status_details validator with circular import

genotype_api/match.py

@@ -23,11 +23,13 @@ def compare_genotypes(genotype_1: Genotype, genotype_2: Genotype) -> str:
 
 
 def check_sex(
-    sample: Sample, analysis_1: Analysis, analysis_2: Analysis
+    sex_1: Optional[str], sex_2: Optional[str], sex_3: Optional[str]
 ) -> Optional[Literal["fail", "pass"]]:
-    if sample.sex in ["unknown", None]:
+    """Compare three sex strings"""
+
+    if sex_1 in ["unknown", None]:
         return "fail"
-    if not sample.sex == analysis_1.sex == analysis_2.sex:
+    if not sex_1 == sex_2 == sex_3:
         return "fail"
     return "pass"
 
@@ -55,9 +57,9 @@ def check_sample(sample: Sample):
     assert len(sample.analyses) == 2, "must load both types of analyses"
     return dict(
         sex=check_sex(
-            sample=sample,
-            analysis_1=sample.genotype_analysis,
-            analysis_2=sample.sequence_analysis,
+            sex_1=sample.sex,
+            sex_2=sample.genotype_analysis.sex,
+            sex_3=sample.sequence_analysis.sex,
         ),
         compare=check_snps(
             analysis_1=sample.genotype_analysis,

genotype_api/models.py

@@ -2,11 +2,11 @@
 from typing import Optional, List, Dict
 from collections import Counter
 
-
-from pydantic import constr, EmailStr, BaseModel, validator
+from pydantic import constr, EmailStr, validator
 from sqlmodel import SQLModel, Field, Relationship
 
 from genotype_api.constants import TYPES, SEXES, STATUS
+from genotype_api.match import check_sex, check_snps, score_no_calls
 
 
 class GenotypeBase(SQLModel):
@@ -177,8 +177,27 @@ class UserReadWithPlates(UserRead):
     plates: Optional[List[Plate]] = []
 
 
+class SampleReadWithStatusDetails(SampleRead):
+    analyses: Optional[List[AnalysisRead]] = []
+    status_details: Optional[str]
+
+    @validator("status_details", always=True)
+    def set_status_details(cls, v, values: dict) -> str:
+        genotype_analysis: Analysis = values["genotype_analysis"]
+        sequence_analysis: Analysis = values["sequence_analysis"]
+        sample_sex = values["sex"]
+
+        sex_status = check_sex(sample_sex, genotype_analysis.sex, sequence_analysis.sex)
+        snp_status = check_snps(genotype_analysis, sequence_analysis)
+        no_calls_status = score_no_calls(genotype_analysis)
+        print(sex_status)
+        print(snp_status)
+        print(no_calls_status)
+        return snp_status
+
+
 class AnalysisReadWithSample(AnalysisRead):
-    sample: Optional[SampleSlim]
+    sample: Optional[SampleReadWithStatusDetails]
 
 
 class PlateReadWithAnalyses(PlateRead):