Fix bug in clinical-density-plot endpoint when mixing sample and patient attributes #8884
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Luke-Sikina
approved these changes
Sep 14, 2021
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| List<Sample> samplesForPatient = patientToSamples.get( | ||
| d.getPatientId() | ||
| ).get(d.getStudyId()); | ||
| if (samplesForPatient != null) { | ||
| for (Sample s: samplesForPatient) { | ||
| ClinicalData newData = new ClinicalData(); | ||
| newData.setAttrId(d.getAttrId()); | ||
| newData.setPatientId(d.getPatientId()); | ||
| newData.setStudyId(d.getStudyId()); | ||
| newData.setAttrValue(d.getAttrValue()); | ||
| newData.setSampleId(s.getStableId()); | ||
| sampleClinicalDataList.add(newData); | ||
| } | ||
| } |
There was a problem hiding this comment.
If you wanted to cut down on your nesting, you could do something like this:
Suggested change
| List<Sample> samplesForPatient = patientToSamples.get( | |
| d.getPatientId() | |
| ).get(d.getStudyId()); | |
| if (samplesForPatient != null) { | |
| for (Sample s: samplesForPatient) { | |
| ClinicalData newData = new ClinicalData(); | |
| newData.setAttrId(d.getAttrId()); | |
| newData.setPatientId(d.getPatientId()); | |
| newData.setStudyId(d.getStudyId()); | |
| newData.setAttrValue(d.getAttrValue()); | |
| newData.setSampleId(s.getStableId()); | |
| sampleClinicalDataList.add(newData); | |
| } | |
| } | |
| List<Sample> samplesForPatient = patientToSamples | |
| .get(d.getPatientId()) | |
| .getOrDefault(d.getStudyId(), new ArrayList<>()); | |
| for (Sample s: samplesForPatient) { | |
| ClinicalData newData = new ClinicalData(); | |
| newData.setAttrId(d.getAttrId()); | |
| newData.setPatientId(d.getPatientId()); | |
| newData.setStudyId(d.getStudyId()); | |
| newData.setAttrValue(d.getAttrValue()); | |
| newData.setSampleId(s.getStableId()); | |
| sampleClinicalDataList.add(newData); | |
| } |
This is really six in one half a dozen in the other though.
…ent attributes New solution always returns counts in terms of samples Signed-off-by: Adam Abeshouse <abeshoua@mskcc.org>
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New solution always returns counts in terms of samples
Part of #8867