Fix violin plot sample filtering and counting issues #11122
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onursumer
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onursumer
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Oct 25, 2024
src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
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onursumer
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Oct 25, 2024
| @@ -33,7 +33,7 @@ public DensityPlotData getDensityPlotData(List<ClinicalData> sampleClinicalData, | |||
| result.setBins(new ArrayList<>()); | |||
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| Map<String, List<ClinicalData>> clinicalDataGroupedBySampleId = sampleClinicalData.stream(). | |||
| collect(Collectors.groupingBy(ClinicalData::getSampleId)); | |||
| collect(Collectors.groupingBy(c -> c.getStudyId() + "_" + c.getSampleId())); | |||
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this may not be necessary, but since we removed the study id from the sample id for clinical data this change will keep the ids same for density plot implementation.
alisman
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Oct 28, 2024
alisman
reviewed
Oct 28, 2024
| if (patientClinicalDataList.isEmpty()) { | ||
| combinedClinicalDataList = sampleClinicalDataList; | ||
| } else { | ||
| // fetch samples again without the numerical clinical data filter |
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@onursumer can you add to comment WHY we fetch again without clinical data filter?
…erting patient clinical data to sample clinical data
…e ids to count samples when internal id is null
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* use samples filtered without numerical clinical data filter when converting patient clinical data to sample clinical data * make clinical data sample/patient ids match legacy ids, and use stable ids to count samples when internal id is null
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Fix #11112