fix circular import

genotype_api/api/endpoints/analyses.py

@@ -15,7 +15,8 @@
     get_analyses_with_skip_and_limit,
 )
 from genotype_api.database.crud.update import refresh_sample_status
-from genotype_api.database.models import Analysis, AnalysisRead, AnalysisReadWithGenotype, User
+from genotype_api.database.models import Analysis, User
+from genotype_api.dto.dto import AnalysisRead, AnalysisReadWithGenotype
 from genotype_api.database.session_handler import get_session
 from genotype_api.file_parsing.files import check_file
 from genotype_api.file_parsing.vcf import SequenceAnalysis

genotype_api/api/endpoints/plates.py

@@ -30,11 +30,13 @@
 from genotype_api.database.models import (
     Analysis,
     Plate,
+    User,
+)
+from genotype_api.dto.dto import (
     PlateCreate,
     PlateReadWithAnalyses,
     PlateReadWithAnalysisDetail,
     PlateReadWithAnalysisDetailSingle,
-    User,
 )
 from genotype_api.database.session_handler import get_session
 from genotype_api.file_parsing.excel import GenotypeAnalysis

genotype_api/api/endpoints/samples.py

@@ -25,10 +25,9 @@
 from genotype_api.database.models import (
     Analysis,
     Sample,
-    SampleRead,
-    SampleReadWithAnalysisDeep,
     User,
 )
+from genotype_api.dto.dto import SampleRead, SampleReadWithAnalysisDeep
 from genotype_api.database.session_handler import get_session
 from genotype_api.models import MatchResult, SampleDetail
 from genotype_api.security import get_active_user

genotype_api/api/endpoints/users.py

@@ -8,7 +8,8 @@
 from starlette.responses import JSONResponse
 
 from genotype_api.database.crud.read import get_user
-from genotype_api.database.models import User, UserCreate, UserRead, UserReadWithPlates
+from genotype_api.database.models import User
+from genotype_api.dto.dto import UserRead, UserCreate, UserReadWithPlates
 from genotype_api.database.session_handler import get_session
 from genotype_api.security import get_active_user
 

genotype_api/database/crud/create.py

@@ -4,7 +4,8 @@
 from sqlmodel import Session
 from sqlmodel.sql.expression import Select, SelectOfScalar
 
-from genotype_api.database.models import Analysis, Plate, PlateCreate, Sample, User, UserCreate
+from genotype_api.database.models import Analysis, Plate, Sample, User
+from genotype_api.dto.dto import UserCreate, PlateCreate
 
 SelectOfScalar.inherit_cache = True
 Select.inherit_cache = True

genotype_api/database/crud/delete.py

@@ -3,7 +3,7 @@
 from sqlmodel import Session
 from sqlmodel.sql.expression import Select, SelectOfScalar
 
-from genotype_api.database.models import Analysis, Plate
+from genotype_api.database.models import Analysis, Plate, Sample
 
 SelectOfScalar.inherit_cache = True
 Select.inherit_cache = True

genotype_api/database/crud/read.py

@@ -15,8 +15,8 @@
     Plate,
     Sample,
     User,
-    PlateReadWithAnalysisDetailSingle,
 )
+from genotype_api.dto.dto import PlateReadWithAnalysisDetailSingle
 
 SelectOfScalar.inherit_cache = True
 Select.inherit_cache = True

genotype_api/database/crud/update.py

@@ -4,10 +4,11 @@
 from genotype_api.database.crud.read import get_sample
 from genotype_api.database.filter_models.plate_models import PlateSignOff
 from genotype_api.database.filter_models.sample_models import SampleSexesUpdate
-from genotype_api.match import check_sample
 from genotype_api.database.models import Sample, Plate
 from sqlmodel.sql.expression import Select, SelectOfScalar
 
+from genotype_api.service.match_genotype_service.match_genotype import MatchGenotypeService
+
 SelectOfScalar.inherit_cache = True
 Select.inherit_cache = True
 
@@ -16,7 +17,7 @@ def refresh_sample_status(sample: Sample, session: Session) -> Sample:
     if len(sample.analyses) != 2:
         sample.status = None
     else:
-        results = check_sample(sample=sample)
+        results = MatchGenotypeService.check_sample(sample=sample)
         sample.status = "fail" if "fail" in results.dict().values() else "pass"
 
     session.add(sample)

genotype_api/database/models.py

@@ -1,13 +1,11 @@
 from collections import Counter
 from datetime import datetime
 
-from pydantic import EmailStr, constr, validator
+from pydantic import EmailStr, constr
 from sqlalchemy import Index
 from sqlmodel import Field, Relationship, SQLModel
 
 from genotype_api.constants import SEXES, STATUS, TYPES
-from genotype_api.models import PlateStatusCounts, SampleDetail
-from genotype_api.service.match_genotype_service.utils import check_snps, check_sex
 
 
 class GenotypeBase(SQLModel):
@@ -36,14 +34,6 @@ def is_ok(self) -> bool:
         return "0" not in self.alleles
 
 
-class GenotypeRead(GenotypeBase):
-    id: int
-
-
-class GenotypeCreate(GenotypeBase):
-    pass
-
-
 class AnalysisBase(SQLModel):
     type: TYPES
     source: str | None
@@ -68,14 +58,6 @@ def check_no_calls(self) -> dict[str, int]:
         return Counter(calls)
 
 
-class AnalysisRead(AnalysisBase):
-    id: int
-
-
-class AnalysisCreate(AnalysisBase):
-    pass
-
-
 class SampleSlim(SQLModel):
     status: STATUS | None
     comment: str | None
@@ -113,14 +95,6 @@ def sequence_analysis(self) -> Analysis | None:
         return None
 
 
-class SampleRead(SampleBase):
-    id: constr(max_length=32)
-
-
-class SampleCreate(SampleBase):
-    pass
-
-
 class SNPBase(SQLModel):
     ref: constr(max_length=1) | None
     chrom: constr(max_length=5) | None
@@ -134,10 +108,6 @@ class SNP(SNPBase, table=True):
     id: constr(max_length=32) | None = Field(default=None, primary_key=True)
 
 
-class SNPRead(SNPBase):
-    id: constr(max_length=32)
-
-
 class UserBase(SQLModel):
     email: EmailStr = Field(index=True, unique=True)
     name: str | None = ""
@@ -149,14 +119,6 @@ class User(UserBase, table=True):
     plates: list["Plate"] = Relationship(back_populates="user")
 
 
-class UserRead(UserBase):
-    id: int
-
-
-class UserCreate(UserBase):
-    pass
-
-
 class PlateBase(SQLModel):
     created_at: datetime | None = datetime.now()
     plate_id: constr(max_length=16) = Field(index=True, unique=True)
@@ -171,94 +133,3 @@ class Plate(PlateBase, table=True):
     id: int | None = Field(default=None, primary_key=True)
     user: "User" = Relationship(back_populates="plates")
     analyses: list["Analysis"] = Relationship(back_populates="plate")
-
-
-class PlateRead(PlateBase):
-    id: str
-    user: UserRead | None
-
-
-class PlateCreate(PlateBase):
-    analyses: list[Analysis] | None = []
-
-
-class UserReadWithPlates(UserRead):
-    plates: list[Plate] | None = []
-
-
-class SampleReadWithAnalysis(SampleRead):
-    analyses: list[AnalysisRead] | None = []
-
-
-class AnalysisReadWithGenotype(AnalysisRead):
-    genotypes: list[Genotype] | None = []
-
-
-class SampleReadWithAnalysisDeep(SampleRead):
-    analyses: list[AnalysisReadWithGenotype] | None = []
-    detail: SampleDetail | None
-
-    @validator("detail")
-    def get_detail(cls, value, values) -> SampleDetail:
-        analyses = values.get("analyses")
-        if len(analyses) != 2:
-            return SampleDetail()
-        genotype_analysis = [analysis for analysis in analyses if analysis.type == "genotype"][0]
-        sequence_analysis = [analysis for analysis in analyses if analysis.type == "sequence"][0]
-        status = check_snps(
-            genotype_analysis=genotype_analysis, sequence_analysis=sequence_analysis
-        )
-        sex = check_sex(
-            sample_sex=values.get("sex"),
-            genotype_analysis=genotype_analysis,
-            sequence_analysis=sequence_analysis,
-        )
-
-        return SampleDetail(**status, sex=sex)
-
-    class Config:
-        validate_all = True
-
-
-class AnalysisReadWithSample(AnalysisRead):
-    sample: SampleSlim | None
-
-
-class AnalysisReadWithSampleDeep(AnalysisRead):
-    sample: SampleReadWithAnalysisDeep | None
-
-
-class PlateReadWithAnalyses(PlateRead):
-    analyses: list[AnalysisReadWithSample] | None = []
-
-
-class PlateReadWithAnalysisDetail(PlateRead):
-    analyses: list[AnalysisReadWithSample] | None = []
-    detail: PlateStatusCounts | None
-
-    @validator("detail")
-    def check_detail(cls, value, values):
-        analyses = values.get("analyses")
-        statuses = [str(analysis.sample.status) for analysis in analyses]
-        commented = sum(1 for analysis in analyses if analysis.sample.comment)
-        status_counts = Counter(statuses)
-        return PlateStatusCounts(**status_counts, total=len(analyses), commented=commented)
-
-    class Config:
-        validate_all = True
-
-
-class PlateReadWithAnalysisDetailSingle(PlateRead):
-    analyses: list[AnalysisReadWithSample] | None = []
-    detail: PlateStatusCounts | None
-
-    @validator("detail")
-    def check_detail(cls, value, values):
-        analyses = values.get("analyses")
-        statuses = [str(analysis.sample.status) for analysis in analyses]
-        commented = sum(1 for analysis in analyses if analysis.sample.comment)
-        status_counts = Counter(statuses)
-        return PlateStatusCounts(**status_counts, total=len(analyses), commented=commented)
-
-    class Config:
-        validate_all = True