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refactor custom data filter util methods
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Bryan Lai committed Sep 20, 2024
1 parent a3e3be0 commit 2740db8
Showing 1 changed file with 60 additions and 49 deletions.
109 changes: 60 additions & 49 deletions src/main/java/org/cbioportal/web/columnar/util/CustomDataFilterUtil.java
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Original file line number Diff line number Diff line change
Expand Up @@ -37,66 +37,28 @@ public List<CustomSampleIdentifier> extractCustomDataSamples(final StudyViewFilt
return null;
}

List<CustomSampleIdentifier> customSampleIdentifiers = new ArrayList<>();

if (CollectionUtils.isEmpty(studyViewFilter.getCustomDataFilters())) {
return null;
}

final List<CustomSampleIdentifier> flattenedSamples = studyViewFilter.getCustomDataFilters().stream()
final List<CustomSampleIdentifier> customSamplesFromProperty = studyViewFilter.getCustomDataFilters().stream()
.flatMap(filter -> {
List<CustomSampleIdentifier> samples = filter.getSamples();
return (samples != null) ? samples.stream() : Stream.empty();
})
.collect(Collectors.toList());

if (!flattenedSamples.isEmpty()) {
customSampleIdentifiers.addAll(flattenedSamples);

List<ClinicalDataFilter> equalityFilters = new ArrayList<>();
List<ClinicalDataFilter> intervalFilters = new ArrayList<>();

studyViewFilter.getCustomDataFilters().forEach(filter -> {
if (filter.getDatatype()
.equals(CustomDatatype.STRING.name())
) {
equalityFilters.add(filter);
} else {
intervalFilters.add(filter);
}
});

MultiKeyMap<String, String> customDataByStudySampleName = new MultiKeyMap<>();

studyViewFilter.getCustomDataFilters().stream().forEach(filter -> {
filter.getSamples().forEach(datum -> {
String value = datum.getValue().toUpperCase();
if (value.equals("NAN") || value.equals("N/A")) {
value = "NA";
}
customDataByStudySampleName.put(datum.getStudyId(), datum.getSampleId(), filter.getDisplayName(), value);
});
});

List<CustomSampleIdentifier> filtered = new ArrayList<>();
customSampleIdentifiers.forEach(customSampleIdentifier -> {
int equalityFilterCount = getFilteredCountByDataEqualityWithStudySampleNameMap(equalityFilters, customDataByStudySampleName,
customSampleIdentifier.getSampleId(), customSampleIdentifier.getStudyId(), false);
int intervalFilterCount = getFilteredCountByDataIntervalWithStudySampleNameMap(intervalFilters, customDataByStudySampleName,
customSampleIdentifier.getSampleId(), customSampleIdentifier.getStudyId());
if (equalityFilterCount == equalityFilters.size()
&& intervalFilterCount == intervalFilters.size()
) {
filtered.add(customSampleIdentifier);
}
else {
customSampleIdentifier.setIsFilteredOut(true);
filtered.add(customSampleIdentifier);
}
});
return filtered;
if (!customSamplesFromProperty.isEmpty()) {
return extractCustomDataSamplesWithoutSession(studyViewFilter, customSamplesFromProperty);
}

else {
return extractCustomDataSamplesWithSession(studyViewFilter);
}
}

private List<CustomSampleIdentifier> extractCustomDataSamplesWithSession(final StudyViewFilter studyViewFilter) {
List<CustomSampleIdentifier> customSampleIdentifiers = new ArrayList<>();

final List<String> attributeIds = studyViewFilter.getCustomDataFilters().stream()
.map(ClinicalDataFilter::getAttributeId)
.collect(Collectors.toList());
Expand Down Expand Up @@ -169,6 +131,55 @@ public List<CustomSampleIdentifier> extractCustomDataSamples(final StudyViewFilt

return filtered;
}

private List<CustomSampleIdentifier> extractCustomDataSamplesWithoutSession(final StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customSamplesFromProperty) {
List<CustomSampleIdentifier> customSampleIdentifiers = new ArrayList<>();

customSampleIdentifiers.addAll(customSamplesFromProperty);

List<ClinicalDataFilter> equalityFilters = new ArrayList<>();
List<ClinicalDataFilter> intervalFilters = new ArrayList<>();

studyViewFilter.getCustomDataFilters().forEach(filter -> {
if (filter.getDatatype()
.equals(CustomDatatype.STRING.name())
) {
equalityFilters.add(filter);
} else {
intervalFilters.add(filter);
}
});

MultiKeyMap<String, String> customDataByStudySampleName = new MultiKeyMap<>();

studyViewFilter.getCustomDataFilters().stream().forEach(filter -> {
filter.getSamples().forEach(datum -> {
String value = datum.getValue().toUpperCase();
if (value.equals("NAN") || value.equals("N/A")) {
value = "NA";
}
customDataByStudySampleName.put(datum.getStudyId(), datum.getSampleId(), filter.getDisplayName(), value);
});
});

List<CustomSampleIdentifier> filtered = new ArrayList<>();
customSampleIdentifiers.forEach(customSampleIdentifier -> {
int equalityFilterCount = getFilteredCountByDataEqualityWithStudySampleNameMap(equalityFilters, customDataByStudySampleName,
customSampleIdentifier.getSampleId(), customSampleIdentifier.getStudyId(), false);
int intervalFilterCount = getFilteredCountByDataIntervalWithStudySampleNameMap(intervalFilters, customDataByStudySampleName,
customSampleIdentifier.getSampleId(), customSampleIdentifier.getStudyId());
if (equalityFilterCount == equalityFilters.size()
&& intervalFilterCount == intervalFilters.size()
) {
filtered.add(customSampleIdentifier);
}
else {
customSampleIdentifier.setIsFilteredOut(true);
filtered.add(customSampleIdentifier);
}
});
return filtered;
}

private Integer getFilteredCountByDataEqualityWithStudySampleNameMap(List<ClinicalDataFilter> attributes, MultiKeyMap<String, String> clinicalDataMap,
String entityId, String studyId, boolean negateFilters) {
Expand Down

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