remove organism validation (#4103)

remove organism existence validation

cg/services/order_validation_service/errors/sample_errors.py

@@ -52,11 +52,6 @@ class VolumeRequiredError(SampleError):
     message: str = "Volume is required"
 
 
-class OrganismDoesNotExistError(SampleError):
-    field: str = "organism"
-    message: str = "Organism does not exist"
-
-
 class SampleNameNotAvailableError(SampleError):
     field: str = "name"
     message: str = "Sample name already used in previous order"

cg/services/order_validation_service/models/order_aliases.py

@@ -11,7 +11,6 @@
 )
 
 OrderWithIndexedSamples = FluffyOrder | RmlOrder
-OrderWithSamplesFromOrganism = MutantOrder | MicrosaltOrder
 OrderWithControlSamples = (
     MetagenomeSample | MicrobialFastqOrder | MicrosaltOrder | MutantOrder | TaxprofilerSample
 )

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

@@ -14,7 +14,6 @@
     IndexSequenceMissingError,
     InvalidVolumeError,
     OccupiedWellError,
-    OrganismDoesNotExistError,
     PoolApplicationError,
     PoolPriorityError,
     SampleNameNotAvailableControlError,
@@ -29,7 +28,6 @@
 from cg.services.order_validation_service.models.order_aliases import (
     OrderWithControlSamples,
     OrderWithIndexedSamples,
-    OrderWithSamplesFromOrganism,
 )
 from cg.services.order_validation_service.models.sample_aliases import IndexedSample
 from cg.services.order_validation_service.rules.sample.utils import (
@@ -211,21 +209,6 @@ def validate_index_sequence_required(
     return errors
 
 
-def validate_organism_exists(
-    order: OrderWithSamplesFromOrganism, store: Store, **kwargs
-) -> list[OrganismDoesNotExistError]:
-    """
-    Validate that the organisms of all samples in the order exist in the database.
-    Only applicable to Microsalt and Mutant orders.
-    """
-    errors: list[OrganismDoesNotExistError] = []
-    for sample_index, sample in order.enumerated_samples:
-        if not store.get_organism_by_internal_id(sample.organism):
-            error = OrganismDoesNotExistError(sample_index=sample_index)
-            errors.append(error)
-    return errors
-
-
 def validate_pools_contain_one_application(
     order: OrderWithIndexedSamples, **kwargs
 ) -> list[PoolApplicationError]:

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

@@ -4,7 +4,6 @@
     validate_applications_not_archived,
     validate_container_name_required,
     validate_non_control_sample_names_available,
-    validate_organism_exists,
     validate_sample_names_unique,
     validate_tube_container_name_unique,
     validate_volume_interval,
@@ -20,7 +19,6 @@
     validate_applications_not_archived,
     validate_container_name_required,
     validate_non_control_sample_names_available,
-    validate_organism_exists,
     validate_sample_names_unique,
     validate_tube_container_name_unique,
     validate_volume_interval,

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

@@ -4,7 +4,6 @@
     validate_applications_not_archived,
     validate_container_name_required,
     validate_non_control_sample_names_available,
-    validate_organism_exists,
     validate_sample_names_unique,
     validate_tube_container_name_unique,
     validate_volume_interval,
@@ -20,7 +19,6 @@
     validate_applications_not_archived,
     validate_container_name_required,
     validate_non_control_sample_names_available,
-    validate_organism_exists,
     validate_volume_required,
     validate_sample_names_unique,
     validate_tube_container_name_unique,

cg/store/crud/read.py

@@ -16,8 +16,8 @@
 )
 from cg.constants.sequencing import DNA_PREP_CATEGORIES, SeqLibraryPrepCategory
 from cg.exc import CaseNotFoundError, CgError, OrderNotFoundError, SampleNotFoundError
-from cg.models.orders.sample_base import SexEnum
 from cg.models.orders.constants import OrderType
+from cg.models.orders.sample_base import SexEnum
 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

tests/fixtures/cgweb_orders/microbial_fastq.json

@@ -16,7 +16,7 @@
             "elution_buffer": "Nuclease-free water",
             "name": "prov1",
             "priority": "priority",
-            "volume": "1",
+            "volume": "100",
             "well_position": ""
         },
         {
@@ -29,7 +29,7 @@
             "elution_buffer": "Nuclease-free water",
             "name": "prov2",
             "priority": "priority",
-            "volume": "2",
+            "volume": "20",
             "well_position": "A:1"
         }
     ]

tests/meta/orders/test_meta_orders_api.py

@@ -72,8 +72,8 @@ def test_too_long_order_name():
         OrderType.FASTQ,
         OrderType.FLUFFY,
         OrderType.METAGENOME,
-        # OrderType.MICROBIAL_FASTQ,
-        # OrderType.MICROSALT,
+        OrderType.MICROBIAL_FASTQ,
+        OrderType.MICROSALT,
         # OrderType.MIP_DNA,
         # OrderType.MIP_RNA,
         # OrderType.PACBIO_LONG_READ,

tests/services/order_validation_service/sample_rules/test_data_validators.py

@@ -4,13 +4,11 @@
     ApplicationNotCompatibleError,
     ApplicationNotValidError,
     InvalidVolumeError,
-    OrganismDoesNotExistError,
 )
 from cg.services.order_validation_service.rules.sample.rules import (
     validate_application_compatibility,
     validate_application_exists,
     validate_applications_not_archived,
-    validate_organism_exists,
     validate_volume_interval,
 )
 from cg.services.order_validation_service.workflows.microsalt.models.order import MicrosaltOrder
@@ -85,29 +83,3 @@ def test_invalid_volume(valid_microsalt_order: MicrosaltOrder, base_store: Store
 
     # THEN the error should concern the invalid volume
     assert isinstance(errors[0], InvalidVolumeError)
-
-
-def test_invalid_organism(valid_microsalt_order: MicrosaltOrder, base_store: Store):
-
-    # GIVEN an order with a sample specifying a non-existent organism
-    valid_microsalt_order.samples[0].organism = "Non-existent organism"
-
-    # WHEN validating that all organisms exist
-    errors = validate_organism_exists(order=valid_microsalt_order, store=base_store)
-
-    # THEN an error should be returned
-    assert errors
-
-    # THEN the error should concern the invalid organism
-    assert isinstance(errors[0], OrganismDoesNotExistError)
-
-
-def test_valid_organisms(valid_microsalt_order: MicrosaltOrder, base_store: Store):
-
-    # GIVEN a valid order
-
-    # WHEN validating that all organisms exist
-    errors = validate_organism_exists(order=valid_microsalt_order, store=base_store)
-
-    # THEN no error should be returned
-    assert not errors