removing old sample and order models pt 1

cg/models/orders/samples.py

@@ -2,7 +2,6 @@
 
 from cg.constants import DataDelivery
 from cg.constants.constants import GenomeVersion, Workflow
-from cg.constants.orderforms import ORIGINAL_LAB_ADDRESSES, REGION_CODES
 from cg.models.orders.constants import OrderType
 from cg.models.orders.sample_base import (
     NAME_PATTERN,
@@ -12,19 +11,7 @@
     SexEnum,
     StatusEnum,
 )
-from cg.store.models import Application, Case, Organism, Panel, Pool, Sample
-
-
-class OptionalIntValidator:
-    @classmethod
-    def str_to_int(cls, v: str) -> int | None:
-        return int(v) if v else None
-
-
-class OptionalFloatValidator:
-    @classmethod
-    def str_to_float(cls, v: str) -> float | None:
-        return float(v) if v else None
+from cg.store.models import Application, Case, Panel, Sample
 
 
 class OrderInSample(BaseModel):
@@ -51,274 +38,6 @@ def is_sample_for(cls, project: OrderType):
         return project == cls._suitable_project
 
 
-class Of1508Sample(OrderInSample):
-    # Orderform 1508
-    # Order portal specific
-    internal_id: constr(max_length=Sample.internal_id.property.columns[0].type.length) | None
-    # "required for new samples"
-    name: (
-        constr(
-            regex=NAME_PATTERN,
-            min_length=2,
-            max_length=Sample.name.property.columns[0].type.length,
-        )
-        | None
-    )
-
-    # customer
-    age_at_sampling: float | None
-    family_name: constr(
-        regex=NAME_PATTERN,
-        min_length=2,
-        max_length=Case.name.property.columns[0].type.length,
-    )
-    case_internal_id: constr(max_length=Sample.internal_id.property.columns[0].type.length) | None
-    sex: SexEnum = SexEnum.unknown
-    tumour: bool = False
-    source: str | None
-    control: ControlEnum | None
-    volume: str | None
-    container: ContainerEnum | None
-    # "required if plate for new samples"
-    container_name: str | None
-    well_position: str | None
-    # "Required if samples are part of trio/family"
-    mother: (
-        constr(regex=NAME_PATTERN, max_length=Sample.name.property.columns[0].type.length) | None
-    )
-    father: (
-        constr(regex=NAME_PATTERN, max_length=Sample.name.property.columns[0].type.length) | None
-    )
-    # This information is required for panel analysis
-    capture_kit: str | None
-    # This information is required for panel- or exome analysis
-    elution_buffer: str | None
-    tumour_purity: int | None
-    # "This information is optional for FFPE-samples for new samples"
-    formalin_fixation_time: int | None
-    post_formalin_fixation_time: int | None
-    tissue_block_size: str | None
-    # "Not Required"
-    cohorts: list[str] | None
-    phenotype_groups: list[str] | None
-    phenotype_terms: list[str] | None
-    require_qc_ok: bool = False
-    quantity: int | None
-    subject_id: (
-        constr(regex=NAME_PATTERN, max_length=Sample.subject_id.property.columns[0].type.length)
-        | None
-    )
-    synopsis: str | None
-
-    @validator("container", "container_name", "name", "source", "subject_id", "volume")
-    def required_for_new_samples(cls, value, values, **kwargs):
-        if not value and not values.get("internal_id"):
-            raise ValueError(f"required for new sample {values.get('name')}")
-        return value
-
-    @validator(
-        "tumour_purity",
-        "formalin_fixation_time",
-        "post_formalin_fixation_time",
-        "quantity",
-        pre=True,
-    )
-    def str_to_int(cls, v: str) -> int | None:
-        return OptionalIntValidator.str_to_int(v=v)
-
-    @validator(
-        "age_at_sampling",
-        "volume",
-        pre=True,
-    )
-    def str_to_float(cls, v: str) -> float | None:
-        return OptionalFloatValidator.str_to_float(v=v)
-
-
-class MipDnaSample(Of1508Sample):
-    _suitable_project = OrderType.MIP_DNA
-    # "Required if data analysis in Scout or vcf delivery"
-    panels: list[constr(min_length=1, max_length=Panel.abbrev.property.columns[0].type.length)]
-    status: StatusEnum
-
-
-class BalsamicSample(Of1508Sample):
-    _suitable_project = OrderType.BALSAMIC
-
-
-class BalsamicQCSample(Of1508Sample):
-    _suitable_project = OrderType.BALSAMIC_QC
-    reference_genome: GenomeVersion | None
-
-
-class BalsamicUmiSample(Of1508Sample):
-    _suitable_project = OrderType.BALSAMIC_UMI
-
-
-class MipRnaSample(Of1508Sample):
-    _suitable_project = OrderType.MIP_RNA
-
-
-class RnafusionSample(Of1508Sample):
-    _suitable_project = OrderType.RNAFUSION
-
-
-class TomteSample(MipDnaSample):
-    _suitable_project = OrderType.TOMTE
-    reference_genome: GenomeVersion | None
-
-
-class FastqSample(OrderInSample):
-    _suitable_project = OrderType.FASTQ
-
-    # Orderform 1508
-    # "required"
-    container: ContainerEnum | None
-    sex: SexEnum = SexEnum.unknown
-    source: str
-    tumour: bool
-    # "required if plate"
-    container_name: str | None
-    well_position: str | None
-    elution_buffer: str
-    # This information is required for panel analysis
-    capture_kit: str | None
-    # "Not Required"
-    quantity: int | None
-    subject_id: str | None
-
-    @validator("quantity", pre=True)
-    def str_to_int(cls, v: str) -> int | None:
-        return OptionalIntValidator.str_to_int(v=v)
-
-
-class PacBioSample(OrderInSample):
-    _suitable_project = OrderType.PACBIO_LONG_READ
-
-    container: ContainerEnum
-    container_name: str | None = None
-    sex: SexEnum = SexEnum.unknown
-    source: str
-    subject_id: str
-    tumour: bool
-    well_position: str | None = None
-
-
-class RmlSample(OrderInSample):
-    _suitable_project = OrderType.RML
-
-    # 1604 Orderform Ready made libraries (RML)
-    # Order portal specific
-    # "This information is required"
-    pool: constr(max_length=Pool.name.property.columns[0].type.length)
-    concentration: float
-    concentration_sample: float | None
-    index: str
-    index_number: str | None
-    # "Required if Plate"
-    rml_plate_name: str | None
-    well_position_rml: str | None
-    # "Automatically generated (if not custom) or custom"
-    index_sequence: str | None
-    # "Not required"
-    control: str | None
-
-    @validator("concentration_sample", pre=True)
-    def str_to_float(cls, v: str) -> float | None:
-        return OptionalFloatValidator.str_to_float(v=v)
-
-
-class FluffySample(RmlSample):
-    _suitable_project = OrderType.FLUFFY
-    # 1604 Orderform Ready made libraries (RML)
-
-
-class MetagenomeSample(Of1508Sample):
-    _suitable_project = OrderType.METAGENOME
-    # "This information is required"
-    source: str
-    # "This information is not required"
-    concentration_sample: float | None
-    family_name: None = None
-    subject_id: None = None
-
-    @validator("concentration_sample", pre=True)
-    def str_to_float(cls, v: str) -> float | None:
-        return OptionalFloatValidator.str_to_float(v=v)
-
-    @validator("subject_id", pre=True)
-    def required_for_new_samples(cls, v: str) -> None:
-        """Overrides the parent validator since subject_id is optional for these samples."""
-        return None
-
-
-class TaxprofilerSample(MetagenomeSample):
-    _suitable_project = OrderType.TAXPROFILER
-
-
-class MicrobialSample(OrderInSample):
-    # 1603 Orderform Microbial WHOLE_GENOME_SEQUENCING
-    # "These fields are required"
-    organism: constr(max_length=Organism.internal_id.property.columns[0].type.length)
-    reference_genome: constr(max_length=Sample.reference_genome.property.columns[0].type.length)
-    elution_buffer: str
-    extraction_method: str | None
-    container: ContainerEnum
-    # "Required if Plate"
-    container_name: str | None
-    well_position: str | None
-    # "Required if "Other" is chosen in column "Species""
-    organism_other: constr(max_length=Organism.internal_id.property.columns[0].type.length) | None
-    verified_organism: bool | None  # sent to LIMS
-    control: str | None
-
-
-class MicrobialFastqSample(OrderInSample):
-    _suitable_project = OrderType.MICROBIAL_FASTQ
-
-    elution_buffer: str
-    container: ContainerEnum
-    # "Required if Plate"
-    container_name: str | None
-    well_position: str | None
-    # "These fields are not required"
-    control: str | None
-
-
-class MicrosaltSample(MicrobialSample):
-    _suitable_project = OrderType.MICROSALT
-    # 1603 Orderform Microbial WHOLE_GENOME_SEQUENCING
-
-
-class SarsCov2Sample(MicrobialSample):
-    _suitable_project = OrderType.SARS_COV_2
-
-    # 2184 Orderform SARS-COV-2
-    # "These fields are required"
-    collection_date: str
-    lab_code: str = None
-    primer: str
-    original_lab: str
-    original_lab_address: str = None
-    pre_processing_method: str
-    region: str
-    region_code: str = None
-    selection_criteria: str
-    volume: str | None
-
-    @validator("lab_code", pre=True, always=True)
-    def set_lab_code(cls, value):
-        return "SE100 Karolinska"
-
-    @validator("region_code", pre=True, always=True)
-    def set_region_code(cls, value, values):
-        return value if value else REGION_CODES[values["region"]]
-
-    @validator("original_lab_address", pre=True, always=True)
-    def set_original_lab_address(cls, value, values):
-        return value if value else ORIGINAL_LAB_ADDRESSES[values["original_lab"]]
-
-
 def sample_class_for(project: OrderType):
     """Get the sample class for the specified project
 

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

@@ -5,8 +5,9 @@
 
 
 def is_sample_missing_capture_kit(sample: BalsamicSample, store: Store) -> bool:
-    application: Application = store.get_application_by_tag(sample.application)
+    application: Application | None = store.get_application_by_tag(sample.application)
     return (
-        application.prep_category == SeqLibraryPrepCategory.TARGETED_GENOME_SEQUENCING
+        application
+        and application.prep_category == SeqLibraryPrepCategory.TARGETED_GENOME_SEQUENCING
         and not sample.capture_kit
     )

cg/services/orders/store_order_services/store_order_service.py

@@ -3,7 +3,6 @@
 import logging
 from abc import ABC, abstractmethod
 
-from cg.models.orders.order import OrderIn
 from cg.services.order_validation_service.models.order import Order
 from cg.services.order_validation_service.models.sample import Sample
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
@@ -12,16 +11,6 @@
 LOG = logging.getLogger(__name__)
 
 
-class ValidateOrderService(ABC):
-    @abstractmethod
-    def __init__(self, status_db: Store):
-        self.status_db = status_db
-
-    @abstractmethod
-    def validate_order(self, order_in: OrderIn):
-        pass
-
-
 class StoreOrderService(ABC):
     @abstractmethod
     def __init__(self, status_db: Store, lims_service: OrderLimsService):

tests/conftest.py

@@ -122,6 +122,7 @@
     "tests.fixture_plugins.orders_fixtures.order_form_fixtures",
     "tests.fixture_plugins.orders_fixtures.order_to_submit_fixtures",
     "tests.fixture_plugins.orders_fixtures.order_fixtures",
+    "tests.fixture_plugins.orders_fixtures.services_and_api_fixtures",
     "tests.fixture_plugins.orders_fixtures.store_fixtures",
     "tests.fixture_plugins.orders_fixtures.store_service_fixtures",
     "tests.fixture_plugins.pacbio_fixtures.context_fixtures",

tests/fixture_plugins/orders_fixtures/order_to_submit_fixtures.py

@@ -22,6 +22,8 @@
 from cg.services.order_validation_service.workflows.pacbio_long_read.models.order import PacbioOrder
 from cg.services.order_validation_service.workflows.rml.models.order import RmlOrder
 from cg.services.order_validation_service.workflows.rna_fusion.models.order import RnaFusionOrder
+from cg.services.order_validation_service.workflows.taxprofiler.models.order import TaxprofilerOrder
+from cg.services.order_validation_service.workflows.tomte.models.order import TomteOrder
 
 
 @pytest.fixture(scope="session")
@@ -56,7 +58,7 @@ def metagenome_order_to_submit(cgweb_orders_dir: Path) -> dict:
     )
 
 
-@pytest.fixture
+@pytest.fixture(scope="session")
 def microbial_fastq_order_to_submit(cgweb_orders_dir: Path) -> dict:
     """Load an example microbial order."""
     return ReadFile.get_content_from_file(
@@ -120,6 +122,14 @@ def sarscov2_order_to_submit(cgweb_orders_dir: Path) -> dict:
     )
 
 
+@pytest.fixture(scope="session")
+def taxprofiler_order_to_submit(cgweb_orders_dir: Path) -> dict:
+    """Load an example Taxprofiler order."""
+    return ReadFile.get_content_from_file(
+        file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "taxprofiler.json")
+    )
+
+
 @pytest.fixture(scope="session")
 def tomte_order_to_submit(cgweb_orders_dir: Path) -> dict:
     """Load an example TOMTE order."""
@@ -142,6 +152,8 @@ def all_orders_to_submit(
     rml_order_to_submit: dict,
     rnafusion_order_to_submit: dict,
     sarscov2_order_to_submit: dict,
+    taxprofiler_order_to_submit: dict,
+    tomte_order_to_submit: dict,
 ) -> dict[OrderType, Order]:
     """Returns a dict of parsed order for each order type."""
     return {
@@ -159,4 +171,6 @@ def all_orders_to_submit(
         OrderType.RML: RmlOrder.model_validate(rml_order_to_submit),
         OrderType.RNAFUSION: RnaFusionOrder.model_validate(rnafusion_order_to_submit),
         OrderType.SARS_COV_2: MutantOrder.model_validate(sarscov2_order_to_submit),
+        OrderType.TAXPROFILER: TaxprofilerOrder.model_validate(taxprofiler_order_to_submit),
+        OrderType.TOMTE: TomteOrder.model_validate(tomte_order_to_submit),
     }