feat(sex): Use Sex

Clinical-Genomics · May 16, 2024 · 8a98147 · 8a98147
1 parent 0750658
commit 8a98147
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Showing 5 changed files with 8 additions and 6 deletions.
diff --git a/tests/mocks/scout.py b/tests/mocks/scout.py
@@ -1,20 +1,21 @@
 """Mock the scout api"""
 
 import logging
-from mock import Mock
 
+from mock import Mock
 from pydantic.v1 import BaseModel, validator
 from typing_extensions import Literal
 
 from cg.apps.scout.scoutapi import ScoutAPI
+from cg.constants.subject import Sex
 from tests.mocks.process_mock import ProcessMock
 
 LOG = logging.getLogger(__name__)
 
 
 class MockScoutIndividual(BaseModel):
     sample_id: str = "sample_id"
-    sex: str = "female"
+    sex: str = Sex.FEMALE
     analysis_type: Literal[
         "external",
         "mixed",

diff --git a/tests/models/mip/conftest.py b/tests/models/mip/conftest.py
@@ -159,7 +159,7 @@ def mip_metrics_deliverables_raw() -> dict:
                 "input": "some_input",
                 "name": "gender",
                 "step": "chanjo_sexcheck",
-                "value": "female",
+                "value": Sex.FEMALE,
             },
             {
                 "id": "another_id",

diff --git a/tests/models/mip/test_mip_metrics_deliverables.py b/tests/models/mip/test_mip_metrics_deliverables.py
@@ -1,5 +1,6 @@
 """Test MIP metrics deliverables"""
 
+from cg.constants.subject import Sex
 from cg.models.mip.mip_metrics_deliverables import (
     DuplicateReads,
     MeanInsertSize,
@@ -163,7 +164,7 @@ def test_instantiate_mip_metrics_set_sample_id_metrics(mip_metrics_deliverables_
             assert sample_id_metric.mapped_reads_step == "bamstats"
             assert sample_id_metric.mean_insert_size == 422.0
             assert sample_id_metric.mean_insert_size_step == "collectmultiplemetricsinsertsize"
-            assert sample_id_metric.predicted_sex == "female"
+            assert sample_id_metric.predicted_sex == Sex.FEMALE
             assert sample_id_metric.predicted_sex_step == "chanjo_sexcheck"
 
 

diff --git a/tests/models/report/test_validators.py b/tests/models/report/test_validators.py
@@ -179,7 +179,7 @@ def test_get_gender_as_string():
     validated_invalid_gender: str = get_gender_as_string(invalid_gender)
 
     # THEN check if the gender has been correctly formatted
-    assert validated_gender == REPORT_GENDER.get("female")
+    assert validated_gender == REPORT_GENDER.get(Sex.FEMALE)
     assert validated_invalid_gender == NA_FIELD
 
 

diff --git a/tests/store/conftest.py b/tests/store/conftest.py
@@ -43,7 +43,7 @@ class StoreConstants(enum.Enum):
     REFERENCE_GENOME_SAMPLE_WITH_ATTRIBUTES: str = "NC_222"
     ORIGINAL_TICKET_SAMPLE_WITH_ATTRIBUTES: str = "ticket"
     FROM_SAMPLE_SAMPLE_WITH_ATTRIBUTES: str = "sample_1"
-    SEX_SAMPLE_WITH_ATTRIBUTES: str = "male"
+    SEX_SAMPLE_WITH_ATTRIBUTES: str = Sex.MALE
     ENTRY_ID_SAMPLE_WITH_ATTRIBUTES: int = 1
     INVOICE_ID_SAMPLE_WITH_ATTRIBUTES: int = 1
     INTERNAL_ID_SAMPLE_WITHOUT_ATTRIBUTES: str = "sample_without_attributes"