Fix clinical data value casing #11281
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onursumer
reviewed
Dec 13, 2024
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| items.forEach(attr -> { | ||
| Map<String, List<ClinicalDataCount>> countsPerType = attr.getCounts().stream() | ||
| .collect(Collectors.groupingBy(ClinicalDataCount::getValue)); | ||
| .collect(Collectors.groupingBy(a -> a.getValue().toLowerCase())); | ||
| List<ClinicalDataCount> res = countsPerType.entrySet().stream().map(entry -> { | ||
| ClinicalDataCount mergedCount = new ClinicalDataCount(); | ||
| mergedCount.setAttributeId(attr.getAttributeId()); | ||
| mergedCount.setValue(entry.getKey()); | ||
| // we are just going to choose the value of the first item | ||
| // due to failure in data normalization in source files, we may find values | ||
| // have inconsistent casing. we choose to merge and choose an arbitrary casing | ||
| mergedCount.setValue(entry.getValue().stream().findFirst().get().getValue()); |
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We can probably avoid modifying this method by reusing normalizeDataCounts. So, something like this after this line might be better.
result.forEach(item -> item.setCounts(StudyViewColumnarServiceUtil.normalizeDataCounts(item.getCounts())));
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Initial SQL was upper casing all clinical data values in order to elide casing inconsistencies. We need to respect the casing of imported data, while still grouping in a case-insensitive way