Update VariantKeyGenerator to use GenomicVariant in place of Variant

exomiser · Jan 18, 2024 · 7ffa16d · 7ffa16d
1 parent 54ac97e
commit 7ffa16d
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Showing 2 changed files with 5 additions and 7 deletions.
diff --git a/...rc/main/java/org/monarchinitiative/exomiser/autoconfigure/genome/VariantKeyGenerator.java b/...rc/main/java/org/monarchinitiative/exomiser/autoconfigure/genome/VariantKeyGenerator.java
@@ -22,6 +22,7 @@
 
 import org.monarchinitiative.exomiser.core.model.AlleleProtoAdaptor;
 import org.monarchinitiative.exomiser.core.model.Variant;
+import org.monarchinitiative.svart.GenomicVariant;
 import org.springframework.cache.interceptor.KeyGenerator;
 import org.springframework.cache.interceptor.SimpleKey;
 
@@ -46,8 +47,8 @@ public static Object generateKey(Object... params) {
         }
         if (params.length == 1) {
             Object param = params[0];
-            if (param instanceof Variant) {
-                return AlleleProtoAdaptor.toAlleleKey((Variant) param);
+            if (param instanceof GenomicVariant genomicVariant) {
+                return AlleleProtoAdaptor.toAlleleKey(genomicVariant);
             }
         }
         return new SimpleKey(params);

diff --git a/...est/java/org/monarchinitiative/exomiser/autoconfigure/genome/VariantKeyGeneratorTest.java b/...est/java/org/monarchinitiative/exomiser/autoconfigure/genome/VariantKeyGeneratorTest.java
@@ -22,10 +22,9 @@
 
 import org.junit.jupiter.api.Test;
 import org.monarchinitiative.exomiser.core.genome.GenomeAssembly;
-import org.monarchinitiative.exomiser.core.model.Variant;
-import org.monarchinitiative.exomiser.core.model.VariantEvaluation;
 import org.monarchinitiative.exomiser.core.proto.AlleleProto;
 import org.monarchinitiative.svart.CoordinateSystem;
+import org.monarchinitiative.svart.GenomicVariant;
 import org.monarchinitiative.svart.Strand;
 import org.springframework.cache.interceptor.SimpleKey;
 
@@ -46,9 +45,7 @@ public void returnsEmptyKeyForEmptyQuery() throws Exception {
 
     @Test
     public void returnsKeyForVariant() throws Exception {
-        Variant variant = VariantEvaluation.builder()
-                .variant(GenomeAssembly.HG19.getContigById(1), Strand.POSITIVE, CoordinateSystem.oneBased(), 2345, "A", "T")
-                .build();
+        GenomicVariant variant = GenomicVariant.of(GenomeAssembly.HG19.getContigById(1), Strand.POSITIVE, CoordinateSystem.oneBased(), 2345, "A", "T");
         // AlleleKey has no genomeAssembly. This might have been a bit of an oversight, but with assembly-specific caches
         // created in version 10.1.1 it's OK to use the AlleleKey as the cache key
         AlleleProto.AlleleKey expected = AlleleProto.AlleleKey.newBuilder()