Add join condition for sample and analysis

genotype_api/database/base_handler.py

@@ -29,4 +29,4 @@ def _get_query(self, table: Type[DeclarativeBase]) -> Query:
         return select(table)
 
     def _get_join_analysis_on_sample(self) -> Query:
-        return self._get_query(table=Sample).join(Analysis)
+        return self._get_query(table=Sample).join(Analysis, Analysis.sample_id == Sample.id)

genotype_api/database/crud/create.py

@@ -1,5 +1,7 @@
 import logging
 
+from sqlalchemy.future import select
+
 from genotype_api.database.base_handler import BaseHandler
 from genotype_api.database.models import SNP, Analysis, Genotype, Plate, Sample, User
 from genotype_api.dto.user import UserRequest
@@ -25,23 +27,32 @@ async def create_plate(self, plate: Plate) -> Plate:
 
     async def create_sample(self, sample: Sample) -> Sample:
         """Creates a sample in the database."""
-        sample_in_db = await self._get_query(Analysis).filter(Sample.id == sample.id).one_or_none()
-        if sample_in_db:
+        sample_in_db_query = self._get_query(Analysis).filter(Sample.id == sample.id)
+        result = await self.session.execute(sample_in_db_query)
+        if sample_in_db := result.one_or_none():
             raise SampleExistsError
         self.session.add(sample)
         await self.session.commit()
         await self.session.refresh(sample)
         return sample
 
     async def create_analyses_samples(self, analyses: list[Analysis]) -> list[Sample]:
-        """creating samples in an analysis if not already in db."""
-        return [
-            await self.create_sample(sample=Sample(id=analysis.sample_id))
-            for analysis in analyses
-            if not await self.session.query(Sample)
-            .filter(Sample.id == analysis.sample_id)
-            .one_or_none()
-        ]
+        """Creating samples in an analysis if not already in db."""
+        created_samples = []
+
+        for analysis in analyses:
+            # Sample already exists in the database
+            sample_in_db_query = self._get_query(Sample).filter(Sample.id == analysis.sample_id)
+            result = await self.session.execute(sample_in_db_query)
+            sample_in_db = result.one_or_none()
+
+            # Sample doesn't exist
+            if not sample_in_db:
+                sample = Sample(id=analysis.sample_id)
+                created_sample = await self.create_sample(sample=sample)
+                created_samples.append(created_sample)
+
+        return created_samples
 
     async def create_user(self, user: User) -> User:
         self.session.add(user)

genotype_api/database/crud/read.py

@@ -9,10 +9,19 @@
 from genotype_api.database.base_handler import BaseHandler
 from genotype_api.database.filter_models.plate_models import PlateOrderParams
 from genotype_api.database.filter_models.sample_models import SampleFilterParams
-from genotype_api.database.filters.analysis_filter import AnalysisFilter, apply_analysis_filter
-from genotype_api.database.filters.genotype_filters import GenotypeFilter, apply_genotype_filter
+from genotype_api.database.filters.analysis_filter import (
+    AnalysisFilter,
+    apply_analysis_filter,
+)
+from genotype_api.database.filters.genotype_filters import (
+    GenotypeFilter,
+    apply_genotype_filter,
+)
 from genotype_api.database.filters.plate_filters import PlateFilter, apply_plate_filter
-from genotype_api.database.filters.sample_filters import SampleFilter, apply_sample_filter
+from genotype_api.database.filters.sample_filters import (
+    SampleFilter,
+    apply_sample_filter,
+)
 from genotype_api.database.filters.snp_filters import SNPFilter, apply_snp_filter
 from genotype_api.database.filters.user_filters import UserFilter, apply_user_filter
 from genotype_api.database.models import SNP, Analysis, Genotype, Plate, Sample, User
@@ -147,7 +156,7 @@ async def get_filtered_samples(self, filter_params: SampleFilterParams) -> list[
             select(Sample)
             .distinct()
             .options(selectinload(Sample.analyses).selectinload(Analysis.genotypes))
-            .join(Analysis)
+            .join(Analysis, Analysis.sample_id == Sample.id)
         )
         if filter_params.sample_id:
             query = self._get_samples(query, filter_params.sample_id)

genotype_api/database/crud/update.py

@@ -8,7 +8,9 @@
 from genotype_api.database.filter_models.sample_models import SampleSexesUpdate
 from genotype_api.database.models import Analysis, Plate, Sample, User
 from genotype_api.exceptions import SampleNotFoundError
-from genotype_api.services.match_genotype_service.match_genotype import MatchGenotypeService
+from genotype_api.services.match_genotype_service.match_genotype import (
+    MatchGenotypeService,
+)
 
 
 class UpdateHandler(BaseHandler):
@@ -69,7 +71,7 @@ async def update_sample_sex(self, sexes_update: SampleSexesUpdate) -> Sample:
             select(Sample)
             .distinct()
             .options(selectinload(Sample.analyses).selectinload(Analysis.genotypes))
-            .join(Analysis)
+            .join(Analysis, Analysis.sample_id == Sample.id)
             .filter(Sample.id == sexes_update.sample_id)
         )