Enum Example for PhenotypeStatus

cg/apps/mip/confighandler.py

@@ -4,7 +4,7 @@
 from marshmallow import Schema, fields, validate
 
 from cg.constants import DEFAULT_CAPTURE_KIT
-from cg.constants.subject import RelationshipStatus
+from cg.constants.subject import PhenotypeStatus, RelationshipStatus
 from cg.exc import PedigreeConfigError
 
 LOG = logging.getLogger(__name__)
@@ -26,9 +26,9 @@ class SampleSchema(Schema):
     )
     father = fields.Str(dump_default=RelationshipStatus.HAS_NO_PARENT)
     mother = fields.Str(dump_default=RelationshipStatus.HAS_NO_PARENT)
-    phenotype = fields.Str(
+    phenotype = fields.Enum(
+        PhenotypeStatus,
         required=True,
-        validate=validate.OneOf(choices=["affected", "unaffected", "unknown"]),
     )
     sex = fields.Str(required=True, validate=validate.OneOf(choices=["female", "male", "unknown"]))
     expected_coverage = fields.Float()

cg/constants/subject.py

@@ -1,4 +1,4 @@
-from enum import IntEnum, StrEnum
+from enum import Enum, IntEnum, StrEnum, auto
 
 
 class Sex(StrEnum):
@@ -9,11 +9,10 @@ class Sex(StrEnum):
     MISSING = ""
 
 
-class PhenotypeStatus(StrEnum):
-    UNKNOWN = "unknown"
-    UNAFFECTED = "unaffected"
-    AFFECTED = "affected"
-    MISSING = ""
+class PhenotypeStatus(Enum):
+    UNKNOWN = auto()
+    UNAFFECTED = auto()
+    AFFECTED = auto()
 
 
 class PlinkPhenotypeStatus(IntEnum):

cg/meta/workflow/raredisease.py

@@ -5,7 +5,7 @@
 
 from cg.constants import GenePanelMasterList, Workflow
 from cg.constants.gene_panel import GENOME_BUILD_37
-from cg.constants.subject import PlinkPhenotypeStatus, PlinkSex
+from cg.constants.subject import PhenotypeStatus, PlinkPhenotypeStatus, PlinkSex
 from cg.meta.workflow.analysis import add_gene_panel_combo
 from cg.meta.workflow.nf_analysis import NfAnalysisAPI
 from cg.models.cg_config import CGConfig
@@ -81,11 +81,11 @@ def get_workflow_parameters(self, case_id: str) -> WorkflowParameters:
         )
 
     @staticmethod
-    def get_phenotype_code(phenotype: str) -> int:
+    def get_phenotype_code(phenotype: PhenotypeStatus) -> int:
         """Return Raredisease phenotype code."""
         LOG.debug("Translate phenotype to integer code")
         try:
-            code = PlinkPhenotypeStatus[phenotype.upper()]
+            code = PlinkPhenotypeStatus[phenotype.name]
         except KeyError:
             raise ValueError(f"{phenotype} is not a valid phenotype")
         return code

cg/models/scout/scout_load_config.py

@@ -6,6 +6,7 @@
 from typing_extensions import Annotated, Literal
 
 from cg.constants.scout import UploadTrack
+from cg.constants.subject import PhenotypeStatus
 from cg.models.scout.validators import field_not_none
 
 
@@ -44,7 +45,7 @@ class ScoutIndividual(BaseModel):
     confirmed_sex: bool | None = None
     father: str | None = None
     mother: str | None = None
-    phenotype: str | None = None
+    phenotype: PhenotypeStatus | None = None
     sample_id: Annotated[str, BeforeValidator(field_not_none)] = None
     sample_name: str | None = None
     sex: Annotated[str | None, BeforeValidator(field_not_none)] = None

cg/store/models.py

@@ -29,6 +29,7 @@
     StatusOptions,
 )
 from cg.constants.priority import SlurmQos
+from cg.constants.subject import PhenotypeStatus
 from cg.constants.symbols import EMPTY_STRING
 
 BigInt = Annotated[int, None]
@@ -618,9 +619,7 @@ class CaseSample(Base):
     id: Mapped[PrimaryKeyInt]
     case_id: Mapped[str] = mapped_column(ForeignKey("case.id", ondelete="CASCADE"))
     sample_id: Mapped[int] = mapped_column(ForeignKey("sample.id", ondelete="CASCADE"))
-    status: Mapped[str] = mapped_column(
-        types.Enum(*(status.value for status in StatusOptions)), default=StatusOptions.UNKNOWN.value
-    )
+    status: Mapped[PhenotypeStatus] = mapped_column(default=StatusOptions.UNKNOWN)
 
     created_at: Mapped[datetime | None]
     updated_at: Mapped[datetime | None]

tests/cli/workflow/mip/conftest.py

@@ -7,7 +7,7 @@
 from cg.apps.scout.scoutapi import ScoutAPI
 from cg.apps.tb import TrailblazerAPI
 from cg.constants import Workflow
-from cg.constants.subject import Sex
+from cg.constants.subject import PhenotypeStatus, Sex
 from cg.meta.compress import CompressAPI
 from cg.meta.workflow.mip_dna import MipDNAAnalysisAPI
 from cg.meta.workflow.mip_rna import MipRNAAnalysisAPI
@@ -149,7 +149,9 @@ def mip_dna_context(
                 customer_id="cust000",
                 sex=Sex.UNKNOWN,
             )
-            helpers.add_relationship(store=_store, sample=sample, case=case_obj, status="affected")
+            helpers.add_relationship(
+                store=_store, sample=sample, case=case_obj, status=PhenotypeStatus.AFFECTED
+            )
     cg_context.meta_apis["analysis_api"] = mip_analysis_api
     return cg_context
 

tests/conftest.py

@@ -32,7 +32,7 @@
 from cg.constants.housekeeper_tags import HK_DELIVERY_REPORT_TAG
 from cg.constants.priority import SlurmQos
 from cg.constants.sequencing import SequencingPlatform
-from cg.constants.subject import Sex
+from cg.constants.subject import PhenotypeStatus, Sex
 from cg.io.controller import WriteFile
 from cg.io.json import read_json, write_json
 from cg.io.yaml import read_yaml, write_yaml
@@ -50,7 +50,10 @@
 from cg.models.flow_cell.flow_cell import FlowCellDirectoryData
 from cg.models.raredisease.raredisease import RarediseaseSampleSheetHeaders
 from cg.models.rnafusion.rnafusion import RnafusionParameters, RnafusionSampleSheetEntry
-from cg.models.taxprofiler.taxprofiler import TaxprofilerParameters, TaxprofilerSampleSheetEntry
+from cg.models.taxprofiler.taxprofiler import (
+    TaxprofilerParameters,
+    TaxprofilerSampleSheetEntry,
+)
 from cg.models.tomte.tomte import TomteSampleSheetHeaders
 from cg.store.database import create_all_tables, drop_all_tables, initialize_database
 from cg.store.models import Bed, BedVersion, Case, Customer, Order, Organism, Sample
@@ -266,7 +269,7 @@ def analysis_family(case_id: str, family_name: str, sample_id: str, ticket_id: s
                 "internal_id": sample_id,
                 "father": "ADM2",
                 "mother": "ADM3",
-                "status": "affected",
+                "status": PhenotypeStatus.AFFECTED,
                 "original_ticket": ticket_id,
                 "reads": 5000000,
                 "capture_kit": "GMSmyeloid",
@@ -275,7 +278,7 @@ def analysis_family(case_id: str, family_name: str, sample_id: str, ticket_id: s
                 "name": "father",
                 "sex": Sex.MALE,
                 "internal_id": "ADM2",
-                "status": "unaffected",
+                "status": PhenotypeStatus.UNAFFECTED,
                 "original_ticket": ticket_id,
                 "reads": 6000000,
                 "capture_kit": "GMSmyeloid",
@@ -284,7 +287,7 @@ def analysis_family(case_id: str, family_name: str, sample_id: str, ticket_id: s
                 "name": "mother",
                 "sex": Sex.FEMALE,
                 "internal_id": "ADM3",
-                "status": "unaffected",
+                "status": PhenotypeStatus.UNAFFECTED,
                 "original_ticket": ticket_id,
                 "reads": 7000000,
                 "capture_kit": "GMSmyeloid",

tests/store_helpers.py

@@ -699,7 +699,7 @@ def add_relationship(
         store: Store,
         sample: Sample,
         case: Case,
-        status: str = PhenotypeStatus.UNKNOWN,
+        status: PhenotypeStatus = PhenotypeStatus.UNKNOWN,
         father: Sample = None,
         mother: Sample = None,
     ) -> CaseSample: