From 7bedd13c0d59d543d56c16af72fe034790f059f2 Mon Sep 17 00:00:00 2001 From: mayabrandi Date: Fri, 12 Nov 2021 12:25:13 +0100 Subject: [PATCH] validated samples for coverage plot function --- statina/API/v2/endpoints/batches.py | 10 +++++++--- statina/crud/find/plots/coverage_plot_data.py | 4 ++-- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/statina/API/v2/endpoints/batches.py b/statina/API/v2/endpoints/batches.py index 40de136d..e8c8bbb1 100644 --- 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 index 0f931532..0b88e8cf 100644 --- 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