Add validations for Nallo orders (#4342)(minor)

## Description

### Added

- Models and validation rules to make Nallo orderable in cg
- Connect Nallo with CaseStoring service
---------

Co-authored-by: Sebastian Diaz <[email protected]>

Author: eliottBo

cg/constants/constants.py

@@ -165,22 +165,22 @@ class SampleType(StrEnum):
 
 
 class DataDelivery(StrEnum):
-    ANALYSIS_FILES: str = "analysis"
-    ANALYSIS_SCOUT: str = "analysis-scout"
-    BAM: str = "bam"
-    FASTQ: str = "fastq"
-    FASTQ_SCOUT: str = "fastq-scout"
-    FASTQ_QC: str = "fastq_qc"
-    FASTQ_ANALYSIS: str = "fastq-analysis"
-    FASTQ_QC_ANALYSIS: str = "fastq_qc-analysis"
-    FASTQ_ANALYSIS_SCOUT: str = "fastq-analysis-scout"
-    NIPT_VIEWER: str = "nipt-viewer"
-    NO_DELIVERY: str = "no-delivery"
-    RAW_DATA_ANALYSIS: str = "raw_data-analysis"
-    RAW_DATA_ANALYSIS_SCOUT: str = "raw_data-analysis-scout"
-    RAW_DATA_SCOUT: str = "raw_data-scout"
-    SCOUT: str = "scout"
-    STATINA: str = "statina"
+    ANALYSIS_FILES = "analysis"
+    ANALYSIS_SCOUT = "analysis-scout"
+    BAM = "bam"
+    FASTQ = "fastq"
+    FASTQ_SCOUT = "fastq-scout"
+    FASTQ_QC = "fastq_qc"
+    FASTQ_ANALYSIS = "fastq-analysis"
+    FASTQ_QC_ANALYSIS = "fastq_qc-analysis"
+    FASTQ_ANALYSIS_SCOUT = "fastq-analysis-scout"
+    NIPT_VIEWER = "nipt-viewer"
+    NO_DELIVERY = "no-delivery"
+    RAW_DATA_ANALYSIS = "raw_data-analysis"
+    RAW_DATA_ANALYSIS_SCOUT = "raw_data-analysis-scout"
+    RAW_DATA_SCOUT = "raw_data-scout"
+    SCOUT = "scout"
+    STATINA = "statina"
 
 
 class HastaSlurmPartitions(StrEnum):

cg/services/orders/constants.py

@@ -11,6 +11,7 @@
     OrderType.MICROSALT: Workflow.MICROSALT,
     OrderType.MIP_DNA: Workflow.MIP_DNA,
     OrderType.MIP_RNA: Workflow.MIP_RNA,
+    OrderType.NALLO: Workflow.NALLO,
     OrderType.PACBIO_LONG_READ: Workflow.RAW_DATA,
     OrderType.RML: Workflow.RAW_DATA,
     OrderType.RNAFUSION: Workflow.RNAFUSION,

cg/services/orders/storing/implementations/case_order_service.py

@@ -85,9 +85,9 @@ def store_order_data_in_status_db(self, order: OrderWithCases) -> list[DbCase]:
                 )
 
             db_order.cases.append(db_case)
-            self.status_db.session.add_all(new_cases)
-            self.status_db.session.add(db_order)
-            self.status_db.session.commit()
+            self.status_db.add_multiple_items_to_store(new_cases)
+            self.status_db.add_item_to_store(db_order)
+            self.status_db.commit_to_store()
         return new_cases
 
     @staticmethod
@@ -129,7 +129,7 @@ def _create_db_sample(
         ordered: datetime,
         sample: SampleInCase,
         ticket: str,
-    ):
+    ) -> DbSample:
         application_tag = sample.application
         application_version: ApplicationVersion = (
             self.status_db.get_current_application_version_by_tag(tag=application_tag)
@@ -144,7 +144,7 @@ def _create_db_sample(
             **sample.model_dump(exclude={"application", "container", "container_name"}),
         )
         db_sample.customer = customer
-        self.status_db.session.add(db_sample)
+        self.status_db.add_item_to_store(db_sample)
         return db_sample
 
     def _create_db_case(
@@ -214,7 +214,7 @@ def _create_db_sample_dict(
         case_samples: dict[str, DbSample] = {}
         for sample in case.samples:
             if sample.is_new:
-                with self.status_db.session.no_autoflush:
+                with self.status_db.no_autoflush_context():
                     db_sample: DbSample = self._create_db_sample(
                         case=case,
                         customer=customer,

cg/services/orders/storing/service_registry.py

@@ -74,6 +74,10 @@ def get_storing_service(self, order_type: OrderType) -> StoreOrderService:
         OrderLimsService,
         StoreCaseOrderService,
     ),
+    OrderType.NALLO: (
+        OrderLimsService,
+        StoreCaseOrderService,
+    ),
     OrderType.PACBIO_LONG_READ: (
         OrderLimsService,
         StorePacBioOrderService,

cg/services/orders/validation/errors/case_sample_errors.py

@@ -175,3 +175,8 @@ class BufferMissingError(CaseSampleError):
 class SampleOutsideOfCollaborationError(CaseSampleError):
     field: str = "internal_id"
     message: str = "Sample cannot be outside of collaboration"
+
+
+class SampleNameAlreadyExistsError(CaseSampleError):
+    field: str = "name"
+    message: str = "Sample name already exists in a previous order"

cg/services/orders/validation/order_type_maps.py

@@ -42,6 +42,11 @@
 )
 from cg.services.orders.validation.order_types.mutant.models.order import MutantOrder
 from cg.services.orders.validation.order_types.mutant.validation_rules import MUTANT_SAMPLE_RULES
+from cg.services.orders.validation.order_types.nallo.models.order import NalloOrder
+from cg.services.orders.validation.order_types.nallo.validation_rules import (
+    NALLO_CASE_RULES,
+    NALLO_CASE_SAMPLE_RULES,
+)
 from cg.services.orders.validation.order_types.order_validation_rules import ORDER_RULES
 from cg.services.orders.validation.order_types.pacbio_long_read.models.order import PacbioOrder
 from cg.services.orders.validation.order_types.pacbio_long_read.validation_rules import (
@@ -104,6 +109,10 @@ class RuleSet(BaseModel):
         case_rules=MIP_RNA_CASE_RULES,
         case_sample_rules=MIP_RNA_CASE_SAMPLE_RULES,
     ),
+    OrderType.NALLO: RuleSet(
+        case_rules=NALLO_CASE_RULES,
+        case_sample_rules=NALLO_CASE_SAMPLE_RULES,
+    ),
     OrderType.PACBIO_LONG_READ: RuleSet(
         sample_rules=PACBIO_LONG_READ_SAMPLE_RULES,
     ),
@@ -136,6 +145,7 @@ class RuleSet(BaseModel):
     OrderType.MICROSALT: MicrosaltOrder,
     OrderType.MIP_DNA: MIPDNAOrder,
     OrderType.MIP_RNA: MIPRNAOrder,
+    OrderType.NALLO: NalloOrder,
     OrderType.PACBIO_LONG_READ: PacbioOrder,
     OrderType.RML: RMLOrder,
     OrderType.RNAFUSION: RNAFusionOrder,

cg/services/orders/validation/order_types/nallo/constants.py

@@ -0,0 +1,13 @@
+from enum import StrEnum
+
+from cg.constants import DataDelivery
+
+
+class NalloDeliveryType(StrEnum):
+    ANALYSIS = DataDelivery.ANALYSIS_FILES
+    ANALYSIS_SCOUT = DataDelivery.ANALYSIS_SCOUT
+    NO_DELIVERY = DataDelivery.NO_DELIVERY
+    SCOUT = DataDelivery.SCOUT
+    RAW_DATA_ANALYSIS = DataDelivery.RAW_DATA_ANALYSIS
+    RAW_DATA_ANALYSIS_SCOUT = DataDelivery.RAW_DATA_ANALYSIS_SCOUT
+    RAW_DATA_SCOUT = DataDelivery.RAW_DATA_SCOUT

cg/services/orders/validation/order_types/nallo/models/case.py

@@ -0,0 +1,23 @@
+from pydantic import Discriminator, Tag
+from typing_extensions import Annotated
+
+from cg.services.orders.validation.models.case import Case
+from cg.services.orders.validation.models.discriminators import has_internal_id
+from cg.services.orders.validation.models.existing_sample import ExistingSample
+from cg.services.orders.validation.order_types.nallo.models.sample import NalloSample
+
+NewSample = Annotated[NalloSample, Tag("new")]
+OldSample = Annotated[ExistingSample, Tag("existing")]
+
+
+class NalloCase(Case):
+    cohorts: list[str] | None = None
+    panels: list[str]
+    synopsis: str | None = None
+    samples: list[Annotated[NewSample | OldSample, Discriminator(has_internal_id)]]
+
+    def get_samples_with_father(self) -> list[tuple[NalloSample | ExistingSample, int]]:
+        return [(sample, index) for index, sample in self.enumerated_samples if sample.father]
+
+    def get_samples_with_mother(self) -> list[tuple[NalloSample | ExistingSample, int]]:
+        return [(sample, index) for index, sample in self.enumerated_samples if sample.mother]

cg/services/orders/validation/order_types/nallo/models/order.py

@@ -0,0 +1,25 @@
+from pydantic import Discriminator, Tag
+from typing_extensions import Annotated
+
+from cg.services.orders.validation.models.discriminators import has_internal_id
+from cg.services.orders.validation.models.existing_case import ExistingCase
+from cg.services.orders.validation.models.order_with_cases import OrderWithCases
+from cg.services.orders.validation.order_types.nallo.constants import NalloDeliveryType
+from cg.services.orders.validation.order_types.nallo.models.case import NalloCase
+from cg.services.orders.validation.order_types.nallo.models.sample import NalloSample
+
+NewCase = Annotated[NalloCase, Tag("new")]
+OldCase = Annotated[ExistingCase, Tag("existing")]
+
+
+class NalloOrder(OrderWithCases):
+    cases: list[Annotated[NewCase | OldCase, Discriminator(has_internal_id)]]
+    delivery_type: NalloDeliveryType
+
+    @property
+    def enumerated_new_samples(self) -> list[tuple[int, int, NalloSample]]:
+        return [
+            (case_index, sample_index, sample)
+            for case_index, case in self.enumerated_new_cases
+            for sample_index, sample in case.enumerated_new_samples
+        ]

cg/services/orders/validation/order_types/nallo/models/sample.py

@@ -0,0 +1,21 @@
+from typing import Annotated
+
+from pydantic import BeforeValidator, Field
+
+from cg.models.orders.sample_base import NAME_PATTERN, SexEnum, StatusEnum
+from cg.services.orders.validation.constants import ElutionBuffer
+from cg.services.orders.validation.models.sample import Sample
+from cg.services.orders.validation.utils import parse_buffer
+
+
+class NalloSample(Sample):
+    elution_buffer: Annotated[ElutionBuffer | None, BeforeValidator(parse_buffer)] = None
+    father: str | None = Field(None, pattern=NAME_PATTERN)
+    mother: str | None = Field(None, pattern=NAME_PATTERN)
+    phenotype_groups: list[str] | None = None
+    phenotype_terms: list[str] | None = None
+    require_qc_ok: bool = False
+    sex: SexEnum
+    source: str
+    status: StatusEnum
+    subject_id: str = Field(pattern=NAME_PATTERN, max_length=128)

cg/services/orders/validation/order_types/nallo/validation_rules.py

@@ -0,0 +1,74 @@
+from cg.services.orders.validation.rules.case.rules import (
+    validate_case_internal_ids_exist,
+    validate_case_names_available,
+    validate_case_names_not_repeated,
+    validate_each_new_case_has_an_affected_sample,
+    validate_existing_cases_belong_to_collaboration,
+    validate_existing_cases_have_an_affected_sample,
+    validate_gene_panels_unique,
+)
+from cg.services.orders.validation.rules.case_sample.rules import (
+    validate_application_compatibility,
+    validate_application_exists,
+    validate_application_not_archived,
+    validate_container_name_required,
+    validate_existing_samples_belong_to_collaboration,
+    validate_fathers_are_male,
+    validate_fathers_in_same_case_as_children,
+    validate_gene_panels_exist,
+    validate_mothers_are_female,
+    validate_mothers_in_same_case_as_children,
+    validate_not_all_samples_unknown_in_case,
+    validate_pedigree,
+    validate_sample_names_available,
+    validate_sample_names_different_from_case_names,
+    validate_sample_names_not_repeated,
+    validate_samples_exist,
+    validate_subject_ids_different_from_case_names,
+    validate_subject_ids_different_from_sample_names,
+    validate_subject_sex_consistency,
+    validate_tube_container_name_unique,
+    validate_volume_interval,
+    validate_volume_required,
+    validate_well_position_format,
+    validate_well_positions_required,
+    validate_wells_contain_at_most_one_sample,
+)
+
+NALLO_CASE_RULES: list[callable] = [
+    validate_case_internal_ids_exist,
+    validate_case_names_available,
+    validate_case_names_not_repeated,
+    validate_each_new_case_has_an_affected_sample,
+    validate_existing_cases_have_an_affected_sample,
+    validate_existing_cases_belong_to_collaboration,
+    validate_gene_panels_exist,
+    validate_gene_panels_unique,
+]
+
+NALLO_CASE_SAMPLE_RULES: list[callable] = [
+    validate_application_compatibility,
+    validate_application_exists,
+    validate_application_not_archived,
+    validate_container_name_required,
+    validate_existing_samples_belong_to_collaboration,
+    validate_fathers_are_male,
+    validate_fathers_in_same_case_as_children,
+    validate_mothers_are_female,
+    validate_mothers_in_same_case_as_children,
+    validate_not_all_samples_unknown_in_case,
+    validate_pedigree,
+    validate_samples_exist,
+    validate_sample_names_available,
+    validate_sample_names_different_from_case_names,
+    validate_sample_names_not_repeated,
+    validate_subject_ids_different_from_case_names,
+    validate_subject_ids_different_from_sample_names,
+    validate_subject_sex_consistency,
+    validate_tube_container_name_unique,
+    validate_volume_interval,
+    validate_volume_required,
+    validate_well_positions_required,
+    validate_wells_contain_at_most_one_sample,
+    validate_well_position_format,
+]

cg/services/orders/validation/rules/case/rules.py

@@ -19,6 +19,7 @@
 from cg.services.orders.validation.order_types.balsamic.models.order import BalsamicOrder
 from cg.services.orders.validation.order_types.balsamic_umi.models.order import BalsamicUmiOrder
 from cg.services.orders.validation.order_types.mip_dna.models.order import MIPDNAOrder
+from cg.services.orders.validation.order_types.nallo.models.order import NalloOrder
 from cg.services.orders.validation.rules.case.utils import (
     contains_duplicates,
     is_case_not_from_collaboration,
@@ -136,7 +137,7 @@ def validate_number_of_normal_samples(
 
 
 def validate_each_new_case_has_an_affected_sample(
-    order: MIPDNAOrder, **kwargs
+    order: MIPDNAOrder | NalloOrder, **kwargs
 ) -> list[NewCaseWithoutAffectedSampleError]:
     """Validates that each case in the order contains at least one sample with affected status."""
     errors: list[NewCaseWithoutAffectedSampleError] = []
@@ -148,7 +149,7 @@ def validate_each_new_case_has_an_affected_sample(
 
 
 def validate_existing_cases_have_an_affected_sample(
-    order: MIPDNAOrder, store: Store, **kwargs
+    order: MIPDNAOrder | NalloOrder, store: Store, **kwargs
 ) -> list[ExistingCaseWithoutAffectedSampleError]:
     errors: list[ExistingCaseWithoutAffectedSampleError] = []
     for case_index, case in order.enumerated_existing_cases:

cg/services/orders/validation/rules/case_sample/rules.py

@@ -23,6 +23,7 @@
     OccupiedWellError,
     PedigreeError,
     SampleDoesNotExistError,
+    SampleNameAlreadyExistsError,
     SampleNameRepeatedError,
     SampleNameSameAsCaseNameError,
     SampleOutsideOfCollaborationError,
@@ -57,8 +58,8 @@
     is_buffer_missing,
     is_concentration_missing,
     is_container_name_missing,
-    is_invalid_plate_well_format,
     is_invalid_capture_kit,
+    is_invalid_plate_well_format,
     is_sample_missing_capture_kit,
     is_sample_not_from_collaboration,
     is_sample_tube_name_reused,
@@ -266,6 +267,8 @@ def validate_wells_contain_at_most_one_sample(
 def validate_sample_names_not_repeated(
     order: OrderWithCases, store: Store, **kwargs
 ) -> list[SampleNameRepeatedError]:
+    """Ensures that sample names are unique within the order
+    and that they not already used in the case previously."""
     old_sample_names: set[str] = get_existing_sample_names(order=order, status_db=store)
     new_samples: list[tuple[int, int, SampleInCase]] = order.enumerated_new_samples
     sample_name_counter = Counter([sample.name for _, _, sample in new_samples])
@@ -494,3 +497,16 @@ def validate_existing_samples_belong_to_collaboration(
                 )
                 errors.append(error)
     return errors
+
+
+def validate_sample_names_available(
+    order: OrderWithCases, store: Store, **kwargs
+) -> list[SampleNameAlreadyExistsError]:
+    """Validates that new sample names are not already used by the customer."""
+    errors: list[SampleNameAlreadyExistsError] = []
+    customer_entry_id: int = store.get_customer_by_internal_id(order.customer).id
+    for case_index, sample_index, sample in order.enumerated_new_samples:
+        if store.is_sample_name_used(sample=sample, customer_entry_id=customer_entry_id):
+            error = SampleNameAlreadyExistsError(case_index=case_index, sample_index=sample_index)
+            errors.append(error)
+    return errors

cg/store/crud/read.py

@@ -1831,3 +1831,11 @@ def get_pacbio_sequencing_runs_by_run_name(self, run_name: str) -> list[PacbioSe
         if runs.count() == 0:
             raise EntryNotFoundError(f"Could not find any sequencing runs for {run_name}")
         return runs.all()
+
+    def is_sample_name_used(self, sample: Sample, customer_entry_id: int) -> bool:
+        """Check if a sample name is already used by the customer"""
+        if self.get_sample_by_customer_and_name(
+            customer_entry_id=[customer_entry_id], sample_name=sample.name
+        ):
+            return True
+        return False

tests/apps/orderform/test_json_orderform_parser.py

@@ -6,9 +6,10 @@
 
 
 @pytest.mark.parametrize(
-    "valid_json_order_type", [OrderType.MIP_DNA, OrderType.BALSAMIC, OrderType.FLUFFY]
+    "valid_json_order_type",
+    [OrderType.MIP_DNA, OrderType.BALSAMIC, OrderType.FLUFFY],
 )
-def test_generate_mip_json_orderform(valid_json_order_type: str, json_order_dict: dict):
+def test_generate_json_orderform(valid_json_order_type: str, json_order_dict: dict):
     """Tests the orderform generation for customer-submitted json files"""
 
     # GIVEN a dictionary from a JSON file of a certain order type