validated samples for coverage plot function

Clinical-Genomics · Nov 12, 2021 · 7bedd13 · 7bedd13
1 parent 8ea3001
commit 7bedd13
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Showing 2 changed files with 9 additions and 5 deletions.
diff --git a/statina/API/v2/endpoints/batches.py b/statina/API/v2/endpoints/batches.py
@@ -274,10 +274,14 @@ def coverage(
     db_samples: List[DataBaseSample] = statina.crud.find.samples.batch_samples(
         batch_id=batch_id, adapter=adapter
     )
-    samples: List[Sample] = [Sample(**db_sample.dict()) for db_sample in db_samples]
+    validated_samples: List[SampleValidator] = [
+        SampleValidator(**db_sample.dict()) for db_sample in db_samples
+    ]
 
-    scatter_data: Dict[str, CoveragePlotSampleData] = get_scatter_data_for_coverage_plot(samples)
-    box_data: Dict[int, List[float]] = get_box_data_for_coverage_plot(samples)
+    scatter_data: Dict[str, CoveragePlotSampleData] = get_scatter_data_for_coverage_plot(
+        validated_samples
+    )
+    box_data: Dict[int, List[float]] = get_box_data_for_coverage_plot(validated_samples)
     return JSONResponse(
         content=jsonable_encoder(
             dict(

diff --git a/statina/crud/find/plots/coverage_plot_data.py b/statina/crud/find/plots/coverage_plot_data.py
@@ -2,11 +2,11 @@
 
 from statina.models.database import DataBaseSample
 from statina.models.server.plots.coverage import CoveragePlotSampleData
-from statina.models.server.sample import Sample, SampleWarning
+from statina.models.server.sample import SampleValidator, SampleWarning
 
 
 def get_scatter_data_for_coverage_plot(
-    samples: List[Sample],
+    samples: List[SampleValidator],
 ) -> Dict["str", CoveragePlotSampleData]:
     """Coverage Ratio data for Coverage Plot.
     Only adding samples with a zscore war