, case in order.enumerated_new_cases:
-        for sample_index, sample in case.enumerated_new_samples:
-            if not sample.source:
-                error = SourceMissingError(case_index=case_index, sample_index=sample_index)
-                errors.append(error)
-    return errors
-
-
 def validate_wells_contain_at_most_one_sample(
     order: OrderWithCases, **kwargs
 ) -> list[OccupiedWellError]:
@@ -350,13 +338,3 @@ def validate_concentration_interval_if_skip_rc(
         )
         errors.extend(case_errors)
     return errors
-
-
-def validate_status_required_if_new(order: OrderWithCases, **kwargs) -> list[StatusMissingError]:
-    errors: list[StatusMissingError] = []
-    for case_index, case in order.enumerated_new_cases:
-        for sample_index, sample in case.enumerated_new_samples:
-            if not sample.status:
-                error = StatusMissingError(case_index=case_index, sample_index=sample_index)
-                errors.append(error)
-    return errors

cg/services/order_validation_service/rules/sample/rules.py

@@ -4,8 +4,6 @@
     ApplicationArchivedError,
     ApplicationNotCompatibleError,
     ApplicationNotValidError,
-    ElutionBufferMissingError,
-    ExtractionMethodMissingError,
     InvalidVolumeError,
     OccupiedWellError,
     OrganismDoesNotExistError,
@@ -68,29 +66,6 @@ def validate_organism_exists(
     return errors
 
 
-def validate_buffer_required(
-    order: OrderWithNonHumanSamples,
-    **kwargs,
-) -> list[ElutionBufferMissingError]:
-    errors: list[ElutionBufferMissingError] = []
-    for sample_index, sample in order.enumerated_samples:
-        if not sample.elution_buffer:
-            error = ElutionBufferMissingError(sample_index=sample_index)
-            errors.append(error)
-    return errors
-
-
-def validate_extraction_method_required(
-    order: OrderWithNonHumanSamples, **kwargs
-) -> list[ExtractionMethodMissingError]:
-    errors: list[ExtractionMethodMissingError] = []
-    for sample_index, sample in order.enumerated_samples:
-        if not sample.extraction_method:
-            error = ExtractionMethodMissingError(sample_index=sample_index)
-            errors.append(error)
-    return errors
-
-
 def validate_application_compatibility(
     order: OrderWithNonHumanSamples,
     store: Store,

cg/services/order_validation_service/workflows/microsalt/models/sample.py

@@ -7,10 +7,10 @@
 
 class MicrosaltSample(Sample):
     control: ControlEnum | None = None
-    elution_buffer: str | None = None
-    extraction_method: ExtractionMethod | None = None
-    organism: str | None = None
-    priority: PriorityEnum | None = None
+    elution_buffer: str
+    extraction_method: ExtractionMethod
+    organism: str
+    priority: PriorityEnum
     quantity: int | None = None
-    reference_genome: str | None = Field(default=None, max_length=255)
+    reference_genome: str = Field(max_length=255)
     sample_concentration: float | None = None

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

@@ -2,7 +2,6 @@
     validate_application_compatibility,
     validate_application_exists,
     validate_applications_not_archived,
-    validate_buffer_required,
     validate_organism_exists,
     validate_sample_names_available,
     validate_sample_names_unique,
@@ -15,7 +14,6 @@
     validate_application_compatibility,
     validate_application_exists,
     validate_applications_not_archived,
-    validate_buffer_required,
     validate_organism_exists,
     validate_sample_names_available,
     validate_sample_names_unique,

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

@@ -20,8 +20,6 @@
     validate_sample_names_not_repeated,
     validate_samples_exist,
     validate_sex_required_for_new_samples,
-    validate_source_required,
-    validate_status_required_if_new,
     validate_subject_ids_different_from_case_names,
     validate_subject_ids_different_from_sample_names,
     validate_volume_interval,
@@ -51,8 +49,6 @@
     validate_samples_exist,
     validate_sample_names_not_repeated,
     validate_sex_required_for_new_samples,
-    validate_source_required,
-    validate_status_required_if_new,
     validate_subject_ids_different_from_case_names,
     validate_subject_ids_different_from_sample_names,
     validate_volume_interval,

cg/services/order_validation_service/workflows/tomte/models/case.py

@@ -8,17 +8,15 @@
     TomteSample,
 )
 
+NewSample = Annotated[TomteSample, Tag("new")]
+OldSample = Annotated[ExistingSample, Tag("existing")]
+
 
 class TomteCase(Case):
     cohorts: list[str] | None = None
     panels: list[str]
     synopsis: str | None = None
-    samples: list[
-        Annotated[
-            Annotated[TomteSample, Tag("new")] | Annotated[ExistingSample, Tag("existing")],
-            Discriminator(has_internal_id),
-        ]
-    ]
+    samples: list[Annotated[NewSample | OldSample, Discriminator(has_internal_id)]]
 
     def get_sample(self, sample_name: str) -> TomteSample | None:
         for sample in self.samples:

cg/services/order_validation_service/workflows/tomte/models/order.py

@@ -9,12 +9,10 @@
 )
 from cg.services.order_validation_service.workflows.tomte.models.case import TomteCase
 
+NewCase = Annotated[TomteCase, Tag("new")]
+OldCase = Annotated[ExistingCase, Tag("existing")]
+
 
 class TomteOrder(OrderWithCases):
-    cases: list[
-        Annotated[
-            Annotated[TomteCase, Tag("new")] | Annotated[ExistingCase, Tag("existing")],
-            Discriminator(has_internal_id),
-        ]
-    ]
+    cases: list[Annotated[NewCase | OldCase, Discriminator(has_internal_id)]]
     delivery_type: TomteDeliveryType

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

@@ -20,15 +20,12 @@
     validate_sample_names_not_repeated,
     validate_samples_exist,
     validate_sex_required_for_new_samples,
-    validate_source_required,
-    validate_status_required_if_new,
     validate_subject_ids_different_from_case_names,
     validate_subject_ids_different_from_sample_names,
     validate_volume_interval,
     validate_wells_contain_at_most_one_sample,
 )
 
-
 CASE_RULES: list[callable] = [
     validate_case_internal_ids_exist,
     validate_case_names_available,
@@ -52,8 +49,6 @@
     validate_samples_exist,
     validate_sample_names_not_repeated,
     validate_sex_required_for_new_samples,
-    validate_source_required,
-    validate_status_required_if_new,
     validate_subject_ids_different_from_case_names,
     validate_subject_ids_different_from_sample_names,
     validate_volume_interval,

tests/services/order_validation_service/sample_rules/conftest.py

@@ -1,9 +1,10 @@
 import pytest
 
 from cg.constants.constants import Workflow
-from cg.models.orders.sample_base import ContainerEnum
+from cg.models.orders.sample_base import ContainerEnum, PriorityEnum
 from cg.services.order_validation_service.constants import (
     MINIMUM_VOLUME,
+    ElutionBuffer,
     ExtractionMethod,
 )
 from cg.services.order_validation_service.workflows.microsalt.constants import (
@@ -25,8 +26,10 @@ def create_microsalt_sample(id: int) -> MicrosaltSample:
         application="MWRNXTR003",
         container=ContainerEnum.plate,
         container_name="ContainerName",
+        elution_buffer=ElutionBuffer.WATER,
         extraction_method=ExtractionMethod.MAELSTROM,
         organism="C. jejuni",
+        priority=PriorityEnum.standard,
         require_qc_ok=True,
         reference_genome="NC_00001",
         well_position=f"A:{id}",

tests/services/order_validation_service/sample_rules/test_data_validators.py

@@ -3,17 +3,13 @@
     ApplicationArchivedError,
     ApplicationNotCompatibleError,
     ApplicationNotValidError,
-    ElutionBufferMissingError,
-    ExtractionMethodMissingError,
     InvalidVolumeError,
     OrganismDoesNotExistError,
 )
 from cg.services.order_validation_service.rules.sample.rules import (
     validate_application_compatibility,
     validate_application_exists,
     validate_applications_not_archived,
-    validate_buffer_required,
-    validate_extraction_method_required,
     validate_organism_exists,
     validate_volume_interval,
 )
@@ -119,33 +115,3 @@ def test_valid_organisms(valid_order: MicrosaltOrder, base_store: Store):
 
     # THEN no error should be returned
     assert not errors
-
-
-def test_buffer_required(valid_order: MicrosaltOrder):
-
-    # GIVEN an order containing a sample with missing buffer
-    valid_order.samples[0].elution_buffer = None
-
-    # WHEN validating that buffers are set for new samples
-    errors = validate_buffer_required(order=valid_order)
-
-    # THEN an error should be returned
-    assert errors
-
-    # THEN the error should concern the missing buffer
-    assert isinstance(errors[0], ElutionBufferMissingError)
-
-
-def test_extraction_method_missing(valid_order: MicrosaltOrder):
-
-    # GIVEN an order containing a sample with missing extraction method
-    valid_order.samples[0].extraction_method = None
-
-    # WHEN validating that the extraction method is set for all new samples
-    errors = validate_extraction_method_required(order=valid_order)
-
-    # THEN an error should be raised
-    assert errors
-
-    # THEN the error should concern the missing extraction method
-    assert isinstance(errors[0], ExtractionMethodMissingError)

tests/services/order_validation_service/test_data_validators.py

@@ -11,7 +11,6 @@
     ApplicationNotValidError,
     SampleDoesNotExistError,
     SexMissingError,
-    SourceMissingError,
 )
 from cg.services.order_validation_service.models.existing_case import ExistingCase
 from cg.services.order_validation_service.models.existing_sample import ExistingSample
@@ -26,7 +25,6 @@
     validate_gene_panels_exist,
     validate_samples_exist,
     validate_sex_required_for_new_samples,
-    validate_source_required,
 )
 from cg.services.order_validation_service.workflows.tomte.models.order import TomteOrder
 from cg.store.models import Application
@@ -172,16 +170,3 @@ def test_sex_missing_for_new_sample(valid_order: TomteOrder):
 
     # THEN the error should concern the missing sex
     assert isinstance(errors[0], SexMissingError)
-
-
-def test_source_missing_for_new_sample(valid_order: TomteOrder):
-
-    # GIVEN an order with a new sample without 'source' set
-    valid_order.cases[0].samples[0].source = None
-
-    # WHEN validating that all new samples have 'source' set
-    errors = validate_source_required(order=valid_order)
-
-    assert errors
-
-    assert isinstance(errors[0], SourceMissingError)