feat(sex): Use Sex

Clinical-Genomics · May 16, 2024 · 0750658 · 0750658
1 parent 0870326
commit 0750658
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Showing 4 changed files with 10 additions and 8 deletions.
diff --git a/tests/meta/report/test_mip_dna_api.py b/tests/meta/report/test_mip_dna_api.py
@@ -1,4 +1,5 @@
 from cg.constants import REPORT_GENDER
+from cg.constants.subject import Sex
 from tests.store_helpers import StoreHelpers
 
 

diff --git a/tests/meta/workflow/test_balsamic.py b/tests/meta/workflow/test_balsamic.py
@@ -19,15 +19,15 @@ def test_get_verified_sex():
 
     # GIVEN a sample object
     sample_obj = {
-        "ACC0000A0": {"sex": "female"},
-        "ACC0000A1": {"sex": "female"},
+        "ACC0000A0": {"sex": Sex.FEMALE},
+        "ACC0000A1": {"sex": Sex.FEMALE},
     }
 
     # WHEN extracting the sex
     retrieved_sex: Sex = BalsamicAnalysisAPI.get_verified_sex(sample_obj)
 
     # THEN sex must match the expected one
-    assert retrieved_sex == "female"
+    assert retrieved_sex == Sex.FEMALE
 
 
 def test_get_verified_sex_error():
@@ -49,8 +49,8 @@ def test_get_verified_sex_unknown(caplog):
 
     # GIVEN a sample object with different sexes
     sample_obj = {
-        "ACC0000A0": {"sex": "unknown"},
-        "ACC0000A1": {"sex": "unknown"},
+        "ACC0000A0": {"sex": Sex.UNKNOWN},
+        "ACC0000A1": {"sex": Sex.UNKNOWN},
     }
 
     # WHEN extracting the sex

diff --git a/tests/mocks/limsmock.py b/tests/mocks/limsmock.py
@@ -4,7 +4,7 @@
 from typing_extensions import Literal
 
 from cg.apps.lims import LimsAPI
-from cg.constants.subject import PhenotypeStatus
+from cg.constants.subject import PhenotypeStatus, Sex
 
 
 class LimsProject(BaseModel):
@@ -23,7 +23,7 @@ class LimsSample(BaseModel):
     id: str
     name: str = None
     customer: str = None
-    sex: Literal["male", "female", "unknown"] = None
+    sex: Literal[Sex.MALE, Sex.FEMALE, Sex.UNKNOWN] = None
     father: str = None
     mother: str = None
     status: Literal[

diff --git a/tests/models/mip/conftest.py b/tests/models/mip/conftest.py
@@ -3,6 +3,7 @@
 import pytest
 
 from cg.constants.priority import SlurmQos
+from cg.constants.subject import Sex
 from cg.models.mip.mip_metrics_deliverables import MIPMetricsDeliverables
 
 
@@ -165,7 +166,7 @@ def mip_metrics_deliverables_raw() -> dict:
                 "input": "some_input",
                 "name": "gender",
                 "step": "chanjo_sexcheck",
-                "value": "male",
+                "value": Sex.MALE,
             },
             {
                 "id": "an_id",