feat(sex): Use Sex

cg/meta/orders/case_submitter.py

@@ -1,7 +1,7 @@
 import datetime as dt
 import logging
 
-from cg.constants import DataDelivery, Priority
+from cg.constants import DataDelivery, Priority, Sex
 from cg.constants.constants import CaseActions, Workflow
 from cg.constants.pedigree import Pedigree
 from cg.exc import OrderError
@@ -38,7 +38,7 @@ def _validate_subject_sex(self, samples: [Of1508Sample], customer_id: str):
             if not subject_id:
                 continue
             new_gender: str = sample.sex
-            if new_gender == "unknown":
+            if new_gender == Sex.UNKNOWN:
                 continue
 
             existing_samples: list[Sample] = self.status.get_samples_by_customer_and_subject_id(
@@ -47,7 +47,7 @@ def _validate_subject_sex(self, samples: [Of1508Sample], customer_id: str):
             existing_sample: Sample
             for existing_sample in existing_samples:
                 previous_gender = existing_sample.sex
-                if previous_gender == "unknown":
+                if previous_gender == Sex.UNKNOWN:
                     continue
 
                 if previous_gender != new_gender:

cg/meta/orders/microbial_submitter.py

@@ -2,7 +2,7 @@
 
 from cg.constants import DataDelivery
 from cg.constants.constants import Workflow
-from cg.constants.subject import Sex
+from cg.constants.subject import PhenotypeStatus, Sex
 from cg.meta.orders.lims import process_lims
 from cg.meta.orders.submitter import Submitter
 from cg.models.orders.order import OrderIn
@@ -146,7 +146,7 @@ def store_items_in_status(
                 priority = new_sample.priority
                 sample_objs.append(new_sample)
                 link: CaseSample = self.status.relate_sample(
-                    case=case, sample=new_sample, status="unknown"
+                    case=case, sample=new_sample, status=PhenotypeStatus.UNKNOWN
                 )
                 self.status.session.add(link)
                 new_samples.append(new_sample)

cg/meta/orders/pool_submitter.py

@@ -2,7 +2,7 @@
 
 from cg.constants import DataDelivery
 from cg.constants.constants import Workflow
-from cg.constants.subject import Sex
+from cg.constants.subject import PhenotypeStatus, Sex
 from cg.exc import OrderError
 from cg.meta.orders.lims import process_lims
 from cg.meta.orders.submitter import Submitter
@@ -162,7 +162,7 @@ def store_items_in_status(
                 )
                 new_samples.append(new_sample)
                 link: CaseSample = self.status.relate_sample(
-                    case=case, sample=new_sample, status="unknown"
+                    case=case, sample=new_sample, status=PhenotypeStatus.UNKNOWN
                 )
                 self.status.session.add(link)
             new_pools.append(new_pool)

cg/meta/upload/gisaid/models.py

@@ -4,6 +4,8 @@
 
 from pydantic import BaseModel, ConfigDict, model_validator
 
+from cg.constants import Sex
+from cg.constants.subject import PhenotypeStatus
 from cg.meta.upload.gisaid.constants import AUTHORS
 
 
@@ -57,9 +59,9 @@ class GisaidSample(BaseModel):
     covv_passage: str | None = "Original"
     covv_location: str | None = None
     covv_host: str | None = "Human"
-    covv_gender: str | None = "unknown"
+    covv_gender: str | None = Sex.UNKNOWN
     covv_patient_age: str | None = "unknown"
-    covv_patient_status: str | None = "unknown"
+    covv_patient_status: str | None = PhenotypeStatus.UNKNOWN
     covv_seq_technology: str | None = "Illumina NovaSeq"
     covv_orig_lab_addr: str | None = None
     covv_subm_lab: str | None = "Karolinska University Hospital"

cg/meta/upload/mutacc.py

@@ -145,7 +145,7 @@ def resolve_parent(scout_parent: str) -> str:
 
 def resolve_phenotype(scout_phenotype: int) -> str:
     """Convert scout phenotype to mutacc phenotype"""
-    mutacc_phenotype = "unknown"
+    mutacc_phenotype = PhenotypeStatus.UNKNOWN
     if scout_phenotype == 1:
         mutacc_phenotype = PhenotypeStatus.UNAFFECTED
     if scout_phenotype == 2:

cg/models/lims/sample.py

@@ -42,7 +42,7 @@ class Udf(BaseModel):
     require_qc_ok: bool = False
     rml_plate_name: str | None
     selection_criteria: str | None
-    sex: Literal["M", "F", "unknown"] = "unknown"
+    sex: Literal["M", "F", "unknown"] = Sex.UNKNOWN
     skip_reception_control: bool | None = None
     source: str = "NA"
     tissue_block_size: str | None
@@ -54,7 +54,7 @@ class Udf(BaseModel):
 
     @validator("sex", pre=True)
     def validate_sex(cls, value: str):
-        return SEX_MAP.get(value, "unknown")
+        return SEX_MAP.get(value, Sex.UNKNOWN)
 
 
 class LimsSample(BaseModel):

cg/models/orders/validators/excel_sample_validators.py

@@ -1,4 +1,5 @@
 from cg.constants.orderforms import REV_SEX_MAP, SOURCE_TYPES
+from cg.constants.subject import Sex
 from cg.models.orders.sample_base import PriorityEnum
 
 
@@ -59,7 +60,7 @@ def convert_sex(sex: str) -> str | None:
     if not sex:
         return None
     sex = sex.strip()
-    return REV_SEX_MAP.get(sex, "unknown")
+    return REV_SEX_MAP.get(sex, Sex.UNKNOWN)
 
 
 def convert_to_lower(value: str) -> str:

tests/apps/madeline/test_madeline.py

@@ -3,6 +3,7 @@
 from pathlib import Path
 
 from cg.apps.madeline.api import MadelineAPI
+from cg.constants.subject import Sex
 
 
 def get_ind_info(columns, line):
@@ -48,7 +49,7 @@ def test_generate_madeline_input_no_sex(madeline_columns, proband):
 
     # GIVEN a case id and a ind with unknown sex
     case_id = "test"
-    proband["sex"] = "unknown"
+    proband["sex"] = Sex.UNKNOWN
     inds = [proband]
     # WHEN generating madeline formated lines
     madeline_lines = MadelineAPI.make_ped(case_id, inds)

tests/meta/archive/conftest.py

@@ -13,7 +13,7 @@
 from cg.constants import SequencingFileTag
 from cg.constants.archiving import ArchiveLocations
 from cg.constants.constants import DataDelivery, FileFormat, Workflow
-from cg.constants.subject import Sex
+from cg.constants.subject import PhenotypeStatus, Sex
 from cg.io.controller import WriteStream
 from cg.meta.archive.archive import SpringArchiveAPI
 from cg.meta.archive.ddn.constants import ROOT_TO_TRIM
@@ -282,7 +282,7 @@ def archive_store(
         ticket="123",
         customer_id=customer_ddn.id,
     )
-    base_store.relate_sample(case=case, sample=new_samples[0], status="unknown")
+    base_store.relate_sample(case=case, sample=new_samples[0], status=PhenotypeStatus.UNKNOWN)
     order = Order(
         customer_id=customer_ddn.id,
         ticket_id=new_samples[0].original_ticket,

tests/meta/orders/test_meta_orders_api.py

@@ -445,7 +445,7 @@ def test_validate_sex_unknown_new_sex(
             name=sample.name,
             subject_id=sample.subject_id,
         )
-        sample.sex = "unknown"
+        sample.sex = Sex.UNKNOWN
         store.session.add(sample_obj)
         store.session.commit()