[ALS-4947] Add anyRecordOfMulti field to the query object #77
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ramari16
commented
Aug 28, 2023
Comment on lines
-263
to
+276
| private void addIdSetsForAnyRecordOf(Query query, ArrayList<Set<Integer>> filteredIdSets) { | ||
| if(!query.getAnyRecordOf().isEmpty()) { | ||
| Set<Integer> patientsInScope = new ConcurrentSkipListSet<Integer>(); | ||
| VariantBucketHolder<VariantMasks> bucketCache = new VariantBucketHolder<VariantMasks>(); | ||
| query.getAnyRecordOf().parallelStream().forEach(path->{ | ||
| if(patientsInScope.size()<Math.max( | ||
| phenotypeMetaStore.getPatientIds().size(), | ||
| variantService.getPatientIds().length)) { | ||
| if(VariantUtils.pathIsVariantSpec(path)) { | ||
| addIdSetsForVariantSpecCategoryFilters(new String[]{"0/1","1/1"}, path, patientsInScope, bucketCache); | ||
| } else { | ||
| patientsInScope.addAll(getCube(path).keyBasedIndex()); | ||
| } | ||
| private void addIdSetsForAnyRecordOf(List<String> anyRecordOfFilters, ArrayList<Set<Integer>> filteredIdSets) { | ||
| if(!anyRecordOfFilters.isEmpty()) { | ||
| VariantBucketHolder<VariantMasks> bucketCache = new VariantBucketHolder<>(); | ||
| Set<Integer> anyRecordOfPatientSet = anyRecordOfFilters.parallelStream().flatMap(path -> { | ||
| if (VariantUtils.pathIsVariantSpec(path)) { | ||
| TreeSet<Integer> patientsInScope = new TreeSet<>(); | ||
| addIdSetsForVariantSpecCategoryFilters(new String[]{"0/1", "1/1"}, path, patientsInScope, bucketCache); | ||
| return patientsInScope.stream(); | ||
| } else { | ||
| return (Stream<Integer>) getCube(path).keyBasedIndex().stream(); |
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This used to add all patients matching any path to patientsInScope which is a hacky way of doing OR.
The new logic creates a set with all patients matching any of the paths (i.e., they have any record of that path) and adds it to filteredIdSets, which is a list of sets that eventually get ANDed with each other. We can then call this method multiple times with multiple different lists of anyRecordOf filters to support AND/OR functionality in this very specific way.
srpiatt
reviewed
Aug 30, 2023
client-api/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/Query.java
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This new field supports separate lists of OR filters where the result of each is ANDed with each other. I also removed some obsolete/redundant java generics