Add empty variant index

hms-dbmi · Jan 3, 2024 · 69c56bb · 69c56bb
1 parent 882b68c
commit 69c56bb
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Showing 3 changed files with 10 additions and 7 deletions.
diff --git a/...src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNodeImpl.java b/...src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNodeImpl.java
@@ -89,7 +89,7 @@ public BigInteger runGetPatientMask(DistributableQuery distributableQuery) {
                 List<VariantIndex> variantSets = getVariantsMatchingFilters(filter);
                 log.info("Found " + variantSets.size() + " groups of sets for patient identification");
                 if(!variantSets.isEmpty()) {
-                    VariantIndex unionOfVariantSets = new SparseVariantIndex(Set.of());
+                    VariantIndex unionOfVariantSets = VariantIndex.empty();
                     for(VariantIndex variantSet : variantSets) {
                         unionOfVariantSets = unionOfVariantSets.union(variantSet);
                     }
@@ -100,8 +100,7 @@ public BigInteger runGetPatientMask(DistributableQuery distributableQuery) {
                         intersectionOfInfoFilters = intersectionOfInfoFilters.intersection(unionOfVariantSets);
                     }
                 } else {
-                    // todo: create an empty variant index implementation
-                    intersectionOfInfoFilters = new SparseVariantIndex(Set.of());
+                    intersectionOfInfoFilters = VariantIndex.empty();
                 }
             }
             // todo: handle empty getVariantInfoFilters()
@@ -194,14 +193,14 @@ private VariantIndex getComputedVariantIndexForCategoryFilter(Map.Entry<String,
                     .reduce(VariantIndex::union)
                     .orElseGet(() -> {
                         log.info("No variant index computed for category filter. This should never happen");
-                        return new SparseVariantIndex(Set.of());
+                        return VariantIndex.empty();
                     });
         } else if(infoKeys.size() == 1) {
             return variantIndexCache.get(column, infoKeys.get(0));
         } else { // infoKeys.size() == 0
             log.info("No indexes found for column [" + column + "] for values [" + Joiner.on(",").join(values) + "]");
             // todo: test this case. should this be empty list or a list with an empty VariantIndex?
-            return new SparseVariantIndex(Set.of());
+            return VariantIndex.empty();
         }
     }
 
@@ -249,7 +248,7 @@ public Collection<String> runGetVariantList(DistributableQuery query) {
                 !variantInfoFilter.categoryVariantInfoFilters.isEmpty() || !variantInfoFilter.numericVariantInfoFilters.isEmpty()
         );
         if(queryContainsVariantInfoFilters) {
-            VariantIndex unionOfInfoFilters = new SparseVariantIndex(Set.of());
+            VariantIndex unionOfInfoFilters = VariantIndex.empty();
 
             // todo: are these not the same thing?
             if(query.getVariantInfoFilters().size()>1) {

diff --git a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantIndex.java b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantIndex.java
@@ -28,4 +28,8 @@ protected VariantIndex intersection(SparseVariantIndex sparseVariantIndex, Dense
                 .collect(Collectors.toSet());
         return new SparseVariantIndex(intersection);
     }
+
+    public static VariantIndex empty() {
+        return new SparseVariantIndex(Set.of());
+    }
 }
diff --git a/...est/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientVariantJoinHandlerTest.java b/...est/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientVariantJoinHandlerTest.java
@@ -119,7 +119,7 @@ public void getPatientIdsForIntersectionOfVariantSets_somePatientsMatchVariants(
 
     @Test
     public void getPatientIdsForIntersectionOfVariantSets_noVariants() {
-        VariantIndex intersectionOfInfoFilters = new SparseVariantIndex(Set.of());
+        VariantIndex intersectionOfInfoFilters = VariantIndex.empty();
 
         Set<Integer> patientIdsForIntersectionOfVariantSets = patientMaskToPatientIdSet(patientVariantJoinHandler.getPatientIdsForIntersectionOfVariantSets(Set.of(), intersectionOfInfoFilters));
         // this should be empty, as there are no variants