Fix missing clinical data NA counts which have been filtered out #11163
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haynescd
reviewed
Nov 11, 2024
| //studyIds, sampleIds, attributes.stream().map(a -> a.getAttributeId()).collect(Collectors.toList())); | ||
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| // fetch the samples by using the provided study view filter | ||
| List<Sample> filteredSamples = studyViewColumnarService.getFilteredSamples(studyViewFilter); |
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I would push this business logic down into the service (eventually business logic shouldn't even be at this layer)
and utilize the studyViewRepository.getFilteredSamplesCount().
Probably wrap this in a function.
haynescd
requested changes
Nov 11, 2024
Comment on lines
165
to
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| resultWithAllAttributes.stream().forEach(attr -> { | ||
| Map<String, List<ClinicalDataCount>> countsPerType = attr.getCounts().stream() | ||
| .collect(Collectors.groupingBy(ClinicalDataCount::getValue)); | ||
| List<ClinicalDataCount> res = countsPerType.entrySet().stream().map((entry)->{ | ||
| ClinicalDataCount mergedCount = new ClinicalDataCount(); | ||
| mergedCount.setAttributeId(attr.getAttributeId()); | ||
| mergedCount.setValue(entry.getKey()); | ||
| mergedCount.setCount(entry.getValue().stream().mapToInt(ClinicalDataCount::getCount).sum()); | ||
| return mergedCount; | ||
| }).collect(Collectors.toList()); | ||
| attr.setCounts(res); | ||
| }); |
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Did you mean to use StudyViewColumnarServiceUtil.mergeClinicalDataCounts?
| var result = studyViewRepository.getClinicalDataCounts(createContext(studyViewFilter), filteredAttributes); | ||
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| // fetch the samples by using the provided study view filter | ||
| List<Sample> filteredSamples = getFilteredSamples(studyViewFilter); |
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I would still suggest this studyViewRepository.getFilteredSamplesCount()
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@haynescd my understanding was just that you wanted me to call the repository directly, right here
haynescd
requested changes
Nov 12, 2024
Comment on lines
167
to
178
| // resultWithAllAttributes.stream().forEach(attr -> { | ||
| // Map<String, List<ClinicalDataCount>> countsPerType = attr.getCounts().stream() | ||
| // .collect(Collectors.groupingBy(ClinicalDataCount::getValue)); | ||
| // List<ClinicalDataCount> res = countsPerType.entrySet().stream().map((entry)->{ | ||
| // ClinicalDataCount mergedCount = new ClinicalDataCount(); | ||
| // mergedCount.setAttributeId(attr.getAttributeId()); | ||
| // mergedCount.setValue(entry.getKey()); | ||
| // mergedCount.setCount(entry.getValue().stream().mapToInt(ClinicalDataCount::getCount).sum()); | ||
| // return mergedCount; | ||
| // }).collect(Collectors.toList()); | ||
| // attr.setCounts(res); | ||
| // }); |
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Fixers #11159